Hiring lab technician / manager

We are recruiting a lab technician / lab manager to join the lab this spring!

The selected candidate will support soil ecology research in in our lab in the Department of Soil Science. They will work closely with the principal investigator and other lab members, managing lab activities and performing research. Our lab is a positive work environment, with lots of potential for growth in this position. UW-Madison is an excellent place to work, and the city of Madison, WI is a wonderful place to live.

Applications are due April 15, 2016.
The position is posted here on the UW Madison jobs site [http://www.ohr.wisc.edu/Weblisting/External/PVLSummaryApply.aspx?pvl_num=85987]

First Month of being an Assistant Professor

Yesterday marked my first month as an Assistant Professor in the Department of Soil Science at UW-Madison! Coming from the fantasyland of a Californian postdoc, I quickly remembered my Canadian instincts, and that wearing three scarves and two pairs of pants was basic common sense in -24°C weather. Fortunately, it’s also beautiful here, the frozen lakes are great for skating (and ice fishing!), and even frigid weather doesn’t stop the bike-crazy Madisonians. It’s been a bit of a whirlwind, but I think I might be coming to the end of the forms I need to fill out, and took the occasion to reflect on what this first month has been like. There are four elements that stand out so far:

IMG_0548

My new office – featuring the amazing Ergotron keyboard and monitor arms and the Canadian Soil Science Society 2016 calendar (February features beautiful Gleyed Gray Luvisols)

Decision fatigue: I have probably never made so many potentially important decisions in such a short time. They’re all decisions I am lucky to have to make – which office to choose (I went with the south-facing windows), which health care options I want (complicated for a Canadian), which courses I am going to teach and when (intro enviro and graduate soil micro next spring) – but each one takes time to reflect on and choose, and sometimes it’s hard to find the data needed to make the best decision.

Diplomacy: It always takes a while to figure out how things operate at a new workplace. The Soil Science department and other colleagues have been awesome – everyone has been so welcoming and helpful – and I have been enjoying getting to know people, learning where the department’s strengths and challenges lie, and just getting a sense for how things work here.

Dollars (hopefully): Yup, I’ve already been submitting grants! My second NSF DEB pre-proposal went in at the end of my second week here, and I’m working on proposals for Hatch, EMSL, JGI, and DOE to submit within the next two months. I actually quite enjoy writing grants, (which is good, because it seems like in this funding climate, one has to submit a lot of them)!

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My office is in King Hall, which is >125 years old!

(Self)-Determination: It is really awesome to “be my own boss”. (Okay, so technically there are a whole host of people with authority over me, but it feels that way.) For example, we got promising reviews back on my final (yay!) Ph.D. paper this week. During my postdoc, I would have waited until the weekend to work on them, but now all my academic responsibilities fall under the same hat again.

I’m really enjoying this time of reflection on how to best set up the lab — establishing systems for electronic lab notebooks and lab inventory management, working on big picture strategy for the lab’s future, and building the heart of the lab: our team!  I’d love to hear from other professors: what are you glad you did when starting your labs, or what decisions might you have made differently?

Effects of char additions to soil on microbial community composition and CO2 emissions

We’ve posted a pre-print version of our paper, Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter, at bioRxiv. The paper is currently under review at ISME J. I’m really pleased to have it submitted, since it is the final piece of my Ph.D. research. (The other part of Chapter 4, the 3-part stable isotope partitioning method, was recently published in Nature Communications.)

Briefly, we added either charred or fresh corn stover to a field soil, and then monitored CO2 emissions and microbial communities over 12 weeks. There are several elements to the paper that I think are pretty cool, but I’ll just focus on what is perhaps my favourite figure from the paper here:

Figure_5_Whitman

This figure represents the response of the microbial community to 350°C charred corn stover (i.e., “pyrogenic organic matter”, or PyOM) on the x-axis, and fresh stover on the y-axis. The scale indicates whether the microbes increased or decreased in relative abundance (“log2-fold change”), as compared to the soil with no organic matter additions, where 0 indicates no change, +1 indicates a doubling in relative abundance, +2 indicates a quadrupling in relative abundance, and so forth. Each point indicates a single microbial “operational taxonomic unit” (OTU) (which you can think of as something like a species, as Robert Edgar discusses here), coloured by the phylum to which they belong – you can see that Proteobacteria and Bacteroidetes are among the strongest responders. The bars on the sides indicate the relative density of the OTUs – you can see that most are grouped around 0, indicating that most OTUs don’t change very much. The black line indicates a 1:1 relationship, where the response to the PyOM is the same as the response to the stover. Any OTU above this line responds more to stover, and any OTU below responds more to PyOM. Thus, the OTUs in the blue-shaded circle respond mostly to stover, those in the pink circle respond to PyOM, but not to stover, and those in the purple circle respond strongly to both. We compare the responses 12 days after the PyOM or stover were added (left panel), and 82 days after (right panel). You can see that some microbes respond immediately to the stover additions, while the response to PyOM takes longer to emerge.

For me, the most exciting about this data is what we can infer from how the OTUs respond to each amendment in isolation vs. together. For example, 70% of the OTUs that respond to PyOM by day 12 also responded to stover. These microbes might be responsible for decomposing the easily-mineralizable C found in PyOM – while much of PyOM is difficult to decompose, there is a fraction of it that is rapidly mineralized to CO2. I am also very interested in the OTUs that respond to PyOM, but not to stover. For example, 7 OTUs from the phylum Gemmatiomnadetes show this response, and 2 of them are among the top 10 most abundant PyOM-responders. These microbes are likely responding to something unique about the PyOM – e.g., its polyaromatic C compounds or its effect on soil pH (although PyOM only increased pH by ~0.75). Focusing on these types of microbes in future studies could help us better understand the effects of PyOM additions on soil C cycling.

Recruiting Graduate Students in Soil Ecology at UW-Madison

We are recruiting 1-2 new graduate students (MS or PhD) to join our Soil Ecology lab starting as soon as January 2016. Students will work with Dr. Thea Whitman as an advisor to develop a project investigating soil microbial ecology and organic matter biogeochemistry in the context of climate change. Potential projects include: (1) Investigating the effects of boreal forest fires on soil microbial communities (2) Determining the mechanisms behind complex, 3-way carbon cycling interactions between soil, plants, and fresh or charred organic matter using a novel stable isotope approach (see our 2015 paper in Nature Communications). The ideal candidates would have a strong interest in soil ecology and experience in at least some of the following: field or laboratory research, microbiology, soil science, biogeochemistry, ecology, statistical analyses, and bioinformatics (Python and R).

Students will be enrolled in the Soil Science graduate research program at the University of Wisconsin-Madison, and the position will be a 50% Research Assistantship that will include a stipend of $1,768/month; stipends run from July 1 to June 30.  Health care benefits are included in the appointment and are dependent on the individual’s needs. UW-Madison has a strong culture of collaboration across fields, and the selected graduate students will interact with researchers from diverse fields, including microbiology, geography, forest ecology, agronomy, and environmental studies.

Applications should be submitted to twhitman@wisc.edu by December 1, 2015, and include a letter describing your interest in the position, a CV, a record of grades (e.g., copy of transcript), and the name and contact information for three references. Successful applicants will need to apply to the Soil Sciences graduate program through the UW Madison graduate school and be accepted (requires GRE scores and TOEFL scores (if applicable), official transcripts, and letters of recommendation).

(Charley Harper)(Illustration by Charley Harper)

Paper in Nature Communications: Three-source dual-isotope partitioning

I am excited to announce that my three-source, dual-isotope partitioning approach has been published at Nature Communications! The paper describes a new technique to separate one pool (e.g., total soil CO2 emissions) into its three different sources (e.g., roots, soil organic carbon, and added plant litter), but still just using two stable isotopes (e.g., 12C/13C or 14N/15N). I’ll leave the details for the paper, which is open-access, but, briefly, it hinges on adding a double-treatment, where the experimental designs are identical, except one component has a different isotopic signature in treatment A vs. treatment B. (The figure below illustrates this graphically). The R code for analysis is published with the paper, so I am hoping it will be easily accessible to people who will find it useful – I think it could be an extremely powerful tool to help advance our understanding of element cycling in systems with more than two components.

A little story behind the paper: this review process was actually a pretty great experience. All the reviewers offered constructive comments, and I really felt like the end manuscript was much stronger after going through several rounds of revisions. One funny thing about this paper is related to the fact that I came up with the method out of necessity: I needed to separate soil, biochar, and plant root-derived CO2 in my field trial, but conventional isotope partitioning couldn’t handle three sources, and I didn’t have access to the resources to partition them by adding a radioactive isotope or something like that. I remember the moment I figured it out, and excitedly scrawling it on the chalkboard in the nook at the end of the hall in Bradfield while showing my labmate. If I had just been trying to showcase a new method, I probably would not have designed a field trial – notoriously messy – to demonstrate it! In my case, though, I just needed the method in order to do the field trial, and finish my Ph.D.. Hence, I’ll be really excited to start applying this new method in my new lab, in order to answer complex and exciting questions about three-(or more!)-way interactions in biogeochemical systems at finer scales.

Shading corresponds to illustrative values representing the isotopic composition (in arbitrary units) of each end-member (A, B and C) or the combined isotopic composition for a given system. Dashed lines along a single combined isotopic composition represent possible partitioning solutions for the combined sources. (a) Given an isotopic composition (here, a shade of grey representing an isotope value of 59) for a two-source system (rectangle between A and B) there is only one solution (that is, 38% from A and 62% from B), but for the three-source system (triangle of A, B and C), there is a range of solutions, shown along the dashed red line, which does not allow the three sources to be conclusively quantified. (b) By designing a system with two treatments, where the third component is present in two different isotopic forms that are otherwise identical (two leftmost triangles, as indicated by different shades for C1and C2), the range of solutions (dashed lines) will intersect at one point, which allows the total emissions to be partitioned conclusively into three parts (intersection of dashed lines in right triangle, indicating 25% A, 25% B and 50% C.

Shading corresponds to illustrative values representing the isotopic composition (in arbitrary units) of each end-member (A, B and C) or the combined isotopic composition for a given system. Dashed lines along a single combined isotopic composition represent possible partitioning solutions for the combined sources. (a) Given an isotopic composition (here, a shade of grey representing an isotope value of 59) for a two-source system (rectangle between A and B) there is only one solution (that is, 38% from A and 62% from B), but for the three-source system (triangle of A, B and C), there is a range of solutions, shown along the dashed red line, which does not allow the three sources to be conclusively quantified. (b) By designing a system with two treatments, where the third component is present in two different isotopic forms that are otherwise identical (two leftmost triangles, as indicated by different shades for C1and C2), the range of solutions (dashed lines) will intersect at one point, which allows the total emissions to be partitioned conclusively into three parts (intersection of dashed lines in right triangle, indicating 25% A, 25% B and 50% C.