@article {3054, title = {Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations.}, journal = {Bioresour Technol}, volume = {345}, year = {2022}, month = {2022 Feb}, pages = {126553}, abstract = {

Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H is actually the electron donor supporting growth has not been rigorously excluded.

}, keywords = {Electrodes, Electron Transport, Electrons, Geobacter, Iron, Oxidation-Reduction, Soil Microbiology}, issn = {1873-2976}, doi = {10.1016/j.biortech.2021.126553}, author = {Lovley, Derek R} } @article {3092, title = {Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils.}, journal = {Appl Environ Microbiol}, volume = {83}, year = {2017}, month = {2017 May 01}, abstract = {

The possibility that (formerly ) and species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of accounted for over half of the PilA gene sequences in metagenomic libraries and 42\% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with species, but sequences most closely related to putative e-pilin genes from genera such as , , , and , were also detected. Approximately 17\% of all metagenomic and metatranscriptomic bacterial sequences clustered with species, and the finding that spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed genes. In addition, homologs of genes encoding OmcS, a -type cytochrome associated with the e-pili of and required for DIET, were also highly expressed in the soils. species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO reduction in Thus, these results are consistent with a model in which species were providing electrons to species for methane production through electrical connections of e-pili. species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for in methanogenic rice paddy soils is important because it demonstrates that the contribution that makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with spp., and possibly other methanogens, via DIET.

}, keywords = {Carbon Dioxide, Electron Transport, Fimbriae Proteins, Gene Expression Profiling, Geobacter, Metagenome, Methane, Methanosarcinaceae, Oryza, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.00223-17}, author = {Holmes, Dawn E and Shrestha, Pravin M and Walker, David J F and Dang, Yan and Nevin, Kelly P and Woodard, Trevor L and Lovley, Derek R} } @article {1417, title = {Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.}, journal = {Mol Ecol}, volume = {23}, year = {2014}, month = {2014 Jun}, pages = {2988-99}, abstract = {

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.

}, keywords = {Agriculture, Carbon Cycle, Ecosystem, Genes, Bacterial, Genes, Fungal, Genetic Variation, Metagenome, Multigene Family, Nitrogen Cycle, Oligonucleotide Array Sequence Analysis, Soil Microbiology, Trees, Tropical Climate}, issn = {1365-294X}, doi = {10.1111/mec.12786}, author = {Paula, Fabiana S and Rodrigues, Jorge L M and Zhou, Jizhong and Wu, Liyou and Mueller, Rebecca C and Mirza, Babur S and Bohannan, Brendan J M and N{\"u}sslein, Klaus and Deng, Ye and Tiedje, James M and Pellizari, Vivian H} } @article {1419, title = {Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.}, journal = {ISME J}, volume = {8}, year = {2014}, month = {2014 Jul}, pages = {1548-50}, abstract = {

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.

}, keywords = {Brazil, Conservation of Natural Resources, DNA Barcoding, Taxonomic, DNA, Fungal, DNA, Ribosomal, Ecosystem, Fungi, Phylogeny, Plant Roots, Soil Microbiology, Trees, Tropical Climate}, issn = {1751-7370}, doi = {10.1038/ismej.2013.253}, author = {Mueller, Rebecca C and Paula, Fabiana S and Mirza, Babur S and Rodrigues, Jorge L M and N{\"u}sslein, Klaus and Bohannan, Brendan J M} } @article {1420, title = {Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.}, journal = {Appl Environ Microbiol}, volume = {80}, year = {2014}, month = {2014 Jan}, pages = {281-8}, abstract = {

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

}, keywords = {Agriculture, Bacteria, Biota, Carbon, Cluster Analysis, Conservation of Natural Resources, Human Activities, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen, Nitrogen Fixation, Oxidoreductases, Phylogeny, Sequence Analysis, DNA, Soil, Soil Microbiology, South America, Trees}, issn = {1098-5336}, doi = {10.1128/AEM.02362-13}, author = {Mirza, Babur S and Potisap, Chotima and N{\"u}sslein, Klaus and Bohannan, Brendan J M and Rodrigues, Jorge L M} } @article {1423, title = {Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, year = {2013}, month = {2013 Jan 15}, pages = {988-93}, abstract = {

The Amazon rainforest is the Earth\&$\#$39;s largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

}, keywords = {Agriculture, Animals, Bacteria, Biodiversity, Brazil, Cattle, Ecosystem, Humans, Phylogeny, Rain, Soil Microbiology, Trees, Tropical Climate}, issn = {1091-6490}, doi = {10.1073/pnas.1220608110}, author = {Rodrigues, Jorge L M and Pellizari, Vivian H and Mueller, Rebecca and Baek, Kyunghwa and Jesus, Ederson da C and Paula, Fabiana S and Mirza, Babur and Hamaoui, George S and Tsai, Siu Mui and Feigl, Brigitte and Tiedje, James M and Bohannan, Brendan J M and N{\"u}sslein, Klaus} } @article {1564, title = {A field trial of nutrient stimulation of methanotrophs to reduce greenhouse gas emissions from landfill cover soils.}, journal = {J Air Waste Manag Assoc}, volume = {63}, year = {2013}, month = {2013 Mar}, pages = {300-9}, abstract = {

UNLABELLED: Landfills are among the major sources of anthropogenic methane (CH4) estimated to reach 40 x 10(9) kg per year worldwide by 2015 (IPCC, 2007). A 2 1/2-year field experiment was conducted at a closed landfill in western Michigan where methanotrophs, methane-consuming bacteria, were stimulated by nutrient addition to the soil without significantly increasing biogenic nitrous oxide (N2O) production. The effects of the nitrogen amendments (KNO3 and NH4Cl), phenylacetylene (a selective inhibitor of nitrifying bacteria that contribute to N2O production), and a canopy (to reduce direct water infiltration) on the vertical soil gas profiles of CH4, CO2, and O2 were measured in the top meter of the soil. Methane and nitrous oxide fluxes were calculated from the corresponding soil gas concentration gradients with respect to depth and a Millington-Quirk diffusivity coefficient in soil derived empirically from soil porosity, water content, and diffusivity coefficients in air from the literature. Methane flux estimates were as high as 218.4 g m(-2) day(-1) in the fall and 12.8 g/m(-2) day(-1) in the summer. During the spring and summer CH4 fluxes were reduced by more than half by adding KNO3 and NH4Cl into the soil as compared to control plots, while N2O fluxes increased substantially. The concurrent addition of phenylacetylene to the amendment decreased peak N2O production by half and the rate of peak methane oxidation by about one-third. The seasonal average methane and N2O flux data were extrapolated to estimate the reduction of CH4 and N2O fluxes into the atmosphere by nitrogen and inhibitor addition to the cover soils. The results suggest that such additions coupled with soil moisture management may provide a potential strategy to significantly reduce greenhouse gas emissions from landfills.

IMPLICATIONS: The results of a 2 1/2-year study of effects of nutrient stimulation on methane oxidation in landfill cover soils demonstrates that nutrient addition does decrease methane emissions. The work further underscores the control which soil moisture exerts on methane oxidation. Water management is critical to the success of methane oxidation strategies.

}, keywords = {Biodegradation, Environmental, Gases, Greenhouse Effect, Methane, Oxidation-Reduction, Soil, Soil Microbiology, Waste Management}, issn = {1096-2247}, author = {Lizik, William and Im, Jeongdae and Semrau, Jeremy D and Barcelona, Michael J} } @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 {369, title = {Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes.}, journal = {Appl Environ Microbiol}, volume = {78}, year = {2012}, month = {2012 Apr}, pages = {2459-61}, abstract = {We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.}, keywords = {Archaea, Bacteria, Biodiversity, Cluster Analysis, Ecosystem, Genes, rRNA, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Trees, Tropical Climate}, issn = {1098-5336}, doi = {10.1128/AEM.07547-11}, author = {Deangelis, Kristen M and Firestone, Mary K} } @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 {374, title = {Effects of selected root exudate components on soil bacterial communities.}, journal = {FEMS Microbiol Ecol}, volume = {77}, year = {2011}, month = {2011 Sep}, pages = {600-10}, abstract = {Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.}, keywords = {Bacteria, DNA, Bacterial, Molecular Sequence Data, Organic Chemicals, Phylogeny, Pinus, Plant Exudates, Plant Roots, Rhizosphere, RNA, Ribosomal, 16S, Soil, Soil Microbiology}, issn = {1574-6941}, doi = {10.1111/j.1574-6941.2011.01150.x}, author = {Shi, Shengjing and Richardson, Alan E and O{\textquoteright}Callaghan, Maureen and Deangelis, Kristen M and Jones, Eirian E and Stewart, Alison and Firestone, Mary K and Condron, Leo M} } @article {1569, title = {Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure.}, journal = {Appl Microbiol Biotechnol}, volume = {89}, year = {2011}, month = {2011 Jan}, pages = {189-200}, abstract = {

Landfills are large sources of CH(4), but a considerable amount of CH(4) can be removed in situ by methanotrophs if their activity can be stimulated through the addition of nitrogen. Nitrogen can, however, lead to increased N(2)O production. To examine the effects of nitrogen and a selective inhibitor on CH(4) oxidation and N(2)O production in situ, 0.5 M of NH(4)Cl and 0.25 M of KNO(3), with and without 0.01\% (w/v) phenylacetylene, were applied to test plots at a landfill in Kalamazoo, MI from 2007 November to 2009 July. Nitrogen amendments stimulated N(2)O production but had no effect on CH(4) oxidation. The addition of phenylacetylene stimulated CH(4) oxidation while reducing N(2)O production. Methanotrophs possessing particulate methane monooxygenase and archaeal ammonia-oxidizers (AOAs) were abundant. The addition of nitrogen reduced methanotrophic diversity, particularly for type I methanotrophs. The simultaneous addition of phenylacetylene increased methanotrophic diversity and the presence of type I methanotrophs. Clone libraries of the archaeal amoA gene showed that the addition of nitrogen increased AOAs affiliated with Crenarchaeal group 1.1b, while they decreased with the simultaneous addition of phenylacetylene. These results suggest that the addition of phenylacetylene with nitrogen reduces N(2)O production by selectively inhibiting AOAs and/or type II methanotrophs.

}, keywords = {Acetylene, Archaea, Archaeal Proteins, Bacteria, Bacterial Proteins, Gases, Greenhouse Effect, Methane, Molecular Sequence Data, Nitrogen, Refuse Disposal, Soil, Soil Microbiology}, issn = {1432-0614}, doi = {10.1007/s00253-010-2811-0}, author = {Im, Jeongdae and Lee, Sung-Woo and Bodrossy, Levente and Barcelona, Michael J and Semrau, Jeremy D} } @article {372, title = {Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.}, journal = {Nature}, volume = {480}, year = {2011}, month = {2011 Dec 15}, pages = {368-71}, abstract = {Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 {\textdegree}C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.}, keywords = {Alaska, Arctic Regions, Bacteria, Carbon, Carbon Cycle, DNA, Freezing, Genes, rRNA, Metagenome, Metagenomics, Methane, Nitrogen, Nitrogen Cycle, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Soil, Soil Microbiology, Temperature, Time Factors}, issn = {1476-4687}, doi = {10.1038/nature10576}, author = {Mackelprang, Rachel and Waldrop, Mark P and Deangelis, Kristen M and David, Maude M and Chavarria, Krystle L and Blazewicz, Steven J and Rubin, Edward M and Jansson, Janet K} } @article {420, title = {Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers.}, journal = {Appl Environ Microbiol}, volume = {77}, year = {2011}, month = {2011 Sep}, pages = {6502-9}, abstract = {Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.}, keywords = {Biodiversity, Deltaproteobacteria, DNA, Bacterial, Gene Expression Profiling, Hydrogensulfite Reductase, Molecular Sequence Data, Oxidation-Reduction, Sequence Analysis, DNA, Soil Microbiology, Sulfates, Water Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.00576-11}, author = {Miletto, M and Williams, K H and N{\textquoteright}Guessan, A L and Lovley, D R} } @article {423, title = {Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies.}, journal = {Appl Environ Microbiol}, volume = {77}, year = {2011}, month = {2011 Jul}, pages = {4597-602}, abstract = {Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.}, keywords = {Acetates, Antibodies, Bacterial, Bacterial Proteins, Geobacter, Petroleum, Quaternary Ammonium Compounds, Soil Microbiology, Water Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.00114-11}, author = {Yun, Jiae and Ueki, Toshiyuki and Miletto, Marzia and Lovley, Derek R} } @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} } @article {447, title = {Role of Geobacter sulfurreducens outer surface c-type cytochromes in reduction of soil humic acid and anthraquinone-2,6-disulfonate.}, journal = {Appl Environ Microbiol}, volume = {76}, year = {2010}, month = {2010 Apr}, pages = {2371-5}, abstract = {Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.}, keywords = {Anthraquinones, Bacterial Proteins, Cytochromes, Gene Deletion, Genes, Bacterial, Geobacter, Humic Substances, Oxidation-Reduction, Soil, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02250-09}, author = {Voordeckers, James W and Kim, Byoung-Chan and Izallalen, Mounir and Lovley, Derek R} } @article {467, title = {Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation.}, journal = {ISME J}, volume = {3}, year = {2009}, month = {2009 Apr}, pages = {454-65}, abstract = {As part of an effort to diagnose the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater, transcript levels for two genes potentially associated with oxidative stress, cydA and sodA, were quantified throughout a bioremediation field study in Rifle, CO, USA. Despite the accumulation of Fe(II) in the groundwater, which is inconsistent with the presence of dissolved oxygen, both genes were highly expressed during the bioremediation process. Therefore, the response to oxidative stress was further evaluated with Geobacter uraniireducens, an isolate from the Rifle site. When G. uraniireducens cultured with fumarate as the electron acceptor was exposed to 5\% oxygen for 8 h, there was a significant increase in cydA and sodA transcripts as well as other genes associated with oxygen respiration or oxidative stress. Oxygen-exposed cells had lower transcript abundance for genes associated with anaerobic respiration, metabolism and motility. Short-term oxygen exposure had little impact on cydA transcript levels, as more than 1 h was required for increases to levels comparable to the subsurface. Abundance of cydA and sodA transcripts for the isolate G. sulfurreducens were always higher in cells cultured with Fe(III) compared with fumarate as an electron acceptor, even when fumarate-grown cells were exposed to oxygen, and Fe(III)-grown cells were grown anaerobically. These results suggest that the apparently high Geobacter cydA and sodA expression during bioremediation cannot necessarily be attributed to oxidative stress and demonstrate that diagnosis of the metabolic status of subsurface microorganisms through transcript analysis should be coupled with appropriate geochemical analyses.}, keywords = {Anaerobiosis, Bacterial Proteins, Biodegradation, Environmental, Colorado, Ferric Compounds, Fumarates, Gene Expression Profiling, Geobacter, Oxidative Stress, Soil Microbiology, Uranium}, issn = {1751-7370}, doi = {10.1038/ismej.2008.126}, author = {Mouser, Paula J and Holmes, Dawn E and Perpetua, Lorrie A and DiDonato, Raymond and Postier, Brad and Liu, Anna and Lovley, Derek R} } @article {378, title = {Selective progressive response of soil microbial community to wild oat roots.}, journal = {ISME J}, volume = {3}, year = {2009}, month = {2009 Feb}, pages = {168-78}, abstract = {Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7\% of the total rhizosphere microbial community (147 of 1917 taxa); the 7\% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.}, keywords = {Avena sativa, Bacteria, Biodiversity, Colony Count, Microbial, Microarray Analysis, Oligonucleotide Array Sequence Analysis, Plant Roots, Polymerase Chain Reaction, RNA, Bacterial, RNA, Ribosomal, 16S, Soil Microbiology}, issn = {1751-7370}, doi = {10.1038/ismej.2008.103}, author = {Deangelis, Kristen M and Brodie, Eoin L and DeSantis, Todd Z and Andersen, Gary L and Lindow, Steven E and Firestone, Mary K} } @article {483, title = {Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes.}, journal = {Microbiology}, volume = {154}, year = {2008}, month = {2008 May}, pages = {1422-35}, abstract = {Previous studies have shown that Geobacter sulfurreducens requires the outer-membrane, multicopper protein OmpB for Fe(III) oxide reduction. A homologue of OmpB, designated OmpC, which is 36 \% similar to OmpB, has been discovered in the G. sulfurreducens genome. Deletion of ompC inhibited reduction of insoluble, but not soluble Fe(III). Analysis of multiple Geobacter and Pelobacter genomes, as well as in situ Geobacter, indicated that genes encoding multicopper proteins are conserved in Geobacter species but are not found in Pelobacter species. Levels of ompB transcripts were similar in G. sulfurreducens at different growth rates in chemostats and during growth on a microbial fuel cell anode. In contrast, ompC transcript levels increased at higher growth rates in chemostats and with increasing current production in fuel cells. Constant levels of Geobacter ompB transcripts were detected in groundwater during a field experiment in which acetate was added to the subsurface to promote in situ uranium bioremediation. In contrast, ompC transcript levels increased during the rapid phase of growth of Geobacter species following addition of acetate to the groundwater and then rapidly declined. These results demonstrate that more than one multicopper protein is required for optimal Fe(III) oxide reduction in G. sulfurreducens and suggest that, in environmental studies, quantifying OmpB/OmpC-related genes could help alleviate the problem that Pelobacter genes may be inadvertently quantified via quantitative analysis of 16S rRNA genes. Furthermore, comparison of differential expression of ompB and ompC may provide insight into the in situ metabolic state of Geobacter species in environments of interest.}, keywords = {Acetates, Amino Acid Sequence, Bacterial Outer Membrane Proteins, Electrodes, Ferric Compounds, Gene Deletion, Gene Expression Profiling, Geobacter, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Sequence Alignment, Sequence Homology, Nucleic Acid, Soil Microbiology, Uranium}, issn = {1350-0872}, doi = {10.1099/mic.0.2007/014365-0}, author = {Holmes, Dawn E and Mester, T{\"u}nde and O{\textquoteright}Neil, Regina A and Perpetua, Lorrie A and Larrahondo, M Juliana and Glaven, Richard and Sharma, Manju L and Ward, Joy E and Nevin, Kelly P and Lovley, Derek R} } @article {746, title = {Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages.}, journal = {FEMS Microbiol Ecol}, volume = {60}, year = {2007}, month = {2007 Apr}, pages = {60-73}, abstract = {Volcanic activity creates new landforms that can change dramatically over time as a consequence of biotic succession. Nonetheless, volcanic deposits present severe constraints for microbial colonization and activity. We have characterized bacterial diversity on four recent deposits at Kilauea volcano, Hawaii (KVD). Much of the diversity was either closely related to uncultured organisms or distinct from any reported 16S rRNA gene sequences. Diversity indices suggested that diversity was highest in a moderately vegetated 210-year-old ash deposit (1790-KVD), and lowest for a 79-year-old lava flow (1921-KVD). Diversity for a 41-year-old tephra deposit (1959-KVD) and a 300-year-old rainforest (1700-KVD) reached intermediate values. The 1959-KVD and 1790-KVD communities were dominated by Acidobacteria, Alpha- and Gammaproteobacteria, Actinobacteria, Cyanobacteria, and many unclassified phylotypes. The 1921-KVD, an unvegetated low pH deposit, was dominated by unclassified phylotypes. In contrast, 1700-KVD was primarily populated by Alphaproteobacteria with very few unclassified phylotypes. Similar diversity indices and levels of trace gas flux were found for 1959-KVD and 1790-KVD; however, statistical analyses indicated significantly different communities. This study not only showed that microorganisms colonize recent volcanic deposits and are able to establish diverse communities, but also that their composition is governed by variations in local deposit parameters.}, keywords = {Bacteria, DNA, Bacterial, Ecosystem, Genes, rRNA, Genetic Variation, Hawaii, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil Microbiology, Time Factors, Volcanic Eruptions}, issn = {0168-6496}, doi = {10.1111/j.1574-6941.2006.00253.x}, author = {Gomez-Alvarez, Vicente and King, Gary M and N{\"u}sslein, Klaus} } @article {744, title = {Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter.}, journal = {Appl Environ Microbiol}, volume = {73}, year = {2007}, month = {2007 Jul}, pages = {4171-9}, abstract = {The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl(-) in a subsurface shale rich in CH(4) derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH(4)-producing zone lacked electron acceptors such as O(2), NO(3)(-), Fe(3+), or SO(4)(2-). Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl(-) concentrations above approximately 1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H(2)/CO(2)) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH(4)-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters.}, keywords = {Archaea, Base Sequence, Cloning, Molecular, DNA Primers, Genes, Archaeal, Genetic Variation, Geologic Sediments, Methane, Michigan, Molecular Sequence Data, Organic Chemicals, Phylogeny, RNA, Archaeal, RNA, Ribosomal, 16S, Sodium Chloride, Soil, Soil Microbiology, Water Microbiology}, issn = {0099-2240}, doi = {10.1128/AEM.02810-06}, author = {Waldron, Patricia J and Petsch, Steven T and Martini, Anna M and N{\"u}sslein, Klaus and N{\"u}slein, Klaus} } @article {748, title = {Distribution of extensive nifH gene diversity across physical soil microenvironments.}, journal = {Microb Ecol}, volume = {51}, year = {2006}, month = {2006 May}, pages = {441-52}, abstract = {The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant-microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 microm to the clay fraction at < 75 microm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.}, keywords = {Bacteria, Base Sequence, DNA Primers, Genes, Bacterial, Multigene Family, Oxidoreductases, Phylogeny, Polymerase Chain Reaction, Soil Microbiology}, issn = {0095-3628}, doi = {10.1007/s00248-006-9044-x}, author = {Izquierdo, Javier A and N{\"u}sslein, Klaus} } @article {545, title = {Dissimilatory Fe(III) and Mn(IV) reduction.}, journal = {Adv Microb Physiol}, volume = {49}, year = {2004}, month = {2004}, pages = {219-86}, abstract = {Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.}, keywords = {Archaea, Biodegradation, Environmental, Ferric Compounds, Geobacter, Manganese, Manganese Compounds, Oxidation-Reduction, Oxides, Shewanella, Soil Microbiology, Soil Pollutants}, issn = {0065-2911}, doi = {10.1016/S0065-2911(04)49005-5}, author = {Lovley, Derek R and Holmes, Dawn E and Nevin, Kelly P} } @article {591, title = {Bioremediation. Anaerobes to the rescue.}, journal = {Science}, volume = {293}, year = {2001}, month = {2001 Aug 24}, pages = {1444-6}, keywords = {Bacteria, Aerobic, Bacteria, Anaerobic, Biodegradation, Environmental, Euryarchaeota, Ferric Compounds, Genome, Archaeal, Genome, Bacterial, Hydrocarbons, Aromatic, Hydrocarbons, Chlorinated, Metals, Methane, Nitrates, Oxidation-Reduction, Oxygen, Soil Microbiology, Sulfates, Sulfur-Reducing Bacteria, Water Pollutants, Chemical}, issn = {0036-8075}, doi = {10.1126/science.1063294}, author = {Lovley, D R} } @article {867, title = {Methane production and release from two New England peatlands.}, journal = {Int Microbiol}, volume = {3}, year = {2000}, month = {2000 Jun}, pages = {89-95}, abstract = {The rate of methane production and release to the atmosphere was determined for two New England peat bogs. Methane production rates from peat sediments, which were measured down to depths of 150 cm, ranged from 1 to 15 micromoles per liter per hour. The highest rates of methane production occurred at depths of 60-100 cm. Methane release from these same peats was quantified from various habitats on the bog using gas collection chambers. The chambers enclose a two-liter volume and cover an area of 0.02 m2. Methane accumulation in the chambers was measured for periods of up to 18 days. Methane release was related to pH and habitat zone. The lowest rates of methane release were from those portions of the bogs that had pH values below 5.0. Peak methane release occurred during or immediately after ice melt in both wetlands with release rates as high as 34 mmoles/m2/d. The overall estimate of yearly release of methane from these bog systems is 2,900 and 14,900 moles per year for Arcadia and Hawley Bogs respectively. Both of these bogs have pH environments close to the lowest limit for methanogenesis, and small differences in pH values can have a large impact on both the rate of methane production and the rate of methane release to the atmosphere.}, keywords = {Anaerobiosis, Euryarchaeota, Hydrogen-Ion Concentration, Methane, New England, Soil, Soil Microbiology}, issn = {1139-6709}, author = {Duval, B and Goodwin, S} } @article {609, title = {Microbes with a mettle for bioremediation.}, journal = {Nat Biotechnol}, volume = {18}, year = {2000}, month = {2000 Jun}, pages = {600-1}, keywords = {Bacterial Adhesion, Cadmium, Cupriavidus necator, Industrial Waste, Metallothionein, Metals, Heavy, Soil Microbiology, Soil Pollutants}, issn = {1087-0156}, doi = {10.1038/76433}, author = {Lovley, D R and Lloyd, J R} } @article {753, title = {Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil.}, journal = {Appl Environ Microbiol}, volume = {65}, year = {1999}, month = {1999 Aug}, pages = {3622-6}, abstract = {The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35\% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63\% G+C content fraction. All three methods showed differences between the forest and pasture habitats, providing evidence that vegetation had a strong influence on microbial community composition at three levels of taxon resolution. The forest soil DNA had a peak in G+C content of 61\%, while the DNA of the pasture soil had a peak in G+C content of 67\%. None of the dominant phylotypes found in the forest soil were detected in the pasture soil. For the 63\% G+C fraction SSU rDNA sequence analysis of the three most dominant members revealed that their phyla changed from Fibrobacter and Syntrophomonas assemblages in the forest soil to Burkholderia and Rhizobium-Agrobacterium assemblages in the pasture soil.}, keywords = {Agriculture, Bacteria, Base Composition, DNA, Bacterial, Ecosystem, Molecular Sequence Data, Soil Microbiology, Trees, Tropical Climate}, issn = {0099-2240}, author = {N{\"u}sslein, K and Tiedje, J M} } @article {754, title = {Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition.}, journal = {Appl Environ Microbiol}, volume = {64}, year = {1998}, month = {1998 Apr}, pages = {1283-9}, abstract = {The small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G + C) content by using bisbenzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63\% G + C fraction) and a fraction with a low biomass (35\% G + C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63\% G + C fraction contained several dominant phylotypes, while the community members that were less successful (35\% G + C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G + C contents used. The dominant phylotypes in the 63\% G + C fraction were members of the Pseudomonas, Rhizobium-Agrobacterium, and Rhodospirillum assemblages, while all of the clones sequenced from the 35\% G + C fraction were affiliated with several Clostridium assemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G + C separation step is also a way to detect some of the less dominant organisms in a community.}, keywords = {Base Composition, Clostridium, DNA, Bacterial, DNA, Ribosomal, Ecosystem, Genetic Variation, Hawaii, Phylogeny, Pseudomonas, Rhizobium, Rhodospirillum, Soil Microbiology}, issn = {0099-2240}, author = {N{\"u}sslein, K and Tiedje, J M} } @article {632, title = {Microbial degradation of hydrochlorofluorocarbons (CHCl2F and CHCl2CF3) in soils and sediments.}, journal = {Appl Environ Microbiol}, volume = {62}, year = {1996}, month = {1996 May}, pages = {1818-21}, abstract = {The ability of microorganisms to degrade trace levels of the hydrochlorofluorocarbons HCFC-21 and HCFC-123 was investigated. Methanotroph-linked oxidation of HCFC-21 was observed in aerobic soils, and anaerobic degradation of HCFC-21 occurred in freshwater and salt marsh sediments. Microbial degradation of HCFC-123 was observed in anoxic freshwater and salt marsh sediments, and the recovery of 1,1,1-trifluoro-2-chloroethane indicated the involvement of reductive dechlorination. No degradation of HCFC-123 was observed in aerobic soils. In some experiments, HCFCs were degraded at low (parts per billion) concentrations, raising the possibility that bacteria in nature remove HCFCs from the atmosphere.}, keywords = {Biodegradation, Environmental, Chlorofluorocarbons, Soil Microbiology}, issn = {0099-2240}, author = {Oremland, R S and Lonergan, D J and Culbertson, C W and Lovley, D R} } @article {642, title = {Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism.}, journal = {Appl Environ Microbiol}, volume = {60}, year = {1994}, month = {1994 Oct}, pages = {3752-9}, abstract = {A dissimilatory metal- and sulfur-reducing microorganism was isolated from surface sediments of a hydrocarbon-contaminated ditch in Norman, Okla. The isolate, which was designated strain PCA, was an obligately anaerobic, nonfermentative nonmotile, gram-negative rod. PCA grew in a defined medium with acetate as an electron donor and ferric PPi, ferric oxyhydroxide, ferric citrate, elemental sulfur, Co(III)-EDTA, fumarate, or malate as the sole electron acceptor. PCA also coupled the oxidation of hydrogen to the reduction of Fe(III) but did not reduce Fe(III) with sulfur, glucose, lactate, fumarate, propionate, butyrate, isobutyrate, isovalerate, succinate, yeast extract, phenol, benzoate, ethanol, propanol, or butanol as an electron donor. PCA did not reduce oxygen, Mn(IV), U(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PCA exhibited dithionite-reduced minus air-oxidized difference spectra which were characteristic of c-type cytochromes. Phylogenetic analysis of the 16S rRNA sequence placed PCA in the delta subgroup of the proteobacteria. Its closest known relative is Geobacter metallireducens. The ability to utilize either hydrogen or acetate as the sole electron donor for Fe(III) reduction makes strain PCA a unique addition to the relatively small group of respiratory metal-reducing microorganisms available in pure culture. A new species name, Geobacter sulfurreducens, is proposed.}, keywords = {Acetic Acid, Acetic Acids, Base Sequence, DNA Primers, DNA, Bacterial, DNA, Ribosomal, Electron Transport, Gram-Negative Anaerobic Bacteria, Hydrogen, Metals, Microscopy, Electron, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Soil Microbiology}, issn = {0099-2240}, author = {Caccavo, F and Lonergan, D J and Lovley, D R and Davis, M and Stolz, J F and McInerney, M J} } @article {656, title = {Dissimilatory Fe(III) and Mn(IV) reduction.}, journal = {Microbiol Rev}, volume = {55}, year = {1991}, month = {1991 Jun}, pages = {259-87}, abstract = {The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater. This process, which may have been the first globally significant mechanism for the oxidation of organic matter to carbon dioxide, plays an important role in the oxidation of natural and contaminant organic compounds in a variety of environments and contributes to other phenomena of widespread significance such as the release of metals and nutrients into water supplies, the magnetization of sediments, and the corrosion of metal. Until recently, much of the Fe(III) and Mn(IV) reduction in sedimentary environments was considered to be the result of nonenzymatic processes. However, microorganisms which can effectively couple the oxidation of organic compounds to the reduction of Fe(III) or Mn(IV) have recently been discovered. With Fe(III) or Mn(IV) as the sole electron acceptor, these organisms can completely oxidize fatty acids, hydrogen, or a variety of monoaromatic compounds. This metabolism provides energy to support growth. Sugars and amino acids can be completely oxidized by the cooperative activity of fermentative microorganisms and hydrogen- and fatty-acid-oxidizing Fe(III) and Mn(IV) reducers. This provides a microbial mechanism for the oxidation of the complex assemblage of sedimentary organic matter in Fe(III)- or Mn(IV)-reducing environments. The available evidence indicates that this enzymatic reduction of Fe(III) or Mn(IV) accounts for most of the oxidation of organic matter coupled to reduction of Fe(III) and Mn(IV) in sedimentary environments. Little is known about the diversity and ecology of the microorganisms responsible for Fe(III) and Mn(IV) reduction, and only preliminary studies have been conducted on the physiology and biochemistry of this process.}, keywords = {Bacteria, Electron Transport, Ferric Compounds, Fungi, Geological Phenomena, Geology, Manganese, Oxidation-Reduction, Soil Microbiology, Water Microbiology}, issn = {0146-0749}, author = {Lovley, D R} } @article {1723, title = {Ecological observation of the 137Cs-contamination in beef of animals from the southern-Bavarian area.}, journal = {Environ Qual Saf}, volume = {4}, year = {1975}, month = {1975}, pages = {24-36}, abstract = {

Certain climatic and edaphic conformations in the Bavarian sub-alpine mountains and in the Alps favor above all the development of a land utilization system and farm structures similar to those in the northern part of Scandinavia. In 1963/64, the years of the highest environmental contamination up to the present, we established in 600 beef samples from the round or shoulder of male and female cattle (mainly Highland cattle) close connections between the 137Cs-contamination of green crop and the long lastnig yearly precipitation quantities, as well as certain relations between the 137Cs-contamination of meat and differences in the feeding and keeping of the animals. During summer-seasons (April-October), beef of cattle from pastures with heavy rainfall (Alps) was contaiminated by 137Cs up to 15 times more than that of confined animals. Hereby the rate of 137Cs-contamination in the meat of grazing cattle was nearly proportional to the quantities of precipitation. When confined cattle were fed on pastures in autumn after harvesting for 2 to 3 weeks, a quick increase of 137Cs-contamination of the meat was caused within this time up to values which in this district were otherwise only observed in grazing cattle. The lower 137Cs-content in meat of cattle housed during the summer season is due to the more varied fodder, which is at that time less contaminated than green crop. During the winter season (November to March), the highest contaminations in the meat of confined (Bohemian Forest) or grazing cattle (Alps) was measured when the animals in these districts were almost exclusively fed with fodder from the own farmground or with leafy silage. The highest contamination was almost regularly noticed in January, February and March, as generally during these months the highly contaminated first cut hay is fed. Here the meat was often even more contaminated than that of grazing cattle. After the quick decrease of 137Cs in fallout noticed in the years 1964 and 1965, in 1965/66 a dependance in the 137Cs-contamination of beef on the methods of keeping and feeding could still be observed in only the extreme cases (Alps, Bavarian- and Bohemian Forest); though in general, meat of animals from districts with heavy rainfall was slightly more contaminated than meat of animals from regions with less precipitation.

}, keywords = {Animals, Cattle, Cesium Radioisotopes, Ecology, Food Contamination, Radioactive, Fungi, Germany, West, Hydrogen-Ion Concentration, Meat, Plants, Radioactive Pollutants, Soil, Soil Microbiology, Time Factors, Trees, Weather}, issn = {0300-824X}, author = {Kreuzer, W} }