In discussion: paper on ecosystem H2 flux measurement techniques

A manuscript I’ve been working on for a good chunk of time now, entitled “Ecosystem fluxes of hydrogen: a comparison of flux-gradient methods,” was just published to Atmospheric Measurement Techniques Discussions (view paper online). Our goal was to present a detailed experimental approach for measuring ecosystem fluxes of H2 and to test different so-called “flux-gradient methods” for calculating the H2 fluxes. Some common trace gas flux methods, e.g. eddy covariance, are not available for species like H2 that cannot be measured precisely at high frequencies (<1Hz). We hope this paper will help inform the design of future studies for which flux-gradient methods might be the best option for measuring trace gas fluxes.

Here are a couple videos on the instrument deployment(1) and design(2) for more information.

H2 flux measurements at Harvard Forest, MA

H2 fluxes were measured at Harvard Forest, MA

 

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Move to Stanford University!

Stanford life

Boston to the Bay Area! This October I began a new academic life at Stanford University where I am a NSF postdoctoral fellow working on questions regarding the microbiology underpinning large trace gas fluxes between the atmosphere and biosphere. I am working under the guidance of Professor Paula Welander who recently joined the Environmental Earth System Science faculty. I am looking forward to learning from her expertise and that of the rest of our group, and working in her brand new lab. With this new move, I also began a new social life, which (after many years in tech schools) included my first-ever college football game and tailgating. Should be a great couple of years.

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Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria

The presence (left) or absence (right) of aerial hyphae in Streptomyces may influence their atmospheric H2 consumption

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.

Much of this work was done with the help of Deepa Rao, an undergraduate researcher at MIT at the time who wrote an award-winning senior thesis on the topic and presented results in a number of venues, including at AGU 2012.

 

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AGU 2013 Session: Linking Microbial Communities and Biogeochemistry to Ecosystem Processes and Environmental Change

I am co-organizing a session at this year’s annual AGU meeting in San Francisco focusing on the microbial influence on atmospheric chemistry and ecosystem processes. We are bringing together a group with diverse disciplinary backgrounds and scientific approaches to share approaches and ideas. We hope to see you there on Friday!

Sessions: B51D (poster), B53D (oral), B54B (oral)

-search the sessions-

microbe-atmosphere

Section/Focus Group:

 

Conveners:

Laura Meredith, MIT, predawn@mit.edu

Catherine Febria, University of Maryland, febria@umces.edu

Jake Hosen, University of Maryland, hosen@cbl.umces.edu

Ed Hall, ed.hall@colostate.edu

Description:

Microbial communities are mediators of all biogeochemical cycles, controlling ecosystem responses to human-induced change. Advances in the molecular characterization of carbon and microbial communities have produced novel datasets that capture large spatiotemporal dynamics. Researchers are now able to address questions about the interactivities of nutrient flux from the microbial community to ecosystem scale. This session will highlight ressearch on the functional role of microbial communities in ecosystem-level biogeochemistry. We encourage contributions that investigate C, N, P, small-scale experiments and syntheses that can inform understanding of ecosystem-level responses to environmental change.

Index Terms:

[0439] BIOGEOSCIENCES / Ecosystems, structure and dynamics
[0470] BIOGEOSCIENCES / Nutrients and nutrient cycling
[0465] BIOGEOSCIENCES / Microbiology: ecology, physiology and genomics
[0428] BIOGEOSCIENCES / Carbon cycling

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Award for best PAOC PhD thesis

At the EAPS 2013 Student Awards ceremony held last week I was awarded the Carl-Gustaf Rossby Prize for best PhD thesis in PAOC for the year! I’m humbled to be a part of the list of recipients of the award over the years. May this be more motivation to finish writing and submitting my papers…

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Deepa blogs about AGU 2012

Connecting H2 consumption to life cycles of soil microbes

Deepa’s AGU Poster “Connecting H2 consumption to life cycles of soil microbes”

Read Deepa Rao’s Blog Post

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.”

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AGU Talk 2012

I was thrilled to give a talk this year at AGU in the full-day, highly subscribed Biosphere-Atmosphere Greenhouse Gas Fluxes in Terrestrial Ecosystems IV session organized by Paul Stoy, Christopher Williams, and Todd Scanlon. I’m looking forward to publishing these results very soon!

AGU 2012 Talk

AGU 2012 Talk

 

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Thesis Defense!

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 .pdfCarl-Gustaf Rossby Prize for best PhD thesis in PAOC for the year). 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.

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ISME 14 – The power of the small

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.

 

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Deepa receives Goetze Prize for Undergraduate Research

 

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 H2 consumption 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.”

Click here for a description of her Senior Thesis Presentation 

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.

 

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