The broad areas of my research include microbial ecology and systematics. My main goal is to understand the dynamics of microbial communities in the natural environment and their response to human intervention. In particular, I am interested in studying the succession and biogeography of microbial communities in soil and how these distribution patterns are influenced by natural and human-induced changes to the soil ecosystem. In addition, I am interested in cultivation and characterization of representatives of those bacterial taxa which show characteristic patterns of geographical selection and/or soil-specific occurrence.
Soils represent one of the largest and most diverse reservoirs of prokaryotes in the biosphere. Induced by both natural and human perturbations, the soil ecosystem is under continuous stress and its microclimate undergoes regular shifts. These changes in-turn impact the existing microbial communities in the soil. With changes in community composition, the distribution patterns of the members of these microbial communities also change. By studying microbial communities in soils from different geographical locations, land management systems, and environments, it is possible to ascertain such distribution patterns.
My research uses gene sequence approach, supplemented with extensive bioinformatics and statistical analyses, phospholipid fatty acid profiling and soil physicochemical analyses, to understand the dynamics of microbial communities in different environments.
Based on the analyses of >11,000 bacterial 16S rRNA gene sequences from soils in Georgia, Kansas, and Michigan, I have identified clusters of closely related species with similar physiological properties, i.e., operational taxonomic units (OTUs), which show two characteristic patterns of distribution. While some of these OTUs are abundant and widely distributed in all soils, others are found only in certain soils exhibiting either geographical selection and/or soil-specific occurrence. Presumably, these OTUs play important roles due to their specific associations and abundance.
My research is aimed at testing this hypothesis and to investigate the contribution of these soil-specific bacterial taxa towards determining the activity and functions of the parent microbial community.
Approximately 5% of all prokaryotic cells on Earth inhabit the soils worldwide. However, only 0.1 to 1.0 % of all prokaryotic taxa have actually been cultured. Obviously, this unexplored majority has a huge impact on prokaryotic phylogeny, where entire lineages may be missing because of the inability to culture that group in the laboratory.
By using a guided-enrichment strategy that combines molecular tools and conventional microbiological cultivation methods, I am now cultivating bacteria with obligate growth requirements from different soils. Strategies such as the use of soil incubation chambers which simulate the natural environment/microclimate of the growing bacteria have been developed, standardized and used for the cultivation of members of the bacterial phylum Acidobacteria and Verrucomicrobia. We are now purifying these bacterial cultures for further characterization.
The environmental distribution of the acyl-homoserine lactone (AHL)-mediated gene expression systems amongst bacteria is poorly understood. Only ~2% of the total bacterial genera listed in the Bergey's Manual of Systematic Bacteriology are known to harbour the AHL producing species. Most of these species have obtained the luxRI homologs from other donors via horizontal gene transfer. A study describing the universal distribution of the luxRI homologs in the genus Aeromonas was recently published.
What is the ecological significance of QS in soil? QS seems to provide a mechanism in soil by which bacteria orchestrate and finetune their behaviour as a group rather than as individual cells, thereby coordinating gene expression and, consequently, the behaviour of the microbial population. However, little information exists as yet about the relevance of in situ AHL-mediated gene regulation in soil. Recent results indicate that cells in aggregates are much more tolerant of desiccation stresses on leaves than are more solitary cells. Thus, it is tempting to speculate that bacterial cells within aggregates may have the ability to modify their microenvironment in soils as well. Similarly, AHLs are known to stimulate the growth of bacteria when supplemented into the growth media. An understanding of the distribution of the quorum sensing genes in soil microbial communities will therefore lead to new insights into the dynamics of microbial communities. In addition, the industrial potential of such study can not be underestimated.