The Microbiome of a Tropical Reservoir

Last changed: 10 June 2021

A project to use environmental genome approaches to explore the hidden microbial diversity of a tropical reservoir.

Reservoirs contribute significantly to global nutrient cycling and greenhouse gas emissions, with many of the key environments located on the regions heavily impacted by the climate change, such as tropical zone. However, the taxonomic identities of the organisms contributing to these processes in the tropical reservoirs are poorly resolved, and the metabolic pathways and strategies that allow these organisms to thrive and perform biogeochemical functions are unknown. To address this, deep metagenomic sequencing and biochemical analyses were performed at two locations within a reservoir in Puerto Rico at four different depths.

In this project you will characterize the changes in biota across depths, and the metabolic functions associated with specific organisms. You will also employ metagenomic binning methods to assemble population genomes which will then be characterized for their metabolic traits. In the project you will combine bioinformatics with ecological theory to provide a first look into some of the unknown microorganisms found in eutrophic reservoirs.

Specific aims of the project

  1. To characterize community changes linked to depth profiles in a eutrophic reservoir
  2. To characterize the metabolic changes linked to chemical gradients over depth profiles
  3. To assemble and characterize novel genomes isolated from a eutrophic reservoir

Techniques and methods to be used in the project

  • Bioinformatics: metagenomic analysis (functional and taxonomic,  annotations), genome assembly, comparative genomics, python/R/bash programming
  • Ecology: multivariate analysis, statistical analysis, data-visualization, aquatic microbial ecology

Facts:

  • Main subject area: Biology
  • Level: Advanced (Master)
  • Length: 30hp/20 weeks or 60 hp/40 weeks
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