← Back to Search
Assessing Bacterial Diversity In Soil
L. Zhang, Z. Xu
Published 2008 · Biology
Save to my Library
Download PDFAnalyze on Scholarcy
Background, aim and scopeBiodiversity 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 featuresSoil 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 perspectivesIn 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.
This paper references
Cross-Polarized Magic-Angle Spinning (sup13)C Nuclear Magnetic Resonance Spectroscopic Characterization of Soil Organic Matter Relative to Culturable Bacterial Species Composition and Sustained Biological Control of Pythium Root Rot.
M. Böhm (1997)
Two Cases of Chromobacterium violaceumInfection after Injury in a Subtropical Region
J. Lee (1999)
Biolog analysis and fatty acid methyl ester profiles indicate that pseudomonad inoculants that promote phytoremediation alter the root-associated microbial community of Bromus biebersteinii
S. Siciliano (1998)
Molecular and Culture-Based Analyses of Prokaryotic Communities from an Agricultural Soil and the Burrows and Casts of the Earthworm Lumbricus rubellus
M. Furlong (2002)
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria
S. Joseph (2003)
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
G. Muyzer (1993)
A Comparison with Biolog and multi-SIR*
S. Chapman (2007)
Changes in soil fungal:bacterial biomass ratios following reductions in the intensity of management of an upland grassland
R. Bardgett (2004)
High diversity in DNA of soil bacteria.
V. Torsvik (1990)
Soil molecular microbial ecology at age 20: methodological challenges for the future
A. Ogram (2000)
The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology
A. Konopka (1998)
Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China
Y. Ge (2008)
Soil carbon and nutrient pools, microbial properties and gross nitrogen transformations in adjacent natural forest and hoop pine plantations of subtropical Australia
Z. Xu (2008)
Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities
C. Campbell (1997)
Phylogenetic analysis of gram-positive bacteria based on grpE, encoded by the dnaK operon.
S. Ahmad (2000)
Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions.
C. Kuske (1997)
Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis
E. Stackebrandt (1993)
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.
Ji-Zheng He (2007)
Characterization of bacteria that suppress rhizoctonia damping-off in bark compost media by analysis of Fatty Acid biomarkers.
A. Tunlid (1989)
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
W. T. Liu (1997)
Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods
E. Smit (2001)
Microbial Dynamics Associated with Multiphasic Decomposition of 14C-Labeled Cellulose in Soil
S. Hu (1997)
Molecular microbial diversity of an agricultural soil in Wisconsin.
J. Borneman (1996)
Diversity in the rhizobia associated with Phaseolus vulgaris L. in Ecuador, and comparisons with Mexican bean rhizobia.
G. Bernal (2001)
Cultivation-Dependent and -Independent Approaches for Determining Bacterial Diversity in Heavy-Metal-Contaminated Soil
R. Ellis (2003)
Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use
H. Yao (2000)
Assessing CLPPs using MicroResp™
S. Chapman (2007)
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
C. Woese (1990)
Effect of introducing genetically engineered microorganisms on soil microbial community diversity
A. Bej (1991)
PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods.
J. Stach (2001)
Structural and functional diversity of soil microbes is affected by elevated [CO2] and N addition in a poplar plantation
A. Lagomarsino (2007)
Novel techniques for analysing microbial diversity in natural and perturbed environments.
V. Torsvik (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
K. Nüsslein (1998)
Long-term fertilization regimes and diversity of an agricultural affect bacterial community structure soil in northern China
Y. Ge (2008)
Screening techniques for detecting allelic variation in DNA sequences
E. Lessa (1993)
Bacterial diversity of terra preta and pristine forest soil from the Western Amazon
Jong-Shik Kim (2007)
Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance
P. E. Axelrood (2002)
Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam.
J. Shen (2008)
Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica.
D. Saul (2005)
DNA fingerprinting techniques for microorganisms
M. Vaneechoutte (1996)
Effect of organic matter decomposition level on bacterial species diversity and composition in relationship to pythium damping-off severity.
M. Böhm (1993)
Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization
A. Derry (1998)
Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.
J. Zhou (1997)
CLPP and EEA profiles of microbial communities in salt marsh sediments
A. L. Costa (2007)
Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils
A. M. Ibekwe (2004)
Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils
L. Zelles (1992)
What type of diversity yields synergy during mixed litter decomposition in a natural forest ecosystem?
S. Chapman (2007)
Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization.
J. Garland (1991)
Functional biodiversity of microbial communities in the rhizospheres of hybrid larch (Larix eurolepis) and Sitka spruce (Picea sitchensis).
S. Grayston (1996)
Incubation time and media requirements of culturable bacteria from different phylogenetic groups
H. Mitsui (1997)
The use of colony development for the characterization of bacterial communities in soil and on roots
F. D. Leij (2004)
METHODS FOR ASSESSING THE COMPOSITION AND DIVERSITY OF SOIL MICROBIAL COMMUNITIES
G. T. Hill (2000)
Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval
R. Grosskopf (1998)
Comparison of Diversities and Compositions of Bacterial Populations Inhabiting Natural Forest Soils
E. Hackl (2004)
Brock Biology of Microorganisms
M. Madigan (1996)
Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes
S. Peters (2000)
Community-level physiological profiles of bacteria and fungi: plate type and incubation temperature influences on contrasting soils.
A. Classen (2003)
Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales.
U. Griepenburg (1999)
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
R. Amann (1995)
Comparison of CLPP and enzyme activity assay for functional characterization of bacterial soil communities
A. Winding (2007)
Microbial communities of continuously cropped, irrigated rice fields.
W. Reichardt (1997)
Functional diversity and community structure of micro-organisms in three arctic soils as determined by sole-carbon-source-utilization
A. Derry (2004)
Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation.
J. Borneman (1997)
DGGE/TGGE a method for identifying genes from natural ecosystems.
G. Muyzer (1999)
Selective influence of plant species on microbial diversity in the rhizosphere
S. Grayston (1998)
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys.
M. Sait (2002)
Soil microbial functional diversity under intensively managed bamboo plantations in southern China
Q. Xu (2008)
Molecular Techniques for Determining Microbial Diversity and Community Structure in Natural Environments
J. Theron (2000)
Effects of metam sodium fumigation on soil microbial activity and community structure
J. Macalady (1998)
Nitrogen limitation of microbial decomposition in a grassland under elevated CO2
S. Hu (2001)
Discrimination of microbial diversity by fatty acid profiles of phospholipids and lipopolysaccharides in differently cultivated soils
L. Zelles (2004)
Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis
J. Dunbar (2000)
Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil.
B. Nogales (1999)
Effect of compost on rhizosphere microflora of the tomato and on the incidence of plant growth-promoting rhizobacteria.
A. M. de Brito (1995)
Response of a Soil Bacterial Community to Grassland Succession as Monitored by 16S rRNA Levels of the Predominant Ribotypes
A. Felske (2000)
Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning
J. Dunbar (1999)
Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.
W. Liesack (1992)
Increasing the efficiency of the plate counting method for estimating bacterial diversity
G. M. Balestra (1997)
Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia.
J. He (2006)
The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.
R. Gupta (2000)
Opening the black box of soil microbial diversity
J. Tiedje (1999)
Antibiotic resistance: genetic mechanisms and mobility.
J. E. Olsen (1999)
Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies?
Y. Ge (2008)
Diversity and dynamics of microbial communities in soils from agro-ecosystems.
D. Buckley (2003)
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis.
F. von Wintzingerode (1997)
Saccharococcus caldoxylosilyticus sp. nov., an obligately thermophilic, xylose-utilizing, endospore-forming bacterium.
S. Ahmad (2000)
Determinants of Soil Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on Phospholipid Fatty Acid Profiles
D. Bossio (1998)
Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia
P. Janssen (2002)
Diversity of microbial communities
R. Atlas (1984)
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.
P. Hugenholtz (1998)
Phospholipid Fatty Acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals.
A. Frostegård (1993)
Phylogenetic Analysis of Microbial Diversity in the Rhizoplane of Oilseed Rape (Brassica napus cv. Westar) Employing Cultivation-Dependent and Cultivation-Independent Approaches
O. Kaiser (2001)
Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source.
M. L. Chow (2002)
Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis.
A. Gelsomino (1999)
Quantification of Ammonia-Oxidizing Bacteria in Arable Soil by Real-Time PCR
A. Hermansson (2001)
Effect of Phenylurea Herbicides on Soil Microbial Communities Estimated by Analysis of 16S rRNA Gene Fingerprints and Community-Level Physiological Profiles
S. El Fantroussi (1999)
Structure and function of alpine and arctic soil microbial communities.
D. Nemergut (2005)
ACIDOPHILIC HETEROTROPHIC BACTERIA ISOLATED FROM ACIDIC MINE DRAINAGE, SEWAGE, AND SOILS
N. Kishimoto (1987)
Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures
A. E. McCaig (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.
I. Marsh (1999)
Microbial Population Changes during Bioremediation of an Experimental Oil Spill
S. Macnaughton (1999)
This paper is referenced by
The isolation, characterization, and identification of a novel species of bacterium in the Enterobacteriaceae family from Kephart Prong, Great Smoky Mountains National Park
L. Dye (2017)
Some Issues and Challenges When Designing Laboratory Bioassays
U. Blum (2014)
RDX Degradation Potential in Soils Previously Unexposed to RDX and the Identification of RDX-Degrading Species in One Agricultural Soil Using Stable Isotope Probing
Indumathy Jayamani (2013)
Molecular investigation of bacterial communities on intravascular catheters: no longer just Staphylococcus
L. Zhang (2014)
Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands
S. Mishra (2013)
Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration
J. Li (2020)
Evaluation of constraints in bioremediation of weathered hydrocarbon-contaminated arid soils through microcosm biopile study
Kavitha Ramadass (2015)
Changes of soil microbial characteristics in saline-sodic soils under drip irrigation
S. H. Liu (2014)
Changes of soil bacterial communities in bamboo plantations at different elevations.
Y. Lin (2015)
Influence of plant species, location, and seasonality on rhizosphere bacterial communities in freshwater wetlands
Hakchul Lee (2016)
Metagenomics pro fi ling for assessing microbial diversity in both active and closed land fi lls
M. Zainun (2017)
Cedar and bamboo plantations alter structure and diversity of the soil bacterial community from a hardwood forest in subtropical mountain
Yu-Te Lin (2017)
Effects of single and mixed species forest ecosystems on diversity and function of soil microbial community in subtropical China
Y. Jiang (2011)
Changes in the Soil Bacterial Communities in a Cedar Plantation Invaded by Moso Bamboo
Y. Lin (2013)
Elevation gradient of soil bacterial communities in bamboo plantations
Y. Lin (2016)
Comparison of plant growth-promoting rhizobacteria in a pine forest soil and an agricultural soil
Víctor M. Flores-Núñez (2018)
Interactions between microbial community structure and pathogen survival in soil
E. Moynihan (2012)
Development of Biomarkers for Assessing I n Situ RDX Biodegradation Potential SERDP Project ER-1606 JUNE 2016
A. Cupples (2013)
Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing
S. Xie (2010)
Soil Organic Matter Dynamics and Structure
N. Nikolaidis (2013)
A Comparison of the Microbial Community and Functional Genes Present in Free-Living and Soil Particle-Attached Bacteria from an Aerobic Bioslurry Reactor Treating High-Molecular-Weight PAHs
Chu-Chun Yu (2019)
Impact of fire on soil gross nitrogen transformations in forest ecosystems
Y. Wang (2014)
Metagenomics profiling for assessing microbial diversity in both active and closed landfills.
M. Zainun (2018)
Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China
Hua Wei (2018)
Development of Biomarkers for Assessing In Situ RDX Biodegradation Potential
A. Cupples (2016)
Variations in Soil Bacterial Community Diversity and Structures Among Different Revegetation Types in the Baishilazi Nature Reserve
Jiaojiao Deng (2018)
Identificação de fungos dos gêneros Aspergillus e Penicillium em solos preservados do cerrado
M. Monteiro (2013)
Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with Salicornia for Treatment of Marine Aquaculture Effluents
Xiaona Ma (2018)
Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer
J. Hu (2011)
Phylogenetic characterization of bacterial populations in different layers of oak forest soil
Song-Ih Han (2015)
Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado
A. S. F. Araujo (2016)
Members of soil bacterial communities sensitive to tillage and crop rotation
C. Yin (2010)See more