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Clay minerals interaction with microorganisms: a review

Published online by Cambridge University Press:  02 January 2018

Javier Cuadros
Javier Cuadros*
Affiliation:
Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
*
*E-mail: [email protected]
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Abstract

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Interest in mineral–microbe interaction has grown enormously over recent decades, providing information in a puzzle-like manner which points towards an ever increasingly intimate relationship between the two; a relationship that can be truly termed co-evolution. Clay minerals play a very central role in this co-evolving system. Some 20 years ago, clay scientists looked at clay mineral–microbe studies as a peripheral interest only. Now, can clay scientists think that they understand the formation of clay minerals throughout geological history if they do not include life in their models? The answer is probably no, but we do not yet know the relative weight of biological and inorganic factors involved in driving clay-mineral formation and transformation. Similarly, microbiologists are missing out important information if they do not investigate the influence and modifications that minerals, particularly clay minerals, have on microbial activity and evolution. This review attempts to describe the several points relating clay minerals and microorganisms that have been discovered so far. The information obtained is still very incomplete and many opportunities exist for clay scientists to help to write the real history of the biosphere.

Keywords

biogeochemistrybio-reduction and oxidationbioweatheringclay biomineralizationCritical Zonemineral-life co-evolution
Type
Research Article
Information
Clay Minerals , Volume 52 , Issue 2 , June 2017 , pp. 235 - 261
Creative Commons
Creative Common License - CCCreative Common License - BY
Copyright © The Mineralogical Society of Great Britain and Ireland 2017 This is an Open Access article, distributed under the terms of the Creative Commons Attribution license. (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © The Mineralogical Society of Great Britain and Ireland 2017

References

Adamo, P. & Violante, P. (2000) Weathering of rocks and neogenesis of minerals associated with lichen activity. Applied Clay Science, 16, 229–256.CrossRefGoogle Scholar
Adeyemi, A.O. & Gadd, G.M. (2005) Fungal degradation of calcium-, lead- and silicon-bearing minerals. BioMetals, 18, 269–281.CrossRefGoogle ScholarPubMed
Alimova, A., Katz, A., Steiner, N., Rudolph, E., Wei, H., Steiner, J.C. & Gottlieb, P. (2009) Bacteria-clay interaction: Structural changes in smectite induced during biofilm formation. Clays and Clay Minerals, 57, 205–212.Google Scholar
Alt, J.C. & Mata, P. (2000) On the role of microbes in the alteration of submarine basaltic glass: a TEM study. Earth and Planetary Science Letters, 181, 301–313.CrossRefGoogle Scholar
Amundson, R., Richter, D.D., Humphreys, G.S., Jobbágy, E. & Gaillardet, J. (2007) Coupling between biota and the Earth materials in the Critical Zone. Elements, 3, 327–332.Google Scholar
Andrade, G., de Azevedo, A., Cuadros, J., Souza Jr, V., Furquim, S., Kiyohara, P. & Vidal-Torrado, P. (2014) Transformation of kaolinite into smectite and ironillite in Brazilian mangrove soils. Soil Science Society of America Journal, 78, 655–672.Google Scholar
Arocena, J.M., Velde, B. & Robertson, S.J. (2012) Weathering of biotite in the presence of arbuscular mycorrhizae in selected agricultural crops. Applied Clay Science, 64, 12–17.CrossRefGoogle Scholar
Ascaso, C. & Galvan, J. (1976) Studies on the pedogenetic action of lichen acids. Pedobiologia, 16, 321–331.Google Scholar
Baldermann, A., Warr, L., Grathoff, G. & Dietzel, M. (2013) The rate and mechanism of deep-sea glauconite formation at the Ivory Coast-Ghana marginal ridge. Clays and Clay Minerals, 61, 258–276.CrossRefGoogle Scholar
Baldermann, A., Warr, L., Letofsky-Papst, I. & Mavromatis, V. (2015) Substantial iron sequestration during greenclay authigenesis in modern deep-sea sediments. Nature Geoscience, 8, 885–890.Google Scholar
Balland, C., Poszwa, A., Leyval, C. & Mustin, C. (2010) Dissolution rates of phyllosilicates as a function of bacterial metabolic diversity. Geochimica et Cosmochimica Acta, 74, 5478–5493.CrossRefGoogle Scholar
Balogh-BrunstadZ., Keller, C.K., Dickinson, J.T., Stevens, F., Li, C.Y. & Bormann, B.T. (2008) Biotite weathering and nutrient uptake by ectomycorrhizal fungus, Suillus tomentosus, in liquid-culture experiments. Geochimica et Cosmochimica Acta, 72, 2601–2618.Google Scholar
Banfield, J.F., Barker, W.W., Welch, S.A. & Taunton, A. (1999) Biological impact on mineral dissolution: Application of the lichen model to understanding mineral weathering in the rhizosphere. Proccedings of the National Academy of Sciences, 96, 3404–3411.Google Scholar
Barker, W.W. & Banfield, J.F. (1996) Biologically versus inorganically mediated weathering reactions: relationships between minerals and extracellular microbial polymers in lithobiontic communities. Chemical Geology, 132, 55–69.Google Scholar
Barker, W.W., Welch, S.A. & Banfield, J.F. (1997) Biogeochemical weathering of silicate minerals. Pp. 392–428 in: Geomicrobiology: Interactions between Microbes and Minerals (Banfield, J.F. and Nealson, K.H., editors). Reviews in Mineralogy and Geochemistry, 35. Mineralogical Society of America, Chantilly, Virginia, USA.Google Scholar
Barker, W.W., Welch, S.A., Chu, S. & Banfield, J.F. (1998) Experimental observations of the effects of bacteria on aluminosilicate weathering. American Mineralogist, 83, 1551–1563.Google Scholar
Battistuzzi, F.U., Feijao, A. & Hedges, S.B. (2004) A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary Biology, 4, 44. DOI: 10.1186/1471-2148-4-44.CrossRefGoogle ScholarPubMed
Belnap, J. (2003) The world at your feet: desert biological soil crusts. Frontiers in Ecology and the Environment, 1, 181–189.Google Scholar
Belnap, J., Büdel, B. & Lange, O.L. (2001) Biological soil crusts: characteristics and distribution. Pp. 3–30 in: Biological Soil Crusts: Structure, Function, and Management (J. Benlap & Lange, O.L., editors). Ecological Studies series vol. 150, Springer, Berlin.Google Scholar
Benzerara, K., Menguy, N., Guyot, F., Vanni, C. & Gillet, P. (2005) TEM study of a silicate–carbonate–microbe interface prepared by focused ion beam milling. Geochimica et Cosmochimica Acta, 69, 1413–1422.Google Scholar
Berger, G., Lacharpagne, J-C., Velde, B., Beaufort, D. & Lanson, B. (1997) Kinetic constraints on illitization reactions and the effects of organic diagenesis in sandstone/shale sequences. Applied Geochemistry, 12, 23–35.Google Scholar
Berner, E. & Berner, R. (2012) Global Environment:Water, Air, and Geochemical Cycles. Princeton University Press, Princeton, New Jersey, USA.Google Scholar
Bigham, J.M., Bhatti, T.M., Vuorinen, A. & Tuovinen, O.H. (2001) Dissolution and structural alteration of phlogopite mediated by proton attack and bacterial oxidation of ferrous iron. Hydrometallurgy, 59, 301–309.CrossRefGoogle Scholar
Boneville, S., Morgan, D.J., Schmalenberger, A., Bray, A., Brown, A., Banwart, S.A. & Benning, L.G. (2011) Treemycorrhiza symbiosis accelerate mineral weathering: Evidence from nanometer-scale elemental fluxes at the hypha-mineral interface. Geochimica et Cosmochimica Acta, 75, 6988–7005.CrossRefGoogle Scholar
Brehm, U., Gorbushina, A. & Mottershead, D. (2005) The role of microorganisms and biofilms in the breakdown and dissolution of quartz and glass. Palaeogeography, Palaeoclimatology, Palaeoecology, 219, 117–129.Google Scholar
Butterfield, N.J. (2000) Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology, 26, 386–404.2.0.CO;2>CrossRefGoogle Scholar
Carson, J.K., Rooney, D., Gleeson, D.B. & Clipson, N. (2007) Altering the mineral composition of soil causes a shift in microbial community structure. FEMS Microbiology Ecology, 61, 414–423. Chamley, H. (1989) Clay Sedimentology. Springer-Verlag, Berlin.Google Scholar
Chen, J., Blume, H.P. & Beyer, L. (2000) Weathering of rocks induced by lichen colonization – a review. Catena, 39, 121–146.Google Scholar
Chorover, J., Kretzschmar, R., Garcia-Pichel, F. & Sparks, D.L. (2007) Soil biogeochemical processes within the Critical Zone. Elements, 3, 321–326.CrossRefGoogle Scholar
Courvoisier, E. & Dukan, S. (2009) Improvement of Escherichia coli growth by kaolinite. Applied Clay Science, 44. 67–70.Google Scholar
Cuadros, J., Afsin, B., Michalski, J.R. & Ardakani, M. (2012) Fast, microscale-controlled weathering of rhyolitic obsidian to quartz and alunite. Earth and Planetary Science Letters, 353–354, 156–162.CrossRefGoogle Scholar
Cuadros, J., Afsin, B., Jadubansa, P., Ardakani, M., Ascaso, C. & Wierzchos, J. (2013a) Microbial and inorganic control on the composition of clay from volcanic glass alteration experiments. American Mineralogist, 98, 319–334.Google Scholar
Cuadros, J., Afsin, B., Jadubansa, P., Ardakani, M., Ascaso, C. & Wierzchos, J. (2013b) Pathways of volcanic glass alteration in laboratory experiments through inorganic and microbially-mediated processes. Clay Minerals, 48, 423–445.Google Scholar
Cuadros, J., Andrade, G., Ferreira, T.O., Partiti, C.S.M., Cohen, R. & Vidal-Torrado, P. (2017) The mangrove reactor: fast clay transformation and potassium sink. Applied Clay Science, 140, 50–58.Google Scholar
Curry, K.J., Bennett, R.H., Mayer, L.M., Curry, A., Abril, M., Biesiot, P.M. & Hulbert, M.H. (2007) Direct visualization of clay microfabric signatures driving organic matter preservation in fine-grained sediment. Geochimica et Cosmochimica Acta, 71, 1709–1720.Google Scholar
de la Torre M.A. & Gomez-Alarcon, G. (1994) Manganese and iron oxidation by fungi isolated from building stone. Microbial Ecology, 27, 177–188.Google Scholar
de los Ríos, A., Wierzchos, J., Sancho, L.G. & Ascaso, C. (2003) Acid microenvironments in microbial biofilms of antarctic endolithic microecosystems. Environmental Microbiology, 5, 231–237.CrossRefGoogle ScholarPubMed
Dong, H. (2012) Clay-microbe interactions and implications for environmental mitigation. Elements, 8, 113–118.CrossRefGoogle Scholar
Dong, H., Jaisi, D., Kim, J. & Zhang, G. (2009) Microbe– clay mineral interactions. American Mineralogist, 94, 1505–1519.Google Scholar
Douglas, S. & Beveridge, T. (1998) Mineral formation by bacteria in natural microbial communities. FEMS Microbiology Ecology, 26, 79–88.CrossRefGoogle Scholar
Dröge, M., Pühler, A.W. & Selbitschka, W. (1999) Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies. Biology and Fertility of Soils, 29, 221–245.Google Scholar
Emerson, D., Fleming, E.J. & McBeth, J.M. (2010) Ironoxidizing bacteria: an environmental and genomic perspective. Annual Review of Microbiology, 64, 561–583.CrossRefGoogle ScholarPubMed
Ernstsen, V., Gates, W. & Stucki, J. (1998) Microbial reduction of structural iron in clays – a renewable source of reduction capacity. Journal of Environmental Quality, 27, 761–766.Google Scholar
Etienne, S. & Dupont, J. (2002) Fungal weathering of basaltic rocks in a cold oceanic environment (Iceland): comparison between experimental and field observations. Earth Surface Processes and Landforms, 27, 737–748.CrossRefGoogle Scholar
Fiore, S., Dumontet, S., Huertas, F.J. & Pasquale, V. (2011) Bacteria-induced crystallization of kaolinite. Applied Clay Science, 53, 566–571.Google Scholar
Frausto da Silva, J.J.R. & Williams, R.J.P. (2001) The Biological Chemistry of the Elements: The Inorganic Chemistry of Life, 2nd Edition. Oxford University Press, Oxford.CrossRefGoogle Scholar
Gazzè, S.A., Saccone, L., Ragnarsdottir, K.V., Smits, M.M., Duran, A.L., Leake, J.R., Banwart, S.A. & McMaster, T.J. (2012) Nanoscale channels on ectomycorrhizalcolonized chlorite: Evidence for plant-driven fungal dissolution. Journal of Geophysical Research, 117, G00N09.CrossRefGoogle Scholar
Gerbl, F.W., Weidler, G.W., Wanek, W., Erhardt, A. & Stan-Lotter, H. (2014) Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Frontiers in Microbiology, 5, Article 225. http://dx.doi.org/10.3389/fmicb.2014.00225 Google Scholar
Grote, E.E., Belnap, J., Housman, D.C. & Sparks, J.P. (2010) Carbon exchange in biological soil crust communities under differential temperatures and soil water contents: implications for global change. Global Change Biology, 16, 2763–2774.Google Scholar
Hama, K., Bateman, K., Coombs, P., Hards, V., Milodowski, A., West, J., Wetton, P., Yoshida, H. & Aoki, K. (2001) Influence of bacteria on rock-water interaction and clay mineral formation in subsurface granitic environments. Clay Minerals, 36, 599–613.Google Scholar
Hausrath, E., Neaman, A. & Brantley, S. (2009) Elemental release rates from dissolving basalt and granite with and without organic ligands. American Journal of Science, 309, 633–660.CrossRefGoogle Scholar
Heberling, C., Lowell, R.P., Liu, L. & Fisk, M.R. (2010) Extent of the microbial biosphere in the oceanic crust. Geochemistry, Geophysics, Geosystems, 11, Q08003.Google Scholar
Hedrich, S., Schlömann, M. & Johnson, D.B. (2011) The iron-oxidizing proteobacteria. Microbiology, 157, 1551–1564.Google Scholar
Hopf, J., Langerhorst, F., Pollok, K., Merten, D. & Kothe, E. (2009) Influence of microorganisms on biotite dissolution: An experimental approach. Chemie der Erde Geochemistry, 69(S2), 45–56.Google Scholar
Huggett, J. & Cuadros, J. (2005) Low-temperature illitization of smectite in the late Eocene and early Oligocene of the Isle ofWight (Hampshire basin), UK. American Mineralogist, 90, 1192–1202.CrossRefGoogle Scholar
Huggett, J. & Cuadros, J. (2010) Glauconite formation in lacustrine/palaeosol sediments, Isle of Wight (Hampshire basin), UK. Clay Minerals, 45, 35–49.CrossRefGoogle Scholar
Huggett, J., McCarty, D., Calvert, C., Gale, A. & Kirk, C. (2006) Serpentine-nontronite-vermiculite mixed-layer clay from the Weches Formation, Claiborne Group, Middle Eocene, Northeast Texas. Clays and Clay Minerals, 54, 101–115.CrossRefGoogle Scholar
Jaisi, D.P., Kukkadapu, R.K., Eberl, D.D. & Dong, H. (2005) Control of Fe(III) site occupancy on the rate and extent of microbial reduction of Fe(III) in nontronite. Geochimica et Cosmochimica Acta, 69, 5429–5440.Google Scholar
Kalinowski, B. & Schweda, P. (1996) Kinetics of muscovite, phlogopite, and biotite dissolution and alteration at pH 1-4, room temperature. Geochimica et Cosmochimica Acta, 60, 367–385.CrossRefGoogle Scholar
Kawano, M. & Tomita, K. (2001) Microbial biomineralization in weathered volcanic ash deposit and formation of biogenic minerals by experimental incubation. American Mineralogist, 86, 400–410.Google Scholar
Kennedy, M., Droser, M., Mayer, L.M., Pevear, D. & Mrofka, D. (2006) Late Precambrian oxygenation; inception of the clay mineral factory. Science, 311, 1446–1449.Google Scholar
Kieft, T.L. (2000) Size matters: Dwarf cells in soil and subsurface terrestrial environments. Pp. 19–46 in: Non-culturable Microorganisms in the Environment (Colwell, R.R. & Grimes, D.J., editors). ASM Press, Washington, D.C. Google Scholar
Konhauser, K. & Urrutia, M. (1999) Bacterial clay authigenesis: a common biogeochemical process. Chemical Geology, 161, 399–413.CrossRefGoogle Scholar
Konhauser, K.O., Fyfe, W.S., Ferris, F.G. & Beveridge, T.J. (1993) Metal sorption and mineral precipitation by bacteria in two Amazonian river systems: Rio Solimoes and Rio Negro, Brazil. Geology, 21, 1103–1106.Google Scholar
Konhauser, K., Schiffman, P. & Fisher, Q. (2002) Microbial mediation of authigenic clays during hydrothermal alteration of basaltic tephra, Kilauea volcano. Geochemistry Geophysics Geosystems, 3, 1075.CrossRefGoogle Scholar
Kuhn, K.M., DuBois, J.L. & Maurice, P.A. (2013) Strategies of aerobic microbial Fe acquisition from Fe-bearing montmorillonite clay. Geochimica et Cosmochimica Acta, 117, 191–202.Google Scholar
Landeweert, R., Hoffland, E., Finlay, R.D., Kuyper, T.W. & van Breemen N. (2001) Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. Trends in Ecology & Evolution, 16, 248–254.CrossRefGoogle ScholarPubMed
Lawrence, C., Harden, J. & Maher, K. (2014) Modeling the influence of organic acids on soil weathering. Geochimica et Cosmochimica Acta, 139, 487–507.Google Scholar
Lenton, T.M., Crouch, M., Johnson, M., Pires, N. & Dolan, L. (2012) First plants cooled the Ordovician. Nature Geoscience, 5, 86–89.Google Scholar
Li, Z., Liu, L., Chen, J. & Teng, H.H. (2016) Cellular dissolution at hypha- and spore-mineral interfaces revealing unrecognized mechanisms and scales of fungal weathering. Geology, G37561.1.Google Scholar
Lian, B., Wang, B., Pan, M., Liu, C. & Teng, H.H. (2008) Microbial release of potassium from Kbearing minerals by thermophilic fungus Aspergillus fumigatus. Geochimica et Cosmochimica Acta, 72, 87–98.Google Scholar
Lücking, R., Huhndorf, S., Pfister, D.H., Plata, E.R. & Lumbsch, H.T. (2009) Fungi evolved right on track. Mycologia, 101, 810–822.Google Scholar
Luef, B., Fakra, S.C., Csencsits, R., Wrighton, K.C., Williams, K.H., Wilkins, M.J., Downing, K.H., Long, P.E., Comolli, L.R. & Banfield, J.F. (2013) Ironreducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. The ISME Journal, 7, 338–350.Google Scholar
Lünsdorf, H., Erb, R.W., Abraham, W.R. & Timmis, K.N. (2000) “Clay Hutches”: a novel interaction between bacteria and clay minerals. Environmental Microbiology, 2, 161–168.CrossRefGoogle ScholarPubMed
McCollom, T.M. & Seewald, J.S. (2013) Serpentinites, hydrogen, and life. Elements, 9, 129–134.CrossRefGoogle Scholar
Ménez, B., Pasini, V. & Brunelli, D. (2012)Life in thehydrated suboceanic mantle. Nature Geoscience, 5, 133–137.Google Scholar
Miller, J.D. (1992) Fungi as contaminants in indoor air. Atmospheric Environment, 26, 2163–2172.Google Scholar
Monreal, C.M. & Kodama, H. (1997) Influence of aggregate architecture and minerals on living habitats and soil organic matter. Canadian Journal of Soil Science, 77, 367–377.Google Scholar
Moore, J., Lichtner, P., White, A. & Brantley, S. (2012) Using a reactive transport model to elucidate differences between laboratory and field dissolution rates in regolith. Geochimica et Cosmochimica Acta, 93, 235–261.CrossRefGoogle Scholar
Morrison, K., Bristow, T. & Kennedy, M. (2013) The reduction of structural iron in ferruginous smectite via the amino acid cysteine: Implications for an electron shuttling compound. Geochimica et Cosmochimica Acta, 104, 152–163.Google Scholar
Müller, B. (2009) Impact of the bacterium Pseudomonas fluorescens and its genetic derivatives on vermiculite: Effect on trace metals contents and clay mineralogical properties. Geoderma, 153, 94–103.Google Scholar
Nealson, K. & Popa, R. (2005) Introduction and overview: what do we know for sure. American Journal of Science, 305, 449–466.Google Scholar
Neumann, A., Petit, S. & Hofstetter, T. (2011) Evaluation of redox-active iron sites in smectites using middle and near infrared spectroscopy. Geochimica et Cosmochimica Acta, 75, 2336–2355.Google Scholar
Ottow, J.C.G. & Von Klopotek, A. (1969) Enzymatic reduction of iron oxide by fungi. Applied Microbiology, 18, 41–43.Google Scholar
Perdrial, J.N., Warr, L.N., Perdrial, N., Lett, M.-C. & Elsass, F. (2009) Interaction between smectite and bacteria: Implications for bentonite as backfill material in the disposal of nuclear waste. Chemical Geology, 264, 281–294.Google Scholar
Perez Rodriguez J.L., Carretero, M.I. & Maqueda, C. (1989) Behaviour of sepiolite, vermiculite and montmorillonite as supports in anaerobic digesters. Applied Clay Science, 4, 69–82.Google Scholar
Pinzari, F., Cuadros, J., Napoli, R., Canfora, L. & Baussà Bardají, D. (2016) Routes of phlogopite weathering by three fungal strains. Fungal Biology, 120, 1582–1599.Google Scholar
Prescott, L., Harley, J. & Klein, D. (1999) Microbiology, 4th edition. McGrawHill, New York. http://www.mhhe.com/biosci/cellmicro/prescott/index.mhtml. Google Scholar
Quirk, J., Leake, J.R., Banwart, S.A., Taylor, L.L. & Beerling, D.J. (2014) Weathering by tree-root-associating fungi diminishes under simulated Cenozoic atmospheric CO2 decline. Biogeosciences, 11, 321–331.Google Scholar
Ransom, B., Bennett, R.H., Baerwald, R., Hulbert, M.H. & Burkett, P.J. (1999) In situ conditions and interactions between microbes and minerals in fine-grained marine sediments: ATEM microfabric perspective. American Mineralogist, 84, 183–192.Google Scholar
Richardson, S.M. & McSween, H.Y. (1998) Geochemistry: Pathways and Processes. Prentice Hall, New Jersey, USA.Google Scholar
Robertson, K., Gauvin, R. & Finch, J. (2005) Application of charge contrast imaging in mineral characterization. Minerals Engineering, 18, 343–352.Google Scholar
Rothschild, L.J. & Mancinelli, R. (2001) Life in extreme environments. Nature, 409, 1092–1101.Google Scholar
Sanchez-Navas, A., Martin-Algarra, A. & Nieto, F. (1998) Bacterially-mediated authigenesis of clays in phosphate stromatolites. Sedimentology, 45, 519–533.Google Scholar
Schopf, J.W. (2006) The first billion years: When did life emerge. Elements, 2, 229–233.Google Scholar
Six, J., Conant, R.T., Paul, E.A. & Paustian, K. (2002) Stabilization mechanisms of soil organic matter: implications for C-saturation of soils. Plant and Soil, 241, 155–176.Google Scholar
Small, J. (1994) Fluid composition, mineralogy and morphological changes associated with the semctiteto- illite reaction: an experimental investigation of the effect of organic acid anions. Clay Minerals, 29, 539–554.Google Scholar
Song, W., Ogawa, N., Oguchi, C.T., Hatta, T. & Matsukura, Y. (2007) Effect of Bacillus subtilis on granite weathering: A laboratory experiment. Catena, 70, 275–281.CrossRefGoogle Scholar
Staudigel, H., Chastain, R.A., Yayanos, A. & Bourcier, W. (1995) Biologically mediated dissolution of glass. Chemical Geology, 126, 147–154.Google Scholar
Staudigel, H., Furnes, H., McLoughlin, N., Banerjee, N.R., Connell, L.B. & Templeton, A. (2008) 3.5 billion years of glass bioalteration: Volcanic rocks as a basis for microbial life. Earth Science Reviews, 89, 156–176.Google Scholar
Tazaki, K. (2005) Microbial formation of a halloysite-like mineral. Clays and Clay Minerals, 53, 224–233.Google Scholar
Thompson, I.A., Huber, D.M., Guest, C.A. & Schulze, D.G. (2005) Fungal manganese oxidation in a reduced soil. Environmental Microbiology, 7, 1480–1487.Google Scholar
Thorseth, I., Furnes, H. & Heldal, M. (1992) The importance of microbiological activity in the alteration of natural basaltic glass. Geochimica et Cosmochimica Acta, 56, 845–850.Google Scholar
Thorseth, I.H., Furnes, H. & Tumyr, O. (1995a) Textural and chemical effects of bacterial activity on basaltic glass: an experimental approach. Chemical Geology, 119, 139–160.Google Scholar
Thorseth, I.H., Torsvik, T., Furnes, H. & Muehlenbachs, K. (1995b)Microbes play an important role in the alteration of oceanic crust. Chemical Geology, 126, 137–146.Google Scholar
Thorseth, I.H., Pedersen, R.B. & Christie, D.M. (2003) Microbial alteration of 0–30-Ma seafloor and subseafloor basaltic glasses from the Australian Antarctic Discordance. Earth and Planetary Science Letters, 215, 237–247.Google Scholar
Todar, K. (2016) Online Textbook of Bacteriology. http://textbookofbacteriology.net/.Google Scholar
Ueshima, M. & Tazaki, K. (2001) Possible role of microbial polysaccharides in nontronite formation. Clays and Clay Minerals, 49, 292–299.Google Scholar
Ullman, W., Kirchman, D., Welch, S. & Vandevivere, P. (1996) Laboratory evidence for microbially mediated silicate mineral dissolution in nature. Chemical Geology, 132, 11–17.Google Scholar
Uroz, S., Calvaruso, C., Turpault, M.P., Sarniguet, A., De Boer, W., Leveau, J.H.J. & Frey-Klett, P. (2009) Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas. Soil Biology and Biochemistry, 41, 2178–2186.Google Scholar
Urrutia, M. & Beveridge, T. (1995) Formation of shortrange ordered aluminosilicates in the presence of a bacterial surface (Bacillus subtilis) and organic ligands. Geoderma, 65, 149–165.Google Scholar
Valsami-Jones, E. & McEldowney, S. (2000) Mineral dissolution by heterotrophic bacteria: principles and methodologies. Pp. 27–55 in: Environmental Mineralogy; Microbial Interactions, Anthropogenic Influences, Contaminated Land and Waste Management (Cotter-Howells, J.D., Campbell, L.S., Valsami-Jones, E. & M. Batchelder, editors). The Mineralogical Society Series, no. 9, Mineralogical Society, London.Google Scholar
Van Veen J.A. & Kuikman, P.J. (1990) Soil structural aspects of decomposition of organic matter by microorganisms. Biogeochemistry, 11, 213–233.Google Scholar
Vieira, M.J. & Melo, L.F. (1995) Effect of clay particles on the behaviour of biofilms formed by Pseudomonas fluorescens. Water Science & Technology, 32, 45–52.Google Scholar
Wei, Z., Kierans, M. & Gadd, G.M. (2012) A model sheet mineral system to study fungal bioweathering of mica. Geomicrobiology Journal, 29, 323–331.Google Scholar
Whitman, W.B., Coleman, D.C. & Wiebe, W.J. (1998) Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences of the USA, 95, 6578–6583.Google Scholar
Wierzchos, J. & Ascaso, C. (1996) Morphological and chemical features of bioweathered granitic biotite induced by lichen activity. Clays and Clay Minerals, 44, 653–657.Google Scholar
Wilson, M.J. & Jones, D. (1983) Lichen weathering of minerals: implications for pedogenesis. Pp. 5–12 in: Residual Deposits: Surface Related Weathering Processes and Materials (Wilson, R.C.L., editor). Geological Society Special Publication no. 11, Geological Society, London.Google Scholar
Xiao, B., Lian, B., Sun, L. & Shao, W. (2012) Gene transcription response to weathering of K-bearing minerals by Aspergillus fumigatus. Chemical Geology, 306–307, 1–9.Google Scholar
Zhang, G., Dong, H., Kim, J. & Eberl, D. (2007a) Microbial reduction of structural Fe3+ in nontronite by a thermophilic bacterium and its role in promoting the smectite to illite reaction. American Mineralogist, 92, 1411–1419.Google Scholar
Zhang, G., Kim, J., Dong, H. & Sommer, A. (2007b) Microbial effects in promoting the smectite to illite reaction: Role of organic matter intercalated in the interlayer. American Mineralogist, 92, 1401–1410.Google Scholar
Zierenberg, R., Adams, M. & Arp, A. (2000) Life in extreme environments: Hydrothermal vents. Proceedings of the National Academy of Sciences, 97, 12961–12962.Google Scholar
Zysset, M. & Schindler, P. (1996) The proton promoted dissolution kinetics of K-montmorillonite. Geochimica et Cosmochimica Acta, 60, 921–931.Google Scholar