Research
Overview:
We study the molecular biology and physiology of bacteria in the ocean to understand how their activities affect elemental cycling. Our lab focuses on heterotrophic bacteria and their consumption of carbon compounds (organic matter). Over 660 gigatons of dissolved organic carbon (DOC) are stored in marine waters, an amount equivalent to all the carbon stored as CO2 in the earth’s atmosphere. As the biogeochemical engines of the ocean, bacteria control the flux of this carbon pool, and even small changes in their activities can result in large impacts on ocean carbon chemistry. Bacteria have a major influence on whether DOC gets converted back to CO2 (remineralization) versus sinking to the bottom of the ocean where it can be stored for thousands of years or more. Therefore, bacteria not only affect the ocean’s carbon cycle, but also have a major influence on the amount of carbon in the earth’s atmosphere.
The diversity of genes, metabolic pathways, and regulatory networks bacteria use to process this carbon is staggering, and presents a significant challenge to connecting bacterial activities to biogeochemical and ecological function. Making these connections is critical for developing models of how bacteria affect marine carbon cycles, and predicting how those cycles may change due to human activities.
Our group investigates the molecular mechanisms within heterotrophic marine bacteria, including their encoding in bacterial genomes and the regulation of their expression, to better understand how their genomic makeup, metabolism, and physiology alter the flow of carbon through the cell and ultimately the marine environment. In particular, we work to make connections between bacteria and the carbon cycle by combining molecular and physiological studies with measurements of oxidation of carbon compounds and total respiration. Towards this aim we have two main approaches:
1) Laboratory studies of gene expression and metabolism using model
bacterial isolates.
2) Field investigations of microbial community genomics and
biogeochemical rates.
Current Research Projects:
Galapagos Marine Microbiome
Marine bacterioplankton communities of the Galápagos Islands. We are currently conducting a multiyear study in collaboration with the Marchetti lab to understand the diversity of microbes that inhabit the waters surrounding the Galápagos Islands. Metagenomic libraries are revealing the types of microbes and their ecological roles in this hot spot of marine carbon cycling.
EXPORTS: Coupling omics technologies to understand carbon production and removal at the oceans surface
EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led field campaign that will provide critical information for quantifying the export and fate of carbon using satellite observations and state of the art ocean technologies. The overarching goal is to understand how the carbon makes it to the twilight zone and deep ocean interior, and how long it stays there, which is vital to understanding present and future ocean ecosystems and global climate.
http://oceanexports.org/
Quantitative genomics
A significant challenge in microbial ecology is connecting the massive amounts of omics data we are currently able to obtain to physiological and biogeochemical rates, a challenge that must be met if we are to increase the predictive nature of microbial ecology. We are working to make these connections using quantitative genomic techniques coupled with in siturate measurements. This is being done first in the laboratory, using our
model OM43 clade isolate NB0046, to identify how the transcripts per cell concentrations for a given process (particularly growth and C1 metabolism) correlate with the corresponding process rates. These results will then be extended into the field, where we are employing both quantitative metagenomics and metatranscriptomics together with oxidation rate measurements.