@article {2626, title = {Membrane-partitioned cell wall synthesis in mycobacteria.}, journal = {Elife}, volume = {10}, year = {2021}, month = {2021 Feb 05}, abstract = {

Many antibiotics target the assembly of cell wall peptidoglycan, an essential, heteropolymeric mesh that encases most bacteria. In rod-shaped bacteria, cell wall elongation is spatially precise yet relies on limited pools of lipid-linked precursors that generate and are attracted to membrane disorder. By tracking enzymes, substrates, and products of peptidoglycan biosynthesis in , we show that precursors are made in plasma membrane domains that are laterally and biochemically distinct from sites of cell wall assembly. Membrane partitioning likely contributes to robust, orderly peptidoglycan synthesis, suggesting that these domains help template peptidoglycan synthesis. The cell wall-organizing protein DivIVA and the cell wall itself promote domain homeostasis. These data support a model in which the peptidoglycan polymer feeds back on its membrane template to maintain an environment conducive to directional synthesis. Our findings are applicable to rod-shaped bacteria that are phylogenetically distant from , indicating that horizontal compartmentalization of precursors may be a general feature of bacillary cell wall biogenesis.

}, issn = {2050-084X}, doi = {10.7554/eLife.60263}, author = {Garc{\'\i}a-Heredia, Alam and Kado, Takehiro and Sein, Caralyn E and Puffal, Julia and Osman, Sarah H and Judd, Julius and Gray, Todd A and Morita, Yasu S and Siegrist, M Sloan} } @article {3085, title = {Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.}, journal = {Microb Ecol}, volume = {76}, year = {2018}, month = {2018 Oct}, pages = {660-667}, abstract = {

Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40~days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.

}, keywords = {Acetates, Biodegradation, Environmental, Geobacter, Groundwater, Methane, Methanosarcina, Oxidation-Reduction, Uranium, Water Pollutants, Chemical}, issn = {1432-184X}, doi = {10.1007/s00248-018-1165-5}, author = {Holmes, Dawn E and Orelana, Roberto and Giloteaux, Ludovic and Wang, Li-Ying and Shrestha, Pravin and Williams, Kenneth and Lovley, Derek R and Rotaru, Amelia-Elena} } @article {1737, title = {Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.}, journal = {Science}, volume = {348}, year = {2015}, month = {2015 Apr 24}, pages = {428-31}, abstract = {

Methane is a key component in the global carbon cycle, with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply substituted "clumped" isotopologues (for example, (13)CH3D) has recently emerged as a proxy for determining methane-formation temperatures. However, the effect of biological processes on methane{\textquoteright}s clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on (13)CH3D abundances and results in anomalously elevated formation-temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.

}, keywords = {Animals, Carbon Cycle, Carbon Isotopes, Cattle, Groundwater, Hydrogen, Methane, Methanomicrobiales, Temperature}, issn = {1095-9203}, doi = {10.1126/science.aaa4326}, author = {Wang, David T and Gruen, Danielle S and Lollar, Barbara Sherwood and Hinrichs, Kai-Uwe and Stewart, Lucy C and Holden, James F and Hristov, Alexander N and Pohlman, John W and Morrill, Penny L and K{\"o}nneke, Martin and Delwiche, Kyle B and Reeves, Eoghan P and Sutcliffe, Chelsea N and Ritter, Daniel J and Seewald, Jeffrey S and McIntosh, Jennifer C and Hemond, Harold F and Kubo, Michael D and Cardace, Dawn and Hoehler, Tori M and Ono, Shuhei} } @article {3119, title = {Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments.}, journal = {Front Microbiol}, volume = {5}, year = {2014}, month = {2014}, pages = {366}, abstract = {

Previous studies have suggested that protozoa prey on Fe(III)- and sulfate-reducing bacteria that are enriched when acetate is added to uranium contaminated subsurface sediments to stimulate U(VI) reduction. In order to determine whether protozoa continue to impact subsurface biogeochemistry after these acetate amendments have stopped, 18S rRNA and {\ss}-tubulin sequences from this phase of an in situ uranium bioremediation field experiment were analyzed. Sequences most similar to Metopus species predominated, with the majority of sequences most closely related to M. palaeformis, a cilitated protozoan known to harbor methanogenic symbionts. Quantification of mcrA mRNA transcripts in the groundwater suggested that methanogens closely related to Metopus endosymbionts were metabolically active at this time. There was a strong correlation between the number of mcrA transcripts from the putative endosymbiotic methanogen and Metopus {\ss}-tubulin mRNA transcripts during the course of the field experiment, suggesting that the activity of the methanogens was dependent upon the activity of the Metopus species. Addition of the eukaryotic inhibitors cyclohexamide and colchicine to laboratory incubations of acetate-amended subsurface sediments significantly inhibited methane production and there was a direct correlation between methane concentration and Metopus {\ss}-tubulin and putative symbiont mcrA gene copies. These results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2014.00366}, author = {Holmes, Dawn E and Giloteaux, Ludovic and Orellana, Roberto and Williams, Kenneth H and Robbins, Mark J and Lovley, Derek R} } @article {3118, title = {Proteome of Geobacter sulfurreducens in the presence of U(VI).}, journal = {Microbiology (Reading)}, volume = {160}, year = {2014}, month = {2014 Dec}, pages = {2607-2617}, abstract = {

Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 {\textmu}M U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance-nodulation-cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.

}, keywords = {Bacterial Proteins, Gene Expression Regulation, Bacterial, Geobacter, Organometallic Compounds, Proteome}, issn = {1465-2080}, doi = {10.1099/mic.0.081398-0}, author = {Orellana, Roberto and Hixson, Kim K and Murphy, Sean and Mester, T{\"u}nde and Sharma, Manju L and Lipton, Mary S and Lovley, Derek R} } @article {1440, title = {Subpolar addition of new cell wall is directed by DivIVA in mycobacteria.}, journal = {Proc Natl Acad Sci U S A}, volume = {111}, year = {2014}, month = {2014 Aug 5}, pages = {E3243-51}, abstract = {

Mycobacteria are surrounded by a complex multilayered envelope and elongate at the poles. The principles that organize the coordinated addition of chemically diverse cell wall layers during polar extension remain unclear. We show that enzymes mediating the terminal cytosolic steps of peptidoglycan, arabinogalactan, and mycolic acid synthesis colocalize at sites of cell growth or division. The tropomyosin-like protein, DivIVA, is targeted to the negative curvature of the pole, is enriched at the growing end, and determines cell shape from this site. In contrast, cell wall synthetic complexes are concentrated at a distinct subpolar location. When viewed at subdiffraction resolution, new peptidoglycan is deposited at this subpolar site, and inert cell wall covers the DivIVA-marked tip. The differentiation between polar tip and cell wall synthetic complexes is also apparent at the biochemical level. Enzymes that generate mycolate precursors interact with DivIVA, but the final condensation of mycolic acids occurs in a distinct protein complex at the site of nascent cell wall addition. We propose an ultrastructural model of mycobacterial polar growth where new cell wall is added in an annular zone below the cell tip. This model may be broadly applicable to other bacterial and fungal organisms that grow via polar extension.

}, keywords = {Bacterial Proteins, Cell Cycle Proteins, Cell Membrane, Cell Polarity, Cell Wall, Models, Biological, Mycobacterium smegmatis, Mycolic Acids, Protein Binding}, issn = {1091-6490}, doi = {10.1073/pnas.1402158111}, author = {Meniche, Xavier and Otten, Renee and Siegrist, M Sloan and Baer, Christina E and Murphy, Kenan C and Bertozzi, Carolyn R and Sassetti, Christopher M} } @article {3154, title = {Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation.}, journal = {ISME J}, volume = {7}, year = {2013}, month = {2013 Feb}, pages = {370-83}, abstract = {

The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the α-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (>60\%) and acr3-1 (>90\%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50\%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.

}, keywords = {Acetates, Arsenate Reductases, Arsenic, Biodegradation, Environmental, Colorado, Gene Expression Regulation, Bacterial, Genes, Bacterial, Geobacter, Groundwater, Transcriptome, Uranium}, issn = {1751-7370}, doi = {10.1038/ismej.2012.109}, author = {Giloteaux, Ludovic and Holmes, Dawn E and Williams, Kenneth H and Wrighton, Kelly C and Wilkins, Michael J and Montgomery, Alison P and Smith, Jessica A and Orellana, Roberto and Thompson, Courtney A and Roper, Thomas J and Long, Philip E and Lovley, Derek R} } @article {1444, title = {Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase.}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, year = {2013}, month = {2013 Dec 24}, pages = {E5069-77}, abstract = {

Bacteria are able to adapt to dramatically different microenvironments, but in many organisms, the signaling pathways, transcriptional programs, and downstream physiological changes involved in adaptation are not well-understood. Here, we discovered that osmotic stress stimulates a signaling network in Mycobacterium tuberculosis regulated by the eukaryotic-like receptor Ser/Thr protein kinase PknD. Expression of the PknD substrate Rv0516c was highly induced by osmotic stress. Furthermore, Rv0516c disruption modified peptidoglycan thickness, enhanced antibiotic resistance, and activated genes in the regulon of the alternative σ-factor SigF. Phosphorylation of Rv0516c regulated the abundance of EspA, a virulence-associated substrate of the type VII ESX-1 secretion system. These findings identify an osmosensory pathway orchestrated by PknD, Rv0516c, and SigF that enables adaptation to osmotic stress through cell wall remodeling and virulence factor production. Given the widespread occurrence of eukaryotic-like Ser/Thr protein kinases in bacteria, these proteins may play a broad role in bacterial osmosensing.

}, keywords = {Adaptation, Biological, Blotting, Western, Gene Expression Regulation, Bacterial, Green Fluorescent Proteins, Microarray Analysis, Mycobacterium tuberculosis, Osmolar Concentration, Osmotic Pressure, Phosphorylation, Protein Kinases, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.1321205110}, author = {Hatzios, Stavroula K and Baer, Christina E and Rustad, Tige R and Siegrist, M Sloan and Pang, Jennifer M and Ortega, Corrie and Alber, Tom and Grundner, Christoph and Sherman, David R and Bertozzi, Carolyn R} } @article {3137, title = {U(VI) reduction by diverse outer surface c-type cytochromes of Geobacter sulfurreducens.}, journal = {Appl Environ Microbiol}, volume = {79}, year = {2013}, month = {2013 Oct}, pages = {6369-74}, abstract = {

Early studies with Geobacter sulfurreducens suggested that outer-surface c-type cytochromes might play a role in U(VI) reduction, but it has recently been suggested that there is substantial U(VI) reduction at the surface of the electrically conductive pili known as microbial nanowires. This phenomenon was further investigated. A strain of G. sulfurreducens, known as Aro-5, which produces pili with substantially reduced conductivity reduced U(VI) nearly as well as the wild type, as did a strain in which the gene for PilA, the structural pilin protein, was deleted. In order to reduce rates of U(VI) reduction to levels less than 20\% of the wild-type rates, it was necessary to delete the genes for the five most abundant outer surface c-type cytochromes of G. sulfurreducens. X-ray absorption near-edge structure spectroscopy demonstrated that whereas 83\% {\textpm} 10\% of the uranium associated with wild-type cells correspond to U(IV) after 4 h of incubation, with the quintuple mutant, 89\% {\textpm} 10\% of uranium was U(VI). Transmission electron microscopy and X-ray energy dispersion spectroscopy revealed that wild-type cells did not precipitate uranium along pili as previously reported, but U(IV) was precipitated at the outer cell surface. These findings are consistent with those of previous studies, which have suggested that G. sulfurreducens requires outer-surface c-type cytochromes but not pili for the reduction of soluble extracellular electron acceptors.

}, keywords = {Cytochromes, Fimbriae, Bacterial, Gene Deletion, Geobacter, Microscopy, Electron, Transmission, Oxidation-Reduction, Uranium, X-Ray Absorption Spectroscopy}, issn = {1098-5336}, doi = {10.1128/AEM.02551-13}, author = {Orellana, Roberto and Leavitt, Janet J and Comolli, Luis R and Csencsits, Roseann and Janot, Noemie and Flanagan, Kelly A and Gray, Arianna S and Leang, Ching and Izallalen, Mounir and Mester, T{\"u}nde and Lovley, Derek R} } @article {1206, title = {Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, year = {2012}, month = {2012 Aug 21}, pages = {13674-9}, abstract = {

Microbial productivity at hydrothermal vents is among the highest found anywhere in the deep ocean, but constraints on microbial growth and metabolism at vents are lacking. We used a combination of cultivation, molecular, and geochemical tools to verify pure culture H(2) threshold measurements for hyperthermophilic methanogenesis in low-temperature hydrothermal fluids from Axial Volcano and Endeavour Segment in the northeastern Pacific Ocean. Two Methanocaldococcus strains from Axial and Methanocaldococcus jannaschii showed similar Monod growth kinetics when grown in a bioreactor at varying H(2) concentrations. Their H(2) half-saturation value was 66 μM, and growth ceased below 17-23 μM H(2), 10-fold lower than previously predicted. By comparison, measured H(2) and CH(4) concentrations in fluids suggest that there was generally sufficient H(2) for Methanocaldococcus growth at Axial but not at Endeavour. Fluids from one vent at Axial (Marker 113) had anomalously high CH(4) concentrations and contained various thermal classes of methanogens based on cultivation and mcrA/mrtA analyses. At Endeavour, methanogens were largely undetectable in fluid samples based on cultivation and molecular screens, although abundances of hyperthermophilic heterotrophs were relatively high. Where present, Methanocaldococcus genes were the predominant mcrA/mrtA sequences recovered and comprised \~{}0.2-6\% of the total archaeal community. Field and coculture data suggest that H(2) limitation may be partly ameliorated by H(2) syntrophy with hyperthermophilic heterotrophs. These data support our estimated H(2) threshold for hyperthermophilic methanogenesis at vents and highlight the need for coupled laboratory and field measurements to constrain microbial distribution and biogeochemical impacts in the deep sea.

}, keywords = {Archaea, Biodiversity, Coculture Techniques, DNA, Ribosomal, Ecosystem, Gases, Geography, Hydrogen, Hydrothermal Vents, Kinetics, Methane, Molecular Sequence Data, Temperature, Time Factors, Water Microbiology}, issn = {1091-6490}, doi = {10.1073/pnas.1206632109}, author = {Ver Eecke, Helene C and Butterfield, David A and Huber, Julie A and Lilley, Marvin D and Olson, Eric J and Roe, Kevin K and Evans, Leigh J and Merkel, Alexandr Y and Cantin, Holly V and Holden, James F} } @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 {424, title = {Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms.}, journal = {Appl Environ Microbiol}, volume = {77}, year = {2011}, month = {2011 May}, pages = {2882-6}, abstract = {Microbial electrosynthesis, a process in which microorganisms use electrons derived from electrodes to reduce carbon dioxide to multicarbon, extracellular organic compounds, is a potential strategy for capturing electrical energy in carbon-carbon bonds of readily stored and easily distributed products, such as transportation fuels. To date, only one organism, the acetogen Sporomusa ovata, has been shown to be capable of electrosynthesis. The purpose of this study was to determine if a wider range of microorganisms is capable of this process. Several other acetogenic bacteria, including two other Sporomusa species, Clostridium ljungdahlii, Clostridium aceticum, and Moorella thermoacetica, consumed current with the production of organic acids. In general acetate was the primary product, but 2-oxobutyrate and formate also were formed, with 2-oxobutyrate being the predominant identified product of electrosynthesis by C. aceticum. S. sphaeroides, C. ljungdahlii, and M. thermoacetica had high (>80\%) efficiencies of electrons consumed and recovered in identified products. The acetogen Acetobacterium woodii was unable to consume current. These results expand the known range of microorganisms capable of electrosynthesis, providing multiple options for the further optimization of this process.}, keywords = {Acetobacterium, Carbon Dioxide, Clostridium, Electrodes, Electrons, Moorella, Organic Chemicals, Oxidation-Reduction, Veillonellaceae}, issn = {1098-5336}, doi = {10.1128/AEM.02642-10}, author = {Nevin, Kelly P and Hensley, Sarah A and Franks, Ashley E and Summers, Zarath M and Ou, Jianhong and Woodard, Trevor L and Snoeyenbos-West, Oona L and Lovley, Derek R} } @article {415, title = {Geobacter: the microbe electric{\textquoteright}s physiology, ecology, and practical applications.}, journal = {Adv Microb Physiol}, volume = {59}, year = {2011}, month = {2011}, pages = {1-100}, abstract = {Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.}, keywords = {Biotechnology, Ecology, Environmental Remediation, Ferric Compounds, Geobacter}, issn = {0065-2911}, doi = {10.1016/B978-0-12-387661-4.00004-5}, author = {Lovley, Derek R and Ueki, Toshiyuki and Zhang, Tian and Malvankar, Nikhil S and Shrestha, Pravin M and Flanagan, Kelly A and Aklujkar, Muktak and Butler, Jessica E and Giloteaux, Ludovic and Rotaru, Amelia-Elena and Holmes, Dawn E and Franks, Ashley E and Orellana, Roberto and Risso, Carla and Nevin, Kelly P} } @article {373, title = {PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.}, journal = {Appl Environ Microbiol}, volume = {77}, year = {2011}, month = {2011 Sep}, pages = {6313-22}, abstract = {Environmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20\% in soil and 60\% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.}, keywords = {Biodiversity, DNA, Complementary, Environmental Microbiology, Metagenomics, Microarray Analysis, Oligonucleotide Array Sequence Analysis, RNA, Ribosomal, 16S, Sensitivity and Specificity}, issn = {1098-5336}, doi = {10.1128/AEM.05262-11}, author = {Deangelis, Kristen M and Wu, Cindy H and Beller, Harry R and Brodie, Eoin L and Chakraborty, Romy and DeSantis, Todd Z and Fortney, Julian L and Hazen, Terry C and Osman, Shariff R and Singer, Mary E and Tom, Lauren M and Andersen, Gary L} } @article {1208, title = {Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea.}, journal = {Appl Environ Microbiol}, volume = {77}, year = {2011}, month = {2011 May}, pages = {3169-73}, abstract = {

Nineteen hyperthermophilic heterotrophs from deep-sea hydrothermal vents, plus the control organism Pyrococcus furiosus, were examined for their ability to grow and produce H$_{2}$ on maltose, cellobiose, and peptides and for the presence of the genes encoding proteins that hydrolyze starch and cellulose. All of the strains grew on these disaccharides and peptides and converted maltose and peptides to H$_{2}$ even when elemental sulfur was present as a terminal electron acceptor. Half of the strains had at least one gene for an extracellular starch hydrolase, but only P. furiosus had a gene for an extracellular β-1,4-endoglucanase. P. furiosus was serially adapted for growth on CF11 cellulose and H$_{2}$ production, which is the first reported instance of hyperthermophilic growth on cellulose, with a doubling time of 64 min. Cell-specific H$_{2}$ production rates were 29 fmol, 37 fmol, and 54 fmol of H$_{2}$ produced cell$^{-}${\textonesuperior} doubling$^{-}${\textonesuperior} on α-1,4-linked sugars, β-1,4-linked sugars, and peptides, respectively. The highest total community H$_{2}$ production rate came from growth on starch (2.6 mM H$_{2}$ produced h$^{-}${\textonesuperior}). Hyperthermophilic heterotrophs may serve as an important alternate source of H$_{2}$ for hydrogenotrophic microorganisms in low-H$_{2}$ hydrothermal environments, and some are candidates for H$_{2}$ bioenergy production in bioreactors.

}, keywords = {Archaea, Carbohydrate Metabolism, Hot Springs, Hydro-Lyases, Hydrogen, Peptides, Seawater}, issn = {1098-5336}, doi = {10.1128/AEM.01366-10}, author = {Oslowski, Daniel M and Jung, Jong-Hyun and Seo, Dong-Ho and Park, Cheon-Seok and Holden, James F} } @article {676, title = {Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules.}, journal = {J Struct Biol}, volume = {175}, year = {2011}, month = {2011 Aug}, pages = {244-52}, abstract = {Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia{\textquoteright}s use for 3D visualization in structure-related pedagogy.}, keywords = {Encyclopedias as Topic, Information Dissemination, Information Management, Information Services, Models, Molecular, Molecular Biology, Online Systems, Protein Conformation, Proteins, User-Computer Interface}, issn = {1095-8657}, doi = {10.1016/j.jsb.2011.04.011}, author = {Prilusky, Jaime and Hodis, Eran and Canner, David and Decatur, Wayne A and Oberholser, Karl and Martz, Eric and Berchanski, Alexander and Harel, Michal and Sussman, Joel L} } @article {490, title = {PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens.}, journal = {J Mol Microbiol Biotechnol}, volume = {16}, year = {2009}, month = {2009}, pages = {146-58}, abstract = {Growth using Fe(III) as a terminal electron acceptor is a critical physiological process in Geobacter sulfurreducens. However, the mechanisms of electron transfer during Fe(III) reduction are only now being understood. It has been demonstrated that the pili in G. sulfurreducens function as microbial nanowires conducting electrons onto Fe(III) oxides. A number of c-type cytochromes have also been shown to play important roles in Fe(III) reduction. However, the regulatory networks controlling the expression of the genes involved in such processes are not well known. Here we report that the expression of pilA, which encodes the pilistructural protein, is directly regulated by a two-component regulatory system in which PilR functions as an RpoN-dependent enhancer binding protein. Surprisingly, a deletion of the pilR gene affected not only insoluble Fe(III) reduction, which requires pili, but also soluble Fe(III) reduction, which, in contrast, does not require pili. Gene expression profiling using whole-genome DNA microarray and quantitative RT-PCR analyses obtained with a PilR-deficient mutant revealed that the expression of pilA and other pilin-related genes are downregulated, while many c-type cytochromes involved in Fe(III) reduction were differentially regulated. This is the first instance of an enhancer binding protein implicated in regulating genes involved in Fe(III) respiratory functions.}, keywords = {Bacterial Proteins, Ferric Compounds, Fimbriae Proteins, Gene Expression Regulation, Bacterial, Genes, Regulator, Geobacter, Oxidation-Reduction, Transcription, Genetic}, issn = {1660-2412}, doi = {10.1159/000115849}, author = {Ju{\'a}rez, Katy and Kim, Byoung-Chan and Nevin, Kelly and Olvera, Leticia and Reguera, Gemma and Lovley, Derek R and Meth{\'e}, Barbara A} } @article {471, title = {Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments.}, journal = {ISME J}, volume = {3}, year = {2009}, month = {2009 Feb}, pages = {216-30}, abstract = {To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.}, keywords = {Colorado, DNA, Bacterial, Environmental Microbiology, Gene Expression Profiling, Geobacter, Geologic Sediments, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Sequence Analysis, DNA, Uranium}, issn = {1751-7370}, doi = {10.1038/ismej.2008.89}, author = {Holmes, Dawn E and O{\textquoteright}Neil, Regina A and Chavan, Milind A and N{\textquoteright}guessan, Lucie A and Vrionis, Helen A and Perpetua, Lorrie A and Larrahondo, M Juliana and DiDonato, Raymond and Liu, Anna and Lovley, Derek R} } @article {360, title = {Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade.}, journal = {J Gen Virol}, volume = {90}, year = {2009}, month = {2009 Feb}, pages = {334-46}, abstract = {Glossina pallidipes and Musca domestica salivary gland hypertrophy viruses (GpSGHV and MdSGHV) replicate in the nucleus of salivary gland cells causing distinct tissue hypertrophy and reduction of host fertility. They share general characteristics with the non-occluded insect nudiviruses, such as being insect-pathogenic, having enveloped, rod-shaped virions, and large circular double-stranded DNA genomes. MdSGHV measures 65x550 nm and contains a 124 279 bp genome (approximately 44 mol\% G+C content) that codes for 108 putative open reading frames (ORFs). GpSGHV, measuring 50x1000 nm, contains a 190 032 bp genome (28 mol\% G+C content) with 160 putative ORFs. Comparative genomic analysis demonstrates that 37 MdSGHV ORFs have homology to 42 GpSGHV ORFs, as some MdSGHV ORFs have homology to two different GpSGHV ORFs. Nine genes with known functions (dnapol, ts, pif-1, pif-2, pif-3, mmp, p74, odv-e66 and helicase-2), a homologue of the conserved baculovirus gene Ac81 and at least 13 virion proteins are present in both SGHVs. The amino acid identity ranged from 19 to 39 \% among ORFs. An (A/T/G)TAAG motif, similar to the baculovirus late promoter motif, was enriched 100 bp upstream of the ORF transcription initiation sites of both viruses. Six and seven putative microRNA sequences were found in MdSGHV and GpSGHV genomes, respectively. There was genome. Collinearity between the two SGHVs, but not between the SGHVs and the nudiviruses. Phylogenetic analysis of conserved genes clustered both SGHVs in a single clade separated from the nudiviruses and baculoviruses. Although MdSGHV and GpSGHV are different viruses, their pathology, host range and genome composition indicate that they are related.}, keywords = {Animals, Chromosome Mapping, Conserved Sequence, Cytomegalovirus, DNA, Viral, Genes, Viral, Genome, Viral, Houseflies, Hypertrophy, Open Reading Frames, Salivary Glands, Tsetse Flies, Virion}, issn = {0022-1317}, doi = {10.1099/vir.0.006783-0}, author = {Garcia-Maruniak, Alejandra and Abd-Alla, Adly M M and Salem, Tamer Z and Parker, Andrew G and Lietze, Verena-Ulrike and van Oers, Monique M and Maruniak, James E and Kim, Woojin and Burand, John P and Cousserans, Fran{\c c}ois and Robinson, Alan S and Vlak, Just M and Bergoin, Max and Boucias, Drion G} } @article {700, title = {Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis.}, journal = {OMICS}, volume = {12}, year = {2008}, month = {2008 Mar}, pages = {33-59}, abstract = {Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate assimilation, and energy metabolism, as well as genes potentially encoding acetate permease. Further, similar TFBS were identified from the analysis of both sets, suggesting that these TFBS are significant in the regulation of metabolism in G. sulfurreducens. In addition, we have utilized microarray data to derive condition specific constraints on the capacity of key enzymes in central metabolism. We have incorporated these constraints into the metabolic model of G. sulfurreducens and simulated Fe(II)-limited growth. The resulting prediction was consistent with data, suggesting that regulatory constraints are important for simulating growth phenotypes in nonoptimal environments.}, keywords = {Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Models, Genetic, Oligonucleotide Array Sequence Analysis, Sequence Analysis, DNA, Transcription, Genetic}, issn = {1536-2310}, doi = {10.1089/omi.2007.0043}, author = {Mahadevan, Radhakrishnan and Yan, Bin and Postier, Brad and Nevin, Kelly P and Woodard, Trevor L and O{\textquoteright}Neil, Regina and Coppi, Maddalena V and Meth{\'e}, Barbara A and Krushkal, Julia} } @article {491, title = {Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {190}, year = {2008}, month = {2008 Apr}, pages = {2266-74}, abstract = {The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were identified and knocked out. Mutants lacking both of these enzymes were auxotrophs for isoleucine, whereas single mutants were capable of growth in the absence of isoleucine. Biochemical characterization of the single mutants revealed deficiencies in citramalate synthase and threonine ammonia-lyase activity. Thus, in G. sulfurreducens, 2-oxobutanoate can be synthesized either from citramalate or threonine, with the former being the main pathway for isoleucine biosynthesis. The citramalate synthase of G. sulfurreducens constitutes the first characterized member of a phylogenetically distinct clade of citramalate synthases, which contains representatives from a wide variety of microorganisms.}, keywords = {Acetyl Coenzyme A, Bacterial Proteins, Biosynthetic Pathways, Butyric Acids, Carbon Isotopes, Geobacter, Isoleucine, Malates, Pyruvic Acid, Threonine, Threonine Dehydratase}, issn = {1098-5530}, doi = {10.1128/JB.01841-07}, author = {Risso, Carla and Van Dien, Stephen J and Orloff, Amber and Lovley, Derek R and Coppi, Maddalena V} } @article {488, title = {Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation.}, journal = {Environ Microbiol}, volume = {10}, year = {2008}, month = {2008 May}, pages = {1218-30}, abstract = {Limitations on the availability of Fe(III) as an electron acceptor are thought to play an important role in restricting the growth and activity of Geobacter species during bioremediation of contaminated subsurface environments, but the possibility that these organisms might also be limited in the subsurface by the availability of iron for assimilatory purposes was not previously considered because copious quantities of Fe(II) are produced as the result of Fe(III) reduction. Analysis of multiple Geobacteraceae genomes revealed the presence of a three-gene cluster consisting of homologues of two iron-dependent regulators, fur and dtxR (ideR), separated by a homologue of feoB, which encodes an Fe(II) uptake protein. This cluster appears to be conserved among members of the Geobacteraceae and was detected in several environments. Expression of the fur-feoB-ideR cluster decreased as Fe(II) concentrations increased in chemostat cultures. The number of Geobacteraceae feoB transcripts in groundwater samples from a site undergoing in situ uranium bioremediation was relatively high until the concentration of dissolved Fe(II) increased near the end of the field experiment. These results suggest that, because much of the Fe(II) is sequestered in solid phases, Geobacter species, which have a high requirement for iron for iron-sulfur proteins, may be limited by the amount of iron available for assimilatory purposes. These results demonstrate the ability of transcript analysis to reveal previously unsuspected aspects of the in situ physiology of microorganisms in subsurface environments.}, keywords = {Bacterial Proteins, Biodegradation, Environmental, Culture Media, Ferric Compounds, Ferrous Compounds, Fresh Water, Gene Expression Regulation, Bacterial, Geobacter, Iron, Multigene Family, Phylogeny, Polymerase Chain Reaction, Repressor Proteins, Reverse Transcriptase Polymerase Chain Reaction, Transcription, Genetic, Uranium, Water Pollution, Radioactive}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2007.01537.x}, author = {O{\textquoteright}Neil, Regina A and Holmes, Dawn E and Coppi, Maddalena V and Adams, Lorrie A and Larrahondo, M Juliana and Ward, Joy E and Nevin, Kelly P and Woodard, Trevor L and Vrionis, Helen A and N{\textquoteright}guessan, Lucie A and Lovley, Derek R} } @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 {479, title = {Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells.}, journal = {Environ Microbiol}, volume = {10}, year = {2008}, month = {2008 Oct}, pages = {2505-14}, abstract = {It has been previously noted that mixed communities typically produce more power in microbial fuel cells than pure cultures. If true, this has important implications for the design of microbial fuel cells and for studying the process of electron transfer on anode biofilms. To further evaluate this, Geobacter sulfurreducens was grown with acetate as fuel in a continuous flow {\textquoteright}ministack{\textquoteright} system in which the carbon cloth anode and cathode were positioned in close proximity, and the cation-selective membrane surface area was maximized in order to overcome some of the electrochemical limitations that were inherent in fuel cells previously employed for the study of pure cultures. Reducing the size of the anode in order to eliminate cathode limitation resulted in maximum current and power densities per m(2) of anode surface of 4.56 A m(-2) and 1.88 W m(-2) respectively. Electron recovery as current from acetate oxidation was c. 100\% when oxygen diffusion into the system was minimized. This performance is comparable to the highest levels previously reported for mixed communities in similar microbial fuel cells and slightly higher than the power output of an anaerobic sludge inoculum in the same ministack system. Minimizing the volume of the anode chamber yielded a volumetric power density of 2.15 kW m(-3), which is the highest power density per volume yet reported for a microbial fuel cell. Geobacter sulfurreducens formed relatively uniform biofilms 3-18 mum thick on the carbon cloth anodes. When graphite sticks served as the anode, the current density (3.10 A m(-2)) was somewhat less than with the carbon cloth anodes, but the biofilms were thicker (c. 50 mum) with a more complex pillar and channel structure. These results suggest that the previously observed disparity in power production in pure and mixed culture microbial fuel cell systems can be attributed more to differences in the fuel cell designs than to any inherent superior capability of mixed cultures to produce more power than pure cultures.}, keywords = {Acetic Acid, Biofilms, Carbon, Electricity, Electrodes, Geobacter, Oxidation-Reduction}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2008.01675.x}, author = {Nevin, K P and Richter, H and Covalla, S F and Johnson, J P and Woodard, T L and Orloff, A L and Jia, H and Zhang, M and Lovley, D R} } @article {500, title = {Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments.}, journal = {Microb Ecol}, volume = {55}, year = {2008}, month = {2008 Apr}, pages = {489-99}, abstract = {The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.}, keywords = {Anaerobiosis, Desulfitobacterium, DNA, Bacterial, DNA, Ribosomal, Gene Expression, Geologic Sediments, Hydrogensulfite Reductase, Molecular Sequence Data, Petroleum, Phylogeny, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, 16S, Temperature}, issn = {0095-3628}, doi = {10.1007/s00248-007-9294-2}, author = {Chin, Kuk-Jeong and Sharma, Manju L and Russell, Lyndsey A and O{\textquoteright}Neill, Kathleen R and Lovley, Derek R} } @article {499, title = {Involvement of Geobacter sulfurreducens SfrAB in acetate metabolism rather than intracellular, respiration-linked Fe(III) citrate reduction.}, journal = {Microbiology}, volume = {153}, year = {2007}, month = {2007 Oct}, pages = {3572-85}, abstract = {A soluble ferric reductase, SfrAB, which catalysed the NADPH-dependent reduction of chelated Fe(III), was previously purified from the dissimilatory Fe(III)-reducing micro-organism Geobacter sulfurreducens, suggesting that reduction of chelated forms of Fe(III) might be cytoplasmic. However, metabolically active spheroplast suspensions could not catalyse acetate-dependent Fe(III) citrate reduction, indicating that periplasmic and/or outer-membrane components were required for Fe(III) citrate reduction. Furthermore, phenotypic analysis of an SfrAB knockout mutant suggested that SfrAB was involved in acetate metabolism rather than respiration-linked Fe(III) reduction. The mutant could not grow via the reduction of either Fe(III) citrate or fumarate when acetate was the electron donor but could grow with either acceptor if either hydrogen or formate served as the electron donor. Following prolonged incubation in acetate : fumarate medium in the absence of hydrogen and formate, an {\textquoteright}acetate-adapted{\textquoteright} SfrAB-null strain was isolated that was capable of growth on acetate : fumarate medium but not acetate : Fe(III) citrate medium. Comparison of gene expression in this strain with that of the wild-type revealed upregulation of a potential NADPH-dependent ferredoxin oxidoreductase as well as genes involved in energy generation and amino acid uptake, suggesting that NADPH homeostasis and the tricarboxylic acid (TCA) cycle were perturbed in the {\textquoteright}acetate-adapted{\textquoteright} SfrAB-null strain. Membrane and soluble fractions prepared from the {\textquoteright}acetate-adapted{\textquoteright} strain were depleted of NADPH-dependent Fe(III), viologen and quinone reductase activities. These results indicate that cytoplasmic, respiration-linked reduction of Fe(III) by SfrAB in vivo is unlikely and suggest that deleting SfrAB may interfere with growth via acetate oxidation by interfering with NADP regeneration.}, keywords = {Acetates, Amino Acid Transport Systems, Bacterial Proteins, Cell Membrane, Citric Acid Cycle, Cytoplasm, Energy Metabolism, Ferric Compounds, Formic Acids, Fumarates, Gene Deletion, Gene Expression Profiling, Geobacter, Hydrogen, NADH, NADPH Oxidoreductases, Oligonucleotide Array Sequence Analysis}, issn = {1350-0872}, doi = {10.1099/mic.0.2007/006478-0}, author = {Coppi, Maddalena V and O{\textquoteright}Neil, Regina A and Leang, Ching and Kaufmann, Franz and Meth{\'e}, Barbara A and Nevin, Kelly P and Woodard, Trevor L and Liu, Anna and Lovley, Derek R} } @article {493, title = {Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments.}, journal = {ISME J}, volume = {1}, year = {2007}, month = {2007 Dec}, pages = {663-77}, abstract = {There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.}, keywords = {Biodegradation, Environmental, Ecosystem, Ferric Compounds, Geobacter, Hydrocarbons, Aromatic, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Uranium}, issn = {1751-7362}, doi = {10.1038/ismej.2007.85}, author = {Holmes, Dawn E and O{\textquoteright}Neil, Regina A and Vrionis, Helen A and N{\textquoteright}guessan, Lucie A and Ortiz-Bernad, Irene and Larrahondo, Maria J and Adams, Lorrie A and Ward, Joy A and Nicoll, Julie S and Nevin, Kelly P and Chavan, Milind A and Johnson, Jessica P and Long, Philip E and Lovley, Derek R} } @article {747, title = {Broad-spectrum antibacterial activity by a novel abiogenic peptide mimic.}, journal = {Microbiology}, volume = {152}, year = {2006}, month = {2006 Jul}, pages = {1913-8}, abstract = {The human-mediated use and abuse of classical antibiotics has created a strong selective pressure for the rapid evolution of antibiotic resistance. As resistance levels rise, and the efficacy of classical antibiotics wanes, the intensity of the search for alternative antimicrobials has increased. One class of molecules that has attracted much attention is the antimicrobial peptides (AMPs). They exhibit broad-spectrum activity, they are potent and they are widespread as part of the innate defence system of both vertebrates and invertebrates. However, peptides are complex molecules that suffer from proteolytic degradation. The ability to capture the essential properties of antimicrobial peptides in simple easy-to-prepare molecules that are abiotic in origin and non-proteolytic offers many advantages. Mechanistic and structural knowledge of existing AMPs was used to design a novel compound that mimics the biochemical activity of an AMP. This report describes the development and in vitro characterization of a small peptide mimic that exhibited quick-acting and selective antibacterial activity against a broad range of bacteria, including numerous clinically relevant strains, at low MIC values.}, keywords = {Anti-Bacterial Agents, Drug Design, Humans, Microbial Sensitivity Tests, Peptides}, issn = {1350-0872}, doi = {10.1099/mic.0.28812-0}, author = {N{\"u}sslein, Klaus and Arnt, Lachelle and Rennie, Jason and Owens, Cullen and Tew, Gregory N} } @article {695, title = {TbGPI16 is an essential component of GPI transamidase in Trypanosoma brucei.}, journal = {FEBS Lett}, volume = {580}, year = {2006}, month = {2006 Jan 23}, pages = {603-6}, abstract = {Glycosylphosphatidylinositol (GPI) is widely used by eukaryotic cell surface proteins for membrane attachment. De novo synthesized GPI precursors are attached to proteins post-translationally by the enzyme complex, GPI transamidase. TbGPI16, a component of the trypanosome transamidase, shares similarity with human PIG-T. Here, we show that TbGPI16 is the orthologue of PIG-T and an essential component of GPI transamidase by creating a TbGPI16 knockout. TbGPI16 forms a disulfide-linked complex with TbGPI8. A cysteine to serine mutant of TbGPI16 was unable to fully restore the surface expression of GPI-anchored proteins upon transfection into the knockout cells, indicating that its disulfide linkage with TbGPI8 is important for the full transamidase activity.}, keywords = {Acyltransferases, Animals, Disulfides, Gene Targeting, Humans, Membrane Glycoproteins, Multiprotein Complexes, Mutation, Protein Subunits, Protozoan Proteins, Trypanosoma brucei brucei}, issn = {0014-5793}, doi = {10.1016/j.febslet.2005.12.075}, author = {Hong, Yeonchul and Nagamune, Kisaburo and Ohishi, Kazuhito and Morita, Yasu S and Ashida, Hisashi and Maeda, Yusuke and Kinoshita, Taroh} } @article {532, title = {Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates.}, journal = {Int J Syst Evol Microbiol}, volume = {55}, year = {2005}, month = {2005 Jul}, pages = {1667-74}, abstract = {Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain Bem(T) was enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35(T) and P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35(T) and P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA and nifD genes indicated that all four strains are delta-proteobacteria and members of the Geobacter cluster of the Geobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genus Geobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain Bem(T) grew fastest at 30 degrees C, whereas strains P11, P35(T) and P39 grew equally well at 17, 22 and 30 degrees C. In addition, strains P11, P35(T) and P39 were capable of growth at 4 degrees C. The names Geobacter bemidjiensis sp. nov. (type strain Bem(T)=ATCC BAA-1014(T)=DSM 16622(T)=JCM 12645(T)) and Geobacter psychrophilus sp. nov. (strains P11, P35(T) and P39; type strain P35(T)=ATCC BAA-1013(T)=DSM 16674(T)=JCM 12644(T)) are proposed.}, keywords = {Bacterial Proteins, Bacterial Typing Techniques, Cold Temperature, DNA, Bacterial, DNA, Ribosomal, Ferric Compounds, Fresh Water, Genes, rRNA, Geobacter, Geologic Sediments, Massachusetts, Minnesota, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S, Species Specificity, Water Supply}, issn = {1466-5026}, doi = {10.1099/ijs.0.63417-0}, author = {Nevin, Kelly P and Holmes, Dawn E and Woodard, Trevor L and Hinlein, Erich S and Ostendorf, David W and Lovley, Derek R} } @article {526, title = {Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI).}, journal = {Environ Sci Technol}, volume = {39}, year = {2005}, month = {2005 Dec 1}, pages = {9039-48}, abstract = {A field-scale acetate amendment experiment was performed in a contaminated aquifer at Old Rifle, CO to stimulate in situ microbial reduction of U(VI) in groundwater. To evaluate the microorganisms responsible for microbial uranium reduction during the experiment, 13C-labeled acetate was introduced into well bores via bio-traps containing porous activated carbon beads (Bio-Sep). Incorporation of the 13C from labeled acetate into cellular DNA and phospholipid fatty acid (PLFA) biomarkers was analyzed in parallel with geochemical parameters. An enrichment of active sigma-proteobacteria was demonstrated in downgradient monitoring wells: Geobacter dominated in wells closer to the acetate injection gallery, while various sulfate reducers were prominent in different downgradient wells. These results were consistent with the geochemical evidence of Fe(III), U(VI), and SO(4)2- reduction. PLFA profiling of bio-traps suspended in the monitoring wells also showed the incorporation of 13C into bacterial cellular lipids. Community composition of downgradient monitoring wells based on quinone and PLFA profiling was in general agreement with the 13C-DNA result. The direct application of 13C label to biosystems, coupled with DNA and PLFA analysis,}, keywords = {Acetates, Biodegradation, Environmental, Carbon Isotopes, Electrophoresis, Polyacrylamide Gel, Geobacter, Phylogeny, Polymerase Chain Reaction, Proteobacteria, Uranium}, issn = {0013-936X}, author = {Chang, Yun-Juan and Long, Philip E and Geyer, Roland and Peacock, Aaron D and Resch, Charles T and Sublette, Kerry and Pfiffner, Susan and Smithgall, Amanda and Anderson, Robert T and Vrionis, Helen A and Stephen, John R and Dayvault, Richard and Ortiz-Bernad, Irene and Lovley, Derek R and White, David C} } @article {530, title = {Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site.}, journal = {Appl Environ Microbiol}, volume = {71}, year = {2005}, month = {2005 Oct}, pages = {6308-18}, abstract = {The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.}, keywords = {Acetates, Biodegradation, Environmental, Deltaproteobacteria, DNA, Bacterial, DNA, Ribosomal, Ferric Compounds, Fresh Water, Geologic Sediments, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sulfates, Uranium, Water Pollution}, issn = {0099-2240}, doi = {10.1128/AEM.71.10.6308-6318.2005}, author = {Vrionis, Helen A and Anderson, Robert T and Ortiz-Bernad, Irene and O{\textquoteright}Neill, Kathleen R and Resch, Charles T and Peacock, Aaron D and Dayvault, Richard and White, David C and Long, Philip E and Lovley, Derek R} } @article {529, title = {Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes.}, journal = {Appl Environ Microbiol}, volume = {71}, year = {2005}, month = {2005 Nov}, pages = {6870-7}, abstract = {The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.}, keywords = {Acetates, Citrate (si)-Synthase, Deltaproteobacteria, DNA, Ribosomal, Electrodes, Ferric Compounds, Fresh Water, Geobacter, Geologic Sediments, Petroleum, Phylogeny, RNA, Ribosomal, 16S, Uranium, Water Pollutants, Chemical, Water Pollutants, Radioactive}, issn = {0099-2240}, doi = {10.1128/AEM.71.11.6870-6877.2005}, author = {Holmes, Dawn E and Nevin, Kelly P and O{\textquoteright}Neil, Regina A and Ward, Joy E and Adams, Lorrie A and Woodard, Trevor L and Vrionis, Helen A and Lovley, Derek R} } @article {555, title = {Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {186}, year = {2004}, month = {2004 May}, pages = {3022-8}, abstract = {Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement. Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors. Hya, in contrast, was not. These findings suggest that Hyb is an essential respiratory hydrogenase in G. sulfurreducens.}, keywords = {Anthraquinones, Ferric Compounds, Fumarates, Geobacter, Hydrogen, Operon, Oxidation-Reduction, Oxidoreductases, Phenotype}, issn = {0021-9193}, author = {Coppi, Maddalena V and O{\textquoteright}Neil, Regina A and Lovley, Derek R} } @article {554, title = {Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant Bacterium from Low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov.}, journal = {Appl Environ Microbiol}, volume = {70}, year = {2004}, month = {2004 May}, pages = {2959-65}, abstract = {A facultatively anaerobic, acid-resistant bacterium, designated strain FRCl, was isolated from a low-pH, nitrate- and U(VI)-contaminated subsurface sediment at site FW-024 at the Natural and Accelerated Bioremediation Research Field Research Center in Oak Ridge, Tenn. Strain FRCl was enriched at pH 4.5 in minimal medium with nitrate as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Clones with 16S ribosomal DNA (rDNA) sequences identical to the sequence of strain FRCl were also detected in a U(VI)-reducing enrichment culture derived from the same sediment. Cells of strain FRCl were gram-negative motile regular rods 2.0 to 3.4 micro m long and 0.7 to 0.9 microm in diameter. Strain FRCl was positive for indole production, by the methyl red test, and for ornithine decarboxylase; it was negative by the Voges-Proskauer test (for acetylmethylcarbinol production), for urea hydrolysis, for arginine dihydrolase, for lysine decarboxylase, for phenylalanine deaminase, for H(2)S production, and for gelatin hydrolysis. Strain FRCl was capable of using O(2), NO(3)(-), S(2)O(3)(2-), fumarate, and malate as terminal electron acceptors and of reducing U(VI) in the cell suspension. Analysis of the 16S rDNA sequence of the isolate indicated that this strain was 96.4\% similar to Salmonella bongori and 96.3\% similar to Enterobacter cloacae. Physiological and phylogenetic analyses suggested that strain FRCl belongs to the genus Salmonella and represents a new species, Salmonella subterranea sp. nov.}, keywords = {Anaerobiosis, Culture Media, DNA, Ribosomal, Fresh Water, Geologic Sediments, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrates, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Salmonella, Sequence Analysis, DNA, Uranium, Water Pollution, Chemical}, issn = {0099-2240}, author = {Shelobolina, Evgenya S and Sullivan, Sara A and O{\textquoteright}Neill, Kathleen R and Nevin, Kelly P and Lovley, Derek R} } @article {544, title = {Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments.}, journal = {Microb Ecol}, volume = {48}, year = {2004}, month = {2004 Aug}, pages = {178-90}, abstract = {The microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. Three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. Fuel cells were also deployed in the field in salt marsh sediments in New Jersey and estuarine sediments in Oregon, USA. All of the sediments produced comparable amounts of power. Analysis of 16S rRNA gene sequences after 3-7 months of incubation demonstrated that all of the energy-harvesting anodes were highly enriched in microorganisms in the delta-Proteobacteria when compared with control electrodes not connected to a cathode. Geobacteraceae accounted for the majority of delta-Proteobacterial sequences or all of the energy-harvesting anodes, except the one deployed at the Oregon estuarine site. Quantitative PCR analysis of 16S rRNA genes and culturing studies indicated that Geobacteraceae were 100-fold more abundant on the marine-deployed anodes versus controls. Sequences most similar to microorganisms in the family Desulfobulbaceae predominated on the anode deployed in the estuarine sediments, and a significant proportion of the sequences recovered from the freshwater anodes were closely related to the Fe(III)-reducing isolate, Geothrix fermentans. There was also a specific enrichment of microorganisms on energy harvesting cathodes, but the enriched populations varied with the sediment/water source. Thus, future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.}, keywords = {Base Sequence, Biodiversity, Bioelectric Energy Sources, Cloning, Molecular, DNA Primers, Electrodes, Gammaproteobacteria, Geologic Sediments, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Restriction Mapping, RNA, Ribosomal, 16S, Sequence Analysis, DNA}, issn = {0095-3628}, doi = {10.1007/s00248-003-0004-4}, author = {Holmes, D E and Bond, D R and O{\textquoteright}Neil, R A and Reimers, C E and Tender, L R and Lovley, D R} } @article {542, title = {Resistance of solid-phase U(VI) to microbial reduction during in situ bioremediation of uranium-contaminated groundwater.}, journal = {Appl Environ Microbiol}, volume = {70}, year = {2004}, month = {2004 Dec}, pages = {7558-60}, abstract = {Speciation of solid-phase uranium in uranium-contaminated subsurface sediments undergoing uranium bioremediation demonstrated that although microbial reduction of soluble U(VI) readily immobilized uranium as U(IV), a substantial portion of the U(VI) in the aquifer was strongly associated with the sediments and was not microbially reducible. These results have important implications for in situ uranium bioremediation strategies.}, keywords = {Acetates, Biodegradation, Environmental, Deltaproteobacteria, Fresh Water, Geologic Sediments, Oxidation-Reduction, Solubility, Uranium, Water Pollutants, Radioactive}, issn = {0099-2240}, doi = {10.1128/AEM.70.12.7558-7560.2004}, author = {Ortiz-Bernad, Irene and Anderson, Robert T and Vrionis, Helen A and Lovley, Derek R} } @article {553, title = {Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater.}, journal = {Appl Environ Microbiol}, volume = {70}, year = {2004}, month = {2004 May}, pages = {3091-5}, abstract = {Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.}, keywords = {Anaerobiosis, Biodegradation, Environmental, Culture Media, Fresh Water, Geobacter, Geologic Sediments, Mining, Oxidation-Reduction, Vanadium, Water Pollution, Chemical}, issn = {0099-2240}, author = {Ortiz-Bernad, Irene and Anderson, Robert T and Vrionis, Helen A and Lovley, Derek R} } @article {1215, title = {Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.}, journal = {J Am Soc Mass Spectrom}, volume = {14}, year = {2003}, month = {2003 Sep}, pages = {957-70}, abstract = {

A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100\% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97\% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50\% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50\% for approximately 70\% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.

}, keywords = {Amino Acid Sequence, Chromatography, Liquid, Databases, Protein, Electrophoresis, Gel, Two-Dimensional, Methanococcus, Molecular Sequence Data, Molecular Weight, Peptide Mapping, Proteins, Pyrococcus furiosus, Sensitivity and Specificity, Software, Spectrometry, Mass, Electrospray Ionization, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Trypsin}, issn = {1044-0305}, author = {Lim, Hanjo and Eng, Jimmy and Yates, John R and Tollaksen, Sandra L and Giometti, Carol S and Holden, James F and Adams, Michael W W and Reich, Claudia I and Olsen, Gary J and Hays, Lara G} } @article {563, title = {Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.}, journal = {Appl Environ Microbiol}, volume = {69}, year = {2003}, month = {2003 Oct}, pages = {5884-91}, abstract = {The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 micro M in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.}, keywords = {Acetates, DNA, Ribosomal, Ecosystem, Fatty Acids, Ferric Compounds, Fresh Water, Geobacter, Mining, Oxidation-Reduction, Phospholipids, RNA, Ribosomal, 16S, Sulfates, Uranium, Water Pollution, Chemical}, issn = {0099-2240}, author = {Anderson, Robert T and Vrionis, Helen A and Ortiz-Bernad, Irene and Resch, Charles T and Long, Philip E and Dayvault, Richard and Karp, Ken and Marutzky, Sam and Metzler, Donald R and Peacock, Aaron and White, David C and Lowe, Mary and Lovley, Derek R} } @article {714, title = {Caveolar endocytosis of simian virus 40 is followed by brefeldin A-sensitive transport to the endoplasmic reticulum, where the virus disassembles.}, journal = {J Virol}, volume = {76}, year = {2002}, month = {2002 May}, pages = {5156-66}, abstract = {Simian virus 40 (SV40) enters cells by atypical endocytosis mediated by caveolae that transports the virus to the endoplasmic reticulum (ER) instead of to the endosomal-lysosomal compartment, which is the usual destination for viruses and other cargo that enter by endocytosis. We show here that SV4O is transported to the ER via an intermediate compartment that contains beta-COP, which is best known as a component of the COPI coatamer complexes that are required for the retrograde retrieval pathway from the Golgi to the ER. Additionally, transport of SV40 to the ER, as well as infection, is sensitive to brefeldin A. This drug acts by specifically inhibiting the ARF1 GTPase, which is known to regulate assembly of COPI coat complexes on Golgi cisternae. Moreover, some beta-COP colocalizes with intracellular caveolin-1, which was previously shown to be present on a new organelle (termed the caveosome) that is an intermediate in the transport of SV40 to the ER (L. Pelkmans, J. Kartenbeck, and A. Helenius, Nat. Cell Biol. 3:473-483, 2001). We also show that the internal SV40 capsid proteins VP2 and VP3 become accessible to immunostaining starting at about 5 h. Most of that immunostaining overlays the ER, with some appearing outside of the ER. In contrast, immunostaining with anti-SV40 antisera remains confined to the ER.}, keywords = {Animals, Antiviral Agents, Biological Transport, Brefeldin A, Capsid, Caveolae, Coatomer Protein, Endocytosis, Endoplasmic Reticulum, Simian virus 40, Virus Replication}, issn = {0022-538X}, author = {Norkin, Leonard C and Anderson, Howard A and Wolfrom, Scott A and Oppenheim, Ariella} } @article {583, title = {Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments.}, journal = {Appl Environ Microbiol}, volume = {68}, year = {2002}, month = {2002 May}, pages = {2300-6}, abstract = {Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40\% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5\% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65\% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.}, keywords = {Gene Library, Geologic Sediments, Iron, Oxidation-Reduction, Proteobacteria, RNA, Ribosomal, 16S, Soil Pollutants, Uranium}, issn = {0099-2240}, author = {Holmes, Dawn E and Finneran, Kevin T and O{\textquoteright}Neil, Regina A and Lovley, Derek R} } @article {400, title = {Evidence for "pre-recruitment" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell.}, journal = {Biochem Biophys Res Commun}, volume = {291}, year = {2002}, month = {2002 Mar 8}, pages = {979-86}, abstract = {In response to the oxidative stress imposed by redox-cycling compounds like paraquat, Escherichia coli induces the synthesis of SoxS, which then activates the transcription of approximately 100 genes. The DNA binding site for SoxS-dependent transcription activation, the "soxbox," is highly degenerate, suggesting that the genome contains a large number of SoxS binding sites. To estimate the number of soxboxes in the cell, we searched the E. coli genome for SoxS binding sites using as query sequence the previously determined optimal SoxS binding sequence. We found approximately 12,500 sequences that match the optimal binding sequence under the conditions of our search; this agrees with our previous estimate, based on information theory, that a random sequence the size of the E. coli genome contains approximately 13,000 soxboxes. Thus, fast-growing cells with 4-6 genomes per cell have approximately 65,000 soxboxes. This large number of potential SoxS binding sites per cell raises the interesting question of how SoxS distinguishes between the functional soxboxes located within the promoters of target genes and the plethora of equivalent but nonfunctional binding sites scattered throughout the chromosome. To address this question, we treated cells with paraquat and used Western blot analysis to determine the kinetics of SoxS accumulation per cell; we also determined the kinetics of SoxS-activated gene expression. The abundance of SoxS reached a maximum of 2,500 molecules per cell 20 min after induction and gradually declined to approximately 500 molecules per cell over the next 1.5 h. Given that activation of target gene expression began almost immediately and given the large disparity between the number of SoxS molecules per cell, 2,500, and the number of SoxS binding sites per cell, 65,000, we infer that SoxS is not likely to activate transcription by the usual "recruitment" pathway, as this mechanism would require a number of SoxS molecules similar to the number of soxboxes. Instead, we propose that SoxS first interacts in solution with RNA polymerase and then the binary complex scans the chromosome for promoters that contain a soxbox properly positioned and oriented for transcription activation. We name this new pathway "pre-recruitment."}, keywords = {Bacterial Proteins, Binding Sites, Blotting, Western, Cell Division, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Kinetics, Numerical Analysis, Computer-Assisted, Oxidative Stress, Paraquat, Protein Transport, Trans-Activators, Transcription Factors, Transcriptional Activation}, issn = {0006-291X}, doi = {10.1006/bbrc.2002.6559}, author = {Griffith, Kevin L and Shah, Ishita M and Myers, Todd E and O{\textquoteright}Neill, Michael C and Wolf, Richard E} } @article {781, title = {Human Stx2-specific monoclonal antibodies prevent systemic complications of Escherichia coli O157:H7 infection.}, journal = {Infect Immun}, volume = {70}, year = {2002}, month = {2002 Feb}, pages = {612-9}, abstract = {Hemolytic-uremic syndrome (HUS) is a serious complication predominantly associated with infection by enterohemorrhagic Escherichia coli (EHEC), such as E. coli O157:H7. EHEC can produce Shiga toxin 1 (Stx1) and/or Shiga toxin 2 (Stx2), both of which are exotoxins comprised of active (A) and binding (B) subunits. In piglets and mice, Stx can induce fatal neurological symptoms. Polyclonal Stx2 antiserum can prevent these effects in piglets infected with the Stx2-producing E. coli O157:H7 strain 86-24. Human monoclonal antibodies (HuMAbs) against Stx2 were developed as potential passive immunotherapeutic reagents for the prevention and/or treatment of HUS. Transgenic mice bearing unrearranged human immunoglobulin (Ig) heavy and kappa light chain loci (HuMAb___Mouse) were immunized with formalin-inactivated Stx2. Thirty-seven stable hybridomas secreting Stx2-specific HuMAbs were isolated: 33 IgG1kappa A-subunit-specific and 3 IgG1kappa and 1 IgG3kappa B-subunit-specific antibodies. Six IgG1kappa A-subunit-specific (1G3, 2F10, 3E9, 4H9, 5A4, and 5C12) and two IgG1kappa B-subunit-specific (5H8 and 6G3) HuMAbs demonstrated neutralization of > 95\% activity of 1 ng of Stx2 in the presence of 0.04 microg of HuMAb in vitro and significant prolongation of survival of mice given 50 microg of HuMAb intraperitoneally (i.p.) and 25 ng of Stx2 intravenously. When administered i.p. to gnotobiotic piglets 6 or 12 h after infection with E. coli O157:H7 strain 86-24, HuMAbs 2F10, 3E9, 5H8, and 5C12 prolonged survival and prevented development of fatal neurological signs and cerebral lesions. The Stx2-neutralizing ability of these HuMAbs could potentially be used clinically to passively protect against HUS development in individuals infected with Stx-producing bacteria, including E. coli O157:H7.}, keywords = {Animals, Antibodies, Bacterial, Antibodies, Monoclonal, Antibody Specificity, Disease Models, Animal, Escherichia coli O157, Female, Germ-Free Life, HeLa Cells, Hemolytic-Uremic Syndrome, Humans, Immunization, Passive, Immunoglobulin G, Immunoglobulin Isotypes, Immunoglobulin kappa-Chains, Mice, Neutralization Tests, Shiga Toxin 2, Swine}, issn = {0019-9567}, author = {Mukherjee, Jean and Chios, Kerry and Fishwild, Dianne and Hudson, Deborah and O{\textquoteright}Donnell, Susan and Rich, Stephen M and Donohue-Rolfe, Arthur and Tzipori, Saul} } @article {589, title = {A hydrogen-based subsurface microbial community dominated by methanogens.}, journal = {Nature}, volume = {415}, year = {2002}, month = {2002 Jan 17}, pages = {312-5}, abstract = {The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90\% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth{\textquoteright}s subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.}, keywords = {Bacteria, DNA, Archaeal, DNA, Bacterial, Ecosystem, Euryarchaeota, Exobiology, Hydrogen, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Water Microbiology}, issn = {0028-0836}, doi = {10.1038/415312a}, author = {Chapelle, Francis H and O{\textquoteright}Neill, Kathleen and Bradley, Paul M and Meth{\'e}, Barbara A and Ciufo, Stacy A and Knobel, LeRoy L and Lovley, Derek R} } @article {779, title = {Infectivity of a Cryptosporidium parvum isolate of cervine origin for healthy adults and interferon-gamma knockout mice.}, journal = {J Infect Dis}, volume = {185}, year = {2002}, month = {2002 May 1}, pages = {1320-5}, abstract = {The infectivity of a Cryptosporidium parvum isolate of cervine origin (type 2, Moredun) propagated in calves was investigated simultaneously in healthy adult human volunteers and in interferon-gamma knockout (GKO) mice. After exposure to 100-3000 oocysts, 16 volunteers recorded, for a duration of 6 weeks, the number and form of stools that they passed and any symptoms that they experienced. Oocyst excretion was assessed by enzyme-linked immunosorbent assay and direct immunofluorescence assay. Eleven subjects (69\%) became ill, and 8 subjects (50\%) shed oocysts in stool. The median duration of illness was 169 h, and the median number of unformed stools passed was 24. The duration and intensity of symptoms were more severe than were those associated with previously studied isolates. The median infectious dose was estimated to be 300 oocysts for humans and 1 oocyst for the GKO mouse model. The Moredun isolate was more pathogenic than the reference GCH-1 isolate. The GKO mouse model of cryptosporidiosis is useful for discerning isolate-specific differences in pathogenicity.}, keywords = {Adult, Animals, Body Weight, Cryptosporidiosis, Cryptosporidium parvum, Deer, Diarrhea, Disease Susceptibility, Female, Humans, Interferon-gamma, Mice, Mice, Knockout}, issn = {0022-1899}, doi = {10.1086/340132}, author = {Okhuysen, Pablo C and Rich, Stephen M and Chappell, Cynthia L and Grimes, Kevin A and Widmer, Giovanni and Feng, Xiaochuan and Tzipori, Saul} } @article {778, title = {Production and characterization of protective human antibodies against Shiga toxin 1.}, journal = {Infect Immun}, volume = {70}, year = {2002}, month = {2002 Oct}, pages = {5896-9}, abstract = {Hemolytic-uremic syndrome (HUS) is a serious complication which is predominantly associated in children with infection by Shiga toxin-producing Escherichia coli (STEC). By using HuMAb-Mouse (Medarex) animals, human monoclonal antibodies (Hu-MAbs) were developed against Shiga toxin 1 (Stx1) for passive immunotherapy of HUS. Ten stable hybridomas comprised of fully human heavy- and light-chain immunoglobulin elements and secreting Stx1-specific Hu-MAbs (seven immunoglobulin M(kappa)() [IgM(kappa)] elements [one specific for the A subunit and six specific for the B subunit] and three IgG1(kappa) elements specific for subunit B) were isolated. Two IgM(kappa) Hu-MAbs (2D9 and 15G9) and three IgG1(kappa) Hu-MAbs (5A4, 10F4, and 15G2), all specific for subunit B, demonstrated marked neutralization of Stx1 in vitro and significant prolongation of survival in a murine model of Stx1 toxicosis.}, keywords = {Animals, Antibodies, Bacterial, Antibodies, Monoclonal, Child, Escherichia coli, Female, HeLa Cells, Hemolytic-Uremic Syndrome, Humans, Hybridomas, Immunization, Passive, Immunoglobulin G, Immunoglobulin M, Mice, Neutralization Tests, Shiga Toxin 1}, issn = {0019-9567}, author = {Mukherjee, Jean and Chios, Kerry and Fishwild, Dianne and Hudson, Deborah and O{\textquoteright}Donnell, Susan and Rich, Stephen M and Donohue-Rolfe, Arthur and Tzipori, Saul} } @article {579, title = {Rapid evolution of redox processes in a petroleum hydrocarbon-contaminated aquifer.}, journal = {Ground Water}, volume = {40}, year = {2002}, month = {2002 Jul-Aug}, pages = {353-60}, abstract = {Ground water chemistry data collected over a six-year period show that the distribution of contaminants and redox processes in a shallow petroleum hydrocarbon-contaminated aquifer has changed rapidly over time. Shortly after a gasoline release occurred in 1990, high concentrations of benzene were present near the contaminant source area. In this contaminated zone, dissolved oxygen in ground water was depleted, and by 1994 Fe(III) reduction and sulfate reduction were the predominant terminal electron accepting processes. Significantly, dissolved methane was below measurable levels in 1994, indicating the absence of significant methanogenesis. By 1996, however, depletion of solid-phase Fe(III)-oxyhydrox ides in aquifer sediments and depletion of dissolved sulfate in ground water resulted in the onset of methanogenesis. Between 1996 and 2000, water-chemistry data indicated that methanogenic metabolism became increasingly prevalent. Molecular analysis of 16S-rDNA extracted from sediments shows the presence of a more diverse methanogenic community inside as opposed to outside the plume core, and is consistent with water-chemistry data indicating a shift toward methanogenesis over time. This rapid evolution of redox processes reflects several factors including the large amounts of contaminants, relatively rapid ground water flow (approximately 0.3 m/day [approximately foot/day]), and low concentrations of microbially reducible Fe(III) oxyhydroxides ( approximately 1 micromol/g) initially present in aquifer sediments. These results illustrate that, under certain hydrologic conditions, redox conditions in petroleum hydrocarbon-contaminated aquifers can change rapidly in time and space, and that the availability of solid-phase Fe(III)-oxyhydroxides affects this rate of change.}, keywords = {Hydrocarbons, Iron, Methane, Oxidation-Reduction, Petroleum, Soil Pollutants, Solubility, Sulfates, Water Pollutants, Water Supply}, issn = {0017-467X}, author = {Chapelle, Francis H and Bradley, Paul M and Lovley, Derek R and O{\textquoteright}Neill, Kathleen and Landmeyer, James E} } @article {618, title = {Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the epsilon Proteobacteria.}, journal = {Int J Syst Bacteriol}, volume = {49 Pt 3}, year = {1999}, month = {1999 Jul}, pages = {1177-80}, abstract = {Two strains of dissimilatory arsenate-reducing vibrio-shaped bacteria are assigned to the genus Sulfurospirillum. These two new species, Sulfurospirillum barnesii strain SES-3T and Sulfurospirillum arsenophilum strain MIT-13T, in addition to Sulfurospirillum sp. SM-5, two strains of Sulfurospirillum deleyianum, and Sulfurospirillum arcachonense, form a distinct clade within the epsilon subclass of the Proteobacteria based on 16S rRNA analysis.}, keywords = {Arsenates, Bacterial Typing Techniques, DNA, Ribosomal, Genes, rRNA, Gram-Negative Bacteria, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Selenium Compounds, Sequence Analysis, DNA}, issn = {0020-7713}, author = {Stolz, J F and Ellis, D J and Blum, J S and Ahmann, D and Lovley, D R and Oremland, R S} } @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 {638, title = {Growth of Strain SES-3 with Arsenate and Other Diverse Electron Acceptors.}, journal = {Appl Environ Microbiol}, volume = {61}, year = {1995}, month = {1995 Oct}, pages = {3556-61}, abstract = {The selenate-respiring bacterial strain SES-3 was able to use a variety of inorganic electron acceptors to sustain growth. SES-3 grew with the reduction of arsenate to arsenite, Fe(III) to Fe(II), or thiosulfate to sulfide. It also grew in medium in which elemental sulfur, Mn(IV), nitrite, trimethylamine N-oxide, or fumarate was provided as an electron acceptor. Growth on oxygen was microaerophilic. There was no growth with arsenite or chromate. Washed suspensions of cells grown on selenate or nitrate had a constitutive ability to reduce arsenate but were unable to reduce arsenite. These results suggest that strain SES-3 may occupy a niche as an environmental opportunist by being able to take advantage of a diversity of electron acceptors.}, issn = {0099-2240}, author = {Laverman, A M and Blum, J S and Schaefer, J K and Phillips, E and Lovley, D R and Oremland, R S} } @article {1739, title = {Bacterial metabolism of resorcinylic compounds: purification and properties of orcinol hydroxylase and resorcinol hydroxylase from Pseudomonas putida ORC.}, journal = {Eur J Biochem}, volume = {61}, year = {1976}, month = {1976 Jan 2}, pages = {259-69}, abstract = {

The hydroxylase activities observed in extracts of Pseudomonas putida ORC after growth on orcinol and resorcinol as sole source of carbon have been purified to homogeneity. Both enzymes were shown to be flavoproteins and to contain approximately 1 mol of FAD for each polypeptide chain, S20,W values for each enzyme are 4.1 +/- 0.1 and are independent of the presence of their aromatic substrates. Molecular weight determinations under native (approximately 68000) and denaturing (approximately 70000) conditions indicated that they are monomeric. The visible absorption spectra identical but the circular dichroic spectra of the two proteins can be distinguished. Although each protein catalyzes the NAD(P)H and O2-dependent hydroxylation of both orcinol and resorcinol, the efficiency of the transformations of the substrates by the two enzymes is radically different; furthermore resorcinol hydroxylase is much more versatile in the aromatic compounds it can utilize as substrates and effectors. Other properties of the enzymes which clearly establish their own identity include their serological characteristics and amino acid composition; the latter property is particularly evident when the quantities of valine and alanine residues are compared. The synthesis of each enzyme is also under different regulatory constraints, being controlled by the substrate used for growth.

}, keywords = {Amino Acids, Circular Dichroism, Flavin-Adenine Dinucleotide, Mixed Function Oxygenases, Molecular Weight, NAD, NADP, Oxidation-Reduction, Protein Conformation, Pseudomonas, Resorcinols, Spectrophotometry, Spectrophotometry, Ultraviolet}, issn = {0014-2956}, author = {Ohta, Y and Ribbons, D W} }