Symbiodiniaceae diversity associated with mesophotic Leptoseris corals on eastern Australian reefs

Symbiodiniaceae diversity associated with mesophotic Leptoseris corals on eastern Australian reefs | 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 Short Report Symbiodiniaceae diversity associated with mesophotic Leptoseris corals on eastern Australian reefs Johanna C Gijsbers, Matthew R Nitschke, Veronica Z Radice, Pim Bongaerts This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9544615/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 7 You are reading this latest preprint version Abstract The intimate relationship between scleractinian corals and endosymbiotic dinoflagellates (Symbiodiniaceae) drives primary production and calcification in reef ecosystems. Despite the extensive research focused on coral-Symbiodiniaceae relationships at shallow depths, only a few studies have assessed the symbiont diversity at mesophotic depths. Here, we examined the Symbiodiniaceae diversity associated with nine putative mesophotic Leptoseris species in Australian reefs using the ITS2 and COI marker regions. Amplicon sequencing revealed an almost exclusive association with the genus Cladocopium . While the COI region retrieved four distinct haplotypes, 17 ITS2 profiles grouped into five clusters were identified. Across the Symbiodiniaceae profiles, 24% were found across wide depth ranges, although 53% were only observed at mesophotic depths. Despite a certain degree of host-symbiont specificity, geography and depth also contributed significantly to the composition of Symbiodiniaceae communities. These findings provide much-needed insights into the diversity of Symbiodiniaceae associations with mesophotic Leptoseris , and emphasize the need for further research to establish to what extent lower mesophotic habitats in the Indo-Pacific harbor unique versus generalist endosymbiont associations. Coral ITS2 Leptoseris Mesophotic Symbiodiniaceae Figures Figure 1 Figure 2 Introduction Tropical coral reefs are globally known for being among the most productive ecosystems, providing habitat for many marine organisms and essential services to coastal communities (LaJeunesse et al. 2018 ; Muscatine and Porter 1977 ). Central to the health, resilience, and productivity in nutrient-poor waters lies a complex symbiotic relationship formed between reef-building corals (i.e., scleractinian corals) and endosymbiotic dinoflagellates (Symbiodiniaceae; Muscatine and Cernichiari 1969 ; reviewed in Davies et al. 2023 ). Corals provide the endosymbiotic algae with carbon dioxide and nitrogen for photosynthesis (Pearse and Muscatine 1971 ), while the symbiont enhances calcification and can support the coral’s metabolism through photosynthetic products (Rädecker et al. 2023 ). However, this association can become disrupted under certain stressors, most notably thermal stress. A major loss of the symbiont population from the coral host tissues can result in mortality of the host (Gates et al. 1992 ; Fagoonee et al. 1999 ). These complex host-symbiont dynamics have been a major research focus due to their ecological significance (Glynn 1993 ; Baker et al. 2008 ), especially in the context of increasing sea temperatures and the frequency of thermal stress events. As the vast majority of this research has focused on shallow reef environments, little remains known about host-symbiont interactions in the mesophotic zone, where reduced light availability must have a profound effect on these relationships. The limited studies that have investigated Symbiodiniaceae diversity at mesophotic depths have revealed contrasting biogeographical patterns in the Caribbean and Indo-Pacific regions. While studies from the Caribbean predominantly report specialized Symbiodiniaceae communities (Frade et al. 2008 ; Bongaerts et al. 2013 , 2015a , 2015b ; Lesser et al. 2010 ; but see Gonzalez-Zapata et al. 2018 ), those from the Indo-Pacific frequently report the presence of depth-generalist symbiont types at mesophotic depths (Chan et al. 2009 ; Bongaerts et al. 2011 ; Pérez-Rosales et al. 2024 ). Nonetheless, the sparse reports from coral colonies at the lower mesophotic limits - such as Leptoseris at 100 m (Chan et al. 2009 ), 125 m (Pochon et al. 2015 ), and 172 m (Rouzé et al. 2021 ) - hypothesize the presence of unique Symbiodiniaceae genotypes potentially adapted to the extreme environmental conditions of mesophotic ecosystems (Ferrier-Pagès et al. 2022 ; Pérez-Rosales et al. 2024 ). Similarly, evidence suggests mesophotic Symbiodiniaceae rely on a photosynthetic adaptive mechanism rather than acclimation strategies to survive and dominate extreme environments (Einbinder et al. 2016 ). Thus far, Cladocopium is the predominant genus associated with scleractinian corals in mesophotic environments (Pochon et al. 2015 ; Pérez-Rosales et al. 2024 ); however, other genera, such as Breviolum , Symbiodinium , and Durusdinium have also been found in those depths to a lesser extent (Frade et al. 2008 ; Bongaerts et al. 2015a ; Ziegler et al. 2015 ; Goulet et al. 2019 ). The genus Leptoseris , within the Agariciidae family, is among the most dominant genera on mesophotic reefs across the Indo-Pacific (Pochon et al. 2015 ; Englebert et al. 2017 ). However, Leptoseris species occur across a wide range of depths and reef environments (Kahng and Kelley 2007 ; Chan et al. 2009 ; Hoeksema 2012 ; Luck et al. 2013 ; Pochon et al. 2015 ; Terraneo et al. 2017 ; Pichon et al. 2020 ; Hoarau et al. 2021 ; Gijsbers et al. 2023 ). In an effort to understand the potential adaptations that enable this genus to thrive in such variable light regimes, earlier studies have reported physiological specializations (Schlichter et al. 1986 ; Schlichter 1991 ; Kahng et al. 2023 ). Yet the specificity of these traits has been challenging to assess, due to the taxonomic uncertainty and ambiguity around the currently acknowledged Leptoseris species (Luck et al. 2013 ; Benzoni 2022 ). A recent phylogenomic assessment of Leptoseris has revealed deep genetic divergences and multiple sympatric, distinct lineages, suggesting a higher level of host diversity than previously recognized (Gijsbers et al. 2023 ). Leveraging samples from this dataset, we use a subset of these Leptoseris specimens to assess Symbiodiniaceae diversity (using ITS2 and COI amplicon sequencing) to explore host-symbiont relationships, taking into account this previously undescribed host diversity. Materials and Methods Representative Leptoseris specimens from each of the nine genetically divergent lineages – encompassing four taxonomically recognized species ( Leptoseris scabra , L. glabra , L. mycetoseroides , and L. hawaiiensis ) — were selected from the Gijsbers et al. ( 2023 ) dataset. These specimens (n = 52) spanned a depth gradient of 10–82 m in the Northern Great Barrier Reef and Western Coral Sea Australia (Gijsbers et al. 2023 ), with two further samples included from 124 and 127 m depth (figure S1 ). Given the previously established genetic divergence and putative species status using species delimitation methods, we refer to these as “species” or “genetic lineage” in this study. The internal transcribed spacer 2 (ITS2) region of Symbiodiniaceae ribosomal DNA was targeted for high-throughput amplicon sequencing from 52 Leptoseris specimens. DNA was extracted following the protocol described by Bongaerts et al. ( 2013 ). PCR amplifications of the ITS2 region were performed using the ITS2-specific primer set “SYM_VAR_5.8S2” and “SYM_VAR_REV” (~ 234–266 bp amplicon; Hume et al. 2013 , 2015 , 2018 ). All PCRs (25 µL reaction) contained 12.5 µL AmpliTaq Gold 360 MasterMix (Applied Biosystems, Life Technologies), 1 µL of forward primer (10 µM), 1 µL of reverse primer (10 µM), 0.75 µL DMSO, 8.25 µL ultrapure DI water, and 1.5 µL gDNA. Amplifications were conducted on a BioRad C1000 Touch Thermal Cycler. DNA concentration was quantified using a QuBit High Sensitivity dsDNA assay (Thermo Fisher Scientific). For the Symbiont mtDNA COI region, PCR amplifications were performed using the “COX1_FOR2” and “COX1_REV1” (~ 1000 bp) primers as described by Pochon et al. ( 2012 ). ITS2 and COI amplicons were sequenced (August 2018) on an Illumina MiSeq platform (2 x 300 bp) at the Australian Genome Research Facility, University of Queensland. Finally, the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence COI count data using default settings. The resulting raw ITS2 sequencing reads were demultiplexed and further analyzed using the SymPortal analytical framework ( https://symportal.org , Hume et al. 2019 ). This pipeline uses a series of steps to filter out non-Symbiodiniaceae sequences and identify ITS2 defining intragenomic variants (DIVs) within Symbiodiniaceae genera. SymPortal performs minimum entropy decomposition (Eren et al. 2015 ) to calculate the amount of genomic variation and classifies this as distinct DIVs. Then, it predicts Symbiodiniaceae ITS2-type profiles (which represent hypothetical Symbiodiniaceae taxa) based on the presence and abundance of the identified DIVs. All statistical tests were conducted in R (v.4.3.0, Team 2023 ). The relative abundance of post-MED ITS2 DIVs were used for statistical analyses, while the ITS2-type profiles were used to visualize different taxonomic units. This provides a more detailed and accurate approach to characterize both intra- and intergenomic variations within Symbiodiniaceae taxa. Before conducting statistical tests, we evaluated the degree of homogeneity of dispersion between-groups (region, site, depth, depth category, genetic lineage) using the vegan (v.2.6-4; Oksanen et al. 2022) function betadisper . Additionally, we checked nestedness among the different environmental and biogeographic factors (depth category: shallow (≤ 30 m), upper-mesophotic (31–59 m), lower-mesophotic (≥ 60 m); site; region; genetic lineage). Furthermore, significant differences among the resulting factors in the Symbiodiniaceae community were assessed using a series of Permutational Multivariate Analysis of Variance (PERMANOVA) tests using the adonis function from the vegan package. A comprehensive PERMANOVA model was conducted to evaluate the simultaneous effects of “ region and site ”, “ depth category ”, and “ genetic lineage ”. To do this, symbiont DIV counts were first Hellinger-transformed and then Bray-Curtis dissimilarity matrices were calculated. Pairwise comparisons were then conducted with 99,999 permutations using the pairwiseAdonis package (v. 0.4.1, Martinez Arbizu 2017 ). Variance partitioning was carried out using the varpart function of the vegan package to quantify the unique contribution of the significant variables to the variability in the symbiont community composition. Furthermore, Principal Coordinates Analysis (PCoA; cmdscale function, vegan package) was used to visualize the Symbiodiniaceae ITS2 sequence structure between Leptoseris focal species and genetic lineages, as well as between regions and across depths. Finally, to identify and visualize ITS2 profiles with specific association with the different host genetic lineages, we conducted an Indicator Species Analysis (IndVal) as part of the Indicspecies package (v. 1.8.0). To do this, we tested which ITS2 profiles were significantly associated specifically with each host genetic lineage using the multipatt function with 999 permutations and generated a network (figure S5) to visualize these associations. Phylogenetic relationships of the host were reconstructed under the maximum likelihood (ML) criterion, as implemented in the program IQ-tree (2.1.4-beta; Nguyen et al. 2015 ) under the GTR + I+G4 nucleotide substitution model with 1000 bootstrap replicates. Based on the ITS2-type profiles' phylogenetic similarities (as determined by UniFrac distances), we generated a hierarchical clustering dendrogram using the R built-in hclust function. Finally, correlation analyses within the symbiont community were performed based on ITS2-type profile relative abundances and UniFrac distances using Spearman’s rank correlation coefficient from the cor function of the corrplot package (v. 0.92; Wei et al. 2021 ; figure S4 ). COI-ITS2 correspondence was assessed based on the symbiont COI mtDNA region of 53 Leptoseris samples, including representatives from the Pochon et al. ( 2015 ) dataset. A COI haplotype network was generated using the PopART open-source software (Leigh and Bryant 2015 ). Results and Discussion Despite three decades of research on Symbiodiniaceae in shallow-water scleractinian corals, few studies have examined mesophotic depths, leaving our understanding of Symbiodiniaceae diversity, ecology, and adaptations to low-light environments severely limited (González-Pech et al. 2019 ; Goulet et al. 2019 ). Leveraging a unique collection of deep-water Leptoseris from the Great Barrier Reef (GBR) and Western Coral Sea (WCS) in Australia, we documented Symbiodiniaceae diversity by genotyping the ITS2 and COI regions, and found limited specificity across the nine Leptoseris species, with Symbiodiniaceae community composition explained through the combination of host species, location and depth. Using the SymPortal framework, 5,342,096 Symbiodiniaceae reads were recovered across all samples, with an average of 97,165 post-MED reads per sample. Of these, 99.89% of the sequences belonged to the genus Cladocopium (table S1 ). A total of 262 DIVs were recovered across all samples. While the majority represented low-abundance background variation, 35 unique DIVs consistently co-occurred to compose 22 ITS2-type profiles (Fig. 1 ). Five profiles were removed due to an overall low representation (< 1% of absolute abundance), resulting in a total of 17 profiles considered for statistical analyses. This pattern is consistent with previous reports of Symbiodiniaceae diversity across Indo-Pacific reefs, where the genus Cladocopium often dominates along an extensive depth gradient, and is frequently a dominant member at mesophotic depths (Chan et al. 2009 ; Goulet et al. 2019 ; Rouzé et al. 2021 ; Terraneo et al. 2023 ; Pérez-Rosales et al. 2024 ; Vimercati et al. 2024 ). Despite recovering 35 unique DIVs, the ITS2 profiles grouped into five genetically distinct clusters (based on UniFrac distances), dominated primarily by variants from the C21, C21x, C3, and C1 radiations (Fig. 1 ; figure S3). The C21/C3 cluster was the largest and dominated by C21/C3-related intragenomic variants (e.g., C21y, C21u, C3at), which is consistent with the evolutionary history of the genus Cladocopium , given that the C21 lineage diverged from the ancestral C3 (LaJeunesse 2005 ). Similarly, the C21x cluster was mainly dominated by C21x/C3-related variants. While based on UniFrac distances, the C21x cluster is closely related to the C21 clade; it formed a distinct genetic and ecological cluster. The C1 cluster was composed mainly of C1 variants (e.g., C1ar), with the exception of one profile where the ancestral variants C1 and C3 were co-dominant. The fourth and fifth cluster contained a single C115f and C116 profiles, respectively. The latter containing two profiles of DIVs C116 was co-dominant with C1 and C3. The most prevalent ITS2 profile was C1/C1ar-C1as-C3-C3co-C41l (table S1 ) and was only observed at mesophotic depths of the WCS. Although C1 represents a geographically and ecologically widespread ancestor (LaJeunesse 2005 ; Chan et al. 2009 ), the combination of these DIVs represents a novel profile with a strong presence at lower mesophotic depths, suggesting this profile might be a specialized lineage and possibly endemic to this region. While the generalists C21 and C3-radiations (e.g., C21/C3-C3at-C3av-C3b-C3dp) have been well-documented in association with plate-like morphologies, and at lower depths and across the Indo-Pacific, including Australian reefs, they are widely distributed across depths, sites, and environments (Bongaerts et al. 2011 ; Wagner et al. 2011 ; Padilla-Gamiño et al. 2012 ; Tonk et al. 2013 ; Grima et al. 2022 ; Marzonie et al. 2024 ). In contrast, the novel C1ar and C21x variants identified in this study exhibited a restricted depth and geographical distribution. Thus far, the C1ar lineage appears exclusive to mesophotic depths at WCS sites, as they have not yet been documented in shallow waters; similarly, the majority of the C21x profiles were restricted to lower mesophotic depths. The betadisper test revealed significant differences in the variability of community composition among depths (F = 3.92, p = 0.00307), indicating that depth, as a continuous variable, exhibited heterogeneous dispersion and could confound the interpretation of PERMANOVA results. Therefore, depths were grouped into depth categories (shallow, upper-mesophotic, lower-mesophotic). Furthermore, to account for the hierarchical structure of our sampling design, region and site were treated as nested variables. PERMANOVA results (table S2) indicated that 56% of the variation in the data was explained by region and site (R2 = 0.25, F = 2.37, p = 0.00017), host genetic lineage (R2 = 0.22, F = 2.11, p = 0.00107), and depth category (R2 = 0.09, F = 3.62, p = 0.00173). Cladocopium diversity varied significantly across host genetic lineages. C21/C3 cluster profiles were more predominantly associated with L. scabra (including L. scabra 1, L. scabra 2, DelineatedSp003), L. glabra , and L. hawaiiensis lineages. In contrast, lineages such as L. glabra / L. scabra , L . cf. mycetoseroides , and Leptoseris sp. 1 were mainly linked to the C. proliferum cluster and C116 cluster profiles (Fig. 1 ). The Indicator Species Analysis identified three ITS2 profiles with significant associations to particular host lineages. The most dominant ITS2 profile, C1/C1ar-C1as-C3-C3co-C41l, exhibited a significant association with L . cf. mycetoseroides , L. glabra/L. scabra , and Leptoseris sp. 1 ( p = 0.001). Similarly, while profile C21x/C3-C3av-C21-C21z-C58a-C21bi was significantly associated with L. hawaiiensis and L. scabra 2 ( p = 0.006), C3/C21x-C21-C3av-C3ag-C58a was significantly associated with DelineatedSp003 ( p = 0.03). These results indicate a strong host-symbiont fidelity, although such interpretations need to be cautioned due to the small sample sizes per lineage. Geographically, the C21/C3 cluster was almost exclusively found in the GBR, which is consistent with the patterns well-documented for these generalist lineages in the GBR (LaJeunesse et al. 2003 ), whereas all clusters were observed in the WCS (although the limited number of GBR representatives may constrain these geographic patterns' robustness). Similarly, significant differences in Cladocopium diversity were found among depth zones, with C21/C3 more common at shallow and upper mesophotic depths, with some exceptions from the C1 cluster. In contrast, profiles from all five clusters were observed at lower mesophotic depths, with the most abundant profiles being C1/C1ar and C21x/C3. Notably, clusters C115f and C116 were exclusively observed at lower mesophotic depths, even though these profiles have been reported at shallow depths across the Indo-Pacific, they are considered rare and opportunistic symbionts (Qin et al. 2019 ; Starko et al. 2023 ; Terraneo et al. 2023 ). Although a degree of host-symbiont and depth specificity was observed, the associations are not as straight-forward as observed previously in Hawai’i (Pochon et al. 2015 ). This flexibility is consistent with taxa that rely on broadcast spawning events as a reproductive strategy, acquiring their symbionts from the environment through horizontal transmission (Quigley et al. 2017 ). Despite sparse evidence, species within this genus are generally considered broadcast spawners (Baird et al. 2009 ); and thus acquiring Symbiodiniaceae from the environment might be an adaptive strategy to extreme depth and ecological gradients (Zarate et al. 2024 ). In addition, the broad geographical and depth distribution of samples and limited representation within each genetic lineage, depth, and location, may mask more defined trends within Leptoseris -Symbiodiniaceae associations. Using the mitochondrial COI marker, we retrieved four different haplotypes, referred to as COI-H1, COI-H2, COI-H3, and COI-H4, and we compared these to the COI-I, COI-II, and COI-III sequences from Pochon et al. ( 2015 ) (table S3). Three of these haplotypes broadly matched the ITS2 clusters (Fig. 2 ). The most abundant haplotypes were COI-H1 (56%) and COI-H3 (42%). COI-H1 matched almost exclusively the ITS2 C21/C3 cluster, with one sample matching the C115f cluster. COI-H2 (2%) corresponded to the C1/C3 type (table S3). COI-H3, which corresponds to the COI-III haplotype from Pochon et al. ( 2015 ), mainly corresponded to the C1 ITS2 profiles with some exceptions, where it matched ITS2 C21x/C21y, and C3/C21x profiles from C21x cluster. In addition, we included two samples from the end of the lower mesophotic zone (124 and 126 m, respectively), including the deepest photosymbiotic Leptoseris colony collected to date from the GBR (124 m, Englebert et al. 2015 ). These samples represented a distinct haplotype (COI-H4). However, we were unable to obtain ITS2 amplicon sequences from these specimens, and thus, their inclusion in the study is limited to providing new insights into the symbiont diversity at these extreme depths based on COI data. Unlike the host-specific haplotypes reported for species within the Leptoseris genus in other regions from the Indo-Pacific, such as Hawaii, where Pochon et al. ( 2015 ) observed strong depth zonation and host-symbiont specificity within L. scabra and L. hawaiiensis , we did not find strong host or depth-specificity on Australian reefs. COI-H1 and COI-H3 haplotypes were found along the depth range and were present broadly in all taxa. Despite their importance in mesophotic coral ecosystems across the Pacific, we are only beginning to understand how Leptoseris taxa can thrive under such low-light conditions. By developing thin, horizontal skeletons, these corals maximize their surface area while maintaining low skeletal investment; an efficient strategy that enables them to capture light and fulfill their metabolic needs through photosynthetic carbon (Carmignani et al. 2023 ; Kahng et al. 2023 , 2024 ). In addition to skeletal morphology, there may be other strategic adaptations such as mixed feeding modes and associations with endolithic green algae as an alternative energy source (Rouzé et al. 2021 ; Backstrom et al. 2024 ). At increasing depth, heterotrophy may become more important, yet autotrophy remains essential for their survival and may be fundamental to the skeletogenesis of these species at mesophotic depths (Backstrom et al. 2024 ), suggesting low-light adapted symbionts may play a critical role in this genus’ ability to occupy different environmental niches (Douglas 1998 ; Stat et al. 2008 ; Backstrom et al. 2024 ; Zarate et al. 2024 ). Conclusion Our findings reveal general signatures of host-symbiont specificity with occasional flexibility, with geography and depth also shaping Leptoseris ’ Symbiodiniaceae diversity. On one hand, the observed wide depth distributions of Symbiodiniaceae types – including the presence of some types found at very shallow and lower mesophotic zones – corroborate previous observations of depth-generalist endosymbionts prevailing at mesophotic depths. Nonetheless, despite the resolution of ITS2 amplicon sequencing, there may be further species- or population-level differentiation at mesophotic depths that cannot be discerned using this approach. On the other hand, the observation of novel Symbiodiniaceae variants that have not been reported before indicates that lower mesophotic specialist types may be present and contribute to the ecological success of deep-water Leptoseris communities. Despite our limited sampling within specific locations or depth zones, these results highlight the complexity of Leptoseris -Symbiodiniaceae interactions and underscore our limited understanding regarding photo-endosymbionts’ role in enabling this genus to inhabit such extreme low-light environments. Overall, these results underscore the need for high-resolution genetic studies, combined with functional assessments, to better understand the prevalence and potential mechanisms underlying low-light adaptation in Symbiodiniaceae at mesophotic depths. Declarations Conflict of Interest The authors declare that the research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. Author Contributions PB conceived and designed the present study. PB conducted the sample collection and taxonomical identifications. VZR conducted DNA extractions and amplicon sequencing. JCG conducted the statistical and bioinformatic analyses, generated the figures, and drafted the manuscript. MRN contributed to the bioinformatic and ecological interpretation. All authors read, edited, and approved the final manuscript. Acknowledgements We thank Norbert Englebert, David Whillas, Kyra Hay, and Paul Muir for their help with the original specimen collections, and the crews from Reef Connections, Mike Ball Dive Expeditions, SY Ethereal, and the Waitt Foundation for field support. Data availability statement This study utilizes a subset of raw nextRAD sequence data previously deposited in the NCBI Sequence Read Archive under BioProject PRJNA970738 (Gijsbers et al. 2023). New raw sequence data for the ITS2 and COI amplicons generated specifically for this study are available under BioProject XXXXX (pending) and will be made public upon acceptance of the manuscript. Funding This work was funded by the XL Catlin Seaview Survey (funded by the XL Catlin Group in partnership with Underwater Earth and The University of Queensland), and an Australian Research Council Discovery Early Career Researcher Award (DE160101433). References Backstrom CH, Padilla-Gamiño JL, Spalding HL, Roth MS, Smith CM, Gates RD, Rodrigues LJ (2024) Mesophotic corals in Hawai‘i maintain autotrophy to survive low-light conditions. 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Nat Commun 14:6948. https://doi.org/10.1038/s41467-023-42579-7 Rouzé H, Galand PE, Medina M, Bongaerts P, Pichon M, Pérez-Rosales G, Torda G, Moya A, Under The Pole Consortium, Bardout G, Périé-Bardout E, Marivint E, Lagarrigue G, Leblond J, Gazzola F, Pujolle S, Mollon N, Mittau A, Fauchet J, Paulme N, Pete R, Peyrusse K, Ferucci A, Magnan A, Horlaville M, Breton C, Gouin M, Markocic T, Jubert I, Herrmann P, Raina J-B, Hédouin L (2021) Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth). ISME J 15:1564–1568. https://doi.org/10.1038/s41396-020-00857-y Schlichter D (1991) A perforated gastrovascular cavity in the symbiotic deep-water coral Leptoseris fragilis : a new strategy to optimize heterotrophic nutrition. Helgoländer Meeresunters 45:423–43. https://doi.org/10.1007/BF02367177 Schlichter D, Fricke HW, Weber W (1986) Light harvesting by wavelength transformation in a symbiotic coral of the Red Sea twilight zone. Mar Biol 91:403–7. https://doi.org/10.1007/BF00428634 Starko S, Fifer JE, Claar DC, Davies SW, Cunning R, Baker AC, Baum JK (2023) Marine heatwaves threaten cryptic coral diversity and erode associations among coevolving partners. Sci Adv 9:32. https://doi.org/10.1126/sciadv.adf0954 Stat M, Morris E, Gates RD (2008) Functional diversity in coral–dinoflagellate symbiosis. Proc Natl Acad Sci U S A 105:9256–61. https://doi.org/10.1073/pnas.0801328105 Team RC (2023) R: a language and environment for statistical computing. R foundation for statistical computing. Vienna, Austria, Terraneo TI, Arrigoni R, Benzoni F, Tietbohl MD, Berumen ML (2017) Exploring the genetic diversity of shallow-water Agariciidae (Cnidaria: Anthozoa) from the Saudi Arabian Red Sea. Mar Biodivers 47:1065–1078. https://doi.org/10.1007/s12526-017-0722-3 Terraneo TI, Ouhssain M, Castano CB, Aranda M, Hume BCC, Marchese F, Vimercati S, Chimienti G, Eweida AA, Voolstra CR, Jones BH, Purkis SJ, Rodrigue M, Benzoni F (2023) From the shallow to the mesophotic: a characterization of Symbiodiniaceae diversity in the Red Sea NEOM region. Front Mar Sci 10:1077805. https://doi.org/10.3389/fmars.2023.1077805 Tonk L, Bongaerts P, Sampayo EM, Hoegh-Guldberg O (2013) SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef. BMC Ecol 13:7. https://doi.org/10.1186/1472-6785-13-7 Vimercati S, Terraneo TI, Castano CB, Barreca F, Hume B, Marchese F, Ouhssain M, Steckbauer A, Chimienti G, Eweida AA, Voolstra CR, Rodrigue M, Pieribone V, Purkis SJ, Qurban Mohammed, Jones BH, Duarte CM, Benzoni F (2024) Consistent symbiodiniaceae community assemblage in a mesophotic-specialist coral along the Saudi Arabian Red Sea. Front Mar Sci 11:1264175 https://doi.org/10.3389/fmars.2024.1264175 Wagner D, Pochon X, Irwin L, Toonen RJ, Gates RD (2011) Azooxanthellate? Most Hawaiian black corals contain Symbiodinium . Proc R Soc B Biol Sci 278:1323–1328. https://doi.org/10.1098/rspb.2010.1681 Wei T, Simko VR, Levy M, Xie Y, Jin Y, Zemla J (2021) Package “corrplot”: Visualization of a correlation matrix. Zarate D, Gary J, Li J (2024) Flexibility in coral–algal symbiosis is positively correlated with the host geographic range. Ecol Lett 27:e14374. https://doi.org/10.1111/ele.14374 Ziegler M, Roder CM, Büchel C, Voolstra CR (2015) Mesophotic coral depth acclimatization is a function of host-specific symbiont physiology. Front Mar Sci 2:4 https://doi.org/10.3389/fmars.2015.00004 Additional Declarations No competing interests reported. Supplementary Files LeptoITS2supplementary20260425.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviewers agreed at journal 13 May, 2026 Reviewers agreed at journal 12 May, 2026 Reviewers agreed at journal 04 May, 2026 Reviewers invited by journal 04 May, 2026 Editor assigned by journal 02 May, 2026 Submission checks completed at journal 27 Apr, 2026 First submitted to journal 27 Apr, 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-9544615","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Short Report","associatedPublications":[],"authors":[{"id":635302099,"identity":"10cfeda8-0e80-455c-b6f9-7c94192a8da7","order_by":0,"name":"Johanna C Gijsbers","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFklEQVRIiWNgGAWjYBACxgbGBgPGBiCLHUg8AAkdIFoLD1BpAjFaoPqAhEQCkVqY+xc3FP7cYZMvP/Pxww8JNXbyfMe70yQYKu7ZNeCyYMbDBmPeM2mWG26nGUskHEs2nHnm7DYJhjPFybi1HGwwZmw7bGAgnQN0G9sBxg03crdJMLYlJOP0BlCL4c+2/wbyM88w/0j4d8B+w/23BLT0NzYY8LYdMGC4wcMmkdh2IHHDDV6wFjvctjCC/JJsYHAmzcwisS85eeaZ3M0WCWcSEnBpMew//szw5w47A/n2w49vfPhmZ9t3/OzGGx8qEuxxapmRwGaALsgCiqPEBhxa5PkPMD9AF2T+ACRw2jIKRsEoGAUjDgAA/9ZljN35yp8AAAAASUVORK5CYII=","orcid":"","institution":"California Academy of Sciences","correspondingAuthor":true,"prefix":"","firstName":"Johanna","middleName":"C","lastName":"Gijsbers","suffix":""},{"id":635302101,"identity":"fe3d4006-93e6-4eb9-a5b3-2d93866f943c","order_by":1,"name":"Matthew R Nitschke","email":"","orcid":"","institution":"Australian Institute of Marine Science","correspondingAuthor":false,"prefix":"","firstName":"Matthew","middleName":"R","lastName":"Nitschke","suffix":""},{"id":635302102,"identity":"4084eea6-8a3c-4cda-9fd5-b589a4cd58e0","order_by":2,"name":"Veronica Z Radice","email":"","orcid":"","institution":"University of Queensland","correspondingAuthor":false,"prefix":"","firstName":"Veronica","middleName":"Z","lastName":"Radice","suffix":""},{"id":635302103,"identity":"0e258372-f7ef-4c61-8c69-ef7a7f9978e3","order_by":3,"name":"Pim Bongaerts","email":"","orcid":"","institution":"California Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Pim","middleName":"","lastName":"Bongaerts","suffix":""}],"badges":[],"createdAt":"2026-04-27 16:54:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9544615/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9544615/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":108995423,"identity":"c9a974d7-d0a8-4511-aae3-869a33adc2c9","added_by":"auto","created_at":"2026-05-11 14:08:01","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":429797,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSymbiodiniaceae community composition across \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eLeptoseris\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e spp. a)\u003c/strong\u003e Distribution of ITS2 profiles across depth. Each circle represents a coral colony with the color corresponding to the \u003cem\u003eCladocopium\u003c/em\u003eITS2 profile identified for the respective sample. \u003cstrong\u003eb) \u003c/strong\u003eEcogeographic association diagram. Dendrogram illustrating UniFrac distances of ITS2 profiles. The left panel connects samples based on geographic regions, GBR (blue) and WCS (red). The right panel connects samples based on three depth categories: shallow, upper mesophotic, and lower mesophotic (indicated by increasing tones of blue).\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-9544615/v1/31f6b2e268521289e6071faa.png"},{"id":108995424,"identity":"7db76469-233e-4675-af98-c780d0af8f50","added_by":"auto","created_at":"2026-05-11 14:08:01","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":347059,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eCOI-ITS2 correspondence within \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eLeptoseris\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e spp. a)\u003c/strong\u003eDistribution of COI haplotypes across depth. Each circle represents a coral colony with the color indicating the \u003cem\u003eCladocopium\u003c/em\u003e COI haplotype identified for the respective sample. \u003cstrong\u003eb) \u003c/strong\u003eHaplotype network of the \u003cem\u003eCladocopium \u003c/em\u003eCOI gene (COI-H1-4) connecting a dendrogram UniFrac distances of ITS2 profiles. Asterisks (*) in the haplotype network represent the COI haplotypes (COI-1, COI-2, COI-3) previously reported by Pochon et al. (\u003ca href=\"https://www.zotero.org/google-docs/?E8oPCr\"\u003e2015\u003c/a\u003e).\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-9544615/v1/47e6073e11cd1c60120fc82b.png"},{"id":108995426,"identity":"2e4e0662-9930-4090-88f0-ef8d927e62e9","added_by":"auto","created_at":"2026-05-11 14:08:06","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":882880,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9544615/v1/fb2f14c7-a1f9-4d50-bfad-c64f04c482e2.pdf"},{"id":108995425,"identity":"0ad0480c-f752-4900-b444-36abfcddd0d9","added_by":"auto","created_at":"2026-05-11 14:08:01","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":3483663,"visible":true,"origin":"","legend":"","description":"","filename":"LeptoITS2supplementary20260425.docx","url":"https://assets-eu.researchsquare.com/files/rs-9544615/v1/ea3ac28b1798f4e2d5d42056.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Symbiodiniaceae diversity associated with mesophotic Leptoseris corals on eastern Australian reefs","fulltext":[{"header":"Introduction","content":"\u003cp\u003eTropical coral reefs are globally known for being among the most productive ecosystems, providing habitat for many marine organisms and essential services to coastal communities (LaJeunesse et al. \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Muscatine and Porter \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e1977\u003c/span\u003e). Central to the health, resilience, and productivity in nutrient-poor waters lies a complex symbiotic relationship formed between reef-building corals (i.e., scleractinian corals) and endosymbiotic dinoflagellates (Symbiodiniaceae; Muscatine and Cernichiari \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e1969\u003c/span\u003e; reviewed in Davies et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Corals provide the endosymbiotic algae with carbon dioxide and nitrogen for photosynthesis (Pearse and Muscatine \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e1971\u003c/span\u003e), while the symbiont enhances calcification and can support the coral\u0026rsquo;s metabolism through photosynthetic products (R\u0026auml;decker et al. \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). However, this association can become disrupted under certain stressors, most notably thermal stress. A major loss of the symbiont population from the coral host tissues can result in mortality of the host (Gates et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e1992\u003c/span\u003e; Fagoonee et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e1999\u003c/span\u003e). These complex host-symbiont dynamics have been a major research focus due to their ecological significance (Glynn \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e1993\u003c/span\u003e; Baker et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2008\u003c/span\u003e), especially in the context of increasing sea temperatures and the frequency of thermal stress events. As the vast majority of this research has focused on shallow reef environments, little remains known about host-symbiont interactions in the mesophotic zone, where reduced light availability must have a profound effect on these relationships.\u003c/p\u003e \u003cp\u003eThe limited studies that have investigated Symbiodiniaceae diversity at mesophotic depths have revealed contrasting biogeographical patterns in the Caribbean and Indo-Pacific regions. While studies from the Caribbean predominantly report specialized Symbiodiniaceae communities (Frade et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Bongaerts et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2013\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2015a\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2015b\u003c/span\u003e; Lesser et al. \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; but see Gonzalez-Zapata et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2018\u003c/span\u003e), those from the Indo-Pacific frequently report the presence of depth-generalist symbiont types at mesophotic depths (Chan et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Bongaerts et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; P\u0026eacute;rez-Rosales et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Nonetheless, the sparse reports from coral colonies at the lower mesophotic limits - such as \u003cem\u003eLeptoseris\u003c/em\u003e at 100 m (Chan et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2009\u003c/span\u003e), 125 m (Pochon et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e), and 172 m (Rouz\u0026eacute; et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) - hypothesize the presence of unique Symbiodiniaceae genotypes potentially adapted to the extreme environmental conditions of mesophotic ecosystems (Ferrier-Pag\u0026egrave;s et al. \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; P\u0026eacute;rez-Rosales et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Similarly, evidence suggests mesophotic Symbiodiniaceae rely on a photosynthetic adaptive mechanism rather than acclimation strategies to survive and dominate extreme environments (Einbinder et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Thus far, \u003cem\u003eCladocopium\u003c/em\u003e is the predominant genus associated with scleractinian corals in mesophotic environments (Pochon et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; P\u0026eacute;rez-Rosales et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2024\u003c/span\u003e); however, other genera, such as \u003cem\u003eBreviolum\u003c/em\u003e, \u003cem\u003eSymbiodinium\u003c/em\u003e, and \u003cem\u003eDurusdinium\u003c/em\u003e have also been found in those depths to a lesser extent (Frade et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Bongaerts et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2015a\u003c/span\u003e; Ziegler et al. \u003cspan citationid=\"CR70\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Goulet et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2019\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe genus \u003cem\u003eLeptoseris\u003c/em\u003e, within the Agariciidae family, is among the most dominant genera on mesophotic reefs across the Indo-Pacific (Pochon et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Englebert et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). However, \u003cem\u003eLeptoseris\u003c/em\u003e species occur across a wide range of depths and reef environments (Kahng and Kelley \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Chan et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Hoeksema \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Luck et al. \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Pochon et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Terraneo et al. \u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Pichon et al. \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Hoarau et al. \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Gijsbers et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). In an effort to understand the potential adaptations that enable this genus to thrive in such variable light regimes, earlier studies have reported physiological specializations (Schlichter et al. \u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e1986\u003c/span\u003e; Schlichter \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e1991\u003c/span\u003e; Kahng et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Yet the specificity of these traits has been challenging to assess, due to the taxonomic uncertainty and ambiguity around the currently acknowledged \u003cem\u003eLeptoseris\u003c/em\u003e species (Luck et al. \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Benzoni \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). A recent phylogenomic assessment of \u003cem\u003eLeptoseris\u003c/em\u003e has revealed deep genetic divergences and multiple sympatric, distinct lineages, suggesting a higher level of host diversity than previously recognized (Gijsbers et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Leveraging samples from this dataset, we use a subset of these \u003cem\u003eLeptoseris\u003c/em\u003e specimens to assess Symbiodiniaceae diversity (using ITS2 and COI amplicon sequencing) to explore host-symbiont relationships, taking into account this previously undescribed host diversity.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cp\u003eRepresentative \u003cem\u003eLeptoseris\u003c/em\u003e specimens from each of the nine genetically divergent lineages \u0026ndash; encompassing four taxonomically recognized species (\u003cem\u003eLeptoseris scabra\u003c/em\u003e, \u003cem\u003eL. glabra\u003c/em\u003e, \u003cem\u003eL. mycetoseroides\u003c/em\u003e, and \u003cem\u003eL. hawaiiensis\u003c/em\u003e) \u0026mdash; were selected from the Gijsbers et al. (\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) dataset. These specimens (n\u0026thinsp;=\u0026thinsp;52) spanned a depth gradient of 10\u0026ndash;82 m in the Northern Great Barrier Reef and Western Coral Sea Australia (Gijsbers et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2023\u003c/span\u003e), with two further samples included from 124 and 127 m depth (figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). Given the previously established genetic divergence and putative species status using species delimitation methods, we refer to these as \u0026ldquo;species\u0026rdquo; or \u0026ldquo;genetic lineage\u0026rdquo; in this study.\u003c/p\u003e \u003cp\u003eThe internal transcribed spacer 2 (ITS2) region of Symbiodiniaceae ribosomal DNA was targeted for high-throughput amplicon sequencing from 52 \u003cem\u003eLeptoseris\u003c/em\u003e specimens. DNA was extracted following the protocol described by Bongaerts et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). PCR amplifications of the ITS2 region were performed using the ITS2-specific primer set \u0026ldquo;SYM_VAR_5.8S2\u0026rdquo; and \u0026ldquo;SYM_VAR_REV\u0026rdquo; (~\u0026thinsp;234\u0026ndash;266 bp amplicon; Hume et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2013\u003c/span\u003e, \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2015\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). All PCRs (25 \u0026micro;L reaction) contained 12.5 \u0026micro;L AmpliTaq Gold 360 MasterMix (Applied Biosystems, Life Technologies), 1 \u0026micro;L of forward primer (10 \u0026micro;M), 1 \u0026micro;L of reverse primer (10 \u0026micro;M), 0.75 \u0026micro;L DMSO, 8.25 \u0026micro;L ultrapure DI water, and 1.5 \u0026micro;L gDNA. Amplifications were conducted on a BioRad C1000 Touch Thermal Cycler.\u003c/p\u003e \u003cp\u003eDNA concentration was quantified using a QuBit High Sensitivity dsDNA assay (Thermo Fisher Scientific). For the Symbiont mtDNA COI region, PCR amplifications were performed using the \u0026ldquo;COX1_FOR2\u0026rdquo; and \u0026ldquo;COX1_REV1\u0026rdquo; (~\u0026thinsp;1000 bp) primers as described by Pochon et al. (\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). ITS2 and COI amplicons were sequenced (August 2018) on an Illumina MiSeq platform (2 x 300 bp) at the Australian Genome Research Facility, University of Queensland. Finally, the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence COI count data using default settings.\u003c/p\u003e \u003cp\u003eThe resulting raw ITS2 sequencing reads were demultiplexed and further analyzed using the SymPortal analytical framework (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://symportal.org\u003c/span\u003e\u003cspan address=\"https://symportal.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, Hume et al. \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). This pipeline uses a series of steps to filter out non-Symbiodiniaceae sequences and identify ITS2 defining intragenomic variants (DIVs) within Symbiodiniaceae genera. SymPortal performs minimum entropy decomposition (Eren et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) to calculate the amount of genomic variation and classifies this as distinct DIVs. Then, it predicts Symbiodiniaceae ITS2-type profiles (which represent hypothetical Symbiodiniaceae taxa) based on the presence and abundance of the identified DIVs.\u003c/p\u003e \u003cp\u003eAll statistical tests were conducted in R (v.4.3.0, Team \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The relative abundance of post-MED ITS2 DIVs were used for statistical analyses, while the ITS2-type profiles were used to visualize different taxonomic units. This provides a more detailed and accurate approach to characterize both intra- and intergenomic variations within Symbiodiniaceae taxa. Before conducting statistical tests, we evaluated the degree of homogeneity of dispersion between-groups (region, site, depth, depth category, genetic lineage) using the \u003cem\u003evegan\u003c/em\u003e (v.2.6-4; Oksanen et al. 2022) function \u003cem\u003ebetadisper\u003c/em\u003e. Additionally, we checked nestedness among the different environmental and biogeographic factors (depth category: shallow (\u0026le;\u0026thinsp;30 m), upper-mesophotic (31\u0026ndash;59 m), lower-mesophotic (\u0026ge;\u0026thinsp;60 m); site; region; genetic lineage). Furthermore, significant differences among the resulting factors in the Symbiodiniaceae community were assessed using a series of Permutational Multivariate Analysis of Variance (PERMANOVA) tests using the \u003cem\u003eadonis\u003c/em\u003e function from the \u003cem\u003evegan\u003c/em\u003e package. A comprehensive PERMANOVA model was conducted to evaluate the simultaneous effects of \u0026ldquo;\u003cem\u003eregion and site\u003c/em\u003e\u0026rdquo;, \u0026ldquo;\u003cem\u003edepth category\u003c/em\u003e\u0026rdquo;, and \u0026ldquo;\u003cem\u003egenetic lineage\u003c/em\u003e\u0026rdquo;. To do this, symbiont DIV counts were first Hellinger-transformed and then Bray-Curtis dissimilarity matrices were calculated. Pairwise comparisons were then conducted with 99,999 permutations using the \u003cem\u003epairwiseAdonis\u003c/em\u003e package (v. 0.4.1, Martinez Arbizu \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). Variance partitioning was carried out using the \u003cem\u003evarpart\u003c/em\u003e function of the \u003cem\u003evegan\u003c/em\u003e package to quantify the unique contribution of the significant variables to the variability in the symbiont community composition. Furthermore, Principal Coordinates Analysis (PCoA; \u003cem\u003ecmdscale\u003c/em\u003e function, \u003cem\u003evegan\u003c/em\u003e package) was used to visualize the Symbiodiniaceae ITS2 sequence structure between \u003cem\u003eLeptoseris\u003c/em\u003e focal species and genetic lineages, as well as between regions and across depths. Finally, to identify and visualize ITS2 profiles with specific association with the different host genetic lineages, we conducted an Indicator Species Analysis (IndVal) as part of the \u003cem\u003eIndicspecies\u003c/em\u003e package (v. 1.8.0). To do this, we tested which ITS2 profiles were significantly associated specifically with each host genetic lineage using the \u003cem\u003emultipatt\u003c/em\u003e function with 999 permutations and generated a network (figure S5) to visualize these associations.\u003c/p\u003e \u003cp\u003ePhylogenetic relationships of the host were reconstructed under the maximum likelihood (ML) criterion, as implemented in the program IQ-tree (2.1.4-beta; Nguyen et al. \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) under the GTR\u0026thinsp;+\u0026thinsp;I+G4 nucleotide substitution model with 1000 bootstrap replicates. Based on the ITS2-type profiles' phylogenetic similarities (as determined by UniFrac distances), we generated a hierarchical clustering dendrogram using the R built-in \u003cem\u003ehclust\u003c/em\u003e function. Finally, correlation analyses within the symbiont community were performed based on ITS2-type profile relative abundances and UniFrac distances using Spearman\u0026rsquo;s rank correlation coefficient from the \u003cem\u003ecor\u003c/em\u003e function of the \u003cem\u003ecorrplot\u003c/em\u003e package (v. 0.92; Wei et al. \u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; \u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003efigure S4\u003c/span\u003e). COI-ITS2 correspondence was assessed based on the symbiont COI mtDNA region of 53 \u003cem\u003eLeptoseris\u003c/em\u003e samples, including representatives from the Pochon et al. (\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) dataset. A COI haplotype network was generated using the PopART open-source software (Leigh and Bryant \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e2015\u003c/span\u003e).\u003c/p\u003e"},{"header":"Results and Discussion","content":"\u003cp\u003eDespite three decades of research on Symbiodiniaceae in shallow-water scleractinian corals, few studies have examined mesophotic depths, leaving our understanding of Symbiodiniaceae diversity, ecology, and adaptations to low-light environments severely limited (Gonz\u0026aacute;lez-Pech et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Goulet et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Leveraging a unique collection of deep-water \u003cem\u003eLeptoseris\u003c/em\u003e from the Great Barrier Reef (GBR) and Western Coral Sea (WCS) in Australia, we documented Symbiodiniaceae diversity by genotyping the ITS2 and COI regions, and found limited specificity across the nine \u003cem\u003eLeptoseris\u003c/em\u003e species, with Symbiodiniaceae community composition explained through the combination of host species, location and depth.\u003c/p\u003e \u003cp\u003eUsing the SymPortal framework, 5,342,096 Symbiodiniaceae reads were recovered across all samples, with an average of 97,165 post-MED reads per sample. Of these, 99.89% of the sequences belonged to the genus \u003cem\u003eCladocopium\u003c/em\u003e (table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). A total of 262 DIVs were recovered across all samples. While the majority represented low-abundance background variation, 35 unique DIVs consistently co-occurred to compose 22 ITS2-type profiles (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Five profiles were removed due to an overall low representation (\u0026lt;\u0026thinsp;1% of absolute abundance), resulting in a total of 17 profiles considered for statistical analyses. This pattern is consistent with previous reports of Symbiodiniaceae diversity across Indo-Pacific reefs, where the genus \u003cem\u003eCladocopium\u003c/em\u003e often dominates along an extensive depth gradient, and is frequently a dominant member at mesophotic depths (Chan et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Goulet et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Rouz\u0026eacute; et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Terraneo et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; P\u0026eacute;rez-Rosales et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Vimercati et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Despite recovering 35 unique DIVs, the ITS2 profiles grouped into five genetically distinct clusters (based on UniFrac distances), dominated primarily by variants from the C21, C21x, C3, and C1 radiations (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e; figure S3). The C21/C3 cluster was the largest and dominated by C21/C3-related intragenomic variants (e.g., C21y, C21u, C3at), which is consistent with the evolutionary history of the genus \u003cem\u003eCladocopium\u003c/em\u003e, given that the C21 lineage diverged from the ancestral C3 (LaJeunesse \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2005\u003c/span\u003e). Similarly, the C21x cluster was mainly dominated by C21x/C3-related variants. While based on UniFrac distances, the C21x cluster is closely related to the C21 clade; it formed a distinct genetic and ecological cluster. The C1 cluster was composed mainly of C1 variants (e.g., C1ar), with the exception of one profile where the ancestral variants C1 and C3 were co-dominant. The fourth and fifth cluster contained a single C115f and C116 profiles, respectively. The latter containing two profiles of DIVs C116 was co-dominant with C1 and C3. The most prevalent ITS2 profile was C1/C1ar-C1as-C3-C3co-C41l (table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e) and was only observed at mesophotic depths of the WCS. Although C1 represents a geographically and ecologically widespread ancestor (LaJeunesse \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2005\u003c/span\u003e; Chan et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2009\u003c/span\u003e), the combination of these DIVs represents a novel profile with a strong presence at lower mesophotic depths, suggesting this profile might be a specialized lineage and possibly endemic to this region. While the generalists C21 and C3-radiations (e.g., C21/C3-C3at-C3av-C3b-C3dp) have been well-documented in association with plate-like morphologies, and at lower depths and across the Indo-Pacific, including Australian reefs, they are widely distributed across depths, sites, and environments (Bongaerts et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Wagner et al. \u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Padilla-Gami\u0026ntilde;o et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Tonk et al. \u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Grima et al. \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Marzonie et al. \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). In contrast, the novel C1ar and C21x variants identified in this study exhibited a restricted depth and geographical distribution. Thus far, the C1ar lineage appears exclusive to mesophotic depths at WCS sites, as they have not yet been documented in shallow waters; similarly, the majority of the C21x profiles were restricted to lower mesophotic depths.\u003c/p\u003e \u003cp\u003eThe \u003cem\u003ebetadisper\u003c/em\u003e test revealed significant differences in the variability of community composition among depths (F\u0026thinsp;=\u0026thinsp;3.92, p\u0026thinsp;=\u0026thinsp;0.00307), indicating that depth, as a continuous variable, exhibited heterogeneous dispersion and could confound the interpretation of PERMANOVA results. Therefore, depths were grouped into depth categories (shallow, upper-mesophotic, lower-mesophotic). Furthermore, to account for the hierarchical structure of our sampling design, region and site were treated as nested variables. PERMANOVA results (table S2) indicated that 56% of the variation in the data was explained by region and site (R2\u0026thinsp;=\u0026thinsp;0.25, F\u0026thinsp;=\u0026thinsp;2.37, p\u0026thinsp;=\u0026thinsp;0.00017), host genetic lineage (R2\u0026thinsp;=\u0026thinsp;0.22, F\u0026thinsp;=\u0026thinsp;2.11, p\u0026thinsp;=\u0026thinsp;0.00107), and depth category (R2\u0026thinsp;=\u0026thinsp;0.09, F\u0026thinsp;=\u0026thinsp;3.62, p\u0026thinsp;=\u0026thinsp;0.00173). \u003cem\u003eCladocopium\u003c/em\u003e diversity varied significantly across host genetic lineages. C21/C3 cluster profiles were more predominantly associated with \u003cem\u003eL. scabra\u003c/em\u003e (including \u003cem\u003eL. scabra\u003c/em\u003e 1, \u003cem\u003eL. scabra\u003c/em\u003e 2, DelineatedSp003), \u003cem\u003eL. glabra\u003c/em\u003e, and \u003cem\u003eL. hawaiiensis\u003c/em\u003e lineages. In contrast, lineages such as \u003cem\u003eL. glabra\u003c/em\u003e/\u003cem\u003eL. scabra\u003c/em\u003e, \u003cem\u003eL\u003c/em\u003e. cf. \u003cem\u003emycetoseroides\u003c/em\u003e, and \u003cem\u003eLeptoseris\u003c/em\u003e sp. 1 were mainly linked to the \u003cem\u003eC. proliferum\u003c/em\u003e cluster and C116 cluster profiles (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The Indicator Species Analysis identified three ITS2 profiles with significant associations to particular host lineages. The most dominant ITS2 profile, C1/C1ar-C1as-C3-C3co-C41l, exhibited a significant association with \u003cem\u003eL\u003c/em\u003e. cf. \u003cem\u003emycetoseroides\u003c/em\u003e, \u003cem\u003eL. glabra/L. scabra\u003c/em\u003e, and \u003cem\u003eLeptoseris\u003c/em\u003e sp. 1 (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.001). Similarly, while profile C21x/C3-C3av-C21-C21z-C58a-C21bi was significantly associated with \u003cem\u003eL. hawaiiensis\u003c/em\u003e and \u003cem\u003eL. scabra\u003c/em\u003e 2 (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.006), C3/C21x-C21-C3av-C3ag-C58a was significantly associated with DelineatedSp003 (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.03). These results indicate a strong host-symbiont fidelity, although such interpretations need to be cautioned due to the small sample sizes per lineage. Geographically, the C21/C3 cluster was almost exclusively found in the GBR, which is consistent with the patterns well-documented for these generalist lineages in the GBR (LaJeunesse et al. \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2003\u003c/span\u003e), whereas all clusters were observed in the WCS (although the limited number of GBR representatives may constrain these geographic patterns' robustness). Similarly, significant differences in \u003cem\u003eCladocopium\u003c/em\u003e diversity were found among depth zones, with C21/C3 more common at shallow and upper mesophotic depths, with some exceptions from the C1 cluster. In contrast, profiles from all five clusters were observed at lower mesophotic depths, with the most abundant profiles being C1/C1ar and C21x/C3. Notably, clusters C115f and C116 were exclusively observed at lower mesophotic depths, even though these profiles have been reported at shallow depths across the Indo-Pacific, they are considered rare and opportunistic symbionts (Qin et al. \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Starko et al. \u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Terraneo et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Although a degree of host-symbiont and depth specificity was observed, the associations are not as straight-forward as observed previously in Hawai\u0026rsquo;i (Pochon et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). This flexibility is consistent with taxa that rely on broadcast spawning events as a reproductive strategy, acquiring their symbionts from the environment through horizontal transmission (Quigley et al. \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). Despite sparse evidence, species within this genus are generally considered broadcast spawners (Baird et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2009\u003c/span\u003e); and thus acquiring Symbiodiniaceae from the environment might be an adaptive strategy to extreme depth and ecological gradients (Zarate et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). In addition, the broad geographical and depth distribution of samples and limited representation within each genetic lineage, depth, and location, may mask more defined trends within \u003cem\u003eLeptoseris\u003c/em\u003e-Symbiodiniaceae associations.\u003c/p\u003e \u003cp\u003eUsing the mitochondrial COI marker, we retrieved four different haplotypes, referred to as COI-H1, COI-H2, COI-H3, and COI-H4, and we compared these to the COI-I, COI-II, and COI-III sequences from Pochon et al. (\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) (table S3). Three of these haplotypes broadly matched the ITS2 clusters (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The most abundant haplotypes were COI-H1 (56%) and COI-H3 (42%). COI-H1 matched almost exclusively the ITS2 C21/C3 cluster, with one sample matching the C115f cluster. COI-H2 (2%) corresponded to the C1/C3 type (table S3). COI-H3, which corresponds to the COI-III haplotype from Pochon et al. (\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e), mainly corresponded to the C1 ITS2 profiles with some exceptions, where it matched ITS2 C21x/C21y, and C3/C21x profiles from C21x cluster. In addition, we included two samples from the end of the lower mesophotic zone (124 and 126 m, respectively), including the deepest photosymbiotic \u003cem\u003eLeptoseris\u003c/em\u003e colony collected to date from the GBR (124 m, Englebert et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). These samples represented a distinct haplotype (COI-H4). However, we were unable to obtain ITS2 amplicon sequences from these specimens, and thus, their inclusion in the study is limited to providing new insights into the symbiont diversity at these extreme depths based on COI data. Unlike the host-specific haplotypes reported for species within the \u003cem\u003eLeptoseris\u003c/em\u003e genus in other regions from the Indo-Pacific, such as Hawaii, where Pochon et al. (\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) observed strong depth zonation and host-symbiont specificity within \u003cem\u003eL. scabra\u003c/em\u003e and \u003cem\u003eL. hawaiiensis\u003c/em\u003e, we did not find strong host or depth-specificity on Australian reefs. COI-H1 and COI-H3 haplotypes were found along the depth range and were present broadly in all taxa.\u003c/p\u003e \u003cp\u003eDespite their importance in mesophotic coral ecosystems across the Pacific, we are only beginning to understand how \u003cem\u003eLeptoseris\u003c/em\u003e taxa can thrive under such low-light conditions. By developing thin, horizontal skeletons, these corals maximize their surface area while maintaining low skeletal investment; an efficient strategy that enables them to capture light and fulfill their metabolic needs through photosynthetic carbon (Carmignani et al. \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Kahng et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2023\u003c/span\u003e, \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). In addition to skeletal morphology, there may be other strategic adaptations such as mixed feeding modes and associations with endolithic green algae as an alternative energy source (Rouz\u0026eacute; et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Backstrom et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). At increasing depth, heterotrophy may become more important, yet autotrophy remains essential for their survival and may be fundamental to the skeletogenesis of these species at mesophotic depths (Backstrom et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2024\u003c/span\u003e), suggesting low-light adapted symbionts may play a critical role in this genus\u0026rsquo; ability to occupy different environmental niches (Douglas \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e1998\u003c/span\u003e; Stat et al. \u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Backstrom et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Zarate et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2024\u003c/span\u003e).\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eOur findings reveal general signatures of host-symbiont specificity with occasional flexibility, with geography and depth also shaping \u003cem\u003eLeptoseris\u003c/em\u003e\u0026rsquo; Symbiodiniaceae diversity. On one hand, the observed wide depth distributions of Symbiodiniaceae types \u0026ndash; including the presence of some types found at very shallow and lower mesophotic zones \u0026ndash; corroborate previous observations of depth-generalist endosymbionts prevailing at mesophotic depths. Nonetheless, despite the resolution of ITS2 amplicon sequencing, there may be further species- or population-level differentiation at mesophotic depths that cannot be discerned using this approach. On the other hand, the observation of novel Symbiodiniaceae variants that have not been reported before indicates that lower mesophotic specialist types may be present and contribute to the ecological success of deep-water \u003cem\u003eLeptoseris\u003c/em\u003e communities. Despite our limited sampling within specific locations or depth zones, these results highlight the complexity of \u003cem\u003eLeptoseris\u003c/em\u003e-Symbiodiniaceae interactions and underscore our limited understanding regarding photo-endosymbionts\u0026rsquo; role in enabling this genus to inhabit such extreme low-light environments. Overall, these results underscore the need for high-resolution genetic studies, combined with functional assessments, to better understand the prevalence and potential mechanisms underlying low-light adaptation in Symbiodiniaceae at mesophotic depths.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eConflict of Interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that the research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePB conceived and designed the present study. PB conducted the sample collection and taxonomical identifications. VZR conducted DNA extractions and amplicon sequencing. JCG conducted the statistical and bioinformatic analyses, generated the figures, and drafted the manuscript. MRN contributed to the bioinformatic and ecological interpretation. All authors read, edited, and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgements \u003cbr\u003e\u003c/strong\u003eWe thank Norbert Englebert, David Whillas, Kyra Hay, and Paul Muir for their help with the original specimen collections, and the crews from Reef Connections, Mike Ball Dive Expeditions, SY Ethereal, and the Waitt Foundation for field support.\u003c/p\u003e\n\n\u003cp\u003e\u003cstrong\u003eData availability statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study utilizes a subset of raw nextRAD sequence data previously deposited in the NCBI Sequence Read Archive under BioProject PRJNA970738 (Gijsbers et al. 2023). New raw sequence data for the ITS2 and COI amplicons generated specifically for this study are available under BioProject XXXXX (pending) and will be made public upon acceptance of the manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was funded by the XL Catlin Seaview Survey (funded by the XL Catlin Group in partnership with Underwater Earth and The University of Queensland), and an Australian Research Council Discovery Early Career Researcher Award (DE160101433).\u003c/p\u003e\n"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eBackstrom CH, Padilla-Gami\u0026ntilde;o JL, Spalding HL, Roth MS, Smith CM, Gates RD, Rodrigues LJ (2024) Mesophotic corals in Hawai\u0026lsquo;i maintain autotrophy to survive low-light conditions. 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Front Mar Sci 2:4 \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fmars.2015.00004\u003c/span\u003e\u003cspan address=\"10.3389/fmars.2015.00004\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\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":"coral-reefs","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"core","sideBox":"Learn more about [Coral Reefs](http://link.springer.com/journal/338)","snPcode":"338","submissionUrl":"https://submission.nature.com/new-submission/338/3","title":"Coral Reefs","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Coral, ITS2, Leptoseris, Mesophotic, Symbiodiniaceae","lastPublishedDoi":"10.21203/rs.3.rs-9544615/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9544615/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe intimate relationship between scleractinian corals and endosymbiotic dinoflagellates (Symbiodiniaceae) drives primary production and calcification in reef ecosystems. Despite the extensive research focused on coral-Symbiodiniaceae relationships at shallow depths, only a few studies have assessed the symbiont diversity at mesophotic depths. Here, we examined the Symbiodiniaceae diversity associated with nine putative mesophotic \u003cem\u003eLeptoseris\u003c/em\u003e species in Australian reefs using the ITS2 and COI marker regions. Amplicon sequencing revealed an almost exclusive association with the genus \u003cem\u003eCladocopium\u003c/em\u003e. While the COI region retrieved four distinct haplotypes, 17 ITS2 profiles grouped into five clusters were identified. Across the Symbiodiniaceae profiles, 24% were found across wide depth ranges, although 53% were only observed at mesophotic depths. Despite a certain degree of host-symbiont specificity, geography and depth also contributed significantly to the composition of Symbiodiniaceae communities. These findings provide much-needed insights into the diversity of Symbiodiniaceae associations with mesophotic \u003cem\u003eLeptoseris\u003c/em\u003e, and emphasize the need for further research to establish to what extent lower mesophotic habitats in the Indo-Pacific harbor unique versus generalist endosymbiont associations.\u003c/p\u003e","manuscriptTitle":"Symbiodiniaceae diversity associated with mesophotic Leptoseris corals on eastern Australian reefs","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-05-11 14:07:38","doi":"10.21203/rs.3.rs-9544615/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewerAgreed","content":"31472918900820974082683308124150100247","date":"2026-05-14T03:48:50+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"157052893174860259099171035494450067652","date":"2026-05-12T15:09:33+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"15576447573391662887719669381515437539","date":"2026-05-04T13:10:14+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-05-04T07:37:34+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-05-03T01:01:24+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-04-27T17:35:35+00:00","index":"","fulltext":""},{"type":"submitted","content":"Coral Reefs","date":"2026-04-27T16:49:02+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"coral-reefs","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"core","sideBox":"Learn more about [Coral Reefs](http://link.springer.com/journal/338)","snPcode":"338","submissionUrl":"https://submission.nature.com/new-submission/338/3","title":"Coral Reefs","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"f57acb11-9771-48d5-95a3-d6f774b6fc02","owner":[],"postedDate":"May 11th, 2026","published":true,"recentEditorialEvents":[{"type":"reviewerAgreed","content":"31472918900820974082683308124150100247","date":"2026-05-14T03:48:50+00:00","index":13,"fulltext":""},{"type":"reviewerAgreed","content":"157052893174860259099171035494450067652","date":"2026-05-12T15:09:33+00:00","index":12,"fulltext":""},{"type":"reviewerAgreed","content":"15576447573391662887719669381515437539","date":"2026-05-04T13:10:14+00:00","index":7,"fulltext":""},{"type":"reviewersInvited","content":"5","date":"2026-05-04T07:37:34+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-05-03T01:01:24+00:00","index":"","fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-11T14:07:38+00:00","versionOfRecord":[],"versionCreatedAt":"2026-05-11 14:07:38","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9544615","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9544615","identity":"rs-9544615","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}