in

Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

[adace-ad id="91168"]
  • 1.

    Mukherjee, S. et al. Genomes OnLine database (GOLD) v.7: Updates and new features. Nucleic Acids Res.47, D649–D659 (2019).

    CAS  PubMed  Google Scholar 

  • 2.

    Agarwala, R. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res.46, D8–D13 (2018).

    Google Scholar 

  • 3.

    Chen, I. M. A. et al. IMG/M v.5.0: An integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res.47, D666–D677 (2019).

    CAS  PubMed  Google Scholar 

  • 4.

    Blakemore, R. P. Magnetotactic Bacteria. Science190, 377–379 (1975).

    ADS  CAS  PubMed  Google Scholar 

  • 5.

    Benoit, M. R. et al. Visualizing implanted tumors in mice with magnetic resonance imaging using magnetotactic bacteria. Clin Cancer Res.15, 5170–5177 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 6.

    Alphandéry, E., Chebbi, I., Guyot, F. & Durand-Dubief, M. Use of bacterial magnetosomes in the magnetic hyperthermia treatment of tumours: A review. Int. J. Hyperth.29, 801–809 (2013).

    Google Scholar 

  • 7.

    Chang, S. & Kirschvink, J. L. Magnetofossils, the magnetization of sediments, and the evolution of magnetite biomineralization. Annu. Rev. Earth Planet. Sci17, 169–95 (1989).

    ADS  CAS  Google Scholar 

  • 8.

    Kodama, K. P., Moeller, R. E., Bazylinski, D. A., Kopp, R. E. & Chen, A. P. The mineral magnetic record of magnetofossils in recent lake sediments of Lake Ely, PA. Glob. Planet. Change110, 350–363 (2013).

    ADS  Google Scholar 

  • 9.

    Kopp, R. E. & Kirschvink, J. L. The identification and biogeochemical interpretation of fossil magnetotactic bacteria. Earth-Science Rev.86, 42–61 (2008).

    ADS  Google Scholar 

  • 10.

    Mckay, C. P., Friedmann, E. I., Frankel, R. B. & Bazylinski, D. A. Magnetotactic bacteria on Earth and on Mars. Astrobiology3, 263–271 (2003).

    ADS  CAS  PubMed  Google Scholar 

  • 11.

    Uebe, R. & Schüler, D. Magnetosome biogenesis in magnetotactic bacteria. Nature Reviews Microbiology14, 621–637 (2016).

    CAS  PubMed  Google Scholar 

  • 12.

    Lin, W., Pan, Y. & Bazylinsky, D. A. Diversity and ecology of and biomineralization by magnetotactic bacteria. Environ. Microbiol. Rep.9, 345–356 (2017).

    CAS  PubMed  Google Scholar 

  • 13.

    Lin, W. et al. Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae. ISME J.8, 2463–2477 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 14.

    Lin, W. & Pan, Y. A putative greigite-type magnetosome gene cluster from the candidate phylum Latescibacteria. Environ. Microbiol. Rep.7, 237–242 (2015).

    CAS  PubMed  Google Scholar 

  • 15.

    Lin, W. et al. Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution. ISME J. 201812, 1508–1519 (2018).

    CAS  Google Scholar 

  • 16.

    Ji, B. et al. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain. Environ. Microbiol.16, 525–544 (2014).

    CAS  PubMed  Google Scholar 

  • 17.

    Koziaeva, V. V. et al. Magnetospirillum kuznetsovii sp. nov., a novel magnetotactic bacterium isolated from a lake in the Moscow region. Int. J. Syst. Evol. Microbiol.69, 1953–1959 (2019).

    CAS  Google Scholar 

  • 18.

    Matsunaga, T. et al. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res.12, 157–166 (2005).

    CAS  PubMed  Google Scholar 

  • 19.

    Smalley, M. D., Marinov, G. K., Bertani, L. E. & DeSalvo, G. Genome sequence of Magnetospirillum magnetotacticum strain MS-1. Genome Announc.3, e00233–15 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 20.

    Koziaeva, V. V. et al. Draft Genome sequences of two magnetotactic bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1. Genome Announc.4, e00814–16 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 21.

    Ke, L., Liu, P., Liu, S. & Gao, M. Complete genome sequence of Magnetospirillum sp. ME-1, a novel magnetotactic bacterium isolated from East Lake, Wuhan, China. Genome Announc.5, e00485–17 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 22.

    Wang, Y. et al. Complete genome sequence of Magnetospirillum sp. Strain XM-1, isolated from the Xi’an City Moat. China. Genome Announc.4, e01171–16 (2016).

    PubMed  Google Scholar 

  • 23.

    Grouzdev, D. S. et al. Draft genome sequence of Magnetospirillum sp. Strain SO-1, a freshwater magnetotactic bacterium isolated from the Ol’khovka River, Russia. Genome Announc.2, e00235–14 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 24.

    Ullrich, S., Kube, M., Schübbe, S., Reinhardt, R. & Schüler, D. A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. J. Bacteriol.187, 7176–7184 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 25.

    Trubitsyn, D. et al. Draft genome sequence of Magnetovibrio blakemorei strain MV-1, a marine vibrioid magnetotactic bacterium. Genome Announc.4, e01330–16 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 26.

    Jogler, C. et al. Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer. Environ. Microbiol.11, 1267–1277 (2009).

    CAS  PubMed  Google Scholar 

  • 27.

    Monteil, C. L. et al. Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis. Environ. Microbiol.20, 4415–4430 (2018).

    CAS  PubMed  Google Scholar 

  • 28.

    Schübbe, S. et al. Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1. Appl. Environ. Microbiol.75, 4835–4852 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 29.

    Ji, B. et al. The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria. Environ. Microbiol.19, 1103–1119 (2017).

    CAS  PubMed  Google Scholar 

  • 30.

    Morillo, V. et al. Isolation, cultivation and genomic analysis of magnetosome biomineralization genes of a new genus of South-seeking magnetotactic cocci within the Alphaproteobacteria. Front. Microbiol.5, 72 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 31.

    Koziaeva, V. et al. Genome-based metabolic reconstruction of a novel uncultivated freshwater magnetotactic coccus “Ca. Magnetaquicoccus inordinatus” UR-1, and proposal of a candidate family “Ca. Magnetaquicoccaceae”. Front. Microbiol.10, 2290 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 32.

    Abreu, F. et al. Deciphering unusual uncultured magnetotactic multicellular prokaryotes through genomics. ISME J.8, 1055–1068 (2014).

    CAS  PubMed  Google Scholar 

  • 33.

    Kolinko, S., Richter, M., Glöckner, F. O., Brachmann, A. & Schüler, D. Single-cell genomics reveals potential for magnetite and greigite biomineralization in an uncultivated multicellular magnetotactic prokaryote. Environ. Microbiol. Rep.6, 524–531 (2014).

    CAS  PubMed  Google Scholar 

  • 34.

    Lefèvre, C. T. et al. Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis. Environ. Microbiol.15, 2712–2735 (2013).

    PubMed  Google Scholar 

  • 35.

    Nakazawa, H. et al. Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria. Genome Res.19, 1801–1808 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 36.

    Lefèvre, C. T. et al. Novel magnetite-producing magnetotactic bacteria belonging to the Gammaproteobacteria. ISME J.6, 440–450 (2012).

    PubMed  Google Scholar 

  • 37.

    Baker, B. J., Lazar, C. S., Teske, A. P. & Dick, G. J. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome3 (2015).

  • 38.

    Jogler, C. et al. Cultivation-independent characterization of ‘Candidatus Magnetobacterium bavaricum’ via ultrastructural, geochemical, ecological and metagenomic methods. Environ. Microbiol.12, 2466–2478 (2010).

    CAS  PubMed  Google Scholar 

  • 39.

    Kolinko, S., Richter, M., Glöckner, F. O., Brachmann, A. & Schüler, D. Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes. Environ. Microbiol.18, 21–37 (2016).

    CAS  PubMed  Google Scholar 

  • 40.

    Lin, W. et al. Origin of microbial biomineralization and magnetotaxis during the Archean. Proc. Natl. Acad. Sci.114, 2171–2176 (2017).

    ADS  CAS  PubMed  Google Scholar 

  • 41.

    Koziaeva, V. V. et al. Biodiversity of magnetotactic bacteria in the freshwater lake Beloe Bordukovskoe, Russia. Microbiology89, 348–358, https://doi.org/10.1134/S002626172003008X (2020).

  • 42.

    Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (80−).337, 1661–1665 (2012).

    ADS  CAS  Google Scholar 

  • 43.

    Kolinko, S. et al. Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3. Environ. Microbiol.14, 1709–1721 (2012).

    CAS  PubMed  Google Scholar 

  • 44.

    BioSample of Candidatus Hydrogenedentes bacterium MAG_17971_hgd_130. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911668 (2020).

  • 45.

    Thrash, C. J. et al. Metagenomic assembly and prokaryotic metagenome-assembled genome sequences from the northern Gulf of Mexico “Dead Zone”. Microbiol. Resour. Announc.7, 4–6 (2018).

    Google Scholar 

  • 46.

    Watson, S. W. & Waterbury, J. B. Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov. gen. nov. sp. Arch. Microbiol.77, 203–230 (1971).

    Google Scholar 

  • 47.

    Tian, R. M. et al. The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur. Environ. Microbiol.18, 2481–2494 (2016).

    CAS  PubMed  Google Scholar 

  • 48.

    BioSample of Deltaproteobacteria bacterium MAG_22309_dsfv_022. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911677 (2020).

  • 49.

    Didonato, R. J. et al. Genome sequence of the deltaproteobacterial strain NaphS2 and analysis of differential gene expression during anaerobic growth on naphthalene. PLos One5, e14072 (2010).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 50.

    Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol.2, 1533–1542 (2017).

    CAS  PubMed  Google Scholar 

  • 51.

    Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data5, 1–8 (2018).

    Google Scholar 

  • 52.

    Sizova, M. V., Panikov, N. S., Spiridonova, E. M., Slobodova, N. V. & Tourova, T. P. Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen. Syst. Appl. Microbiol.30, 213–220 (2007).

    CAS  PubMed  Google Scholar 

  • 53.

    Bazylinski, D. A. et al. Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int. J. Syst. Evol. Microbiol.63, 801–808 (2013).

    CAS  PubMed  Google Scholar 

  • 54.

    Lebedeva, E. V. et al. Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol. Ecol.75, 195–204 (2011).

    CAS  PubMed  Google Scholar 

  • 55.

    Lefèvre, C. T. et al. Moderately thermophilic magnetotactic bacteria from hot springs in Nevada. Appl. Environ. Microbiol.76, 3740–3743 (2010).

    PubMed  PubMed Central  Google Scholar 

  • 56.

    Lefèvre, C. T. et al. Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis. Syst. Appl. Microbiol.40, 280–289 (2017).

    PubMed  Google Scholar 

  • 57.

    Mikaelyan, A. et al. High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates. Environ. Microbiol. Rep.9, 477–483 (2017).

    CAS  PubMed  Google Scholar 

  • 58.

    Izawa, K. et al. Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites. Environ. Microbiol. Rep.9, 411–418 (2017).

    CAS  PubMed  Google Scholar 

  • 59.

    Ohkuma, M. et al. The candidate phylum ‘Termite Group 1’ of bacteria: Phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists. FEMS Microbiol. Ecol.60, 467–476 (2007).

    CAS  PubMed  Google Scholar 

  • 60.

    Dufour, S. C. et al. Magnetosome-containing bacteria living as symbionts of bivalves. ISME J.8, 2453–2462 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 61.

    Monteil, C. L. et al. Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. Nat. Microbiol.4, 1088–1095 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 62.

    Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature499, 431–437 (2013).

    ADS  CAS  PubMed  Google Scholar 

  • 63.

    Probst, A. J. et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environ. Microbiol.19, 459–474 (2016).

    PubMed  Google Scholar 

  • 64.

    Tully, B. J., Wheat, C. G., Glazer, B. T. & Huber, J. A. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME J.12, 1–16 (2018).

    CAS  PubMed  Google Scholar 

  • 65.

    Lücker, S., Nowka, B., Rattei, T., Spieck, E. & Daims, H. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front. Microbiol.4, 27 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 66.

    Mendler, K. et al. Annotree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res.47, 4442–4448 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 67.

    Laczny, C. C. et al. BusyBee Web: Metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res.45, W171–W179 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 68.

    Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics32, 605–607 (2016).

    CAS  Google Scholar 

  • 69.

    Lin, H. H. & Liao, Y. C. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci. Rep.6, 12–19 (2016).

    Google Scholar 

  • 70.

    Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol.3, 836–843 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 71.

    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res.25, 1043–1055 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 72.

    Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics29, 1072–1075 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 73.

    Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun.9, 5114 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 74.

    Murali, A., Bhargava, A. & Wright, E. S. IDTAXA: A novel approach for accurate taxonomic classification of microbiome sequences. Microbiome6, 140 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 75.

    Chaumeil, P., Mussig, A. J., Parks, D. H. & Hugenholtz, P. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 1–3, https://doi.org/10.1093/bioinformatics/btz848 (2019).

  • 76.

    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol.36, 996 (2018).

    CAS  PubMed  Google Scholar 

  • 77.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol.30, 772–80 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 78.

    Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol.17, 540–552 (2000).

    CAS  PubMed  Google Scholar 

  • 79.

    Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol.32, 268–274 (2015).

    CAS  PubMed  Google Scholar 

  • 80.

    Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Haeseler, A. V. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods14, 587–589 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 81.

    Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol.35, 518–522 (2018).

    CAS  PubMed  Google Scholar 

  • 82.

    Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res.47, W256–W259 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 83.

    ASM268676v1 assembly for Magnetovibrio sp. NCBI Assembly https://identifiers.org/ncbi/insdc.gca:GCA_002686765.1 (2013).

  • 84.

    ASM240148v1assembly for Elusimicrobia bacterium NORP122. NCBI Assembly https://identifiers.org/ncbi/insdc.gca:GCA_002401485.1 (2017).

  • 85.

    BioSample of Candidatus Hydrogenedentes bacterium MAG_17963_hgd_111. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911667 (2020).

  • 86.

    BioSample of Deltaproteobacteria bacterium MAG_00134_naph_006. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911648 (2020).

  • 87.

    BioSample of Deltaproteobacteria bacterium MAG_00241_naph_010. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911655 (2020).

  • 88.

    BioSample of Deltaproteobacteria bacterium MAG_00792_naph_016. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911656 (2020).

  • 89.

    BioSample of Deltaproteobacteria bacterium MAG_09788_naph_37. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911662 (2020).

  • 90.

    BioSample of Deltaproteobacteria bacterium MAG_15370_dsfb_81. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911665 (2020).

  • 91.

    BioSample of Deltaproteobacteria bacterium MAG_17929_sntb_26. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911666 (2020).

  • 92.

    BioSample of Deltaproteobacteria bacterium MAG_17996_sntb_20. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911670 (2020).

  • 93.

    BioSample of Deltaproteobacteria bacterium MAG_22204_dsfv_001. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911675 (2020).

  • 94.

    BioSample of Gammaproteobacteria bacterium MAG_00150_gam_010. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911649 (2020).

  • 95.

    BioSample of Gammaproteobacteria bacterium MAG_00160_gam_009. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911650 (2020).

  • 96.

    BioSample of Gammaproteobacteria bacterium MAG_00172_gam_018. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911651 (2020).

  • 97.

    BioSample of Gammaproteobacteria bacterium MAG_00188_gam_006. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911652 (2020).

  • 98.

    BioSample of Gammaproteobacteria bacterium MAG_00212_gam_1. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911653 (2020).

  • 99.

    BioSample of Gammaproteobacteria bacterium MAG_00215_gam_020. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911654 (2020).

  • 100.

    BioSample of Magnetococcales bacterium MAG_21055_mgc_1. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911672 (2020).

  • 101.

    BioSample of Nitrospinae bacterium MAG_09705_ntspn_70. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911661 (2020).

  • 102.

    BioSample of Nitrospirae bacterium MAG_10313_ntr_31. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911663 (2020).

  • 103.

    BioSample of Desulfuromonadales bacterium MAG_21601_9_030. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911674 (2020).

  • 104.

    BioSample of Desulfuromonadales bacterium MAG_13126_9_058. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911678 (2020).

  • 105.

    BioSample of Desulfuromonadales bacterium MAG_21600_9_004. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911673 (2020).

  • 106.

    BioSample of Planctomycetes bacterium MAG_11118_pl_115. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911664 (2020).

  • 107.

    BioSample of Planctomycetes bacterium MAG_17991_pl_60. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911669 (2020).

  • 108.

    BioSample of Planctomycetes bacterium MAG_18080_pl_157. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911671 (2020).

  • 109.

    BioSample of Rhodospirillaceae bacterium MAG_04806_tlms_2. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911657 (2020).

  • 110.

    BioSample of Rhodospirillaceae bacterium MAG_05422_2-02_14. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911658 (2020).

  • 111.

    BioSample of Rhodospirillaceae bacterium MAG_05596_2-02_51. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911659 (2020).

  • 112.

    BioSample of Rhodospirillaceae bacterium MAG_06104_tlms_034. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911660 (2020).

  • 113.

    BioSample of Rhodospirillaceae bacterium MAG_22225_2-02_112. NCBI BioSample https://identifiers.org/ncbi/biosample:SAMN14911676 (2020).

  • 114.

    Assembly for unclassified Nitrospina Bin 25. IMG https://identifiers.org/img.taxon:2651870060 (2016).

  • 115.

    Assembly for Planctomycetes bacterium SCGC JGI090-P21. IMG Assembly https://identifiers.org/img.taxon:2264265205 (2015).

  • 116.

    Assembly for Omnitrophica bacterium SCGC_AG-290-C17. IMG Assembly https://identifiers.org/img.taxon:3300015153 (2017).

  • 117.

    Assembly for uncultured microorganism SbSrfc.SA12.01.D19. IMG Assembly https://identifiers.org/img.taxon:3300022116 (2017).

  • 118.

    Uzun, M., Alekseeva, L., Krutkina, M., Koziaeva, V. & Grouzdev, D. Analysis: unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases. fighsare https://doi.org/10.6084/m9.figshare.c.4883706 (2020).

  • 119.

    Espínola, F. et al. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb. Ecol.75, 123–139 (2018).

    PubMed  Google Scholar 

  • 120.

    Wu, X. et al. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations. ISME J.10, 1192–1203 (2016).

    CAS  PubMed  Google Scholar 


  • Source: Ecology - nature.com

    Peering into peer review

    Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia