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Assessing bacterial diversity in soil

A brief review

  • SOILS, SEC 1 • SOIL ORGANIC MATTER DYNAMICS • REVIEW ARTICLE
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Background, aim and scope

Biodiversity has been defined as the total number of species present, i.e. species richness or species abundance, and the distribution of individuals among those species, i.e. species evenness or species equitability. Recently, the biodiversity of soil biota is becoming increasingly essential with the requirement of preserving the integrity, function and long-term sustainability of natural and managed terrestrial ecosystems. The aim of this paper was to review, commonly used methods for the detection of microbial diversity in soils and characteristics of commonly presented soil bacterial communities. It is expected that this review could provide a platform for future studies of bacterial diversity in soils.

Main features

Soil is a complex, dynamic and living habitat for a large number of organisms. Bacteria are an important part of the soil micro-flora because of their abundance, their species diversity and the multiplicity of their metabolic activities. They also have the potential to reflect the past history of a given environment. It is therefore essential to understand the interrelationships between bacteria and their environment by studying the structural and functional diversity of soil bacterial communities and how they would respond to various natural or man-made disturbances. Conventional culture-dependent techniques have been used for the measurement of soil microbial composition, but only 0.1–1% of soil bacteria are accessible by these approaches, which make the wide phylogenetic diversity remaining sparsely studied. Culture-independent molecular techniques can overcome this problem since they use DNA extracted directly from soils. Although the application of these molecular techniques has greatly improved the understanding of structures and dynamics of microbial communities in soils, it still has some limitations, for example the DNA is often extremely difficult to extract and purify from the organic-rich environmental samples. Different methods that complemented each other are recommended to combine the examination of soil microbial communities. Culture-dependent and culture-independent methods discover different phylogenetic information. Phyla Proteobacteria, Cytophagales, Actinobacteria and Firmicutes are well represented by cultivated organisms and these four phyla account for 90% of all cultivated bacteria characterised by 16S rRNA sequences. Some phyla which are revealed by clonal analysis, such as Acidobacteria and Verrucomicrobia, are poorly represented by sequences from cultivated organisms.

Conclusions and perspectives

In conclusion, we have described soil component and compared culture-dependent and culture-independent methods in assessing bacterial diversity in soils. These methods are all feasible to assess the bacterial communities in soils; however, each method has its limitation and only provides a partial picture of one aspect of soil microbial diversity. It is suggested in this paper to combine different methods that complemented each other to obtain a more complete picture of bacterial diversity. The conflict information from studies using culture-dependent and culture-independent methods is also reviewed. It is found that members of four major phylogenetic groups are ubiquitous to almost all soil types: class α-proteobacteria and phyla Actinobacteria, Acidobacteria and Verrucomicrobia; phyla Proteobacteria, Cytophagales, Actinobacteria and Firmicutes are well represented by cultivated organisms. New species and taxa are constantly described, adding to the bacterial list. Consequently, some species or even higher taxa may be transferred to a newly described taxon with more suitable descriptions. Described taxa may be merged together to form a more coherent arrangement, and high rank taxa may be sub-divided or even raised to a higher rank. Our knowledge of bacterial diversity on soils is limited because of the taxonomic and methodological limitations. There is a need now for further examining and comparing these methods to gain assurance that the best methods are used to assess bacterial communities and that we can interpret new information. The association between diversity and function will be clarified with our understanding increasing and knowledge expanding.

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References

  • Ahmad S, Selvapandiyan A, Bhatnagar RK (2000) Phylogenetic analysis of Gram-positive bacteria based on grpE, encoded by the dnaK operon. Int J Syst Evol Microbiol 50:1761–1766

    CAS  Google Scholar 

  • Alvarez MAD, Gagne S, Antoun H (1995) Effect of compost on rhizosphere microflora of the tomato and on the incidence of plant growth-promoting rhizobacteria. Appl Environ Microbiol 61:194–199

    CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  Google Scholar 

  • Atlas RM (1984) Diversity of microbial communities. Adv Microbial Ecol 7:1–47

    Google Scholar 

  • Axelrood PE, Chow ML, Radomski CC, McDermott JM, Davies J (2002) Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can J Microbiol 48:655–674

    Article  CAS  Google Scholar 

  • Balestra GM, Misaghi IJ (1997) Increasing the efficiency of the plate counting method for estimating bacterial diversity. J Microbiol Methods 30:111–117

    Article  Google Scholar 

  • Bardgett RD, Hobbs PJ, Frostegard A (1996) Changes in soil fungal:bacterial biomass ratios following reductions in the intensity of management of an upland grassland. Biol Fertil Soils 22:261–264

    Article  Google Scholar 

  • Bej AK, Perlin M, Atlas RM (1991) Effect of introducing genetically engineered microorganisms on soil microbial community diversity. FEMS Microbiol Ecol 86:169–176

    Article  Google Scholar 

  • Bernal G, Graham PH (2001) Diversity in the rhizobia associated with Phaseolus vulgaris L. in Ecuador, and comparisons with Mexican bean rhizobia. Can J Microbiol 47:526–534

    Article  CAS  Google Scholar 

  • Boehm MJ, Madden LV, Hoitink HAJ (1993) Effect of organic-matter decomposition level on bacterial species-diversity and composition in relationship to pythium damping-off severity. Appl Environ Microbiol 59:4171–4179

    CAS  Google Scholar 

  • Boehm MJ, Wu TY, Stone AG, Kraakman B, Iannotti DA, Wilson GE, Madden LV, Hoitink HAJ (1997) Cross-polarized magic-angle spinning C-13 nuclear magnetic resonance spectroscopic characterization of soil organic matter relative to culturable bacterial species composition and sustained biological control of Pythium root rot. Appl Environ Microbiol 63:162–168

    CAS  Google Scholar 

  • Borneman J, Skroch PW, O’Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943

    CAS  Google Scholar 

  • Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653

    CAS  Google Scholar 

  • Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1–12

    Article  CAS  Google Scholar 

  • Buckley DH, Schmidt TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5:441–52

    Article  Google Scholar 

  • Campbell CD, Grayston SJ, Hirst DJ (1997) Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities. J Microbiol Methods 30:33–41

    Article  Google Scholar 

  • Chapman SK, Koch GW (2007) What type of diversity yields synergy during mixed litter decomposition in a natural forest ecosystem? Plant Soil 299:153–162

    Article  CAS  Google Scholar 

  • Chapman SJ, Campbell CD, Artz RRE (2007) Assessing CLPPs using MicroResp™. A comparison with Biolog and multi-SIR. J Soils Sediments 7(6):406–410

    Article  Google Scholar 

  • Chow ML, Radomski CC, McDermott JM, Davies J, Axelrood PE (2002) Molecular characterization of bacterial diversity in lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357

    Article  CAS  Google Scholar 

  • Classen AT, Boyle SI, Haskins KE, Overby ST, Hart SC (2003) Community-level physiological profiles of bacteria and fungi: plate type and incubation temperature influences on contrasting soils. FEMS Microbiol Ecol 44:319–328

    Article  CAS  Google Scholar 

  • Costa AL, Paixão SM, Caçador I, Carolino M (2007) CLPP and EEA profiles of microbial communities in salt marsh sediments. J Soils Sediments 7(6):418–425

    Article  CAS  Google Scholar 

  • de Leij FAAM, Whipps JM, Lynch JM (1993) The use of colony development for the characterization of bacterial communities in soil and on roots. Microb Ecol 27:81–97

    Google Scholar 

  • Derry AM, Staddon WJ, Kevan PG, Trevors JT (1999) Functional diversity and community structure of micro-organisms in three arctic soils as determined by sole-carbon-source-utilization. Biodiv Conserv 8:205–221

    Article  Google Scholar 

  • Derry AM, Staddon WJ, Trevors JT (1998) Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization. World J Microbiol Biotechnol 14:571–578

    Article  Google Scholar 

  • Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669

    CAS  Google Scholar 

  • Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66:2943–2950

    Article  CAS  Google Scholar 

  • el Fantroussi S, Verschuere L, Verstraete W, Top EM (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65:982–988

    Google Scholar 

  • Ellis RJ, Morgan P, Weightman AJ, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223–3230

    Article  CAS  Google Scholar 

  • Felske A, Wolterink A, Van Lis R, De Vos WM, Akkermans AD (2000) Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66:3998–4003

    Article  CAS  Google Scholar 

  • Frostegard A, Tunlid A, Baath E (1993) Phospholipid fatty-acid composition, biomass, and activity of microbial communities from 2 soil types experimentally exposed to different heavy-metals. Appl Environ Microbiol 59:3605–3617

    CAS  Google Scholar 

  • Furlong MA, Singleton DR, Coleman DC, Whitman WB (2002) Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl Environ Microbiol 68:1265–1279

    Article  CAS  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source utilization. Appl Environ Microbiol 57:2352–2359

    Google Scholar 

  • Garrity GM, Holt JG (2001) Bergey’s manual of systematic bacteriology, 2nd edition, vol. 1. Springer, New York

    Google Scholar 

  • Ge Y, He JZ, Zhu YG, Zhang JB, Xu ZH, Zhang LM, Zheng YM (2008a) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2:254–264

    Article  CAS  Google Scholar 

  • Ge Y, Zhang JB, Zhang LM, Yang M, He JZ (2008b) Long-term fertilization regimes and diversity of an agricultural affect bacterial community structure soil in northern China. J Soils Sediments 8:43–50

    Article  CAS  Google Scholar 

  • Gelsomino A, Keijzer-Wolters AC, Cacco G, van Elsas JD (1999) Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J Microbiol Methods 38:1–15

    Article  CAS  Google Scholar 

  • Grayston SJ, Campbell CD (1996) Functional biodiversity of microbial communities in the rhizospheres of hybrid larch (Larix eurolepis) and Sitka spruce (Picea sitchensis). Tree Physiol 16:1031–1038

    Google Scholar 

  • Grayston SJ, Wang SQ, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378

    Article  CAS  Google Scholar 

  • Griepenburg U, Ward-Rainey N, Mohamed S, Schlesner H, Marxsen H, Rainey FA, Stackebrandt E, Auling G (1999) Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales. Int J Syst Evol Bacteriol 49:689–696

    Article  CAS  Google Scholar 

  • Großkropf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64:960–969

    Google Scholar 

  • Gupta RS (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402

    Article  CAS  Google Scholar 

  • Hackl E, Zechmeister-Boltenstern S, Bodrossy L, Sessitsch A (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70:5057–5065

    Article  CAS  Google Scholar 

  • He JZ, Xu ZH, Hughes J (2006) Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. FEMS Microbiol Ecol 55:38–47

    Article  CAS  Google Scholar 

  • He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di HJ (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:3152–3152

    Article  CAS  Google Scholar 

  • Hermansson A, Lindgren PE (2001) Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl Environ Microbiol 67:972–976

    Article  CAS  Google Scholar 

  • Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A, Maldonado-Ramireza S, Lyncha ST, Nelson EB (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15:25–36

    Article  Google Scholar 

  • Hu S, van Bruggen AHC (1997) Microbial dynamics associated with multiphasic decomposition of C-14-labeled cellulose in soil. Microb Ecol 33:134–143

    Article  CAS  Google Scholar 

  • Hu S, Chapin FS III, Firestone MK, Field CB, Chiariello NR (2001) Nitrogen limitation of microbial decomposition in a grassland under elevated CO2. Nature 409:188–191

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    CAS  Google Scholar 

  • Ibekwe AM, Kennedy AC (1998) Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils. Plant Soil 206:151–161

    Article  CAS  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  Google Scholar 

  • Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215

    Article  CAS  Google Scholar 

  • Kaiser O, Puhler A, Selbitschka W (2001) Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microb Ecol 42:136–149

    CAS  Google Scholar 

  • Kim JS, Sparovek G, Longo RM, De Melo WJ, Crowley D (2007) Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol Biochem 39:684–690

    Article  CAS  Google Scholar 

  • Kishimoto N, Tano T (1987) Acidophilic heterotrophic bacteria isolated from acidic mine drainage, sewage and soils. J Gen Appl Microbiol 33:11–25

    Article  CAS  Google Scholar 

  • Konopka A, Oliver L, Turco RF (1998) The use of carbon substrate utilization patterns in environmental and ecological microbiology. Microb Ecol 35:103–115

    Article  CAS  Google Scholar 

  • Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63:3614–3621

    CAS  Google Scholar 

  • Lagomarsino A, Knapp BA, Moscatelli MC, De Angelis P, Grego S, Insam H (2007) Structural and functional diversity of soil microbes is affected by elevated [CO2] and N addition in a poplar plantation. J Soils Sediments 7(6):399–405

    Article  CAS  Google Scholar 

  • Lee J, Kim JS, Nahm CH, Choi JW, Kim J, Pai SH, Moon KH, Lee K, Chong Y (1999) Two cases of Chromobacterium violaceum infection after injury in a subtropical region. J Clin Microbiol 37:2068–2070

    CAS  Google Scholar 

  • Lessa EP, Applebaum G (1993) Screening techniques for detecting allelic variation in DNA-sequences. Mol Ecol 2:119–129

    Article  CAS  Google Scholar 

  • Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078

    CAS  Google Scholar 

  • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

    CAS  Google Scholar 

  • Macalady JL, Fuller ME, Scow KM (1998) Effects of metam sodium fumigation on soil microbial activity and community structure. J Environ Qual 27:54–63

    Article  CAS  Google Scholar 

  • MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang YJ, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65:3566–3574

    CAS  Google Scholar 

  • Madigan M, Martinko J (ed). (2005) Brock biology of microorganisms, 11 edn. Prentice Hall, Upper Saddle River, NJ

  • Marsh I, Whittington R, Cousins D (1999) PCR-restriction endonuclease analysis for identification and strain typing of Mycobacterium avium subsp. paratuberculosis and Mycobacterium avium subsp. avium based on polymorphisms in IS1311. Mol Cellular Probes 13:115–126

    Article  CAS  Google Scholar 

  • Martins-Loução MA, Cruz C (2007) Microbial communities (Editorial). J Soils Sediments 7(6):398

    Article  Google Scholar 

  • McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730

    CAS  Google Scholar 

  • Mitsui H, Gorlach K, Lee HJ, Hattori R, Hattori T (1997) Incubation time and media requirements of culturable bacteria from different phylogenetic groups. J Microbiol Methods 30:103–110

    Article  CAS  Google Scholar 

  • Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322

    Article  CAS  Google Scholar 

  • Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Appl Environ Microbiol 59:695–700

    CAS  Google Scholar 

  • Nemergut DR, Costello EK, Meyer AF, Pescador MY, Weintraub MN, Schmidt SK (2005) Structure and function of alpine and arctic soil microbial communities. Res Microbiol 156:775–784

    Article  Google Scholar 

  • Nogales B, Moore ER, Abraham WR, Timmis KN (1999) Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environ Microbiol 1:199–212

    Article  CAS  Google Scholar 

  • Nusslein K, Tiedje JM (1998) Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl Environ Microbiol 64:1283–1289

    CAS  Google Scholar 

  • Ogram A (2000) Soil molecular microbial ecology at age 20: methodological challenges for the future. Soil Biol Biochem 32:1499–1504

    Article  CAS  Google Scholar 

  • Olsen JE (1999) Antibiotic resistance: genetic mechanisms and mobility. Acta Vet Scand Suppl 92:15–22

    CAS  Google Scholar 

  • Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936

    Article  CAS  Google Scholar 

  • Reichardt W, Mascarina G, Padre B, Doll J (1997) Microbial communities of continuously cropped, irrigated rice fields. Appl Environ Microbiol 63:233–238

    CAS  Google Scholar 

  • Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666

    Article  CAS  Google Scholar 

  • Saul DJ, Aislabie JM, Brown CE, Harris L, Foght JM (2005) Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53:141–155

    Article  CAS  Google Scholar 

  • Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10:1601–1611

    Article  CAS  Google Scholar 

  • Siciliano SD, Germida JJ, Siciliano SD (1998) Biolog analysis and fatty acid methyl ester profiles indicate that pseudomonad inoculants that promote phytoremediation alter the root-associated microbial community of Bromus biebersteinii. Soil Biol Biochem 30:1717–1723

    Article  CAS  Google Scholar 

  • Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wemars K (2001) Diversity and seasonal fluctuations of the dominat members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291

    Article  CAS  Google Scholar 

  • Stach JE, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol Ecol 36:139–151

    Article  CAS  Google Scholar 

  • Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236

    CAS  Google Scholar 

  • Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37–57

    Article  CAS  Google Scholar 

  • Tiedje JM, Asming-Brempong S, Nüsslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122

    Article  Google Scholar 

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

    CAS  Google Scholar 

  • Torsvik V, Daae FL, Sandaa RA, Ovreas L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62

    Article  CAS  Google Scholar 

  • Tunlid A, Hoitink HAJ, Low CA, White DC (1989) Characterization of bacteria that suppress Rhizoctonia damping-off in bark compost media by analysis of fatty acid biomarkers. Appl Environ Microbiol 55:1368–1374

    CAS  Google Scholar 

  • Vaneechoutte M (1996) DNA fingerprinting techniques for microorganisms—a proposal for classification and nomenclature. Mol Biotechnol 6:115–142

    Article  CAS  Google Scholar 

  • Winding A, Hendriksen NB (2007) Comparison of CLPP and enzyme activity assay for functional characterization of bacterial soil communities. J Soils Sediments 7(6):411–417

    Article  CAS  Google Scholar 

  • Wintzingerode FV, Gobel UB, Staackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc National Academy Sci U S A 87:4576–4579

    Article  CAS  Google Scholar 

  • Xu Q, Jiang P, Xu ZH (2008a) Soil microbial functional diversity under intensively managed bamboo plantations in southern China. J Soils Sediments 8(3):177–183

    Article  CAS  Google Scholar 

  • Xu Z, Ward S, Chen C, Blumfield T, Prasolova N, Liu J (2008b) Soil carbon and nutrient pools, microbial properties and gross nitrogen transformations in adjacent natural forest and hoop pine plantations of subtropical Australia. J Soils Sediments 8(2):99–105

    Article  CAS  Google Scholar 

  • Yao H, He Z, Wilson MJ, Campbell CD (2000) Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 40:223–237

    CAS  Google Scholar 

  • Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty-acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323

    Article  CAS  Google Scholar 

  • Zelles L, Rackwitz R, Bai QY, Beck T, Beese F (1995) Discrimination of microbial diversity by fatty-acid profiles of phospholipids and lipopolysaccharides in differently cultivated soils. Plant Soil 170:115–122

    Article  CAS  Google Scholar 

  • Zhou J, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913–3919

    Article  CAS  Google Scholar 

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  1. Microbial Discovery Research Unit, Griffith University, Brisbane, Queensland, 4111, Australia

    Li Zhang

  2. Center for Forestry and Horticultural Research, School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, 4111, Australia

    Zhihong Xu

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Correspondence to Li Zhang.

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Zhang, L., Xu, Z. Assessing bacterial diversity in soil. J Soils Sediments 8, 379–388 (2008). https://doi.org/10.1007/s11368-008-0043-z

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