Worldwide the resources for mineral fertiliser are diminishing. Growth of healthy, high-yielding crop plants requires a stable input not only of nitrogen and phosphorus, but also of sulfur (S). In natural ecosystems, nutrient cycling is mainly mediated by soil microorganisms, and much research is devoted to optimisation of microbial nutrient cycling for agricultural ecosystems. Several rhizosphere microorganisms are able to mobilise plant-unavailable soil S, and two bacterial genes that may be involved in the process are atsA, which encodes arylsulfatase, and ssuD which encodes alkanesulfonate monooxygenase. This study investigated the impact of agricultural practices on the overall rhizosphere microbial community and on functional diversity of S-mobilising organisms. Five wheat genotypes with different root-structures were inoculated with different strains of Azospirillum brasilense to determine the influence of wheat genotype and inoculation treatment in a continuous wheat field trial at Narrabri, New South Wales (Australia). Pot trials with vertisol soil from the field-site were carried out to investigate the effect of wheat variety and different inoculation treatments under controlled conditions. For the analysis of the ssuD gene diversity degenerate primers were designed and tested for specificity through cloning and sequencing. Both exploratory NMDS-Analysis and redundancy analysis (RDA) of fingerprinting profiles obtained by T-RFLP (Terminal restriction fragment length polymorphism) showed that wheat variety has a significant (p< 0.05) impact on the ssuD gene diversity in the rhizosphere. No significant wheat-genotype related effect could be found for the rhizosphere diversity of the16S rRNA gene. A comparison of two crop rotations, (field pea/sorghum/wheat or Indian mustard/sorghum/wheat) also showed clear differences between the 16S rRNA gene and ssuD gene diversity in the two treatments. In addition, an effect of the interaction between crop rotation (field pea-sorghum-wheat and mustard-sorghum-wheat) and two different N fertiliser levels was found on ssuD gene diversity but not on overall bacterial diversity. These findings indicate that cropping measures, including plant genotype, rotation and N-fertiliser level influence not only overall bacterial, but also ssuD gene functional diversity. This study proves that changes in ssuD gene functional and overall bacterial diversity are not congruent, thus pointing out the importance of a detailed analysis of the functional microbial diversity involved in nutrient cycling. Furthermore major environmental drivers correlated with ssuD gene diversity in wheat and canola rhizospheres across NSW and Victoria were assessed with T-RFLP fingerprints. The information about treatment-related changes, and geographical changes in ssuD gene diversity offers the first information that sulfonate-mobilising communities in soil can be influenced. The development of ssuD degenerate primers for pyrosequencing approaches offers a tool to identify key organisms and to measure their behaviour in rhizospheres and impact on plant nutrition. Optimising farm management by taking into account the genetic potential of rhizosphere microorganisms can help to tailor more resource-efficient crop production systems
