Draft genome sequence of a predatory bacterium from northern peatland soil

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Männistö" }, { "@type": "Person", "name": "Jenni Hultman" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": "Predatory bacteria are abundant in soil, but their diversity and functions remain not fully understood, especially in subarctic regions. Here, we report strain 1-FT3.2, a predatory bacterium obtained from peatland soil in Northern Finland (Pallas, 68 °N). The bacterium was cultivated on Mucilaginibacter cryoferens FT3.2 as prey. Although a pure culture of strain 1-FT3.2 was not obtained, its draft genome was assembled from sequencing reads derived from the co-culture with its prey. The draft genome of 1-FT3.2 is 7.2 Mb in length and 81% complete. Genome analyses suggested that 1-FT3.2 belongs to the family Polyangiaceae (phylum Myxococcota), which comprises predatory bacteria. The genome annotation revealed (near-)complete metabolic modules of central carbon metabolism and aerobic respiration. Two proviral regions were predicted in the draft genome, both putatively representing tailed phages of the class Caudoviricetes. Several CRISPR-Cas system proteins were also identified. The draft genome sequence could be used in future comparative studies assessing the diversity of predatory bacteria in northern soils or other environments." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/14-1153/v1", "name": "Draft genome sequence of a predatory bacterium from northern peatland..." } } ] } Home Browse Draft genome sequence of a predatory bacterium from northern peatland... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Demina T, Ihonen R, Männistö MK and Hultman J. Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.12688/f1000research.171863.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] Tatiana Demina https://orcid.org/0000-0003-3746-5533 1 , Riina Ihonen 1,2 , Minna K. Männistö 2 , Jenni Hultman 1,2 Tatiana Demina https://orcid.org/0000-0003-3746-5533 1 , Riina Ihonen 1,2 , Minna K. Männistö 2 , Jenni Hultman 1,2 PUBLISHED 21 Oct 2025 Author details Author details 1 Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland 2 Natural Resources Institute Finland, Helsinki, Finland Tatiana Demina Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Riina Ihonen Roles: Investigation, Writing – Review & Editing Minna K. Männistö Roles: Conceptualization, Resources, Writing – Review & Editing Jenni Hultman Roles: Conceptualization, Methodology, Resources, Supervision, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Pathogens gateway. This article is included in the Genomics and Genetics gateway. Abstract Predatory bacteria are abundant in soil, but their diversity and functions remain not fully understood, especially in subarctic regions. Here, we report strain 1-FT3.2, a predatory bacterium obtained from peatland soil in Northern Finland (Pallas, 68 °N). The bacterium was cultivated on Mucilaginibacter cryoferens FT3.2 as prey. Although a pure culture of strain 1-FT3.2 was not obtained, its draft genome was assembled from sequencing reads derived from the co-culture with its prey. The draft genome of 1-FT3.2 is 7.2 Mb in length and 81% complete. Genome analyses suggested that 1-FT3.2 belongs to the family Polyangiaceae (phylum Myxococcota ), which comprises predatory bacteria. The genome annotation revealed (near-)complete metabolic modules of central carbon metabolism and aerobic respiration. Two proviral regions were predicted in the draft genome, both putatively representing tailed phages of the class Caudoviricetes. Several CRISPR-Cas system proteins were also identified. The draft genome sequence could be used in future comparative studies assessing the diversity of predatory bacteria in northern soils or other environments. READ ALL READ LESS Keywords subarctic soil, predatory bacteria, Myxococcota, Polyangiaceae, Mucilaginibacter cryoferens, short-read sequencing, bacterial genome Corresponding Author(s) Tatiana Demina ( [email protected] ) Close Corresponding author: Tatiana Demina Competing interests: No competing interests were disclosed. Grant information: The work was supported by the Research Council of Finland (TD: grant 330977, JH: grant 354462) and the Kone Foundation (TD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2025 Demina T et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Demina T, Ihonen R, Männistö MK and Hultman J. Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.12688/f1000research.171863.1 ) First published: 21 Oct 2025, 14 :1153 ( https://doi.org/10.12688/f1000research.171863.1 ) Latest published: 28 Apr 2026, 14 :1153 ( https://doi.org/10.12688/f1000research.171863.2 )  There is a newer version of this article available. Suppress this message for one day. Introduction Predatory bacteria are important players in microbial food webs ( Hungate et al. 2021 ). Myxobacteria are a group of bacteria associated with the phylum Myxococcota , characterised by group predatory behaviour and a complex lifestyle, where rod-shaped vegetative cells can aggregate into multicellular fruiting bodies and produce spores ( Saggu et al. 2023 ). Myxobacteria are globally distributed and especially abundant in soil ( Zhou et al. 2014 ; Wang et al. 2021 ). Together with other micropredators, myxobacteria play leading roles in carbon sequestration and mineralization in soil ( Lueders et al. 2006 ). Moreover, myxobacteria may dominate among other potential bacterivores and have been suggested to represent one of the keystone taxa in soil microbial food webs ( Petters et al. 2021 ). Still, more data are needed to resolve their taxonomic diversity as well as metabolic and lifestyle capacities across environments, including relatively underexplored subarctic regions. Since soil microbial communities are highly diverse, obtaining complete genomes through metagenomics may be a challenging task ( Anthony et al. 2024 ). Cultivating soil microbes makes it possible to reconstruct their genome sequences reliably and link genetic information to the observed phenotype. In this study, we obtained strain 1-FT3.2, a predatory bacterium from northern peatland soil in the Pallas region, Finland, using Mucilaginibacter cryoferens FT3.2 ( Kumar et al. 2025 ) as prey. M. cryoferens , recently described as a new species, was isolated from Arctic tundra soils in the Kilpisjärvi region, Finland, where it may play important roles in litter decomposition and carbon recycling together with other Mucilaginibacter species ( Männistö et al. 2009 ; Kumar et al. 2025 ). Strain 1-FT3.2 remained in a mixed culture with its prey, but the analyses of its draft genome sequence obtained from the co-culture suggest that it belongs to the Polyangiaceae family. Methods Soil sampling, isolation and cultivation conditions A soil sample was collected from peatland in the Pallas area, Northern Finland, in September 2022 (N67°59’ E24°13’, Figure 1A ). The vegetation was mainly sedges ( Figure 1B ). The sample was collected from a depth of 5 cm with sterile instruments and stored at 4°C. The pure culture of Mucilaginibacter cryoferens FT3.2 ( Kumar et al. 2025 ), was used as the prey for isolating predatory bacteria from the soil sample. Bacteria were cultivated using R2A medium (Neogen, NCM0188A), which contained 0.5 g L −1 yeast extract, 0.5 g L −1 meat peptone, 0.5 g L −1 casamino acid, 0.5 g L −1 glucose, 0.5 g L −1 starch, 0.3 g L −1 K 2 PO 4 , 0.05 g L −1 MgSO 4 , and 0.3 g L −1 C 3 H 3 NaO 3 , and was adjusted to pH 6. For solid and top agar, 15 and 4 g L −1 of agar (Sigma-Aldrich, A4550) were added, respectively. The cultures were grown aerobically at room temperature (RT). Figure 1. (A, B) Sampling location, Pallas, and (C) strain 1-FT3.2 growing on plate. In (A), Kilpisjärvi, the original isolation location for the prey strain, Mucilaginibacter cryoferens FT3.2, is additionally shown. Map modified from Wikimedia Commons (NordNordWest). In (C), a representative plate with lysis zones on the M. cryoferens FT3.2 lawn after 14 days of incubation is shown, scale bar, 1 cm. For the isolation, 5 g of the soil sample (wet weight) was resuspended in 50 ml of R2A broth and incubated on a shaker (~200 rpm) at RT for two weeks for the sample enrichment. The enriched sample was centrifuged (ThermoScientific F15-6x100y, 30 min, 2,500 g, 20°C) and 100 μl of non-diluted supernatant plated with 300 μl of the M. cryoferens FT3.2 liquid culture and 3 ml of R2A soft agar (46°C) as a top layer on R2A solid agar plates. The plates were incubated aerobically at RT. The observed growth inhibition/lysis zone was picked up with a sterile pipette tip, resuspended in R2A broth, and plated in a top agar layer as before, which was repeated three consecutive times. DNA extraction and sequencing The top agar layers of the semi-confluent plates were collected and resuspended in R2A broth (3 ml per plate), incubated with shaking (~200 rpm) at RT for one hour and centrifuged (ThermoScientific F15-6x100y, 30 min, 10,000 g, 4°C). The supernatant was collected and stored at 4°C. The stock titers were determined by plating serial dilutions in a top agar layer as described above. DNA was extracted with the GeneJET Genomic DNA Purification Kit (Thermo Scientific, K0721) using the manufacturer’s protocol for Gram-negative bacteria and 20 ml of the agar stock as input. Note that the agar stocks contained cells from both M. cryoferens FT3.2 and the new strain. For sequencing, 100 ng of genomic DNA was converted to a sequencing library using the Illumina DNA prep. Samples were dual indexed using the sequencing core unit’s own Nextera primers. Seven cycles were used in the PCR step and DNA was pooled and purified using Illumina’s SPB bead purification. The Library pool was sequenced at 12 pM on the AVITI sequencer (Element Biosciences) using the AVITI 2x150 Sequencing kit Cloudbreak FreeStyle High Output. Sequencing was performed at the DNA Sequencing and Genomics Laboratory (supported by HiLIFE and Biocenter Finland funding), Institute of Biotechnology, University of Helsinki. Genome annotation FastQC v. 0.11.9 ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) was used to assess the quality of reads. Raw reads were trimmed and adaptors removed with Cutadapt v. 2.7 (-m 50 --nextseq-trim 20) ( Martin 2011 ). Read-based taxonomic profiling was performed using PhyloFlash v. 3.4.2 and SILVA138.1.eukmod database ( Gruber-Vodicka et al. 2020 ). Since the sample contained a mixed culture of the prey strain M. cryoferens FT3.2 and a new potentially predatory strain, SPAdes v. 3.15.5 was used in the --meta mode for genome assembly ( Bankevich et al. 2012 ). BBTools Stats was used for assessing the assembly statistics, Reformat for sorting scaffolds by their GC content, and Dedupe for dereplicating scaffolds (minidentity = 95 absorbrc = t absorbmatch = t sort = length) ( sourceforge.net/projects/bbmap/ ). The full-length SSU rRNA gene sequences obtained from the PhyloFlash run and the assembled scaffolds of ≥10 kbp in length were searched with BLASTN ( Altschul et al. 1990 ) against the NCBI nt database using an E-value cutoff of 0.001. The quality of the draft genome of a new strain was assessed with CheckM2 v. 1.0.1 ( Chklovski et al. 2023 ). GTDB-Tk v. 2.3.2 with GTDB release 226 database ( Chaumeil et al. 2022 ) was used for assigning a taxonomic classification. For the genome annotation, DRAM v. 0.1.2 ( Shaffer et al. 2020 ) was used at KBase ( Arkin et al. 2018 ). Putative (pro)viral sequences were predicted by geNomad v. 1.7 ( Camargo et al. 2023 ) and their quality and completeness were assessed with CheckV v. 0.8.1 ( Nayfach et al. 2021 ). Bowtie2 v. 2.5.3 was used for the additional mapping of reads to putative viral sequences ( Langmead and Salzberg 2012 ). Results Isolation After about two weeks of incubating the plates, growth inhibition/lysis areas of 4-5 mm were observed. In subsequent platings, the size of lytic zones reached up to ~1 cm ( Figure 1C ). The central parts of these zones were clear, while edges were hazier. Agar stocks produced lysis zones on the M. cryoferens FT3.2 lawn when diluted up to 10000-fold, but no lysis zones could be observed when titrating filtered stocks (0.22 and 0.45 μm PES LLG-Syringe filters Spheros), suggesting that the origin of the observed lytic zones was not viral. Very small, almost transparent or whitish colonies growing over the lysis zones were observed ( Figure 1C ), but no aggregated structures like fruiting bodies were seen. Despite our attempts, these tiny colonies could not be transferred to a fresh plate for independent growth. An alternative cultivation approach using the myxobacterium-suited CY-C10 medium (( Karwowski et al. 1996 ) modified by omitting antibiotics) and higher incubation temperature (28°C) for stock titration did not improve colony growth visibility. We named the strain causing lytic zones on M. cryoferens FT3.2 as 1-FT3.2. Genome sequencing and assembly Sequencing genomic DNA of a mixed culture resulted in 245,936,278 raw read pairs (150 bp + 150 bp), of which 245,436,350 pairs were retained after read trimming and quality control. With the read-based profiling by PhyloFlash, 225,532 reads (0.092% of all reads) could be mapped to SSU rRNA sequences in SILVA database. Of the mapped reads, 212,996 (94%) were assigned to the order Sphingobacteriales ( Bacteroidota ), where the genus Mucilaginibacter belongs to, and 9,050 (4%) were assigned to the order Polyangiales ( Myxococcota ). The rest of the hits constituted less than 0.01% of mapped reads each. Thus, read-based profiling suggested two strains present in the sample, comprising about 98% of reads together. Furthermore, full-length SSU rRNA gene sequences assembled by SPAdes, matched to SILVA database, were only two OTUs with the closest-matching references of Mucilaginibacter sp. M20-56 ( Sphingobacteriales ; GenBank acc. no.: KP899210.1, 99% id., 100% cov.) and Phaselicystis metagenome ( Polyangiales ; GenBank acc. no.: FPLS01001412.1, 95% id., 99% cov.). Additional BLASTN searches of the two detected OTUs against the NCBI nt database resulted in hits to 16S rRNA gene sequences of Mucilaginibacter sp. strain FT3.2 (100% id., 100% cov., 0 E-value) and the members of the order Polyangiales (the genera Minicystis, Sorangium, Chondromyces, Labilithrix, Polyangium, and uncultured bacterium, 91-92% id., 100% cov., 0 E-value), respectively. The assembly of the mixed culture consisted of 6,318 scaffolds, of which 140 scaffolds were longer than 10 kbp and represented 95% of the total length of all scaffolds ( Table 1 ). Most scaffolds longer than 10 kb were characterised by a GC content of either 41-43% (71 scaffolds) or 64-66% (56 scaffolds) ( Figure 2 ). The Mucilaginibacter cryoferens FT3.2 genome GC content is known to be 42.1 % (Genbank acc. no. CP183228.1). Therefore, 56 scaffolds with a GC content of 64-66% were separated from the rest of the assembly, representing strain 1-FT3.2. Dedupe run confirmed the non-redundancy of the assembled draft genome. The total length of the 1-FT3.2 draft genome was 7,202,438 bp with the scaffolds ranging from 13,622 to 664,534 bp in length ( Table 2 ). Based on the CheckM2 assessment, the genome is 81.3% complete and 0.5% contaminated. Table 1. Statistics for the mixed culture assembly, listed as of different minimal scaffold length thresholds. Minimum scaffold length, bp Number of scaffolds Number of contigs Total scaffold length, bp Total contig length, bp Scaffold contig coverage, % 50 6,318 6,369 15,040,305 15,035,385 99.97 100 1,456 1,507 14,717,700 14,712,780 99.97 250 299 350 14,552,681 14,547,761 99.97 500 222 271 14,529,291 14,524,391 99.97 1,000 201 250 14,513,761 14,508,861 99.97 2,500 168 217 14,459,058 14,454,158 99.97 5,000 155 203 14,409,144 14,404,344 99.97 10,000 140 188 14,302,883 14,298,083 99.97 25,000 116 161 13,895,326 13,890,826 99.97 50,000 93 136 13,006,064 13,001,764 99.97 100,000 56 89 10,405,941 10,402,641 99.97 250,000 6 12 2,322,273 2,321,673 99.97 500,000 1 3 664,534 664,334 99.97 Figure 2. The distribution of GC content across assembled scaffolds longer than 10 kbp. Table 2. 1-FT3.2 draft genome features. Feature Number of scaffolds 56 Total length, bp 7,202,438 Longest scaffold, bp 664,534 Contig N50, bp 171,520 Completeness, % 81.29 Contamination, % 0.5 Total number of coding sequences (CheckM2) 5,629 GC content, % 65 Number of tRNA genes 67 Number of proviruses 2 Genome classification and annotation In the BLASTN search, the 1-FT3.2 draft genome scaffolds recruited numerous hits to sequences representing the phylum Myxococcota. GTDB-Tk run on the draft genome suggested classifying 1-FT3.2 within the family Polyangiaceae , order Polyangiales , class Polyangia , phylum Myxococcota. With DRAM, no rRNA encoding genes were identified in the draft genome scaffolds. DRAM-based annotations ( Figure 3 ) revealed a few complete metabolic modules: pentose phosphate cycle, citrate cycle (TCA cycle), glyoxylate cycle, cytochrome c oxidase, and F-type ATPase, as well as a near-complete (8/9) glycolysis module, suggesting robust central carbon metabolism and aerobic respiration. Also, arsenate reductase (glutaredoxin), acetyl-CoA synthetase, acetate kinase, and alcohol dehydrogenase were predicted, but no CAZy enzymes. The incomplete nature of the draft genome sequence precludes full understanding of metabolic capacities or the lack of those in 1-FT3.2. Among other DRAM predictions, several different CRISPR-Cas system proteins were identified (Cas1, Cas2, Cas3, CasA, CasB, CasC, CasD, CasE, Cmr1, Cmr2, Cmr3, Cmr4, Cmr5, and Cmr6). About 36% of all predicted proteins had no significant hits to any DRAM database. Figure 3. Metabolic functions of 1-FT3.2 strain predicted with DRAM. Using geNomad with all scaffolds from the mixed-culture assembly resulted in the prediction of two proviral sequences on scaffolds that belonged to the 1-FT3.2 draft genome: at coordinates 58-30,107 nt in NODE_10_length_239568_cov_144.087670 and 23,906-79,669 nt in NODE_67_length_79671_cov_165.578627. These proviral elements were medium-quality (80 and 53 % complete, respectively) and both assigned as tailed phages within the class Caudoviricetes. In addition, three other short scaffolds (0.2, 5.4, and 6.9 kbp), were identified as viral by geNomad, although the presence of viral genes could be confirmed by CheckV only for one of them. Mapping reads to these three short scaffolds resulted in an overall alignment rate of only 0.00002%, confirming that the nature of the observed lysis zones is unlikely to be viral. Conclusions The genome analysis of 1-FT3.2, the new predatory bacterium strain reported here, placed it within the family Polyangiaceae ( Myxococcota ). Members of this family are terrestrial isolates mainly from soil and plant decay material, characterised by large genomes and high GC content, with some strains being able to degrade cellulose and produce various secondary metabolites ( Garcia and Müller 2014 ). Polyangiaceae representatives are rarely isolated from subarctic soils ( Dawid 2000 ). The draft genome sequence of 1-FT3.2 could be used in future comparative studies aiming to resolve the diversity of the family Polyangiaceae and/or more broadly, predatory bacteria residing in subarctic soils. Although the reported genome is incomplete, it still contributes to increasing the sequenced space of the soil microbiome. Having the strain available for future laboratory studies makes it possible to explore its lifestyle and metabolic capacities in more detail. Data availability Raw reads from the mixed culture are available from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA): PRJNA1337162. The new strain 1-FT3.2 draft genome is available from Figshare: https://doi.org/10.6084/m9.figshare.30277690.v1 [ Demina et al. (2025) ]. Data are available under license CC BY 4.0 Acknowledgements We thank Erin Way and Essi Suomilammi for technical assistance. We acknowledge DNA Sequencing and Genomics Laboratory (supported by HiLIFE and Biocenter Finland funding), Institute of Biotechnology, University of Helsinki for sequencing and CSC – IT Center for Science, Finland, for computational resources as well as for technical support. This work is supported as part of the Genomic Sciences Program DOE Systems Biology Knowledgebase (KBase) funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886. When preparing the manuscript, ChatGPT 5 (OpenAI) was used to suggest language improvements, which were reviewed and further edited by TD. Open access funded by Helsinki University Library. References Altschul SF, Gish W, Miller W, et al. : Basic Local Alignment Search Tool. J. Mol. Biol. 1990; 215 (3): 403–410. 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Publisher Full Text Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 21 Oct 2025 ADD YOUR COMMENT Comment Author details Author details 1 Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland 2 Natural Resources Institute Finland, Helsinki, Finland Tatiana Demina Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Riina Ihonen Roles: Investigation, Writing – Review & Editing Minna K. Männistö Roles: Conceptualization, Resources, Writing – Review & Editing Jenni Hultman Roles: Conceptualization, Methodology, Resources, Supervision, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information The work was supported by the Research Council of Finland (TD: grant 330977, JH: grant 354462) and the Kone Foundation (TD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (2) version 2 Revised Published: 28 Apr 2026, 14:1153 https://doi.org/10.12688/f1000research.171863.2 version 1 Published: 21 Oct 2025, 14:1153 https://doi.org/10.12688/f1000research.171863.1 Copyright © 2025 Demina T et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Demina T, Ihonen R, Männistö MK and Hultman J. Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.12688/f1000research.171863.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 21 Oct 2025 Views 0 Cite How to cite this report: Blin K and Szenei J. Reviewer Report For: Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.5256/f1000research.189522.r429010 ) The direct URL for this report is: https://f1000research.com/articles/14-1153/v1#referee-response-429010 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 25 Nov 2025 Kai Blin , Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Capital Region of Denmark, Denmark Judit Szenei , Technical University of Denmark The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Capital Region of Denmark, Denmark Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.189522.r429010 In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored ... Continue reading READ ALL In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: de-novo sequencing, genome mining, natural products We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Blin K and Szenei J. Reviewer Report For: Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.5256/f1000research.189522.r429010 ) The direct URL for this report is: https://f1000research.com/articles/14-1153/v1#referee-response-429010 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 28 Apr 2026 Tatiana Demina , Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland 28 Apr 2026 Author Response First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers ... Continue reading First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers to all the comments below, reflecting the changes introduced in the updated manuscript (version 2). Reviewers’ comment: In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Answer: Indeed, the genome analyses suggested that 1-FT3.2 is only distantly related to other members of family Polyangiaceae and may represent a novel genus within it. We agree that this finding deserved more emphasis and have now highlighted it in the Abstract and Conclusions. We have also clarified in the text that the closest related genomes identified by autoMLST2.0 (Automated Multi-Locus Species Tree) share only ~76% ANI with 1-FT3.2, supporting its placement in a distinct and underexplored lineage within Myxococcota. A phylogenetic tree was not included in the manuscript because low ANI values indicate deep divergence from reference genomes, and the incompleteness of the 1-FT3.2 genome means that some single-copy marker genes may be missing, which could compromise the reliability of the phylogenetic placement. Reviewers’ comment: Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Answer: Following reviewers’ recommendations, we added long-read data into analyses in the updated manuscript, which helped to improve the assembly quality considerably. We first obtained a complete genome sequence of the prey bacterium, M. cryoferens FT3.2, from long reads and used it as a reference to remove prey-derived sequences from short and long reads prior to assembly. We then performed a hybrid assembly using both short and long reads from which prey sequences had been excluded. While genome completeness and contamination estimates improved only slightly (completeness: 81.29% -> 81.91%; contamination: 0.5% -> 0.38%), several other assembly metrics improved significantly, reflecting a more contiguous assembly: total length 7,202,438 -> 7,638,883 bp; number of scaffolds: 56 -> 13; longest scaffold: 664,534 -> 2,109,807 bp; contig N50: 171.520 Kb -> 452.545 Kb; number of tRNA genes: 67 -> 79; number of rRNA genes: 0 -> 15. The new assembly was also subjected to more thorough annotation, which included additional CAZyme profiling with dbCAN2 and prediction of biosynthetic gene clusters with antiSMASH. Reviewers’ comment: Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. Answer: Yes, the updated draft genome of 1-FT3.2 was deposited to ENA as a MAG. New long read data were saved to SRA. Reviewers’ comment: All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Answer: We thank the reviewers for their positive assessment and constructive comments. In addition to improved genome assembly and more thorough genome annotation, the updated manuscript version contains new microscopy images and more information about 1-FT3.2 cultivation. We believe that the improved manuscript provides more insights into the diversity and functional potential of yet underexplored members of Myxococcota . First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers to all the comments below, reflecting the changes introduced in the updated manuscript (version 2). Reviewers’ comment: In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Answer: Indeed, the genome analyses suggested that 1-FT3.2 is only distantly related to other members of family Polyangiaceae and may represent a novel genus within it. We agree that this finding deserved more emphasis and have now highlighted it in the Abstract and Conclusions. We have also clarified in the text that the closest related genomes identified by autoMLST2.0 (Automated Multi-Locus Species Tree) share only ~76% ANI with 1-FT3.2, supporting its placement in a distinct and underexplored lineage within Myxococcota. A phylogenetic tree was not included in the manuscript because low ANI values indicate deep divergence from reference genomes, and the incompleteness of the 1-FT3.2 genome means that some single-copy marker genes may be missing, which could compromise the reliability of the phylogenetic placement. Reviewers’ comment: Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Answer: Following reviewers’ recommendations, we added long-read data into analyses in the updated manuscript, which helped to improve the assembly quality considerably. We first obtained a complete genome sequence of the prey bacterium, M. cryoferens FT3.2, from long reads and used it as a reference to remove prey-derived sequences from short and long reads prior to assembly. We then performed a hybrid assembly using both short and long reads from which prey sequences had been excluded. While genome completeness and contamination estimates improved only slightly (completeness: 81.29% -> 81.91%; contamination: 0.5% -> 0.38%), several other assembly metrics improved significantly, reflecting a more contiguous assembly: total length 7,202,438 -> 7,638,883 bp; number of scaffolds: 56 -> 13; longest scaffold: 664,534 -> 2,109,807 bp; contig N50: 171.520 Kb -> 452.545 Kb; number of tRNA genes: 67 -> 79; number of rRNA genes: 0 -> 15. The new assembly was also subjected to more thorough annotation, which included additional CAZyme profiling with dbCAN2 and prediction of biosynthetic gene clusters with antiSMASH. Reviewers’ comment: Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. Answer: Yes, the updated draft genome of 1-FT3.2 was deposited to ENA as a MAG. New long read data were saved to SRA. Reviewers’ comment: All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Answer: We thank the reviewers for their positive assessment and constructive comments. In addition to improved genome assembly and more thorough genome annotation, the updated manuscript version contains new microscopy images and more information about 1-FT3.2 cultivation. We believe that the improved manuscript provides more insights into the diversity and functional potential of yet underexplored members of Myxococcota . Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 28 Apr 2026 Tatiana Demina , Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland 28 Apr 2026 Author Response First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers ... Continue reading First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers to all the comments below, reflecting the changes introduced in the updated manuscript (version 2). Reviewers’ comment: In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Answer: Indeed, the genome analyses suggested that 1-FT3.2 is only distantly related to other members of family Polyangiaceae and may represent a novel genus within it. We agree that this finding deserved more emphasis and have now highlighted it in the Abstract and Conclusions. We have also clarified in the text that the closest related genomes identified by autoMLST2.0 (Automated Multi-Locus Species Tree) share only ~76% ANI with 1-FT3.2, supporting its placement in a distinct and underexplored lineage within Myxococcota. A phylogenetic tree was not included in the manuscript because low ANI values indicate deep divergence from reference genomes, and the incompleteness of the 1-FT3.2 genome means that some single-copy marker genes may be missing, which could compromise the reliability of the phylogenetic placement. Reviewers’ comment: Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Answer: Following reviewers’ recommendations, we added long-read data into analyses in the updated manuscript, which helped to improve the assembly quality considerably. We first obtained a complete genome sequence of the prey bacterium, M. cryoferens FT3.2, from long reads and used it as a reference to remove prey-derived sequences from short and long reads prior to assembly. We then performed a hybrid assembly using both short and long reads from which prey sequences had been excluded. While genome completeness and contamination estimates improved only slightly (completeness: 81.29% -> 81.91%; contamination: 0.5% -> 0.38%), several other assembly metrics improved significantly, reflecting a more contiguous assembly: total length 7,202,438 -> 7,638,883 bp; number of scaffolds: 56 -> 13; longest scaffold: 664,534 -> 2,109,807 bp; contig N50: 171.520 Kb -> 452.545 Kb; number of tRNA genes: 67 -> 79; number of rRNA genes: 0 -> 15. The new assembly was also subjected to more thorough annotation, which included additional CAZyme profiling with dbCAN2 and prediction of biosynthetic gene clusters with antiSMASH. Reviewers’ comment: Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. Answer: Yes, the updated draft genome of 1-FT3.2 was deposited to ENA as a MAG. New long read data were saved to SRA. Reviewers’ comment: All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Answer: We thank the reviewers for their positive assessment and constructive comments. In addition to improved genome assembly and more thorough genome annotation, the updated manuscript version contains new microscopy images and more information about 1-FT3.2 cultivation. We believe that the improved manuscript provides more insights into the diversity and functional potential of yet underexplored members of Myxococcota . First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers to all the comments below, reflecting the changes introduced in the updated manuscript (version 2). Reviewers’ comment: In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Answer: Indeed, the genome analyses suggested that 1-FT3.2 is only distantly related to other members of family Polyangiaceae and may represent a novel genus within it. We agree that this finding deserved more emphasis and have now highlighted it in the Abstract and Conclusions. We have also clarified in the text that the closest related genomes identified by autoMLST2.0 (Automated Multi-Locus Species Tree) share only ~76% ANI with 1-FT3.2, supporting its placement in a distinct and underexplored lineage within Myxococcota. A phylogenetic tree was not included in the manuscript because low ANI values indicate deep divergence from reference genomes, and the incompleteness of the 1-FT3.2 genome means that some single-copy marker genes may be missing, which could compromise the reliability of the phylogenetic placement. Reviewers’ comment: Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Answer: Following reviewers’ recommendations, we added long-read data into analyses in the updated manuscript, which helped to improve the assembly quality considerably. We first obtained a complete genome sequence of the prey bacterium, M. cryoferens FT3.2, from long reads and used it as a reference to remove prey-derived sequences from short and long reads prior to assembly. We then performed a hybrid assembly using both short and long reads from which prey sequences had been excluded. While genome completeness and contamination estimates improved only slightly (completeness: 81.29% -> 81.91%; contamination: 0.5% -> 0.38%), several other assembly metrics improved significantly, reflecting a more contiguous assembly: total length 7,202,438 -> 7,638,883 bp; number of scaffolds: 56 -> 13; longest scaffold: 664,534 -> 2,109,807 bp; contig N50: 171.520 Kb -> 452.545 Kb; number of tRNA genes: 67 -> 79; number of rRNA genes: 0 -> 15. The new assembly was also subjected to more thorough annotation, which included additional CAZyme profiling with dbCAN2 and prediction of biosynthetic gene clusters with antiSMASH. Reviewers’ comment: Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. Answer: Yes, the updated draft genome of 1-FT3.2 was deposited to ENA as a MAG. New long read data were saved to SRA. Reviewers’ comment: All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Answer: We thank the reviewers for their positive assessment and constructive comments. In addition to improved genome assembly and more thorough genome annotation, the updated manuscript version contains new microscopy images and more information about 1-FT3.2 cultivation. We believe that the improved manuscript provides more insights into the diversity and functional potential of yet underexplored members of Myxococcota . Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 21 Oct 2025 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 Version 2 (revision) 28 Apr 26 Version 1 21 Oct 25 read Kai Blin , Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark Judit Szenei , Technical University of Denmark The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Blin K et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 25 Nov 2025 | for Version 1 Kai Blin , Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Capital Region of Denmark, Denmark Judit Szenei , Technical University of Denmark The Novo Nordisk Foundation Center for Biosustainability, Lyngby, Capital Region of Denmark, Denmark 0 Views copyright © 2025 Blin K et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise de-novo sequencing, genome mining, natural products We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 28 Apr 2026 Tatiana Demina, Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland First of all, we sincerely thank the reviewers for the provided comments, which we found very useful and did our best to implement changes accordingly. Please find our point-by-point answers to all the comments below, reflecting the changes introduced in the updated manuscript (version 2). Reviewers’ comment: In their manuscript "Draft genome sequence of a predatory bacterium from northern peatland soil", Demina et al. present the genome of a Polyangiaceae family bacterium isolated from nothern peatland soil. This genome adds another puzzle part a currently underexplored branch of the Myxococcota. It's currently the least fragmented genome of a number of genomes that look vaguely related to Labilithrix based on ANI, but that form a distinct cluster when looking at an MLST tree. I think the authors could have pushed that fact a bit more than they modestly did. Answer: Indeed, the genome analyses suggested that 1-FT3.2 is only distantly related to other members of family Polyangiaceae and may represent a novel genus within it. We agree that this finding deserved more emphasis and have now highlighted it in the Abstract and Conclusions. We have also clarified in the text that the closest related genomes identified by autoMLST2.0 (Automated Multi-Locus Species Tree) share only ~76% ANI with 1-FT3.2, supporting its placement in a distinct and underexplored lineage within Myxococcota. A phylogenetic tree was not included in the manuscript because low ANI values indicate deep divergence from reference genomes, and the incompleteness of the 1-FT3.2 genome means that some single-copy marker genes may be missing, which could compromise the reliability of the phylogenetic placement. Reviewers’ comment: Unfortunately, the genome is only estimated to be ~ 80 % complete by CheckM, and I can't help to wonder if part of that isn't driven by the method the authors chose to separate their target DNA reads from the prey bacterium reads by running a mixed assembly first and then discarding small scaffolds while binning based on GC content. As the authors' group did recently publish the prey bacterium's genome, I wonder why they did not remove reads by mapping all reads against the prey bacterium's genome and only keeping reads that fail to match. On that cleaned up set, I'd imagine that an assembler would have had an easier job to create a more complete assembly. If I got the numbers right, the authors sequenced the ~ 14 Mbp combined genome to a coverate of ~ 35x, which is a bit low coverage for a 150 bp read assembly. As the authors did manage to get their bacterium in (co-)culture, they should have been able to isolate enough DNA to get a long-read sequencing run, which would have allowed for a much better de novo assembly. Answer: Following reviewers’ recommendations, we added long-read data into analyses in the updated manuscript, which helped to improve the assembly quality considerably. We first obtained a complete genome sequence of the prey bacterium, M. cryoferens FT3.2, from long reads and used it as a reference to remove prey-derived sequences from short and long reads prior to assembly. We then performed a hybrid assembly using both short and long reads from which prey sequences had been excluded. While genome completeness and contamination estimates improved only slightly (completeness: 81.29% -> 81.91%; contamination: 0.5% -> 0.38%), several other assembly metrics improved significantly, reflecting a more contiguous assembly: total length 7,202,438 -> 7,638,883 bp; number of scaffolds: 56 -> 13; longest scaffold: 664,534 -> 2,109,807 bp; contig N50: 171.520 Kb -> 452.545 Kb; number of tRNA genes: 67 -> 79; number of rRNA genes: 0 -> 15. The new assembly was also subjected to more thorough annotation, which included additional CAZyme profiling with dbCAN2 and prediction of biosynthetic gene clusters with antiSMASH. Reviewers’ comment: Do the authors plan to submit their genome to EBI/NCBI instead of just depositing it on figshare? This would make it much easier for people to actually find the genome. Answer: Yes, the updated draft genome of 1-FT3.2 was deposited to ENA as a MAG. New long read data were saved to SRA. Reviewers’ comment: All in all, the authors have made a nice contribution to the available data on Myxococcota. With not much more effort, I think they could have made this data even better, but maybe that is something the authors can consider in the future. Answer: We thank the reviewers for their positive assessment and constructive comments. In addition to improved genome assembly and more thorough genome annotation, the updated manuscript version contains new microscopy images and more information about 1-FT3.2 cultivation. We believe that the improved manuscript provides more insights into the diversity and functional potential of yet underexplored members of Myxococcota . View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Blin K and Szenei J. Peer Review Report For: Draft genome sequence of a predatory bacterium from northern peatland soil [version 1; peer review: 1 approved with reservations] . F1000Research 2025, 14 :1153 ( https://doi.org/10.5256/f1000research.189522.r429010) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-1153/v1#referee-response-429010 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. 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