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Assessing Bacterial Diversity In Soil

L. Zhang, Z. Xu
Published 2008 · Biology

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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.
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