Computational Biology Research Scientist position available in our group.
Computational Biology Research Scientist-76312
Scientist to interface cutting-edge omics technologies with terrestrial biogeochemical models. The position requires expertise with high-throughput sequencing as applied to microbial ecological questions in addition to experience with metabolic and trait-based modeling. The successful candidate will analyze existing or newly generated omics datasets (metagenomics, metatranscriptomics, metaproteomics and isolate genome sequences) using existing or novel methods to define and extract microbial molecular traits for linking ecosystem processes, response to environmental change, and community dynamics.
Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H2 cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.
Beller, H.R., Han, R. Lim, HC. and E.L. Brodie. 2013. Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1. Appl. Environ. Microbiol. 79:63-73
Microorganisms feature a variety of states that permit survival through harsh conditions, such as those they experience in the soil environment during a hot, dry Mediterranean-climate summer. Many microbes produce small cyst-like cells restructured from vegetative cells; others produce spores. Each response provides protection from certain kinds of environmental stress, (e.g., high heat, lack of water). Although these mechanisms may be important for surviving an extended drought, organisms that have entered a dormant state must return to an active state once the rains return. This resuscitation process can be responsible for extremely large increases in respiration (and thus CO2 release to the atmosphere). A high degree of gene coordination may be necessary for surviving the sudden deluge, as well as for entry into and resuscitation from dormant states.
In this paper we show that phylogenetically related groups of soil microbes have similar response trajectories following a rainfall event. Read more about this on the ESD news blog
Placella, S.A., E.L. Brodie, and M.K. Firestone (2012), Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. PNAS, DOI: www.pnas.org/cgi/doi/10.1073/pnas.1204306109. [sorry it’s not open access – please contact Eoin for a reprint if you don’t have access]
Congrats to Ulisses who was awarded an NSF Science Education Leadership Award for his work with SynBERC (Synthetic Biology Engineering Research Center), who recognized Ulisses for his significant contribution to the SynBERC’s educational mission and for leadership in synthetic biology education, outreach, and training. For the last year, Ulisses has served as a mentor of high school students through iCLEM, The Introductory College Level Experience in Microbiology program. He has also mentored community college students through TTE, The Transfer To Excellence program.
read the full story in ESD news
Nicholas J. Bouskill
Developing a Mechanistic High-Latitude Soil Carbon and Nitrogen Cycle Model in TOUGHREACT
Eoin L. Brodie
Integrative Mapping of Soil Heterogeneity at the Microbial Scale
see ESD news item