Microbial diversity through time in sediment cores of Sider’s Pond

Sediment cores have provided us with a great deal of information about the past. By taking cores and analyzing the chemical and biological components of the sediments therein, we have been able to glimpse what life on Earth was like thousands of years ago and how it evolved in response to changing climate, ecological and geological conditions (Hays et al., 1976; Smol et al., 2005; Tierney et al., 2010; Zachos et al., 2001). Recently, with the development of next generation sequencing technologies, we have become better able to utilize a new component of these sediments in our reconstructions: DNA. (Giguet Covex et al., 2014; Redou et al., 2014).

While next generation sequencing techniques provide an advantage for analyzing the more degraded DNA found within sediment cores, the depositional environment controls how much DNA degradation occurs. For this reason, we have chosen a study site that exhibits many DNA preserving qualities. Our site, Sider’s Pond, is a small, meromictic kettle pond located in the town of Falmouth, MA just 550 meters from the open ocean. The pond’s meromixis is maintained by the balance of fresh groundwater inputs and salt water inflows during exceptionally high tides. These conditions combined with the pond’s location in a cold temperate environment, lead us to believe that its sediments likely provide a high quality archive of DNA. Here we propose to obtain this DNA by piston coring Sider’s Pond. Through next generation sequencing and our bioinformatics pipeline, we propose to use these DNA analyses to understand how disturbances, both natural and anthropogenic, affected the biological diversity and composition of Sider’s Pond over the last 1,000 years.

Given that the pond has experienced increased nutrient loading in a developed watershed, we expect commensurate change in species composition and genetic diversity. As the pond became increasingly eutrophied, we predict that species diversity decreased as fewer and fewer species could cope with this new, more extreme environment. We also predict that metagenomic diversity would decrease and become more specialized to cope with the environment.

We will use piston cores to sample the sediment in Sider’s pond.  Core chronologies will be inferred using 210Pb analyses, and these data will be correlated with microbial 16S rRNA sequence data from Illumina libraries of core sections that sample multiple time slices through the core.  Our goal is to test the hypothesis that microbial diversity shows a shift in composition associated with increased evidence for human impact as European settlers and suburbanization altered the nutrient input to the pond over the past few centuries.