NSF Postdoctoral Fellow – Stanford Environmental Earth System Science
Category Archives: H2 Soil Microbiology
Soil microorganisms utilize H2 from the atmosphere so strongly as to comprise its largest sink; however, many fundamental questions surrounding this process remain. Which microorganisms possess the ability to utilize atmospheric H2 at such low concentrations (~500 ppbv)? What, if any, competitive advantage is gained via access to the atmospheric H2 reservoir? Which environmental processes most strongly influence the rate of H2 uptake by these microorganisms?
We hope to contribute to our understanding of these questions with our explorations into the microbiology of H2 uptake at Harvard Forest.
The presence (left) or absence (right) of aerial hyphae in Streptomyces may be linked to atmospheric H2 consumption
Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2). In a recent study (early view in Environmental Microbiology Reports), we probed the advantage of atmospheric H2 consumption to microbes and relationship between environmental conditions, physiology of soil microbes, and H2. First, we were interested in whether environmental isolates and culture collection strains with the genetic potential for atmospheric H2 uptake (a specific NiFe-hydrogenase gene) actually exhibit atmospheric H2 uptake. To expand the library of atmospheric H2-oxidizing bacteria, we quantify H2 uptake rates by novel Streptomyces soil isolates that contain the hhyL and by three previously isolated and sequenced strains of actinobacteria whose hhyL sequences span the known hhyL diversity. Second, we investigated how H2 uptake varies over organismal life cycle in one sporulating and one non-sporulating microorganism, Streptomyces sp. HFI8 and Rhodococcus equi, respectively. Our observations suggest that conditions favoring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.
It’s a wonderful piece (highlighted on the EAPS department website) about her first the AGU experience written through her uniquely balanced scientific and artistic perspective. For example, she writes, “Science, nature, life, emergence, and the universe have always inspired my art. And it is the unnecessary beauty of science that makes it deeply mysterious and so inviting to my mind… AGU was an incredible week of reconnecting with friends, advisors, professors, fellow researchers. It was also unexpectedly a way for me to connect a path to a foreseeable future where my two passions can be combined, perhaps even muddled, into an exciting career.”
I defended my thesis entitled “Field Measurement of the Fate of Atmospheric H2 in a Forest Environment: from Canopy to Soil” on October 4, 2012.
It was an incredible relief to finish the thesis document itself (link to .pdf). I really enjoyed preparing and giving my thesis defense presentation. It’s not often that one gets to present the culmination of six years of hard work and personal development to colleagues, family, and friends. I am grateful for mentorship from my advisor Ron Prinn, my thesis committee (Steve Wofsy – Harvard, Bill Munger – Harvard, Tanja Bosak – MIT, Colleen Hansel – WHOI, Shuhei Ono – MIT), and many others along the way!
I am continuing at MIT for a short (approximately 9 month) postdoctoral position with Ron Prinn to translate the work described in my thesis to publications. I am currently exploring possibilities for a postdoctoral position at the intersection of microbial ecology and atmospheric chemistry (trace gas cycles or aerosols) by searching advertised positions and writing fellowship proposals.
Presenting a poster on “Physiology of the microbe-mediated soil sink for atmospheric H2″ at ISME in Copenhagen, Denmark. Deepa Rao contributed greatly to this work.
Last week I attended ISME 14 (International Symposium on Microbial Ecology) in Copenhagen, Denmark. It was a delight to see the city – its juxtaposed giant modern, cool, sterile buildings surrounding the historic old city. More of a delight was unexpectedly running into friends from the MBL Microbial Diversity summer school (2010) and realizing they are now my colleagues.
Wind turbines and modern architecture outside of Copenhagen
The conference itself was quite good. I appreciated the range of content from very big picture and abstract to focused experimental projects. One message I took away from the community was a sort of -omics backlash, or perhaps whiplash, to the idea that generating more and more -omics data is the sole future for microbial ecology. It seems that presenters coming from both the -omics and experimental side were acknowledging the importance of both tools, and especially of using them together. Those seem to be a lot of tools for any one scientist to master, so I am encouraged that the tone was of collaborative holistic approaches for tackling scientific questions.
Tuborg beer and the Royal Copenhagen porcelain company
I really enjoyed a somewhat unique session. It was a discussion entitled “Frontiers in microbial ecosystem science: Energizing the research agenda” sponsored at this and other conferences by the US National Science Foundation. All sorts of issues were raised in a discussion of “what needs to be done” – what are the important topics and how should we advance microbial ecology. I was struck by how strong the arguments were that microbial ecology is important for understanding, and possibly mitigating, climate change. This is my main interest, but I often find the microbial ecology literature and research interests so focused on minute points (I think my own project included), that it is difficult to see the link between the microbial and global scales. At this session I learned that it is not only because it is difficult to do, but also because the funding agencies seem to push scientists to write grants in one or the other. It is difficult to be interdisciplinary (falling under more than one NSF department). It has been a (fun) challenge for me to try to get a foot in both atmospheric and microbial ecology science, and it was encouraging to hear from the community that the intersection of the two is valued.
Deepa Rao accepting the award from her academic advisor Sam Bowring
At the 2012 EAPS Student Awards Ceremony Deepa Rao received the Christopher Goetze Prize for Undergraduate Research for her thesis entitled : “Exploring the Microbe-mediated Soil H2 sink: A lab-based study of the physiology and related H2consumption of isolates from the Harvard Forest LTER.” The award recognizes “ innovative experimental design, care in data collection, and sensitive application of results to research problems.”
It has been a pleasure to supervise Deepa’s thesis research and her results will contribute to our research efforts to understand the mechanisms driving the soil sink for atmospheric H2. Professor Ron Prinn acts as the faculty advisor for both Deepa and I.
Topic: Soil microorganisms dominate the fate of atmospheric molecular hydrogen (H2 ) and comprise an estimated 75-80% of its global sink. Recent work has linked atmospheric H2 uptake to a novel high-affinity [NiFe]-hydrogenase expressed in active Streptomyces sp. cells , and is perhaps not driven by abiotic hydrogenases as was previously thought. Consequently, atmospheric hydrogen may be a 60-85 Tg yr−1 energetic supplement to microbes in Earth’s uppermost soil horizon. Continue reading →