Bacterial communities are key drivers of soil fertility and agriculture productivity. Understanding how soil bacterial communities change in response to different conditions is an important aspect in the development of sustainable agriculture. There is a desire to reduce the current reliance on high inputs of chemicals and fertilisers in agriculture, but limited data are available on how this might impact soil bacterial communities. This study investigated the bacterial communities in a spring barley monoculture site subjected to two different input regimes for over 12 years: a conventional chemical/fertiliser regime, and a reduced input regime. A culture independent approach was performed to compare the bacterial communities through 16S rRNA gene PCR-DGGE. PCO analysis revealed that the rhizosphere has a strong structuring effect on the bacterial community. Moreover, high inputs of agrichemicals lead to an increase of phosphorus level in the soil and a concomitant reduction of the bacterial diversity. These results may help to evaluate the environmental risks associated with agrichemical usage.

To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.

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