@article {368,
	title = {Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia.},
	journal = {MBio},
	volume = {3},
	year = {2012},
	month = {2012},
	abstract = {Tropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of the Firmicutes, Bacteroidetes, and Alphaproteobacteria as dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure. IMPORTANCE: After multiple transfers, we established microbial consortia derived from two tropical forest soils with different native redox conditions. Communities derived from the rapidly fluctuating redox environment maintained a capacity to use added terminal electron acceptors (TEAs) after multiple transfers, though they were not present during the enrichment. Communities derived from lower-redox soils were not responsive to TEA addition but were much more efficient at switchgrass decomposition. Though the communities were different, diversity was not, and both were dominated by many of the same species of clostridia. This reflects the inadequacy of rRNA for determining the function of microbial communities, in this case the retained ability to utilize TEAs that were not part of the selective growth conditions. More importantly, this suggests that microbial community function is shaped by life history, where environmental factors produce heritable traits through natural selection over time, creating variation in the community, a phenomenon not well documented for microbes.},
	keywords = {Adaptation, Physiological, Alphaproteobacteria, Anaerobiosis, Bacteroidetes, Biota, Biotransformation, Carbon, Electron Transport, Enzyme Activation, Ferric Compounds, Genes, rRNA, Microbial Consortia, Nitrates, Oxidation-Reduction, Panicum, Phylogeny, Rain, Soil Microbiology, Sulfates, Trees, Tropical Climate},
	issn = {2150-7511},
	doi = {10.1128/mBio.00249-11},
	author = {Deangelis, Kristen M and Fortney, Julian L and Borglin, Sharon and Silver, Whendee L and Simmons, Blake A and Hazen, Terry C}
}
@article {367,
	title = {Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {109},
	year = {2012},
	month = {2012 Aug 7},
	pages = {E2173-82},
	abstract = {To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.},
	issn = {1091-6490},
	doi = {10.1073/pnas.1112750109},
	author = {Khudyakov, Jane I and D{\textquoteright}haeseleer, Patrik and Borglin, Sharon E and Deangelis, Kristen M and Woo, Hannah and Lindquist, Erika A and Hazen, Terry C and Simmons, Blake A and Thelen, Michael P}
}
