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Harvard Forest REU Symposium Abstract 2021

  • Title: Utilizing Traits-based Clustering Analysis to Find Genomic Evidence of Substrate Utilization Adaptation in LTER Warming Plot Isolates
  • Author: Theresa C Caso-McHugh (Massachusetts Institute of Technology)
  • Abstract:

    Anthropogenic climate change significantly influences many facets of life on Earth. A noteworthy example is the soil microbiome, which may be substantially affected by the warming expected to occur due to rising global temperatures. Microbes are key forces in the carbon cycle and produce extracellular enzymes that process and create soil organic matter (SOM). In studies conducted at the Harvard Forest Long-Term Ecological Research (LTER) site warming experiment, long-term warming of soils affects the community structure and genetic profile of microbial soil communities. Long-term warming has also been found to lower the quantity of SOM, alter the relative abundance of SOM’s various types in the soil, and increase the ability of soil microbes to degrade SOM, particularly more complex types. The aim of this project was to analyze the genomes from 42 different isolates that have been collected from both the control and warmed LTER plots for adaptive traits. A computational method detailed in Finn et al., 2021 clusters predicted genes from genome collections based on pairwise similarity. Each of the clusters is annotated with the protein group’s function, and a matrix of genomes with their associated trait data is produced. These methods are of particular relevance to the substrate utilization results seen in the LTER, because they have allowed me to determine genomic traits associated with the observed growth phenotypes seen in the substrate utilization data. Using the 42 genomes of various taxa sequenced from LTER warming plot isolates, I have utilized the clustering method detailed above to find traits-based evidence of adaptation in the LTER warming plot isolates, as well as analyzed the extent to which this evidence corroborates the substrate utilization changes observed previously. I expect that evidence of adaptation will be seen in the form of a statistically significant difference in the enrichment of traits related to substrate utilization between the warm plot isolates and the control plot isolates.

  • Research Category: Soil Carbon and Nitrogen Dynamics; Large Experiments and Permanent Plot Studies