End of Year Update

Well, I must admit that I have been remiss in updating my website, but things have been pretty busy. I've been working on book chapters, manuscripts, grant proposals, proposal and manuscripts reviews, and so on. As the year closes, I've been focused on examining denitrification in the uranium- and nitrate- contaminated subsurface at Oak Ridge, TN. The lab is taking a number of cultivation-based and molecular approaches to the characterization of denitrifying microorganisms in acidic- and circumneutral contaminated sediments. As part of this work, the Joint Genome Institute (JGI) has approved our previously submitted grant proposal and is working to sequence the genomes of six denitrifying bacteria isolated from the subsurface. Also, I was featured in the Mo Bio newsletter (fame reaches me at last).

In other news, the on-line versions of two of my book chapters are now available:

(1) Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis in "Handbook of Hydrocarbon and Lipid Microbiology", published by Springer.

(2) Compost Microbial Populations and Interactions with Plants in "Microbes at Work", also published by Springer.

Best wishes for a happy new year.
Cheers,
Stefan

Update, 2009

Well, I hope this isn't a trend - updating my site only annually! Anyway, some nice news to relate. First, I have a manuscript recently published in the Nature ISME Journal with my friend and colleague Jamie Foster on the subject of cyanobacteria in marine stromatolites. Currently, this article is freely available to download. Also, Jen Blank and I have published an article on the alkaline spring system in the Del Puerto Ophiolite (described in an earlier post). This article is available as a corrected proof. Also, quite exciting, as part of the research with my new laboratory, we have just described a new species of Geobacter, name Geobacter daltonii FRC-32. This article is now in press in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Amazingly, G. daltonii and its nearest neighbor G. uraniireducens Rf4, are highly similar by 16S rRNA gene sequence (98.1% similar), but have divergent genomes (21% by DNA-DNA hybridization analysis). This should be published and available in the near future.

New Publication in the ISME Journal

Well, it seems like I've only been posting when I get a manuscript published. We'll see how long this system can keep up!

Anyway, the new manuscript is:

Green SJ, Blackford CA, Bucki P, Jahnke LL and Prufert-Bebout L. 2008. A salinity and sulfate manipulation of hypersaline microbial mats reveals stasis in the cyanobacterial community structure. ISME Journal 2:457-470

In this study we examined the effect of salinity and sulfate manipulations on cyanobacterial community composition and relative abundance in hypersaline microbial mats. To do so, we employed several cultivation-independent molecular analyses, including: cyanobacterial-specific PCR-DGGE analysis and colony-PCR with cyanobacterial primers. We demonstrate that the relative abundance of cyanobacteria, as assayed by PCR, was not significantly affected by the manipulations. We demonstrate how colony-PCR with specific population primers can be used to monitor relative abundance without heavy sequencing. Furthermore, the overall cyanobacterial community was only modestly impacted by the salinity and sulfate manipulations, and the cyanobacterial populations that developed under the lowered sulfate and salinity conditions were most closely affiliated with other hypersaline microbial mat cyanobacteria.

This article is a featured article in the current issue of the ISME Journal, and is therefore freely accessible. But please contact me if you cannot get a copy.

Cheers,
Stefan

New Position and New Publication

Well, it has been a while since I updated my blog. My apologies, but the last few months have been quite hectic. I have taken a new position in the Oceanography Department of Florida State University (Tallahassee, FL). I am working for Dr. Joel Kostka on a Department of Energy project exploring bioremediation (or bioimobilization) and natural attenuation of Uranium-contaminated sites.

A paper from the project I was working on at NASA has just been published online at Environmental Microbiology. If you are interested, see: Smith et al. 2008. Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environmental Microbiology 10(2):386–394.
Hope you had a great new year.

Cheers,
Stefan

New Publication

I'm pleased to report that the final manuscript from my thesis has just been published online in the new "International Society for Microbial Ecology (ISME) Journal". This manuscript is the culmination of my doctoral research and describes how the rhizosphere effect can affect different microbial taxa differently.

The manuscript is now available in print. Enjoy!

Green, S.J., Michel Jr., F.C., Hadar, Y. and D. Minz. [2007]. Contrasting patterns of seed and root colonization by bacteria from the genus Chryseobacterium and from the family Oxalobacteraceae. ISME Journal. 1:291-299.

Kiva.org

I know this is off-topic, but I recently discovered this organization: www.kiva.org. It is an organization which allows you to extent credit via micro loans ($25 or greater) to individuals. It is not a charitable contribution, but rather a zero-interest loan to help people start or expand businesses. It is amazing to see how a little bit of money can go so far. I am not affiliated or paid by Kiva in anyway. I simply think it is a wonderful idea that appears to be implemented in a well-organized manner. Cheers, Stefan

New Position

My friend Dave chided me for not updating my blog frequently enough. I must admit it is true. It is hard to believe that it has already been over 3 months since I last updated it. Anyway, I now have a new position as a research scientist at the SETI Institute. I am still working at the NASA-Ames Research Center, however. I am currently working on a few different projects, including hypersaline microbial mats from Guerrero Negro, Baja, Mexico. The Exobiology Department at NASA-ARC is planning another trip to the salt production facility - Exportadora de Sal S.A. de C.V. - located in Guerrero Negro, Baja, California Sur, Mexico. This trip we're planning to study some of the higher salinity ponds (on the order of 150 ppt salinity) as opposed to the lower, but still hypersaline ponds of about 85 ppt.

I also have an ongoing project with Dr. Jen Blank of the SETI Institute to study the geology, chemistry and biology of ophiolite rocks found in certain locations in Northern California. Ophiolites are pieces of ocean crust that have been lifted up to the surface and exposed. When these rocks undergo weathering, a number of interesting abiotic chemical reactions can occur, and the water chemistry is highly modified. For example, in the system we are studying (see below), the pH of the water in local streams is roughly 9.0, and the water has high levels of carbonate and magnesium. In addition, we are finding unique microbial communities associated with these waters. More on this as the work progresses.
Cheers,
Stefan