Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust
Himadri Bose
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Avishek Dutta
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Ajoy Roy
Department of Biotechnology, National Institute of Technology
Durgapur, Durgapur, 713209, West Bengal, India
Abhishek Gupta
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Sourav Mukhopadhyay
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Balaram Mohapatra
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Jayeeta Sarkar
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Sukanta Roy
Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, 415114, Maharashtra, India
Sufia K. Kazy
Department of Biotechnology, National Institute of Technology
Durgapur, Durgapur, 713209, West Bengal, India
Pinaki Sar
CORRESPONDING AUTHOR
Environmental Microbiology and Genomics Laboratory, Department of
Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302,
West Bengal, India
Related authors
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H. Gupta, S. Nayak, W. Ellsworth, Y. J. B. Rao, S. Rajan, B. K. Bansal, N. Purnachandra Rao, S. Roy, K. Arora, R. Mohan, V. M. Tiwari, H. V. S. Satyanarayana, P. K. Patro, D. Shashidhar, and K. Mallika
Sci. Dril., 18, 5–9, https://doi.org/10.5194/sd-18-5-2014, https://doi.org/10.5194/sd-18-5-2014, 2014
Short summary
Short summary
During May 16-18, 2014, the ICDP Workshop on Scientific Deep Drilling in the Koyna region of western India was held in Koyna to review the progress made in the preparatory phase and the preparation of a full drilling proposal. 49 participants came from Canada, France, Germany, India, Japan, New Zealand, Norway, Spain, and USA. It was recommended to have two pilot and two main boreholes, hosting comprehensive sets of monitoring instruments to better comprehend reservoir-triggered earthquakes.
Related subject area
Location/Setting: Continental | Subject: Microbiology | Geoprocesses: Deep biosphere
Drilling into an active mofette: pilot-hole study of the impact of CO2-rich mantle-derived fluids on the geo–bio interaction in the western Eger Rift (Czech Republic)
Workshop to develop deep-life continental scientific drilling projects
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Sci. Dril., 19, 43–53, https://doi.org/10.5194/sd-19-43-2015, https://doi.org/10.5194/sd-19-43-2015, 2015
Cited articles
Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R.,
and Fierer, N.: Examining the global distribution of dominant archaeal
populations in soil, ISME J., 5, 908–917, https://doi.org/10.1038/ismej.2010.171, 2010.
Beeman, R. E. and Suflita, J. M.: Evaluation of deep subsurface sampling procedures using serendipitous microbial contaminats as tracers organisms, Geomicrobiol. J., 7, 223–233, https://doi.org/10.1080/01490458909377868, 1989.
Borgonie, G., Magnabosco, C., García-Moyano, A., Linage-Alvarez, B.,
Ojo, A. O., Freese, L. B., Van Jaarsveld, C., Van Rooyen, C., Kuloyo, O.,
Cason, E. D., and Vermeulen, J.: New ecosystems in the deep subsurface follow
the flow of water driven by geological activity, Sci. Rep., 9, 3310, https://doi.org/10.1038/s41598-019-39699-w, 2019.
Borsodi, A. K., Micsinai, A., Kovacs, G., Toth, E., Schumann, P., Kovacs,
A. L., Böddi, B., and Marialigeti, K.: Pannonibacter phragmitetus gen. nov., sp. nov., a novel
alkalitolerant bacterium isolated from decomposing reed rhizomes in a
Hungarian soda lake, Int. J. Syst. Evol. Microbiol., 53, 555–561,
https://doi.org/10.1099/ijs.0.02356-0, 2003.
Breuker, A., Köweker, G., Blazejak, A., and Schippers, A.: The deep
biosphere in terrestrial sediments in the Chesapeake Bay area, Virginia,
USA, Front. Microbiol., 2, 156, https://doi.org/10.3389/fmicb.2011.00156, 2011.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D.,
Costello, E. K., Fierer, N., Pena, A. G., Goodrich, J. K., Gordon, J. I., and
Huttley, G. A.: QIIME allows analysis of high-throughput community sequencing
data, Nat. Methods, 7, 335–336, 2010.
Chakraborty, A., Ellefson, E., Li, C., Gittins, D., Brooks, J. M., Bernard,
B. B., and Hubert, C. R.: Thermophilic endospores associated with
migrated thermogenic hydrocarbons in deep Gulf of Mexico marine
sediments, ISME J., 12, 1895–1906, 2018.
Colwell, F. S. and D'Hondt, S.: Nature and extent of the deep biosphere, Rev.
Mineral. Geochem., 75, 547–574, https://doi.org/10.2138/rmg.2013.75.17, 2013.
Deep, K., Poddar, A., and Das, S. K.: Anoxybacillus suryakundensis sp. nov, a moderately thermophilic,
alkalitolerant bacterium isolated from hot spring at Jharkhand, India, PloS
One, 8, e85493, https://doi.org/10.1371/journal.pone.0085493, 2013.
Dias, M., Salvado, J. C., Monperrus, M., Caumette, P., Amouroux, D., Duran,
R., and Guyoneaud, R.: Characterization of Desulfomicrobium salsuginis sp. nov. and Desulfomicrobium aestuarii sp. nov., two new
sulfate-reducing bacteria isolated from the Adour estuary (French Atlantic
coast) with specific mercury methylation potentials, Syst.
Appl. Microbiol., 31, 30–37,
https://doi.org/10.1016/j.syapm.2007.09.002, 2008.
Dutta, A., Dutta Gupta, S., Gupta, A., Sarkar, J., Roy, S., Mukherjee, A.,
and Sar, P.: Exploration of deep terrestrial subsurface microbiome in Late
Cretaceous Deccan traps and underlying Archean basement, India, Sci. Rep.,
8, 17459, https://doi.org/10.1038/s41598-018-35940-0, 2018.
Emmerich, M., Bhansali, A., Lösekann-Behrens, T., Schröder, C.,
Kappler, A., and Behrens, S.: Abundance, distribution, and activity of Fe
(II)-oxidizing and Fe (III)-reducing microorganisms in hypersaline sediments
of Lake Kasin, southern Russia, Appl. Environ. Microbiol., 78, 4386–4399,
https://doi.org/10.1128/AEM.07637-11, 2012.
Engle, M., Li, Y., Woese, C., and Wiegel, J.: Isolation and characterization
of a novel alkalitolerant thermophile, Anaerobranca horikoshii gen. nov., sp. nov., Int. J. Syst.
Evol. Microbiol., 45, 454–461, https://doi.org/10.1099/ijs.0.004218-0, 1995.
Escudero, C., Oggerin, M., and Amils, R.: The deep continental subsurface:
The dark biosphere, Int. Microbiol., 21.3–14, https://doi.org/10.1007/s10123-018-0009-y, 2018.
Fang, J., Kato, C., Runko, G.M., Nogi, Y., Hori, T., Li, J., Morono, Y., and
Inagaki, F.: Predominance of viable spore-forming piezophilic bacteria in
high-pressure enrichment cultures from ∼1.5 to 2.4 km-deep
coal-bearing sediments below the ocean floor, Front. Microbiol., 8, 137, https://doi.org/10.3389/fmicb.2017.00137, 2017.
Flemming, H. C. and Wuertz, S.: Bacteria and archaea on Earth and their
abundance in biofilms, Nat. Rev. Microbiol., 17, 247–260, https://doi.org/10.1038/s41579-019-0158-9, 2019.
França, L., Rainey, F. A., Nobre, M. F., and Da Costa, M. S.: Tepidicella xavieri gen. nov.,
sp. nov., a betaproteobacterium isolated from a hot spring runoff, Int. J.
Syst. Evol. Microbiol., 56, 907–912, https://doi.org/10.1099/ijs.0.64193-0, 2006.
Fredrickson, J. K. and Balkwill, D. L.: Geomicrobial processes and
biodiversity in the deep terrestrial subsurface, Geomicrobiol. J., 23,
345–356, https://doi.org/10.1080/01490450600875571, 2006.
Fullerton, H. and Moyer, C. L.: Comparative single-cell genomics of
Chloroflexi from the Okinawa Trough deep subsurface biosphere, Appl. Environ.
Microbiol., 82, 3000–3008, https://doi.org/10.1128/AEM.00624-16, 2016.
Gaboyer, F., Burgaud, G., and Alain, K.: Physiological and evolutionary
potential of microorganisms from the Canterbury Basin subseafloor, a
metagenomic approach, FEMS Microbiol. Ecol., 9, 5,
https://doi.org/10.1093/femsec/fiv029, 2015.
Gandhi, S. M. and Sarkar, B. C. (Eds.): Essentials of Mineral Exploration
and Evaluation, Elsevier, Amesterdam, the Netherlands, 2003.
Gibiino, G., Lopetuso, L. R., Scaldaferri, F., Rizzatti, G., Binda, C., and
Gasbarrini, A.: Exploring Bacteroidetes: Metabolic key points and
immunological tricks of our gut commensals, Dig. Liver Dis., 50, 635–639,
https://doi.org/10.1016/j.dld.2018.03.016, 2018.
Glaring, M. A., Vester, J. K., Lylloff, J. E., Al-Soud, W. A., Sørensen,
S. J., and Stougaard, P.: Microbial diversity in a permanently cold and
alkaline environment in Greenland, PloS One, 10, e0124863,
https://doi.org/10.1371/journal.pone.0124863, 2015.
Gorlenko, V., Tsapin, A., Namsaraev, Z., Teal, T., Tourova, T., Engler, D.,
Mielke, R., and Nealson, K.: Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic,
fermentative bacterium isolated from a hot spring on Mono Lake, Syst.
Evol. Microbiol., 54, 739–743, https://doi.org/10.1099/ijs.0.02909-0, 2004.
Guerra, A. B., Oliveira, J. S., Silva-Portela, R. C., Araujo, W., Carlos, A. C.,
Vasconcelos, A. T. R., Freitas, A. T., Domingos, Y. S., de Farias, M. F.,
Fernandes, G. J. T., and Agnez-Lima, L. F.: Metagenome enrichment approach used
for selection of oil-degrading bacteria consortia for drill cutting residue
bioremediation, Environ. Pollut., 235,
869–880, https://doi.org/10.1016/j.envpol.2018.01.014, 2018.
Gupta, A., Dutta, A., Sarkar, J., Panigrahi, M. K., and Sar, P.: Low-Abundance
Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic
Mine Drainage From the Malanjkhand Copper Project, India, Front. Microbiol.,
9, 2882, https://doi.org/10.3389/fmicb.2018.02882, 2018.
Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P., and Minghim,
R.: InteractiVenn: a web-based tool for the analysis of sets through Venn
diagrams, BMC Bioinformatics, 16, 169, https://doi.org/10.1186/s12859-015-0611-3, 2015.
Hoehler, T. M. and Jørgensen, B. B.: Microbial life under extreme energy
limitation, Nat. Rev. Microbiol., 11, 83–94, 2013.
Hong, H., Kim, S. J., Min, U. G., Lee, Y. J., Kim, S. G., Jung, M. Y., Seo, Y. S.,
and Rhee, S. K.: Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated
from an oil-contaminated site, Antonie van Leeuwenhoek, 107, 971–977,
https://doi.org/10.1007/s10482-015-0389-3, 2015.
Horino, H., Fujita, T., and Tonouchi, A.: Description of Anaerobacterium
chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from
Clostridium rRNA cluster III isolated from soil of a Japanese rice field,
and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov., Int.
J. Syst. Evol. Microbiol., 64, 1296–1303, https://doi.org/10.1099/ijs.0.059378-0, 2014.
Hubalek, V., Wu, X., Eiler, A., Buck, M., Heim, C., Dopson, M., Bertilsson,
S., and Ionescu, D.: Connectivity to the surface determines diversity
patterns in subsurface aquifers of the Fennoscandian shield, ISME J., 10, 2556, https://doi.org/10.1038/ismej.2016.94, 2016.
Ino, K., Hernsdorf, A. W., Konno, U., Kouduka, M., Yanagawa, K., Kato, S.,
Sunamura, M., Hirota, A., Togo, Y. S., Ito, K., and Fukuda, A.: Ecological
and genomic profiling of anaerobic methane-oxidizing archaea in a deep
granitic environment, ISME J., 12, 31–47, https://doi.org/10.1038/ismej.2017.140, 2017.
İşçi, E. and Turutoğlu, S. İ.: Stabilization of the
mixture of bentonite and sepiolite as a water based drilling fluid, J. Pet.
Sci. Eng., 76, 1–5, https://doi.org/10.1016/j.petrol.2010.11.021, 2011.
Ishikawa, M., Tanasupawat, S., Nakajima, K., Kanamori, H., Ishizaki, S.,
Kodama, K., Okamoto-Kainuma, A., Koizumi, Y., Yamamoto, Y., and Yamasato,
K.: Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and
alkaliphilic marine lactic acid bacteria isolated from marine organisms and
salted foods collected in Japan and Thailand, Int. J. Syst. Evol.
Microbiol., 59, 1215–1226, https://doi.org/10.1099/ijs.0.65602-0, 2009.
Islam, E., Paul, D., and Sar, P.: Microbial diversity in Uranium deposits
from Jaduguda and Bagjata Uranium mines, India as revealed by clone library
and denaturing gradient gel electrophoresis analyses, Geomicrobiol. J., 31,
862–874, https://doi.org/10.1080/01490451.2014.907375, 2014.
Kanso, S., Greene, A. C., and Patel, B. K.: Bacillus subterraneus sp. nov., an iron-and
manganese-reducing bacterium from a deep subsurface Australian thermal
aquifer, Int. J. Syst. Evol. Microbiol., 52, 869–874,
https://doi.org/10.1099/00207713-52-3-869, 2002.
Kieft, T. L.: Sampling the deep sub-surface using drilling and coring
techniques, in: Handbook of Hydrocarbon and Lipid Microbiology, edited by:
Timmis, K. N., Springer, Berlin, Heidelberg, 3427–3441,
https://doi.org/10.1007/978-3-540-77587-4_267, 2010.
Kieft, T. L.: Microbiology of the Deep Continental Biosphere, in: Their
World: A Diversity of Microbial Environments, edited by: Hurst, C.,
Springer, Cham, 225–249, https://doi.org/10.1007/978-3-319-28071-4, 2016.
Kieft, T. L., Phelps, T. J., and Fredrickson, J. K.: Drilling, coring, and
sampling subsurface environments, in: Manual of Environmental Microbiology,
3rd edition, edited by: Hurst, C. J., ASM Press, Washington, D.C., USA, 799–817, https://doi.org/10.1128/9781555815882.ch66, 2007.
Kjeldsen, K. U., Loy, A., Jakobsen, T. F., Thomsen, T. R., Wagner, M., and
Ingvorsen, K.: Diversity of sulfate-reducing bacteria from an extreme
hypersaline sediment, Great Salt Lake (Utah), FEMS Microbiol. Ecol.,
60, 287–298, https://doi.org/10.1111/j.1574-6941.2007.00288.x, 2007.
Klouche, N., Fardeau, M. L., Lascourreges, J. F., Cayol, J. L., Hacene, H.,
Thomas, P., and Magot, M.: Geosporobacter subterraneus gen. nov., sp. nov., a
spore-forming bacterium isolated from a deep subsurface aquifer, Int. J.
Syst. Evol. Microbiol., 57, 1757–1761, https://doi.org/10.1099/ijs.0.64642-0, 2007.
Kumar, P. A., Srinivas, T. N. R., Madhu, S., Sravan, R., Singh, S., Naqvi,
S. W. A., Mayilraj, S., and Shivaji, S.: Cecembia lonarensis gen. nov., sp.
nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae, isolated from a
haloalkaline lake and emended descriptions of the genera Indibacter, Nitritalea and
Belliella, Int. J. Syst. Evol. Microbiol., 62, 2252–2258, https://doi.org/10.1099/ijs.0.038604-0, 2012.
Kumar, S., Stecher, G., and Tamura, K.: MEGA7: molecular evolutionary
genetics analysis version 7.0 for bigger datasets, Mol. Biol Evol., 33,
1870–1874, https://doi.org/10.1093/molbev/msw054, 2016.
Labonté, J. M., Lever, M. A., Edwards, K. J., and Orcutt, B. N.: Influence
of igneous basement on deep sediment microbial diversity on the eastern Juan
de Fuca ridge flank, Front.
Microbiol., 8, 1434, https://doi.org/10.3389/fmicb.2017.01434, 2017.
Lakhal, R., Pradel, N., Postec, A., Ollivier, B., Cayol, J. L., Godfroy, A.,
Fardeau, M. L., and Galés, G.: Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine
bacterium isolated from deep-sea sediments, Int. J. Syst. Evol.
Microbiol., 65, 3097–3102, https://doi.org/10.1099/ijsem.0.000386, 2015.
Leandro, T., Rodriguez, N., Rojas, P., Sanz, J. L., da Costa, M. S., and
Amils, R.: Study of methanogenic enrichment cultures of rock cores from the
deep subsurface of the Iberian Pyritic Belt, Heliyon, 4, e00605,
https://doi.org/10.1016/j.heliyon.2018.e00605, 2018.
Leblanc, V., Hellal, J., Fardeau, M.L., Khelaifia, S., Sergeant, C.,
Garrido, F., Ollivier, B., and Joulian, C.: Microbial and Geochemical
Investigation down to 2000 m Deep Triassic Rock (Meuse/Haute Marne,
France), Geosciences, 9, 3, https://doi.org/10.3390/geosciences9010003, 2019.
Leboulanger, C., Agogué, H., Bernard, C., Bouvy, M., Carré, C.,
Cellamare, M., Duval, C., Fouilland, E., Got, P., Intertaglia, L., and
Lavergne, C.: Microbial diversity and cyanobacterial production in Dziani
Dzaha crater lake, a unique tropical thalassohaline environment, PloS
One, 12, e0168879, https://doi.org/10.1371/journal.pone.0168879, 2017.
Lee, S. J., Lee, Y. J., Ryu, N., Park, S., Jeong, H., Lee, S. J., Kim, B. C.,
Lee, D. W., and Lee, H. S.: Draft genome sequence of the thermophilic
bacterium Anoxybacillus kamchatkensis G10, J. Bacteriol., 194, 6684–6685,
https://doi.org/10.1128/JB.01877-12, 2012.
Lin, S. Y., Hameed, A., Wen, C. Z., Hsu, Y. H., Liu, Y. C., Lai, W. A., and Young,
C. C.: Hydrogenophaga aquatica sp. nov., isolated from a hot spring, Int. J. Syst. Evol.
Microbiol., 67, 3716–3721, https://doi.org/10.1099/ijsem.0.002146,
2017.
Liu, S. V., Zhou, J., Zhang, C., Cole, D. R., Gajdarziska-Josifovska, M., and Phelps, T. J.: Thermophilic Fe (III)-reducing bacteria from the deep subsurface: the evolutionary implications, Science, 277, 1106–1109, https://doi.org/10.1126/science.277.5329.1106, 1997.
Magnabosco, C., Lin, L. H., Dong, H., Bomberg, M., Ghiorse, W., Stan-Lotter,
H., Pedersen, K., Kieft, T. L., van Heerden, E., and Onstott, T. C.: The
biomass and biodiversity of the continental subsurface, Nat.
Geosci., 11, 707–717, 2018.
Masui, N., Morono, Y., and Inagaki, F.: Microbiological assessment of
circulation mud fluids during the first operation of riser drilling by the
deep-earth research vessel Chikyu, Geomicrobiol. J., 25, 274–282,
https://doi.org/10.1080/01490450802258154, 2008.
McMahon, S. and Parnell, J.: Weighing the deep continental biosphere, FEMS
Microbiol. Ecol., 87, 113–120, https://doi.org/10.1111/1574-6941.12196,
2014.
McMahon, S. and Parnell, J.: The deep history of Earth's biomass, J. Geol.
Soc., 175, 716–720, https://doi.org/10.1144/jgs2018-061, 2018.
Montmorillonite – Handbook of Mineralogy: Mineral data, available at: http://rruff.geo.arizona.edu/doclib/hom/montmorillonite.pdf, (last access: 28 January 2020)
2000.
Misra, S., Roy, S., Bartakke, V., Athavale, G., and Gupta, H.: Fissures and
fractures in the Koyna seismogenic zone, western India, J. Geol. Soc. India,
90, 131–137, https://doi.org/10.1007/s12594-017-0690-z, 2017.
Miteva, V., Burlingame, C., Sowers, T., and Brenchley, J.: Comparative
evaluation of the indigenous microbial diversity vs. drilling fluid
contaminants in the NEEM Greenland ice core, FEMS Microbiol. Ecol., 89,
238–256, https://doi.org/10.1111/1574-6941.12286, 2014.
Moore, E. R., Tindall, B. J., Dos Santos, V. A. M., Pieper, D. H., Ramos, J. L.,
and Palleroni, N. J.: Nonmedical: pseudomonas, in: The prokaryotes,
Springer, New York, NY, USA, 646–703, https://doi.org/10.1007/0-387-30746-x_21, 2006.
Nyyssönen, M., Hultman, J., Ahonen, L., Kukkonen, I., Paulin, L., Laine,
P., Itävaara, M., and Auvinen, P.: Taxonomically and functionally
diverse microbial communities in deep crystalline rocks of the Fennoscandian
shield, ISME J., 8, 126–138, 2014.
Ogg, C. D. and Patel, B. K.: Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic
bacterium from the Great Artesian Basin of Australia aquifer, Int. J. Syst.
Evol. Microbiol., 59, 964–971, https://doi.org/10.1099/ijs.0.004218-0, 2009.
Ogg, C. D., Greene, A. C., and Patel, B. K.: Thermovenabulum gondwanense sp. nov., a thermophilic anaerobic
Fe (III)-reducing bacterium isolated from microbial mats thriving in a Great
Artesian Basin bore runoff channel, Int. J. Syst. Evol.
Microbiol., 60, 1079–1084, https://doi.org/10.1099/ijs.0.009886-0, 2010.
Onstott, T. C., Phelps, T. J., Colwell, F. S., Ringelberg, D., White, D. C., and
Boone, D. R.: Observations pertaining to the origin and ecology of
microorganisms recovered from the deep subsurface of Taylorsville Bain,
Virginia, Geomicrobiol. J., 15, 353–385,
https://doi.org/10.1080/01490459809378088, 1998.
Palleroni, N. J.: Introduction to the Family Pseudomonadaceae, in: The
Prokaryotes, edited by: Starr, M. P., Stolp, H., Trüper, H. G., Balows, A., and
Schlegel, H. G., Springer, Berlin, Heidelberg,
https://doi.org/10.1007/978-3-662-13187-9_59, 1981.
Pedersen, K., Hallbeck, L., Arlinger, J., Erlandson, A. C., and Jahromi, N.:
Investigation of the potential for microbial contamination of deep granitic
aquifers during drilling using 16S rRNA gene sequencing and culturing
methods, J. Microbiol. Meth., 30, 179–192,
https://doi.org/10.1016/S0167-7012(97)00066-3, 1997.
Pielou, E. C.: Species-diversity and pattern-diversity in the study of
ecological succession, J. Theor. Biol., 10, 370–383,
https://doi.org/10.1016/0022-5193(66)90133-0, 1966.
Pinnaka, A. K. and Tanuku, N. R. S.: The Family Cyclobacteriaceae, in: The Prokaryotes, edited by: Rosenberg, E., DeLong, E. F.,
Lory, S., Stackebrandt, E., and Thompson, F., Springer,
Berlin, Heidelberg, https://doi.org/10.1007/978-3-642-38954-2_139, 2014.
Postgate, J. R.: Versatile medium for the enumeration of sulfate-reducing
bacteria, Appl. Environ. Microbiol., 11, 265–267, 1963.
Puente-Sánchez, F., Moreno-Paz, M., Rivas, L.A., Cruz-Gil, P.,
García-Villadangos, M., Gómez, M.J., Postigo, M., Garrido, P.,
González-Toril, E., Briones, C., and Fernández-Remolar, D.: Deep
subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt
revealed through geochemistry and molecular biomarkers, Geobiology, 12,
34–47, https://doi.org/10.1111/gbi.12065, 2014.
Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M.,
García-Villadangos, M., Moreno-Paz, M., Blanco, Y., Rodríguez, N.,
Bird, L., Lincoln, S. A., Tornos, F., and Prieto-Ballesteros, O.: Viable
cyanobacteria in the deep continental subsurface, Pr. Natl. Acad.
Sci. USA, 115, 10702–10707, https://doi.org/10.1073/pnas.1808176115, 2018.
Pujalte, M. J., Lucena, T., Ruvira, M. A., Arahal, D. R., and Macián, M. C.: The
Family Rhodobacteraceae, in: The Prokaryotes, edited by: Rosenberg, E., DeLong, E. F., Lory, S.,
Stackebrandt, E., and Thompson, F., Springer, Berlin, Heidelberg, https://doi.org/10.1007/978-3-642-30197-1_377, 2014.
Purkamo, L., Bomberg, M., Nyyssönen, M., Ahonen, L., Kukkonen, I., and
Itävaara, M.: Response of deep subsurface microbial community to
different carbon sources and electron acceptors during ∼2 months
incubation in microcosms, Front. Microbiol., 8, 232,
https://doi.org/10.3389/fmicb.2017.00232, 2017.
Purkamo, L., Kietäväinen, R., Miettinen, H., Sohlberg, E., Kukkonen,
I., Itävaara, M., and Bomberg, M.: Diversity and functionality of
archaeal, bacterial and fungal communities in deep Archaean bedrock
groundwater, FEMS Microbiol. Ecol., 94, 8, https://doi.org/10.1093/femsec/fiy116, 2018.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
Peplies, J., and Glöckner, F. O.: The SILVA ribosomal RNA gene database
project: improved data processing and web-based tools, Nucleic Acids Res., 41,
D590–D596, https://doi.org/10.1093/nar/gks1219, 2012.
Rabia, H. (Ed.): Oil Well Drilling Engineering: Principles and Practice, Graham & Trotman. Inc., London, UK, 1985.
Rainey, F. and Oren, A. (Eds.): Taxonomy of prokaryotes, Academic Press, London, UK, 2011.
Rempfert, K. R., Miller, H. M., Bompard, N., Nothaft, D., Matter, J. M.,
Kelemen, P., Fierer, N., and Templeton, A. S.: Geological and geochemical
controls on subsurface microbial life in the Samail Ophiolite, Oman, Front.
Microbiol., 8, 56,
https://doi.org/10.3389/fmicb.2017.00056, 2017.
Reyes, C., Schneider, D., Thürmer, A., Kulkarni, A., Lipka, M.,
Sztejrenszus, S. Y., Böttcher, M. E., Daniel, R., and Friedrich, M. W.:
Potentially active iron, sulfur, and sulfate reducing bacteria in Skagerrak
and Bothnian Bay sediments, Geomicrobiol. J., 34, 840–850,
https://doi.org/10.1080/01490451.2017.1281360, 2017.
Roh, Y., Liu, S. V., Li, G., Huang, H., Phelps, T. J., and Zhou, J.: Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado, Appl. Environ. Microbiol., 68, 6013–6020, https://doi.org/10.1128/AEM.68.12.6013-6020.2002, 2002.
Roy, S. and Rao, R. U. M.: Geothermal investigations in the 1993 Latur
earthquake area, Deccan volcanic province, India, Tectonophysics, 306,
237–252, https://doi.org/10.1016/S0040-1951(99)00051-7, 1999.
Roy, S. and Rao, R. U. M.: Heat flow in the Indian shield, J. Geophys. Res.-Sol. Ea., 105, 25587–25604, https://doi.org/10.1029/2000JB900257, 2000.
Russell, J. A., León-Zayas, R., Wrighton, K., and Biddle, J. F.: Deep
subsurface life from North Pond: enrichment, isolation, characterization and
genomes of heterotrophic bacteria, Front. Microbiol., 7, 678, https://doi.org/10.3389/fmicb.2016.00678, 2016.
Sahl, J. W., Schmidt, R., Swanner, E. D., Mandernack, K. W., Templeton, A. S.,
Kieft, T. L., Smith, R. L., Sanford, W. E., Callaghan, R. L., Mitton, J. B., and
Spear, J. R.: Subsurface microbial diversity in deep-granitic-fracture water
in Colorado, Appl. Environ. Microbiol., 74,
143–152, https://doi.org/10.1128/AEM.01133-07, 2008.
Sakamoto, M.: The Family Porphyromonadaceae, in: The Prokaryotes, Springer, Berlin, Heidelberg,
811–824, https://doi.org/10.1007/978-3-642-38954-2_132, 2014.
Salah, Z. B., Rout, S. P., and Humphreys, P. N.: Draft whole-genome sequence of
the alkaliphilic Alishewanella aestuarii strain HH-ZS, isolated from historical lime kiln
waste-contaminated soil, Genome Announce., 4, e01447-16,
https://doi.org/10.1128/genomeA.01447-16, 2016.
Sar, P.: Terrestrial deep subsurface Raw sequence reads, available at: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA482760/ (last access: 10 February 2020), 2018.
Schlumberger Oilfield Glossary: Terms: Electrical Stability Test, Electrical Resitivity, Invert Emulsion, available at: http://glossary.connect.slb.com (last access: 28 January 2020), 2010.
Simpson, E. H.: Measurement of species diversity, Nature, 163, 688, https://doi.org/10.1038/163688a0, 1949.
Slobodkin, A.: The Family Peptostreptococcaceae, in: The Prokaryotes, Springer, Berlin,
Heidelberg, 291–302,
https://doi.org/10.1007/978-3-642-30120-9_217, 2014.
Slobodkina, G. B., Kolganova, T. V., Kostrikina, N. A., Bonch-Osmolovskaya,
E. A., and Slobodkin, A. I.: Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic
bacterium from an underground gas storage reservoir, Int. J. Syst. Evol.
Microbiol., 62, 1543–1547, https://doi.org/10.1099/ijs.0.033076-0, 2012.
Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A., and Staudigel, H.:
Tracer-based estimates of drilling-induced microbial contamination of deep
sea crust, Geomicrobiol. J., 17, 207–219,
https://doi.org/10.1080/01490450050121170, 2000.
Soares, A., Edwards, A., An, D., Bagnoud, A., Bomberg, M., Budwill, K.,
Caffrey, S., Fields, M., Toner, B., Gralnick, J., and Kadnikov, V.: A global
perspective on microbial diversity in the terrestrial deep
subsurface, bioRxiv, p602672, https://doi.org/10.1101/602672, in review, 2019.
Sokolova, T., González Grau, J. M., Kostrikina, N. A., Chernyh, N. A., Kochetkova, T. V., Bonch-Osmolovskaya, E. A., and Robb, F.: Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park, Int. J. Syst. Evol. Microbiol., 54, 2353–2359, https://doi.org/10.1099/ijs.0.63186-0, 2004.
Song, L. and Dong, X.: Hydrogenoanaerobacterium saccharovorans gen. nov., sp. nov., isolated from
H2-producing UASB granules, Int. J. Syst. Evol. Microbiol., 59,
295–299, https://doi.org/10.1099/ijs.0.000349-0, 2009.
Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., and Schmidt, T.
M.: rrn DB: Improved tools for interpreting rRNA gene abundance in bacteria
and archaea and a newfoundation for future development, Nucleic Acids Res., 43,
D593–D598, https://doi.org/10.1093/nar/gku1201, 2015.
Struchtemeyer, C. G., Davis, J. P., and Elshahed, M. S.: Influence of the
drilling mud formulation process on the bacterial communities in thermogenic
natural gas wells from the Barnett Shale, Appl. Environ. Microbiol, 7,
AEM-00233, https://doi.org/10.1128/AEM.00233-11, 2011.
Sylvan, J. B., Hoffman, C. L., Momper, L. M., Toner, B. M., Amend, J. P., and
Edwards, K. J.: Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately
halophilic bacterium isolated from deep subseafloor basaltic crust, Int. J.
Syst. Evol. Microbiol., 65, 1992–1998, https://doi.org/10.1099/ijs.0.000211, 2015.
Toffin, L., Zink, K., Kato, C., Pignet, P., Bidault, A., Bienvenu, N.,
Birrien, J. L., and Prieur, D.: Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid
bacterium isolated from deep sub-seafloor sediment of the Nankai
Trough, Int. J. Syst. Evol. Microbiol., 55, 345–351,
https://doi.org/10.1099/ijs.0.63236-0, 2005.
Tomás, A. F., Karakashev, D., and Angelidaki, I.:
Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extremely thermophilic, high ethanol-yielding
bacterium isolated from household waste, Int. J. Syst. Evol. Microbiol., 63,
2396–2404, https://doi.org/10.1099/ijs.0.045211-0, 2013.
Ueda, K., Yamashita, A., Ishikawa, J., Shimada, M., Watsuji, T. O., Morimura,
K., Ikeda, H., Hattori, M., and Beppu, T.: Genome sequence of
Symbiobacterium thermophilum, an uncultivable bacterium that depends on
microbial commensalism, Nucleic. Acids. Res., 32, 4937–4944,
https://doi.org/10.1093/nar/gkh830, 2004.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J.: Prokaryotes: the unseen
majority, P. Natl. Acad. Sci. USA, 95, 6578–6583,
https://doi.org/10.1073/pnas.95.12.6578, 1998.
Willems, A.: The Family Comamonadaceae, in: The Prokaryotes, edited by: Rosenberg, E., DeLong,
E. F., Lory, S., Stackebrandt, E., and Thompson, F., Springer, Berlin, Heidelberg, Germany,
2014.
Willems, A., Busse, J., Goor, M., Pot, B., Falsen, E., Jantzen, E., Hoste,
B., Gillis, M., Kersters, K., Auling, G., and De Ley, J.: Hydrogenophaga, a new genus of
hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava),
Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and “Pseudomonas carboxydoflava”), and
Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis), Int. J. Syst. Evol. Microbiol., 39, 319–333,
https://doi.org/10.1099/00207713-39-3-319, 1989.
Wu, X. Y., Zheng, G., Zhang, W. W., Xu, X. W., Wu, M., and Zhu, X. F.:
Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda
lake, Int. J. Syst. Evol. Microbiol., 60, 2540–2543,
https://doi.org/10.1099/ijs.0.018259-0, 2010.
Yanagawa, K., Nunoura, T., McAllister, S., Hirai, M., Breuker, A., Brandt,
L., House, C., Moyer, C. L., Birrien, J. L., Aoike, K., and Sunamura, M.: The
first microbiological contamination assessment by deep-sea drilling and
coring by the D/V Chikyu at the Iheya North hydrothermal field in the
Mid-Okinawa Trough (IODP Expedition 331), Front. Microbiol., 4, 327, https://doi.org/10.3389/fmicb.2013.00327, 2013.
Yang, C. X., Liu, Y. P., Bao, Q. H., Feng, F. Y., Liu, H. R., Zhang, X. J., and
Zhao, Y. L.: Mongoliitalea lutea gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium
isolated from a haloalkaline lake, Int. J. Syst. Evol.
Microbiol., 62, 647–653, https://doi.org/10.1099/ijs.0.031286-0, 2012.
Zavarzina, D. G., Sokolova, T. G., Tourova, T. P., Chernyh, N. A., Kostrikina,
N. A., and Bonch-Osmolovskaya, E. A.: Thermincola ferriacetica sp. nov., a new anaerobic, thermophilic,
facultatively chemolithoautotrophic bacterium capable of dissimilatory Fe
(III) reduction. Extremophiles, 11, 1–7, https://doi.org/10.1007/s00792-006-0004-7, 2007.
Zhang, G., Dong, H., Xu, Z., Zhao, D., and Zhang, C.: Microbial diversity in ultra-high-pressure rocks and fluids from the Chinese Continental Scientific Drilling Project in China, Appl. Environ. Microbiol., 71, 3213–3227, https://doi.org/10.1128/AEM.71.6.3213-3227.2005, 2005.
Zhang, G., Dong, H., Jiang, H., Xu, Z., and Eberl, D. D.: Unique microbial
community in drilling fluids from Chinese continental scientific
drilling, Geomicrobiol. J., 23, 499–514,
https://doi.org/10.1080/01490450600875860, 2006.
Short summary
Drilling fluid (DF) used in the drilling of crystalline continental crust is considered a potent contaminant for subsurface rock samples, though it could provide a glimpse into the nature of deep subsurface life. Microbial communities of DF retrieved from Koyna pilot borehole (3000 m) in the Deccan Traps was explored through 16S rRNA and other diagnostic marker genes. Detection of extremophilic and other deep biosphere relevant microorganisms in DF redefined the role of DF in deep life research.
Drilling fluid (DF) used in the drilling of crystalline continental crust is considered a potent...