Environmental Geomicrobiology
Making quantitative links between microbial diversity and biogeochemical cycles
Environmental Geomicrobiology
Making quantitative links between microbial diversity and biogeochemical cycles
Research areas
Our Motivation
Microorganisms influence the composition of the atmosphere, the cycling of elements within and through ecosystems, and the functioning of ecosystems. Microorganisms are also the most metabolically flexible, and the most taxonomically and evolutionarily diverse organisms on Earth. Yet deciphering how that diversity influences biogeochemical processes at larger scales is a challenge, because of the overwhelming complexity of microbial communities makes it difficult to quantify how microbial taxa assimilate and transform elements in the environment.
We use a combination of methods that blend traditions from microbial ecology including stable isotope probing, genomic, gene expression, and GC-MS tools to investigate how the diversity and physiology of microorganisms shape carbon cycling of ecosystems. Our research is derived primarily from field observations, as well as DNA and RNA stable isotope labeling experiments. We are focused on the microbial and biochemical mechanisms underlying the biogeochemical cycling of carbon, and its processing through microbial feeding chains.
Linking microbial diversity to ecological functions
We are interested in deciphering the identify of key microbial groups and or species that are responsible for important C and N cycling processes in nature. To this end, we often use a method called quantitative DNA stable isotope probing that measures the amount of assimilated 13C, 15N, or 18O (stable isotopes) by each and every microbial taxon that is detectable in an environmental sample. Because microbial communities are extremely diverse, this allows us to systematically investigate which microbes are more important than others for assimilation of specific C and N chemicals. Experimental designs allow for controlled testing of hypotheses that can be explored with further experiments or methods. Stable isotope labeling experiments are combined with GC-MS measurements of 13CO2 and 13CH4 to quantify C remineralization rates and estimate microbial carbon use efficiencies.
Microbial metabolism in early earth analog environments
At deep sea low temperature hydrothermal vents chemolithoautotrophic microbes are able to fix CO2 in the absence of sunlight, fueled by geological energy sources. These settings exhibit water-rock interactions and abiotic chemistry called serpentinization, whereby the abiotic synthesis of organic molecules occurs in a naturally exiting proton gradient. This is hypothesized to be analogous to the metabolism of the first cell and the chemolithoautotrophic microbes living at these settings today obtain energy through a similar carbon fixation and bioenergetic pathway. We are interested how this ancient bioenergetic pathway functions in simulated ferruginous environments characteristic of the Archaean and Hadean ocean, its potential role in the origins of life, and the mechanisms by which it supports life and ecosystems. We are able to reproduce "green smoker" hydrothermal chimneys under strictly anoxic conditions, allowing for testing hypotheses surrounding how this primordial metabolism could have supported microbial habitability of early earth habitats and potential exoplanets.
Energetic limits to life
We are interested in how life survives under persistent energy limitation, at or close to the energy limits to life, below the seafloor over relatively long timescales (thousands to millions of years). Deep subseafloor and subsurface habitats offer a unique opportunity to study how life can survive over geological timescales without receiving relatively young, freshly produced organic matter from oxygenic photosynthesis and in the absence of higher energy terminal electron acceptors for cellular respiration. Our interest in this topic has led us to investigate microbial communities subsisting in a wide range of energy-limited depositional settings spanning million-year-old deep sea red clay to sandy continental margin sediments. We are particularly interested in understanding how abiotic and biological hydrogen production supports ecosystems at thermodynamic conditions close to energetic limit to life.