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Harvard Forest REU Symposium Abstract 2011
- Title: Using computational genomic methods to address microbial community function within experimentally warmed soils
- Author: Tara Mahendrarajah (University of Massachusetts Amherst)
- Abstract:
Long-term soil manipulations at the Harvard Forest are being used to investigate the role of microorganisms on community structure within an experimentally warmer world. Microbial communities are a major component of soils and are therefore intrinsically linked to the global carbon cycle. Evidence suggests that global climate change has the potential to alter microbial community composition and subsequently lead to communities that are able to use a wider range of carbon sources within the soil – ultimately altering the global carbon cycle. Therefore, it is imperative to understand the association between microbial species diversity and function within soil ecosystems. The primary objective of this research project focused on evaluating microbial community composition using laboratory and computational techniques. Soil samples collected at four time points from a long-term experimentally warmed plot in Barre Woods were processed and had the DNA extracted using molecular laboratory procedures. Following the final soil sampling period in August, 100 samples will be pooled and sent for sequencing in order to obtain metagenomic data that will be analyzed for microbial species taxonomy counts and classification, and gene prevalence and function. In addition, a secondary goal of this study was to develop strategies to effectively integrate analyses of species diversity and microbial function, in order to understand how community dynamics may differ in warmed soil. The National Ecological Observatory Network (NEON) collected a soil sample from Prospect Hill, and provided us with metagenomic data in the form of amino acid and nucleotide sequence files. Ribosomal 16S rRNA sequences were processed through the Ribosomal Database Project Classifier and revealed that the soil sample was dominated by members belonging to the phyla Acidobacteria (28%) and Proteobacteria (22%). This suggests that soil on Prospect Hill is composed of a plethora of bacteria involved in several ecologically significant processes including chemical decomposition, nitrogen fixation, and carbon cycling. The amino acid metagenomic data was processed through the Basic Local Alignment Search Tool, which compared the query sequences to an extensive database of protein domains of known function. We found that 16% of the proteins present within the NEON soil sample are involved in carbohydrate metabolism and energy production, suggesting that a majority of genetic material within microbial communities is allotted to biomass degradation. Methods used to evaluate microbial diversity and community function, as performed in this study, will be used in parallel with enzyme activity assays, in future analyses of data collected from the Barre Woods warming plot, in order to understand changing community dynamics in response to a warming climate.
- Research Category: Biodiversity Studies; Physiological Ecology, Population Dynamics, and Species Interactions
