Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment

Fitness drift of an atrazine-degrading population under atrazine selection pressure

International audiencePseudomonas sp. ADP harbouring the atrazine catabolic plasmid ADP1 was subcultured in liquid medium containing atrazine as sole source of nitrogen. After approximately 320 generations, a new population evolved which replaced the initial population. This newly evolved population grew faster and degraded atrazine more rapidly than the initial population. Plasmid profiles and Southern blot analyses revealed that the evolved strain, unlike the ancestral strain, presented a tandem duplication of the atzB gene encoding the second enzyme of the atrazine catabolic pathway responsible for the transformation of hydroxyatrazine to N-isopropylammelide. This duplication resulted from a homologous recombination that occurred between two direct repeats of 6.2 kb flanking the atzB gene and constituted by the insertion sequences IS1071, ISPps1 and a pdhL homologous sequence. This study highlights the IS-mediated plasticity of atrazine-degrading potential and demonstrates that insertion sequences not only help to disperse the atrazine-degrading gene but also improve the fitness of the atrazine-degrading population

Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams

1. To assess the impact of metal mixtures on microbial decomposition of leaf litter, we exposed leaves previously immersed in a stream to environmentally realistic concentrations of copper (Cu) and zinc (Zn) (three levels), alone and in all possible combinations. The response of the microbial community was monitored after 10, 25 and 40 days of metal exposure by examining leaf mass loss, fungal and bacterial biomass, fungal reproduction and fungal and bacterial diversity.2. Analysis of microbial diversity, assessed by denaturing gradient gel electrophoresis and identification of fungal spores, indicated that metal exposure altered the structure of fungal and bacterial communities on decomposing leaves.3. Exposure to metal mixtures or to the highest Cu concentration significantly reduced leaf decomposition rates and fungal reproduction, but not fungal biomass. Bacterial biomass was strongly inhibited by all metal treatments.4. The effects of Cu and Zn mixtures on microbial decomposition of leaf litter were mostly additive, because observed effects did not differ from those expected as the sum of single metal effects. However, antagonistic effects on bacterial biomass were found in all metal combinations and on fungal reproduction in metal combinations with the highest Cu concentrations, particularly at longer exposure times.Portuguese Foundation for the Science and the Technology supported S. Duarte (SFRH/BD/13482/ 2003) and A. Alves (SFRH/BPD/24509/2005