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Role of Microorganisms in Soil Genesis and Functions

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Abstract

The soil is an eminent gift from nature encompassing numerous essential minerals and nutrients for maintaining the vivacity of living biota such as plants, animals, and microorganisms. Soil genesis or pedogenesis is an imperative phenomenon, where biological activities shown by microorganisms which open numerous ways for promoting the process of soil formation. Microorganisms including bacteria, fungi, cyanobacteria, and lichens are said to be well-known ‘soil engineers’ actively participate in pedogenesis through commencing the process of biological weathering of rocks, decomposition of organic matters and nutrient cycling. However, the study on soil microorganisms is an important aspect for depicting their role in soil genesis and it is also apparent to determine both culturable and unculturable diversity of soil inhabitant microbiota. In this view, the present manuscript is focused on depicting the role of microorganisms in soil formation and the mechanisms for weathering process employed by such micro-flora with highlighting the current and advanced molecular approaches for determining microbial diversity in soil.

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References

  • Acosta Martínez, V., Dowd, S., Sun, Y., & Allen, V. (2008). Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry, 40, 2762–2770.

    Article  CAS  Google Scholar 

  • Agrawal, P. K., Agrawal, S., & Shrivastava, R. (2015). Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem. 3 Biotech, 5, 853–866.

    Article  PubMed  PubMed Central  Google Scholar 

  • Amann, R., & Ludwig, W. (2000). Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiology Reviews, 24(5), 555–565.

    Article  CAS  PubMed  Google Scholar 

  • Andriuzzi, W. S., Ngo, P. T., Geisen, S., Keith, A. M., Dumack, K., & Bolger, T. (2016). Organic matter composition and the protist and nematode communities around anecic earthworm burrows. Biology and Fertility of Soils, 52, 91–100.

    Article  CAS  Google Scholar 

  • April, R., & Keller, D. (1990). Mineralogy of the rhizosphere in forest soils of the eastern United States. Biogeochemistry, 9, 1–18.

    Article  Google Scholar 

  • Arino, X., Gomez-Bolea, A., & Saiz-Jimenez, C. (1997). Lichens on ancient mortars. International Biodeterioration & Biodegradation, 40, 217–224.

    Article  Google Scholar 

  • Bae, K. S., & Barton, L. L. (1989). Alkaline phosphates and other hydrolyases produced by Cenococcum graniforme, an ectomycorrhizal fungus. Applied and Environmental Microbiology, 55, 2511–2516.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Balesdent, J., Chenu, C., & Balabane, M. (2000). Relationship of soil organic matter dynamics to physical protection and tillage. Soil and Tillage Research, 53, 215–230.

    Article  Google Scholar 

  • Balogh-Brunstad, Z., Keller, C. K., Bormann, B. T., O’Brien, R., Wang, D., & Hawley, G. (2008). Chemical weathering and chemical denudation dynamics through ecosystem development and disturbance. Global Biogeochemical Cycles, 22, 1007.

    Article  CAS  Google Scholar 

  • Barber, D. A., & Lynch, J. M. (1977). Microbial growth in the rhizosphere. Soil Biology and Biochemistry, 9, 305–308.

    Article  CAS  Google Scholar 

  • Barker, W. W., Welch, S. A., & Banfield, J. F. (1997). Biogeochemical weathering of silicate minerals. In J. F. Banfield & K. H. Nealson (Eds.), Geomicrobiology: Interactions between microbes and minerals (Reviews in mineralogy) (Vol. 35, pp. 391–428). Chelsea: Mineralogical Society of America.

    Chapter  Google Scholar 

  • Baudoin, E., Benizri, E., & Guckert, A. (2002). Impact of growth stages on bacterial community structure along maize roots by metabolic and genetic fingerprinting. Applied Soil Ecology, 19, 135–145.

    Article  Google Scholar 

  • Benizri, E., Baudoin, E., & Guckert, A. (2001). Root colonization by inoculated plant growth promoting rhizobacteria. Biocontrol Science and Technology, 11(5), 557–574.

    Article  Google Scholar 

  • Benizri, E., Dedourge, O., Di Battista-Leboeuf, C., Nguyen, C. S., & Piutti, G. A. (2002). Effect of maize rhizodeposits on soil microbial community structure. Applied Soil Ecology, 21, 261–265.

    Article  Google Scholar 

  • Benson, D. R. (1988). The genus Frankia: Actinomycetes symbionts of plants. Microbiological Sciences, 5, 9–12.

    CAS  PubMed  Google Scholar 

  • Berthelin, J. (1983). Microbial weathering processes. Microbial geochemistry (pp. 223–262). London: Blackwell.

    Google Scholar 

  • Buckley, D. H., & Schmidt, T. M. (2001). The structure of microbial communities in soil and the lasting impact of cultivation. Microbial Ecology, 42, 11–21.

    CAS  PubMed  Google Scholar 

  • Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R. H., Uroz, S., & Martin, F. (2009). 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184(2), 449–456.

    Article  CAS  Google Scholar 

  • Burgess, K. S., Fazekas, A. J., Kesanakurti, P. R., Graham, S. W., Husband, B. C., Newmaster, S. G., Percy, D. M., Hajibabaei, M., & Barrett, S. C. H. (2011). Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods in Ecology and Evolution, 2, 333–340.

    Article  Google Scholar 

  • Buscot, F., & Varma, A. (2005). Microorganisms in soils: Roles in genesis and functions (pp. 159–171). New York: Berlin Heidelberg/Springer.

    Google Scholar 

  • Calvaruso, C., Turpault, M. P., & Frey-Klett, P. (2006). Root-associated bacteria contribute to mineral weathering and to mineral nutrition in trees: A budgeting analysis. Applied Environmental Microbiology, 72, 1258–1266.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chalot, M., Javelle, A., Blaudez, D., Lambilliote, R., Cooke, R., Sentenac, H., Wip, F. D., & Botton, B. (2002). An uptake on nutrient transport processes in ectomycorrhizas. Plant and Soil, 244, 165–175.

    Article  CAS  Google Scholar 

  • Chang, T. T., & Li, C. Y. (1998). Weathering of limestone, marble, and calcium phosphate by ectomycorrhizal fungi and associated microorganisms. Taiwan Journal of Forest Science, 13, 85–90.

    Google Scholar 

  • Chen, J., Blume, H. P., & Beyer, L. (2000). Weathering of rocks induced by lichen colonization –a review. Catena, 39, 121–146.

    Article  CAS  Google Scholar 

  • Chen, J., Kadlubar, F. F., & Chen, J. Z. (2007). DNA supercoiling suppresses real-time PCR: A new approach to the quantification of mitochondrial DNA damage and repair. Nucleic Acids Research, 35, 1377–1388.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng, J., Pinnell, L., Engel, K., Neufeld, J. D., & Charles, T. C. (2014). Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. Journal of Microbiological Methods, 99, 27–34.

    Article  CAS  PubMed  Google Scholar 

  • Chenu, C. (1993). Clay-or-sand polysaccharide associations as models for the interface between micro-organisms and soil: Water-related properties and microstructure. Geoderma, 56, 143–156.

    Article  CAS  Google Scholar 

  • Chorover, J., Kretzschmar, R., Garcia-Pichel, F., & Sparks, D. L. (2007). Soil biogeochemical processes within the critical zone. Elements, 35, 321–326.

    Article  Google Scholar 

  • Chotte, J. L. (2005). Importance of microorganisms for soil aggregation. In F. Buscot & A. Varma (Eds.), Microorganisms in soils: Roles in genesis and functions (pp. 107–119). Berlin: Springer.

    Chapter  Google Scholar 

  • Clarholm, M. (1985). Possible roles of roots, bacteria, protozoa and fungi in supplying nitrogen to plants. In A. H. Fitter, D. Atkinson, D. J. Read, & M. B. Usher (Eds.), Ecological interactions in soil (pp. 297–317). Oxford: Blackwell.

    Google Scholar 

  • Cockell, C. S., Olsson, K., Herrera, A., & Meunier, A. (2009). Alteration textures in terrestrial volcanic glass and the associated bacterial community. Geobiology, 7, 50–65.

    Article  CAS  PubMed  Google Scholar 

  • Condron, L., Strak, C., O’Callaghan, M., Clinton, P., & Huang, Z. (2010). The role of microbial communities in the formation and decomposition of soil organic matter. In G. Dixon & E. Tilson (Eds.), Soil microbiology and sustainable crop production. Dordrecht: Springer.

    Google Scholar 

  • Cromack, K., & Caldwell, B. A. (1992). The role of fungi in litter decomposition and nutrient cycling. In G. C. Carroll & D. T. Wicklow (Eds.), The fungal community, its organization and role in the ecosystem (pp. 601–618). New York: Dekker.

    Google Scholar 

  • Davinic, M., Fultz, L. M., Acosta-Martinez, V., Caldero´ n, F. J., Cox, S. B., Dowd, S. E., Allen, V. G., Zak, J. C., & Moore-Kucera, J. (2012). Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biology and Biochemistry, 46, 63–72.

    Article  CAS  Google Scholar 

  • De Long, E. F., & Pace, N. R. (2001). Environmental diversity of bacteria and archaea. Systematic Biology, 50(4), 470–478.

    Article  Google Scholar 

  • De Macedo, J. R., Meneguelli, N. D., Ottoni Filho, T. B., & De Sousa Lima, J. A. (2002). Estimation of field capacity and moisture retention based on regression analysis involving chemical and physical properties in Alfisols and Ultisols of the state of Rio de Janeiro. Communications in Soil Science and Plant Analysis, 33(13–14), 2037–2055.

    Article  Google Scholar 

  • De ta Torre, M. A., Gome Z-Alarcon, G., & Palacios, J. M. (1993). In vitro biofilm formation by Penidllium frequentans strain on sandstone, granite, and limestone. Applied Microbiology and Biotechnology, 40, 408–415.

    Article  Google Scholar 

  • Esposito, A., Colantuono, C., Ruggieri, V., & Chiusano, M. L. (2016). Bioinformatics for agriculture in the next-generation sequencing era. Chemical and Biological Technologies in Agriculture, 3, 1–12.

    Article  CAS  Google Scholar 

  • Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008). The microbial engines that drive Earth’s biogeochemical cycles. Science, 320, 1034–1039.

    Article  CAS  PubMed  Google Scholar 

  • Feeney, D. S., Crawford, J. W., Daniell, T., Hallett, P. D., Nunan, N., Ritz, K., Rivers, M., & Young, I. M. (2006). Three-dimensional microorganization of the soil–root–microbe system. Microbial Ecology, 52(1), 151–158.

    Article  PubMed  Google Scholar 

  • Fierer, N., Jackson, J. A., Vilgalys, R., & Jackson, R. B. (2005). Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology, 71(7), 4117–4120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R. A., Felts, B., Rayhawk, S., Knight, R., Rohwer, F., & Jackson, R. B. (2007). Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and Environmental Microbiology, 73, 7059–7066.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frey-Klett, J., Garbaye, J., & Tarkka, M. (2007). The mycorrhiza helper bacteria revisited. New Phytologist, 176, 22–36.

    Article  CAS  Google Scholar 

  • Gadd, G. M. (1993). Interactions of fungi with toxic metals. New Phytologist, 124, 25–60.

    Article  CAS  Google Scholar 

  • Gadd, G. M. (2007). Geomycology: Biogeochemical transformation of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation. Mycological Research, 111, 3–49.

    Article  CAS  PubMed  Google Scholar 

  • Gadd, G. M. (2010). Metals, minerals and microbes: Geomicrobiology and bioremediation. Microbiology, 156, 609–643.

    Article  CAS  PubMed  Google Scholar 

  • Gilbert, J. A., & Neufeld, J. D. (2014). Life in a world without microbes. PLoS Biology, 12(12), e1002020.

    Article  PubMed  PubMed Central  Google Scholar 

  • Giller, K. E., Beare, M. H., Lavelle, P., Izac, A. M. N., & Swift, M. J. (1997). Agricultural intensification, soil biodiversity and agroecosystem function. Applied Soil Ecology, 6, 3–16.

    Article  Google Scholar 

  • Giri, B., Giang, P. H., Kumari, R., Prasad, R., & Varma, A. (2005). Microbial diversity in soils. In A. Varma & F. Buscot (Eds.), Microorganisms in soils: Roles in genesis and functions (Soil biology, Vol. 3). Berlin, Heidelberg: Springer.

    Google Scholar 

  • Gleeson, D. B., Kennedy, N. M., Clipson, N., Melville, K., Gadd, G. M., & McDermott, F. P. (2006). Mineralogical influences on bacterial community structure on a weathered pegmatitic granite. Microbial Ecology, 51, 526–534.

    Article  PubMed  Google Scholar 

  • Glenn, T. C. (2011). Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759–769.

    Article  CAS  PubMed  Google Scholar 

  • Hajibabaei, M., Singer, G. A. C., Clare, E. L., & Hebert, P. D. N. (2007). Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology, 5(1), 24.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hawksworth, D. L. (1991a). The biodiversity of microorganisms and invertebrates: Its role in sustainable agriculture (p. 302). Melksham: CAB International/Redwood Press.

    Google Scholar 

  • Hawksworth, D. L. (1991b). The fungal dimension of biodiversity: Magnitude, significance, and conservation. Mycological Research, 95, 641–655.

    Article  Google Scholar 

  • Hawksworth, D. L., & Mound. (1991). Biodiversity databases: The crucial significance of collections. In D. L. Hawksworth (Ed.), The biodiversity of microorganisms and invertebrates: Its role in sustainable agriculture (pp. 17–29). Wallingford: CAB International.

    Google Scholar 

  • Haynes, R. J. (2014). Nature of the belowground ecosystem and its development during Pedogenesis. Advances in Agronomy, 127, 43–109.

    Article  Google Scholar 

  • Hebert, P. D. N., Ratnasingham, S., & de Waard, J. R. (2003). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences, 270, 96–99.

    Google Scholar 

  • Hirsch, P., Eckhardt, F. E. W., & Palmer, R. J., Jr. (1995). Methods for the study of rock-inhabitating microorganisms—A mini review. Journal of Microbiological Methods, 23, 143–167.

    Article  Google Scholar 

  • Huang, D. L., Zeng, G. M., Feng, C. L., Hu, S., Jiang, X. Y., Tang, L., Su, F. F., Zhang, Y., Zeng, W., & Liu, H. L. (2008). Degradation of lead-contaminated lignocellulosic waste by Phanerochaete chrysosporium and the reduction of lead toxicity. Environmental Science & Technology, 42(13), 4946–4951.

    Article  CAS  Google Scholar 

  • Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C., & Stetter, K. O. (2002). A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature, 417, 63–67.

    Article  CAS  PubMed  Google Scholar 

  • Jansson, J. K., van Elsas, J. D., & Bailey, M. J. (2000). Tracking genetically engineered microorganisms. Georgetown: Landes Bioscience.

    Google Scholar 

  • Kallenbach, C. M., Frey, D. S., & Grandy, A. S. (2016). Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nature Communications, 7, 13630.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kandeler, E., Tscherko, D., Bruce, K. D., Stemmer, M., Hobbs, P. J., Bardgett, R. D., & Amelung, W. (2000). The structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biology and Fertility of Soils, 32, 390–400.

    Article  CAS  Google Scholar 

  • Kaplan, W. A. (1983). Nitrification. In E. J. Carpenter & D. G. Capone (Eds.), Nitrogen in the marine environment (pp. 139–190). New York: Academic.

    Chapter  Google Scholar 

  • Kuzyakov, Y. (2010). Priming effects: Interactions between living and dead organic matter. Soil Biology and Biochemistry, 42, 1363–1371.

    Article  CAS  Google Scholar 

  • Kyrpides, N. C., & Olsen, G. J. (1999). Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry. Trends in Genetics, 15, 298–299.

    Article  CAS  PubMed  Google Scholar 

  • Lakhanpal, T. N. (2000). Ectomycorrhiza–an overview. In K. G. Mukerji, B. P. Chamola, & J. Singh (Eds.), Mycorrhizal biology (pp. 101–118). New York: Kluwer/Plenum.

    Chapter  Google Scholar 

  • Lam, K. N., & Charles, T. C. (2015). Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. Microbiome, 3, 22.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee, K. E. (1985). Earthworms their ecology and relationships with soils and land use. Sydney: Academic.

    Google Scholar 

  • Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., Schuster, S. C., & Schleper, C. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature, 442, 806–809.

    Article  CAS  PubMed  Google Scholar 

  • Leita, L., De Nobili, M., Muhlbachova, G., Mondini, C., Marchiol, L., & Zerbi, G. (1995). Bioavailability and effects of heavy metals on soil microbial biomass survival during laboratory incubation. Biology and Fertility of Soils, 19, 103–108.

    Article  CAS  Google Scholar 

  • Lian, B., Chen Ye, Z. H. U., Lijun, Y., & Ruidong. (2008a). Effect of microbial weathering on carbonate rocks. Earth Science Frontiers, 15(6), 90–99.

    Article  Google Scholar 

  • Lian, B., Wang, B., Pan, M., Liu, C., & Teng, H. (2008b). Microbial release of potassium from K-bearing minerals by thermophilic fungus Aspergillus fumigatus. Geochimica et Cosmochimica Acta, 72, 87–98.

    Article  CAS  Google Scholar 

  • Lipiec, J., Brzezińska, M., Turski, M., Szarlip, P., & Frąc, M. (2015). Wettability and biogeochemical properties of the drilosphere and casts of endogeic earthworms in pear orchard. Soil and Tillage Research, 145, 55–61.

    Article  Google Scholar 

  • Lipiec, J., Frąc, M., Brzezińska, M., Turski, M., & Oszust, K. (2016). Linking microbial enzymatic activities and functional diversity of soil around earthworm burrows and casts. Frontiers in Microbiology, 7, 1361.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lynch, J. M. (1987). Microbial interactions in the rhizosphere. Soil Microorganisms, 30, 33–41.

    Google Scholar 

  • Lynch, J. M. (1990). The rhizosphere. New York: Wiley.

    Google Scholar 

  • Lynch, J. M., & Hobbie, J. B. (1988). Microorganisms in action: Concepts and application in microbial ecology (p. 36). Oxford: Blackwell.

    Google Scholar 

  • Madigan, M. T., Martinko, J. M., Stahl, D. A., & David, P. (2011). Clark Brock biology of microorganisms (13th ed.). QR41.2.B77, 579—dc22.

    Google Scholar 

  • Mamta, R. J. R., & Khursheed, A. W. (2015). Bioremediation of pesticides under the influence of bacteria and fungi Chapter 3. In Handbook of research on uncovering new methods for ecosystem management through bioremediation (pp. 51–72). Hershey: IGI Global.

    Chapter  Google Scholar 

  • Metting, B. (1988). Micro-algae in agriculture. In M. A. Borowitzka & L. A. Borowitzka (Eds.), Microalgal biotechnology (pp. 288–304). Cambridge: Cambridge University Press.

    Google Scholar 

  • Mirdamadian, S. H., Emtiazi, G., Golabi, M. H., & Ghanavati, H. (2010). Biodegradation of petroleum and aromatic hydrocarbons by Bacteria isolated from petroleum-contaminated soil. Journal of Petroleum & Environmental Biotechnology, 1, 102.

    Article  CAS  Google Scholar 

  • Moses, C. A., & Smith, B. J. (1993). A note on the role of the lichen Collema auriforma in solution basin development on a carboniferous limestone substrate. Earth Surface Processes and Landforms, 18, 363–368.

    Article  Google Scholar 

  • Nannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G., & Renella, G. (2017). Microbial diversity and soil functions. European Journal of Soil Science, 68, 1–26.

    Article  Google Scholar 

  • Nilsson, R. H., Kristiansson, E., Ryberg, M., Hallenberg, N., & Larsson, K. H. (2008). Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and ITS implications for molecular species identification. Evolutionary Bioinformatics, 4, 193–201.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nunan, N. (2017). The microbial habitat in soil. Scale, heterogeneity and functional consequences. Journal of Plant Nutrition and Soil Science, 180, 425–429.

    Article  CAS  Google Scholar 

  • O’Donnell, A. G., Seasman, M., Macrae, A., Waite, I., & Davies, J. T. (2001). Plants and fertilizers as drivers of change in microbial community structure and function in soil. Plant and Soil, 232, 135–145.

    Article  Google Scholar 

  • Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science, 276(5313), 734–740.

    Article  CAS  PubMed  Google Scholar 

  • Pace, N. R. (1999). Microbial ecology and diversity. ASM News, 65, 328–333.

    Google Scholar 

  • Pace, N. R., Olsen, G. J., & Woese, C. R. (1986). Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell, 45, 325–326.

    Article  CAS  PubMed  Google Scholar 

  • Paterson, E., Osler, G., Dawson, L. A., Gebbing, T., Sim, A., & Ord, B. (2008). Labile and recalcitrant plant fractions are utilised by distinct microbial communities in soil: Independent of the presence of roots and mycorrhizal fungi. Soil Biology and Biochemistry, 40, 1103–1113.

    Article  CAS  Google Scholar 

  • Payne, J. W. (1981). Denitrification. New York: Wiley.

    Google Scholar 

  • Pizl, V., & Novakova, A. (2003). Interactions between microfungi and Eisenia andrei (Oligochaeta) during cattle manure vermicomposting. Pedobiologia, 47, 895–899.

    Google Scholar 

  • Prescott, L. M., Harley, J. P., & Klein, D. A. (1996). The diversity of the microbial world. In L. M. Prescott, J. P. Harley, & D. A. Klein (Eds.), Microbiology. Dubuque: WCB Publishers.

    Google Scholar 

  • Prosser, J. I. (2002). Molecular and functional diversity in soil micro-organisms. Plant and Soil, 244, 9–17.

    Article  CAS  Google Scholar 

  • Puente, M. E., Bashan, Y., Li, C. Y., & Lebsky, V. K. (2004). Microbial populations and activities in the rhizoplane of rock-weathering desert plants I. Root colonization and weathering of igneous rocks. Plant Biology, 6, 629–642.

    Article  CAS  PubMed  Google Scholar 

  • Puente, M. E., Rodriguez-Jaramillo, M. C., Li, C. Y., & Bashan, Y. (2006). Image analysis for quantification of bacterial rock weathering. Journal of Microbiological Methods, 64, 275–286.

    Article  PubMed  Google Scholar 

  • Quejigo, J. R., Dominguez-Garay, A., Dorfler, A., Schroll, R., & Esteve-Nunez, A. (2018). Anodic shifting of the microbial community profile to enhance oxidative metabolism in soil. Soil Biology and Biochemistry, 116, 131–138.

    Article  CAS  Google Scholar 

  • Ren, R., Sun, Y., Zhao, Y., Geiser, D., Ma, H., & Zhou, X. (2016). Phylogenetic resolution of deep eukaryotic and fungal relationships using highly conserved low-copy nuclear genes. Genome Biology and Evolution, 8(9), 2683–2701.

    Article  PubMed  PubMed Central  Google Scholar 

  • Richter, D. D., Oh, N. H., Fimmen, R., & Jackson, J. (2007). The rhizosphere and soil formation. In The rhizosphere: An ecological perspective (pp. 179–200). Cambridge: Academic.

    Chapter  Google Scholar 

  • Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G., Km, A., Kent, A. D., Daroub, S. H., Camargo, F. A. O., Farmerie, W. G., & Triplett, E. W. (2007). Pyrosequencing enumerates and contracts soil microbial diversity. The ISME Journal, 1, 283–290.

    Article  CAS  PubMed  Google Scholar 

  • Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R., & Fierer, N. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal, 4, 1340–1351.

    Article  PubMed  Google Scholar 

  • Schimel, J. (1995). Ecosystem consequences of microbial diversity and community structure. In F. S. Chapin & C. Korner (Eds.), Arctic and alpine biodiversity: Patterns, causes and ecosystem consequences. Ecological studies (Analysis and syntehsis, Vol. 113). Berlin, Heidelberg: Springer.

    Google Scholar 

  • Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, 1794–1805.

    Article  CAS  PubMed  Google Scholar 

  • Singh, A. V., Sharma, A., & Johri, B. N. (2012). Phylogenetic profiling of culturable bacteria associated with early phase of mushroom composting assessed by amplified rDNA restriction analysis. Annals of Microbiology, 62, 675–682.

    Article  Google Scholar 

  • Smitha, M. S., Singh, S., & Singh, R. (2017). Microbial biotransformation: A process for chemical alterations. Journal of Bacteriology & Mycology: Open Access, 4(2), 00085.

    Google Scholar 

  • Sollins, P., Cromack, K., Jr., Li, C. Y., & Fogel, R. (1981). Role of low-molecular weight organic acids in the inorganic nutrition of fungi and higher plants. In G. C. Carroll & D. T. Wicklow (Eds.), The fungal community, its organization and role in ecosystem. New York: Dekker.

    Google Scholar 

  • Sterflinger, K., & Krumbein, W. E. (1997). Dematiaceous fungi as a major agent for biopitting on Mediterranean marbles and limestones. Geomicrobiology Journal, 14, 219–222.

    Article  Google Scholar 

  • SubbaRao, N. S. (1997). Soil microbiology. Oxford: IBH Publ.

    Google Scholar 

  • Szalay, A. (1964). Cation exchange properties of humic acids and their importance in the geochemical enrichment of UO2 ++ and other cations. Geochimica et Cosmochimica Acta, 28, 1605–1614.

    Article  CAS  Google Scholar 

  • Tabatabai, M. A. (1982). Soil enzymes. In A. L. Page, M. Rh, & D. R. Keeney (Eds.), Methods of soil analysis, part 2. Chemical and microbiological properties – Agronomy. Madison: American Society of Agronomy, Soil Science Society of America.

    Google Scholar 

  • Tate, K. R., Parshotam, A., & Ross, D. J. (1995). Soil carbon storage and turnover in temperate forests and grasslands – A New Zealand perspective. Journal of Biogeography, 22, 695–700.

    Article  Google Scholar 

  • Temperton, B., Field, D., Oliver, A., Tiwari, B., Mühling, M., & Joint, I. (2009). Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. The ISME Journal, 3, 792–796.

    Article  CAS  PubMed  Google Scholar 

  • Tiedje, J. M., Asuming-Brempong, S., Nüsslein, K., Marsh, T. L., & Flynn, S. J. (1999). Opening the black box of soil microbial diversity. Applied Soil Ecology, 13, 109–122.

    Article  Google Scholar 

  • Torsvik, V., Goksoyr, J., & Daae, F. L. (1990). High diversity in DNA of soil bacteria. Applied Environmental and Microbiology, 56, 782–787.

    CAS  Google Scholar 

  • Tourasse, N. J., & Gouy, M. (1997). Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Molecular Biology and Evolution, 14(3), 287–298.

    Article  CAS  PubMed  Google Scholar 

  • Uroz, S., Calvaruso, C., Marie-Pierre, T., & Frey-Klett, P. (2009). Mineral weathering by bacteria: Ecology, actors and mechanisms. Trends in Microbiology, 17, 378–387.

    Article  CAS  PubMed  Google Scholar 

  • Wainwright, M. (1992). The impact of fungi on environmental biogeochemistry. In G. C. Carroll & D. T. Wicklow (Eds.), The fungal community, its organization and role in the ecosystem (pp. 601–618). New York: Dekker.

    Google Scholar 

  • Welch, D. B. M., & Huse, S. M. (2011). Microbial diversity in the deep sea and the underexplored “Rare Biosphere”. In Handbook of molecular microbial ecology II: Metagenomics in different habitats (pp. 243–252). Hoboken: Wiley-Blackwell. https://doi.org/10.1002/9781118010549.ch24.

    Chapter  Google Scholar 

  • Welch, S., & McPhail, D. (2003). Mobility of major and trace elements during biologically mediated weathering of granite. In I. C. Roach (Ed.), CRC LEME Regional Regolith Symposia (pp. 437–440). Millaa Millaa: CRC LEME.

    Google Scholar 

  • Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088–5090.

    Article  CAS  Google Scholar 

  • Woese, C. R., Kandler, O., & Wheelis, M. L. (1990). Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eucarya. Proceedings of the National Academy of Sciences, 87, 4576–4579.

    Article  CAS  Google Scholar 

  • Wolters, V. (1991). Soil invertebrates – Effects on nutrient turnover and soil structure: A review. Zeitschrift für Pflanzenernährung und Bodenkunde, 154, 389–402.

    Article  Google Scholar 

  • Zambell, C. B., Adams, J. M., Gorring, M. L., & Schwartzman, D. W. (2012). Effect of lichen colonization on chemical weathering of hornblende granite as estimated by aqueous elemental flux. Chemical Geology, 291, 166–174.

    Article  CAS  Google Scholar 

  • Zhang, J., Chiodini, R., Badr, A., & Zhang, G. (2011). The impact of next generation sequencing on genomics. Journal of Genetics and Genomics, 38, 95–109.

    Article  PubMed  PubMed Central  Google Scholar 

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Kaviya, N., Upadhayay, V.K., Singh, J., Khan, A., Panwar, M., Singh, A.V. (2019). Role of Microorganisms in Soil Genesis and Functions. In: Varma, A., Choudhary, D. (eds) Mycorrhizosphere and Pedogenesis. Springer, Singapore. https://doi.org/10.1007/978-981-13-6480-8_2

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