One man's trash is another's treasure: Understanding microbial diversity and community structure via metagenomic analysis in sediments near a sewage outfall

Just as different human communities may grow up depending on the type of jobs available (think Silicon Valley), microbial community structures depend on the resources available. One question researchers have asked is whether the response to resource availability is primarily reflected in shifting species, or if there is a “lottery” system, in which any species that satisfies a certain functional niche can enter and remain. Our project examines the functional and taxonomic structure of microbial communities along Greenwood Creek in the Plum Island Estuary Long Term Ecological Research (LTER) site. Due to the presence of a sewage outfall at the top of the creek, a strong gradient of nitrogen and other compounds has existed in Greenwood Creek for many years, which could have substantial effects on community structure. Since this nitrogen gradient co-occurs with a strong salinity gradient, we also took sediment samples from a nearby creek with a similar salinity gradient to put our findings in context. Following sampling, we extracted DNA from the soil and used “next-generation” sequencing technology to sequence millions of random DNA fragments from the community of microbes in the sediment. We will compare these sequences to DNA sequences in existing databases to determine the presence and abundance of different functional genes and taxonomic groups along the two creeks. This combination of field ecology, environmental biology, high-throughput sequencing and bioinformatics allows us to get a full picture of the otherwise invisible structure and function of microbial communities and address basic hypotheses regarding microbial ecology.