New Articles

Well, as usual, a long time has passed since I have updated my site. A few new publications:

Gihring, T. M., Z. Gengxin, S. C. Brooks, J. H. Campbell, D. B. Watson, C. C. Brandt, Z. Yang, C. S. Criddle, K. Lowe, W. A. Overholt, W.-M. Wu, T. Mehlhorn, J. E. Kostka, S. J. Green, and C. W. Schadt. 2011. A limited microbial consortium is responsible for longer-term bioreduction of uranium in a contaminated aquifer. Appl Environ Microbiol In press.

Gihring, T. M., S. J. Green, and C. W. Schadt. 2011. Massively-parallel rRNA gene sequencing demonstrates substantial potential for biased community comparisons due to sample size dependence and diversity index underestimation. Environ Microbiol In press.

Kostka, J. E., and S. J. Green. 2011. Microorganisms and processes linked to uranium reduction and immobilization, p. 117-138. In J. F. Stolz and R. S. Oremland (ed.), Microbial Metal and Metalloid Metabolism: Advances and Applications. ASM Press, Washington, D.C.

Foster, J. S., and S. J. Green. 2011. Microbial diversity in modern stromatolites, p. 383-405. In V. C. Tewari and J. Seckbach (ed.), Stromatolites: Interaction of Microbes with Sediments, vol. 18. Springer-Verlag, Heidelberg, Germany.

Other than that, things are moving along at the DNA Services Facility. We have just purchased an Ion Torrent, and are looking to purchase another next-gen sequencer by the end of the year. Will keep you up to date.

Cheers,
Stefan

New Job / New Manuscript

Well, I now have a new position as Director of the DNA Services Facility at the University of Illinois at Chicago. Please feel free to continue to contact me for DGGE advice or other, and also feel free to contact me regarding any work you might be interested in having my facility perform. Our website is: http://www.rrc.uic.edu/dnas [Sorry for the advertisement!]. My official new email address is: GreenDNA@uic.edu

I also have a new manuscript in press that will hopefully be published soon in Soil Biology and Biochemistry:

Khodadad, C.L.M, A.R. Zimmerman, S. Uthandi, S.J. Green, and J.S. Foster (2010) Taxa-specific changes in soil microbial community composition induced by pyrogenic carbon amendments. Soil Biology & Biochemistry, DOI 10.1016/j.soilbio.2010.11.005

Best wishes,
Stefan

New Manuscripts

Well, a few new manuscripts and a book chapter to relate:

Myshrall, K.L., Mobberley, J.M., Green, S.J., Visscher, P.T., Havemann, S.A., Reid, R.P. and Foster, J.S. 2010. Biogeochemical cycling and microbial diversity in the thrombolitic microbialites of Highborne Cay, Bahamas. Geobiology. 8(4):337-354.

Green, S. J., and L. L. Jahnke. 2010. Molecular investigations and experimental manipulations of microbial mats: A view to paleo-microbial ecosystems, p. 183-206. In J. Seckbach and A. Oren (ed.), Molecular Investigations and Experimental Manipulations of Microbial Mats: A View to Paleomicrobial Ecosystems, vol. 14. Springer, Heidelberg, Germany.

Wu, W-M, Carley, J., Green, S.J., Luo, J., Kelly, S.D., Nostrand, J., Lowe, K., Mehlhorn, T., Carroll, S., Boonchayanant, B., Lofler, F.E., Watson, D.B., Kemner, K.M., Zhou, J., Kitanidis, P.K., Kostka, J.E., Jardine, P.M., Criddle, C.S. 2010. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environ. Sci. Technol. 44: 5104–5111.

Butler, C., Clauwaert, P., Green, S.J., Verstraete, W. and Nerenberg, R. 2010. Bioelectrochemical perchlorate reduction in a microbial fuel cell. Environ. Sci. Technol. 44:4685-4691.

Hope all is well. Cheers, Stefan

Manuscript on denitrifying bacteria from the contaminated subsurface

Well, good news here. Our manuscript describing denitrifying bacteria isolated from a contaminated subsurface environment has been accepted for publication in Applied and Environmental Microbiology. In addition, the manuscript examines primers targeting key denitrification genes (nitrite reductase - nirK, and nitrous oxide reductase, nosZ), and shows that commonly employed primer sets are unlikely to target many known denitrifying organisms.

Enjoy,
Stefan

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