Microbial ecology of terrestrial and subterrestrial ecosystems

Research Focus and Target Areas

Communities, not total biomass, control net process rates and drive the biogeochemical cycles that sustain the biosphere. Thus, descriptions of the temporal and spatial dimensions of microbial community structure and the complex gene expression patterns that underlie trophic interactions are fundamental to a more complete understanding of our biosphere.

Our research interests are focused on (I) the adaptation of microbial community structure and activity to external stress factors, and (II) the role microorganisms play in biogeochemical cycles. To aid our research we currently focus on three defined terrestrial microbial systems:

  • The lack of electron donors in deep subsurface systems,
  • the stress of land use change and intensive agriculture on soil systems, and
  • the extreme conditions in sediments under acid mine drainage. 

Current Projects

BioEnergy from the Deep Subsurface

BioEnergy from the Deep SubsurfaceIncreasing demand for natural gas in the United States has resulted in the development of unconventional sources of this valuable resource, including coalbed and shale methane. When we started to investigate biogeochemical cycles in deep subsurface systems we were confronted with the question, what enables microorganisms in the deep subsurface to break down coal polymer in a sustainable way without the continuous replenishment of electron acceptors. During ongoing research we gained a deeper understanding how to convert unmineable coal to methane in-situ. Through the development of novel technologies that stimulate the bottle necks within the metabolic chain of endogenous coal bed methane microbial communities, we intend to provide long-term biotechnology-driven solutions for enhancement and sustained production of natural gas. More details on Burcu Ünsal's page.

Hotspots of Soil Diversity and Activity

Hotspots of Soil Diversity and ActivityWe recently initiated a Microbial Observatory in the Amazon rainforest, focused on documenting the diversity of Amazon rainforest soil bacteria (collaborators see below). In this four-year project it is especially imperative to characterize the microbial diversity of the Amazon rainforest, because this ecosystem is under great threat. An increasing demand for grain, fibers, and biofuel has accelerated the conversion of the Amazon rainforest to agriculture, creating a new frontier of deforestation of 1 million sq. km.  This shift is predicted to have significant effects on global emissions of greenhouse gases, global warming, soil degradation, and water resources. Understanding the consequences of this conversion will require insight into the diversity of rainforest microbes and their response to deforestation. This project will establish baseline estimates of soil bacterial diversity at broad coverage in the Amazon rainforest, and will determine how microbial diversity changes in response to ecosystem conversion from rainforest to agriculture.  To answer these questions, this research combines extensive surveys of bacterial diversity using novel high-throughput approaches such as 454 pyrosequencing technology targeting a suite of phylogenetically informative markers to achieve “ultra deep sequencing” of the soil microbial community. This will be coupled to selective isolation and analyses of two contrasting bacterial groups, the Burkholderia and Acidobacteria, which will serve as proxies of the group-level genetic diversity. High-throughput identification in addition to extensive surveys documenting functional gene diversity both employ DNA microarrays. More details on George Hamaoui's and Kyung-Hwa Baek's pages.

Brendan Bohannan at the University of Oregon
Jorge Rodrigues at the University of Texas at Arlington
James Tiedje at Michigan State University

Acid Mine Drainage and Perchlorate Bioremediation

Acid Mine Drainage and Perchlorate BioremediationAcid mine drainage causes environmental contamination worldwide. We investigate an acid mine stream that is self attenuating. This project seeks to understand the biogeochemistry of Fe(III) and SO42- reduction, and their role in the natural attenuation of extreme acidity in a long-abandoned pyrite mine, Davis Mine, in western Massachusetts. Isolation of acidophilic sulfate reducers parallel sulfate reduction kinetics and the determination of gene dosage for the functional keystone gene. More details on Caryl Ann Becerra's and Brendan Murphy's pages.

Perchlorate is a wide spread groundwater contaminant. This project investigates the microbiology of a novel process to entirely break down perchlorate in contaminated ground and surface waters to innocuous products. We have enriched a microbial consortium capable of coupling elemental sulfur oxidation with perchlorate reduction. This stable consortium not only successfully degrades perchlorate using S0 as the sole electron donor, but also does this at NaCl concentrations typical of ion exchange brines, currently a common removal technique. More details on Teresa Conneely's and Nazita Gamini's pages.

Sarina Ergas, University of Massachusetts Amherst

Open Positions

Please refer to the contact page for information on current open positions.