The Thrash lab investigates the relationships among and between aquatic microorganisms and their environment. We combine cultivation independent methods (e.g., metagenomics, metatranscriptomics, and single-cell genomics) with high throughput culturing, physiology, and microbial genomics, and comparisons to chemical and physical measurements. We seek to understand why microorganisms occur where they do and what they are doing there. See our Publications page to get a sense of our recent work.

High throughput culturing

We conduct high throughput cultivation (HTC) experiments using tailored, defined media from a number of environments, including the coastal Gulf of Mexico, Lake Michigan, the Eastern Tropical North Pacific, and the San Pedro Ocean Time Series. We also collect water chemistry and microbial community data from the source water to evaluate cultivation efficacy and refine our defined media recipes. To date, we have isolated over 400 microorganisms, many of which represent some of the most abundant taxa in the sampled environments. Prominent examples include the first isolation of a freshwater SAR11 (a.k.a. LD12) representative, members of SAR11 subclade IIIa, OM43, OM182, SAR92, SAR116, Limnohabitans, Polynucleobacter, Actinobacter acIV, and many others.

Bacterioplankton characterization

TEM of dividing Fonsibacter ubiquis cells, obtained by V. Celeste Lanclos

Isolates obtained via HTC that have prominent roles in their community, are phylogenetically novel, and/or have the potential to contribute to our understanding of ecosystem functions are investigated further. We conduct a battery of physiological experiments to determine optimum growth conditions, comparative genomics to facilitate metabolic reconstruction, and genome-informed tests of metabolic capability. Isolates from the SAR11, SAR116, and OM252 subclades are currently under investigation, and we have many others on deck!

Evolution of salinity tolerance in SAR11

We have NSF-funded support for a collaboration with Liz Kujawinski (WHOI) to quantify the mechanistic differences between sister clades of SAR11 that have evolved to inhabit environments with very different ionic strength regimes. We are using a combination of field observations and culture-based experiments with (meta)transcriptomics and metabolomics. The field portion of this work has concluded, with sequencing and pure culture work in progress.

Microbial ecology of the northern Gulf of Mexico “dead zone”

ESOM of GOM hypoxia metagenomic bins (and cover of the 2017 mBio issue in which our paper appeared)

We have collaborated with Nancy Rabalais (LSU/LUMCON), Olivia Mason (Florida State University), and Brett Baker (University of Texas) in deploying a wide range of cultivation-independent techniques to learn about the microbial communities and genetics associated with the generation and maintenance of seasonal bottom water hypoxia on the Northern Gulf of Mexico shelf region (see lab blog entries for 2013 and 2014 cruise information). New work will begin in mid-2020. The main page will have updates.

Isolating new microbes capable of metabolizing greenhouse gasses

We have funding from the USC Provost’s office that supports high-risk research to isolate novel microorganisms (targeting Archaea) that can metabolize greenhouse gasses like nitrous oxide, methane, and carbon dioxide. We are collaborating with Jan Amend’s lab (lead team) and Adam Smith’s lab. Research will begin in earnest in 2020 upon acquisition of new anaerobic and microaerophilic cultivation equipment. Stay tuned!

Other projects

Microbial degradation of photooxidized hydrocarbons. A one-year study with Christoph Aeppli’s lab (lead team) to determine how natural weathering of oil affects microbial biodegradation. This work is funded by the National Academies of Science, Engineering, and Medicine Gulf Research Program.

Microbial ecology of the Mississippi River. An ongoing project that makes use of samples collected via a citizen science effort in collaboration with OAR Northwest.

last updated 12/20/19