JOB POST: Postdoc position in microbe-mineral interfaces

The Hanson and Chan laboratories at the University of Delaware are seeking motivated geomicrobiologists in training to work at the microbe-mineral interface. Our NSF funded project (award # 1244373) seeks to understand how the phototrophic bacterium Chlorobaculum tepidum both produces and consumes extracellular elemental sulfur. This is a new and rapidly developing system in microbe-mineral interactions. The project utilizes (and provides extensive training opportunities in) anaerobic microbial genetics, systems biology, electron microscopy, and nanoscale geochemical analysis methods. Our laboratories are located at the Delaware Biotechnology Institute (www.dbi.udel.edu), the newly constructed Interdisciplinary Science and Engineering Laboratory (www.udel.edu/iselab/), and we will make extensive use of advanced capabilities in UD’s BioImaging center (bioimaging.dbi.udel.edu). UD offers a number of programs for professional development and networking specifically targeted at postdoctoral researchers. We are committed to providing an environment where enthusiastic and talented postdoctoral researchers can advance their careers. 

Tom Hanson (tehanson@udel.edu)

Clara Chan (cschan@udel.edu) 

New Experimental Field Site? Maybe….

Just finished a lengthy grant proposal effort. For those of you who don’t know it can be an arduous process; coming up with new ideas, thoroughly researching them, writing the 15 pages of the proposal, getting all the collaborators to agree on it, and making sure you have the other 15 pages of junk that is required all formated correctly. Always difficult at best, painful at worst. At the end you are never quite sure whether to declare victory or accept defeat. Then it disappears for 9 months, and just when you have forgot about it, it either reemerges as a project that you have to figure out how to really accomplish, or it collects dust until the next RFP deadline. I’m happy to say, I am now in the waiting faze.

Anyway, this is one of the sites we chose to propose to work in, when I hiked up to check out this place last week on a ridgetop about 2 miles from my office. Definitely would be great to get the opportunity to visit this place more often! Here is a link to the Project Summary for those that are curious. Thanks to Aimee Classen, Greg Hurst, and Emily Austin for all there help in putting this together!

Job Post: Ph.D.-positions in Biodiversity Research (Netherlands Institute of Ecology)

The Deutsche Forschungsgemeinschaft (DFG) funds a large-scale grassland project “The Jena Experiment” (www.the-jena-experiment.de) on the relationship between Biodiversity and Ecosystem Functioning (Grant FOR 1451). On a 10ha field site in Jena, more than 470 grassland plots have been established where plant diversity is manipulated to measure the effect of diversity on multi-trophic interactions and nutrient cycling. Applications are sought for the following position:

Ph.D. position (PhD-TE-013060) - A short description of the position is given below.

The project is an international collaborative research effort of 11 universities and research institutes in Germany, three universities in Switzerland, two in The Netherlands as well as universities and research institutes in Austria, France and Canada. All Ph.D.-students will benefit from an already existing experimental set up and the interaction with other PhDs and researchers in an international research team. The ability to speak and write German will be appreciated but is not indispensable for candidates fluent in English. A full description of the project and more details about the positions can be found under: www.the-jena-experiment.de

Selection of applicants starts 10. April 2013 and continues until positions are filled. Starting dates depend on the position on offer. Applications – in a single pdf-file only – should be sent to the addresses given below.

Ph.D.-positions in Soil/Plant Ecology

We offer a PhD position in Wageningen at the department of Terrestrial Ecology at The Netherlands Institute of Ecology (NIOO-KNAW, Prof. Wim van der Putten), in close collaboration with the Soil Quality department at Wageningen University (Dr. Gerlinde De Deyn) and the department of Ecology and Biodiversity at Utrecht University (Prof. George Kowalchuk).

The research focuses on the role of plant-soil feedbacks in the relation between plant (trait) diversity and ecosystem functioning. Plant species influence the composition of soil biota and these influences have feedback effects to the role of plant species in plant communities and the ecosystem processes that emerge from these communities. Previous research has shown that plant species differ in the strength and direction of plant-soil feedback. However, the roles of different soil microorganisms (bacteria, fungi) have yet to be elucidated.  In the present project, you will relate the composition of soil microorganisms to plant traits in plant communities and consequent ecosystem functioning. We intend to investigate to what extent plant species create specific rhizosphere communities and how these communities differentially impact on plant growth. Candidates should have a MSc degree in soil biology/ecology, microbiology or plant ecology. We are looking for candidates with:

• good ability to think conceptually and quantitatively
• good knowledge of plant-soil (biotic) interactions
• experience with working with soil organisms
• affinity with state-of-the art soil molecular biological techniques
• excellent ability to communicate in English, both orally and in writing
• experience with writing scientific papers is highly appreciated
• good organisational skills and ability to work independently
• ability to work in multidisciplinary research teams

Contact: Dr. Gerlinde De Deyn, Dept. of Soil Quality, Wageningen University, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands. Email: gerlinde.dedeyn@wur.nl

Applications: Please send your application with vacancy number (PhD-TE-013060), including a cover letter detailing your motivation for and expectations from this position, your CV including a summary of your past research, and contact information for three references to vacature@nioo.knaw.nl. The closing date is 10^th of April 2013.

Modeling microbial communities and two new papers

There is a lot of emphasis these days in my field on figuring out how to best translate our results from gene-based microbial community studies, into predictive mathematical models of (eco)system functions.  While still not easy, the new methods we now have on hand for microbial community analyses do finally allow us to collect enough data, on enough replicates, that it is no longer impossible.

Thanks to the work of a talented scientist I got to work with at ORNL named Gouping Tang, I can finally say we (mostly Gouping) have been able to make the leap from our data sets to mathematical models.  These two new papers take the data and theoretical model we proposed in a paper led by Tom Gihring in late 2011, and develop full mathematical simulations of our experimental systems.  These data are from a large scale field test we worked on with numerous collaborators that demonstrated the use of emulsified vegetable oil to stimulate reducing conditions in a contaminated groundwater system. This is somewhat bittersweet though as due to funding changes, these may be some of the final opportunities our lab will have for work on metal bioreduction in groundwater microbial communities that I have toiled on ever since leaving graduate school and coming to Oak Ridge.

Here are the citations with the links to PDF files.

Tang, G., Wu, W. M., Watson, D. B., Parker, J. C., Schadt, C., Shi, X., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor–Microcosm Tests and Model Development. Environmental Science & Technology.  (Tang_EST_MicrocosmModel)

Tang, G., Watson, D. B., Wu, W. M., Schadt, C., Parker, J. C., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron donor–Model Application to a Field Test. Environmental Science & Technology. (Tang_EST_FieldModel)

Off to Asilomar Fungal Genetics Conference on Tuesday…

Just finished up my poster for the Fungal Genetics Meeting at Asilomar coming up on Tuesday and dropped the file off at the printer.  Very excited to attend for the first time.  I’ve been hearing great things about this conference for years and it certainly looks to be a great location.  Finally got the excuse I needed to add yet another meeting to my schedule when I was asked to help organize a session on metagenomics.  Looking forward to the session, conference and the chance for a stroll or two on the beach!

Job Post: Two Postdoctoral Positions in Australia with Ian Anderson and Jeff Powell

Ref 114/13 Postdoctoral Research Fellow in Eucalypt – Fungal Associations, Hawkesbury Institute for the Enivronment 

For a position description and application instructions, go to: 

http://bit.ly/XJzE0D

This is an exciting opportunity to undertake research related to an Australian Research Council Discovery (ARCD) grant (‘Switching partners: a driving force for tree productivity in a changing environment?’). Many eucalypts form mycorrhizal associations with two different and diverse groups of fungi, a trait shared by only a few ecologically and economically significant tree species. While each of these groups of fungi are important contributors to global primary productivity, the benefits that trees derive from these dual associations are not fully known. This research will explain the basis for this diversity and determine whether trees will make greater demands of their partners in future climates.

Applicants should have expertise within the broad areas of plant-microbe associations, molecular microbial ecology, soil science, or related fields. A background in the generation and analysis of next-generation sequence data will also be well regarded.

This is a full time, fixed term (2.5 years) appointment based at our Hawkesbury campus.

Remuneration Package: Academic Level A $91,289 to $96,851 p.a. (comprising Salary $77,140 to $81,840 p.a., plus 17% Superannuation and Leave Loading).

Position Enquiries: Dr Jeff Powell, +61 (0) 2 4570 1093 jeff.powell@uws.edu.au
Closing Date: 21 March 2013

__________________________________________

Ref 161/13 Postdoctoral Research Fellow in Plant-Fungal Associations, Hawkesbury Institute for the Environment

For a position description and application instructions, go to:  

http://bit.ly/XlK7mL

This is an exciting opportunity to undertake research related to an Australian Research Council Discovery (ARCD) grant (Plant : fungal symbioses in Australian forests – new perspectives using laser microdissection). The main goal of this project is to understand the importance of interactions between basidiomycete fungi and the roots of understorey Ericaceae shrubs, and determine the potential for these fungi to form mycelial linkages between the understorey shrubs and overstorey trees in Australian forests.

The successful applicant will have experience in the use of microscopy and/or molecular microbial ecology technigues in studying plant:microbe associations.

This is a full time, fixed term (2 years) appointment based at our HAwkesbury campus.

Remuneration Package: Academic Level A $91,289 to $96,851 p.a. (comprising Salary $77,140 to $81,840 p.a., plus 17% Superannuation and Leave Loading).

Position Enquiries: Professor Ian Anderson, Director of Research, +61 (0) 4570 1993 or  i.anderson@uws.edu.au
Closing Date: 21 March 2013

Cool toys = Hot data? (part 1)

As part of our work on a the SPRUCE experiment, we have been quantifying the various microbial activities in a peat bog in MN. We have also been lucky enough to explore some new approaches to improve our research methods as part of this. Two of these efforts involve some pretty cool science ‘toys’. Im going to discuss one below, and save the other for a future post.

One of the ways we are trying to accomplish the above, is to understand more thoroughly how the enzyme activities of microorganisms may vary in response to a range of temperatures. These enzyme potential analyses have been around for years and allow us to understand how microbial activity contributes to the cycling of carbon and nutrients under various specific stimuli. These work are possible now, thanks to work in the past by Bob Sinsabaugh, Don Zak, and many others. We accomplish this by adding peat (or soil) to mixtures that contain a fluorescent dye labeled substrate compound, that the enzymes the microorganisms secrete into the soil (or peat) can breakdown. When the fluorescent label is liberated from the the substrate compound, it fluoresces, and we can quantify it. If we want to quantify this response over a range of temperatures, it usually involves hunting up a host of large incubators in which to do the studies. At most usually 4 or 5 of these are available at any given time. Last month, Meg Steinweg and I visited the lab of collaborator Joel Kostka at Georgia Tech that had a cool toy that allowed us to do this much more efficiently.

This is a gradient heat block (much like those used for PCR, but bigger) that allowed us to fairly precisely conduct our experiments. It is a custom designed tool that was machined from a block of solid aluminum, and has an electric heater attached on the high temperature end, as well as ports that allow circulation of a chilled glycol solution on the low temperature end. To this they added holes at an even spacing that we can add test tubes too. This creates a precise gradient of temperatures over a range of about 0 to 40 degrees Celsius (~32 to 104 degrees Fahrenheit) to do our enzyme assays. Once we set the temperature, this gradient was repeatable each day as seen below (there are three separate measurements in the graph, taken over two days, that largely overlap!)

This science ‘toy’ is translating to some really cool data sets for our SPRUCE projet. In SPRUCE we will be using a belowground heating system to warm up the peat in the bog to understand how all the carbon stored in the peat will respond (a paper on this technology is here). This could have implications for the potential of future climate change to feedback and cause additional releases of carbon dioxide and methane to the atmosphere from bogs and other ecosystems. To get an initial handle on this in laboratory experiments, we used the ‘toy’ above to look at three different microbial enzyme responses tied to carbon, nitrogen and phosphorus cycling using peat collected from Minnesota at different times of the year. Typically we would expect responses leading to a rather smooth exponential curve showing increased activity with increased temperature (up to the point where the enzymes become denatured and activity drops off). Somewhat surprisingly, Meg’s work using this tool, looks to be showing two different responses in at least some samples. In an example of one of our Beta-Galactosidase activity assays below, we see a linear response at lower temperatures (below about 15C), and what seems to be a separate linear response at higher temperatures (above about 15C), instead of the expected exponential curve. While this graph is only showing a set of data originating from one peat sample, for one enzyme activity, collected at one time of year… When we look at a range of such samples, Meg’s data is showing trends that vary by depth in the peat, and time of year the samples were taken.

Im not sure exactly how these data should be interpreted yet (we need more of them of course), but what it could suggest, is that what we are seeing is enzyme responses from multiple communities of microorganisms, that exist separated by space (depth in the peat) and time (season in which the samples are collected). That would be pretty cool to prove, as it might effect the interpretation of the seasonal responses we will see in Minnesota when we heat up the bog. This is not unprecedented, as we saw similar phenomena when I was studying alpine tundra communities in Colorado during graduate school. However, this could justify more winter trips to MN, which believe it or not, I enjoy!

We have recently began some work collaborating with a group that does sensor development at ORNL, that is related to the SPRUCE project objectives. Hopefully in the near future I will be able to blog about it as well. However, as of now, while im convinced we are producing some really cool toys, the project has yet to produce any cool data. When the data arrives I am hoping to post about it in the near future.

Job Post: Mycology postdoc with Andrew Miller and Illinois Natural History Survey

The Illinois Natural History Survey is offering a competitive Post Doctoral Research Associate position for 2 years
which includes a generous salary, benefits, funds for research expenses, and the opportunity to live in glorious East-Central Illinois. Research in Mycology that would add new directions and build on my lab’s strengths include endophytes and environmental sampling, although I am open to additional suggestions. Applications are due March 15, 2013. Please contact Dr. Andrew Miller (amiller@inhs.illinois.edu) if you are interested to discuss this position further.

Please see the position announcement at:
http://wwx.inhs.illinois.edu/opportunities/post-doctoral/postdoc-sponsors/

Job Post: Postdoctoral opportunity in Jim Spain’s Lab at Georgia Tech

Postdoctoral Fellowships – Microbial Physiology/Ecology

Postdoctoral positions are available to explore metabolic diversity among bacteria that synthesize and degrade organic compounds. The emphasis is on discovery of novel enzymes and catabolic pathways using microbial physiology, genomics, and molecular biology. The successful candidate will work in close collaboration with a team using systems biology techniques, physiological experiments, enzymology and analytical chemistry to discover new enzymes and harness them to synthesize new compounds. The laboratory is well equipped with analytical instruments and all the facilities needed for cell cultivation and molecular biology. Applicants should have a recent PhD and a strong background in microbiology, biochemistry, molecular biology, environmental engineering or microbial ecology. The successful applicant will be expected to design and execute laboratory experiments, analyze quantitative data, write and communicate results to the scientific community.

Send CV to: Jim Spain jspain@ce.gatech.edu Environmental Engineering Program, 311 Ferst Dr., Georgia Institute of Technology, Atlanta, GA 30332-0512, 404-894-2265.

Job Post: Graduate Student/Postdoctoral openings In Anna Rosling’s new lab in Uppsala

Multiple Positions in the Department of Evolutionary Biology, EBC, Uppsala University exploring life strategies in the Archaeorhizomycetes

-PhD position in Soil fungal ecology
-Post doc fellowship

Deadline for application is March 15, 2013.

More information as well as links to the position advertisements on her homepage:
http://www.ebc.uu.se/Research/IEG/evbiol/research/rosling/