Environmental distribution and functions of the Atribacteria
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    Abstract:

    Atribacteria is a new phylum covering the lineages of OP9 and JS1. Most of the members are uncultivated microorganisms, which are distributed widely in the natural environments and dominant in some environments, such as deep marine sediments, geothermal springs, and oil reservoirs. Studies based on genomic information indicate that Atribacteria are strictly anaerobic microorganisms and have the ability to degrade sugars, organic acids, and short chain n-alkanes, suggesting that they may play a key role in subsurface carbon cycling. However, due to the lack of representative pure culture strains, the physiological and biochemical functions of Atribacteria remain to be verified. In this paper, the discovery and development history of Atribacteria, and their environmental distribution and diversity were reviewed. The three proposed metabolic modes of Atribacteria were analyzed and future research directions in this field were also discussed.

    Reference
    [1] Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron Thrash J. High proportions of bacteria and archaea across most biomes remain uncultured. The ISME Journal, 2019, 13(12):3126-3130.
    [2] Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products. Chemistry & Biology, 1998, 5(10):R245-R249.
    [3] Kalisky T, Blainey P, Quake SR. Genomic analysis at the single-cell level. Annual Review of Genetics, 2011, 45:431-445.
    [4] Youssef NH, Blainey PC, Quake SR, Elshahed MS. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Applied and Environmental Microbiology, 2011, 77(21):7804-7814.
    [5] Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, Woyke T, Hentschel U. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME Journal, 2013, 7(12):2287-2300.
    [6] Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PSG, Scholz MB, Lo CC, Raymond J. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications, 2013, 4(1):1854-1854.
    [7] Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, Schwientek P, Kille P, Parkes RJ, Sass H. Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. The ISME Journal, 2016, 10(2):273-286.
    [8] Webster G, Yarram L, Freese E, Köster J, Sass H, Parkes RJ, Weightman AJ. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiology Ecology, 2007, 62(1):78-89.
    [9] Hoshino T, Toki T, Ijiri A, Morono Y, Machiyama H, Ashi J, Okamura K, Inagaki F. Atribacteria from the subseafloor sedimentary biosphere disperse to the hydrosphere through submarine mud volcanoes. Frontiers in Microbiology, 2017, 8:1135.
    [10] Lau MCY, Aitchison JC, Pointing SB. Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet. Extremophiles, 2009, 13(1):139-149.
    [11] Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, DeSantis TZ, Hugenholtz P, Andersen GL, Coates JD. A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME Journal, 2008, 2(11):1146-1156.
    [12] Pham VD, Hnatow LL, Zhang SP, Fallon RD, Jackson SC, Tomb JF, DeLong EF, Keeler SJ. Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environmental Microbiology, 2009, 11(1):176-187.
    [13] Katayama T, Nobu MK, Kusada H, Meng XY, Hosogi N, Uematsu K, Yoshioka H, Kamagata Y, Tamaki H. Isolation of a member of the candidate phylum 'Atribacteria' reveals a unique cell membrane structure. Nature Communications, 2020, 11(1):1-9.
    [14] Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology, 1998, 180(2):366-376.
    [15] Webster G, Parkes RJ, Fry JC, Weightman AJ. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Applied and Environmental Microbiology, 2004, 70(9):5708-5713.
    [16] Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology, 2014, 12(9):635-645.
    [17] Chakraborty A, Ruff SE, Dong XY, Ellefson ED, Li C, Brooks JM, McBee J, Bernard BB, Hubert CRJ. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(20):11029-11037.
    [18] Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(8):2815-2820.
    [19] Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature, 2013, 499(7459):431-437.
    [20] Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, McManus J, Stewart FJ. Adaptations of Atribacteria to life in methane hydrates:hot traits for cold life. bioRxiv, 2019.
    [21] Liu YF, Qi ZZ, Shou LB, Liu JF, Yang SZ, Gu JD, Mu BZ. Anaerobic hydrocarbon degradation in candidate phylum 'Atribacteria' (JS1) inferred from genomics. The ISME Journal, 2019, 13(9):2377-2390.
    [22] Vick TJ, Dodsworth JA, Costa KC, Shock EL, Hedlund BP. Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera. Geobiology, 2010, 8(2):140-154.
    [23] Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP. Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles, 2009, 13(3):447-459.
    [24] Wemheuer B, Taube R, Akyol P, Wemheuer F, Daniel R. Microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the Kamchatka peninsula. Archaea, 2013:1-13.
    [25] Levén L, Eriksson ARB, Schnürer A. Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste. FEMS Microbiology Ecology, 2007, 59(3):683-693.
    [26] Rivière D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li TL, Camacho P, Sghir A. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. The ISME Journal, 2009, 3(6):700-714.
    [27] Tang YQ, Ji P, Hayashi J, Koike Y, Wu XL, Kida K. Characteristic microbial community of a dry thermophilic methanogenic digester:its long-term stability and change with feeding. Applied Microbiology and Biotechnology, 2011, 91(5):1447-1461.
    [28] Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiology Ecology, 2008, 66(2):181-196.
    [29] Gittel A, Sørensen KB, Skovhus TL, Ingvorsen K, Schramm A. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Applied and Environmental Microbiology, 2009, 75(22):7086-7096.
    [30] Carr SA, Orcutt BN, Mandernack KW, Spear JR. Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica. Frontiers in Microbiology, 2015, 6:872.
    [31] Lee YM, Hwang K, Lee JI, Kim M, Hwang CY, Noh HJ, Choi H, Lee HK, Chun J, Hong SG, Shin SC. Genomic insight into the predominance of candidate phylum atribacteria JS1 lineage in marine sediments. Frontiers in Microbiology, 2018, 9:2909.
    [32] Blazejak A, Schippers A. High abundance of JS-1-and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiology Ecology, 2010, 72(2):198-207.
    [33] Zhang Y, Su X, Chen F, Jiao L, Jiang HC, Dong HL, Ding GC. Abundance and diversity of candidate division JS1-and Chloroflexi-related bacteria in cold seep sediments of the northern South China Sea. Frontiers of Earth Science, 2012, 6(4):373-382.
    [34] Kobayashi H, Endo K, Sakata S, Mayumi D, Kawaguchi H, Ikarashi M, Miyagawa Y, Maeda H, Sato K. Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir. Journal of Bioscience and Bioengineering, 2012, 113(2):204-210.
    [35] Cheng L, Shi SB, Li Q, Chen JF, Zhang H, Lu YH. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. PLoS One, 2014, 9(11):e113253.
    [36] Toth CRA, Gieg LM. Time course-dependent methanogenic crude oil biodegradation:dynamics of fumarate addition metabolites, biodegradative genes, and microbial community composition. Frontiers in Microbiology, 2017, 8:2610.
    [37] Webster G, Watt LC, Rinna J, Fry JC, Evershed RP, Parkes RJ, Weightman AJ. A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environmental Microbiology, 2006, 8(9):1575-1589.
    [38] Hicks RE, Amann RI, Stahl DA. Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Applied and Environmental Microbiology, 1992, 58(7):2158-2163.
    [39] Zheng D, Alm EW, Stahl DA, Raskin L. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Applied and Environmental Microbiology, 1996, 62(12):4504-4513.
    [40] Teske A, Hinrichs KU, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. Microbial diversity of hydrothermal sediments in the Guaymas basin:evidence for anaerobic methanotrophic communities. Applied and Environmental Microbiology, 2002, 68(4):1994-2007.
    [41] Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. The ISME Journal, 2010, 4(5):642-647.
    [42] Gies EA, Konwar KM, Beatty JT, Hallam SJ. Illuminating microbial dark matter in meromictic sakinaw lake. Applied and Environmental Microbiology, 2014, 80(21):6807-6818.
    [43] Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Applied and Environmental Microbiology, 1998, 64(2):795-799.
    [44] Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jørgensen BB. Predominant archaea in marine sediments degrade detrital proteins. Nature, 2013, 496(7444):215-218.
    [45] Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. The ISME Journal, 2015, 9(8):1710-1722.
    [46] Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature, 1998, 392(6678):801-805.
    [47] Radajewski S, Ineson P, Parekh NR, Colin Murrell J. Stable-isotope probing as a tool in microbial ecology. Nature, 2000, 403(6770):646-649.
    [48] Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 1993, 59(3):695-700.
    [49] Webster G, Sass H, Cragg BA, Gorra R, Knab NJ, Green CJ, Mathes F, Fry JC, Weightman AJ, Parkes RJ. Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiology Ecology, 2011, 77(2):248-263.
    [50] Müller B, Sun L, Schnürer A. First insights into the syntrophic acetate-oxidizing bacteria-a genetic study. MicrobiologyOpen, 2013, 2(1):35-53.
    [51] Aoyagi T, Inaba T, Aizawa H, Mayumi D, Sakata S, Charfi A, Suh C, Lee JH, Sato Y, Ogata A, Habe H, Hori T. Unexpected diversity of acetate degraders in anaerobic membrane bioreactor treating organic solid waste revealed by high-sensitivity stable isotope probing. Water Research, 2020, 176:115750.
    [52] Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Computational Biology, 2014, 10(10):e1003898.
    [53] Kirst H, Kerfeld CA. Bacterial microcompartments:catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering. BMC Biology, 2019, 17(1):79.
    [54] Tan B, Jane Fowler S, Laban NA, Dong XL, Sensen CW, Foght J, Gieg LM. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. The ISME Journal, 2015, 9(9):2028-2045.
    [55] Hu P, Tom L, Singh A, Thomas BC, Baker BJ, Piceno YM, Andersen GL, Banfield JF. Genome-resolved metagenomic analysis reveals roles for candidate phyla and other microbial community members in biogeochemical transformations in oil reservoirs. mBio, 2016, 7(1):e01669-15.
    [56] Sierra-Garcia IN, Belgini DRB, Torres-Ballesteros A, Paez-Espino D, Capilla R, Santos Neto EV, Gray N, de Oliveira VM. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. Science of the Total Environment, 2020, 715:136646.
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Zhonglin Liu, Yifan Liu, Dandan Lin, Lei Zhou, Bo-Zhong Mu. Environmental distribution and functions of the Atribacteria. [J]. Acta Microbiologica Sinica, 2021, 61(6): 1416-1427

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  • Received:March 23,2021
  • Revised:April 18,2021
  • Online: June 05,2021
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