Conclusions. Community analysis by T-RFLP of 16S rRNA
genes proved to be a highly suitable and sensitive tool with
which to investigate the microbial community structures in
different particle size fractions and treatments. Three normalized
replicate samples of each fraction and treatment showed
comparable population profiles and grouped well in a cluster
analysis. Quantitative T-RFLP analysis has to be treated with
caution due to biases inherent to PCR amplification (53) and
variations in the copy number of the 16S rRNA gene in different
bacterial species (8). However, with awareness of these
limitations, T-RFLP analysis can be used for a semiquantitative
analysis of bacterial community structures (12, 47). In this
experiment, the microbial composition was mainly affected by
the particle size fraction and did respond to a lesser extent to
organic amendments. Therefore, our results demonstrate specific
microbe-particle associations that are affected to a smaller
extent by external factors such as fertilization or heavy metal
pollution (32). Knowledge of the microbial community structure
represents a first step toward understanding soil function
in response to the environment. In addition to community
structure, the analysis of functional genes within a given population
will greatly increase our comprehension of the role of
bacteria in soil processes important for geochemical dynamics
of elements, specifically carbon, nitrogen, and sulfur.
Conclusions. Community analysis by T-RFLP of 16S rRNAgenes proved to be a highly suitable and sensitive tool withwhich to investigate the microbial community structures indifferent particle size fractions and treatments. Three normalizedreplicate samples of each fraction and treatment showedcomparable population profiles and grouped well in a clusteranalysis. Quantitative T-RFLP analysis has to be treated withcaution due to biases inherent to PCR amplification (53) andvariations in the copy number of the 16S rRNA gene in differentbacterial species (8). However, with awareness of theselimitations, T-RFLP analysis can be used for a semiquantitativeanalysis of bacterial community structures (12, 47). In thisexperiment, the microbial composition was mainly affected bythe particle size fraction and did respond to a lesser extent toorganic amendments. Therefore, our results demonstrate specificmicrobe-particle associations that are affected to a smallerextent by external factors such as fertilization or heavy metalpollution (32). Knowledge of the microbial community structurerepresents a first step toward understanding soil functionin response to the environment. In addition to communitystructure, the analysis of functional genes within a given populationwill greatly increase our comprehension of the role ofbacteria in soil processes important for geochemical dynamicsof elements, specifically carbon, nitrogen, and sulfur.
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