@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 {375,
	title = {Characterization of trapped lignin-degrading microbes in tropical forest soil.},
	journal = {PLoS One},
	volume = {6},
	year = {2011},
	month = {2011},
	pages = {e19306},
	abstract = {Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.},
	keywords = {Biodiversity, Biomass, Ecosystem, Gases, Lignin, Oligonucleotide Array Sequence Analysis, Phylogeny, Plants, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil Microbiology, Trees},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0019306},
	author = {Deangelis, Kristen M and Allgaier, Martin and Chavarria, Yaucin and Fortney, Julian L and Hugenholtz, Phillip and Simmons, Blake and Sublette, Kerry and Silver, Whendee L and Hazen, Terry C}
}
@article {376,
	title = {Microbial communities acclimate to recurring changes in soil redox potential status.},
	journal = {Environ Microbiol},
	volume = {12},
	year = {2010},
	month = {2010 Dec},
	pages = {3137-49},
	abstract = {Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO$_{2}$ respiration, methanogenesis, N$_{2}$O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA:DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.},
	keywords = {Acclimatization, Archaea, Bacteria, Carbon Dioxide, DNA, Archaeal, DNA, Bacterial, Iron, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, RNA, Archaeal, RNA, Bacterial, Soil, Soil Microbiology, Trees},
	issn = {1462-2920},
	doi = {10.1111/j.1462-2920.2010.02286.x},
	author = {Deangelis, Kristen M and Silver, Whendee L and Thompson, Andrew W and Firestone, Mary K}
}
