Environmental Microbial Ecology

Prof Sanjay SWARUP's group studies how microbial communities or "microbiomes" and their life at interfaces of solid, liquid or air as "biofilms" drive the processes occurring in natural environments, such as, in surface freshwater or on plant surfaces. Member species of these communities share resources, such as metabolites or metabolic signals and they have diverse interactions with their hosts and immediate environments, all based on ecological principles. Due to mainstreaming of next generation DNA and RNA sequencing technologies, microbial ecologists can now directly sequence DNA/RNA of these community members, thus bypassing laboratory-based culturing, which can only lead to recovery of <5% of microbes in most environmental niches sampled routinely. Hence, most of the classical understanding of microbes that was based on cultured single species in free living forms, is now going through a paradigm shift.
Understanding of microbiome and biofilm processes, using a combination of ecological, life sciences and computational approaches can benefit different sectors, such as, agriculture, the environment or human health, among many others. Utilisation of these processes can lead to sustainable management interventions that are based on ecological principles.
Prof Swarup's research group studies metabolic and microbial processes from microscale to catchment or regional scales in two natural ecosystems surface freshwater systems and plant surfaces, for which they use both field- and laboratory-based studies. They have been studying the assemblages of microbiomes in biofilms and their functioning in sediment-water-plant interactions in urban waterways and reservoirs of Singapore; and in degraded tropical peatlands in Sumatra, where land use changes are leading to peat loss and greenhouse gas emissions by microbial oxidation. In these natural systems, they focus on the metabolites, which are the key drivers of interactions between microbial community members and their interactions with plant hosts.
Their plant-microbial studies are aimed at elucidating metabolites of plant origin that either actively exude into the immediate surrounding region of roots called the rhizosphere in both aquatic or soil systems or they are released from degrading plant materials in peatlands. In both freshwater and plant research, they have introduced modern life science approaches such as omics (technologies that elucidate cellular molecules) data-driven systems level analyses at the field scales, which is pushing frontiers in environmental sciences. Among these, they have taken leadership in the field of metabolomics, which involves the study of the metabolite complement of a given cell, tissue or exudate at any given time. In 2003, the team pioneered "rhizosphere metabolomics" to understand the role of metabolites in root exudates in influencing rhizosphere ecology. Integration of genomics data from nextgen sequencing of DNA and RNA with metabolomics data using computational approaches and in-house developed pipelines, is providing insights into the complex biological processes in both laboratory- and field-based studies.