Reading material: Darkness visiable, reflections on the underground ecology
Diversity is a critical environmental topic that concerned people from all walks of life are rallying around(Kennedy & Smith 1995).
Soil probably harbours most of our planet’s undiscovered biodiversity. Recent results from both, culturing and nucleic acidbased approaches indicate soil microbial diversity is even higher than previously imagined(Tiedje et al. 1999), the highly diverse bacterial communities with up to 50,000 or even up to millions of different 16S rRNA gene sequences. So far, it has remained unclear whether functional redundancy or a multitude of ecological niches and adaptive mechanisms governs the composition of soil bacterial communities(Zul et al. 2007).
Soil bacteria and fungi play pivotal roles in various biogeochemical cycles(BGC), they also play important roles in soil quality and plant productivity.
The methods for analysis composition and diversity of soil microbial has advantaged in the past years. Traditionally, taxonomic classification of bacteria has been determined based on metabolic, morphologic, and physiological traits. This approach emulates the methodological approach of botanists and zoologists; however, it requires the isolation and cultivation of individual bacterial species. Assessments of bacterial communities from a number of environments have found that the fraction of cells that may be cultured is not representative of the abundance or diversity of the microbial community present in the environment; it is often observed that direct microscopic counts exceed viable cell counts by several orders of magnitude. Trosvik et al.(1990)have suggested that typical soils may contain 104 species g-1, at least half(and perhaps as many as 95%) of which are likely to be unculturable by current techniques.Clearly, culture-based methodology is inadequate to serve the needs of microbial ecologists seeking to describe the diversity of bacterial communities in environmental samples, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil.(Kent and Triplett 2002)
Methods for acessing composition and diversity of soil microbial community
As the methods is very important for us to analysis the divertity of soil mirobialcommunity, I ‘ll introduce two main group methods (Hill et al. 2000, Kirk et al. 2004).
1. Biochemical-based techniques to study microbial diversity
1.1 Dilution plating and culturing methods.
1.2 Sole carbon source utilization patterns/community level physiological profiling for measuring microbial diversity.
1.3 Fatty acid methyl ester (FAME) analysis
2. Molecular-based techniques to study microbial diversity.
2.1 Guanine plus cytosine (G+C) content.
2.2 Nucleic acid reassociation and hybridization.
2.3 DNA microarrays.
2.4 PCR-based approaches.
2.4.1 Denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel. electrophoresis (TGGE).
2.4.2 Single strand conformation polymorphism (SSCP).
2.4.3 Restriction fragment length polymorphism (RFLP)/amplified ribosomal DNA restriction analysis (ARDRA).
2.4.4 Terminal restriction fragment length polymorphism (T-RFLP) Ribosomal intergenic spacer analysis (RISA)/ automated ribosomal intergenic spacer analysis (ARISA).
2.4.5 Highly repeated sequence characterization or microsatellite regions.
Althrough the methods is advantaged, it is difficult for us to know the diversity and composition of soil microbial community clearly. Not only did us lack of knowledge about the soil microbe, but also the soil environment is strongly infecting the diversity and function of soil microbial community (Yang 2000, Zul et al. 2007). There are many factor significantly effecting the diversity of soil microbe.
1. Soil bacterial diversity was found to be dependent on soil pH.
2. Site temperature, latitude also the important factor effect on the soil microbe.
3. Organic carbon content and C:N ratio is very important for soil microorganism.
4. The structure of the soil is effecting on the water content of soil, it’s relatting to the micro-environment of soil microorganism .
5. Plant diversity, it’s especially effect on the rhizospheric microorganism.
In the end , as soil is very important for human, many scientists also thought that the soil microbial diversity is a black box. Understanding the dynamics of microbial communities is at the heart of contemporary microbial ecology, and understanding of the soil microbial community is probably the most challenging because of the exceptionally high microbial diversity in soil and the complex and variable matrix in which soil microbes are embedded. Nonetheless, it is time to open the soil black box.
Reference
Hill, G. T., N. A. Mitkowski, L. Aldrich-Wolfe, L. R. Emele, D. D. Jurkonie, A. Ficke, S. Maldonado-Ramirez, S. T. Lynch, and E. B. Nelson. 2000. Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology 15:25-36.
Kennedy, A. and K. Smith. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant and Soil 170:75-86.
Kent, A. D. and E. W. Triplett. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annual Reviews in Microbiology 56:211-236.
Kirk, J. L., L. A. Beaudette, M. Hart, P. Moutoglis, J. N. Klironomos, H. Lee, and J. T. Trevors. 2004. Methods of studying soil microbial diversity. Journal of Microbiological Methods 58:169-188.
Tiedje, J., S. Asuming-Brempong, K. Nüsslein, T. Marsh, and S. Flynn. 1999. Opening the black box of soil microbial diversity. Applied Soil Ecology 13:109-122.
Torsvik, V., J. Goksoyr, and F. Daae. 1990. High diversity in DNA of soil bacteria. Applied and Environmental Microbiology 56:782-787.
Yang, Y. H. 2000. Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: a study with RAPD marker. Microbial Ecology 39:72-79.
Zul, D., S. Denzel, A. Kotz, and J. Overmann. 2007. Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity? Applied and Environmental Microbiology 73:6916-6929.