Abstract
Cultivation-independent genomic approaches have greatly advanced our understanding of the ecology and diversity of microbial communities involved in biodegradation processes. However, much still needs to be resolved in terms of the structure, composition and dynamics of the microbial community in impacted ecosystems. Here we report on the RNA activity of the microbial community during the bioremediation process using RNA Temperature Gradient Gel Electrophoresis (RNA-TGGE). Dendrograms constructed from similarity matching data produced from the TGGE profiles separated a community exhibiting high remediation potential. Overall, increased Shannon Weaver Diversity indices (1–2.4) were observed in the high potential remediation treatment samples. The functionality of the microbial community was compared, with the microbial community showing the greatest organisation also showing the highest levels of hydrocarbon degradation. Subsequent sequencing of excised bands from the microbial community identified the presence of Gammaproteobacteria together with a number of uncultured bacteria. The data shows that RNA TGGE represents a simple, reproducible and effective tool for use in the assessment of a commercial bioremediation event, in terms of monitoring either the natural or augmented hydrocarbon-degrading microbial community.
Highlights
In the past, detection and analysis of bacteria in the environment was performed mainly by methods based on bacterial culture [1]
In terms of commercial bioremediation and the management of a bioremediation event, this technology has only been of limited value due to the length of time required for isolation [4]; on many occasions by the time a drop in hydrocarbonoclastic organisms has been observed [5], the bioremediation has already stalled
Developments in cultivation-independent genomic approaches have greatly advanced our understanding of the ecology and diversity of microbial communities [6]
Summary
Detection and analysis of bacteria in the environment was performed mainly by methods based on bacterial culture [1]. The separation or detection of small differences in specific DNA sequences can give important information about community structure and the diversity of microbes containing critical genes [4,7]. Molecular genetic fingerprinting techniques provide a pattern or profile of the community diversity on the basis of the physical separation of unique nucleic acid species. The general strategy for genetic fingerprinting of microbial communities consist of first, the extraction of nucleic acids (DNA and RNA), second the amplification of genes encoding 16S rRNA and third, the analysis of PCR products by a genetic fingerprinting technique [9,10]. Different amplified products can be separated by electrophoresis to create banding patterns known as a molecular fingerprint. Changes in the molecular fingerprint can be analysed to identify the microbial community structure in space and in time [11]
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