Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains

Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains Batuhan Dogan, Janne A. Ihalainen, Yonghui Zeng, Riitta Nissinen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9081327/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 9 You are reading this latest preprint version Abstract Solar radiation impacts most life forms on Earth by acting as a energy source or a regulatory signal. However, relatively little is still known about phototrophic potential and strategies of environmental bacteria beyond Cyanobacteria. This study explores the phototrophy related genomic diversity of Sphingomonas faeni strains from Arctic and sub-Arctic regions. We analyzed the genomes of 25 plant-associated S.faeni strains isolated from Vaccinium myrtillus , Oxyria digyna , Vaccinium vitis-idaea , and Bistorta vivipara , along with a reference S. faeni genome MA-olki. The strains showed diversity both in overall genome level but also in phototrophic capabilities: Seven strains were identified as aerobic anoxygenic phototrophic (AAP) bacteria with a complete photosynthetic gene cluster, 16 strains contained Xanthorhodopsin (XR) genes, and three strains were non-phototrophic, possessing no AAP or XR genes. The AAP strains were found exclusive from Vaccinium hosts. O. digyna contained only XR containing strains and B. vivipara showed XR genes and one non-phototrophic strain. V. vitis-idaea hosted strains for all three different phototrophy categories. Phylogenetic analyses using 16S rRNA gene and whole genome alignments showed AAP positive strains forming a tight phylogenetic group. We found no strong evidence of horizontal gene transfer of photosynthetic gene cluster. XR strains and non-phototrophic strains clustered into three different subgroups. Phototrophic strains had more photoreceptors, and AAP strains exhibited dual copies of the 5-aminolevulinic acid (5-ALA) gene within the photosynthetic gene cluster (PGC). Our genomic analysis suggests a relationship between phototrophic strategies and host plant specificity. Figures Figure 1 Figure 2 Figure 3 Figure 4 2. Introduction The Arctic and sub-Arctic regions represent environments where low temperatures, and variable light conditions pose challenges to all life forms [ 1 ]. In these environments, microorganisms have evolved a variety of adaptive strategies to exploit available resources and cope with environmental stressors. Enabling organisms to utilize light as an energy source may confer an advantage in harsh ecosystems [ 2 ]. Photosynthetic microorganisms like cyanobacteria and algae adapt to low temperatures and light levels by optimizing their membrane lipid compositions to maintain fluidity at low temperatures and by evolving specialized pigments to maximize light absorption even in low light conditions [ 2 , 3 ]. These adaptations enable them to thrive in cold environments, where seasonally low light availability and nutrient scarcity would otherwise limit growth. Anoxygenic phototrophic bacteria use bacteriochlorophyll (BChl) based reaction centers and light harvesting antennas to capture light [ 4 ]. Some of those require oxygen rich environments for growth and electron transport reactions [ 5 ]. These organisms are known as aerobic anoxygenic phototrophic bacteria (AAPB) and thrive in aerobic settings, using various organic compounds as electron donors in their phototrophic processes [ 6 ]. Initially identified in nutrient poor marine environments [ 7 ], AAPB are now known to be widespread in both marine and freshwater ecosystems [ 6 , 8 ]. In these aquatic environments, they may represent up to one-third of all bacterial populations, playing an important role in the carbon cycling processes of aquatic systems [ 9 , 10 ]. AAPB have also been observed in terrestrial habitats such as soil biocrusts [ 11 ] and Antarctic soils [ 12 ]. Additionally, AAPB have been detected within the metagenomes of plant phyllospheres and are found in both epi- and endophytic niche communities of diverse plant species in Arctic and boreal zones [ 13 – 15 ]. The ecology of AAPB is not well understood. Kolber et al. [ 16 ], and Koblížek [ 6 ] speculated that the ability to utilize light may be especially beneficial in nutrient poor marine environments. Retinal based phototrophy involves microorganisms that use rhodopsins to capture light energy. Proteorhodopsin genes, found across all three domains of life, are most extensively studied in marine bacteria, and they are present in approximately half of all surface ocean heterotrophic bacteria [ 17 , 18 ]. Xanthorhodopsins enable microorganisms to utilize light as an energy source, thereby conferring an adaptive advantage in nutrient poor environments [ 19 – 21 ]. Structurally, XRs are transmembrane proteins with seven transmembrane helices, a configuration crucial for their function in creating a proton gradient across the membrane upon light exposure [ 22 – 24 ]. The retinal molecule, covalently bound to a lysine residue within the protein, undergoes isomerization upon light absorption, initiating a series of conformational changes that result in proton pumping across the membrane [ 19 , 20 , 22 – 26 ]. Hence, AAPB utilize BChl a to absorb blue and near-infrared light, while rhodopsins utilize green light for ATP synthesis. The biosynthesis of rhodopsin based proton pumps is energetically more frugal than the complex photosynthetic machinery required by bacteria [ 27 ]. Due to larger light harvesting capability the photosynthetic machinery can function in lower light regimes than the rhodopsin systems, however. Naturally, phototrophic bacteria require detailed sensing of light and possess a set of photoreceptor proteins [ 28 ]. All photosensors operate through a similar mechanism: photon absorption by the chromophore induces physical changes in the chromophore and its surrounding environment. Flavin containing systems like Blue Light Using Flavin domain (BLUF) complex undergo charge transfer processes following photon absorption [ 29 ]. In contrast, bacteriophytochromes (BphP) utilize a photoinduced isomerization process of bilin chromophores [ 30 , 31 ]. These chromophore changes lead to alterations in the protein environment of the photosensory domain. The biochemical signaling occurs through the effector domain of the complex, which often binds to or separates from its corresponding response regulator (RR), acting as a gene expression regulator. In summary, while the architecture of the photosensory domain is largely conserved across life forms, the effector domain exhibits significant variability [ 32 ]. This variability allows effector domains to control a wide range of functions through their interactions with their respective RRs or other suppressor/effector domains. Numerous studies detail the variability and functional mechanisms of microbial photosensory systems [ 30 , 33 – 37 ]. Sphingomonas faeni is a Gram-negative, non-spore-forming, psychrotolerant bacterium that was first described by Busse et al. [ 38 ]. having been originally isolated from straw. This species is part of the genus Sphingomonas , which is characterized by its distinctive sphingoglycolipids, ubiquinone Q-10, and the presence of sym-homospermidine as the predominant polyamine [ 39 , 40 ]. S. faeni has been repeatedly isolated from endophytic leaf and root tissues of an arcto-alpine pioneer plant Oxyria digyna [ 41 , 42 ], from leaves of a high altitude medicinal plant Arnebia euchorma [ 43 ], and it has been shown to be consistently present in leaves and photosynthetic stems of Vaccinium vitis-idaea and V. myrtillus in several sampling locations in Finland [ 15 ]. The S. faeni strains from Vaccinium species were shown to be AAP positive by BChl a fluorescence imaging and targeted PCR [ 15 , 44 ]. In contrast, none of the strains isolated from O. digyna were AAP positive ([ 41 , 42 ] and Nissinen, unpublished). Likewise, genomes of S. faeni strain ALB2 from A. euchorma , or the type strain of the species, MA-Olki, indicated no presence of AAP related genes [ 38 , 45 ]. Although S. faeni strains have previously been isolated from various regions and plant species, the genomic correlations among the strains along different phototrophic characteristics within the same bacterial species are missing, however. For this, we isolated S. faeni strains from V. vitis-idaea , and together with our strain collection from various plants from different locations (Table 1 ), we obtained the whole genome sequences of both AAP positive and AAP negative S. faeni strains. With these collected strains, we conducted a comparative genomic analysis, concentrating on their entire genomic sequence profiles and phototrophic characters. This allowed to explore the host specific commonalities among these groups and further pinpoint genomic variations on the protein composition level of the photosynthetic gene clusters and photoreceptor sites, all the way to single site information with potential structural implications of the XR proteins. 3. Materials and Methods 3.1. Selection and Isolation of studied strains We utilized S. faeni strains isolated during previous studies from phyllo-, endosphere and seeds of O. digyna , V. myrtillus , V. vitis-idaea and B. vivipara ( [ 15 , 42 ] and Nissinen, unpublished). The isolation sites spanned across diverse geographical locations in Finland and in Svalbard (Supplementary Fig. 1). We screened the strains from O. digyna (37 strains) and B vivipara (3 strains) for presence of BChl a and thus for AAP type phototrophy by NIR-fluorescence imaging of bacterial colonies [ 44 ]. All strains from O. digyna and B. vivipara were negative in NIR-imaging (data not shown). Still, 11 strains from O.digyna and 2 strains from B. vivipara were selected for full genome sequencing (Table 1 ). Additional AAP negative S. faeni strains were isolated from V. vitis-idaea (this study) as described in Nissinen et al. [ 42 ]. Post incubation, colonies exhibiting characteristic features of Sphingomonas were identified and subcultured onto sterile ½ R2A agar plates. Criteria for selection included colony size exceeding 2 millimeters and a distinct orange-light red pigmentation. Polymerase Chain Reaction (PCR) was performed to identify isolates in genus Sphingomonas . The primers used were SA429f (5' TAAAGCTCTTTTACCCG 3'), and SA933r (5' AAACCACATGCTCCACC 3') [ 46 ]. Colonies positively identified as Sphingomonas were then propagated on fresh ½ R2A media and identified by near full length amplicidation and sequencing of 16S rRNA gene with primers 27f (5'-AGAGTTTGATCMTGGCTCAG-3') and 1492r (5'- TACGGYTACCTTGTTACGACTT-3'). In addition to AAP negative strains, seven AAP positive strains from previous study [ 15 ] were selected for this study. The extraction of genomic DNA was carried out with MasterPure™ Complete DNA & RNA Purification Kit in accordance with the manufacturer’s instructions. 3.2. Genome sequencing and processsing The whole genome sequences of the strains were obtained using DNBseq technology, ensuring a read length of PR150 and allocating 2 GB per sample. The sequencing was conducted at BGI (bgi.com). The quality of the resultant sequencing reads was assessed and adapter sequences, contaminants, and low quality reads were removed using SOAPnuke [ 47 ], with the quality threshold set to Q > 20. The reads were then assembled into 7-132 contigs per genome using Unicycler v0.5.0 [ 48 ], further uploaded to the RAST Annotation Server [ 49 ] where the automated gene annotations were performed. Genomes in this study were deposited in the NCBI Genome Database under BioProject ID PRJNA1202125. NCBI’s Average Nucleotide Identity (ANI) analysis confirmed that all strains belong to species S. faeni . The corresponding accession numbers are SAMN45951201, SAMN45951202, SAMN45951203, SAMN45951204, SAMN45951205, SAMN45951206, SAMN45951208, SAMN45951209, SAMN45951210, SAMN45951211, SAMN45951212, SAMN45951213, SAMN45951214, SAMN45951215, SAMN45951216, SAMN45951217, SAMN45951218, SAMN45951219, SAMN45951220, SAMN45951221, SAMN45951222, SAMN45951223, SAMN45951224, SAMN45951225, and SAMN45951226. 3.3. Comparative genome analyses and bioinformatics The whole genome sequences were initially transferred to Geneious Prime v2024.0 (geneious.com) for processing, where sequence isolations were conducted. Isolated sequences were enhanced through in-house BLAST-P and the Biopython library function pairwise2.align.globalxx. These methodologies were implemented via in-house Python scripts to conduct searches on individual genomes. Phylogenetic trees based on these whole genome sequences were constructed by uploading the sequences to the Type Strain Genome Server (TYGS) [ 50 ]. Amino acid sequences for chosen proteins and protein complexes were aligned using ClustalW [ 51 ], and the aligned amino acid sequences were visualized using JalView [ 52 ]. Core genome alignment was generated using MAFFT (-e -n) [ 53 , 54 ] for further analysis. The core genome refers to the set of genes shared by all strains within a given species or group, representing essential functions and common characteristics. PGC synteny was constructed using EasyFig version 2.2.5 [ 55 ]. Phylogenetic trees were assembled in Geneious Prime and MEGA v 11 [ 56 ] and subsequently refined and visualized using the Interactive Tree Of Life (iTOL) platform [ 57 ]. ANIs for the whole genome and core genome sequences were calculated using fastANI [ 58 ]. A multidimensional scaling (MDS) graph, illustrating the genetic distances among the strains based on fastANI results, was constructed using in-house Python script (Supplementary Fig. 2). Plasmid sequences within the utilized strains were extracted using the Platon Plasmid Finder tool [ 59 ]. Generally, visualizations of the results were generated with home-built Python scripts. MDS was applied to visualize the clustering of strains based on the distance matrix, and the results were plotted with annotated strain identifiers, and labels indicating the proportion of variance explained by the principal coordinates. Statistical analyses and MSA were performed using custom Python scripts. 3.4. Structure predictions of the Xanthorhodopsin Amino acid sequences of the XR proteins from 17 strains were aligned using ClustalW [ 51 ] to identify conserved motifs and polymorphisms. Protein structure predictions were performed using SWISS MODEL [ 60 – 64 ], which also provided Protein Data Bank (PDB) files for further analysis. The sequences were uploaded to UniProt to identify binding sites and functional motifs. DeepTMHMM − 1.0 [ 65 ] was used to predict the transmembrane locations of the proteins. The resulting protein structures and motifs were visualized using PyMOL 3.0 (pymol.org), highlighting key functional regions and conserved features essential for XR function. 4. Results 4.1. Genome sequence screenings The genomes of 26 S. faeni strains varied in size from 4.1 to 5.4 Megabases (Mb). Although it was not possible to extract plasmid sequences from three strains, the number of plasmid sequences is estimated to range from one to seven. Supplementary Table 1 provides a detailed overview of the general characteristics of the 26 S. faeni strains examined in this study. All the seven strains, which showed positive NIR-fluorescence signal in the bacterial imaging analysis (not shown), contained complete PGC sequences in their genome. This confirmed the AAP character of these strains and we named these strains as AAP positive strains. We detected XR genes in 16 of the 20 AAP negative strains. Despite lacking the AAP genes, this subgroup is also classified as phototrophic, as they have potential to utilize light-driven redox reactions through a retinal-rhodopsin-based proton pumping mechanism. Here, we call these XR strains. To summarize, in our analysis we have AAP positive group, which contain the PGC, XR group, which contain XR gene, and a “none” group that contain neither of those phototrophic gene patterns (four strains) (Table 1 ). Thirteen of the strains, all belonging to the “none” or XR groups, were isolated from endosphere, phyllosphere or seeds of O. digyna and B. vivipara in oroarctic and arctic regions. The seven AAP positive strains were collected from subarctic V. myrtillus or V. vitis-idaea plants, both from endosphere and phyllosphere, without any specifity of the location (Table 1 ). In addition one none-strain and four XR strains originated from V. vitis-idaea plants. Table 1 Strains used in this study. The NCBI accession number of MA-Olki type-strain is under the “Location”. The strains are ordered according to their isolation source and phototrophy. FI: Finland, SV: Svalbard. The map of locations is shown in Supplementary Fig. 1. Strain Host Location Niche Phototrophy Source VOU02AS02 V.myrtillus Oulu, FI Endophytic AAP [ 15 ] VTK02DS03 V.myrtillus Turku, FI Endophytic AAP [ 15 ] VUT02AP02 V.myrtillus Utsjoki, FI Epiphytic AAP [ 15 ] VTK02EP11 V.myrtillus Turku, FI Epiphytic AAP [ 15 ] VKS02BS02 V.myrtillus Kuusamo, FI Endophytic AAP [ 15 ] PTK02CS01 V.vitis-idaea Turku, FI Endophytic AAP [ 15 ] PES02AP01 V.vitis-idaea Espoo, FI Epiphytic AAP [ 15 ] POU06NBS01 V.vitis-idaea Oulu, FI Endophytic XR This study POU06NCP01 V.vitis-idaea Oulu, FI Epiphytic XR This study POU06NBP02 V.vitis-idaea Oulu, FI Epiphytic XR This study POU06NCP02 V.vitis-idaea Oulu, FI Epiphytic XR This study POU06NBS02 V.vitis-idaea Oulu, FI Endophytic None This study L1DT4B O. digyna Longyearbyen, SV Epiphytic XR This study L1BT3 O. digyna Longyearbyen, SV Epiphytic XR This study L1BD2 O. digyna Longyearbyen, SV Epiphytic XR This study S2H28 O. digyna Kilpisjärvi, FI Endophytic XR [ 42 ] 9OR8 O. digyna Kilpisjärvi, FI Seed XR This study 26OR1 O. digyna Kilpisjärvi, FI Seed XR This study JPL28 O. digyna Kilpisjärvi, FI Endophytic XR [ 41 ] S3H21 O. digyna Kilpisjärvi, FI Endophytic XR [ 42 ] JWL30 O. digyna Kilpisjärvi, FI Endophytic XR [ 41 ] JWL22 O. digyna Kilpisjärvi, FI Endophytic XR [ 41 ] JWL2 O. digyna Kilpisjärvi, FI Endophytic XR [ 41 ] JOBD13 B. vivipara Kilpisjärvi, FI Epiphytic XR This study JOBD21 B. vivipara Kilpisjärvi, FI Epiphytic None This study MA-Olki NCBI GCA_003053745.1 N/A None NCBI 4.2. Phototrophicity correlates with overall genomic composition A phylogenetic tree of the 26 S. faeni strains was established using the full length 16S rRNA gene (Fig. 1 A). No differences were found in the 16S rRNA gene sequences among the AAP strains, which shared 100% similarity. 16S sequence differences between the AAP and none groups were 0.7 ± 0.1%, and between the AAP and XR groups, 0.47 ± 0.2%. Subsequently, we aligned the whole genomes to construct a phylogenetic tree, presented in Fig. 1 B. In whole genome alignment, the maximum difference between AAP and XR strains was 15 ± 1.5%, while the difference between AAP and none strains was 10.7 ± 1%. Whole genome similarity among the AAP strains was 96 ± 0.7%. We distributed the whole genome sequences into four lineages (L1-L4, Fig. 1 B). The AAP positive S. faeni strains (L3 lineage) cluster within the same phylogenetic group. The XR and none groups predominantly cluster according to their host. The L1 contains strains only from V. vitis-idaea . All epiphytic O. digyna strains locate in lineage L2. The L4 is the most heterogeneous linage in terms of the host or niche having strains from B.vivipara , O. digyna and V. vitis-idaea , and both XR and none phototrophic groups, including the model strain of the study (Fig. 1 B). 4.3. Photosynthetic gene cluster sequence and Xanthorhodopsin structures The phototrophic strains have either a PGC or an XR gene. The PGC is very conserved in gene syntheny in the all studied S. faeni AAP strains and only minor changes in the sequences of unknown hypotetical proteins exist (Supplementary Fig. 3). Due to the large size of the PGC, we did not perform a single amino acid level analysis for this region. Such detailed analysis was conducted, however, for the 17 obtained XR sequences. The amino acid similarity within the XR sequences ranged from a minimum of 79.6% to a maximum of 100% between strains. The phylogenetic tree presented in Fig. 2 shows that, with the exception of strain S3H21, the XR sequences group according to the same lineages as observed in the whole genome analysis presented in Fig. 1 B. To explore potential structural differences, XR sequences from each lineages were selected for detailed structural analysis. Amino acid sequences were aligned to well known XR sequences from Salinibacter ruber [ 25 , 26 , 66 ], Kin4B8 from Bdellovibrionota bacterium [ 67 ], and AAP5 from S. glacialis [ 68 , 69 ]. Alignment is shown in Supplementary Fig. 4. The secondary structure predictions indicated that the all XR proteins consist of seven alpha-helices (Fig. 3 ) and show very similar structural motifs with seven transmembrane regions, marked from 1 to 7. Key conserved motifs essential for XR function were identified. The primary proton acceptor Asp96 in S. ruber [ 66 ] corresponds the Asp92 in S. faeni strains (Fig. 3 A and Supplementary Fig. 4). In S. ruber , the amino acid functioning as the proton donor at position Glu107 [ 66 ] corresponds to Glu103 in S. faeni strains. The Schiff base binding residue, located at Lys240 in S. ruber [ 66 ], is observed at Lys228 in S. faeni . Carotenoid binding sites in S. faeni strains exhibit substitutions compared to those in S. ruber which binds salinixanthin as a carotenoid, but show closer correspondence with those of Kin4B8 ( B. bacterium ) and AAP5 ( S. glacialis ) which bind zeaxanthin and nostoxanthin, respectively [ 67 , 69 ]. The Gly153 in Kin4B8 (Gly156 in S. ruber ), which facilitates a so called fenestration and therefore energy transfer from a carotenoid to retinal, can be found in all studied S. faeni strains as Gly149. Other common residues in the carotenoid binding sites are listed in Supplementary Table 2 and show closer correspondence to those of the Kin4B8 and AAP5 sequences, particularly to a tyrosine residue (Y209) in Kin4B8, which has been shown to be important for carotenoid hydroxyl group binding [ 67 ], than that of S. ruber . It is also interesting to note that in our protein models, together with the alignment of Kin4B8 (with PDB code 8I2Z), a Lys184 site in the studied S. faeni strains resembles, structurally, the Asn188 position in Kin4B8 among several other amino acids along the carotenoid molecule (Fig. 3 C), suggesting that S. faeni XRs bind a hydroxyl containing carotenoid molecule, like zeaxanthin or nostoxanthin, instead of a 4-keto group carotenoid, such as salinixanthin or echinenone. A few carotenoid binding sites show variation among the S. faeni groups; the L1 (POU06-group) lineage has a Val145 instead of Ala145 in other lineages, but also lineage independent variation at the positions Arg184 versus Lys184 and Ser153 versus Ala153 can be pinpointed (Supplementary Fig. 4 and Supplementary table 2). It will be interesting to investigate in future studies whether these amino acids play a critical role in determining the carotenoid type or the energy transfer efficiency in these strains and how the carotenoid is located in these XR proteins, as the SWISS-MODEL structural predictions lack the positioning of the cofactors of the proteins. The conserved 3-omega motif, a characteristic of various eubacterial rhodopsins, is partially present in the S. faeni strains. In S. ruber , the first aromatic amino acid of this motif is Tyr13 in helix A [ 66 ], while in S. faeni , it corresponds to Tyr9 in POU06NCP02, and Phe9 in JWL30 strains (Supplementary Fig. 4). The second aromatic component, Trp70 in helix B of S. ruber , is Trp66 in S. faeni . However, instead of the third aromatic component in the B-C loop, Tyr81 in S. ruber , non-aromatic residues Val77 and Ile77 exists in L1 and L4 strains, respectively. In summary, the analysis identified key conserved motifs, primary proton donor, the retinal binding pocket with the critical proton acceptor and another proton donor, the proton release group, and the Schiff base for which carotenoid can transfer excitation energy. The carotenoid binding site suggests for a hydroxyl grouped carotenoid and some amino acid variations among and between the lineages can be observed, which may indicate different type of carotenoid binding in each of the S. faeni strains. 4.4. 5-ALA Sequences 5-ALA is a crucial precursor in the biosynthesis of tetrapyrroles, which include essential molecules such as chlorophyll, heme, and vitamin B12 [ 70 ]. In phototrophic bacteria, 5-ALA is synthesized through two main pathways: the C4 pathway (also known as the Shemin pathway) and the C5 pathway [ 71 ]. The C4 pathway involves the condensation of glycine and succinyl-CoA, catalyzed by the enzyme 5-ALA synthase, which is encoded by the hemA gene. During the analysis of PGC’s of AAP strains, 5-ALA, a precursor in heme synthesis [ 72 ] was found. As expected, 5-ALA sequences were identified in all strains, regardless of the phototrophic group. Intriguingly, the AAP positive strains exhibited the presence of two copies of the gene involved in 5-ALA synthesis, with one copy consistently located within the PGC, while the other is situated outside of the PGC. In contrast, AAP negative strains (both ‘XR’ and ‘none’ group) contained only a single copy. We extracted the 5-ALA sequences from our strains, and then performed an alignment. In the alignment results, the amino acid sequences of 5-ALA across phototrophic groups demonstrate a minimum similarity of 87%. However, within the PGC, the 5-ALA sequences exhibit a maximum similarity of only 67% when compared with 5-ALA sequences from outside the PGC. Conversely, non-PGC 5-ALA sequences from AAP strains show up to 96% similarity with those from XR and other none group 5-ALA sequences.This difference can be observed in the phylogenetic tree constructed based on the alignment results (Fig. 4 ), which also shows that the 5-ALA phylogeny follows the host species distribution, marked as different lineages, as described in the Fig. 1 B. 4.5. Photosensors in different phototrophic groups We analyzed the photosensor capacity of the strains in two fold. First the number of Blue Light Using Flavin (BLUF), bacteriophytochromes (BphP), sensory rhodopsins (SR), and photoactive yellow proteins (PYP) for each strain, are identified as presented in Table 2 . The photosensor content followed largerly the lineages based on whole genome similarity, presented in Fig. 1 B. The strains in lineage L1 contained BLUFs and BPhPs, but none of these strain contained PYP or SR. On the other hand, all BLUF sensors were absent in the lineage L2, but multiple PYPs, BphPs and SR were present in this lineage. The L3 strains, which all contain PGC, had on average the highest number and the most versatile set of photosensors. The lineage L4 had the largest range in number of photoreceptors per strain, from the least amount but also one of the highest amount of photosensors of our strain collection. This lineage shows also that the non-phototrophic strains had generally the least amount of photosensors, as also observed in Ihalainen et al [ 28 ]. In the second analysis, the neighbouring genes of the identified photosensors associated with each lineage were investigated (Supplementary Table 3). Several patterns of functional groups could be identified in the analysis. The BLUF photoreceptors were flanked by Superoxide dismutase on the 5' side in the L1BT3 strain and 9OR8, belonging to the lineage L4. The BLUFs in strains of the lineage L1 all had a N5-carboxyaminoimidazole ribonucleotide synthase on the 3' side. In terms of BphP genes, we identified that in all studied strains one BphP is related with a sodium/bile acid transporter in the 5’ neighboring site. With the same BphP gene the 3’ side varied according to the lineages. The L1 showed a hypotetical protein, the L2 lineage indicated an estrase/lipase gene, the L3 a M38 beta-aspartyl dipeptidase gene and L4 an uncharacterized MFS-transporter or a ferrichrome-iron receptor. An exception was JOBD21 strain which also showed a M38 gene on the 3’ side from the BphP gene. The second dominating BphP related 5’ gene was a cAMP-binding proteins - catabolite gene activator gene, which could be found from strains from the L1, L3 and L4 lineages. The L2 lineage lacked these BphP related cAMP-binding protein genes but contained mannonate dehydratase genes on 3’ side in the few strains. An oxidoreductase gene on the 3’ side was found from the few strains of L4 lineage and transposase genes could be also identified from L1 and L4 strains. In the analysis of PYP-flanking genes we found that some strains of the L2 lineage showed a chloride channel protein as a 5’ neighbor whereas AAP or XR containing strains from L3 and L4 lineages typically have GAF domain/GGDEF domain/EAL domain proteins in their 5' neighborhood. We found a PYP related or BphP related transcriptional regulator in one L2 strain (5’ side) and in two L3 strains (3’ side), respectively. All in all, multitude of potentially important gene products related to photosensor proteins could be identified, and it is highly interesting to test their functionality in biochemical and biophysical terms in the future. Table 2 Types of light-harvesting systems, rhodopsins, and the number of photoreceptor proteins in the studied S. faeni strains. Rho: Rhodopsin Type, SR: Sensory Rhodopsin, XR: Xanthorhodopsin, LH: Light-Harvesting System, BLUF: BLUF Domain (Blue Light Using Flavin), BphP: Bacteriophytochrome, PYP: Photoactive Yellow Protein Strain LH Rho BLUF BphP PYP Phototrophy Lineage PES02AP01 (P) LH1 - 1 3 1 AAP 3 VTK02DS03 (P) LH1 - 1 3 1 AAP 3 VTK02EP11 (M) LH1 SR - 2 1 AAP 3 VUT02AP02 (M) LH1 SR 1 2 1 AAP 3 VOU02AS02 (M) LH1 SR 1 2 1 AAP 3 PTK02CS01 (P) LH1 - 1 2 1 AAP 3 VKS02BS02 (M) LH1 - 2 3 1 AAP 3 POU06NCP02 (P) - XR 1 3 - Rho 1 POU06NBS01 (P) - XR 1 1 - Rho 1 POU06NCP01 (P) - XR 1 3 - Rho 1 POU06NBP02 (P) - XR 1 2 - Rho 1 L1BD2 (O) - XR - 2 3 Rho 2 L1DT4B(O) - XR - 2 2 Rho 2 L1BT3 (O) - SR & XR 2 1 1 Rho - S2H28 (O) - XR 1 4 1 Rho 4 JOBD13 (B) - XR - 5 1 Rho 4 9OR8 (O) - XR 1 3 2 Rho 4 26OR1 (O) - SR & XR - 2 1 Rho 4 JPL28 (O) - XR - 2 1 Rho 4 S3H21 (O) - XR - 1 1 Rho 4 JWL30 (O) - XR - 1 1 Rho 4 JWL22 (O) - XR - 1 1 Rho 4 JWL2 (O) - XR - 1 1 Rho 4 JOBD21 (B) - - 1 2 1 None 4 MA-Olki (NCBI) - - 1 2 - None 4 POU06NBS02 (P) - - 1 3 - None 4 5. Discussion The genetic composition of individual bacterial strains among the same species can be quite divergent. Here, we demonstrate this with 25 S. faeni strains isolated from various plant hosts, O. digyna, V. myrtillus , V. vitis-idaea, and B. vivipara , from boreal, sub-arctic and arctic regions. The strains could be divided into four different lineages based on whole genome alignment, which was also reflected in more detailed genomic analysis along this study. The lineages based on whole genome alignment correlated with three phototrophic strategies of these strains: AAP positive, XR containing, and non-phototrophic bacterial strains. Interestingly, their overall phylogeny together with their phototrophy correlated also with the plant from which these strains were isolated. Our AAP positive strains were all from Vaccinium species, from phyllo- or endosphere of V. myrtillus or from V. vitis-idaea plants. Both of these plant species are perennial shrubs dominating in boreal forests and common also in arctic fell flora, and thus, offer a long term habitat for their microbial companions. In our previous study, we detected a high abundance of AAPB - in particular endospheric AAPB - in perennial plants that retain their photosynthetic tissues also through winter months [ 15 ]. In that same study, we isolated diverse AAP positive Methylobacteria from these Vaccinium species [ 15 ]. What might be the role, if any, of AAP in the interaction with Vaccinium sp. and AAPB, remains to be investigated. Our preliminary analysis of the genes other than PGC specific to AAP positive, Vaccinium associated strains did not offer any obvious clues to this, but are an obvious target for further studies. Curiously, throughout our campaigns we never found any AAP positive S. faeni strains from O. digyna or from B. vivipara , although S. faeni has been shown to be abundant in these plants [[ 15 ] and Nissinen, unpublished]. The endophytic strains from O. digyna formed their own lineage in whole genome alignment. Instead we found that the strains from O. digyna contained an XR protein indicating therefore a potential for phototrophy but without “an expensive” photosynthetic machinery. Unlike V. myrtillus and V. vitis-idaea , O. digyna and B. vivipara overwinter as rhizomes, with decidious above-ground stems and leaves. Curiously, most of the AAP negative XR containing S. faeni strains formed an own genomic linage, clearly distinct from AAP positive Vaccinium -associated strains. The genomic composition of this linage (L1 in Fig. 1 B) is particularly similar in the multidimensional scaling, XR sequence, and photosensor composition. In the predicted XR structures, the 3-omega motif of a Xanthorhodopsin containing AAP Rhodobacter strain, the third position is substituted by a non-aromatic Ile77 residue [ 24 , 69 ], replacing the Tyr81 residue observed in S. ruber XR. Similarly, substitutions in the 3-omega motifs of S. faeni strains, involving non-aromatic residues such as valine and isoleucine, highlight the plasticity of this motif in XR proteins. The amino acid substitutions observed in S. faeni XR proteins suggest both conservation of function and potential adaptive modifications. Key proton transfer residues, including Asp92 (Asp96 in S. ruber ), Glu103 (Glu107 in S. ruber ), and Lys228 (Lys240 in S. ruber ), remain unchanged, indicating that the retinal Schiff base binding and proton pumping mechanism are likely preserved. However, notable substitutions in the carotenoid binding region (Fig. 3 , Supplementary Fig. 4, Supplementary Table 2) suggest a nostoxanthin or zeaxanthin binding, similar to a comparable sequence of AAP5 [ 69 ], which shows even a dual phototrophic character. Notably, the C-terminal structure of S. faeni strains resembles to some extend that of light-gated cation channel rhodopsins [ 23 ]. Across all S. faeni strains in this study regardless of phototrophic group, the core genome, which consists of genes shared among all strains, exhibits minimal nucleotide variation (~ 1%), highlighting a high degree of genetic consistency across the species. Furthermore, genome analytics such as ANI analysis and MDS based on ANI values highlight genetic consistency within phototrophic groups. These results align with our findings, as the phylogenetic trees in this study also exhibit a similar topology, suggesting a long term evolution of the PGC with the overall genome of these strains. This pattern is consistent with observations in other species, such as Citromicrobium sp ., which harbors two distinct phototrophic groups [ 73 ], and haloalkaliphilic Rhodobacterales [ 74 ] which suggests that AAP strains have undergone stronger genetic conservation compared to other phototrophic or non-phototrophic groups. The plant-associated S. faeni strains share their ecological niche with many other bacteria, making horizontal gene transfer plausible. However, the absence of significant differences in GC content between plasmids, PGC, and chromosomal DNA in this study indicates that the PGC has been co-evolving with the core genome for an extended period, with no strong evidence of recent horizontal gene transfer. Rather, it highlights that their genetic characteristics are closely integrated with the chromosomal genome. 5-ALA sequences were found in all S. faeni strains used in the study. However, while the XR and none strains have only one 5-ALA gene, the AAP strains have two 5-ALA genes, one of which is always in the PGC. This situation resembles a common feature in AAP species [ 74 ]. Heme, being an essential component in various proteins, including those integral to photosynthesis and electron transport [ 75 ], implicates the necessity for more robust biosynthetic pathways in these phototrophs. The duplication of the 5-ALA gene in AAP positive strains, especially the positioning of one copy within the PGC, might reflect an evolutionary adaptation, providing a means for more nuanced regulation of heme synthesis. This positioning could cater specifically to the photosynthetic machinery, while the other gene copy addresses general cellular functions that require heme. Conversely, the single gene copy in AAP negative strains suggests a simpler heme biosynthesis pathway, sufficient for their non-photosynthetic metabolic demands. Furthermore, 5-ALA is not just a precursor in heme synthesis but also plays a role in the biosynthesis of various tetrapyrroles, like bacteriochlorophylls [ 76 ]. Our photosensor analysis revealed here and in our previous study the wider need for photosensing among phototrophs [ 28 ]. However, the limited number of strains from the non-phototrophic group analyzed poses challenges in drawing statistically significant conclusions about this group. Still, the photosensor composition followed the linages in phylogeny grouping, but direct functional properties for particualr photosensors is challenging to propose. For example, we could not pinpoint any particular BphP genes near PGC regulating its function, similar as found for microsymbiotic nitrogen fixing bacteria Bradyrhizobium japonicum [ 77 ]. On the other hand, one BphP was associated with sodium/bile acid symporters in every strain in this study (Supplementary Table 3). Together with presence of transcriptional regulators of the LysR family, this suggests a network where light sensing proteins influence membrane transport and gene expression, aligning with previous findings that highlight the role of photoreceptors in environmental adaptation [ 78 ]. Similarly, the proximity of PYP photoreceptors to GAF domain proteins and chloride channel proteins suggests their potential role in signal transduction and ion transport. This photoreceptor has already been shown to regulate biofilm formation in Idiomarina loihiensis [ 79 ]. The frequent co-localization of BLUF photoreceptors with superoxide dismutase genes suggests a role in regulating the oxidative stress response. For instance, in Acinetobacter baumannii , BlsA, a BLUF-type photoreceptor, has been shown to effectively stimulate catalase activity, trehalose production, fluoroquinolone antibiotic tolerance, and the Type VI secretion system (T6SS) a macromolecular secretion machinery used by many Gram-negative bacteria to eliminate competitors [ 80 , 81 ]. Recent studies further show the role of blue light photoreceptors in regulating photosynthetic and stress adaptive responses. In Dinoroseobacter shibae , the LOV-domain-containing protein LdaP was identified as a light dependent antirepressor that interacts with PpsR to regulate the photosynthetic gene cluster, demonstrating how photoreceptors modulate light driven gene expression at a transcriptional level [ 82 ]. To conclude, the genomic sequencing of 25 S. faeni strains, along with the type strain MA-Olki from the NCBI Genome Database, revealed genome sizes ranging from 4.1 to 5.4 Mb. Members of the XR group were the most prevalent, suggesting a widespread distribution of this photoreceptor among the strains. Our study enhances the understanding of microbial adaptation and the ecological dynamics of S. faeni in Arctic and boreal environments. The findings highlight the complex relationship between genetic diversity and environmental adaptability, emphasizing the need for further investigation into the ecological impacts and evolutionary pathways of phototrophic strains, including both AAP and XR containing strains. Declarations Used Python Scripts All custom Python scripts can be found in this repository github.com/batuhanthebioinformatician/Plant_Microbiome_Phototrophy Competing Interests: The authors declare that they have no relevant financial or non-financial interests to disclose. Author Contribution J.A.I and R.N. conceptualized the work. R.N. and B.D performed the experimental work. B.D. wrote the genome analysis scripts and together with R.N. and Y.Z performed the genomic analysis. B.D., J.A.I,R.N.,Y.Z. analyzed the data and wrote the manuscript. B.D. prepared all figures and tables of the manuscript. Acknowledgement The financial support for the study originates from KONE foundation (grant “Jaettu Valo”) and Science Council Finland (grant #259180 for Riitta Nissinen). Puhti supercomputer at the CSC - IT Center for Science in Finland was utilized to handle the demanding data processing and analysis tasks efficiently. This infrastructure provided the necessary computational power to conduct intensive genomic analyses and support the advanced bioinformatics processing required for this research. Ole Franz is acknowledged for instructive comments on the manuscript. The authors wish to thank Jani Hohti and Joonas Ikävalko for isolating the strains from O. digyna seeds. Data Availability Genomes in this study were deposited in the NCBI Genome Database under BioProject ID PRJNA1202125. NCBI’s Average Nucleotide Identity (ANI) analysis confirmed that all strains belong to species S. faeni. The corresponding accession numbers are SAMN45951201, SAMN45951202, SAMN45951203, SAMN45951204, SAMN45951205, SAMN45951206, SAMN45951208, SAMN45951209, SAMN45951210, SAMN45951211, SAMN45951212, SAMN45951213, SAMN45951214, SAMN45951215, SAMN45951216, SAMN45951217, SAMN45951218, SAMN45951219, SAMN45951220, SAMN45951221, SAMN45951222, SAMN45951223, SAMN45951224, SAMN45951225, and SAMN45951226.All custom Python scripts can be found in this repository github.com/batuhanthebioinformatician/Plant_Microbiome_Phototrophy References Holmberg, S. M., & Jørgensen, N. O. G. (2023). Insights into abundance, adaptation and activity of prokaryotes in arctic and Antarctic environments. Polar Biology , 46 (5), 381–396. Morgan-Kiss, R. M., et al. (2006). 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Supplementary Files SupplementaryFileFaeni.pdf Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 04 May, 2026 Reviews received at journal 04 May, 2026 Reviews received at journal 14 Apr, 2026 Reviewers agreed at journal 09 Apr, 2026 Reviewers agreed at journal 16 Mar, 2026 Reviewers invited by journal 11 Mar, 2026 Editor assigned by journal 10 Mar, 2026 Submission checks completed at journal 10 Mar, 2026 First submitted to journal 10 Mar, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9081327","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":604669653,"identity":"4f7ec85a-037c-432a-b297-d65e0561e2dc","order_by":0,"name":"Batuhan Dogan","email":"","orcid":"","institution":"University of Jyväskylä","correspondingAuthor":false,"prefix":"","firstName":"Batuhan","middleName":"","lastName":"Dogan","suffix":""},{"id":604669654,"identity":"6db0a927-a2d9-4992-ba75-c2b6421cbf1b","order_by":1,"name":"Janne A. Ihalainen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA90lEQVRIiWNgGAWjYBACxgYwJZHAwM7AcADIkgOLVBgQo4UZosUYLHIGjxYYAGsBgUSwGWfwKGVuP3vswQcGizz+ZuaHhwsq7qQ3z8gxYDhQgMdhPXnphjMYJIolDrMZHJ5x5lluI1gLXr/kmEnzMEgkNhxmMDjM23YYrIX5Az4t/W/MpP8Atcw/zP7hMO+/w+mMBG2ZAbQFGGKJGw7zAG1pOJxAhJY3ZpI9BhKJGw/zFBzmOXbYsLHnWcEBfFoM+3PMJH5U1CXOO96++TNPzWF5w/bkjQ8O/MGjpQFEIptpOCEBHKc4gTymCD9eDaNgFIyCUTACAQCqf1Y7OQJOrAAAAABJRU5ErkJggg==","orcid":"","institution":"University of Jyväskylä","correspondingAuthor":true,"prefix":"","firstName":"Janne","middleName":"A.","lastName":"Ihalainen","suffix":""},{"id":604669655,"identity":"967636bc-9fd2-44de-99ab-551daf143877","order_by":2,"name":"Yonghui Zeng","email":"","orcid":"","institution":"University of Copenhagen","correspondingAuthor":false,"prefix":"","firstName":"Yonghui","middleName":"","lastName":"Zeng","suffix":""},{"id":604669656,"identity":"dde62f38-44a4-4c25-b8fa-991419ed44a6","order_by":3,"name":"Riitta Nissinen","email":"","orcid":"","institution":"University of Turku","correspondingAuthor":false,"prefix":"","firstName":"Riitta","middleName":"","lastName":"Nissinen","suffix":""}],"badges":[],"createdAt":"2026-03-10 08:38:34","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9081327/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9081327/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104781618,"identity":"32cf1add-e308-4e76-a110-c15d328100b6","added_by":"auto","created_at":"2026-03-17 07:56:01","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":238274,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogeny tree of 26 \u003cem\u003eS. faeni\u003c/em\u003e strains built with Neighbour-Joining method A) Tree based on 16S rRNA gene alignment B) Tree of whole genome alignment. The phylogenetic tree features strains color-coded as follows: purple for XR strains, dark blue for AAP strains, and gray for non-phototrophic strains. Strains are distinguished by text formatting, with bold text representing endophytic strains and non-bold text for epiphytic strains. Isolation sources are indicated as: O for \u003cem\u003eO. digyna\u003c/em\u003e, P for \u003cem\u003eV. vitis-idaea\u003c/em\u003e, V for \u003cem\u003eV. myrtillus\u003c/em\u003e, and B for \u003cem\u003eB. vivipara\u003c/em\u003e. Seed isolated are marked in parenthesis. The lineages (L1-L4) used to categorize the strains in this study are color-coded as follows: L1 (brown), L2 (yellow), L3 (green), and L4 (cyan). Note that the strain L1BT3 is uncategorized and its phylogenetic branch is shown as a black line.\u003c/p\u003e","description":"","filename":"Fig1.png","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/27fd7e47341014117dc4fea6.png"},{"id":104586662,"identity":"e0a0d52f-8838-44c8-9cdc-e59b60b68f9e","added_by":"auto","created_at":"2026-03-13 15:56:12","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":128277,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic tree of XR sequences. Bold text indicates XR from endophytic strains, while plain text shows epiphytic strains. Isolation sources are specified as follows: O for \u003cem\u003eOxyria digyna\u003c/em\u003e, P for \u003cem\u003eV. vitis-idaea\u003c/em\u003e, and B for \u003cem\u003eB. vivipara\u003c/em\u003e. Seed isolates are listed in parentheses.\u003c/p\u003e","description":"","filename":"Fig2.png","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/72d167c1e1be8058e04da64b.png"},{"id":104586657,"identity":"02d85744-9298-4fd2-b3f0-8f40709ec59b","added_by":"auto","created_at":"2026-03-13 15:56:12","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":527741,"visible":true,"origin":"","legend":"\u003cp\u003e(A) Protein model of \u003cem\u003eS. faeni\u003c/em\u003estrain POU06NBP02 generated by SWISS-MODEL. (B) The cryo-EM structure of Kin4B8 (\u003cem\u003eB.\u003c/em\u003ebacterium) XR (pale green), the zeaxanthin is shown in orange and the all-trans-retinal (ATR) in purple. Carotenoid binding region in \u003cem\u003eS. faeni\u003c/em\u003estrains F156, K184 (or R184 in some strains; see Supplementary Table 2), L187, F190, A191, G194, P197, and I198 are highlighted in yellow. Fenestration-associated region R146, G149, S153 (or A153 in some strains; see Supplementary Table 2), Y200, M201, Y204, and A205 are shown in pink. The B-C loop is colored orange. For \u003cem\u003eS. faeni\u003c/em\u003e, proton donor region is shown in purple, proton acceptor region in blue, Schiff base residues in brown, and the Omega motif in cyan. (C) Structural alignment of \u003cem\u003eS. faeni\u003c/em\u003e POU06NBP02 (pale gray) and Kin4B8 (pale green) and its zeaxanthin binding positions in \u003cem\u003eS. faeni\u003c/em\u003e. The key residues positioned according to the SWISS-MODEL are possibly involved in carotenoid binding and fenestration points in the \u003cem\u003eS. faeni\u003c/em\u003e strains.\u003c/p\u003e","description":"","filename":"Fig3.png","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/acd9b651d808353e6092767e.png"},{"id":104586659,"identity":"81f4f765-9588-4fe0-bb1b-cbe5cad0a33c","added_by":"auto","created_at":"2026-03-13 15:56:12","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":171391,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogeny tree of 5-aminolevulinic acid nucleotide sequences built with Neighbour-Joining method. Strain name+PGC indicates the sequence is in the PGC. The phylogenetic tree features strains color-coded as follows: purple for XR strains, dark blue for AAP strains, and gray for non-phototrophic strains. Strains are distinguished by text formatting, with bold text representing endophytic strains and plain text for epiphytic strains. The seed isolates are indicated inside parantheses. The specific isolation sources are detailed as: O for \u003cem\u003eOxyria digyna\u003c/em\u003e, P for \u003cem\u003eV. vitis-idaea\u003c/em\u003e, V for \u003cem\u003eV. myrtillus\u003c/em\u003e, and B for \u003cem\u003eB. vivipara\u003c/em\u003e. The phylogeny tree deviates again as lineages, marked as L1 to L4, along the same strains as in Figure 1B.\u003c/p\u003e","description":"","filename":"Fig4.png","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/d21adf15508d7c5af8d90e1b.png"},{"id":104787924,"identity":"fc650ed5-5089-4608-8260-f68ae4e4fd21","added_by":"auto","created_at":"2026-03-17 08:23:15","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2210035,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/0c73a803-249e-4349-8838-dc8fd669f802.pdf"},{"id":104586658,"identity":"cda18d1e-b7dd-4449-8d89-7ebf7e4cc37f","added_by":"auto","created_at":"2026-03-13 15:56:12","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":832855,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFileFaeni.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9081327/v1/21402a79e1c0573adbdb0385.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains","fulltext":[{"header":"2. Introduction","content":"\u003cp\u003eThe Arctic and sub-Arctic regions represent environments where low temperatures, and variable light conditions pose challenges to all life forms [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. In these environments, microorganisms have evolved a variety of adaptive strategies to exploit available resources and cope with environmental stressors. Enabling organisms to utilize light as an energy source may confer an advantage in harsh ecosystems [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Photosynthetic microorganisms like cyanobacteria and algae adapt to low temperatures and light levels by optimizing their membrane lipid compositions to maintain fluidity at low temperatures and by evolving specialized pigments to maximize light absorption even in low light conditions [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. These adaptations enable them to thrive in cold environments, where seasonally low light availability and nutrient scarcity would otherwise limit growth.\u003c/p\u003e \u003cp\u003eAnoxygenic phototrophic bacteria use bacteriochlorophyll (BChl) based reaction centers and light harvesting antennas to capture light [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Some of those require oxygen rich environments for growth and electron transport reactions [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. These organisms are known as aerobic anoxygenic phototrophic bacteria (AAPB) and thrive in aerobic settings, using various organic compounds as electron donors in their phototrophic processes [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Initially identified in nutrient poor marine environments [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e], AAPB are now known to be widespread in both marine and freshwater ecosystems [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. In these aquatic environments, they may represent up to one-third of all bacterial populations, playing an important role in the carbon cycling processes of aquatic systems [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. AAPB have also been observed in terrestrial habitats such as soil biocrusts [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e] and Antarctic soils [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Additionally, AAPB have been detected within the metagenomes of plant phyllospheres and are found in both epi- and endophytic niche communities of diverse plant species in Arctic and boreal zones [\u003cspan additionalcitationids=\"CR14\" citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. The ecology of AAPB is not well understood. Kolber et al. [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e], and Kobl\u0026iacute;žek [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e] speculated that the ability to utilize light may be especially beneficial in nutrient poor marine environments.\u003c/p\u003e \u003cp\u003eRetinal based phototrophy involves microorganisms that use rhodopsins to capture light energy. Proteorhodopsin genes, found across all three domains of life, are most extensively studied in marine bacteria, and they are present in approximately half of all surface ocean heterotrophic bacteria [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e, \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. Xanthorhodopsins enable microorganisms to utilize light as an energy source, thereby conferring an adaptive advantage in nutrient poor environments [\u003cspan additionalcitationids=\"CR20\" citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Structurally, XRs are transmembrane proteins with seven transmembrane helices, a configuration crucial for their function in creating a proton gradient across the membrane upon light exposure [\u003cspan additionalcitationids=\"CR23\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. The retinal molecule, covalently bound to a lysine residue within the protein, undergoes isomerization upon light absorption, initiating a series of conformational changes that result in proton pumping across the membrane [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e, \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan additionalcitationids=\"CR23 CR24 CR25\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Hence, AAPB utilize BChl \u003cem\u003ea\u003c/em\u003e to absorb blue and near-infrared light, while rhodopsins utilize green light for ATP synthesis. The biosynthesis of rhodopsin based proton pumps is energetically more frugal than the complex photosynthetic machinery required by bacteria [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Due to larger light harvesting capability the photosynthetic machinery can function in lower light regimes than the rhodopsin systems, however.\u003c/p\u003e \u003cp\u003eNaturally, phototrophic bacteria require detailed sensing of light and possess a set of photoreceptor proteins [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. All photosensors operate through a similar mechanism: photon absorption by the chromophore induces physical changes in the chromophore and its surrounding environment. Flavin containing systems like Blue Light Using Flavin domain (BLUF) complex undergo charge transfer processes following photon absorption [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. In contrast, bacteriophytochromes (BphP) utilize a photoinduced isomerization process of bilin chromophores [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. These chromophore changes lead to alterations in the protein environment of the photosensory domain. The biochemical signaling occurs through the effector domain of the complex, which often binds to or separates from its corresponding response regulator (RR), acting as a gene expression regulator. In summary, while the architecture of the photosensory domain is largely conserved across life forms, the effector domain exhibits significant variability [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. This variability allows effector domains to control a wide range of functions through their interactions with their respective RRs or other suppressor/effector domains. Numerous studies detail the variability and functional mechanisms of microbial photosensory systems [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan additionalcitationids=\"CR34 CR35 CR36\" citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cem\u003eSphingomonas faeni\u003c/em\u003e is a Gram-negative, non-spore-forming, psychrotolerant bacterium that was first described by Busse et al. [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. having been originally isolated from straw. This species is part of the genus \u003cem\u003eSphingomonas\u003c/em\u003e, which is characterized by its distinctive sphingoglycolipids, ubiquinone Q-10, and the presence of sym-homospermidine as the predominant polyamine [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cem\u003eS. faeni\u003c/em\u003e has been repeatedly isolated from endophytic leaf and root tissues of an arcto-alpine pioneer plant \u003cem\u003eOxyria digyna\u003c/em\u003e [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e], from leaves of a high altitude medicinal plant \u003cem\u003eArnebia euchorma\u003c/em\u003e [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e], and it has been shown to be consistently present in leaves and photosynthetic stems of \u003cem\u003eVaccinium vitis-idaea\u003c/em\u003e and \u003cem\u003eV. myrtillus\u003c/em\u003e in several sampling locations in Finland [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. The \u003cem\u003eS. faeni\u003c/em\u003e strains from \u003cem\u003eVaccinium\u003c/em\u003e species were shown to be AAP positive by BChl \u003cem\u003ea\u003c/em\u003e fluorescence imaging and targeted PCR [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. In contrast, none of the strains isolated from \u003cem\u003eO. digyna\u003c/em\u003e were AAP positive ([\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e] and Nissinen, unpublished). Likewise, genomes of \u003cem\u003eS. faeni\u003c/em\u003e strain ALB2 from \u003cem\u003eA. euchorma\u003c/em\u003e, or the type strain of the species, MA-Olki, indicated no presence of AAP related genes [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAlthough \u003cem\u003eS. faeni\u003c/em\u003e strains have previously been isolated from various regions and plant species, the genomic correlations among the strains along different phototrophic characteristics within the same bacterial species are missing, however. For this, we isolated \u003cem\u003eS. faeni\u003c/em\u003e strains from \u003cem\u003eV. vitis-idaea\u003c/em\u003e, and together with our strain collection from various plants from different locations (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e), we obtained the whole genome sequences of both AAP positive and AAP negative \u003cem\u003eS. faeni\u003c/em\u003e strains. With these collected strains, we conducted a comparative genomic analysis, concentrating on their entire genomic sequence profiles and phototrophic characters. This allowed to explore the host specific commonalities among these groups and further pinpoint genomic variations on the protein composition level of the photosynthetic gene clusters and photoreceptor sites, all the way to single site information with potential structural implications of the XR proteins.\u003c/p\u003e"},{"header":"3. Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003e3.1. Selection and Isolation of studied strains\u003c/h2\u003e \u003cp\u003eWe utilized \u003cem\u003eS. faeni\u003c/em\u003e strains isolated during previous studies from phyllo-, endosphere and seeds of \u003cem\u003eO. digyna\u003c/em\u003e, \u003cem\u003eV. myrtillus\u003c/em\u003e, \u003cem\u003eV. vitis-idaea\u003c/em\u003e and \u003cem\u003eB. vivipara (\u003c/em\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e] and Nissinen, unpublished). The isolation sites spanned across diverse geographical locations in Finland and in Svalbard (Supplementary Fig.\u0026nbsp;1). We screened the strains from \u003cem\u003eO. digyna\u003c/em\u003e (37 strains) and \u003cem\u003eB vivipara\u003c/em\u003e (3 strains) for presence of BChl \u003cem\u003ea\u003c/em\u003e and thus for AAP type phototrophy by NIR-fluorescence imaging of bacterial colonies [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. All strains from \u003cem\u003eO. digyna\u003c/em\u003e and \u003cem\u003eB. vivipara\u003c/em\u003e were negative in NIR-imaging (data not shown). Still, 11 strains from \u003cem\u003eO.digyna\u003c/em\u003e and 2 strains from \u003cem\u003eB. vivipara\u003c/em\u003e were selected for full genome sequencing (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Additional AAP negative \u003cem\u003eS. faeni\u003c/em\u003e strains were isolated from \u003cem\u003eV. vitis-idaea\u003c/em\u003e (this study) as described in Nissinen et al. [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. Post incubation, colonies exhibiting characteristic features of \u003cem\u003eSphingomonas\u003c/em\u003e were identified and subcultured onto sterile \u0026frac12; R2A agar plates. Criteria for selection included colony size exceeding 2 millimeters and a distinct orange-light red pigmentation. Polymerase Chain Reaction (PCR) was performed to identify isolates in genus \u003cem\u003eSphingomonas\u003c/em\u003e. The primers used were SA429f (5' TAAAGCTCTTTTACCCG 3'), and SA933r (5' AAACCACATGCTCCACC 3') [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e]. Colonies positively identified as \u003cem\u003eSphingomonas\u003c/em\u003e were then propagated on fresh \u0026frac12; R2A media and identified by near full length amplicidation and sequencing of 16S rRNA gene with primers 27f (5'-AGAGTTTGATCMTGGCTCAG-3') and 1492r (5'- TACGGYTACCTTGTTACGACTT-3'). In addition to AAP negative strains, seven AAP positive strains from previous study [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e] were selected for this study.\u003c/p\u003e \u003cp\u003eThe extraction of genomic DNA was carried out with MasterPure\u0026trade; Complete DNA \u0026amp; RNA Purification Kit in accordance with the manufacturer\u0026rsquo;s instructions.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003e3.2. Genome sequencing and processsing\u003c/h2\u003e \u003cp\u003eThe whole genome sequences of the strains were obtained using DNBseq technology, ensuring a read length of PR150 and allocating 2 GB per sample. The sequencing was conducted at BGI (bgi.com). The quality of the resultant sequencing reads was assessed and adapter sequences, contaminants, and low quality reads were removed using SOAPnuke [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e], with the quality threshold set to Q\u0026thinsp;\u0026gt;\u0026thinsp;20. The reads were then assembled into 7-132 contigs per genome using Unicycler v0.5.0 [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e], further uploaded to the RAST Annotation Server [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e] where the automated gene annotations were performed. Genomes in this study were deposited in the NCBI Genome Database under BioProject ID PRJNA1202125. NCBI\u0026rsquo;s Average Nucleotide Identity (ANI) analysis confirmed that all strains belong to species \u003cem\u003eS. faeni\u003c/em\u003e. The corresponding accession numbers are SAMN45951201, SAMN45951202, SAMN45951203, SAMN45951204, SAMN45951205, SAMN45951206, SAMN45951208, SAMN45951209, SAMN45951210, SAMN45951211, SAMN45951212, SAMN45951213, SAMN45951214, SAMN45951215, SAMN45951216, SAMN45951217, SAMN45951218, SAMN45951219, SAMN45951220, SAMN45951221, SAMN45951222, SAMN45951223, SAMN45951224, SAMN45951225, and SAMN45951226.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003e3.3. Comparative genome analyses and bioinformatics\u003c/h2\u003e \u003cp\u003eThe whole genome sequences were initially transferred to Geneious Prime v2024.0 (geneious.com) for processing, where sequence isolations were conducted. Isolated sequences were enhanced through in-house BLAST-P and the Biopython library function pairwise2.align.globalxx. These methodologies were implemented via in-house Python scripts to conduct searches on individual genomes. Phylogenetic trees based on these whole genome sequences were constructed by uploading the sequences to the Type Strain Genome Server (TYGS) [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. Amino acid sequences for chosen proteins and protein complexes were aligned using ClustalW [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e], and the aligned amino acid sequences were visualized using JalView [\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. Core genome alignment was generated using MAFFT (-e -n) [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e, \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e] for further analysis. The core genome refers to the set of genes shared by all strains within a given species or group, representing essential functions and common characteristics. PGC synteny was constructed using EasyFig version 2.2.5 [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e].\u003c/p\u003e \u003cp\u003ePhylogenetic trees were assembled in Geneious Prime and MEGA v 11 [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e] and subsequently refined and visualized using the Interactive Tree Of Life (iTOL) platform [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e]. ANIs for the whole genome and core genome sequences were calculated using fastANI [\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. A multidimensional scaling (MDS) graph, illustrating the genetic distances among the strains based on fastANI results, was constructed using in-house Python script (Supplementary Fig.\u0026nbsp;2). Plasmid sequences within the utilized strains were extracted using the Platon Plasmid Finder tool [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e]. Generally, visualizations of the results were generated with home-built Python scripts. MDS was applied to visualize the clustering of strains based on the distance matrix, and the results were plotted with annotated strain identifiers, and labels indicating the proportion of variance explained by the principal coordinates. Statistical analyses and MSA were performed using custom Python scripts.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003e3.4. Structure predictions of the Xanthorhodopsin\u003c/h2\u003e \u003cp\u003eAmino acid sequences of the XR proteins from 17 strains were aligned using ClustalW [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e] to identify conserved motifs and polymorphisms. Protein structure predictions were performed using SWISS MODEL [\u003cspan additionalcitationids=\"CR61 CR62 CR63\" citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e], which also provided Protein Data Bank (PDB) files for further analysis. The sequences were uploaded to UniProt to identify binding sites and functional motifs. DeepTMHMM\u0026thinsp;\u0026minus;\u0026thinsp;1.0 [\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e] was used to predict the transmembrane locations of the proteins. The resulting protein structures and motifs were visualized using PyMOL 3.0 (pymol.org), highlighting key functional regions and conserved features essential for XR function.\u003c/p\u003e \u003c/div\u003e"},{"header":"4. Results","content":"\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003e4.1. Genome sequence screenings\u003c/h2\u003e \u003cp\u003eThe genomes of 26 \u003cem\u003eS. faeni\u003c/em\u003e strains varied in size from 4.1 to 5.4 Megabases (Mb). Although it was not possible to extract plasmid sequences from three strains, the number of plasmid sequences is estimated to range from one to seven. Supplementary Table\u0026nbsp;1 provides a detailed overview of the general characteristics of the 26 S. \u003cem\u003efaeni\u003c/em\u003e strains examined in this study.\u003c/p\u003e \u003cp\u003eAll the seven strains, which showed positive NIR-fluorescence signal in the bacterial imaging analysis (not shown), contained complete PGC sequences in their genome. This confirmed the AAP character of these strains and we named these strains as AAP positive strains. We detected XR genes in 16 of the 20 AAP negative strains. Despite lacking the AAP genes, this subgroup is also classified as phototrophic, as they have potential to utilize light-driven redox reactions through a retinal-rhodopsin-based proton pumping mechanism. Here, we call these XR strains. To summarize, in our analysis we have AAP positive group, which contain the PGC, XR group, which contain XR gene, and a \u0026ldquo;none\u0026rdquo; group that contain neither of those phototrophic gene patterns (four strains) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Thirteen of the strains, all belonging to the \u0026ldquo;none\u0026rdquo; or XR groups, were isolated from endosphere, phyllosphere or seeds of \u003cem\u003eO. digyna\u003c/em\u003e and \u003cem\u003eB. vivipara\u003c/em\u003e in oroarctic and arctic regions. The seven AAP positive strains were collected from subarctic \u003cem\u003eV. myrtillus\u003c/em\u003e or \u003cem\u003eV. vitis-idaea\u003c/em\u003e plants, both from endosphere and phyllosphere, without any specifity of the location (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). In addition one none-strain and four XR strains originated from \u003cem\u003eV. vitis-idaea\u003c/em\u003e plants.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003e\u003cb\u003eStrains used in this study.\u003c/b\u003e The NCBI accession number of MA-Olki type-strain is under the \u0026ldquo;Location\u0026rdquo;. The strains are ordered according to their isolation source and phototrophy. FI: Finland, SV: Svalbard. The map of locations is shown in Supplementary Fig.\u0026nbsp;1.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eStrain\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHost\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLocation\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNiche\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003ePhototrophy\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eSource\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVOU02AS02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.myrtillus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVTK02DS03\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.myrtillus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTurku, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVUT02AP02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.myrtillus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eUtsjoki, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVTK02EP11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.myrtillus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTurku, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVKS02BS02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.myrtillus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKuusamo, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePTK02CS01\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTurku, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePES02AP01\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eEspoo, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NBS01\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NCP01\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NBP02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NCP02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NBS02\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eV.vitis-idaea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eOulu, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1DT4B\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLongyearbyen, SV\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1BT3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLongyearbyen, SV\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1BD2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLongyearbyen, SV\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eS2H28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9OR8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSeed\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e26OR1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSeed\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJPL28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eS3H21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJWL30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJWL22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJWL2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eO. digyna\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEndophytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJOBD13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eB. vivipara\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJOBD21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eB. vivipara\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKilpisj\u0026auml;rvi, FI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEpiphytic\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eThis study\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMA-Olki\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNCBI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_003053745.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eN/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNCBI\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003e4.2. Phototrophicity correlates with overall genomic composition\u003c/h2\u003e \u003cp\u003eA phylogenetic tree of the 26 \u003cem\u003eS. faeni\u003c/em\u003e strains was established using the full length 16S rRNA gene (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA). No differences were found in the 16S rRNA gene sequences among the AAP strains, which shared 100% similarity. 16S sequence differences between the AAP and none groups were 0.7\u0026thinsp;\u0026plusmn;\u0026thinsp;0.1%, and between the AAP and XR groups, 0.47\u0026thinsp;\u0026plusmn;\u0026thinsp;0.2%. Subsequently, we aligned the whole genomes to construct a phylogenetic tree, presented in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB. In whole genome alignment, the maximum difference between AAP and XR strains was 15\u0026thinsp;\u0026plusmn;\u0026thinsp;1.5%, while the difference between AAP and none strains was 10.7\u0026thinsp;\u0026plusmn;\u0026thinsp;1%. Whole genome similarity among the AAP strains was 96\u0026thinsp;\u0026plusmn;\u0026thinsp;0.7%. We distributed the whole genome sequences into four lineages (L1-L4, Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). The AAP positive \u003cem\u003eS. faeni\u003c/em\u003e strains (L3 lineage) cluster within the same phylogenetic group. The XR and none groups predominantly cluster according to their host. The L1 contains strains only from \u003cem\u003eV. vitis-idaea\u003c/em\u003e. All epiphytic \u003cem\u003eO. digyna\u003c/em\u003e strains locate in lineage L2. The L4 is the most heterogeneous linage in terms of the host or niche having strains from \u003cem\u003eB.vivipara\u003c/em\u003e, \u003cem\u003eO. digyna\u003c/em\u003e and \u003cem\u003eV. vitis-idaea\u003c/em\u003e, and both XR and none phototrophic groups, including the model strain of the study (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003e4.3. Photosynthetic gene cluster sequence and Xanthorhodopsin structures\u003c/h2\u003e \u003cp\u003eThe phototrophic strains have either a PGC or an XR gene. The PGC is very conserved in gene syntheny in the all studied \u003cem\u003eS. faeni\u003c/em\u003e AAP strains and only minor changes in the sequences of unknown hypotetical proteins exist (Supplementary Fig.\u0026nbsp;3). Due to the large size of the PGC, we did not perform a single amino acid level analysis for this region. Such detailed analysis was conducted, however, for the 17 obtained XR sequences. The amino acid similarity within the XR sequences ranged from a minimum of 79.6% to a maximum of 100% between strains. The phylogenetic tree presented in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e shows that, with the exception of strain S3H21, the XR sequences group according to the same lineages as observed in the whole genome analysis presented in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB.\u003c/p\u003e \u003cp\u003eTo explore potential structural differences, XR sequences from each lineages were selected for detailed structural analysis. Amino acid sequences were aligned to well known XR sequences from \u003cem\u003eSalinibacter ruber\u003c/em\u003e [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e, \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e], Kin4B8 from \u003cem\u003eBdellovibrionota bacterium\u003c/em\u003e [\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e], and AAP5 from \u003cem\u003eS. glacialis\u003c/em\u003e [\u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e68\u003c/span\u003e, \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e]. Alignment is shown in Supplementary Fig.\u0026nbsp;4. The secondary structure predictions indicated that the all XR proteins consist of seven alpha-helices (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e) and show very similar structural motifs with seven transmembrane regions, marked from 1 to 7.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eKey conserved motifs essential for XR function were identified. The primary proton acceptor Asp96 in \u003cem\u003eS. ruber\u003c/em\u003e [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e] corresponds the Asp92 in \u003cem\u003eS. faeni\u003c/em\u003e strains (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eA and Supplementary Fig.\u0026nbsp;4). In \u003cem\u003eS. ruber\u003c/em\u003e, the amino acid functioning as the proton donor at position Glu107 [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e] corresponds to Glu103 in \u003cem\u003eS. faeni\u003c/em\u003e strains. The Schiff base binding residue, located at Lys240 in \u003cem\u003eS. ruber\u003c/em\u003e [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e], is observed at Lys228 in \u003cem\u003eS. faeni\u003c/em\u003e. Carotenoid binding sites in \u003cem\u003eS. faeni\u003c/em\u003e strains exhibit substitutions compared to those in \u003cem\u003eS. ruber\u003c/em\u003e which binds salinixanthin as a carotenoid, but show closer correspondence with those of Kin4B8 (\u003cem\u003eB. bacterium\u003c/em\u003e) and AAP5 (\u003cem\u003eS. glacialis\u003c/em\u003e) which bind zeaxanthin and nostoxanthin, respectively [\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e, \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e]. The Gly153 in Kin4B8 (Gly156 in \u003cem\u003eS. ruber\u003c/em\u003e), which facilitates a so called fenestration and therefore energy transfer from a carotenoid to retinal, can be found in all studied \u003cem\u003eS. faeni\u003c/em\u003e strains as Gly149. Other common residues in the carotenoid binding sites are listed in Supplementary Table\u0026nbsp;2 and show closer correspondence to those of the Kin4B8 and AAP5 sequences, particularly to a tyrosine residue (Y209) in Kin4B8, which has been shown to be important for carotenoid hydroxyl group binding [\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e], than that of \u003cem\u003eS. ruber\u003c/em\u003e. It is also interesting to note that in our protein models, together with the alignment of Kin4B8 (with PDB code 8I2Z), a Lys184 site in the studied \u003cem\u003eS. faeni\u003c/em\u003e strains resembles, structurally, the Asn188 position in Kin4B8 among several other amino acids along the carotenoid molecule (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eC), suggesting that \u003cem\u003eS. faeni\u003c/em\u003e XRs bind a hydroxyl containing carotenoid molecule, like zeaxanthin or nostoxanthin, instead of a 4-keto group carotenoid, such as salinixanthin or echinenone. A few carotenoid binding sites show variation among the \u003cem\u003eS. faeni\u003c/em\u003e groups; the L1 (POU06-group) lineage has a Val145 instead of Ala145 in other lineages, but also lineage independent variation at the positions Arg184 versus Lys184 and Ser153 versus Ala153 can be pinpointed (Supplementary Fig.\u0026nbsp;4 and Supplementary table 2). It will be interesting to investigate in future studies whether these amino acids play a critical role in determining the carotenoid type or the energy transfer efficiency in these strains and how the carotenoid is located in these XR proteins, as the SWISS-MODEL structural predictions lack the positioning of the cofactors of the proteins.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe conserved 3-omega motif, a characteristic of various eubacterial rhodopsins, is partially present in the \u003cem\u003eS. faeni\u003c/em\u003e strains. In \u003cem\u003eS. ruber\u003c/em\u003e, the first aromatic amino acid of this motif is Tyr13 in helix A [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e], while in \u003cem\u003eS. faeni\u003c/em\u003e, it corresponds to Tyr9 in POU06NCP02, and Phe9 in JWL30 strains (Supplementary Fig.\u0026nbsp;4). The second aromatic component, Trp70 in helix B of \u003cem\u003eS. ruber\u003c/em\u003e, is Trp66 in \u003cem\u003eS. faeni\u003c/em\u003e. However, instead of the third aromatic component in the B-C loop, Tyr81 in \u003cem\u003eS. ruber\u003c/em\u003e, non-aromatic residues Val77 and Ile77 exists in L1 and L4 strains, respectively.\u003c/p\u003e \u003cp\u003eIn summary, the analysis identified key conserved motifs, primary proton donor, the retinal binding pocket with the critical proton acceptor and another proton donor, the proton release group, and the Schiff base for which carotenoid can transfer excitation energy. The carotenoid binding site suggests for a hydroxyl grouped carotenoid and some amino acid variations among and between the lineages can be observed, which may indicate different type of carotenoid binding in each of the \u003cem\u003eS. faeni\u003c/em\u003e strains.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003e4.4. 5-ALA Sequences\u003c/h2\u003e \u003cp\u003e5-ALA is a crucial precursor in the biosynthesis of tetrapyrroles, which include essential molecules such as chlorophyll, heme, and vitamin B12 [\u003cspan citationid=\"CR70\" class=\"CitationRef\"\u003e70\u003c/span\u003e]. In phototrophic bacteria, 5-ALA is synthesized through two main pathways: the C4 pathway (also known as the Shemin pathway) and the C5 pathway [\u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e71\u003c/span\u003e]. The C4 pathway involves the condensation of glycine and succinyl-CoA, catalyzed by the enzyme 5-ALA synthase, which is encoded by the \u003cem\u003ehemA\u003c/em\u003e gene. During the analysis of PGC\u0026rsquo;s of AAP strains, 5-ALA, a precursor in heme synthesis [\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e] was found. As expected, 5-ALA sequences were identified in all strains, regardless of the phototrophic group. Intriguingly, the AAP positive strains exhibited the presence of two copies of the gene involved in 5-ALA synthesis, with one copy consistently located within the PGC, while the other is situated outside of the PGC. In contrast, AAP negative strains (both \u0026lsquo;XR\u0026rsquo; and \u0026lsquo;none\u0026rsquo; group) contained only a single copy. We extracted the 5-ALA sequences from our strains, and then performed an alignment. In the alignment results, the amino acid sequences of 5-ALA across phototrophic groups demonstrate a minimum similarity of 87%. However, within the PGC, the 5-ALA sequences exhibit a maximum similarity of only 67% when compared with 5-ALA sequences from outside the PGC. Conversely, non-PGC 5-ALA sequences from AAP strains show up to 96% similarity with those from XR and other none group 5-ALA sequences.This difference can be observed in the phylogenetic tree constructed based on the alignment results (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e), which also shows that the 5-ALA phylogeny follows the host species distribution, marked as different lineages, as described in the Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003e4.5. Photosensors in different phototrophic groups\u003c/h2\u003e \u003cp\u003eWe analyzed the photosensor capacity of the strains in two fold. First the number of Blue Light Using Flavin (BLUF), bacteriophytochromes (BphP), sensory rhodopsins (SR), and photoactive yellow proteins (PYP) for each strain, are identified as presented in Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e. The photosensor content followed largerly the lineages based on whole genome similarity, presented in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB. The strains in lineage L1 contained BLUFs and BPhPs, but none of these strain contained PYP or SR. On the other hand, all BLUF sensors were absent in the lineage L2, but multiple PYPs, BphPs and SR were present in this lineage. The L3 strains, which all contain PGC, had on average the highest number and the most versatile set of photosensors. The lineage L4 had the largest range in number of photoreceptors per strain, from the least amount but also one of the highest amount of photosensors of our strain collection. This lineage shows also that the non-phototrophic strains had generally the least amount of photosensors, as also observed in Ihalainen et al [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn the second analysis, the neighbouring genes of the identified photosensors associated with each lineage were investigated (Supplementary Table\u0026nbsp;3). Several patterns of functional groups could be identified in the analysis. The BLUF photoreceptors were flanked by Superoxide dismutase on the 5' side in the L1BT3 strain and 9OR8, belonging to the lineage L4. The BLUFs in strains of the lineage L1 all had a N5-carboxyaminoimidazole ribonucleotide synthase on the 3' side. In terms of BphP genes, we identified that in all studied strains one BphP is related with a sodium/bile acid transporter in the 5\u0026rsquo; neighboring site. With the same BphP gene the 3\u0026rsquo; side varied according to the lineages. The L1 showed a hypotetical protein, the L2 lineage indicated an estrase/lipase gene, the L3 a M38 beta-aspartyl dipeptidase gene and L4 an uncharacterized MFS-transporter or a ferrichrome-iron receptor. An exception was JOBD21 strain which also showed a M38 gene on the 3\u0026rsquo; side from the BphP gene. The second dominating BphP related 5\u0026rsquo; gene was a cAMP-binding proteins - catabolite gene activator gene, which could be found from strains from the L1, L3 and L4 lineages. The L2 lineage lacked these BphP related cAMP-binding protein genes but contained mannonate dehydratase genes on 3\u0026rsquo; side in the few strains. An oxidoreductase gene on the 3\u0026rsquo; side was found from the few strains of L4 lineage and transposase genes could be also identified from L1 and L4 strains. In the analysis of PYP-flanking genes we found that some strains of the L2 lineage showed a chloride channel protein as a 5\u0026rsquo; neighbor whereas AAP or XR containing strains from L3 and L4 lineages typically have GAF domain/GGDEF domain/EAL domain proteins in their 5' neighborhood. We found a PYP related or BphP related transcriptional regulator in one L2 strain (5\u0026rsquo; side) and in two L3 strains (3\u0026rsquo; side), respectively. All in all, multitude of potentially important gene products related to photosensor proteins could be identified, and it is highly interesting to test their functionality in biochemical and biophysical terms in the future.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003e\u003cb\u003eTypes of light-harvesting systems, rhodopsins, and the number of photoreceptor proteins in the studied\u003c/b\u003e \u003cb\u003eS. faeni\u003c/b\u003e \u003cb\u003estrains.\u003c/b\u003e Rho: Rhodopsin Type, SR: Sensory Rhodopsin, XR: Xanthorhodopsin, LH: Light-Harvesting System, BLUF: BLUF Domain (Blue Light Using Flavin), BphP: Bacteriophytochrome, PYP: Photoactive Yellow Protein\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eStrain\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBLUF\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eBphP\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePYP\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003ePhototrophy\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eLineage\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePES02AP01 (P)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eVTK02DS03 (P)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVTK02EP11 (M)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVUT02AP02 (M)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eVOU02AS02 (M)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003ePTK02CS01 (P)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eVKS02BS02 (M)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLH1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAAP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NCP02 (P)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003ePOU06NBS01 (P)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NCP01 (P)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePOU06NBP02 (P)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1BD2 (O)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1DT4B(O)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eL1BT3 (O)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSR \u0026amp; XR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eS2H28 (O)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJOBD13 (B)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e9OR8 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e26OR1 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSR \u0026amp; XR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eJPL28 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eS3H21 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eJWL30 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eJWL22 (O)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJWL2 (O)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eXR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRho\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eJOBD21 (B)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMA-Olki (NCBI)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003ePOU06NBS02 (P)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e"},{"header":"5. Discussion","content":"\u003cp\u003eThe genetic composition of individual bacterial strains among the same species can be quite divergent. Here, we demonstrate this with 25 \u003cem\u003eS. faeni\u003c/em\u003e strains isolated from various plant hosts, \u003cem\u003eO. digyna, V. myrtillus\u003c/em\u003e, \u003cem\u003eV. vitis-idaea, and B. vivipara\u003c/em\u003e, from boreal, sub-arctic and arctic regions. The strains could be divided into four different lineages based on whole genome alignment, which was also reflected in more detailed genomic analysis along this study. The lineages based on whole genome alignment correlated with three phototrophic strategies of these strains: AAP positive, XR containing, and non-phototrophic bacterial strains. Interestingly, their overall phylogeny together with their phototrophy correlated also with the plant from which these strains were isolated. Our AAP positive strains were all from \u003cem\u003eVaccinium\u003c/em\u003e species, from phyllo- or endosphere of \u003cem\u003eV. myrtillus\u003c/em\u003e or from \u003cem\u003eV. vitis-idaea\u003c/em\u003e plants. Both of these plant species are perennial shrubs dominating in boreal forests and common also in arctic fell flora, and thus, offer a long term habitat for their microbial companions. In our previous study, we detected a high abundance of AAPB - in particular endospheric AAPB - in perennial plants that retain their photosynthetic tissues also through winter months [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. In that same study, we isolated diverse AAP positive Methylobacteria from these \u003cem\u003eVaccinium\u003c/em\u003e species [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. What might be the role, if any, of AAP in the interaction with \u003cem\u003eVaccinium sp.\u003c/em\u003e and AAPB, remains to be investigated. Our preliminary analysis of the genes other than PGC specific to AAP positive, Vaccinium associated strains did not offer any obvious clues to this, but are an obvious target for further studies.\u003c/p\u003e \u003cp\u003eCuriously, throughout our campaigns we never found any AAP positive \u003cem\u003eS. faeni\u003c/em\u003e strains from \u003cem\u003eO. digyna\u003c/em\u003e or from \u003cem\u003eB. vivipara\u003c/em\u003e, although \u003cem\u003eS. faeni\u003c/em\u003e has been shown to be abundant in these plants [[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e] and Nissinen, unpublished]. The endophytic strains from \u003cem\u003eO. digyna\u003c/em\u003e formed their own lineage in whole genome alignment. Instead we found that the strains from \u003cem\u003eO. digyna\u003c/em\u003e contained an XR protein indicating therefore a potential for phototrophy but without \u0026ldquo;an expensive\u0026rdquo; photosynthetic machinery. Unlike \u003cem\u003eV. myrtillus\u003c/em\u003e and \u003cem\u003eV. vitis-idaea\u003c/em\u003e, \u003cem\u003eO. digyna\u003c/em\u003e and \u003cem\u003eB. vivipara\u003c/em\u003e overwinter as rhizomes, with decidious above-ground stems and leaves.\u003c/p\u003e \u003cp\u003eCuriously, most of the AAP negative XR containing \u003cem\u003eS. faeni\u003c/em\u003e strains formed an own genomic linage, clearly distinct from AAP positive \u003cem\u003eVaccinium\u003c/em\u003e-associated strains. The genomic composition of this linage (L1 in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB) is particularly similar in the multidimensional scaling, XR sequence, and photosensor composition.\u003c/p\u003e \u003cp\u003eIn the predicted XR structures, the 3-omega motif of a Xanthorhodopsin containing AAP Rhodobacter strain, the third position is substituted by a non-aromatic Ile77 residue [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e, \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e], replacing the Tyr81 residue observed in \u003cem\u003eS. ruber\u003c/em\u003e XR. Similarly, substitutions in the 3-omega motifs of \u003cem\u003eS. faeni\u003c/em\u003e strains, involving non-aromatic residues such as valine and isoleucine, highlight the plasticity of this motif in XR proteins. The amino acid substitutions observed in \u003cem\u003eS. faeni\u003c/em\u003e XR proteins suggest both conservation of function and potential adaptive modifications. Key proton transfer residues, including Asp92 (Asp96 in \u003cem\u003eS. ruber\u003c/em\u003e), Glu103 (Glu107 in \u003cem\u003eS. ruber\u003c/em\u003e), and Lys228 (Lys240 in \u003cem\u003eS. ruber\u003c/em\u003e), remain unchanged, indicating that the retinal Schiff base binding and proton pumping mechanism are likely preserved. However, notable substitutions in the carotenoid binding region (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, Supplementary Fig.\u0026nbsp;4, Supplementary Table\u0026nbsp;2) suggest a nostoxanthin or zeaxanthin binding, similar to a comparable sequence of AAP5 [\u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e], which shows even a dual phototrophic character. Notably, the C-terminal structure of \u003cem\u003eS. faeni\u003c/em\u003e strains resembles to some extend that of light-gated cation channel rhodopsins [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAcross all \u003cem\u003eS. faeni\u003c/em\u003e strains in this study regardless of phototrophic group, the core genome, which consists of genes shared among all strains, exhibits minimal nucleotide variation (~\u0026thinsp;1%), highlighting a high degree of genetic consistency across the species. Furthermore, genome analytics such as ANI analysis and MDS based on ANI values highlight genetic consistency within phototrophic groups. These results align with our findings, as the phylogenetic trees in this study also exhibit a similar topology, suggesting a long term evolution of the PGC with the overall genome of these strains. This pattern is consistent with observations in other species, such as \u003cem\u003eCitromicrobium sp\u003c/em\u003e., which harbors two distinct phototrophic groups [\u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e], and haloalkaliphilic Rhodobacterales [\u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e74\u003c/span\u003e] which suggests that AAP strains have undergone stronger genetic conservation compared to other phototrophic or non-phototrophic groups.\u003c/p\u003e \u003cp\u003eThe plant-associated \u003cem\u003eS. faeni\u003c/em\u003e strains share their ecological niche with many other bacteria, making horizontal gene transfer plausible. However, the absence of significant differences in GC content between plasmids, PGC, and chromosomal DNA in this study indicates that the PGC has been co-evolving with the core genome for an extended period, with no strong evidence of recent horizontal gene transfer. Rather, it highlights that their genetic characteristics are closely integrated with the chromosomal genome.\u003c/p\u003e \u003cp\u003e5-ALA sequences were found in all \u003cem\u003eS. faeni\u003c/em\u003e strains used in the study. However, while the XR and none strains have only one 5-ALA gene, the AAP strains have two 5-ALA genes, one of which is always in the PGC. This situation resembles a common feature in AAP species [\u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e74\u003c/span\u003e]. Heme, being an essential component in various proteins, including those integral to photosynthesis and electron transport [\u003cspan citationid=\"CR75\" class=\"CitationRef\"\u003e75\u003c/span\u003e], implicates the necessity for more robust biosynthetic pathways in these phototrophs. The duplication of the 5-ALA gene in AAP positive strains, especially the positioning of one copy within the PGC, might reflect an evolutionary adaptation, providing a means for more nuanced regulation of heme synthesis. This positioning could cater specifically to the photosynthetic machinery, while the other gene copy addresses general cellular functions that require heme. Conversely, the single gene copy in AAP negative strains suggests a simpler heme biosynthesis pathway, sufficient for their non-photosynthetic metabolic demands. Furthermore, 5-ALA is not just a precursor in heme synthesis but also plays a role in the biosynthesis of various tetrapyrroles, like bacteriochlorophylls [\u003cspan citationid=\"CR76\" class=\"CitationRef\"\u003e76\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOur photosensor analysis revealed here and in our previous study the wider need for photosensing among phototrophs [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. However, the limited number of strains from the non-phototrophic group analyzed poses challenges in drawing statistically significant conclusions about this group. Still, the photosensor composition followed the linages in phylogeny grouping, but direct functional properties for particualr photosensors is challenging to propose. For example, we could not pinpoint any particular BphP genes near PGC regulating its function, similar as found for microsymbiotic nitrogen fixing bacteria \u003cem\u003eBradyrhizobium japonicum\u003c/em\u003e [\u003cspan citationid=\"CR77\" class=\"CitationRef\"\u003e77\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOn the other hand, one BphP was associated with sodium/bile acid symporters in every strain in this study (Supplementary Table\u0026nbsp;3). Together with presence of transcriptional regulators of the LysR family, this suggests a network where light sensing proteins influence membrane transport and gene expression, aligning with previous findings that highlight the role of photoreceptors in environmental adaptation [\u003cspan citationid=\"CR78\" class=\"CitationRef\"\u003e78\u003c/span\u003e]. Similarly, the proximity of PYP photoreceptors to GAF domain proteins and chloride channel proteins suggests their potential role in signal transduction and ion transport. This photoreceptor has already been shown to regulate biofilm formation in \u003cem\u003eIdiomarina loihiensis\u003c/em\u003e [\u003cspan citationid=\"CR79\" class=\"CitationRef\"\u003e79\u003c/span\u003e]. The frequent co-localization of BLUF photoreceptors with superoxide dismutase genes suggests a role in regulating the oxidative stress response. For instance, in \u003cem\u003eAcinetobacter baumannii\u003c/em\u003e, BlsA, a BLUF-type photoreceptor, has been shown to effectively stimulate catalase activity, trehalose production, fluoroquinolone antibiotic tolerance, and the Type VI secretion system (T6SS) a macromolecular secretion machinery used by many Gram-negative bacteria to eliminate competitors [\u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e80\u003c/span\u003e, \u003cspan citationid=\"CR81\" class=\"CitationRef\"\u003e81\u003c/span\u003e]. Recent studies further show the role of blue light photoreceptors in regulating photosynthetic and stress adaptive responses. In \u003cem\u003eDinoroseobacter shibae\u003c/em\u003e, the LOV-domain-containing protein LdaP was identified as a light dependent antirepressor that interacts with PpsR to regulate the photosynthetic gene cluster, demonstrating how photoreceptors modulate light driven gene expression at a transcriptional level [\u003cspan citationid=\"CR82\" class=\"CitationRef\"\u003e82\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTo conclude, the genomic sequencing of 25 \u003cem\u003eS. faeni\u003c/em\u003e strains, along with the type strain MA-Olki from the NCBI Genome Database, revealed genome sizes ranging from 4.1 to 5.4 Mb. Members of the XR group were the most prevalent, suggesting a widespread distribution of this photoreceptor among the strains. Our study enhances the understanding of microbial adaptation and the ecological dynamics of \u003cem\u003eS. faeni\u003c/em\u003e in Arctic and boreal environments. The findings highlight the complex relationship between genetic diversity and environmental adaptability, emphasizing the need for further investigation into the ecological impacts and evolutionary pathways of phototrophic strains, including both AAP and XR containing strains.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eUsed Python Scripts\u003c/h2\u003e\n\u003cp\u003eAll custom Python scripts can be found in this repository\u003c/p\u003e\n\u003cp\u003egithub.com/batuhanthebioinformatician/Plant_Microbiome_Phototrophy\u003c/p\u003e\n\u003ch2\u003eCompeting Interests:\u003c/h2\u003e\n\u003cp\u003eThe authors declare that they have no relevant financial or non-financial interests to disclose.\u003c/p\u003e\n\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\n\u003cp\u003eJ.A.I and R.N. conceptualized the work. R.N. and B.D performed the experimental work. B.D. wrote the genome analysis scripts and together with R.N. and Y.Z performed the genomic analysis. B.D., J.A.I,R.N.,Y.Z. analyzed the data and wrote the manuscript. B.D. prepared all figures and tables of the manuscript.\u003c/p\u003e\n\u003ch2\u003eAcknowledgement\u003c/h2\u003e\n\u003cp\u003eThe financial support for the study originates from KONE foundation (grant \u0026ldquo;Jaettu Valo\u0026rdquo;) and Science Council Finland (grant #259180 for Riitta Nissinen). Puhti supercomputer at the CSC - IT Center for Science in Finland was utilized to handle the demanding data processing and analysis tasks efficiently. This infrastructure provided the necessary computational power to conduct intensive genomic analyses and support the advanced bioinformatics processing required for this research. Ole Franz is acknowledged for instructive comments on the manuscript. The authors wish to thank Jani Hohti and Joonas Ik\u0026auml;valko for isolating the strains from O. digyna seeds.\u003c/p\u003e\n\u003ch2\u003eData Availability\u003c/h2\u003e\n\u003cp\u003eGenomes in this study were deposited in the NCBI Genome Database under BioProject ID PRJNA1202125. NCBI\u0026rsquo;s Average Nucleotide Identity (ANI) analysis confirmed that all strains belong to species S. faeni. The corresponding accession numbers are SAMN45951201, SAMN45951202, SAMN45951203, SAMN45951204, SAMN45951205, SAMN45951206, SAMN45951208, SAMN45951209, SAMN45951210, SAMN45951211, SAMN45951212, SAMN45951213, SAMN45951214, SAMN45951215, SAMN45951216, SAMN45951217, SAMN45951218, SAMN45951219, SAMN45951220, SAMN45951221, SAMN45951222, SAMN45951223, SAMN45951224, SAMN45951225, and SAMN45951226.All custom Python scripts can be found in this repository github.com/batuhanthebioinformatician/Plant_Microbiome_Phototrophy\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eHolmberg, S. M., \u0026amp; J\u0026oslash;rgensen, N. O. G. (2023). Insights into abundance, adaptation and activity of prokaryotes in arctic and Antarctic environments. \u003cem\u003ePolar Biology\u003c/em\u003e, \u003cem\u003e46\u003c/em\u003e(5), 381\u0026ndash;396.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMorgan-Kiss, R. M., et al. (2006). 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(2024). \u003cem\u003eThe blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression\u003c/em\u003e. \u003cem\u003eFrontiers in Microbiology\u003c/em\u003e, 15.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"photochemical-and-photobiological-sciences","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ppss","sideBox":"Learn more about [Photochemical \u0026 Photobiological Sciences](https://link.springer.com/journal/43630)","snPcode":"43630","submissionUrl":"https://www.editorialmanager.com/ppss/","title":"Photochemical \u0026 Photobiological Sciences","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-9081327/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9081327/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSolar radiation impacts most life forms on Earth by acting as a energy source or a regulatory signal. However, relatively little is still known about phototrophic potential and strategies of environmental bacteria beyond Cyanobacteria. This study explores the phototrophy related genomic diversity of \u003cem\u003eSphingomonas faeni\u003c/em\u003e strains from Arctic and sub-Arctic regions. We analyzed the genomes of 25 plant-associated \u003cem\u003eS.faeni\u003c/em\u003e strains isolated from \u003cem\u003eVaccinium myrtillus\u003c/em\u003e, \u003cem\u003eOxyria digyna\u003c/em\u003e, \u003cem\u003eVaccinium vitis-idaea\u003c/em\u003e, and \u003cem\u003eBistorta vivipara\u003c/em\u003e, along with a reference \u003cem\u003eS. faeni\u003c/em\u003e genome MA-olki. The strains showed diversity both in overall genome level but also in phototrophic capabilities: Seven strains were identified as aerobic anoxygenic phototrophic (AAP) bacteria with a complete photosynthetic gene cluster, 16 strains contained Xanthorhodopsin (XR) genes, and three strains were non-phototrophic, possessing no AAP or XR genes. The AAP strains were found exclusive from \u003cem\u003eVaccinium\u003c/em\u003e hosts. \u003cem\u003eO. digyna\u003c/em\u003e contained only XR containing strains and \u003cem\u003eB. vivipara\u003c/em\u003e showed XR genes and one non-phototrophic strain. \u003cem\u003eV. vitis-idaea\u003c/em\u003e hosted strains for all three different phototrophy categories. Phylogenetic analyses using 16S rRNA gene and whole genome alignments showed AAP positive strains forming a tight phylogenetic group. We found no strong evidence of horizontal gene transfer of photosynthetic gene cluster. XR strains and non-phototrophic strains clustered into three different subgroups. Phototrophic strains had more photoreceptors, and AAP strains exhibited dual copies of the 5-aminolevulinic acid (5-ALA) gene within the photosynthetic gene cluster (PGC). Our genomic analysis suggests a relationship between phototrophic strategies and host plant specificity.\u003c/p\u003e","manuscriptTitle":"Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-13 15:56:01","doi":"10.21203/rs.3.rs-9081327/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-05-04T20:33:30+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-05-04T18:23:37+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-14T08:13:11+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"258217702497695294307143766045909228419","date":"2026-04-09T14:21:41+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"151561940341456901848457332738022795720","date":"2026-03-16T13:06:02+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-11T12:45:16+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-10T14:28:48+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-10T14:12:37+00:00","index":"","fulltext":""},{"type":"submitted","content":"Photochemical \u0026 Photobiological Sciences","date":"2026-03-10T08:28:42+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"photochemical-and-photobiological-sciences","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ppss","sideBox":"Learn more about [Photochemical \u0026 Photobiological Sciences](https://link.springer.com/journal/43630)","snPcode":"43630","submissionUrl":"https://www.editorialmanager.com/ppss/","title":"Photochemical \u0026 Photobiological Sciences","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"765a06d8-bc31-4f9a-aaa6-245a04ec4b34","owner":[],"postedDate":"March 13th, 2026","published":true,"recentEditorialEvents":[{"type":"decision","content":"Revision requested","date":"2026-05-04T20:33:30+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-05-04T18:23:37+00:00","index":22,"fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2026-05-04T20:38:40+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-13 15:56:01","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9081327","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9081327","identity":"rs-9081327","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}