Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods

Abstract

SummarySeveral biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizospheremicrobial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.

Use of Multiplex Terminal Restriction Fragment Length Polymorphism for Rapid and Simultaneous Analysis of Different Components of the Soil Microbial Community ▿

“…Similar results have been obtained previously for the same site for the fungal community using DGGE (2). In addition, several previous studies produced similar results, where habitat or soil type had a stronger impact on microbial communities than the individual plant species had (1,7,8,17,26,35). Again, a slight difference between the PCO plots generated from individual and M-TRFLP analyses may be attributed to the method used to identify TRFs.…”

“…Nucleic acid techniques have gained prominence recently because of their greater resolving power compared with methods such as phospholipid fatty acid analysis (33,35). Most of these molecular methods are PCR based and target the rRNA gene cluster.…”

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

“…Some other profiling techniques, such as community-level physiological profiling, restriction fragment length polymorphism, denaturing gradient gel electrophoresis, and phospholipid fatty acid profiling, have been applied to investigate the composition of bacterial community in contaminated aquifers near MSW composting sites (Röling et al, 2000;Tian et al, 2005;Yu et al, 2010). Among available DNA profiling techniques, TRFLP has been used to monitor structural changes of various soil microbial communities (Dunbar et al, 2000;Singh et al, 2006;Grant et al, 2007). However, to the best of our knowledge, this is the first report to investigate the change of the bacterial community in the MSW composting soil in response to anthracene amendment and subsequent biodegradation.…”

Influence of Long Term Irrigation with Pulp and Paper Mill Effluent on the Bacterial Community Structure and Catabolic Function in Soil

“…Soil microbial communities play a vital role in nutrient cycling, the decomposition of organic matter, carbon sequestration, soil genesis, soil structure and consequently water retention of the soil [2]. Therefore the study of soil community structure and function is an important aspect in assessing soil health.…”