A sulfurous symbiosis: Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett salt marsh
Here's the story behind my recent publication (with many talented coauthors) on the pink berries, the marvelous, macroscopic microbial aggregates of the Sippewissett.A bit of background:
The wild microbe rarely eats alone. The microbial world is a jungle far more exotic than those we can see (metabolically and phylogenetically, at least), one rife with fierce competition, intimate cooperation, and intricately inter-dependent food webs. Eavesdropping on the metabolic conversations of uncultured microbes, though, remains a major technical challenge. It requires tools to navigate the world from the microbe's-eye view. Your binoculars just aren't gonna cut it... (image source ) |
Let's get one thing straightened out:
(image source: my own, here, and here) |
My first encounter....
And people wonder why I think sulfide smells like beautiful summers and nostalgia? (image source: my own) |
(image source: my own) |
Me, awfully excited and really "diving-in" to the project. Can't remember how many times TA Annie Rowe and others had to fish me out of the mud that summer! (image source: Melissa Cregger :) |
Berries: an MBL Microbial Diversity legacy.
My obviously-not-to-scale cartoon of berry spearing with oxygen microsensors. |
Peering into the pink berries with a dissection microscope (real color!). Pink blobs are islands of purple sulfur bacterial cells. (image source: Verena Salman) |
The hypothesis! Purple sulfur bacteria in pink, sulfate reducing bacteria in green. (image source: my own, modified version of Figure 9 from our paper) |
Project launch: Team berry 2010
The first few weeks at the MBL course were bonanza of microbial excitement for me as a huge metabolism geek. My mornings were spent trying to drink from the fire hose of information in lecture, followed by afternoons of lab, then dinner, more lab, and finally trying to piece together the day's ideas over beers.
"Drinking from a fire hose" - another gem from PhDComics |
To track the flow of our isotopically labelled sulfur, we planned to image thin sections of the incubated berries using nanometer scale secondary ion mass spectrometry (nanoSIMS), an instrument commonly used by the Orphan lab for studying anaerobic methane oxidizing consortia.
Using the nanoSIMS to blast sections of pink berries with focused cesium beam (~50nm spot size) and generate spatial maps of isotopic and elemental abundance. (image source: my own). |
The nanoSIMS beast in its subterranean lair @ the Caltech Microanalysis Center. (image source: my own) |
Can't stop, won't stop... the side-project that ate my thesis.
After returning to Davis, passing my qualify exam and wrapping up prior projects, I was determined to get back to berries but wasn't sure exactly how. Victoria suggested that she could include berries in a collaborative NSF proposal on the biogeochemistry of tightly coupled sulfur cycling consortia (along with David Fike, Greg Druschel and Jesse Dillon). When their funding came through, it held out the safety net I needed to work on berries full time. With approval from Victoria and my co-advisers at Davis, I jumped!Returning as a TA to the MBL Microbial Diversity course in 2011, I had a chance to conduct follow up isotope experiments, and collaborate with course student and co-author Verena Salman on developing species-specific FISH probes to identify the spatial arrangements of the two berry symbiotic. Since then, I've followed up on our initial metagenomic sequencing to reconstruct near-complete genomes for the two berry symbionts, demonstrating the genetic potential for a complete sulfur cycle.
David Fike, Greg Druschel, and their groups. With high resolution geochemistry equipment aboard our homemade raft, we were able to link our existing microbiological measurements with microscale geochemical signatures in the berries.
(image sources: my own) |
Conclusions:
FAQ:
- My naturalist's answer is: because they're the pink, charasmatic macrofauana of the microbial world. They're nifty, and we don't know what they do. But seriously...
- Microbial metabolism is the engine that drives the nutrient (biogeochemical) cycling that shapes the health of both our planet and our bodies.
- However, many key transformations in these cycles are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches.
- The berries provide a tractable, reproducible model microbial consortia for developing methods to eavesdrop on these otherwise cryptic metabolic conversations between the wild microbes.
- Understanding the biosignatures (e.g. sulfur isotopic fractionation) produced by microbial communities like the pink berries improves our ability to interpret the rock record and construct models of ecosystem function in both ancient and modern environments.
Thank you:
Through this project, I've had the privilege of working with truly amazing people and making life-long friends. The author list and acknowledgement are just the tip of the iceberg in terms of people who have contributed to this project in one way or another. You all know who you are; I feel so lucky to have gotten to know and work with you. THANK YOU!This project was started as grass-roots style, curiosity-driven student research, and as such, the funding for it has been fairly eclectic. I want to take a moment to acknowledge those organizations that have supported this kind of research and made my work possible.
Funding to the MBL Microbial Diversity course from:
- Howard Hughes Medical Institute
- Gordon and Betty Moore Foundation (#2493)
- National Science Foundation (DEB-0917499)
- US Department of Energy (DE-FG02-10ER13361)
- NASA Astrobiology Institute (NAI)
- NSF (EAR-1124389 & EAR-1123391)
- Gordon and Betty Moore Foundation (#3306)
- National Science Foundation Graduate Research Fellowship
- UC Davis Dissertation Year Fellowship
- P.E.O. Scholar Award
- NAI/APS Lewis and Clark Fund in Astrobiology
- NSF Doctoral Dissertation Improvement Grant (DEB-1310168)