Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif
Autoři:
Irina V. Khilyas aff001; Alyona V. Sorokina aff001; Anna A. Elistratova aff001; Maria I. Markelova aff001; Maria N. Siniagina aff001; Margarita R. Sharipova aff001; Tatyana A. Shcherbakova aff002; Megan E. D’Errico aff003; Michael F. Cohen aff004
Působiště autorů:
Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
aff001; FSUE Central Research Institute of Geology of Non-metallic Mineral Resources, Kazan, Russian Federation
aff002; School of Science and Technology, Sonoma State University, Rohnert Park, CA, United States of America
aff003; Department of Biology, Sonoma State University, Rohnert Park, CA, United States of America
aff004
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0225929
Souhrn
Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.
Klíčová slova:
Actinobacteria – Bacteria – Geochemistry – Magnesium – Mineralogy – Minerals – Ribosomal RNA – X-ray diffraction
Zdroje
1. Brazelton WJ, Morrill PL, Szponar N, Schrenk MO. Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs. Appl Environ Microbiol. 2013;79(13):3906–16. Epub 2013/04/16. doi: 10.1128/AEM.00330-13 23584766; PubMed Central PMCID: PMC3697581.
2. Douglas S, Beveridge TJ. Mineral formation by bacteria in natural microbial communities. FEMS Microbiol Ecol. 1998;26(2):79–88. doi: 10.1111/j.1574-6941.1998.tb00494.x
3. Gadd GM. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology. 2010;156(Pt 3):609–43. Epub 2009/12/19. doi: 10.1099/mic.0.037143-0 20019082.
4. Sleep NH. Geological and geochemical constraints on the origin and evolution of life. Astrobiology. 2018;18(9):1199–219. Epub 2018/08/21. doi: 10.1089/ast.2017.1778 30124324.
5. Garzanti E, Doglioni C, Vezzoli G, Ando S. Orogenic belts and orogenic sediment provenance. J Geol. 2007;115(3):315–34. doi: 10.1086/512755
6. Bach W, Früh-Green GL. Alteration of the oceanic lithosphere and implications for seafloor processes. Elements. 2010;6(3):173–8. doi: 10.2113/gselements.6.3.173
7. Schrenk MO, Brazelton WJ, Lang SQ. Serpentinization, carbon, and deep life. Rev Mineral Geochem. 2013;75(1):575–606. doi: 10.2138/rmg.2013.75.18
8. Brazelton WJ, Thornton CN, Hyer A, Twing KI, Longino AA, Lang SQ, et al. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ. 2017;5:e2945. Epub 2017/02/06. doi: 10.7717/peerj.2945 28149702; PubMed Central PMCID: PMC5274519.
9. Evans BW, Hattori K, Baronnet A. Serpentinite: What, Why, Where? Elements. 2013;9(2):99–106. doi: 10.2113/gselements.9.2.99
10. Barnes I, O'Neill JR, Rapp JB, White DE. Silica-carbonate alteration of serpentine; wall rock alteration in mercury deposits of the California Coast Ranges. Econ Geol. 1973;68(3):388–98. doi: 10.2113/gsecongeo.68.3.388
11. Venturelli G, Contini S, Bonazzi A. Weathering of ultramafic rocks and element mobility at Mt. Prinzera, Northern Apennines, Italy. Mineral Mag. 1997;61(6):765–78.
12. Viti C, Collettini C, Tesei T, Tarling M, Smith S. Deformation processes, textural evolution and weakening in retrograde serpentinites. Minerals. 2018;8:241. doi: 10.3390/min8060241
13. Scherbakova TA, Shevelev AI. Magnesite raw material base of Russia and prospects of its development Georesursy [Georesources]. 2016;18(1):75–8. doi: 10.18599/grs.18.1.14
14. Gannoun A, Tessalina S, Bourdon B, Orgeval J-J, Birck JL, Allègre CJ. Re–Os isotopic constraints on the genesis and evolution of the Dergamish and Ivanovka Cu (Co, Au) massive sulphide deposits, south Urals, Russia. Chem Geol. 2003;196:193–207. doi: 10.1016/S0009-2541(02)00413-8
15. Crump BC, Armbrust EV, Baross JA. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol. 1999;65(7):3192–204. 10388721.
16. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1. Epub 2012/08/31. doi: 10.1093/nar/gks808 22933715; PubMed Central PMCID: PMC3592464.
17. Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M. Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing. PloS one. 2014;9(8):e105592. Epub 2014/08/22. doi: 10.1371/journal.pone.0105592 25144201; PubMed Central PMCID: PMC4140814.
18. Boyd ES, Spear JR, Peters JW. [FeFe] hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl Environ Microbiol. 2009;75(13):4620–3. doi: 10.1128/AEM.00582-09 19429563
19. Luton PE, Wayne JM, Sharp RJ, Riley PW. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology. 2002;148(Pt 11):3521–30. Epub 2002/11/13. doi: 10.1099/00221287-148-11-3521 12427943.
20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 2010;7:335. doi: 10.1038/nmeth.f.303 20383131
21. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–D6. Epub 11/28. doi: 10.1093/nar/gks1219 23193283.
22. Stamatakis M, Mitsis I. The occurrences of Mg-hydroxycarbonates in serpentinites of the western section of the South Aegean volcanic arc (West Attica peninsula-Northeastern Argolis peninsula), Greece. Geol Soc Am Bull. 2013;47:427. doi: 10.12681/bgsg.11018
23. Mellini M. Structure and microstructure of serpentine minerals. Minerals at the Nanoscale. In: Nieto F, Livi KJT, Oberti R, editors.: Mineralogical Society of Great Britain and Ireland; 2013.
24. Brazelton WJ, Ludwig KA, Sogin ML, Andreishcheva EN, Kelley DS, Shen C-C, et al. Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proc Natl Acad Sci USA. 2010:200905369.
25. Daae FL, Okland I, Dahle H, Jorgensen SL, Thorseth IH, Pedersen RB. Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex. Geobiology. 2013;11(4):318–39. Epub 2013/04/05. doi: 10.1111/gbi.12035 23551703.
26. Gravuer K, Eskelinen A. Nutrient and rainfall additions shift phylogenetically estimated traits of soil microbial communities. Front Microbiol. 2017;8(1271). doi: 10.3389/fmicb.2017.01271 28744266
27. Mei N, Zergane N, Postec A, Erauso G, Ollier A, Payri C, et al. Fermentative hydrogen production by a new alkaliphilic Clostridium sp. (strain PROH2) isolated from a shallow submarine hydrothermal chimney in Prony Bay, New Caledonia. Int J Hydrogen Energ. 2014;39(34):19465–73.
28. Oline DK. Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils. Appl Environ Microbiol. 2006;72(11):6965–71. Epub 2006/09/05. doi: 10.1128/AEM.00690-06 16950906; PubMed Central PMCID: PMC1636195.
29. Ronholm J, Goordial J, Sapers HM, Izawa MRM, Applin DM, Pontefract A, et al. Characterization of microbial communities hosted in quartzofeldspathic and serpentinite lithologies in Jeffrey Mine, Canada. Astrobiology. 2018;18(8):1008–22. Epub 2018/07/11. doi: 10.1089/ast.2017.1685 29989429.
30. Suzuki S, Ishii S, Wu A, Cheung A, Tenney A, Wanger G, et al. Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem. Proc Natl Acad Sci USA. 2013;110(38):15336–41. Epub 2013/09/05. doi: 10.1073/pnas.1302426110 24003156; PubMed Central PMCID: PMC3780913.
31. Tiago I, Veríssimo A. Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization. Environ Microbiol. 2013;15(6):1687–706. doi: 10.1111/1462-2920.12034 23731249
32. Woycheese KM, Meyer-Dombard DAR, Cardace D, Argayosa AM, Arcilla CA. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines). Front Microbiol. 2015;6:44. doi: 10.3389/fmicb.2015.00044 25745416
33. Ettenauer J, Piñar G, Sterflinger K, Gonzalez-Muñoz MT, Jroundi F. Molecular monitoring of the microbial dynamics occurring on historical limestone buildings during and after the in situ application of different bio-consolidation treatments. Sci Total Environ. 2011;409(24):5337–52. Epub 09/22. doi: 10.1016/j.scitotenv.2011.08.063 21944202.
34. Frank YA, Kadnikov VV, Gavrilov SN, Banks D, Gerasimchuk AL, Podosokorskaya OA, et al. Stable and variable parts of microbial community in Siberian deep subsurface thermal aquifer system revealed in a long-term monitoring study. Front Microbiol. 2016;7(2101). doi: 10.3389/fmicb.2016.02101 28082967
35. Miettinen H, Kietavainen R, Sohlberg E, Numminen M, Ahonen L, Itavaara M. Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhasalmi mine Finland. Front Microbiol. 2015;6:1203. Epub 2015/11/19. doi: 10.3389/fmicb.2015.01203 26579109; PubMed Central PMCID: PMC4626562.
36. Hänchen M, Prigiobbe V, Baciocchi R, Mazzotti M. Precipitation in the Mg-carbonate system effects of temperature and CO2 pressure. Chemical Engineering Science—Chem Eng Sci. 2008;63:1012–28. doi: 10.1016/j.ces.2007.09.052
37. McCutcheon J, Southam G. Advanced biofilm staining techniques for TEM and SEM in geomicrobiology: Implications for visualizing EPS architecture, mineral nucleation, and microfossil generation. Chem Geol. 2018;498. doi: 10.1016/j.chemgeo.2018.09.016
38. Yao M, Lian B, Teng H, Tian Y, Yang X. Serpentine dissolution in the presence of bacteria Bacillus mucilaginosus. J Geomicrobiol. 2012;30. doi: 10.1080/01490451.2011.653087
39. Crespo-Medina M, Twing KI, Sánchez-Murillo R, Brazelton WJ, McCollom TM, Schrenk MO. Methane dynamics in a tropical serpentinizing environment: the Santa Elena Ophiolite, Costa Rica. Front Microbiol. 2017;8:916. doi: 10.3389/fmicb.2017.00916 28588569
40. Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A, Debroas D, et al. Diversity of rare and abundant prokaryotic phylotypes in the Prony Hydrothermal Field and comparison with other serpentinite-hosted ecosystems. Front Microbiol. 2018;9:102. doi: 10.3389/fmicb.2018.00102 29467733
41. Sánchez-Murillo R, Gazel E, Schwarzenbach EM, Crespo-Medina M, Schrenk MO, Boll J, et al. Geochemical evidence for active tropical serpentinization in the Santa Elena Ophiolite, Costa Rica: An analog of a humid early Earth? Geochem Geophy Geosy. 2014;15(5):1783–800. doi: 10.1002/2013GC005213
42. Brazelton WJ, Nelson B, Schrenk MO. Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities. Front Microbiol. 2012;2:268–. doi: 10.3389/fmicb.2011.00268 22232619.
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