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Recent Advances and Perspectives in Metagenomic Studies of Soil Microbial Communities

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Management of Microbial Resources in the Environment

Abstract

Metagenomics is a modern and rapidly growing field of molecular genetics and ecology that studies the “collective” genome of the microbial community and is based on the analysis of environmental DNA, extracted directly from a variety of natural habitats. The advent of high-throughput sequencing techniques had opened the principally new opportunities in studies of the genetic structure of microbial communities, but at the same time highlighted significant difficulties, arising particularly during the investigation of the soil metagenome.

Soil is the most densely populated habitat on the planet, and can contain up to 1,000 Gbp of genetic information per gram suggesting the great misfortune during the analysis of the soil metagenome consisting in the preferential analysis of only a small fraction of the total soil metagenome with relatively low accuracy. We emphasize the necessity for structuring of the soil metagenome and identification of its main components. Considering that modern metagenomics should first be addressed to the “eternal” questions of soil microbiology, in this review we tried to identify the meaningful parts of soil metagenome primarily by the analysis of soil microbial communities. We discussed in detail the spatial organization of soil metagenome associated with micro- and macrostructure of the soil matrix, the structural organization of soil metagenome associated with the presence of heterogeneous pools of soil DNA, taxonomical and functional organization of the soil metagenome revealed from the investigation of global patterns of distribution of microbial communities in relation to the specific environmental factors.

We demonstrated that soil microbial communities are characterized by a presence of a restricted number of taxonomic organization types, which are based on the most powerful ecological factors such as soil pH and moisture. Comparing to more or less labile taxonomic structure, the functional structure of the soil metagenome is rather conservative and is maintained primarily by two factors – the microbial co-operation and the maintenance of high levels of genetic diversity. Finally we come to a conclusion that the soil metagenome represents an integrative hereditary system for maintenance of the basic soil functions under the variable ecological conditions.

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References

  • Agnelli A, Ascherb J, Cortia G, Ceccherini MT, Nannipieri P, Pietramellara G (2004) Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36:859–868

    Article  CAS  Google Scholar 

  • Andreetta A, Macci C, Ceccherini MT, Cecchini G, Masciandaro G, Pietramellara G, Carnicelli S (2004) Microbial dynamics in Mediterranean Moder humus. Biol Fertil Soils 48:259–270

    Article  CAS  Google Scholar 

  • Ascher J, Ceccherini MT, Nannipieri P, Pietramellara G (2005) Extracellular DNA rise up in soil by water capillarity. Geophys Res Abstr 7:07946

    Google Scholar 

  • Bakken L, Frostegård Ǻ (2006) Nucleic acid extraction from soil. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin

    Google Scholar 

  • Baveye PC (2009) To sequence or not to sequence the whole-soil metagenome? Nat Rev Microbiol 7(10):756

    Article  CAS  PubMed  Google Scholar 

  • Bent SJ, Forney LJ (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME 2:689–695

    Article  CAS  Google Scholar 

  • Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N (2011) The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 43:1450–1455

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bietz MJ, Lee CP (2009) Collaboration in metagenomics: sequence databases and the organization of scientific work. In: Balka E, Ciolfi L, Simone C, Tellioğlu H, Wagner I (eds) ECSCW 2009: Proceedings of the 11th European conference on computer supported cooperative work. Springer, London

    Google Scholar 

  • Böckelmann U, Lünsdorf H, Szewzyk U (2007) The detection of extracellular DNA as a structural component in the EPS of bacterial strains. Geophys Res Abstr 9:01325

    Google Scholar 

  • Brockett BFT, Prescott CE, Grayston SJ (2012) Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in Western Canada. Soil Biol Biochem 44:9–20

    Article  CAS  Google Scholar 

  • Bru D, Ramette A, Saby NP, Dequiedt S, Ranjard L, Jolivet C, Arrouays D, Philippot L (2011) Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J 5:532–542

    Article  CAS  PubMed  Google Scholar 

  • Bürgmann H, Pesaro M, Widmer F, Zeyer J (2001) A strategy for optimizing quality and quantity of DNA extracted from soil. J Microbiol Methods 45:7–20

    Article  PubMed  Google Scholar 

  • Burmølle M, Hansen LH, Sørensen SJ (2006) Reporter gene technology in soil ecology: detection of bioavailability and microbial interactions. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin

    Google Scholar 

  • Burmølle M, Johnsen K, Abu Al-Soud W, Hansen LH, Sørensen SJ (2009) The presence of embedded bacterial pure cultures in agar plates stimulate the culturability of soil bacteria. J Microbiol Methods 79:166–173

    Article  PubMed  Google Scholar 

  • Cai P, Huang Q, Zhang X (2006) Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by DNase. Environ Sci Technol 40:2971–2976

    Article  CAS  PubMed  Google Scholar 

  • Carson JK, Gonzalez-Quiñones V, Murphy DV, Hinz C, Shaw JA, Gleeson DB (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76:3936–3942

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76:999–1007

    Article  CAS  PubMed  Google Scholar 

  • Ceccherini MT, Aschera J, Pietramellara G, Vogel TM, Nannipieri P (2007) Vertical advection of extracellular DNA by water capillarity in soil columns. Soil Biol Biochem 39:158–163

    Article  CAS  Google Scholar 

  • Ceccherini MT, Ascher J, Agnelli A, Borgogni F, Pantani OL, Pietramellara G (2009) Experimental discrimination and molecular characterization of the extracellular soil DNA fraction. Antonie Van Leeuwenhoek 96:653–657

    Article  CAS  PubMed  Google Scholar 

  • Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18:324–330

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chau JF, Bagtzoglou AC, Willig MR (2011) The effect of soil texture on richness and diversity of bacterial communities. Environ Forensics 12:333–341

    Article  CAS  Google Scholar 

  • Chiang W, Tolker-Nielsen T (2010) Extracellular DNA as matrix component in microbial biofilms. In: Kikuchi Y, Rykova EY (eds) Extracellular nucleic acids. Springer, Berlin

    Google Scholar 

  • Chong CW, Pearce DA, Convey P, Yew WS, Tan IKP (2012) Patterns in the distribution of soil bacterial 16S rRNA gene sequences from different regions of Antarctica. Geoderma 181–182:45–55

    Article  Google Scholar 

  • Chotte J (2005) Importance of microorganisms for soil aggregation. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions. Springer, Berlin

    Google Scholar 

  • Chowdhury SP, Schmid M, Hartmann A, Tripathi AK (2009) Diversity of 16S-rRNA and nifH genes derived from rhizosphere soil and roots of an endemic drought tolerant grass, Lasiurus sindicus. Eur J Soil Biol 45:114–122

    Article  CAS  Google Scholar 

  • Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12:2998–3006

    Article  CAS  PubMed  Google Scholar 

  • Connon SA, Lester ED, Shafaat HS, Obenhuber DC, Ponce A (2007) Bacterial diversity in hyperarid Atacama Desert soils. J Geophys Res 112:G04S17. doi:10.1029/2006JG000311

    Article  CAS  Google Scholar 

  • Craig JW, Chang F, Kim JH, Obiajulu SC, Brady SF (2010) Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse Proteobacteria. Appl Environ Microbiol 76(5):1633–1641. doi:10.1128/AEM.02169-09

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Daniel R (2004) The soil metagenome – a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:199–204

    Article  CAS  PubMed  Google Scholar 

  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478

    Article  CAS  PubMed  Google Scholar 

  • Davinic M, Fultz LM, Acosta-Martinez V, Calderón FJ, Cox SB, Dowd SE, Allen VG, Zak JC, Moore-Kucera J (2012) Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biol Biochem 46:63–72

    Article  CAS  Google Scholar 

  • Dechesne A, Pallud C, Debouzie D, Flandrois JP, Vogel TM, Gaudet JP, Grundmann GL (2003) A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil. Soil Biol Biochem 35:1537–1546

    Article  CAS  Google Scholar 

  • Demanèche S, David MM, Navarro E, Simonet P, Vogel TM (2009) Evaluation of functional gene enrichment in a soil metagenomic clone library. JMicrobiol Methods 76:105–107

    Article  CAS  Google Scholar 

  • Eickhorst T, Tippkötter R (2008) Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods. Soil Biol Biochem 40:284–1293

    Google Scholar 

  • Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, Roe BA, Davis JP, Schloss PD, Bailey VL, Krumholz LR (2008) Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 74:5422–5428

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ettema CH, Wardle DA (2002) Spatial soil ecology. Trends Ecol Evol 17:177–183

    Article  Google Scholar 

  • Feinstein LM, Sul WJ, Blackwood CB (2009) Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol 75:5428–5433

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88(6):1354–1364

    Article  PubMed  Google Scholar 

  • Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7:210–220

    Article  CAS  PubMed  Google Scholar 

  • Garbeva P, de Boer W (2009) Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression. Microb Ecol 58:36–46

    Article  CAS  PubMed  Google Scholar 

  • Gerlach W, Jünemann S, Tille F et al (2009) WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 10:430

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gilbert JA, Dupont CL (2011) Microbial metagenomics: beyond the genome. Annu Rev Mar Sci 3:347–371

    Article  Google Scholar 

  • Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gomez-Silva B, Rainey FA, Warren-Rhodes KA, McKay CP, Navarro-Gonzalez R (2008) Atacama desert soil microbiology. In: Dion P, Nautiyal CS (eds) Microbiology of extreme soils. Springer, Berlin

    Google Scholar 

  • Grundmann GL (2004) Spatial scales of soil bacterial diversity – the size of a clone. FEMS Microbiol Ecol 48:119–127

    Article  CAS  PubMed  Google Scholar 

  • Grundmann LG, Gourbiere F (1999) A micro-sampling approach to improve the inventory of bacterial diversity in soil. Appl Soil Ecol 13:123–126

    Article  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42:878–887

    Article  CAS  Google Scholar 

  • Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TL (2010) Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME 4:829–838

    Article  CAS  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rDNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria, proteobacteria, and verrucomicrobia. Appl Environ Microbiol 68:2391–2396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kakirde KS, Parsley LC, Liles MR (2010) Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem 42:1911–1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • King AJ, Freeman KR, Mccormick KF, Lynch RC, Lozupone C, Knight R, Schmidt SK (2010) Biogeography and habitat modelling of high-alpine bacteria. Nature Commun 1:53. doi:10.1038/ncomms1055

    Article  CAS  Google Scholar 

  • Kostychev PA (1937) The soils of chernozem region of Russia: their origin, composition and properties. Selchozgiz, Moscow-Leningrad

    Google Scholar 

  • Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuske CR, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68(4):1854–1863. doi:10.1128/AEM.68.4.1854-1863.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lämmle K, Zipper H, Breuer M, Hauer B, Buta C, Brunner H, Rupp S (2010) Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 127:575–592. doi:10.1016/j.jbiotec.2006.07.036

    Article  CAS  Google Scholar 

  • Lauber CL, Strickland MS, Bradford MA, Fierer N (2008) The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 40:2407–2415

    Article  CAS  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75(15):5111–5120. doi:10.1128/AEM.00335-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S, Cho J (2009) Distribution patterns of the members of phylum Acidobacteria in global soil samples. J Microbiol Biotechnol 19:1281–1287

    CAS  PubMed  Google Scholar 

  • Lee S, Ka J, Cho J (2008) Members of the phylum Acidobacteria are dominant and metabolicallyactive in rhizosphere soil. FEMS Microbiol Lett 285:263–269

    Article  CAS  PubMed  Google Scholar 

  • Levy-Bootha DJ, Campbell RG, Gulden RH, Harta MM, Powellc JR, Klironomos JN, Pauls KP, Swanton CJ, Trevorsa JT, Dunfieldd KE (2007) Cycling of extracellular DNA in the soil environment. Soil Biol Biochem 39:2977–2991

    Article  CAS  Google Scholar 

  • Lombard N, Prestat E, Elsas JDV, Simonet P (2011) Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol Ecol 78:31–49

    Article  CAS  PubMed  Google Scholar 

  • Lorenz P, Liebeton K, Niehaus F, Eck J (2002) Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 13:572–577

    Article  CAS  PubMed  Google Scholar 

  • Lorenz P, Liebeton K, Niehaus F, Schleper C, Eck J (2003) The impact of non-cultivated biodiversity on enzyme discovery and evolution. Biocatal Biotransfor 21(2):87–91

    Article  CAS  Google Scholar 

  • Lu N, Zilles JL, Nguyen TH (2010) Adsorption of extracellular chromosomal dna and its effects on natural transformation of Azotobacter vinelandii. Appl Environ Microbiol 76(13):4179–4184. doi:10.1128/AEM.00193-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mercier A, Kay E, Simonet P (2006) Horizontal gene transfer by natural transformation in soil environment. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin

    Google Scholar 

  • Meyer F, Paarmann D, D’Souza MD, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497–505. doi:10.1016/j.resmic.2010.04.010

    Article  PubMed  Google Scholar 

  • Mummey DL, Stahl PD (2004) Analysis of soil whole- and inner-microaggregate bacterial communities. Microbial Ecol 48:41–50

    Article  CAS  Google Scholar 

  • Mummey D, Holben W, Six J, Stahl P (2006) Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microbial Ecol 51:404–411

    Article  Google Scholar 

  • Nielsen KM, Calamai L, Pietramellara G (2006) Stabilization of extracellular DNA and proteins by transient binding to various soil components. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin

    Google Scholar 

  • Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosafety Res 6:37–53. doi:10.1051/ebr:2007031

    Article  CAS  PubMed  Google Scholar 

  • Nunan N, Wu K, Young IM, Crawford JW, Ritz K (2003) Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol 44:203–215

    Article  CAS  PubMed  Google Scholar 

  • Paget E, Lebrun M, Freyssinet G, Simonet P (1998) The fate of recombinant plant DNA in soil. Eur J Soil Biol 34(2):81–88

    Article  CAS  Google Scholar 

  • Pershina EV, Tamazyan GS, Dolnik AS, Pinaev AG, Sergaliev NH, Andronov EE (2012) Studying the structure of soil microbial community in saline soils by high-throughput pyrosequencing. Ecol Genet 2(10):31–38 (in russian)

    Google Scholar 

  • Pettit RK (2004) Soil DNA libraries for anticancer drug discovery. Cancer Chemother Pharmacol 54:1–6. doi:10.1007/s00280-004-0771-8

    Article  CAS  PubMed  Google Scholar 

  • Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G, Nannipieri P (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45:219–235

    Article  CAS  Google Scholar 

  • Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M (2007) Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73(10):3205–3214. doi:10.1128/AEM.02985-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raes J, Foerstner UK, Bork P (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10:1–9

    Article  CAS  Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics, genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    Article  CAS  PubMed  Google Scholar 

  • Robe P, Nalin R, Capellano C, Vogel TM, Simonet P (2003) Extraction of DNA from soil. Eur J Soil Biol 39:183–190

    Article  CAS  Google Scholar 

  • Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    CAS  PubMed  PubMed Central  Google Scholar 

  • Romanowski G, Lorenz MG, Sayler G, Wackernagel W (1992) Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl Environ Microbiol 58:3012–3019

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruberto LAM, Vazquez SC, Mac Cormack WP (2008) Bacteriology of extremely cold soils exposed to hydrocarbon pollution. In: Dion P, Nautiyal CS (eds) Microbiology of extreme soils. Springer, Berlin

    Google Scholar 

  • Saeki K, Kunito T (2010) Adsorptions of DNA molecules by soils and variable-charged soil constituents. In: Méndez-Vilas A (ed) Current research technology and education topics in applied microbiology and microbial biotechnology. FORMATEX, Badajoz

    Google Scholar 

  • Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J (2008) Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol 74:2902–2907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schink B (2002) Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81:257–261

    Article  CAS  PubMed  Google Scholar 

  • Schipper C, Hornung C, Bijtenhoorn P, Quitschau M, Grond S, Streit WR (2009) Metagenome-derived clones encoding two novel lactonase family proteins involved in biofilm inhibition in Pseudomonas aeruginosa. Appl Environ Microbiol 75(1):224–233. doi:10.1128/AEM.01389-08

    Article  CAS  PubMed  Google Scholar 

  • Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153–1161. doi:10.1128/AEM.02345-10

    Article  CAS  PubMed  Google Scholar 

  • Singh BK, Campbell CD, Sorenson SD, Zhou J (2009a) Soil genomics. Nat Rev Microbiol 7:756. doi:10.1038/nrmicro2119-c1

    Article  CAS  PubMed  Google Scholar 

  • Singh BK, Dawson LA, Macdonald CA, Buckland SM (2009b) Impact of biotic and abiotic interction on soil microbial communities and functions: a field study. Appl Soil Ecol 41:239–248. doi:10.1016/j.apsoil.2008.10.003

    Article  Google Scholar 

  • Spain AM, Krumholz LR, Elshahed MS (2009) Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 3:992–1000

    Article  CAS  PubMed  Google Scholar 

  • Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske SR (2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ Microbiol Rep 4(2):248–256

    Article  PubMed  Google Scholar 

  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil, from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  CAS  PubMed  Google Scholar 

  • Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56(3):782–787

    CAS  PubMed  PubMed Central  Google Scholar 

  • Trap J, Laval K, Akpa-Vinceslas M, Gangneux C, Bureau F, Decaëns T, Aubert M (2011) Humus macro-morphology and soil microbial community changes along a 130-yr-old Fagus sylvatica chronosequence. Soil Biol Biochem 43:1553–1562. doi:10.1016/j.soilbio.2011.04.005

    Article  CAS  Google Scholar 

  • Trevors JT (2010) One gram of soil: a microbial biochemical gene library. Antonie Van Leeuwenhoek 97:99–106. doi:10.1007/s10482-009-9397-5

    Article  CAS  PubMed  Google Scholar 

  • Tringe SG, Hugenholtz P (2009) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11:442–446

    Article  CAS  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    Article  CAS  PubMed  Google Scholar 

  • Tsai S, Selvam A, Chang Y, Yang S (2009) Soil bacterial community composition across different topographic sites characterized by 16S rRNA gene clones in the Fushan Forest of Taiwan. Bot Stud 50:57–68

    CAS  Google Scholar 

  • Tyson GW, Banfield JF (2005) Cultivating the uncultivated: a community genomics perspective. Trends Microbiol 13(9):411–415

    Article  CAS  PubMed  Google Scholar 

  • Ussery DW, Wassenaar TM, Borini S (2009) Computing for comparative microbial genomics. Springer, Berlin

    Book  Google Scholar 

  • Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2010) Molecular methods to study complex microbial communities. In: Streit WR, Daniel R (eds) Metagenomics. Methods and protocols. Humana Press, c/o Springer Science  +  Business Media, New York

    Google Scholar 

  • Vogel TM, Simonet P, Jansson JK, Hirsh PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R, Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252

    Article  CAS  Google Scholar 

  • Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69(10):6235–6242. doi:10.1128/AEM.69.10.6235-6242.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voroney RP (2010) The soil habitat. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry, 3rd edn. Academic, Burlington

    Google Scholar 

  • Wackernagel W (2006) The various sources and the fate of nucleic acids in soil. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin

    Google Scholar 

  • Wagner D (2008) Microbial communities and processes in arctic permafrost environments. In: Dion P, Nautiyal CS (eds) Microbiology of extreme soils. Springer, Berlin

    Google Scholar 

  • Wexler M, Johnston AWB (2010) Wide host-range cloning for functional metagenomics. In: Streit WR, Daniel R (eds) Metagenomics. Methods and protocols. Humana Press, c/o Springer Science  +  Business Media, New York

    Google Scholar 

  • Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R (2010) Horizon-specific bacterial community composition of german grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76(20):6751–6759. doi:10.1128/AEM.01063-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wooley JC, Ye Y (2009) Metagenomics: facts and artifacts, and computational challenges. J Comp Sci Technol 25:71–81

    Article  Google Scholar 

  • Young IM, Crawford JW (2004) Interactions and selforganization in the soil-microbe complex. Science 304:1634–1637

    Article  CAS  PubMed  Google Scholar 

  • Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci USA 99:15681–15686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia

    E. V. Pershina, E. E. Andronov, A. G. Pinaev & N. A. Provorov

Authors
  1. E. V. Pershina
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  2. E. E. Andronov
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  3. A. G. Pinaev
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  4. N. A. Provorov
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Correspondence to N. A. Provorov .

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Editors and Affiliations

  1. Department of Agricultural Microbiology Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India

    Abdul Malik (Visiting Professor/Scientist) (Visiting Professor/Scientist)

  2. Division of Infectious Diseases, University Medical Center Freiburg, Freiburg, Germany

    Abdul Malik (Visiting Professor/Scientist) & Elisabeth Grohmann (Visiting Professor/Scientist) & 

  3. Center of Biological Engineering, University of Minho, Braga, Portugal

    Madalena Alves

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Pershina, E.V., Andronov, E.E., Pinaev, A.G., Provorov, N.A. (2013). Recent Advances and Perspectives in Metagenomic Studies of Soil Microbial Communities. In: Malik, A., Grohmann, E., Alves, M. (eds) Management of Microbial Resources in the Environment. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5931-2_7

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