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Sample records for linking microbial oxidation

  1. Oxidation-induced unfolding facilitates Myosin cross-linking in myofibrillar protein by microbial transglutaminase.

    PubMed

    Li, Chunqiang; Xiong, Youling L; Chen, Jie

    2012-08-15

    Myofibrillar protein from pork Longissimus muscle was oxidatively stressed for 2 and 24 h at 4 °C with mixed 10 μM FeCl(3)/100 μM ascorbic acid/1, 5, or 10 mM H(2)O(2) (which produces hydroxyl radicals) and then treated with microbial transglutaminase (MTG) (E:S = 1:20) for 2 h at 4 °C. Oxidation induced significant protein structural changes (P < 0.05) as evidenced by suppressed K-ATPase activity, elevated Ca-ATPase activity, increased carbonyl and disulfide contents, and reduced conformational stability, all in a H(2)O(2) dose-dependent manner. The structural alterations, notably with mild oxidation, led to stronger MTG catalysis. More substantial amine reductions (19.8-27.6%) at 1 mM H(2)O(2) occurred as compared to 11.6% in nonoxidized samples (P < 0.05) after MTG treatment. This coincided with more pronounced losses of myosin in oxidized samples (up to 33.2%) as compared to 21.1% in nonoxidized (P < 0.05), which was attributed to glutamine-lysine cross-linking as suggested by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PMID:22809283

  2. Disruption of secondary structure by oxidative stress alters the cross-linking pattern of myosin by microbial transglutaminase.

    PubMed

    Li, Chunqiang; Xiong, Youling L

    2015-10-01

    Porcine myofibrillar protein (MP) was oxidatively stressed in an iron-H2O2 radical-producing system then subjected to microbial transglutaminase (TGase, E:S=1:20) at 4°C. Changes in the MP secondary structure and cross-linking site on myosin (subfragments S1, S2, rod, light meromyosin, and heavy meromyosin) after TGase treatment were investigated. Circular dichroism and FTIR recorded unraveling of helixes caused by both oxidation and TGase. The loss of α-helix due to TGase treatment was oxidation-dependent, namely, mild oxidation (0.1-1mM H2O2)>non-oxidation>moderate oxidation (5-20mM H2O2). Moreover, oxidation altered the myosin cross-linking pattern: TGase-initiated S1 cross-linking (which dominated non-oxidized MP) partially shifted to the rod under 0.1-0.5mM H2O2 and extensively to the S2 site with 20mM H2O2. Unraveling of the helical structure and formation of disulfide bonds due to oxidation were implicated in the altered myosin cross-linking pattern during subsequent TGase reactions. PMID:26068405

  3. Formation of Deep Sea Umber Deposits Linked to Microbial Metal Oxidation at the South Atlantic Ridge

    NASA Astrophysics Data System (ADS)

    Peng, Xiaotong; Ta, Kaiwen; Chen, Shun; Zhang, Lijuan; Xu, Hengchao

    2015-04-01

    Umber deposits are important metalliferous deposits, which occur in off-axis half-graben structures at ancient and modern ocean floor. The genesis of umber deposits has remained controversial for several decades. Recently, microbial Fe(II) oxidation associated with low-temperature diffuse venting has been identified as a key process for the formation of umber deposits, but the exact biochemical mechanisms involved to the precipitation of Mn oxides and co-precipitation of Fe oxyhydroxides and Mn oxides in umber deposits still remain unknown. Here, we used nano secondary ion mass spectrometer, synchrotron-based X-ray absorption spectroscopy, electron microscopy, and molecular techniques to demonstrate the coexistence of two types of metal-oxidizing bacteria within deep-sea hydrothermal umber deposits at the South Atlantic Ridge, where we found unique spheroids composed of biogenic Fe oxyhydroxides and Mn oxides in the deposits. Our data suggest that Fe oxyhydroxides and Mn oxides are metabolic by-products of lithotrophic Fe(II)-oxidizing bacteria and heterotrophic Mn(II)-oxidizing bacteria, respectively. The hydrothermal vents fuel lithotrophic Fe(II)-oxidizing bacteria, which constitute a trophic base that may support the activities of heterotrophic Mn(II)-oxidizing bacteria. The biological origin of umber deposits underscore the importance of geomicrobiologcial interaction in triggering the formation of deep-sea deposits, with important implications for the generation of submarine Mn deposits and crusts.

  4. Linking methane oxidation with perchlorate reduction: a microbial base for possible Martian life

    NASA Astrophysics Data System (ADS)

    Miller, L. G.; Carlstrom, C.; Baesman, S. M.; Coates, J. D.; Oremland, R. S.

    2011-12-01

    Recent observations of methane (CH4) and perchlorate (ClO4-) within the atmosphere and surface of Mars, respectively, provide impetus for establishing a metabolic linkage between these compounds whereby CH4 acts as an electron donor and perchlorate acts as an electron acceptor. Direct linkage through anaerobic oxidation of methane (AOM) has not been observed. However, indirect syntrophic oxygenase-dependent oxidation of CH4 with an aerobic methane oxidizer is feasible. The pathway for anaerobic dissimilatory perchlorate reduction includes 3 steps. The first 2 are sequential reductions of (1) perchlorate to chlorate and (2) chlorate to chlorite, mediated by perchlorate reductase. The third step is disproportionation of chlorite to chloride and molecular oxygen, mediated by chlorite dismutase. Utilization of thusly derived oxygen by hydrocarbon-degrading organisms in anoxic environments was first demonstrated by Coates et. al. (1998)1, however the link to aerobic methane oxidation was not examined at that time. Here, we systematically explore the potential for several species of aerobic methanotrophs to couple with chlorite during dissimilatory perchlorate reduction. In one experiment, 0.5 kPa CH4 was completely removed in one day from the headspace of combined cell suspensions of Dechloromonas agitata strain CKB and Methylococcus capsulatus in the presence of 5 mM chlorite. Oxidation of labeled 14CH4 to 14CO2 under similar conditions was later confirmed. Another experiment demonstrated complete removal of 0.2 kPa CH4 over several days by Methylobacter albus strain BG8 with strain CKB in the presence of 5 mM chlorite. Finally, we observed complete removal of 0.2 kPa CH4 in bottles containing natural soil (enriched in methanotrophs by CH4 additions over several weeks) and strain CKB and in the presence of 10 mM chlorite. This soil, collected from a pristine lake shoreline, demonstrated endogenous methane, perchlorate, chlorate and chlorite uptake. Other soil and

  5. Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.

    PubMed

    Hamamura, N; Macur, R E; Korf, S; Ackerman, G; Taylor, W P; Kozubal, M; Reysenbach, A-L; Inskeep, W P

    2009-02-01

    The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA-like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA-like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6-3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2-8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and beta-Proteobacteria. Modified primers designed around previously characterized and newly identified aroA-like genes successfully amplified new lineages of aroA-like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA-like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences

  6. Protein oxidation at different salt concentrations affects the cross-linking and gelation of pork myofibrillar protein catalyzed by microbial transglutaminase.

    PubMed

    Li, Chunqiang; Xiong, Youling L; Chen, Jie

    2013-06-01

    In a fabricated then restructured meat product, protein gelation plays an essential role in producing desirable binding and fat-immobilization properties. In the present study, myofibrillar protein (MFP) suspended in 0.15, 0.45, and 0.6 M NaCl was subjected to hydroxyl radical stress for 2 or 24 h and then treated with microbial transglutaminase (MTGase) in 0.6 M NaCl (E : S = 1 : 20) at 4 and 15 °C for 2 h. Protein cross-linking and dynamic rheological tests were performed to assess the efficacy of MTGase for mediating the gelation of oxidized MFP. MTGase treatments affected more remarkable polymerization of myosin in oxidized MFP than in nonoxidized, especially for samples oxidized at 0.6 M NaCl. Notably, the extent of MTGase-induced myosin cross-linking at 15 °C in oxidized MFP improved up to 46.8%, compared to 31.6% in nonoxidized MFP. MTGase treatment at 4 °C for MFP oxidized in 0.6 M NaCl, but not MFP oxidized in 0.15 M NaCl, produced stronger gels than nonoxidized MFP (P < 0.05). The final (75 °C) storage modulus (G') of oxidized MFP gels was significantly greater than that of nonoxidized, although the G' of the transient peak (∼44.5 °C) showed the opposite trend. Overall, oxidation at high salt concentrations significantly improved MTGase-mediated myosin cross-linking and MFP gelation. This might be because under this condition, MTGase had an increased accessibility to glutamine and lysine residues to effectively initiate protein-protein interactions and gel network formation. PMID:23627930

  7. Linked metatranscriptomic and geochemical data indicate microbial succession in naturally reduced aquifer sediments dominated by H2-oxidizing Comamonadaceae

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Bill, M.; Chakraborty, R.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2015-12-01

    In this study, we sought to better understand what natural organic matter fuels heterotrophic microbial communities in the anoxic subsurface at the Rifle (CO) site and what genes may be diagnostic of that activity. We conducted a 20-day microcosm experiment with naturally reduced zone (NRZ) sediments and collected replicate samples every 5 days for omics (metagenome and metatranscriptome) and biogeochemical measurements (e.g., continuous CO2 production, H2, CH4, acetate, DOC, Fe(II), sulfate, NH4+, spectroscopic analyses of sediment OM). No electron donors were added other than the NRZ sediment, which is enriched in organic matter relative to typical Rifle aquifer material. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with a N2headspace. Biogeochemical measurements indicate that the decomposition of native organic matter occurred in different phases, including depletion of DOC and release of CO2 during the first week of incubation, followed by a pulse of acetogenesis and methanogenesis after 2 weeks (with acetogenesis dominating carbon flux after 2 weeks). While H2 remained below detection levels throughout the study, a peak of [NiFe] uptake hydrogenase, acetyl-CoA synthetase, urease, and nitrate reductase transcripts belonging to the Comamonadaceae family occurred at day 15. Some members of Comamonadaceae are facultative H2-oxidizing chemolithoautotrophs and fix carbon via the acetogenic Wood-Ljungdahl pathway. Comamonadaceae plateaued at 73% of the metagenome at this time and represented 69% of the metatranscriptome, succeeding the S-oxidizing Sulfurimonas genus. Sulfurimonas species were the dominant group at day 0, accounting for 43% of the metagenome and 25% of the metatranscriptome, decreasing to 11% in both the metagenome and metatranscriptome by day 10. Less abundant but still present were transcripts for genes involved in cellulose degradation (glycosyl hydrolases), and glycolysis (phosphofructokinase

  8. Biological consilience of hydrogen sulfide and nitric oxide in plants: Gases of primordial earth linking plant, microbial and animal physiologies.

    PubMed

    Yamasaki, Hideo; Cohen, Michael F

    2016-05-01

    Hydrogen sulfide (H2S) is produced in the mammalian body through the enzymatic activities of cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (3MST). A growing number of studies have revealed that biogenic H2S produced in tissues is involved in a variety of physiological responses in mammals including vasorelaxation and neurotransmission. It is now evident that mammals utilize H2S to regulate multiple signaling systems, echoing the research history of the gaseous signaling molecules nitric oxide (NO) and carbon monoxide (CO) that had previously only been recognized for their cytotoxicity. In the human diet, meats (mammals, birds and fishes) and vegetables (plants) containing cysteine and other sulfur compounds are the major dietary sources for endogenous production of H2S. Plants are primary producers in ecosystems on the earth and they synthesize organic sulfur compounds through the activity of sulfur assimilation. Although plant H2S-producing activities have been known for a long time, our knowledge of H2S biology in plant systems has not been updated to the extent of mammalian studies. Here we review recent progress on H2S studies, highlighting plants and bacteria. Scoping the future integration of H2S, NO and O2 biology, we discuss a possible linkage between physiology, ecology and evolutional biology of gas metabolisms that may reflect the historical changes of the Earth's atmospheric composition. PMID:27083071

  9. Microbial Formaldehyde Oxidation

    SciTech Connect

    Timothy J. Donohue

    2004-12-09

    This project analyzed how cells sense and generate energy from formaldehyde oxidation. Formaldehyde is a toxin that is produced naturally, chemically or by metabolism of a wide variety of methyl-containing compounds. Our goals are to identify how cells sense the presence of this toxic compound and determine how they generate energy and nutrients from the oxidation of formaldehyde. This research capitalizes on the role of the Rhodobacter sphaeroides glutathione dependent formaldehyde dehydrogenase (GSH FDH) in a formaldehyde oxidation pathway that is apparently found in a wide variety of microbes, plants and animals. Thus, our findings illustrate what is required for a large variety of cells to metabolize this toxic compound. A second major focus of our research is to determine how cells sense the presence of this toxic compound and control the expression of gene products required for its detoxification.

  10. A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat

    PubMed Central

    2015-01-01

    Background Dietary intakes of red meat and fat are established risk factors for both colorectal cancer (CRC) and cardiovascular disease (CVDs). Recent studies have shown a mechanistic link between TMAO, an intestinal microbial metabolite of red meat and fat, and risk of CVDs. Data linking TMAO directly to CRC is, however, lacking. Here, we present an unbiased data-driven network-based systems approach to uncover a potential genetic relationship between TMAO and CRC. Materials and methods We constructed two different epigenetic interaction networks (EINs) using chemical-gene, disease-gene and protein-protein interaction data from multiple large-scale data resources. We developed a network-based ranking algorithm to ascertain TMAO-related diseases from EINs. We systematically analyzed disease categories among TMAO-related diseases at different ranking cutoffs. We then determined which genetic pathways were associated with both TMAO and CRC. Results We show that CVDs and their major risk factors were ranked highly among TMAO-related diseases, confirming the newly discovered mechanistic link between CVDs and TMAO, and thus validating our algorithms. CRC was ranked highly among TMAO-related disease retrieved from both EINs (top 0.02%, #1 out of 4,372 diseases retrieved based on Mendelian genetics and top 10.9% among 882 diseases based on genome-wide association genetics), providing strong supporting evidence for our hypothesis that TMAO is genetically related to CRC. We have also identified putative genetic pathways that may link TMAO to CRC, which warrants further investigation. Through systematic disease enrichment analysis, we also demonstrated that TMAO is related to metabolic syndromes and cancers in general. Conclusions Our genome-wide analysis demonstrates that systems approaches to studying the epigenetic interactions among diet, microbiome metabolisms, and disease genetics hold promise for understanding disease pathogenesis. Our results show that TMAO is

  11. Role of oxidants in microbial pathophysiology.

    PubMed Central

    Miller, R A; Britigan, B E

    1997-01-01

    Reactive oxidant species (superoxide, hydrogen peroxide, hydroxyl radical, hypohalous acid, and nitric oxide) are involved in many of the complex interactions between the invading microorganism and its host. Regardless of the source of these compounds or whether they are produced under normal conditions or those of oxidative stress, these oxidants exhibit a broad range of toxic effects to biomolecules that are essential for cell survival. Production of these oxidants by microorganisms enables them to have a survival advantage in their environment. Host oxidant production, especially by phagocytes, is a counteractive mechanism aimed at microbial killing. However, this mechanism may be contribute to a deleterious consequence of oxidant exposure, i.e., inflammatory tissue injury. Both the host and the microorganism have evolved complex adaptive mechanisms to deflect oxidant-mediated damage, including enzymatic and nonenzymatic oxidant-scavenging systems. This review discusses the formation of reactive oxidant species in vivo and how they mediate many of the processes involved in the complex interplay between microbial invasion and host defense. PMID:8993856

  12. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  13. Microbial geomorphology: A neglected link between life and landscape

    NASA Astrophysics Data System (ADS)

    Viles, Heather A.

    2012-07-01

    Whilst recognition is increasing that life and landscapes are intimately related, as evidenced by growing research into ecosystem engineering, biogeomorphology and allied topics, the microbial contribution to such interactions has been relatively neglected. A revolution in environmental microbiology, based on molecular techniques, is now driving a reconsideration of the role of microbial processes in geomorphology at all scales. Recent research illustrates the hitherto unknown microbial diversity present in many extreme geomorphic environments, such as hyperarid deserts, subglacial lakes, hot springs, and much richer microbial life than previously suspected within the soils and sediments that blanket most other landscapes. Such microbial communities have been found to play important geomorphic roles across a wide range of environments, notably in weathering, precipitation of minerals and protecting surfaces from erosion. These geomorphic roles can also be conceptualised as examples of ecosystem engineering, and can pave the way for further plant-geomorphology and zoogeomorphology processes. Three key aspects which emerge from a review of microbial influences on Earth surface processes are a) that microbes play roles on a continuum from full control to passive involvement, b) that complex and widespread communities of microorganisms are involved and c) that microbial activity usually affects several Earth surface processes at once. Examples of the contribution of microbial life to geomorphology over long, medium and short timescales suggest that microorganisms play key geomorphological roles in two major situations; on the cusp between stable states, and in extreme environments where higher plant and animal life is limited and many abiotic processes are also constrained. The dominant link between microbial life and geomorphology appears to take on different forms depending on the timescale under consideration, with a stabilising microbial role apparent over short

  14. Microbial oxidation of pyrrhotites in coal chars

    USGS Publications Warehouse

    Miller, K.W.; Risatti, J.B.

    1988-01-01

    The ability of Thiobacillus ferrooxidans to oxidize pyrrhotite minerals occurring in coal chars was investigated, to evaluate the feasibility of microbial char desulphurization. Bio-oxidation of pyrrhotites in chars produced by two different processes was demonstrated conclusively. Microbial removal of sulphur from a char and its parent coal proceeded at the rate of 3.5% and 12% day-1, respectively with a total of 48% and 81% removal after 27 days. The pH of shake flask cultures containing the coal dropped naturally to a final value of 2.2, while the pH of cultures containing the corresponding char rose and had to be lowered artificially with additional acid. Amending char cultures with elemental sulphur to increase acidity upon bio-oxidation and prevent precipitation of ferric iron was successful; however, the extent of pyrrhotite removal, as demonstated by X-ray diffraction analysis, was not improved. As yet, there is no explanation for the failure of microbial removal of pyrrhotitic sulphur to go to completion. ?? 1988.

  15. [Competitive Microbial Oxidation and Reduction of Arsenic].

    PubMed

    Yang, Ting-ting; Bai, Yao-hui; Liang, Jin-song; Huo, Yang; Wang, Ming-xing; Yuan, Lin-ijang

    2016-02-15

    Filters are widely applied in drinking water treatment plants. Our previous study, which explored the asenic redox in a filter of drinking water plant treating underground water, found that As3+ could be oxidized to As5+ by biogenic manganese oxides, while As5+ could be reduced to As3+ by some microbial arsenic reductases in the biofilter system. This microbial competition could influence the system stability and treatment efficiency. To explore its mechanism, this study selected a manganese-oxidizing bacterial strain (Pseudomonas sp. QJX-1) and a arsenic-reducing strain (Brevibacterium sp. LSJ-9) to investigate their competitive relationship in nutrient acquisition and arsenic redox in the presence of Mn2+, As3+ or As5+ The results revealed that the concentration and valence of Mn and As varied with different reaction time; biological manganese oxides dominated the arsenic redox by rapidly oxidizing the As3+ in the existing system and the As3+ generated by arsenic reductase into As. PCR and RT-PCR results indicated that the arsenic reductase (arsC) was inhibited by the manganese oxidase (cumA). The expression of 16S rRNA in QJX-1 was two orders of magnitude higher than that in LSJ-9, which implied QJX-1 was dominant in the bacterial growth. Our data revealed that hydraulic retention time was critical to the valence of arsenic in the effluent of filter in drinking water treatment plant. PMID:27363151

  16. Carbon isotope fractionation during microbial methane oxidation

    NASA Astrophysics Data System (ADS)

    Barker, James F.; Fritz, Peter

    1981-09-01

    Methane, a common trace constituent of groundwaters, occasionally makes up more than 20% of the total carbon in groundwaters1,2. In aerobic environments CH4-rich waters can enable microbial food chain supporting a mixed culture of bacteria with methane oxidation as the primary energy source to develop3. Such processes may influence the isotopic composition of the residual methane and because 13C/12C analyses have been used to characterize the genesis of methanes found in different environments, an understanding of the magnitude of such effects is necessary. In addition, carbon dioxide produced by the methane-utilizing bacteria can be added to the inorganic carbon pool of affected groundwaters. We found carbon dioxide experimentally produced by methane-utilizing bacteria to be enriched in 12C by 5.0-29.6‰, relative to the residual methane. Where methane-bearing groundwaters discharged into aerobic environments microbial methane oxidation occurred, with the residual methane becoming progressively enriched in 13C. Various models have been proposed to explain the 13C/12C and 14C content of the dissolved inorganic carbon (DIC) of groundwaters in terms of additions or losses during flow in the subsurface4,5. The knowledge of both stable carbon isotope ratios in various pools and the magnitude of carbon isotope fractionation during various processes allows geochemists to use the 13C/12C ratio of the DIC along with water chemistry to estimate corrected 14C groundwater ages4,5. We show here that a knowledge of the carbon isotope fractionation between CH4 and CO2 during microbial methane-utilization could modify such models for application to groundwaters affected by microbial methane oxidation.

  17. Altering petrology through microbial dissimilatory phosphite oxidation

    NASA Astrophysics Data System (ADS)

    Zhu, H.; Figueroa, I.; Coates, J. D.

    2013-12-01

    Microbial enhanced oil recovery (MEOR) takes advantage of various microbial metabolisms to increase hydrocarbon and energy yield by improving oil flow and flood water sweep in a reservoir during tertiary recovery. Wormholing at the injection well is believed to be the result of the large drop in pressure when water exits the injection well and enters the unconsolidated reservoir matrix. One possible means of prevent this event is to consolidate the rock matrix immediately around the injection well to create a permeable zone of stable petrology. Many microbial processes are known to result in the precipitation of ionic components into their environment creating solid-phase minerals. Such processes could be judiciously applied to bind unconsolidated matrices in order to form a permeable concreted rock matrix, which would minimize wormholing events and thus improve floodwater sweep. However, to date, apart from the application of urea oxidation creating calcium carbonate precipitation, there has been little investigation of the applicability of these precipitated bioconcretions to MEOR strategies and none to control wormholing events. Here we present a novel approach to altering rock petrology to concrete unconsolidated matrices in the near well environment by the biogenesis of authigenic minerals through microbial dissimilatory phosphite oxidation. Desulfotignum phosphitoxidans, strain FiPS-3 is currently the only isolated organism capable of using phosphite (HPO32-) as an electron donor for growth. This process, known as dissimilatory phosphite oxidation (DPO), can be coupled to either sulfate reduction or homoacetogenesis and leads to the accumulation of inorganic phosphate in the medium. The resulting insoluble mineral phases can coat the rock environment resulting in a concretion binding the unconsolidated matrix particles into a single phase. In this study we demonstrate that DPO can effectively produce calcium or magnesium phosphate minerals in packed glass

  18. Linking microbial comunity composition and soil processes in acalifornia annual grassland and mixed-conifer forest

    SciTech Connect

    Balser, T.C.; Firestone, M.K.

    2003-07-21

    To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbon dioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO2 production and soil NH4+ concentration, while microbial community characteristics correlated with N2O production, nitrification potential, gross N-mineralization, and soil NO3 concentration, independent of environmental controllers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes, particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.

  19. Exploring Microbial Iron Oxidation in Wetland Soils

    NASA Astrophysics Data System (ADS)

    Wang, J.; Muyzer, G.; Bodelier, P. L. E.; den Oudsten, F.; Laanbroek, H. J.

    2009-04-01

    Iron is one of the most abundant elements on earth and is essential for life. Because of its importance, iron cycling and its interaction with other chemical and microbial processes has been the focus of many studies. Iron-oxidizing bacteria (FeOB) have been detected in a wide variety of environments. Among those is the rhizosphere of wetland plants roots which release oxygen into the soil creating suboxic conditions required by these organisms. It has been reported that in these rhizosphere microbial iron oxidation proceeds up to four orders of magnitude faster than strictly abiotic oxidation. On the roots of these wetland plants iron plaques are formed by microbial iron oxidation which are involved in the sequestering of heavy metals as well organic pollutants, which of great environmental significance.Despite their important role being catalysts of iron-cycling in wetland environments, little is known about the diversity and distribution of iron-oxidizing bacteria in various environments. This study aimed at developing a PCR-DGGE assay enabling the detection of iron oxidizers in wetland habitats. Gradient tubes were used to enrich iron-oxidizing bacteria. From these enrichments, a clone library was established based on the almost complete 16s rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly α- and β-Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, and the PCR products were used in denaturing gradient gel electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene

  20. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

    PubMed

    Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

    2014-11-28

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  1. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    PubMed Central

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  2. Cross-linking of bovine and caprine caseins by microbial transglutaminase and their use as microencapsulating agents for n-3 fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine and caprine caseins were cross-linked with microbial transglutaminase (mTG). The mTG-cross-linked bovine or caprine casein dispersion, mixed with 14.5% maltodextrin (DE = 40), was used to prepare emulsions with 10.5% algae oil. Oxidative stability of emulsions was evaluated by peroxide valu...

  3. Microbially Produced Acetate: A "Missing Link" in Understanding Obesity?

    PubMed

    Trent, Chad M; Blaser, Martin J

    2016-07-12

    Numerous studies have connected the gut microbiome with diet-induced obesity; however, mechanistic explanations for the host-microbial interactions are needed. Perry et al. (2016) present studies suggesting that microbially produced acetate (MPA) increases post-prandial insulin release via a sequential and integrated gut, brain, and pancreatic signaling network promoting energy retention. PMID:27411005

  4. Geothermal Systems in Yellowstone National Park are Excellent Model Environments for Linking Microbial Processes and Geochemical Cycling

    NASA Astrophysics Data System (ADS)

    Inskeep, W. P.; Jay, Z.

    2008-12-01

    Geothermal systems in Yellowstone National Park (YNP) are geochemically diverse, span pH values from approximately 2 to 10, and generally contain a plethora of reduced constituents that may serve as electron donors for chemotrophic microorganisms. One of our long-term goals has been to determine linkages between geochemical processes and the distribution of microbial populations in high-temperature environments, where geochemical conditions often constrain microbial community diversity. Although geochemical characteristics vary greatly across the world's largest geothermal basin, there exist key geochemical attributes that are likely most important for defining patterns in microbial distribution. For example, excellent model systems exist in YNP, where the predominant geochemical and microbial processes are focused on either S species and or Fe-oxidation-reduction. In such cases, we hypothesize that genetic diversity and functional gene content will link directly with habitat parameters. Several cases studies will be presented where pilot metagenomic data (random shotgun sequencing of environmental DNA) was used to identify key functional attributes and confirm that specific patterns of microbial distribution are indeed reflected in other gene loci besides the 16S rRNA gene. These model systems are excellent candidates for elucidating definitive linkages between S, As, and or Fe cycling, genomics and microbial regulation.

  5. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

    2014-12-01

    Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that

  6. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

    2015-04-01

    Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

  7. Microbial metabolic exchange—the chemotype-to-phenotype link

    PubMed Central

    Phelan, Vanessa V; Liu, Wei-Ting; Pogliano, Kit

    2013-01-01

    The function of microbial interactions is to enable microorganisms to survive by establishing a homeostasis between microbial neighbors and local environments. A microorganism can respond to environmental stimuli using metabolic exchange—the transfer of molecular factors, including small molecules and proteins. Microbial interactions not only influence the survival of the microbes but also have roles in morphological and developmental processes of the organisms themselves and their neighbors. This, in turn, shapes the entire habitat of these organisms. Here we highlight our current understanding of metabolic exchange as well as the emergence of new technologies that are allowing us to eavesdrop on microbial conversations comprising dozens to hundreds of secreted metabolites that control the behavior, survival and differentiation of members of the community. The goal of the rapidly advancing field studying multifactorial metabolic exchange is to devise a microbial ‘Rosetta stone’ in order to understand the language by which microbial interactions are negotiated and, ultimately, to control the outcome of these conversations. PMID:22173357

  8. Linking Microbial Community Structure to Function in Representative Simulated Systems

    PubMed Central

    Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

    2013-01-01

    Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

  9. Linking microbial ultrastructure and physiology to iron depositional processes in deep sea hydrothermal environments

    NASA Astrophysics Data System (ADS)

    Chan, C. S.; Fleming, E. J.; Emerson, D.; Edwards, K. J.

    2008-12-01

    Clara S. Chan, Emily Fleming, David Emerson, Katrina J. Edwards Iron microbial mats have been discovered in a variety of deep-sea hydrothermal environments and are increasingly being recognized as more seafloor is explored. The predominant structures found in many of these mats are iron oxyhydroxide-rich filaments. One of the most common structures is a helical stalk bearing a resemblance to the twisted stalk of the terrestrial iron-oxidizing microbe, Gallionella ferruginea. While Gallionella has not been detected in, or isolated from, these mats microaerophilic iron-oxidizing, a stalk- forming bacterium, Mariprofundus ferrooxydans (PV-1 and related strains) has been isolated from mats at the Loihi seamount in Hawaii (Emerson et al. 2007, PLoS One 2(8): e667). Fossilized aggregates of iron filaments have been observed in the rock record (e.g. Little et al. 2004, Geomicrobiol. J. 21:415), and may represent ancient versions of these microbial mats. If this is shown to be true, such filaments would represent one of the few microfossil morphologies that can be linked to a specific microbial metabolism. We have used a combination of test tube culturing, microslide culturing, time lapse microscopy, and electron microscopy to study Mariprofundus stalk morphology and genesis and link these details to physiological responses to environmental chemistry. The goals include determining specific attributes of stalk morphology that can be used to determine the biogenicity of putative iron microfossils, and interpret the conditions of the depositional environment. Light microscopic observation of microslide cultures over the course of several days allowed for determination of bacterial response to developing oxygen and Fe(II) gradients. Once gradients have been established, given an abundant supply of oxygen, cells congregate in a band perpendicular to the gradient and stalks are formed, growing in the direction of increasing oxygen (and decreasing Fe) concentration. This

  10. Methane oxidation linked to chlorite dismutation

    PubMed Central

    Miller, Laurence G.; Baesman, Shaun M.; Carlström, Charlotte I.; Coates, John D.; Oremland, Ronald S.

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO−2) dismutation. Although dissimilatory reduction of ClO−4 and ClO−3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO−2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO−2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO−2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO−2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO−4 or ClO−3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs. PMID:24987389

  11. Methane oxidation linked to chlorite dismutation

    USGS Publications Warehouse

    Miller, Laurence G.; Baesman, Shaun M.; Carlström, Charlotte I.; Coates, John D.; Oremland, Ronald S.

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO−2) dismutation. Although dissimilatory reduction of ClO−4 and ClO−3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO−2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO−2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO−2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO−2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO−4 or ClO−3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

  12. Methane oxidation linked to chlorite dismutation.

    PubMed

    Miller, Laurence G; Baesman, Shaun M; Carlström, Charlotte I; Coates, John D; Oremland, Ronald S

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO(-) 2) dismutation. Although dissimilatory reduction of ClO(-) 4 and ClO(-) 3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO(-) 2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO(-) 2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO(-) 2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO(-) 2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO(-) 4 or ClO(-) 3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs. PMID:24987389

  13. Linking microbial carbon utilization with microbially-derived soil organic matter

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

    Soil microbial communities are fundamental to plant C turnover, as all C inputs eventually pass through the microbial biomass. In turn, there is increasing evidence that this biomass accumulates as a significant portion of stable soil organic matter (SOM) via physiochemical interactions with the soil matrix. However, when exploring SOM dynamics, these two processes are often regarded as discrete from one another, despite potentially important linkages between microbial C utilization and the fate of that biomass C as SOM. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil C inputs that influence microbial biomass production and microbial C allocation. Microbial physiology, such as microbial growth efficiency (MGE), growth rate and turnover have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM accumulation may not necessarily be a function of resistance to decay but the degree to which it optimizes microbial biomass production. To examine the relationship between microbial C utilization and microbial contributions to SOM, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine 1) if, in absence of plant-derived C, chemically complex SOM similar to natural soils can accumulate through the production of microbial residues and 2) how differences in C utilization of simple substrates, varying in energy yields, influence the quantity and chemistry of newly formed SOM. Over the course of the incubation, MGE

  14. [Aqueous oxidation of SO2 with microbial method].

    PubMed

    Jiang, Wen-ju; Tong, Xiao-shuang; Zhu, Xiao-fan; Zhu, Lian-xi; Jin, Yan

    2006-05-01

    The desulfurizations in dilute sulfuric acid solution, acidic ferric solution, acidic ferrous solution, microbial solution (Thiobacillus ferrooridans) and microbial culture medium solution were conducted to discuss biodesulfurization mechanism. The effect of Fe3+ concentration, Fe2+ concentration, SO2 concentration and temperature on biodesulfurization was examined on SO4(2-) concentration in the solution. Biodesulfurization has two ways: direct oxidation and indirect oxidation. In direct oxidation, Thiobacillus ferrooxridans oxidize S(IV) to S(VI). In indirect oxidation, Thiobacillus ferrooxidans can fast transform Fe2+ to Fe3+ in acidic conditions and then increase aqueous catalytic oxidation capacity of Fe3+ on SO2. It shows that indirect oxidation is the dominant way in biodesulfurization process. The desulfurization efficiency increase with concentration of Fe3+ or Fe2+ in the range of 0-1.2 g/L. Thiobacillus ferrooxidans enforce oxidation of SO2 in Fe3+ /Fe2+ system. The removal of SO2 decrease as concentration of SO2 increase, however, concentrations of SO4(2-) in the solution do not vary much in different inlet concentrations of SO2. Temperature has important effect on biodesulfurization. The optimal operative temperature range is 30-40 degrees C. PMID:16850819

  15. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

    SciTech Connect

    Shelobolina, Evgenya S.; Xu, Huifang; Konishi, Hiromi; Kukkadapu, Ravi K.; Wu, Tao; Blothe, Marco; Roden, Eric E.

    2012-06-08

    Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through production of organic ligands and acids, and through uptake of products of weathering. Here we show that a lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture (Straub, 6 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Moessbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 107 cells were produced per {micro}mol Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including decrease in unit cell b-dimension toward dioctahedral levels and iron and potassium release. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms may be directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.

  16. Potential for microbial oxidation of ferrous iron in basaltic glass.

    PubMed

    Xiong, Mai Yia; Shelobolina, Evgenya S; Roden, Eric E

    2015-05-01

    Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and

  17. CKD impairs barrier function and alters microbial flora of the intestine: a major link to inflammation and uremic toxicity

    PubMed Central

    Vaziri, Nosratola D.

    2013-01-01

    Purpose of review Chronic kidney disease (CKD) is associated with oxidative stress and inflammation which contribute to progression of kidney disease and its numerous complications. Until recently, little attention had been paid to the role of the intestine and its microbial flora in the pathogenesis of CKD-associated inflammation. This article is intended to provide an over view of the impact of uremia on the structure and function of the gut and its microbial flora and their potential link to the associated systemic inflammation. Recent findings Recent studies conducted in the author’s laboratories have demonstrated marked disintegration of the colonic epithelial barrier structure and significant alteration of the colonic bacterial flora in humans and animals with advanced CKD. The observed disruption of the intestinal epithelial barrier complex can play an important part in the development of systemic inflammation by enabling influx of endotoxin and other noxious luminal contents into the systemic circulation. Similarly via disruption of the normal symbiotic relationship and production, absorption and retention of noxious products, alteration of the microbial flora can contribute to systemic inflammation and uremic toxicity. In fact recent studies have documented the role of colonic bacteria as the primary source of several well known pro-inflammatory/pro-oxidant uremic toxins as well as many as-yet unidentified retained compounds. Summary CKD results in disruption of the intestinal barrier structure and marked alteration of its microbial flora –events that play a major role in the pathogenesis of inflammation and uremic toxicity. PMID:23010760

  18. Microbial-mediated method for metal oxide nanoparticle formation

    SciTech Connect

    Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

    2015-09-08

    The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

  19. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

    PubMed Central

    Xu, Huifang; Konishi, Hiromi; Kukkadapu, Ravi; Wu, Tao; Blöthe, Marco; Roden, Eric

    2012-01-01

    Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 107 cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere. PMID:22685132

  20. Linking Toluene Degradation with Specific Microbial Populations in Soil

    PubMed Central

    Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

    1999-01-01

    Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

  1. Oxidation of aromatic contaminants coupled to microbial iron reduction

    USGS Publications Warehouse

    Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

    1989-01-01

    THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

  2. Microbial production and oxidation of methane in deep subsurface

    NASA Astrophysics Data System (ADS)

    Kotelnikova, Svetlana

    2002-10-01

    The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized

  3. Microbially mediated cobalt oxidation in seawater revealed by radiotracer experiments

    SciTech Connect

    Lee, B.G.; Fisher, N.S. )

    1993-12-01

    The influence of microbial activity on Co and Mn oxidation in decomposing diatom cultures was determined with radiotracer techniques. Adding a consortium of microorganisms collected from coastal seawater (0.2-3-[mu]m size fraction) to the cultures increased particulate Co formation rates at 18[degrees]C by an order of magnitude (to 3.8% d[sup [minus]1]) and particulate Mn formation rates 3-fold (to 7.9% d[sup [minus

  4. Linking Microbial Heterotrophic Activity and Sediment Lithology in Oxic, Oligotrophic Sub-Seafloor Sediments of the North Atlantic Ocean

    PubMed Central

    Picard, Aude; Ferdelman, Timothy G.

    2011-01-01

    Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7–8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with 14C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO2 (with O2 as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm−3 d−1) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm−3 d−1). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link. PMID:22207869

  5. Microbially Induced Iron Oxidation: What, Where, How

    SciTech Connect

    SCHIERMEYER,ELISA M.; PROVENCIO,PAULA P.; NORTHUP,DIANA E.

    2000-08-15

    From the results of the different bacterial cells seen, it is fairly certain that Gallionella is present because of the bean-shaped cells and twisted stalks found with the TEM. The authors cannot confirm, though, what other iron-oxidizing genera exist in the tubes, since the media was only preferential and not one that isolated a specific genus of bacteria. Based on the environment in which they live and the source of the water, they believe their cultures contain Gallionella, Leptothrix, and possibly Crenothrix and Sphaerotilus. They believe the genus Leptothrix rather than Sphaerotilus exist in the tubes because the water source was fresh, unlike the polluted water in which Sphaerotilus are usually found. The TEM preparations worked well. The cryogenic method rapidly froze the cells in place and allowed them to view their morphology. The FAA method, as stated previously, was the best of the three methods because it gave the best contrast. The gluteraldehyde samples did not come out as well. It is possible that the gluteraldehyde the authors prepared was still too concentrated and did not mix well. Although these bacteria were collected from springs and then cultured in an environment containing a presumably pure iron-bearing metal, it seems the tube already containing Manganese Gradient Medium could be used with a piece of metal containing these bacteria. A small piece of corroding metal could then be inserted into the test tube and cultured to study the bacteria.

  6. Microbial Ecophysiology is a Missing Link in Emerging Microbial-based Soil Organic Matter Frameworks

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.; Frey, S. D.

    2012-12-01

    Recently, our epistemology of soil C dynamics has been undergoing a major transformation; where in the past soil organic matter (SOM) formation was attributed to the biochemical recalcitrance of plant litter, we now know that microbially transformed plant residues and microbial necromass are key precursors of SOM formation. SOM formation is thus a result of complex ecological interactions between substrate availability, the soil biological community, and the decomposing environment, and is a function of multiple ecosystem processes related to climate, soil type and their interactions with resident decomposer communities. Under this emerging new view, microbial biomass is treated generally, without consideration of the ecophysiological processes that regulate the chemistry and abundance of biomass production. In reality, biomass inputs are far more complex in terms of their input rates and potential to serve as a precursor to SOM formation. We explore microbial growth efficiencies (MGE) and growth rates and how their expression across different soil environments can be incorporated into our emerging conceptual models of microbial-mediated SOM formation. MGE and growth rates are both poorly understood despite their direct impact on SOM formation. Specifically, the physiological trade-offs associated with growth rates and MGE need to be assessed in terms of their relative influence on microbial inputs to SOM. Additionally, we need a better understanding of the variation in chemistry of cellular biomass, metabolites and exocellular excretions across species. At a broad level, we know that fungal and bacterial cell walls differ in their chemical recalcitrance and organo-mineral interactions but the degree to which this variation results in long-term differences in SOM dynamics remains unknown. To explore these uncertainties, we use a model-based approach to examine how potential tradeoffs between MGE and growth rates, and their responses to varying environmental

  7. Anoxic Oxidation of Arsenite Linked to Denitrification in Sludges and Sediments

    PubMed Central

    Sun, Wenjie; Sierra, Reyes; Field, Jim A.

    2008-01-01

    In this study, denitrification linked to the oxidation of arsenite (As(III)) to arsenate (As(V)) was shown to be a widespread microbial activity in anaerobic sludge and sediment samples that were not previously exposed to arsenic contamination. When incubated with 0.5 mM As(III) and 10 mM NO3−, the anoxic oxidation of As(III) commenced within a few days, achieving specific activities of up to 1.24 mmol As(V) formed g−1 volatile suspended solids d−1 due to growth (doubling times of 0.74 to 1.4 d). The anoxic oxidation of As(III) was partially to completely inhibited by 1.5 and 5 mM As(III), respectively. Inhibition was minimized by adding As(III) adsorbed onto activated aluminum (AA). The oxidation of As(III) was shown to be linked to the complete denitrification of NO3− to N2 by demonstrating a significantly enhanced production of N2 beyond the background endogenous production as a result of adding As(III)-AA to the cultures. The N2 production corresponded closely the expected stoichiometry of the reaction, 2.5 mol As(III) mol−1 N2-N. The oxidation of As(III) linked to the use of common occuring nitrate as an electron acceptor may be an important missing link in the biogeochemical cycling of arsenic. PMID:18762312

  8. Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

    NASA Technical Reports Server (NTRS)

    Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

    2001-01-01

    In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical

  9. Increased electrical output when a bacterial ABTS oxidizer is used in a microbial fuel cell

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. The present study examined the formation in culture of an unidentified bacterial oxidant and investigated the ...

  10. Complete cobalt recovery from lithium cobalt oxide in self-driven microbial fuel cell - Microbial electrolysis cell systems

    NASA Astrophysics Data System (ADS)

    Huang, Liping; Yao, Binglin; Wu, Dan; Quan, Xie

    2014-08-01

    Complete cobalt recovery from lithium cobalt oxide requires to firstly leach cobalt from particles LiCoO2 and then recover cobalt from aqueous Co(II). A self-driven microbial fuel cell (MFC)-microbial electrolysis cell (MEC) system can completely carry out these two processes, in which Co(II) is firstly released from particles LiCoO2 on the cathodes of MFCs and then reduced on the cathodes of MECs which are powered by the cobalt leaching MFCs. A cobalt leaching rate of 46 ± 2 mg L-1 h-1 with yield of 1.5 ± 0.1 g Co g-1 COD (MFCs) and a Co(II) reduction rate of 7 ± 0 mg L-1 h-1 with yield of 0.8 ± 0.0 g Co g-1 COD (MECs), as well as a overall system cobalt yield of 0.15 ± 0.01 g Co g-1 Co can be achieved in this self-driven MFC-MEC system. Coulombic efficiencies reach 41 ± 1% (anodic MFCs), 75 ± 0% (anodic MECs), 100 ± 2% (cathodic MFCs), and 29 ± 1% (cathodic MECs) whereas overall system efficiency averages 34 ± 1%. These results provide a new process of linking MFCs to MECs for complete recovery of cobalt and recycle of spent lithium ion batteries with no external energy consumption.

  11. Sources and Contributions of Oxygen During Microbial Pyrite Oxidation: the Triple Oxygen Isotopes of Sulfate

    NASA Astrophysics Data System (ADS)

    Ziegler, K.; Coleman, M. L.; Mielke, R. E.; Young, E. D.

    2008-12-01

    complimentary chemistry data (in progress), we interpret our isotope data to indicate that the biotic fractionation factor ɛ18OSO4-O2 of at least ~ -25 to - 35‰ is augmented by microbially induced kinetic fractionation; it is larger than expected based on published equilibrium values [2,3,4]. Our inferred ɛ18OSO4-H2O of at least ~+10‰ is similar to some reported values. These new insights into the close links between microbial life cycle and sources of sulfate oxygen during sulfide oxidation, and their oxygen isotopic expressions, will help elucidate the role of microbial oxidation in natural systems. If microbial populations in natural systems remain in a perpetual lag-phase due to constrains of chemistry, atmospheric oxygen will imprint its isotopic signature onto sulfate deposits. Ultimately, such data could be used as biosignatures on Early Earth or Mars. [1] Brunner and Coleman (2008) EPSL 270, 63-72. [2] Balci et al. (2007) GCA 71, 3796-3811. [3] Pisapia et al. (2007) GCA 71, 2474-2490. [4] Taylor et al. (1984) GCA 48, 2669-2678.

  12. Microbial Diversity in Sediments of Saline Qinghia Lake, China:Linking Geochemical Controls to Microbial Ecoloby

    SciTech Connect

    Dong, Hailiang; Zhang, Gengxin; Jiang, Hongchen; Yu, Bingsong; Chapman, Leah R.; Lucas, Courtney R.; Fields, Matthew W.

    2007-03-30

    Saline lakes at high altitudes represent an important andextreme microbial ecosystem, yet little is known about microbialdiversity in such environments. The objective of this study was toexamine the change of microbial diversity from the bottom of the lake tosediments of 40 cm in depth in a core from Qinghai Lake. The lake issaline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on theQinghai-Tibetan Plateau at an altitude of 3196 m above sea level. Porewater chemistry of the core revealed low concentrations of sulfate andiron (<1 mM), but high concentrations of acetate (40-70 mM) anddissolved organic carbon (1596-5443 mg/L). Total organic carbon and totalnitrogen contents in the sediments were approximately 2 and<0.5percent, respectively. Acridine orange direct count data indicated thatcell numbers decreased from 4 x 10(9) cells/g at the water-sedimentinterface to 6 x 10(7) cells/g wet sediment at the 40-cm depth. Thischange in biomass was positively correlated with acetate concentration inpore water. Phospholipid fatty acid (PLFA) community structure analysesdetermined decrease in the proportion of the Proteobacteria and increasein the Firmicutes with increased depth. Characterization of small subunit(SSU) rRNA genes amplified from the sediments indicated a shift in thebacterial community with depth. Whereas the alpha-, beta-, andgamma-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB)were dominant at the water-sediment interface, low G + C gram-positivebacteria (a subgroup of Firmicutes) became the predominant group in theanoxic sediments. Both PLFA and the sequence data showed similar trend.The Proteobacteria, CFB, and gram-positive bacteria are present in othersaline lakes, but the presence of Actinobacteria andAcidobacteria/Holophaga in significant proportions in the Qinghai Lakesediments appears to be unique. The archaeal diversity was much lower,and clone sequences could be grouped in the Euryarchaeota andCrenarchaeota domains. The

  13. Linking Microbial Ecology to Geochemistry in Sulfate Reducing Systems

    NASA Astrophysics Data System (ADS)

    Drennan, D. M.; Lee, I.; Landkamer, L.; Almstrand, R.; Figueroa, L. A.; Sharp, J. H.

    2013-12-01

    community composition. CCA of Shannon diversity data after one pore volume revealed that zinc removal, walnut shell content, and abundance of delta-Proteobacteria (sulfate reducing organisms) were all corresponding elements. However, after several pore volumes, the walnut shell column was no longer removing Zn as effectively, and community shifts were observed throughout the columns. Analysis of field and laboratory scale microbiological and geochemical shifts, in parallel, gives insight into key biogeochemical variables linked to the performance of passive remediation systems used for the treatment of contaminated MIW, while also providing further insight into metal immobilization at the microbe-mineral interface.

  14. Microbial reduction of manganese oxides - Interactions with iron and sulfur

    NASA Technical Reports Server (NTRS)

    Myers, Charles R.; Nealson, Kenneth H.

    1988-01-01

    Alteromonas putrefaciens (strain MR-1) is capable of rapid Mn(IV) reduction under conditions of neutral pH and temperatures characteristic of the Oneida Lake, New York, sediments from which it was isolated. MR-1 also reduces Fe(3+) to Fe(2+), and disproportionates thiosulfate to sulfide and sulfite; independently, the Fe(2+) and sulfide act as rapid reductants of Mn. The addition of Fe(3+) or thiosulfate to cultures of MR-1 in the presence of oxidized Mn increases the rate and the extent of Mn reduction relative to that observed in the absence of Fe(3+) or thiosulfate. Furthermore, when Fe(3+) and Mn oxides are present conjointly, Fe(2+) does not appear until the reduction of the oxidized Mn is complete. These results demonstrate that the observed rates of Fe(2+) and sulfide production may underestimate the total rates of Fe and sulfate reduction in those environments containing oxidized Mn. These results also demonstrate the potential impact that a single microbe can exert on sediment geochemistry, and provide the basis for preliminary models of the complexity of microbial and geochemical interactions that occur.

  15. Microbial Methane Oxidation Rates in Guandu Wetland of northern Taiwan

    NASA Astrophysics Data System (ADS)

    Yu, Zih-Huei; Wang, Pei-Ling; Lin, Li-Hung

    2016-04-01

    Wetland is one of the major sources of atmospheric methane. The exact magnitude of methane emission is essentially controlled by microbial processes. Besides of methanogenesis, methanotrophy oxidizes methane with the reduction of various electron acceptors under oxic or anoxic conditions. The interplay of these microbial activities determines the final methane flux under different circumstances. In a tidal wetland, the cyclic flooding and recession of tide render oxygen and sulfate the dominant electron acceptors for methane oxidation. However, the details have not been fully examined, especially for the linkage between potential methane oxidation rates and in situ condition. In this study, a sub-tropical wetland in northern Taiwan, Guandu, was chosen to examine the tidal effect on microbial methane regulation. Several sediment cores were retrieved during high tide and low tide period and their geochemical profiles were characterized to demonstrate in situ microbial activities. Incubation experiments were conducted to estimate potential aerobic and anaerobic methane oxidation rates in surface and core sediments. Sediment cores collected in high tide and low tide period showed different geochemical characteristics, owning to tidal inundation. Chloride and sulfate concentration were lower during low tide period. A spike of enhanced sulfate at middle depth intervals was sandwiched by two sulfate depleted zones above and underneath. Methane was accumulated significantly with two methane depletion zones nearly mirroring the sulfate spike zone identified. During the high tide period, sulfate decreased slightly with depth with methane production inhibited at shallow depths. However, a methane consumption zone still occurred near the surface. Potential aerobic methane oxidation rates were estimated between 0.7 to 1.1 μmole/g/d, showing no difference between the samples collected at high tide or low tide period. However, a lag phase was widely observed and the lag phase

  16. Regioselective oxidation of unprotected 1,4 linked glucans.

    PubMed

    Eisink, Niek N H M; Lohse, Jonas; Witte, Martin D; Minnaard, Adriaan J

    2016-06-01

    Palladium-catalyzed alcohol oxidation allows the chemo- and regioselective modification of unprotected 1,4 linked glucans. This is demonstrated in the two-step bisfunctionalization of 1,4 linked glucans up to the 7-mer. Introduction of an anomeric azide is followed by a highly regioselective mono-oxidation of the terminal C3-OH functionality. The resulting orthogonal bis-functionalized oligosaccharides are a viable alternative to PEG-spacers as demonstrated in the conjugation of a cysteine mutant of 4-oxalocrotonate tautomerase with biotin. PMID:27159790

  17. Biologically relevant oxidants cause bound proteins to readily oxidatively cross-link at Guanine.

    PubMed

    Solivio, Morwena J; Nemera, Dessalegn B; Sallans, Larry; Merino, Edward J

    2012-02-20

    Oxidative DNA-protein cross-links have received less attention than other types of DNA damage and remain as one of the least understood types of oxidative lesion. A model system using ribonuclease A and a 27-nucleotide DNA was used to determine the propensity of oxidative cross-linking to occur in the presence of oxidants. Cross-link formation was examined using four different oxidation systems that generate singlet oxygen, superoxide, and metal-based Fenton reactions. It is shown that oxidative cross-linking occurs in yields ranging from 14% to a maximal yield of 61% in all oxidative systems when equivalent concentrations of DNA and protein are present. Because singlet oxygen is the most efficient oxidation system in generating DNA-protein cross-links, it was chosen for further analyses. Cross-linking occurred with single-stranded DNA binding protein and not with bovine serum albumin. Addition of salt lowered nonspecific binding affinity and lowered cross-link yield by up to 59%. The yield of cross-linking increased with increased ratios of protein compared with DNA. Cross-linking was highly dependent on the number of guanines in a DNA sequence. Loss of guanine content on the 27-nucleotide DNA led to nearly complete loss in cross-linking, while primer extension studies showed cross-links to predominantly occur at guanine base on a 100-nucleotide DNA. The chemical species generated were examined using two peptides derived from the ribonuclease A sequence, N-acetyl-AAAKF and N-acetyl-AYKTT, which were cross-linked to 2'-deoxyguanosine. The cross-link products were spiroiminodihydantoin, guanidinohydantoin, and tyrosyl-based adducts. Formation of tyrosine-based adducts may be competitive with the more well-studied lysine-based cross-links. We conclude that oxidative cross-links may be present at high levels in cells since the propensity to oxidatively cross-link is high and so much of the genomic DNA is coated with protein. PMID:22216745

  18. Linking Microbial Dynamics and Physicochemical Processes in High-temperature Acidic Fe(III)- Mineralizing Systems

    NASA Astrophysics Data System (ADS)

    Inskeep, W.

    2014-12-01

    Microbial activity is responsible for the mineralization of Fe(III)-oxides in high-temperature chemotrophic communities that flourish within oxygenated zones of low pH (2.5 - 4) geothermal outflow channels (Yellowstone National Park, WY). High-temperature Fe(II)-oxidizing communities contain several lineages of Archaea, and are excellent model systems for studying microbial interactions and spatiotemporal dynamics across geochemical gradients. We hypothesize that acidic Fe(III)-oxide mats form as a result of constant interaction among primary colonizers including Hydrogenobaculum spp. (Aquificales) and Metallosphaera spp. (Sulfolobales), and subsequent colonization by archaeal heterotrophs, which vary in abundance as a function of oxygen, pH and temperature. We are integrating a complementary suite of geochemical, stable isotope, genomic, proteomic and modeling analyses to study the role of microorganisms in Fe(III)-oxide mat development, and to elucidate the primary microbial interactions that are coupled with key abiotic events. Curated de novo assemblies of major phylotypes are being used to analyze additional -omics datasets from these microbial mats. Hydrogenobaculum spp. (Aquificales) are the dominant bacterial population(s) present, and predominate during early mat development (< 30 d). Other Sulfolobales populations known to oxidize Fe(II) and fix carbon dioxide (e.g., Metallosphaera spp.) represent a secondary stage of mat development (e.g., 14 - 30 d). Hydrogenobaculum filaments appear to promote the nucleation and subsequent mineralization of Fe(III)-oxides, which likely affect the growth and turnover rates of these organisms. Other heterotrophs colonize Fe(III)-oxide mats during succession (> 30 d), including novel lineages of Archaea and representatives within the Crenarchaeota, Euryarchaeota, Thaumarchaeota and Nanoarchaeota. In situ oxygen consumption rates show that steep gradients occur within the top 1 mm of mat surface, and which correlate with

  19. Sorption of trivalent cerium by a mixture of microbial cells and manganese oxides: Effect of microbial cells on the oxidation of trivalent cerium

    NASA Astrophysics Data System (ADS)

    Ohnuki, Toshihiko; Jiang, Mingyu; Sakamoto, Fuminori; Kozai, Naofumi; Yamasaki, Shinya; Yu, Qianqian; Tanaka, Kazuya; Utsunomiya, Satoshi; Xia, Xiaobin; Yang, Ke; He, Jianhua

    2015-08-01

    Sorption of Ce by mixtures of synthetic Mn oxides and microbial cells of Pseudomonas fluorescens was investigated to elucidate the role of microorganisms on Ce(III) oxidative migration in the environment. The mixtures, upon which Ce was sorbed following exposure to solutions containing 1.0 × 10-4 or 1.0 × 10-5 mol L-1 Ce(III), were analyzed by scanning electron microscopy energy dispersive X-ray spectroscopy (SEM-EDS) and micro-X-ray fluorescence (micro-XRF) at synchrotron facilities. A Ce LIII-edge micro XANES spectra analysis was also performed to determine the oxidation states of Ce adsorbed to the Mn oxides and microbial cells in the mixtures. The distribution ratios (Kd) of Ce between the individual solids and solution increased with increasing pH of the solution, and was nearly the same in mixtures containing varying amounts of microbial cells. SEM-EDS and micro-XRF analyses showed that Ce was sorbed by both MnO2 and microbial cells (1.7 × 10-1 or 3.3 × 10-1 g L-1). In addition, nano-particles containing Ce and P developed on the surface of the microbial cells. XANES analysis showed that lower fractions of Ce(III) were oxidized to Ce(IV) in the mixtures containing greater amounts of microbial cells. Micro-XANES analysis revealed that Ce was present as Ce(III) on the microbial cells and as Ce(IV) on Mn oxides. These results strongly suggest that the association of Ce(III) with the microbial cell surface and the formation of Ce phosphate nano-particles are responsible for suppressing the oxidation of Ce(III) to Ce(IV) in the mixtures.

  20. Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments.

    PubMed

    Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip J R; Boschker, Henricus T S

    2015-09-01

    Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following (13)C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas (13)C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and

  1. Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments

    PubMed Central

    Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip JR; Boschker, Henricus TS

    2015-01-01

    Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following 13C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas 13C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and

  2. Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide

    PubMed Central

    Glass, Jennifer B.; Orphan, Victoria J.

    2011-01-01

    Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO2 cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH4), and nitrous oxide (N2O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH4 and N2O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH4 oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N2O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N2O reductase, the only known enzyme capable of microbial N2O conversion to N2, have only been found in classical denitrifiers. Accumulation of N2O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N2O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide

  3. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    NASA Astrophysics Data System (ADS)

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-05-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbially-mediated processes. Soil amended with biochar has been demonstrated to reduce N2O emissions in the field and in laboratory experiments. Although N2O emission mitigation following soil biochar amendment has been reported frequently the underlying processes and specific role of the nitrogen cycling microbial community in decreasing soil N2O emissions has not been subject of systematic investigation. To investigate the impact of biochar on the microbial community of nitrogen-transforming microorganisms we performed a microcosm study with arable soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature wood derived biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative real-time PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil.

  4. [Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

    PubMed

    Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

    2012-01-01

    Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community. PMID:23330391

  5. Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda; Orphan, Victoria; Turk, Kendra; Embaye, Tsegereda; Kubo, Mike; Summons, Roger

    2005-01-01

    Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

  6. Microbial-based inoculants impact nitrous oxide emissions from an incubated soil medium containing urea fertilizers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current study was conducted to test the hypothesis that microbial-based inoculants known to promote root growth and nutrient uptake will reduce emission of nitrous oxide in the presents of nitrogen fertilizers under controlled condition. The microbial based treatments were SoilBuilder (SB), a m...

  7. Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

    SciTech Connect

    Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.; McCue, Lee Ann

    2013-10-01

    To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.

  8. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    PubMed Central

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-01-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  9. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community.

    PubMed

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-03-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  10. Linking protein oxidation to environmental pollutants: redox proteomic approaches.

    PubMed

    Braconi, Daniela; Bernardini, Giulia; Santucci, Annalisa

    2011-10-19

    Environmental pollutants, such as compounds used in agriculture or deriving from vehicles, industries and human activities, can represent major concern for human health since they are considered to contribute significantly to many diseased states with major public health significance. Besides considerable epidemiological evidence linking environmental pollutants with adverse health effects, little information is provided on the effects of these compounds at the cellular and molecular level. Though oxidative stress is generally acknowledged as one of the most important mechanisms of action for pollutant-induced toxicity, redox proteomics, the elective tool to identify post-translationally oxidized proteins, is still in its very infancy in this field of investigation. This review will provide the readers with an outline of the use of redox proteomics in evaluating pollutant-induced oxidative damage to proteins in various biological systems. Future potential applications of redox proteomic approaches from an environmental point of view will be discussed as well. PMID:21767673

  11. Microbial oxidation of methane from old landfills in biofilters

    SciTech Connect

    Streese, J.; Stegmann, R

    2003-07-01

    Landfill gas emissions are among the largest sources of the greenhouse gas methane. For this reason, the possibilities of microbial methane degradation in biofilters were investigated. Different filter materials were tested in two experimental plants, a bench-scale plant (total filter volume 51 l) and a pilot plant (total filter volume 4 m{sup 3}). Three months after the beginning of the experiment, very high degradation rates of up to 63 g CH{sub 4}/(m{sup 3}h) were observed in the bench-scale plant at mean methane concentrations of 2.5% v/v and with fine-grained compost as biofilter material. However, the degradation rates of the compost biofilter decreased in the fifth month of the experiment, probably due to the accumulation of exopolymeric substances formed by the microorganisms. A mixture of compost, peat, and wood fibers showed stable and satisfactory degradation rates around 20 g/(m{sup 3}h) at mean concentrations of 3% v/v over a period of one year. In this material, the wood fibers served as a structural material and prevented clogging of the biofilter. Extrapolation of the experimental data indicates that biofilters for methane oxidation have to be at least 100 times the volume of biofilters for odor control to obtain the same cleaning efficiency per unit volume flow of feed gas.

  12. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    PubMed Central

    Al-Najjar, Mohammad A. A.; Ramette, Alban; Kühl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. PMID:25147548

  13. Deposition of Biogenic Iron Minerals in a Methane Oxidizing Microbial Mat

    PubMed Central

    Wrede, Christoph; Dreier, Anne; Heller, Christina; Reitner, Joachim; Hoppert, Michael

    2013-01-01

    The syntrophic community between anaerobic methanotrophic archaea and sulfate reducing bacteria forms thick, black layers within multi-layered microbial mats in chimney-like carbonate concretions of methane seeps located in the Black Sea Crimean shelf. The microbial consortium conducts anaerobic oxidation of methane, which leads to the formation of mainly two biomineral by-products, calcium carbonates and iron sulfides, building up these chimneys. Iron sulfides are generated by the microbial reduction of oxidized sulfur compounds in the microbial mats. Here we show that sulfate reducing bacteria deposit biogenic iron sulfides extra- and intracellularly, the latter in magnetosome-like chains. These chains appear to be stable after cell lysis and tend to attach to cell debris within the microbial mat. The particles may be important nuclei for larger iron sulfide mineral aggregates. PMID:23843725

  14. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats.

    PubMed

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J; Salzman, Nita H; Baker, John E

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host's metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  15. Microbial Anaerobic Ammonium Oxidation Under Iron Reducing Conditions, Alternative Electron Acceptors

    NASA Astrophysics Data System (ADS)

    Ruiz-Urigüen, M.; Jaffe, P. R.

    2015-12-01

    Autotrophic Acidimicrobiaceae-bacterium named A6 (A6), part of the Actinobacteria phylum have been linked to anaerobic ammonium (NH4+) oxidation under iron reducing conditions. These organisms obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, the TEAs are iron oxides [Fe(III)], which are reduced to Fe(II), this process is known as Feammox. Our studies indicate that alternative forms of TEAs can be used by A6, e.g. iron rich clays (i.e. nontronite) and electrodes in bioelectrochemical systems such as Microbial Electrolysis Cells (MECs), which can sustain NH4+removal and A6 biomass production. Our results show that nontronite can support Feammox and promote bacterial cell production. A6 biomass increased from 4.7 x 104 to 3.9 x 105 cells/ml in 10 days. Incubations of A6 in nontronite resulted in up to 10 times more NH4+ removal and 3 times more biomass production than when ferrihydrite is used as the Fe(III) source. Additionally, Fe in nontronite can be reoxidized by aeration and A6 can reutilize it; however, Fe is still finite in the clay. In contrast, in MECs, A6 harvest electrons from NH4+ and use an anode as an unlimited TEA, as a result current is produced. We operated multiple MECs in parallel using a single external power source, as described by Call & Logan (2011). MECs were run with an applied voltage of 0.7V and different growing mediums always containing initial 5mM NH4+. Results show that current production is favored when anthraquinone-2,6-disulfonate (AQDS), an electron shuttled, is present in the medium as it facilitates the transfer of electrons from the bacterial cell to the anode. Additionally, A6 biomass increased from 1 x 104 to 9.77 x 105cells/ml in 14 days of operation. Due to Acidimicrobiaceae-bacterium A6's ability to use various TEAs, MECs represent an alternative, iron-free form, for optimized biomass production of A6 and its application in NH4

  16. The use of controlled microbial cenoses in producers' link to increase steady functioning of artificial ecosystems

    NASA Astrophysics Data System (ADS)

    Somova, Lydia; Mikheeva, Galina; Somova, Lydia

    The life support systems (LSS) for long-term missions are to use cycling-recycling systems, including biological recycling. Simple ecosystems include 3 links: producers (plants), consumers (man, animals) and reducers (microorganisms). Microorganisms are substantial component of every link of LSS. Higher plants are the traditional regenerator of air and producer of food. They should be used in many successive generations of their reproduction in LSS. Controlled microbiocenoses can increase productivity of producer's link and protect plants from infections. The goal of this work was development of methodological bases of formation of stable, controlled microbiocenoses, intended for increase of productivity of plants and for obtaining ecologically pure production of plants. Main results of our investigations: 1. Experimental microbiocenoses, has been produced in view of the developed methodology on the basis of natural association of microorganisms by long cultivation on specially developed medium. Dominating groups are bacteria of genera: Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Rhodopseudomonas and yeast of genera: Kluyveromyces, Saccharomyces, Torulopsis. 2. Optimal parameters of microbiocenosis cultivation (t, pH, light exposure, biogenic elements concentrations) were experimentally established. Conditions of cultivation on which domination of different groups of microbiocenosis have been found. 3. It was shown, that processing of seeds of wheat, oats, bulbs and plants Allium cepa L. (an onions) with microbial association raised energy of germination of seeds and bulbs and promoted the increase (on 20-30 %) of growth green biomass and root system of plants in comparison with the control. This work is supported by grant, Yenissey , 07-04-96806

  17. Palaeoarchean Barite Deposits in the Barberton Greenstone Belt: Origin and Links to Early Microbial Life

    NASA Astrophysics Data System (ADS)

    Mason, P. R.; Peters, A.; Nijman, W.; Reimer, T. O.; Whitehouse, M. J.

    2008-12-01

    Barite deposits are considered important for identifying microbial S cycling in Archean rocks since they can provide information about S isotopes in coexisting sulfate and sulfide minerals. However the degree to which barite and pyrite in metasedimentary rocks are related remains unclear. In this study we have investigated the origin of barite and pyrite in four main horizons seen in both outcrop and fresh drill core material from the Lower Mapepe formation (3.26 to 3.23 Ga), Barberton Greenstone Belt, South Africa. Host rocks include shales, cherts, tuffs and conglomerates that are variably silicified and/or affected by carbonate alteration. The high-energy depositional environment of the host rocks, mineralogical textures, barite chemistry and the occurrence of feldspars from the rarely-found celsian-hyalophane-orthoclase series suggest a seafloor exhalative origin for the barite. In contrast pyrite is closely associated with cherts and dolomitic units where rare earth element and Y data support a marine influence. Pyrite chemistry (Co/Ni= 0.1-1, Se/S <5 x 10- 5) also indicates a low temperature sedimentary origin. Multiple S isotope data (32S, 33S, 34S, determined by SIMS) for pyrite indicates a number of arrays with limited δ34S fractionation at constant Δ33S associated with individual syn-sedimentary microcrystalline pyrite layers. Isolated euhedral pyrites in massive chert and barite rich units show much more scatter and larger degrees of Δ33S variation (-1 to +4 ). Our results are consistent with models invoking microbial mass dependent fractionation of a heterogeneous elemental sulfur source derived from atmospheric photolysis. The sulfate reservoir can also be linked to photolysis but there is no clear relationship between the barite and pyrite S isotope data, suggesting that microbial (or abiotic) sulfate reduction was absent at this time or that the basinal sulfate concentration must have remained significantly lower than the mM level prior to barite

  18. Linking Microbial Activity with Arsenic Fate during Cow Dung Disposal of Arsenic-Bearing Wastes

    NASA Astrophysics Data System (ADS)

    Clancy, T. M.; Reddy, R.; Tan, J.; Hayes, K. F.; Raskin, L.

    2014-12-01

    To address widespread arsenic contamination of drinking water sources numerous technologies have been developed to remove arsenic. All technologies result in the production of an arsenic-bearing waste that must be evaluated and disposed in a manner to limit the potential for environmental release and human exposure. One disposal option that is commonly recommended for areas without access to landfills is the mixing of arsenic-bearing wastes with cow dung. These recommendations are made based on the ability of microorganisms to create volatile arsenic species (including mono-, di-, and tri-methylarsine gases) to be diluted in the atmosphere. However, most studies of environmental microbial communities have found only a small fraction (<0.1 %) of the total arsenic present in soils or rice paddies is released via volatilization. Additionally, past studies often have not monitored arsenic release in the aqueous phase. Two main pathways for microbial arsenic volatilization are known and include methylation of arsenic during methanogenesis and methylation by arsenite S-adenosylmethionine methyltransferase. In this study, we compare the roles of these two pathways in arsenic volatilization and aqueous mobilization through mesocosm experiments with cow dung and arsenic-bearing wastes produced during drinking water treatment in West Bengal, India. Arsenic in gaseous, aqueous, and solid phases was measured. Consistent with previous reports, less than 0.02% of the total arsenic present was volatilized. A much higher amount (~5%) of the total arsenic was mobilized into the liquid phase. Through the application of molecular tools, including 16S rRNA sequencing and quantification of gene transcripts involved in methanogenesis, this study links microbial community activity with arsenic fate in potential disposal environments. These results illustrate that disposal of arsenic-bearing wastes by mixing with cow dung does not achieve its end goal of promoting arsenic volatilization

  19. Morphology of biogenic iron oxides records microbial physiology and environmental conditions: toward interpreting iron microfossils.

    PubMed

    Krepski, S T; Emerson, D; Hredzak-Showalter, P L; Luther, G W; Chan, C S

    2013-09-01

    Despite the abundance of Fe and its significance in Earth history, there are no established robust biosignatures for Fe(II)-oxidizing micro-organisms. This limits our ability to piece together the history of Fe biogeochemical cycling and, in particular, to determine whether Fe(II)-oxidizers played a role in depositing ancient iron formations. A promising candidate for Fe(II)-oxidizer biosignatures is the distinctive morphology and texture of extracellular Fe(III)-oxyhydroxide stalks produced by mat-forming microaerophilic Fe(II)-oxidizing micro-organisms. To establish the stalk morphology as a biosignature, morphologic parameters must be quantified and linked to the microaerophilic Fe(II)-oxidizing metabolism and environmental conditions. Toward this end, we studied an extant model organism, the marine stalk-forming Fe(II)-oxidizing bacterium, Mariprofundus ferrooxydans PV-1. We grew cultures in flat glass microslide chambers, with FeS substrate, creating opposing oxygen/Fe(II) concentration gradients. We used solid-state voltammetric microelectrodes to measure chemical gradients in situ while using light microscopy to image microbial growth, motility, and mineral formation. In low-oxygen (2.7-28 μm) zones of redox gradients, the bacteria converge into a narrow (100 μm-1 mm) growth band. As cells oxidize Fe(II), they deposit Fe(III)-oxyhydroxide stalks in this band; the stalks orient directionally, elongating toward higher oxygen concentrations. M. ferrooxydans stalks display a narrow range of widths and uniquely biogenic branching patterns, which result from cell division. Together with filament composition, these features (width, branching, and directional orientation) form a physical record unique to microaerophilic Fe(II)-oxidizer physiology; therefore, stalk morphology is a biosignature, as well as an indicator of local oxygen concentration at the time of formation. Observations of filamentous Fe(III)-oxyhydroxide microfossils from a ~170 Ma marine Fe

  20. From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

    NASA Technical Reports Server (NTRS)

    Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

  1. Microbial Methane Oxidation Processes and Technologies for Mitigation of Landfill Gas Emissions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this paper is to review the present knowledge regarding the microbial methane oxidation in natural or engineered landfill environments with focus on process understanding, engineering experiences and modeling. This review includes seven sections. First, the methane oxidation is put in con...

  2. Use of a Burkholderia cenocepacia ABTS Oxidizer in a Microbial Fuel Cell

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial fuel cells (MFCs) often use biological processes to generate electrons from organic material contained in the anode chamber and abiotic processes employing atmospheric oxygen as the oxidant in the cathode chamber. This study investigated the accumulation of an oxidant in bacterial cultures...

  3. Development of microbial spoilage and lipid and protein oxidation in rabbit meat.

    PubMed

    Nakyinsige, K; Sazili, A Q; Aghwan, Z A; Zulkifli, I; Goh, Y M; Abu Bakar, F; Sarah, S A

    2015-10-01

    This experiment aimed to determine microbial spoilage and lipid and protein oxidation during aerobic refrigerated (4°C) storage of rabbit meat. Forty male New Zealand white rabbits were slaughtered according to the Halal slaughter procedure. The hind limbs were used for microbial analysis while the Longissimus lumborum m. was used for determination of lipid and protein oxidation. Bacterial counts generally increased with aging time and the limit for fresh meat (10(8)cfu/g) was reached at d 7 postmortem. Significant differences in malondialdehyde content were observed after 3d of storage. The thiol concentration significantly decreased with increase in aging time. The band intensities of myosin heavy chain and troponin T significantly reduced with increased refrigerated storage while actin remained relatively stable. This study thus proposes protein oxidation as a potential deteriorative change in refrigerated rabbit meat along with microbial spoilage and lipid oxidation. PMID:26115345

  4. Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis).

    PubMed

    VanderWaal, Kimberly L; Atwill, Edward R; Isbell, Lynne A; McCowan, Brenda

    2014-03-01

    Although network analysis has drawn considerable attention as a promising tool for disease ecology, empirical research has been hindered by limitations in detecting the occurrence of pathogen transmission (who transmitted to whom) within social networks. Using a novel approach, we utilize the genetics of a diverse microbe, Escherichia coli, to infer where direct or indirect transmission has occurred and use these data to construct transmission networks for a wild giraffe population (Giraffe camelopardalis). Individuals were considered to be a part of the same transmission chain and were interlinked in the transmission network if they shared genetic subtypes of E. coli. By using microbial genetics to quantify who transmits to whom independently from the behavioural data on who is in contact with whom, we were able to directly investigate how the structure of contact networks influences the structure of the transmission network. To distinguish between the effects of social and environmental contact on transmission dynamics, the transmission network was compared with two separate contact networks defined from the behavioural data: a social network based on association patterns, and a spatial network based on patterns of home-range overlap among individuals. We found that links in the transmission network were more likely to occur between individuals that were strongly linked in the social network. Furthermore, individuals that had more numerous connections or that occupied 'bottleneck' positions in the social network tended to occupy similar positions in the transmission network. No similar correlations were observed between the spatial and transmission networks. This indicates that an individual's social network position is predictive of transmission network position, which has implications for identifying individuals that function as super-spreaders or transmission bottlenecks in the population. These results emphasize the importance of association patterns in

  5. Oxidative Stress in Patients with X-Linked Adrenoleukodystrophy.

    PubMed

    Deon, Marion; Marchetti, Desirèe P; Donida, Bruna; Wajner, Moacir; Vargas, Carmen

    2016-05-01

    X-linked adrenoleukodystrophy (X-ALD) is the most frequent peroxisomal disorder that is characterized by progressive demyelination of the white matter, adrenal insufficiency, and accumulation of very long-chain fatty acids in body fluid and tissues. This disorder is clinically heterogeneous with seven different phenotypes in male patients and five phenotypes in female carriers. An ultimate treatment for X-ALD is not available. Depending on the rate of the disease progression and the degree of an individual handicap, special needs and challenges vary greatly. The exact mechanisms underlying the pathophysiology of this multifactorial neurodegenerative disorder remains obscure. Previous studies has been related oxidative stress with the pathogenesis of several disease that affecting the central nervous system, such as neurodegenerative disease, epilepsy, multiple sclerosis, Alzheimer, and Parkinson diseases. In addition, oxidative damage has been observed in various in vivo and in vitro studies with inborn errors of metabolism, including X-ALD. In this context, this review is focused on oxidative stress in X-ALD, with emphasis on studies using biological samples from patients affected by this disease. PMID:26169524

  6. Linking potential denitrification rates to microbial gene abundances in multiple boreal ecosystems

    NASA Astrophysics Data System (ADS)

    Petersen, D. G.; Blazewicz, S.; Herman, D. J.; Firestone, M. K.; Waldrop, M. P.

    2010-12-01

    The composition and functioning of boreal ecosystems are vulnerable to changes in climate, leading to changes in season length, fire regimes, and soil moisture status. To investigate the influence of vegetation and soil moisture on microbial nitrogen cycling several disparate boreal ecosystems was studied. The two primary objectives were to: (1) determine whether process rates could be predicted solely from soil physical and chemical characteristics and (2) determine if the abundance of functional genes could be an additional explanatory variable. Surface soils were sampled along an elevation-driven hydrologic gradient at the Bonanza Creek LTER that corresponds with five plant communities typical of interior Alaska. The plant communities included a black spruce stand, a deciduous stand, a tussock grassland, an emergent fen, and a rich fen. We examined the chemical composition of the surface organic moss and soil, measured gross N-mineralization, potential rates of nitrification and denitrification (DEA), and abundances of several functional groups of microorganisms from soil cores collected in mid summer. We used quantitative PCR to assess the gene abundances of ammonia oxidizers and denitrifiers based on a functional gene approach. Here, we focus on potential denitrification rates (PDR), and abundance of denitrifyers carrying NirS and NirK genes (nitrate reductase) and NosZ genes (nitrous oxide reductase). PDR increased dramatically with increasing soil moisture along the gradient, from 1 mg N/m2/h at the dry black spruce site to 300 mg N/m2/h in the rich fen, which is very high compared to other poorly drained soil environments. PDR were linearly related to the abundance of functional genes from the microorganisms responsible for this process. Abundances of NirS, NirK and NosZ genes correlated significantly to PDR (r2 = 0.61 p < 0.0001, r2 = 0.45 p < 0.0003, r2 = 0.81 p < 0.0001, respectively). In addition, PDR were better explained by functional gene abundances

  7. Thermodynamic controls on the kinetics of microbial low-pH Fe(II) oxidation.

    PubMed

    Larson, Lance N; Sánchez-España, Javier; Kaley, Bradley; Sheng, Yizhi; Bibby, Kyle; Burgos, William D

    2014-08-19

    Acid mine drainage (AMD) is a major worldwide environmental threat to surface and groundwater quality. Microbial low-pH Fe(II) oxidation could be exploited for cost-effective AMD treatment; however, its use is limited because of uncertainties associated with its rate and ability to remove Fe from solution. We developed a thermodynamic-based framework to evaluate the kinetics of low-pH Fe(II) oxidation. We measured the kinetics of low-pH Fe(II) oxidation at five sites in the Appalachian Coal Basin in the US and three sites in the Iberian Pyrite Belt in Spain and found that the fastest rates of Fe(II) oxidation occurred at the sites with the lowest pH values. Thermodynamic calculations showed that the Gibbs free energy of Fe(II) oxidation (ΔG(oxidation)) was also most negative at the sites with the lowest pH values. We then conducted two series of microbial Fe(II) oxidation experiments in laboratory-scale chemostatic bioreactors operated through a series of pH values (2.1-4.2) and found the same relationships between Fe(II) oxidation kinetics, ΔG(oxidation), and pH. Conditions that favored the fastest rates of Fe(II) oxidation coincided with higher Fe(III) solubility. The solubility of Fe(III) minerals, thus plays an important role on Fe(II) oxidation kinetics. Methods to incorporate microbial low-pH Fe(II) oxidation into active and passive AMD treatment systems are discussed in the context of these findings. This study presents a simplified model that describes the relationship between free energy and microbial kinetics and should be broadly applicable to many biogeochemical systems. PMID:25072394

  8. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats

    PubMed Central

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J.; Salzman, Nita H.

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host’s metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  9. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    SciTech Connect

    Bargar, John; Fuller, Christopher; Marcus, Matthew A.; Brearley, Adrian J.; Perez De la Rosa, M.; Webb, Samuel M.; Caldwell, Wendel A.

    2008-03-19

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick x 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-A basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mnoxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

  10. The role of microbial diversity in the dynamics and stability of global methane consumption: microbial methane oxidation as a model-system for microbial ecology (ESF EuroDiversity METHECO)

    NASA Astrophysics Data System (ADS)

    Frenzel, P.; Metheco-Team

    2009-04-01

    Ecosystems collectively determine biogeochemical processes that regulate the Earth System. Loss of biodiversity is detrimental to ecosystems and therefore has been a central issue for environmental scientists. Although microorganisms form a major part of the Earth's biomass and biodiversity, and have a critical role in biogeochemistry and ecosystem functioning, they do not feature highly in ongoing debates about global biodiversity loss, global change and conservations issues. The neglect of microbial diversity in conservation issues is because microbial communities are regarded as being highly redundant, omnipresent, and therefore inextinguishable. This, however, is a misconception. Recently, the application of advanced molecular techniques has indicated that microbial communities display habitat preferences and are not universally distributed. Even the highly diverse microbial communities in soils can be affected by agricultural use, indicating that genetic erosion may potentially affect these communities as well. Moreover, many important environmental functions are catalyzed by specific groups of microbes with a very narrow ecological range. Recovery of these functional microbial communities after disturbance may take decades. Even if the species making up the community do not become extinct and eventually re-colonize an environment, the function and service to the biosphere is lost long enough to exert permanent, irreversible damage to the environment. Considering the global importance of microbes, combined with our ignorance of how the composition and functioning of these communities is affected, necessitates the assessment of the vulnerability and the resilience of microbial diversity. The latter is a pressing concern in biodiversity research and conservation policy, urgently needing attention in order to be able to anticipate environmental challenges we are facing. Our general hypothesis is: microbial diversity is linked to important ecosystem services and

  11. Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth

    PubMed Central

    Grivennikov, Sergei I.; Wang, Kepeng; Mucida, Daniel; Stewart, C. Andrew; Schnabl, Bernd; Jauch, Dominik; Taniguchi, Koji; Yu, Guann-Yi; Osterreicher, Christoph H.; Hung, Kenneth E.; Datz, Christian; Feng, Ying; Fearon, Eric R.; Oukka, Mohamed; Tessarollo, Lino; Coppola, Vincenzo; Yarovinsky, Felix; Cheroutre, Hilde; Eckmann, Lars; Trinchieri, Giorgio; Karin, Michael

    2013-01-01

    Approximately 2% of colorectal cancer is linked to pre-existing inflammation known as colitis-associated cancer, but most develops in patients without underlying inflammatory bowel disease. Colorectal cancer often follows a genetic pathway whereby loss of the adenomatous polyposis coli (APC) tumour suppressor and activation of β-catenin are followed by mutations in K-Ras, PIK3CA and TP53, as the tumour emerges and progresses1,2. Curiously, however, ‘inflammatory signature’ genes characteristic of colitis-associated cancer are also upregulated in colorectal cancer3,4. Further, like most solid tumours, colorectal cancer exhibits immune/inflammatory infiltrates5, referred to as ‘tumour elicited inflammation’6. Although infiltrating CD4+ TH1 cells and CD8+ cytotoxic T cells constitute a positive prognostic sign in colorectal cancer7,8, myeloid cells and T-helper interleukin (IL)-17-producing (TH17) cells promote tumorigenesis5,6, and a ‘TH17 expression signature’ in stage I/II colorectal cancer is associated with a drastic decrease in disease-free survival9. Despite its pathogenic importance, the mechanisms responsible for the appearance of tumour-elicited inflammation are poorly understood. Many epithelial cancers develop proximally to microbial communities, which are physically separated from immune cells by an epithelial barrier10. We investigated mechanisms responsible for tumour-elicited inflammation in a mouse model of colorectal tumorigenesis, which, like human colorectal cancer, exhibits upregulation of IL-23 and IL-17. Here we show that IL-23 signalling promotes tumour growth and progression, and development of a tumoural IL-17 response. IL-23 is mainly produced by tumour-associated myeloid cells that are likely to be activated by microbial products, which penetrate the tumours but not adjacent tissue. Both early and late colorectal neoplasms exhibit defective expression of several barrier proteins. We propose that barrier deterioration induced by

  12. The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

    PubMed Central

    Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

    2015-01-01

    Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided

  13. Micro-scale morphology and texture of biogenic iron oxide mats provide a physical record of microbial physiology and oxygen conditions

    NASA Astrophysics Data System (ADS)

    Krepski, S. T.; Hredzak-showalter, T.; Luther, G. W.; Chan, C. S.

    2011-12-01

    The ability of certain bacteria to deposit Fe oxide minerals has long been recognized. However, we are only beginning to gain greater insights into the physiology and mechanisms of microbial Fe(II) oxidation and biomineralization, due to a small but growing number of isolates and studies on Fe(II)-oxidizing bacteria (FeOB). We recently isolated a novel microaerophilic FeOB, Betaproteobacterium Gallionellales strain R-1 (Genbank accession number JN377592) from a freshwater Fe seep in Newark, Delaware, USA. Much like Gallionella ferruginea (93.6% 16S gene sequence similarity), this organism is a bean-shaped cell that forms mineralized extracellular Fe twisted stalks. Strain R-1 shows remarkable physiologic and morphological similarity to the marine Zetaproteobacterium FeOB Mariprofundus ferrooxydans, despite being distantly related. We use M. ferrooxydans and strain R-1 as model organisms to study microbial Fe biomineralization and link the formation of microbial Fe oxide mats to environmental conditions and FeOB physiology. To accomplish this, we construct flat glass microslide growth chambers, used in conjunction with solid-state voltammetric microelectrodes to measure the chemistry of FeOB microenvironments in situ while studying undisturbed microbial growth, motility, and mineral formation. The development of microbial Fe oxide bands (analogs of mats) begins when cells attach to a surface and deposit minerals. In low-oxygen zones of redox gradients, formed in part by microbial respiration, the bacteria converge into a narrow, mineralized growth band. Filaments orient directionally, as quantified with ArcGIS, towards increasing oxygen, and display uniquely biological characteristics such as branching and a narrow range of widths. Thus, the mineralized structures provide a physical record of FeOB physiology. Observations of putative filamentous Fe microfossils in thin section show that these characteristics can be preserved in the geologic record, even if some

  14. Oxidative Stress: A Link between Diabetes Mellitus and Periodontal Disease

    PubMed Central

    Mezei, Tibor; Popsor, Sorin; Monea, Monica

    2014-01-01

    Objective. To investigate oxidative stress (OS) and histological changes that occur in the periodontium of subjects with type 2 diabetes mellitus without signs of periodontal disease and to establish if oxidative stress is a possible link between diabetes mellitus and periodontal changes. Materials and Methods. Tissue samples from ten adult patients with type 2 diabetes mellitus (T2D) and eight healthy adults were harvested. The specimens were examined by microscope using standard hematoxylin-eosin stain, at various magnifications, and investigated for tissue levels of malondialdehyde (MDA) and glutathione (GSH). Results. Our results showed that periodontal tissues in patients with T2D present significant inflammation, affecting both epithelial and connective tissues. Mean MDA tissue levels were 3.578 ± 0.60 SD in diabetics versus 0.406 ± 0.27 SD in controls (P < 0.0001), while mean GSH tissue levels were 2.48 ± 1.02 SD in diabetics versus 9.7875 ± 2.42 SD in controls (P < 0.0001). Conclusion. Diabetic subjects had higher MDA levels in their periodontal tissues, suggesting an increased lipid peroxidation in T2D, and decreased GSH tissue levels, suggesting an alteration of the local antioxidant defense mechanism. These results are in concordance with the histological changes that we found in periodontal tissues of diabetic subjects, confirming the hypothesis of OS implication, as a correlation between periodontal disease incidence and T2D. PMID:25525432

  15. Effects of temperature on rates and mineral products of microbial Fe(II) oxidation by Leptothrix cholodnii at microaerobic conditions

    NASA Astrophysics Data System (ADS)

    Vollrath, Susann; Behrends, Thilo; Koch, Christian Bender; Cappellen, Philippe Van

    2013-05-01

    Oxygen concentrations are important in constraining the geochemical niche of neutrophilic iron oxidizers. However, other factors like temperature may affect the competition between microbial and abiotic Fe(II) oxidation and may cause community changes. Here, rates and mineral products of Fe(II) oxidation (initial concentration 150 μmol Fe(II)/l) by the Fe(II) oxidizing bacterial strain Leptothrix cholodnii Appels were compared to those of abiotic oxidation in the temperature range 11-37 °C. Experiments were carried out in a batch reactor at 12-13 μmol O2/l (0.92-1% O2 saturation), pH 7 and, for the microbial experiments, a cell density of around 108 cells/ml. The iron precipitates formed at the different temperatures were characterized by SEM, XRD, FTIR and Mössbauer spectroscopy. Abiotic and microbial Fe(II) oxidation proceeded in two stages. During the initial stage, rates of microbial oxidation exhibited a temperature optimum curve. In contrast, the temperature dependency of abiotic Fe(II) oxidation rate followed the Arrhenius equation. As a consequence, microbial oxidation rates were about 10 times higher compared to the abiotic oxidation at 30 °C. During the second stage, microbial and abiotic rates and their temperature dependencies were similar. Independent of temperature or presence of bacteria, lepidocrocite and ferrihydrite were identified as reaction products, but the characteristics of the precipitates differed. At 37 °C, less lepidocrocite was precipitated in microbial and abiotic experiments due to high oxidation rates. Abiotic oxidation produced larger lepidocrocite crystals mixed with smaller, less crystalline oxides. Large crystals were absent in the microbial products, possibly due to growth inhibition of the minerals by EPS substances. Nevertheless, Mössbauer spectra revealed a better crystal structure of the smaller, microbial precipitates compared to the abiotically formed oxides.

  16. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.

    PubMed

    Beam, Jacob P; Bernstein, Hans C; Jay, Zackary J; Kozubal, Mark A; Jennings, Ryan deM; Tringe, Susannah G; Inskeep, William P

    2016-01-01

    Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3-3.5; temperature = 68-75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4-40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14-30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1-2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day(-1), and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems. PMID:26913020

  17. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs

    PubMed Central

    Beam, Jacob P.; Bernstein, Hans C.; Jay, Zackary J.; Kozubal, Mark A.; Jennings, Ryan deM.; Tringe, Susannah G.; Inskeep, William P.

    2016-01-01

    Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems. PMID:26913020

  18. Enhancement of Electricity Production by Graphene Oxide in Soil Microbial Fuel Cells and Plant Microbial Fuel Cells

    PubMed Central

    Goto, Yuko; Yoshida, Naoko; Umeyama, Yuto; Yamada, Takeshi; Tero, Ryugo; Hiraishi, Akira

    2015-01-01

    The effects of graphene oxide (GO) on electricity generation in soil microbial fuel cells (SMFCs) and plant microbial fuel cell (PMFCs) were investigated. GO at concentrations ranging from 0 to 1.9 g⋅kg−1 was added to soil and reduced for 10 days under anaerobic incubation. All SMFCs (GO-SMFCs) utilizing the soils incubated with GO produced electricity at a greater rate and in higher quantities than the SMFCs which did not contain GO. In fed-batch operations, the overall average electricity generation in GO-SMFCs containing 1.0 g⋅kg−1 of GO was 40 ± 19 mW⋅m−2, which was significantly higher than the value of 6.6 ± 8.9 mW⋅m−2 generated from GO-free SMFCs (p < 0.05). The increase in catalytic current at the oxidative potential was observed by cyclic voltammetry (CV) for GO-SMFC, with the CV curve suggesting the enhancement of electron transfer from oxidation of organic substances in the soil by the reduced form of GO. The GO-containing PMFC also displayed a greater generation of electricity compared to the PMFC with no added GO, with GO-PMFC producing 49 mW⋅m−2 of electricity after 27 days of operation. Collectively, this study demonstrates that GO added to soil can be microbially reduced in soil, and facilitates electron transfer to the anode in both SMFCs and PMFCs. PMID:25883931

  19. Postprandial Oxidative Stress and Gastrointestinal Hormones: Is There a Link?

    PubMed Central

    Malinska, Hana; Kahleova, Hana; Topolcan, Ondrej; Vrzalova, Jindra; Oliyarnyk, Olena; Kazdova, Ludmila; Belinova, Lenka; Hill, Martin; Pelikanova, Terezie

    2014-01-01

    direct link observed between gastrointestinal hormones and oxidative stress markers in diabetic patients. Trial Registration ClinicalTrials.gov NCT01572402 PMID:25141237

  20. Oxygen Effects on Thermophilic Microbial Populations in Biofilters Treating Nitric Oxide Containing Off-Gas Streams

    SciTech Connect

    Lee, Brady Douglas; Apel, William Arnold; Smith, William Aaron

    2004-04-01

    Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost-effective strategies to control nitrogen oxides (NOx) from coal-fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.

  1. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, D F; Thompson, D N; Noah, K S

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, Leptospirillum, Ferromicrobium, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  2. In Vivo Oxidative Stability Changes of Highly Cross-Linked Polyethylene Bearings: An Ex Vivo Investigation.

    PubMed

    Rowell, Shannon L; Reyes, Christopher R; Malchau, Henrik; Muratoglu, Orhun K

    2015-10-01

    The development of highly cross-linked UHMWPEs focused on stabilizing radiation-induced free radicals as the sole precursor to oxidative degradation. However, secondary in vivo oxidation mechanisms have been discovered. After a preliminary post-operative analysis, we subjected highly cross-linked retrievals with 1-4 years in vivo durations and never-implanted controls to accelerated aging to predict the extent to which their oxidative stability was compromised in vivo. Lipid absorption, oxidation, and hydroperoxides were measured using infrared spectroscopy. Gravimetric swelling was used to measure cross-link density. After aging, all retrievals, except vitamin E-stabilized components, regardless of initial lipid levels or oxidation, showed significant oxidative degradation, demonstrated by subsurface oxidative peaks, increased hydroperoxides and decreased cross-link density, compared to their post-operative material properties and never-implanted counterparts, confirming oxidative stability changes. PMID:26048729

  3. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

    SciTech Connect

    Adams, MM; Hoarfrost, AL; Bose, A; Joye, SB; Girguis, PR

    2013-05-14

    Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C-2), propane (C-3), and butane (C-4) in anoxic sediments in contrast to methane (C-1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C-1-C-4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C-1-C-4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75 degrees C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C-1-C-4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C-2-C-4 alkanes. Maximum C-1-C-4 alkane oxidation rates occurred at 55 degrees C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C-3 was oxidized at the highest rate over time, then C-4, C-2, and C-1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C-2-C(4)alkanes with AOM for available oxidants and the influence on the fate of C-1 derived from these hydrothermal systems.

  4. Microbial As(III) Oxidation in Water Treatment Plant Filters

    EPA Science Inventory

    Arsenic exists in two oxidation states in water - arsenite [As(III)] and arsenate [As(V)]. As(III) is relatively mobile in water and difficult to remove by arsenic-removal treatment processes. Source waters that contain As(III) must add a strong oxidant such as free chlorine or p...

  5. [Research progress in microbial methane oxidation coupled to denitrification].

    PubMed

    Zhu, Jing; Yuan, Meng-Dong; Liu, Jing-Jing; Huang, Xiao-Xiao; Wu, Wei-Xiang

    2013-12-01

    Methane oxidation coupled to denitrification is an essential bond to connect carbon- and nitrogen cycling. To deeply research this process will improve our understanding on the biochemical cycling of global carbon and nitrogen. As an exogenous gaseous carbon source of denitrification, methane can both regulate the balance of atmospheric methane to effectively mitigate the greenhouse effect caused by methane, and reduce the cost of exogenous carbon source input in traditional wastewater denitrification treatment process. As a result, great attention has being paid to the mechanical study of the process. This paper mainly discussed the two types of methane oxidation coupled to denitrification, i. e., aerobic methane oxidation coupled to denitrification (AME-D) and anaerobic methane oxidation coupled to denitrification (ANME-D), with the focus on the microbiological coupling mechanisms and related affecting factors. The existing problems in the engineering application of methane oxidation coupled to denitrification were pointed out, and the application prospects were approached. PMID:24697087

  6. Application of microbial inoculants as tools for reducing nitrous oxide emissions from different nitrogen fertilizers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Emissions of nitrous oxide (N2O) are increasing due to several factors, including increased use of nitrogen fertilizers. New management tools are needed to reduce N2O emissions from production agriculture. One potential such tool is the use of microbial inoculants, which are increasingly being used ...

  7. Increased electrical output when a bacterial ABTS oxidizer is used in a microbial fuel cell.

    PubMed

    Hunter, William J; Manter, Daniel K

    2011-02-01

    Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. This study examined the formation in culture of an unidentified bacterial oxidant and investigated the performance of this oxidant in a two-chambered MFC with a proton exchange membrane and an uncoated carbon cathode. DNA, FAME profile and characterization studies identified the microorganism that produced the oxidant as Burkholderia cenocepacia. The oxidant was produced by log phase cells, oxidized the dye 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), had a mass below 1 kD, was heat stable (121°C) and was soluble in ethanol. In a MFC with a 1000 Ω load and ABTS as a mediator, the oxidizer increased cell voltage 11 times higher than atmospheric oxygen and 2.9 times higher than that observed with ferricyanide in the cathode chamber. No increase in cell voltage was observed when no mediator was present. Organisms that produce and release oxidizers into the media may prove useful as bio-cathodes by improving the electrical output of MFCs. PMID:20853166

  8. An Experiment in Autotrophic Fermentation: Microbial Oxidation of Hydrogen Sulfide.

    ERIC Educational Resources Information Center

    Sublette, Kerry L.

    1989-01-01

    Described is an experiment which uses an autotrophic bacterium to anaerobically oxidize hydrogen sulfide to sulfate in a batch-stirred tank reactor. Discusses background information, experimental procedure, and sample results of this activity. (CW)

  9. Iron and sulfide oxidation within the basaltic ocean crust: implications for chemolithoautotrophic microbial biomass production

    NASA Astrophysics Data System (ADS)

    Bach, Wolfgang; Edwards, Katrina J.

    2003-10-01

    Microbial processes within the ocean crust are of potential importance in controlling rates of chemical reactions and thereby affecting chemical exchange between the oceans and lithosphere. We here assess the oxidation state of altered ocean crust and estimate the magnitude of microbial biomass production that might be supported by oxidative and nonoxidative alteration. Compilations of Fe 2O 3, FeO, and S concentrations from DSDP/ODP drill core samples representing upper basaltic ocean crust suggest that Fe 3+/ΣFe increases from 0.15 ± 0.05 to 0.45 ± 0.15 within the first 10-20 Myr of crustal evolution. Within the same time frame 70 ± 25% of primary sulfides in basalt are oxidized. With an annual production of 4.0 ± 1.8 × 10 15 g of upper (500 ± 200 m) crust and average initial concentrations of 8.0 ± 1.3 wt% Fe and 0.125 ± 0.020 wt% S, we estimate annual oxidation rates of 1.7 ± 1.2 × 10 12 mol Fe and 1.1 ± 0.7 × 10 11 mol S. We estimate that 50% of Fe oxidation may be attributed to hydrolysis, producing 4.5 ± 3.0 × 10 11 mol H 2/yr. Thermodynamic and bioenergetic calculations were used to estimate the potential chemolithoautotrophic microbial biomass production within ridge flanks. Combined, aerobic and anaerobic Fe and S oxidation may support production of up to 48 ± 21 × 10 10 g cellular carbon (C). Hydrogen-consuming reactions may support production of a similar or larger microbial biomass if iron reduction, nitrate reduction, or hydrogen oxidation by O 2(aq) are the prevailing metabolic reactions. If autotrophic sulfate reduction or methanogenesis prevail, the potential biomass production is 9 ± 7 × 10 10 g C/yr and 3 ± 2 × 10 10 g C/yr, respectively. Combined primary biomass production of up to ˜1 × 10 12 g C/yr may be similar to that fueled by anaerobic oxidation of organic matter in deep-seated heterotrophic systems. These estimates suggest that water-rock reactions may support significant microbial life within ridge flank

  10. LABORATORY AND FIELD RESULTS LINKING HIGH BULK CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

    EPA Science Inventory

    Diesel contaminated layer (i.e. 32-45 cm) was the most geoelectrically conductive and showed the peak microbial activity. Below the saturated zone microbial enhanced mineral weathering increases the ionic concentration of pore fluids, leading to increased bulk electrical conducit...

  11. Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition

    PubMed Central

    Ma, Wai K.; Farrell, Richard E.; Siciliano, Steven D.

    2011-01-01

    Nitrous oxide (N2O) is a greenhouse gas with a global warming potential far exceeding that of CO2. Soil N2O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N2O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N2O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and N15O3− pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N2O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N2O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N2O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N2O emission. PMID:21712943

  12. The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

    PubMed

    Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

    2016-07-01

    Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota. PMID:27090902

  13. Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

    PubMed Central

    Sutton, Nora B.; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H. M.

    2015-01-01

    While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

  14. S-peptide as a potent peptidyl linker for protein cross-linking by microbial transglutaminase from Streptomyces mobaraensis.

    PubMed

    Kamiya, Noriho; Tanaka, Tsutomu; Suzuki, Tsutomu; Takazawa, Takeshi; Takeda, Shuji; Watanabe, Kimitsuna; Nagamune, Teruyuki

    2003-01-01

    We have found that ribonuclease S-peptide can work as a novel peptidyl substrate in protein cross-linking reactions catalyzed by microbial transglutaminase (MTG) from Streptomyces mobaraensis. Enhanced green fluorescent protein tethered to S-peptide at its N-terminus (S-tag-EGFP) appeared to be efficiently cross-linked by MTG. As wild-type EGFP was not susceptible to cross-linking, the S-peptide moiety is likely to be responsible for the cross-linking. A site-directed mutation study assigned Gln15 in the S-peptide sequence as the sole acyl donor. Mass spectrometric analysis showed that two Lys residues (Lys5 and Lys11) in the S-peptide sequence functioned as acyl acceptors. We also succeeded in direct monitoring of the cross-linking process by virtue of fluorescence resonance energy transfer (FRET) between S-tag-EGFP and its blue fluorescent color variant (S-tag-EBFP). The protein cross-linking was tunable by either engineering S-peptide sequence or capping the S-peptide moiety with S-protein, the partner protein of S-peptide for the formation of ribonuclease A. The latter indicates that S-protein can be used as a specific inhibitor of S-peptide-directed protein cross-linking by MTG. The controllable protein cross-linking of S-peptide as a potent substrate of MTG will shed new light on biomolecule conjugation. PMID:12643745

  15. Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure▿

    PubMed Central

    Bassin, J. P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; van Loosdrecht, M. C. M.

    2011-01-01

    The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “Candidatus Accumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal (“Candidatus Accumulibacter”). PMID:21926194

  16. Textural and Mineralogical Characteristics of Microbial Fossils in Modern and Ancient Iron (oxyhydr)oxides

    NASA Astrophysics Data System (ADS)

    Potter, S. L.; Chan, M. A.; McPherson, B. J.

    2012-12-01

    The Jurassic Brushy Basin Member of the Morrison Formation contains extensive alkaline saline lacustrine deposits rich in diagenetic iron (oxyhydr)oxides that are well exposed on the Colorado Plateau of the southwestern USA. These early diagenetic iron (oxyhydr)oxide minerals are associated with preserved diatoms and other algal forms, identified via scanning electron microscope (SEM) in thin sections of representative samples. The minerals are also associated with macroscopic bioturbation features (e.g., charophytes, burrows and fossilized dinosaur bones). Algal forms with cellular elaboration are identified by HF dissolution of bioturbation structures and examination with SEM. Collectively, these features suggest biomediated textures are preserved in early diagenetic iron (oxyhydr)oxides, and can persist for tens of millions of years. Modern microbially precipitated iron (oxyhydr)oxides and ~100ka tufa terraces from a cold spring system along Ten Mile Graben in southern Utah, USA are compared with the Morrison examples to identify modern microbial fossils and document any differences and preservation changes during diagenesis over geologic time. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se) are associated with microbial fossils in both the modern and ancient tufas, as well as the ancient Morrison specimens. The occurrence of these distinctive trace element configurations in the iron (oxyhydr)oxide minerals suggest the suites could be potential markers for biosignatures. The presence of ferrihydrite in ~100ka fossil microbial mats suggests this thermodynamically unstable mineral may also be used as a biomarker. Diagnostic trace element suites and unusual mineral phases warrant further study for their potential as biomarkers. These terrestrial iron (oxyhydr)oxide examples will: 1) document specific biomediated textures and what their origins might be (related to different processes or species), 2) show how they might persist or respond to

  17. Microbial Communities Associated with Biogenic Iron Oxide Mineralization in Circumneutral pH Environments

    NASA Astrophysics Data System (ADS)

    Chan, C. S.; Banfield, J. F.

    2002-12-01

    Lithotrophic growth on iron is a metabolism that has been found in a variety of neutral pH environments and is likely important in sustaining life in microaerophilic solutions, especially those low in organics. The composition of the microbial communities, especially the organisms that are responsible for iron oxidation, and carbon and nitrogen fixation, are not known, yet the ability to recognize these contributions is vital to our understanding of iron cycling in natural environments. Our approach has been to study the microbial community structure, mineralogy, and geochemistry of ~20 cm thick, 100's meters long, fluffy iron oxide-encrusted biological mats growing in the Piquette Mine tunnel, and to compare the results to those from geochemically similar environments. In situ measurements (Hydrolab) and geochemical characterization of bulk water samples and peepers (dialysis sampling vials) indicate that the environment is microaerobic, with micromolar levels of iron, high carbonate and sulfate, and typical groundwater nitrate and nitrite concentrations. 16S rDNA clone libraries show that the microbial mat and water contain communities with considerable diversity within the Bacterial domain, a large proportion of Nitrospira and Betaproteobacteria, and no Archaea. Because clone library data are not necessarily indicative of actual abundance, fluorescence in-situ hybridization (FISH) was performed on water, mat, and sediment samples from the Piquette mine and two circumneutral iron- and carbonate-rich springs in the Oregon Cascade Range. Domain- and phylum-level probes were chosen based on the clone library results (Nitrospira, Beta- and Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Planctomyces). FISH data reveal spatial associations between specific microbial groups and mineralized structures. The organisms responsible for making the mineralized sheaths that compose the bulk of the iron oxide mat are Betaproteobacteria (probably Leptothrix

  18. Two-stage conversion of crude glycerol to energy using dark fermentation linked with microbial fuel cell or microbial electrolysis cell.

    PubMed

    Chookaew, Teera; Prasertsan, Poonsuk; Ren, Zhiyong Jason

    2014-03-25

    Crude glycerol is a main byproduct of the biodiesel industry, and the beneficial use of waste glycerol has been a major challenge. This study characterises the conversion of crude glycerol into bioenergy such as H2 and electricity using a two-stage process linking dark fermentation with a microbial fuel cell (MFC) or microbial electrolysis cell (MEC). The results showed that fermentation achieved a maximum H2 rate of 332 mL/L and a yield of 0.55 mol H2/mol glycerol, accompanied by 20% of organic removal. Fed with the raw fermentation products with an initial COD of 7610 mg/L, a two-chamber MFC produced 92 mW/m(2) in power density and removed 50% of COD. The Columbic efficiency was 14%. When fed with 50% diluted fermentation product, a similar power output (90m W/m(2)) and COD removal (49%) were obtained, but the CE doubled to 27%. Similar substrates were used to produce H2 in two-chamber MECs, and the diluted influent had a higher performance, with the highest yield at 106 mL H2/g COD and a CE of 24%. These results demonstrate that dark fermentation linked with MFC/MEC can be a feasible option for conversion of waste glycerol into bioenergy. PMID:24380781

  19. Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

    USGS Publications Warehouse

    Dowdle, P.R.; Oremland, R.S.

    1998-01-01

    The microbial oxidation of elemental selenium [Se(O)] was studied by employing 75Se(O) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.The microbial oxidation of elemental selenium [Se(0)] was studied by employing 75Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation

  20. Microbial oxidation of mixtures of methylmercaptan and hydrogen sulfide.

    PubMed

    Subramaniyan, A; Kolhatkar, R; Sublette, K L; Beitle, R

    1998-01-01

    Refinery spent-sulfidic caustic, containing only inorganic sulfides, has previously been shown to be amenable to biotreatment with Thiobacillus denitrificans strain F with complete oxidation of sulfides to sulfate. However, many spent caustics contain mercaptans that cannot be metabolized by this strict autotroph. An aerobic enrichment culture was developed from mixed Thiobacilli and activated sludge that was capable of simultaneous oxidation of inorganic sulfide and mercaptans using hydrogen sulfide (H2S) and methylmercaptan (MeSH) gas feeds used to simulate the inorganic and organic sulfur of a spent-sulfidic caustic. The enrichment culture was also capable of biotreatment of an actual mercaptan-containing, spent-sulfidic caustic but at lower rates than predicted by operation on MeSH and H2S fed to the culture in the gas phase, indicating that the caustic contained other inhibitory components. PMID:18576062

  1. LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

    EPA Science Inventory

    The results of a field and laboratory investigation of unconsolidated sediments contaminated by petroleum hydrocarbons and undergoing natural biodegradation are presented. Fundamental to geophysical investigations of hydrocarbon impacted sediments is the assessment of how microbi...

  2. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, Debby Fox; Thompson, David Neal; Noah, Karl Scott

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, “Leptospirillum”, “Ferromicrobium”, and Acidiphilium. Two temperatures (30°C and 45°C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to low the pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  3. Analysis of a microbial community oxidizing inorganic sulfide and mercaptans.

    PubMed

    Duncan, K E; Sublette, K L; Rider, P A; Stepp, A; Beitle, R R; Conner, J A; Kolhatkar, R

    2001-01-01

    Successful treatment of refinery spent-sulfidic caustic (which results from the addition of sodium hydroxide solutions to petroleum refinery waste streams) was achieved in a bioreactor containing an enrichment culture immobilized in organic polymer beads with embedded powdered activated carbon (Bio-Sep). The aerobic enrichment culture had previously been selected using a gas mixture of hydrogen sulfide and methyl mercaptan (MeSH) as the sole carbon and energy sources. The starting cultures for the enrichment consisted of several different Thiobacilli spp. (T. thioparus, T. denitrificans, T. thiooxidans, and T. neopolitanus), as well as activated sludge from a refinery aerobic wastewater treatment system and sludge from an industrial anaerobic digester. Microscopic examination (light and SEM) of the beads and of microbial growth on the walls of the bioreactor revealed a great diversity of microorganisms. Further characterization was undertaken starting with culturable aerobic heterotrophic microorganisms (sequencing of PCR-amplified DNA coding for 16S rRNA, Gram staining) and by PCR amplification of DNA coding for 16S rRNA extracted directly from the cell mass, followed by the separation of the PCR products by DGGE (denaturing gradient gel electrophoresis). Eight prominent bands from the DGGE gel were sequenced and found to be closest to sequences of uncultured Cytophagales (3 bands), Gram-positive cocci (Micrococcineae), alpha proteobacteria (3 bands), and an unidentified beta proteobacterium. Culturable microbes included several genera of fungi as well as various Gram-positive and Gram-negative heterotrophic bacteria not seen in techniques using direct DNA extraction. PMID:11485441

  4. Anaerobic oxidation of methane: an "active" microbial process.

    PubMed

    Cui, Mengmeng; Ma, Anzhou; Qi, Hongyan; Zhuang, Xuliang; Zhuang, Guoqiang

    2015-02-01

    The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. AOM was first found to be coupled with sulfate reduction and mediated by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). ANME, often forming consortia with SRB, are phylogenetically related to methanogenic archaea. ANME-1 is even able to produce methane. Subsequently, it has been found that AOM can also be coupled with denitrification. The known microbes responsible for this process are Candidatus Methylomirabilis oxyfera (M. oxyfera) and Candidatus Methanoperedens nitroreducens (M. nitroreducens). Candidatus Methylomirabilis oxyfera belongs to the NC10 bacteria, can catalyze nitrite reduction through an "intra-aerobic" pathway, and may catalyze AOM through an aerobic methane oxidation pathway. However, M. nitroreducens, which is affiliated with ANME-2d archaea, may be able to catalyze AOM through the reverse methanogenesis pathway. Moreover, manganese (Mn(4+) ) and iron (Fe(3+) ) can also be used as electron acceptors of AOM. This review summarizes the mechanisms and associated microbes of AOM. It also discusses recent progress in some unclear key issues about AOM, including ANME-1 in hypersaline environments, the effect of oxygen on M. oxyfera, and the relationship of M. nitroreducens with ANME. PMID:25530008

  5. Anaerobic oxidation of methane: an “active” microbial process

    PubMed Central

    Cui, Mengmeng; Ma, Anzhou; Qi, Hongyan; Zhuang, Xuliang; Zhuang, Guoqiang

    2015-01-01

    The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. AOM was first found to be coupled with sulfate reduction and mediated by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). ANME, often forming consortia with SRB, are phylogenetically related to methanogenic archaea. ANME-1 is even able to produce methane. Subsequently, it has been found that AOM can also be coupled with denitrification. The known microbes responsible for this process are Candidatus Methylomirabilis oxyfera (M. oxyfera) and Candidatus Methanoperedens nitroreducens (M. nitroreducens). Candidatus Methylomirabilis oxyfera belongs to the NC10 bacteria, can catalyze nitrite reduction through an “intra-aerobic” pathway, and may catalyze AOM through an aerobic methane oxidation pathway. However, M. nitroreducens, which is affiliated with ANME-2d archaea, may be able to catalyze AOM through the reverse methanogenesis pathway. Moreover, manganese (Mn4+) and iron (Fe3+) can also be used as electron acceptors of AOM. This review summarizes the mechanisms and associated microbes of AOM. It also discusses recent progress in some unclear key issues about AOM, including ANME-1 in hypersaline environments, the effect of oxygen on M. oxyfera, and the relationship of M. nitroreducens with ANME. PMID:25530008

  6. Linking geology, fluid chemistry, and microbial activity of basalt- and ultramafic-hosted deep-sea hydrothermal vent environments.

    PubMed

    Perner, M; Hansen, M; Seifert, R; Strauss, H; Koschinsky, A; Petersen, S

    2013-07-01

    Hydrothermal fluids passing through basaltic rocks along mid-ocean ridges are known to be enriched in sulfide, while those circulating through ultramafic mantle rocks are typically elevated in hydrogen. Therefore, it has been estimated that the maximum energy in basalt-hosted systems is available through sulfide oxidation and in ultramafic-hosted systems through hydrogen oxidation. Furthermore, thermodynamic models suggest that the greatest biomass potential arises from sulfide oxidation in basalt-hosted and from hydrogen oxidation in ultramafic-hosted systems. We tested these predictions by measuring biological sulfide and hydrogen removal and subsequent autotrophic CO2 fixation in chemically distinct hydrothermal fluids from basalt-hosted and ultramafic-hosted vents. We found a large potential of microbial hydrogen oxidation in naturally hydrogen-rich (ultramafic-hosted) but also in naturally hydrogen-poor (basalt-hosted) hydrothermal fluids. Moreover, hydrogen oxidation-based primary production proved to be highly attractive under our incubation conditions regardless whether hydrothermal fluids from ultramafic-hosted or basalt-hosted sites were used. Site-specific hydrogen and sulfide availability alone did not appear to determine whether hydrogen or sulfide oxidation provides the energy for primary production by the free-living microbes in the tested hydrothermal fluids. This suggests that more complex features (e.g., a combination of oxygen, temperature, biological interactions) may play a role for determining which energy source is preferably used in chemically distinct hydrothermal vent biotopes. PMID:23647923

  7. Advanced experimental analysis of controls on microbial Fe(III) oxide reduction. 1998 annual progress report

    SciTech Connect

    Roden, E.E.; Urrutia, M.M.

    1998-06-01

    'Understanding factors which control the long-term survival and activity of Fe(III)-reducing bacteria (FeRB) in subsurface sedimentary environments is important for predicting their ability to serve as agents for bioremediation of organic and inorganic contaminants. This project seeks to refine the authors quantitative understanding of microbiological and geochemical controls on bacterial Fe(III) oxide reduction and growth of FeRB, using laboratory reactor systems which mimic to varying degrees the physical and chemical conditions of subsurface sedimentary environments. Methods for studying microbial Fe(III) oxide reduction and FeRB growth in experimental systems which incorporate advective aqueous phase flux are being developed for this purpose. These methodologies, together with an accumulating database on the kinetics of Fe(III) reduction and bacterial growth with various synthetic and natural Fe(III) oxide minerals, will be applicable to experimental and modeling studies of subsurface contaminant transformations directly coupled to or influenced by bacterial Fe(III) oxide reduction and FeRB activity. This report summarizes research accomplished after approximately 1.5 yr of a 3-yr project. A central hypothesis of the research is that advective elimination of the primary end-product of Fe(III) oxide reduction, Fe(II), will enhance the rate and extent of microbial Fe(III) oxide reduction in open experimental systems. This hypothesis is based on previous studies in the laboratory which demonstrated that association of evolved Fe(II) with oxide and FeRB cell surfaces (via adsorption or surface precipitation) is a primary cause for cessation of Fe(III) oxide reduction activity in batch culture experiments. Semicontinuous culturing was adopted as a first approach to test this basic hypothesis. Synthetic goethite or natural Fe(III) oxide-rich subsoils were used as Fe(III) sources, with the Fe(III)-reducing bacterium Shewanella alga as the test organism.'

  8. Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics

    PubMed Central

    Quaiser, Achim; Bodi, Xavier; Dufresne, Alexis; Naquin, Delphine; Francez, André-Jean; Dheilly, Alexandra; Coudouel, Sophie; Pedrot, Mathieu; Vandenkoornhuyse, Philippe

    2014-01-01

    A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem. PMID:25033299

  9. Modeling carbon cycle responses to tree mortality: linking microbial and biogeochemical changes

    NASA Astrophysics Data System (ADS)

    Moore, D. J.; Trahan, N. A.; Dynes, E. L.; Zobitz, J. M.; Gallery, R.

    2013-12-01

    Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have killed billions of trees from Mexico to Alaska in the last 13 years. This mortality is predicted to influence important carbon, water and energy balance feedbacks on the Earth system. We studied changes in soil biogeochemical cycling and microbial community structure after tree mortality. We show, using a decade long chronosequence, that tree mortality causes no increase in total respiration from local to watershed scales, with corresponding changes in biogeochemical pools of nitrogen and phosphorus. We also found comparable declines in both gross primary productivity and respiration suggesting little change in net flux. We tested the mechanisms controlling these patterns using an ecosystem model; contrasting a simplified microbial subroutine with a 'dead soil' model. We coupled our modeling work with direct measurements of microbial biomass, enzyme kinetics and community structure. The transitory recovery of respiration 6-7 years after mortality was associated with increased microbial biomass, increased incorporation of leaf litter carbon into soil organic matter, and was followed by a secondary decline in respiration during years 8-10. Our findings are consistent with the mechanism of reduced input of new carbon causing a decline in microbial biomass rather than an increased output of older carbon.

  10. ISOGENIE: Linking geochemistry, isotopic chemistry and microbial dynamics & community composition in a thawing permafrost peatland, Stordalen Mire, Abisco, Sweden.

    NASA Astrophysics Data System (ADS)

    Chanton, J.; Crill, P. M.; Rich, V.; McCalley, C. K.; Hodgkins, S. B.; Tyson, G.; Logan, T.; Wehr, R.; Mondav, R.; Li, C.; Frolking, S.; Saleska, S. R.

    2011-12-01

    As permafrost thaws, increasing CH4 emissions from northern wetlands are likely to cause positive feedback to atmospheric warming. One of the over-arching goals of this project is to connect geochemical processes, particularly focusing on methane production, to underlying microbial population dynamics and genomics. Recent transformative technical advances in both high throughput investigations of microbial communities and high temporal resolution biogeochemical isotope measurements now permit a uniquely comprehensive approach to opening the microbial "black boxes" that impact carbon cycling on global scales. This project links detailed microbial sampling with detailed geochemical and isotopic sampling on seasonal and diel timescales and has an extensive modeling component. Gas exchange is monitored across the wetland gradients in a series of automated chambers and isotopes of emitted and belowground methane and carbon dioxide are measured with a QC laser system. The mire is in a state of partial thaw. With this thaw is an apparent ecological session in wetland community structure and associated changes in organic matter lability, rates of methane production and microbial community. Our group's study sites range from palsa with underlying permanently frozen peat, to recently collapsed and flooded palsa, to flooded palsa colonized by Sphagnum, to flooded eriophorum sites, to sites populated by Carex, to open water lakes. Across this environmental gradient pH ranges from 4 to 6.5. This change is driven by changes in hydrology as the surface of the thawing permafrost subsides and an adjacent lake drains into the mire. Along this environmental gradient, from palsa to Carex, the lability of the peat increases significantly as determined in incubations of peat material and monitoring of methane and carbon dioxide production rates. Coincident with this environmental gradient is a decrease in the apparent fractionation factor between methane and carbon dioxide and methane

  11. Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

    SciTech Connect

    Dowdle, P.R.; Oremland, R.S.

    1998-12-01

    The microbial oxidation of elemental selenium [Se(0)] was studied by employing {sup 75}Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(0) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(0) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(0) oxidation ranged from 0.0009 to 0.0117 day{sup {minus}1} which were 3--4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.

  12. Electrospun gelatin nanofibers: a facile cross-linking approach using oxidized sucrose.

    PubMed

    Jalaja, K; James, Nirmala R

    2015-02-01

    Gelatin nanofibers were fabricated via electrospinning with minimal toxicity from solvents and cross-linking agents. Electrospinning was carried out using a solvent system based on water and acetic acid (8:2, v/v). Acetic acid concentration was kept as minimum as possible to reduce the toxic effects. Electrospun gelatin nanofibers were cross-linked with oxidized sucrose. Sucrose was oxidized by periodate oxidation to introduce aldehyde functionality. Cross-linking with oxidized sucrose could be achieved without compromising the nanofibrous architecture. Cross-linked gelatin nanofibers maintained the fibrous morphology even after keeping in contact with aqueous medium. The morphology of the cross-linked nanofibrous mats was examined by scanning electron microscopy (SEM). Oxidized sucrose cross-linked gelatin nanofibers exhibited improved thermal and mechanical properties. The nanofibrous mats were evaluated for cytotoxicity and cell viability using L-929 fibroblast cells. The results confirmed that oxidized sucrose cross-linked gelatin nanofibers were non-cytotoxic towards L-929 cells with good cell viability. PMID:25478965

  13. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    PubMed

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  14. Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

    PubMed Central

    Haverkamp, Thomas H. A.; Hammer, Øyvind; Jakobsen, Kjetill S.

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  15. Linking geochemistry to microbial ecology in hot springs: examples from southeastern Asia (Invited)

    NASA Astrophysics Data System (ADS)

    Dong, H.; Jiang, H.; Hou, W.; Wang, S.; Huang, Q.; Briggs, B. R.; Huang, L.; Hust, W.; Hedlund, B. P.; Zhang, C.; Hartnett, H. E.; Dijkstra, P.; Hungate, B. A.

    2013-12-01

    Despite recent advances in our understanding of microbial ecology in high temperature environments, important questions remain as to how geochemical conditions shape microbial ecology in hot springs. In the past three years, we have surveyed a large number of hot springs in three regions of southeastern Asia: Tengchong of Yunnan Province, China; Tibet in China; and the Philippines. These springs possess large gradients in pH (2.5-9.4), temperature (22.1-93.6oC), and water and sediment geochemistry. Within each region, these geochemical conditions are important in shaping microbial community structure and diversity. For example, in the Rehai geothermal field of Tengchong, dominant taxa within the dominant bacterial phylum Aquificae and archaeal phylum Crenarchaeota depended on pH (2.5-9.4), temperature (55.1-93.6), Na-Cl-HCO3 water type and silicate rock lithology. In the Ruidian geothermal region, springs with circum-neutral pH (6.71-7.29), moderate temperature (50-82oC), Na-HCO3 water type, and carbonate-dominated lithology, Hydrogenobacter of Aquificae dominated spring water, but the microbial community in sediments was diverse with abundant novel groups. In Tibet springs with low-moderate temperature (22-75oC) and circum-neutral pH (7.2-8.1), temperature appeared to be the most important factor in determining diversity and community structure. In acidic hot springs of the Philippines (Temperature: 60-92°C, pH 3.72-6.58), microbial communities were predominated by those related to sulfur metabolism, which are different from those in acidic springs of Tengchong. When these three regions are considered together, environmental conditions play a major role in controlling microbial community structure, but geographical location appears to be an important factor as well.

  16. Microbial iron oxidation in the Arctic tundra and its implications for biogeochemical cycling.

    PubMed

    Emerson, David; Scott, Jarrod J; Benes, Joshua; Bowden, William B

    2015-12-01

    The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long -149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. PMID:26386054

  17. Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

    PubMed Central

    Scott, Jarrod J.; Benes, Joshua; Bowden, William B.

    2015-01-01

    The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long −149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. PMID:26386054

  18. Experimental Evidence Linking Elevated CO2, Rhizosphere C/N Stoichiometry and Microbial Efficiency

    NASA Astrophysics Data System (ADS)

    Carrillo, Y.; Dijkstra, F. A.; Pendall, E.; LeCain, D. R.; Morgan, J.

    2012-12-01

    Soil C storage is a keystone of the global response to climate change. What the relationship between the efficiency of microbial decomposers and soil C storage is, and how changes in atmospheric CO2 concentration and nutrient availability will affect this relationship is not understood. Although mechanisms are elusive, there is increased recognition of the importance of the plant rhizosphere in mediating ecosystem-scale impacts of climate change. We investigated the impact of elevated CO2 (eCO2), soil N availability and root tissue stoichiometry on microbial use of soil C. Starting from seed, we grew a temperate grass in its native soil, under 13C labelled ambient and eCO2 atmospheres. This approach enabled us to assess incorporation of plant-derived and native soil organic matter (SOM) C into microbes, dissolved organic C (DOC) and respiration via isotopic partitioning. N availability was modified via alteration of root tissue stoichiometry (with foliar N application) and direct N addition to soil. Microbial communities were assessed with phospholipid fatty acids (PLFA). eCO2 increased the respiration of plant-derived C, but decreased CO2production from SOM. This was accompanied by an increase in the SOM-derived microbial C, so that the amount of SOM-derived CO2 per unit of microbial C decreased with eCO2 (lower metabolic quotient, an index of microbial efficiency). SOM-derived microbial C was strongly and negatively related to the pool of SOM-derived DOC, supporting enhanced use of this C source. Together, these results indicate that eCO2 led to an increase in size and efficiency of the microbial populations utilizing SOM-C. Increased grazing, as indicated by more abundant PLFA markers of protozoa under eCO2, may have lowered maintenance-associated respiration, thus increasing efficiency. Greater plant inputs with eCO2 may have provided readily available C for labile-C consuming microbes, thus reducing competitive pressure on SOM-consuming populations, who are

  19. Biomineralization associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals

    USGS Publications Warehouse

    Zhang, G.; Dong, H.; Jiang, H.; Kukkadapu, R.K.; Kim, J.; Eberl, D.; Xu, Z.

    2009-01-01

    Iron-reducing and oxidizing microorganisms gain energy through reduction or oxidation of iron, and by doing so play an important role in the geochemical cycling of iron. This study was undertaken to investigate mineral transformations associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals. A fluid sample from the 2450 m depth of the Chinese Continental Scientific Drilling project was collected, and Fe3+-reducing and Fe2+-oxidizing microorganisms were enriched. The enrichment cultures displayed reduction of Fe3+ in nontronite and ferric citrate, and oxidation of Fe2+ in vivianite, siderite, and monosulfide (FeS). Additional experiments verified that the iron reduction and oxidation was biological. Oxidation of FeS resulted in the formation of goethite, lepidocrocite, and ferrihydrite as products. Although our molecular microbiological analyses detected Thermoan-aerobacter ethanolicus as a predominant organism in the enrichment culture, Fe3+ reduction and Fe2+ oxidation may be accomplished by a consortia of organisms. Our results have important environmental and ecological implications for iron redox cycling in solid minerals in natural environments, where iron mineral transformations may be related to the mobility and solubility of inorganic and organic contaminants.

  20. Explicit Microbial Processes to Simulate Methane Production and Oxidation in Wetlands in the GFDL Land Model

    NASA Astrophysics Data System (ADS)

    Smolander, S.; Sulman, B. N.; Shevliakova, E.

    2015-12-01

    Recent observational studies highlighted the need to include explicit treatment of the soil microbial processes into the next generation of Earth System Models (ESMs). These processes shape most soil biogeochemical cycles and control releases of the most potent greenhouses gases carbon dioxide and methane. Currently global ecosystem models usually parameterize methane production as a fraction of soil heterotrophic respiration. This lumps the pathways of several different functional groups of microbes into one production rate, possibly modified by a number of environmental factor multipliers. Methane oxidation is usually more explicitly modeled by Michaelis-Menten kinetics, but if the maximum rate, before environmental multipliers, is a constant parameter, this essentially implies a constant methanotrophic microbe population size. We present an explicit model for wetland soil microbial processes in an ESM context. We introduce a growth and decomposition model for four functional groups of microbes involved in methane production and oxidation, so microbial populations can grow when conditions are favorable and substrate is available. When soil conditions are anoxic, fermenting microbes transform available soil carbon into intermediate substrates, and two different kinds of methanogenic microbes live on their preferred substrates producing methane. Methane is transported through aerobic layers of the soil column, where methanotrophic microbes oxidize part of the methane, and the rest escapes to the atmosphere. We present initial simulations using the new model in the context of existing measurements of methane emissions and microbial populations at the site level, and discuss the implications of including these processes in an ESM. This explicit process model establishes a foundation for improving dynamic ecosystem-climate feedbacks in ESM simulations, and facilitates more detailed experimental verification of wetland biogeochemical processes.

  1. Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

    NASA Astrophysics Data System (ADS)

    Francis, C.

    2015-12-01

    Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention

  2. Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...

  3. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    SciTech Connect

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  4. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

    PubMed Central

    Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

    2016-01-01

    Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the

  5. Linking Predation Risk, Herbivore Physiological Stress and Microbial Decomposition of Plant Litter

    PubMed Central

    Schmitz, Oswald J.; Bradford, Mark A.; Strickland, Michael S.; Hawlena, Dror

    2013-01-01

    The quantity and quality of detritus entering the soil determines the rate of decomposition by microbial communities as well as recycle rates of nitrogen (N) and carbon (C) sequestration1,2. Plant litter comprises the majority of detritus3, and so it is assumed that decomposition is only marginally influenced by biomass inputs from animals such as herbivores and carnivores4,5. However, carnivores may influence microbial decomposition of plant litter via a chain of interactions in which predation risk alters the physiology of their herbivore prey that in turn alters soil microbial functioning when the herbivore carcasses are decomposed6. A physiological stress response by herbivores to the risk of predation can change the C:N elemental composition of herbivore biomass7,8,9 because stress from predation risk increases herbivore basal energy demands that in nutrient-limited systems forces herbivores to shift their consumption from N-rich resources to support growth and reproduction to C-rich carbohydrate resources to support heightened metabolism6. Herbivores have limited ability to store excess nutrients, so stressed herbivores excrete N as they increase carbohydrate-C consumption7. Ultimately, prey stressed by predation risk increase their body C:N ratio7,10, making them poorer quality resources for the soil microbial pool likely due to lower availability of labile N for microbial enzyme production6. Thus, decomposition of carcasses of stressed herbivores has a priming effect on the functioning of microbial communities that decreases subsequent ability to of microbes to decompose plant litter6,10,11. We present the methodology to evaluate linkages between predation risk and litter decomposition by soil microbes. We describe how to: induce stress in herbivores from predation risk; measure those stress responses, and measure the consequences on microbial decomposition. We use insights from a model grassland ecosystem comprising the hunting spider predator (Pisuarina

  6. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation.

    PubMed

    Agler, Matthew T; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M

    2016-01-01

    Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe-microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial "hubs," are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on "hub" microbes, which, via microbe-microbe interactions, transmit the effects to the microbial community. We analyzed two "hub" microbes (the obligate biotrophic

  7. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

    PubMed Central

    Adams, Melissa M.; Hoarfrost, Adrienne L.; Bose, Arpita; Joye, Samantha B.; Girguis, Peter R.

    2013-01-01

    Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C2), propane (C3), and butane (C4) in anoxic sediments in contrast to methane (C1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV, Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C1–C4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C1–C4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75°C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C1–C4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C2–C4 alkanes. Maximum C1–C4 alkane oxidation rates occurred at 55°C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C3 was oxidized at the highest rate over time, then C4, C2, and C1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C2–C4alkanes with AOM for available oxidants and the influence on the fate of C1 derived from these hydrothermal systems. PMID:23717305

  8. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    NASA Astrophysics Data System (ADS)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  9. Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates.

    PubMed

    Hu, Hang-Wei; Chen, Deli; He, Ji-Zheng

    2015-09-01

    The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions. PMID:25934121

  10. Soluble microbial products decrease pyrite oxidation by ferric iron at pH < 2.

    PubMed

    Yacob, Tesfayohanes; Pandey, Sachin; Silverstein, Joann; Rajaram, Harihar

    2013-08-01

    Research on microbial activity in acid mine drainage (AMD) has focused on transformations of iron and sulfur. However, carbon cycling, including formation of soluble microbial products (SMP) from cell growth and decay, is an important biogeochemical component of the AMD environment. Experiments were conducted to study the interaction of SMP with soluble ferric iron in acidic conditions, particularly the formation of complexes that inhibit its effectiveness as the primary oxidant of pyrite during AMD generation. The rate of pyrite oxidation by ferric iron in sterile suspensions at pH 1.8 was reduced by 87% in the presence of SMP produced from autoclaved cells at a ratio of 0.3 mg DOC per mg total soluble ferric iron. Inhibition of pyrite oxidation by SMP was shown to be comparable to, but weaker than, the effect of a chelating synthetic siderophore, DFAM. Two computational models incorporating SMP complexation were fitted to experimental results. Results suggest that bacterially produced organic matter can play a role in slowing pyrite oxidation. PMID:23777272

  11. Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park.

    PubMed

    Fortney, N W; He, S; Converse, B J; Beard, B L; Johnson, C M; Boyd, E S; Roden, E E

    2016-05-01

    Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was investigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sustained DIR driven by oxidation of acetate, lactate, and H2 . Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abiotic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides. Pyrosequencing of 16S rRNA genes from enrichment cultures showed dominant sequences closely affiliated with Geobacter metallireducens, a mesophilic Fe(III) oxide reducer. Shotgun metagenomic analysis of enrichment cultures confirmed the presence of a dominant G. metallireducens-like population and other less dominant populations from the phylum Ignavibacteriae, which appear to be capable of DIR. Gene (protein) searches revealed the presence of heat-shock proteins that may be involved in increased thermotolerance in the organisms present in the enrichments as well as porin-cytochrome complexes previously shown to be involved in extracellular electron transport. This analysis offers

  12. Cr(III) Oxidation Coupled With Microbially-Mediated Mn(II) Oxidation

    SciTech Connect

    Youxian Wu; Baolin Deng

    2006-04-05

    Cr(VI) can be reduced to less toxic and mobile Cr(III) species through abiotic and biological processes. Reductive immobilization of Cr(VI) has been widely explored as a cost effective technology for site remediation; Mn oxides are regarded as primary oxidants for Cr(III) oxidation in the environment; and Generation of Mn oxides from Mn(II) in natural environments is believed to be biologically catalyzed.

  13. Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form

    PubMed Central

    Nielsen, Morten T.; Ranberg, Johan Andersen; Christensen, Ulla; Christensen, Hanne Bjerre; Harrison, Scott J.; Olsen, Carl Erik; Hamberger, Björn; Møller, Birger Lindberg

    2014-01-01

    Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals. PMID:25239892

  14. Zinc oxide nanoparticles cause inhibition of microbial denitrification by affecting transcriptional regulation and enzyme activity.

    PubMed

    Zheng, Xiong; Su, Yinglong; Chen, Yinguang; Wan, Rui; Liu, Kun; Li, Mu; Yin, Daqiang

    2014-12-01

    Over the past few decades, human activities have accelerated the rates and extents of water eutrophication and global warming through increasing delivery of biologically available nitrogen such as nitrate and large emissions of anthropogenic greenhouse gases. In particular, nitrous oxide (N2O) is one of the most important greenhouse gases, because it has a 300-fold higher global warming potential than carbon dioxide. Microbial denitrification is a major pathway responsible for nitrate removal, and also a dominant source of N2O emissions from terrestrial or aquatic environments. However, whether the release of zinc oxide nanoparticles (ZnO NPs) into the environment affects microbial denitrification is largely unknown. Here we show that the presence of ZnO NPs lead to great increases in nitrate delivery (9.8-fold higher) and N2O emissions (350- and 174-fold higher in the gas and liquid phases, respectively). Our data further reveal that ZnO NPs significantly change the transcriptional regulations of glycolysis and polyhydroxybutyrate synthesis, which causes the decrease in reducing powers available for the reduction of nitrate and N2O. Moreover, ZnO NPs substantially inhibit the gene expressions and catalytic activities of key denitrifying enzymes. These negative effects of ZnO NPs on microbial denitrification finally cause lower nitrate removal and higher N2O emissions, which is likely to exacerbate water eutrophication and global warming. PMID:25384038

  15. Polysulfides Link H2S to Protein Thiol Oxidation

    PubMed Central

    Greiner, Romy; Pálinkás, Zoltán; Bäsell, Katrin; Becher, Dörte; Antelmann, Haike; Nagy, Péter

    2013-01-01

    Abstract Aims: Hydrogen sulfide (H2S) is suggested to act as a gaseous signaling molecule in a variety of physiological processes. Its molecular mechanism of action was proposed to involve protein S-sulfhydration, that is, conversion of cysteinyl thiolates (Cys-S−) to persulfides (Cys-S-S−). A central and unresolved question is how H2S—that is, a molecule with sulfur in its lowest possible oxidation state (−2)—can lead to oxidative thiol modifications. Results: Using the lipid phosphatase PTEN as a model protein, we find that the “H2S donor” sodium hydrosulfide (NaHS) leads to very rapid reversible oxidation of the enzyme in vitro. We identify polysulfides formed in NaHS solutions as the oxidizing species, and present evidence that sulfane sulfur is added to the active site cysteine. Polysulfide-mediated oxidation of PTEN was induced by all “H2S donors” tested, including sodium sulfide (Na2S), gaseous H2S, and morpholin-4-ium 4-methoxyphenyl(morpholino) phosphinodithioate (GYY4137). Moreover, we show that polysulfides formed in H2S solutions readily modify PTEN inside intact cells. Innovation: Our results shed light on the previously unresolved question of how H2S leads to protein thiol oxidation, and suggest that polysulfides formed in solutions of H2S mediate this process. Conclusion: This study suggests that the effects that have been attributed to H2S in previous reports may in fact have been mediated by polysulfides. It also supports the notion that sulfane sulfur rather than sulfide is the actual in vivo agent of H2S signaling. Antioxid. Redox Signal. 19, 1749–1765. PMID:23646934

  16. Linking phosphorus availability with photo-oxidative stress in plants.

    PubMed

    Hernández, Iker; Munné-Bosch, Sergi

    2015-05-01

    Plants have evolved a plethora of mechanisms to circumvent the potential damaging effects of living under low phosphorus availability in the soil. These mechanisms include different levels of organization, from root-shoot signalling at the whole-plant level to specific biochemical responses at the subcellular level, such as reductions in photosynthesis and the consequent activation of photo- and antioxidant mechanisms in chloroplasts. Some recent studies clearly indicate that severe phosphorus deficiency can lead to alterations in the photosynthetic apparatus, including reductions in CO2 assimilation rates, a down-regulation of photosynthesis-related genes and photoinhibition at the photosystem II level, thus causing potential photo-oxidative stress. Photo-oxidative stress is characterized by an increased production of reactive oxygen species in chloroplasts, which at low concentrations can serve a signalling, protective role, but when present at high concentrations can cause damage to lipids, proteins and nucleic acids, thus leading to irreversible injuries. We discuss here the mechanisms that phosphate-starved plants have evolved to withstand photo-oxidative stress, including changes at the subcellular level (e.g. activation of photo- and antioxidant protection mechanisms in chloroplasts), cellular and tissular levels (e.g. activation of photorespiration and anthocyanin accumulation) and whole-plant level (alterations in source-sink relationships modulated by hormones). Of particular importance is the current evidence demonstrating that phosphate-starved plants activate simultaneous responses at multiple levels, from transcriptional changes to root-shoot signalling, to prevent oxidative damage. In this review, we summarize current knowledge about the occurrence of photo-oxidative stress in phosphate-starved plants and highlight the mechanisms these plants have evolved to prevent oxidative damage under phosphorus limitation at the subcellular, cellular and whole

  17. (abstract) High-T(sub c) SNS Weak Links Using Oxide Normal Metals

    NASA Technical Reports Server (NTRS)

    Hunt, B. D.; Barner, J. B.; Foote, M. C.; Vasquez, R. P.

    1993-01-01

    This work examines device results for edge-geometry SNS weak links utilizing a variety of oxide normal metals. A comparison of the electrical properties of fabricated devices and the magnetic field response will be presented. Device reproducibility will also be discussed. This talk will also examine recent progress in fabrication of epitaxial SNS weak links on silicon-on-sapphire (SOS) substrates. SNS weak links fabricated recently are under investigation, and preliminary results on these devices will be discussed.

  18. Comparison of Anodic Community in Microbial Fuel Cells with Iron Oxide-Reducing Community.

    PubMed

    Yokoyama, Hiroshi; Ishida, Mitsuyoshi; Yamashita, Takahiro

    2016-04-28

    The group of Fe(III) oxide-reducing bacteria includes exoelectrogenic bacteria, and they possess similar properties of transferring electrons to extracellular insoluble-electron acceptors. The exoelectrogenic bacteria can use the anode in microbial fuel cells (MFCs) as the terminal electron acceptor in anaerobic acetate oxidation. In the present study, the anodic community was compared with the community using Fe(III) oxide (ferrihydrite) as the electron acceptor coupled with acetate oxidation. To precisely analyze the structures, the community was established by enrichment cultures using the same inoculum used for the MFCs. High-throughput sequencing of the 16S rRNA gene revealed considerable differences between the structure of the anodic communities and that of the Fe(III) oxide-reducing community. Geobacter species were predominantly detected (>46%) in the anodic communities. In contrast, Pseudomonas (70%) and Desulfosporosinus (16%) were predominant in the Fe(III) oxide-reducing community. These results demonstrated that Geobacter species are the most specialized among Fe(III)-reducing bacteria for electron transfer to the anode in MFCs. In addition, the present study indicates the presence of a novel lineage of bacteria in the genus Pseudomonas that highly prefers ferrihydrite as the terminal electron acceptor in acetate oxidation. PMID:26767577

  19. Statistical Properties of Short Subsequences in Microbial Genomes and Their Link to Pathogen Identification and Evolution

    NASA Astrophysics Data System (ADS)

    Zhang, Meizhuo; Putonti, Catherine; Chumakov, Sergei; Gupta, Adhish; Fox, George E.; Graur, Dan; Fofanov, Yuriy

    2006-09-01

    Numerous sequencing projects have unveiled partial and full microbial genomes. The data produced far exceeds one person's analytical capabilities and thus requires the power of computing. A significant amount of work has focused on the diversity of statistical characteristics along microbial genomic sequences, e.g. codon bias, G+C content, the frequencies of short subsequences (n-mers), etc. Based upon the results of these studies, two observations were made: (1) there exists a correlation between regions of unusual statistical properties, e.g. difference in codon bias, etc., from the rest of the genomic sequence, and evolutionary significant regions, e.g. regions of horizontal gene transfer; and (2) because no two microbial genomes look statistically identical, statistical properties can be used to distinguish between genomic sequences. Recently, we conducted extensive analysis on the presence/absence of n-mers for many microbial genomes as well as several viral and eukaryotic genomes. This analysis revealed that the presence of n-mers in all genomes considered (in the range of n, when the condition M<<4n holds, where M is the genome length) can be treated as a nearly random and independent process. Thus we hypothesize that one may use relatively small sets of randomly picked n-mers for differentiating between different microorganisms. Recently, we analyzed the frequency of appearance of all 8- to 12-mers present in each of the 200+ publicly available microbial genomes. For nearly all of the genomes under consideration, we observed that some n-mers are present much more frequently than expected: from 50 to over a thousand copies. Upon closer inspection of these sequences, we found several cases in which an overrepresented n-mer exhibits a bias towards being located in the coding or being located in the non-coding region. Although the evolutionary reason for the conservation of such sequences remains unclear, in some cases it is plausible to believe that sequences

  20. Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and microbial physiology.

    PubMed

    Wagai, Rota; Kishimoto-Mo, Ayaka W; Yonemura, Seiichiro; Shirato, Yasuhito; Hiradate, Syuntaro; Yagasaki, Yasumi

    2013-04-01

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by microbial physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure microbial respiration and quantified easily soluble C as well as microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for

  1. Endogenous and enhanced oxidative cross-linking in wheat flour mill streams

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The oxidative cross-linking of arabinoxylan and protein polymers is partially responsible for variation in end-use quality of wheat flour; specifically, differences in batter viscosity as well as variation in bread and cookie quality. A better understanding of the variation in oxidative cross-linkin...

  2. Power of Proteomics in Linking Oxidative Stress and Female Infertility

    PubMed Central

    Gupta, Sajal; Sharma, Rakesh; Agarwal, Ashok

    2014-01-01

    Endometriosis, PCOS, and unexplained infertility are currently the most common diseases rendering large numbers of women infertile worldwide. Oxidative stress, due to its deleterious effects on proteins and nucleic acids, is postulated to be the one of the important mechanistic pathways in differential expression of proteins and in these diseases. The emerging field of proteomics has allowed identification of proteins involved in cell cycle, as antioxidants, extracellular matrix (ECM), cytoskeleton, and their linkage to oxidative stress in female infertility related diseases. The aim of this paper is to assess the association of oxidative stress and protein expression in the reproductive microenvironments such as endometrial fluid, peritoneal fluid, and follicular fluid, as well as reproductive tissues and serum. The review also highlights the literature that proposes the use of the fertility related proteins as potential biomarkers for noninvasive and early diagnosis of the aforementioned diseases rather than utilizing the more invasive methods used currently. The review will highlight the power of proteomic profiles identified in infertility related disease conditions and their linkage with underlying oxidative stress. The power of proteomics will be reviewed with regard to eliciting molecular mechanisms for early detection and management of these infertility related conditions. PMID:24900998

  3. POSSIBLE LINK BETWEEN METHIONINE OXIDATION AND PROTEIN PHOSPHORYLATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aerobic metabolism leads to the production of reactive oxygen species that may damage proteins. Methionine residues in proteins are particularly susceptible to oxidation to methionine sulfoxide (MetSO) converting its side chain from hydrophobic to hydrophilic. We postulated that this could have a si...

  4. Spontaneous arsenic (III) oxidation with bioelectricity generation in single-chamber microbial fuel cells.

    PubMed

    Li, Yunlong; Zhang, Baogang; Cheng, Ming; Li, Yalong; Hao, Liting; Guo, Huaming

    2016-04-01

    Arsenic is one of the most toxic elements commonly found in groundwater. With initial concentration of 200μgL(-1), spontaneous As(III) oxidation is realized completely during 7 days operation in single-chamber microbial fuel cells (MFCs) in the present study, with the maximum power density of 752.6±17mWm(-2). The product is less toxic and mobile As(V), which can be removed from aqueous solution more easily. High-throughput 16S rRNA gene pyrosequencing analysis indicates the existence of arsenic-resistant bacteria as Actinobacteria, Comamonas, Pseudomonas and arsenic-oxidizing bacteria as Enterobacter, with electrochemically active bacteria as Lactococcus, Enterobacter. They interact together and are responsible for As(III) oxidation and bioelectricity generation in MFCs. This study offers a potential attractive method for remediation of arsenic-polluted groundwater. PMID:26685120

  5. Dissimilatory perchlorate reduction linked to aerobic methane oxidation via chlorite dismutase

    NASA Astrophysics Data System (ADS)

    Oremland, R. S.; Baesman, S. M.; Miller, L. G.

    2013-12-01

    The presence of methane (CH4) in the atmosphere of Mars is controversial yet the evidence has aroused scientific interest, as CH4 could be a harbinger of extant or extinct microbial life. There are various oxidized compounds present on the surface of Mars that could serve as electron acceptors for the anaerobic oxidation of CH4, including perchlorate (ClO4-). We examined the role of perchlorate, chlorate (ClO3-) and chlorite (ClO2-) as oxidants linked to CH4 oxidation. Dissimilatory perchlorate reduction begins with reduction of ClO4- to ClO2- and ends with dismutation of chlorite to yield chloride (Cl-) and molecular oxygen (O2). We explored the potential for aerobic CH4 oxidizing bacteria to couple with oxygen derived from chlorite dismutation during dissimilatory perchlorate reduction. Methane (0.2 kPa) was completely removed within several days from the N2-flushed headspace above cell suspensions of methanotrophs (Methylobacter albus strain BG8) and perchlorate reducing bacteria (Dechloromonas agitata strain CKB) in the presence of 5 mM ClO2-. Similar rates of CH4 consumption were observed for these mixed cultures whether they were co-mingled or segregated under a common headspace, indicating that direct contact of cells was not required for methane consumption to occur. We also observed complete removal of 0.2 kPa CH4 in bottles containing dried soil (enriched in methanotrophs by CH4 additions over several weeks) and D. agitata CKB and in the presence of 10 mM ClO2-. This soil (seasonally exposed sediment) collected from the shoreline of a freshwater lake (Searsville Lake, CA) demonstrated endogenous CH4 uptake as well as perchlorate, chlorate and chlorite reduction/dismutation. However, these experiments required physical separation of soil from the aqueous bacterial culture to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although dissimilatory reduction of ClO4- and ClO3- could be inferred from the

  6. Linking lignocellulosic dietary patterns with gut microbial Enterotypes of Tsaitermes ampliceps and comparison with Mironasutitermes shangchengensis.

    PubMed

    Su, L-J; Liu, Y-Q; Liu, H; Wang, Y; Li, Y; Lin, H-M; Wang, F-Q; Song, A-D

    2015-01-01

    Tsaitermes ampliceps (lower termites) and Mironasutitermes shangchengensis (higher termites) are highly eusocial insects that thrive on recalcitrant lignocellulosic diets through nutritional symbioses with gut dwelling prokaryotes and eukaryotes. We used denaturing gradient gel electrophoresis and a 16S rRNA clone library to investigate i) how microbial communities adapt to lignocellulosic diets with different cellulose and lignin content, ii) the differences in the dominant gut microbial communities of the 2 types of termites. The results indicated that gut microbiota composition in T. ampliceps was profoundly affected by 2-week diet shifts. Comparison of these changes indicated that Bacteroidetes and Spirochaetes act in cellulose degradation, while Firmicutes were responsible for lignin degradation. Additionally, Proteobacteria consistently participated in energy production and balanced the gut environment. Bacteroidetes may function without hindgut protozoans in higher termites. The diversity of enteric microorganisms in M. shangchengensis was higher than that in T. ampliceps, possibly because of the more complicated survival mechanisms of higher termites. PMID:26535711

  7. Linking Sediment Microbial Communities to Carbon Cycling in High-Latitude Lakes

    NASA Astrophysics Data System (ADS)

    Emerson, J. B.; Varner, R. K.; Johnson, J. E.; Owusu-Dommey, A.; Binder, M.; Woodcroft, B. J.; Wik, M.; Freitas, N. L.; Boyd, J. A.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

    2015-12-01

    It is well recognized that thawing permafrost peatlands are likely to provide a positive feedback to climate change via CH4 and CO2 emissions. High-latitude lakes in these landscapes have also been identified as sources of CH4 and CO2 loss to the atmosphere. To investigate microbial contributions to carbon loss from high-latitude lakes, we characterized sediment geochemistry and microbiota via cores collected from deep and shallow regions of two lakes (Inre Harrsjön and Mellersta Harrsjön) in Arctic Sweden in July, 2012. These lakes are within the Stordalen Mire long-term ecological area, a focal site for investigating the impacts of climate change-related permafrost thaw, and the lakes in this area are responsible for ~55% of the CH4 loss from this hydrologically interconnected system. Across 40 samples from 4 to 40 cm deep within four sediment cores, Illumina 16S rRNA gene sequencing revealed that the sedimentary microbiota was dominated by candidate phyla OP9 and OP8 (Atribacteria and Aminicenantes, respectively, including putative fermenters and anaerobic respirers), predicted methanotrophic Gammaproteobacteria, and predicted methanogenic archaea from the Thermoplasmata Group E2 clade. We observed some overlap in community structure with nearby peatlands, which tend to be dominated by methanogens and Acidobacteria. Sediment microbial communities differed significantly between lakes, by overlying lake depth (shallow vs. deep), and by depth within a core, with each trend corresponding to parallel differences in biogeochemical measurements. Overall, our results support the potential for significant microbial controls on carbon cycling in high-latitude lakes associated with thawing permafrost, and ongoing metagenomic analyses of focal samples will yield further insight into the functional potential of these microbial communities and their dominant members.

  8. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

    PubMed Central

    Muller, Emilie E. L.; Pinel, Nicolás; Laczny, Cédric C.; Hoopmann, Michael R.; Narayanasamy, Shaman; Lebrun, Laura A.; Roume, Hugo; Lin, Jake; May, Patrick; Hicks, Nathan D.; Heintz-Buschart, Anna; Wampach, Linda; Liu, Cindy M.; Price, Lance B.; Gillece, John D.; Guignard, Cédric; Schupp, James M.; Vlassis, Nikos; Baliga, Nitin S.; Moritz, Robert L.; Keim, Paul S.; Wilmes, Paul

    2014-01-01

    Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ. PMID:25424998

  9. Linking microbial exo-enzyme production to biomass stoichiometry, resource availability and soil respiration

    NASA Astrophysics Data System (ADS)

    Ballantyne, F.; Billings, S. A.

    2013-12-01

    The rate of decomposition of soil organic matter (SOM) is influenced by substrate composition, the diffusion of substrates and exoenzymes secreted by microbes to reaction sites, and the reaction kinetics of those exoenzymes. Predicting carbon (C) flow from SOM into respired CO2 thus requires an understanding of microbial resource allocation and physiological responses to their environment, as these are the factors governing exoenzyme synthesis. Without such an understanding, it is difficult to project how warming and changing edaphic characteristics will influence respiratory CO2 losses from soils. In essence, we need to know how changing environmental conditions directly influence microbial resource demands and reaction kinetics in the soil matrix, and how microbes alter their behavior to maintain metabolic function and balanced acquisition of resources. Here, we present elements of a general theoretical framework describing the consequences of interactions between exoenzymes, SOM substrates, microbial resource allocation and microbial stoichiometry. Our model incorporates the kinetics of exoenzyme-substrate interactions, the costs and benefits associated with producing different exoenzymes, regulation of biomass C:N, and substrate availability in the soil matrix. First, we articulate how resource limitation can become manifest during resource allocation to exoenzymes and acquisition from decaying SOM, and the feedbacks between these two types of limitation. Second, we explore how shifting resource availability forces microbes to alter their strategies for synthesizing exoenzymes to promote acquisition of C and N that satisfies demand. In particular, we study how increases and decreases in total SOM substrate availability influence biomass stoichiometry, how changes in relative exoenzyme-substrate reaction kinetics predicted with warming constrain strategies for regulating relative rates of C and N acquisition, and how strategies for stoichiometric regulation

  10. Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

    2014-12-01

    Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a

  11. Biogeophysical interactions control the formation of iron oxide microbial biofilms in acidic geothermal outflow channels of Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Beam, J.; Berstein, H. C.; Jay, Z.; Kozubal, M. A.; Jennings, R. D.; Inskeep, W. P.

    2012-12-01

    Amorphous iron oxyhydroxide microbial mats in acidic (pH ~ 3) geothermal outflow channels of Yellowstone National Park (YNP) are habitats for diverse populations of autotrophic and heterotrophic microorganisms from the domains Archaea and Bacteria. These systems have been extensively characterized with regards to geochemical, physical, and microbiological (e.g., metagenomics) analyses; however, there is minimal data describing the formation of these iron oxide microbial mats. A conceptual model of Fe(III)-oxide microbial mat development was created, which includes four distinct stages. Autotrophic archaea (Metallosphaera yellowstonensis) and bacteria (Hydrogenobaculum spp.) are the first colonizers (Stage I) that provide pools of organic carbon for heterotrophic thermophiles (Stage II). M. yellowstonensis is an autotrophic Sulfolobales that is responsible for the oxidation of Fe(II) and can thus be defined as the mat 'architect' creating suitable habitats for microbial niches (e.g., anaerobic microorganisms) (Stage III). The last phase of mat formation (Stage IV) represents a pseudo-steady state mature microbial mat, which has been the subject of all previous microbial surveys of these systems. The conceptual model for Fe(III)-oxide microbial mat development was tested by inserting glass (SiO2) microscope slides into the main flow channels of two acidic geothermal springs in YNP. Slides were removed at various time intervals and analyzed for total iron accretion, microbial community structure (i.e., 16S rRNA gene abundance), and mRNA expression of community members. Routine geochemical and physical (e.g., flow) parameters were also measured to decipher their relative contribution to mat development. Initial and previous results show that autotrophic microorganisms (e.g, M. yellowstonensis) are often the first to colonize the glass slides and their activity was confirmed by mRNA expression of genes related to iron oxidation and carbon fixation. Heterotrophs are rare

  12. Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles.

    PubMed

    Byrne, James M; van der Laan, Gerrit; Figueroa, Adriana I; Qafoku, Odeta; Wang, Chongmin; Pearce, Carolyn I; Jackson, Michael; Feinberg, Joshua; Rosso, Kevin M; Kappler, Andreas

    2016-01-01

    The ability for magnetite to act as a recyclable electron donor and acceptor for Fe-metabolizing bacteria has recently been shown. However, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. Here we examine this issue for the phototrophic Fe(II)-oxidizing bacteria Rhodopseudomonas palustris TIE-1 and the Fe(III)-reducing bacteria Geobacter sulfurreducens, comparing magnetite nanoparticles (d ≈ 12 nm) against microparticles (d ≈ 100-200 nm). By integrating surface-sensitive and bulk-sensitive measurement techniques we observed a particle surface that was enriched in Fe(II) with respect to a more oxidized core. This enables microbial Fe(II) oxidation to occur relatively easily at the surface of the mineral suggesting that the electron transfer is dependent upon particle size. However, microbial Fe(III) reduction proceeds via conduction of electrons into the particle interior, i.e. it can be considered as more of a bulk electron transfer process that is independent of particle size. The finding has potential implications on the ability of magnetite to be used for long range electron transport in soils and sediments. PMID:27492680

  13. Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles

    PubMed Central

    Byrne, James M.; van der Laan, Gerrit; Figueroa, Adriana I.; Qafoku, Odeta; Wang, Chongmin; Pearce, Carolyn I.; Jackson, Michael; Feinberg, Joshua; Rosso, Kevin M.; Kappler, Andreas

    2016-01-01

    The ability for magnetite to act as a recyclable electron donor and acceptor for Fe-metabolizing bacteria has recently been shown. However, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. Here we examine this issue for the phototrophic Fe(II)-oxidizing bacteria Rhodopseudomonas palustris TIE-1 and the Fe(III)-reducing bacteria Geobacter sulfurreducens, comparing magnetite nanoparticles (d ≈ 12 nm) against microparticles (d ≈ 100–200 nm). By integrating surface-sensitive and bulk-sensitive measurement techniques we observed a particle surface that was enriched in Fe(II) with respect to a more oxidized core. This enables microbial Fe(II) oxidation to occur relatively easily at the surface of the mineral suggesting that the electron transfer is dependent upon particle size. However, microbial Fe(III) reduction proceeds via conduction of electrons into the particle interior, i.e. it can be considered as more of a bulk electron transfer process that is independent of particle size. The finding has potential implications on the ability of magnetite to be used for long range electron transport in soils and sediments. PMID:27492680

  14. Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles

    NASA Astrophysics Data System (ADS)

    Byrne, James M.; van der Laan, Gerrit; Figueroa, Adriana I.; Qafoku, Odeta; Wang, Chongmin; Pearce, Carolyn I.; Jackson, Michael; Feinberg, Joshua; Rosso, Kevin M.; Kappler, Andreas

    2016-08-01

    The ability for magnetite to act as a recyclable electron donor and acceptor for Fe-metabolizing bacteria has recently been shown. However, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. Here we examine this issue for the phototrophic Fe(II)-oxidizing bacteria Rhodopseudomonas palustris TIE-1 and the Fe(III)-reducing bacteria Geobacter sulfurreducens, comparing magnetite nanoparticles (d ≈ 12 nm) against microparticles (d ≈ 100–200 nm). By integrating surface-sensitive and bulk-sensitive measurement techniques we observed a particle surface that was enriched in Fe(II) with respect to a more oxidized core. This enables microbial Fe(II) oxidation to occur relatively easily at the surface of the mineral suggesting that the electron transfer is dependent upon particle size. However, microbial Fe(III) reduction proceeds via conduction of electrons into the particle interior, i.e. it can be considered as more of a bulk electron transfer process that is independent of particle size. The finding has potential implications on the ability of magnetite to be used for long range electron transport in soils and sediments.

  15. Effect of Phospholipid on Pyrite Oxidation and Microbial Communities under Simulated Acid Mine Drainage (AMD) Conditions.

    PubMed

    Pierre Louis, Andro-Marc; Yu, Hui; Shumlas, Samantha L; Van Aken, Benoit; Schoonen, Martin A A; Strongin, Daniel R

    2015-07-01

    The effect of phospholipid on the biogeochemistry of pyrite oxidation, which leads to acid mine drainage (AMD) chemistry in the environment, was investigated. Metagenomic analyses were carried out to understand how the microbial community structure, which developed during the oxidation of pyrite-containing coal mining overburden/waste rock (OWR), was affected by the presence of adsorbed phospholipid. Using columns packed with OWR (with and without lipid adsorption), the release of sulfate (SO4(2-)) and soluble iron (FeTot) was investigated. Exposure of lipid-free OWR to flowing pH-neutral water resulted in an acidic effluent with a pH range of 2-4.5 over a 3-year period. The average concentration of FeTot and SO4(2-) in the effluent was ≥20 and ≥30 mg/L, respectively. In contrast, in packed-column experiments where OWR was first treated with phospholipid, the effluent pH remained at ∼6.5 and the average concentrations of FeTot and SO4(2-) were ≤2 and l.6 mg/L, respectively. 16S rDNA metagenomic pyrosequencing analysis of the microbial communities associated with OWR samples revealed the development of AMD-like communities dominated by acidophilic sulfide-oxidizing bacteria on untreated OWR samples, but not on refuse pretreated with phospholipid. PMID:26018867

  16. Unexpected Microbial Diversity in Anaerobically Methane-oxidizing Mats of the Black Sea

    NASA Astrophysics Data System (ADS)

    Friedrich, M. W.; Pommerenke, B.; Seifert, R.; Krueger, M.

    2007-12-01

    Sediments of the Black Sea harbour consortia of anaerobically methane-oxidizing microorganisms in dense microbial mats, incrusted in large chimney structures consisting of carbonate precipitate. A number of convincing facts collected previously suggests that anaerobically methane-oxidizing Archaea (ANME) as well as delta- proteobacterial sulphate-reducing bacteria are the key players in anaerobic methane oxidation in Black Sea Mats: their presence has been shown by fluorescent-in-situ hybridization (FISH) with 16S rRNA-targeting probes, lipid biomarkers have typical, low delta13C ratios in archaeal and bacterial lipids, a methyl coenzyme M reductase-like protein was purified from the mat, and mat samples exhibit anaerobic methane oxidation. Here, we show that the diversity of Bacteria in both, pink and black mat samples, is larger than previously known. T-RFLP analysis of 16S rRNA and 16S rRNA genes and cloning and sequencing of randomly selected clones revealed the presence of taxa hitherto unknown to be present in anaerobically methane-oxidizing consortia. Besides the previously known delta-proteobacterial sulphate reducers, clones fell into 7 and 5 different phyla in pink and black coloured mats, respectively. Our findings suggest that the turnover of carbon in anaerobically methane-oxidizing communities might involve a larger diversity of microorganisms than was previously assumed.

  17. Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

    PubMed Central

    Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

    2015-01-01

    Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

  18. Initial Characterization of Carbon Metabolism in Iron Oxidizing Microbial Communities of Acidic Hot Springs in Norris Geyser Basin, Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Kreuzer, H. W.; Jennings, R. D.; Whitmore, L.; Inskeep, W. P.; Moran, J.

    2012-12-01

    the organism produces during autotrophic growth, and are conducting isotopic labeling experiments to determine if these compounds serve as substrates for the iron oxide mat communities. However, isotopic analysis of DIC in the springs as well as bulk iron oxide mat definitively show that fixation of DIC by M. yellowstonensis is not the only source of C within the mats. Metagenome analysis of the microbial communities and genome analysis of isolates suggest the presence of heterotrophic metabolic pathways. Indeed, initial labeling experiments demonstrate strong heterotrophic metabolism in the iron oxide mats as well as in M. yellowstonensis. Several potential sources of reduced C are available in the springs, but whether any of these potential substrates actually feed the iron mat communities is yet to be determined. Carbon isotope ratios of the bulk iron mat communities and potential heterotrophic C sources suggest that heterotrophic uptake of these sources, like autotrophy of DIC, is not the only source of C in the system. Identifying the major active carbon pools and potential geochemical and microbial carbon links will illuminate carbon cycling in this system and should provide insights into how energy is transferred from key chemolithotrophic reactions to other components of the microbial system.

  19. A methodological framework for linking bioreactor function to microbial communities and environmental conditions.

    PubMed

    de los Reyes, Francis L; Weaver, Joseph E; Wang, Ling

    2015-06-01

    In the continuing quest to relate microbial communities in bioreactors to function and environmental and operational conditions, engineers and biotechnologists have adopted the latest molecular and 'omic methods. Despite the large amounts of data generated, gaining mechanistic insights and using the data for predictive and practical purposes is still a huge challenge. We present a methodological framework that can guide experimental design, and discuss specific issues that can affect how researchers generate and use data to elucidate the relationships. We also identify, in general terms, bioreactor research opportunities that appear promising. PMID:25710123

  20. Anaerobic Microbial-Mineral Processes with Fe(III) Oxides: Experimental Considerations and Approaches

    SciTech Connect

    Zachara, John M.; Fredrickson, Jim K.; Kukkadapu, Ravi K.; Gorby, Yuri A.

    2007-07-01

    The biogeochemical cycle of Fe is a one of the dominant redox cycles operative in surface waters and sediments, soils and vadose zones, and groundwater systems. In this cycle which is pronounced at oxic-anoxic boundaries, Fe compounds and microorganisms couple to mediate the oxidation of organic matter by molecular oxygen. The cycle includes: i.) the reductive dissolution of Fe(III) oxides by biogenic organic acids and organic matter oxidizing-metal reducing bacteria yielding Fe2+(aq) and ferrous containing minerals as products, and ii.) the oxidation of dissolved and solid-phase ferrous iron by molecular oxygen and microaerophilic Fe(II)-oxidizing bacteria with subsequent precipitation of poorly crystalline Fe(III) oxides (e.g., ferrihydrite). These Fe(III) oxides; that may recrystallize slowly with time to goethite, hematite, and lepidocrocite; represent a primary redox buffering agent (in terms of electron equivalents) in soils, sediments, and subsurface materials. Manganese (III/IV) oxides are also important in this regard. Because of the high surface area and surface chemical reactivity of Fe(III) oxides and Fe(II) containing mineral phases, the Fe biogeochemical cycle is closely linked to those of the trace metals, phosphorous, and various organic and inorganic anthropogenic contaminants.

  1. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  2. Carbon Monoxide Cycling in Hot Spring Microbial Communities and Links to the Composition of the Archean Atmosphere

    NASA Astrophysics Data System (ADS)

    Colman, A. S.; Techtmann, S.; He, B.; Robb, F.

    2010-12-01

    Carbon monoxide (CO) budgets for the Archean atmosphere generally treat the early biosphere as a major sink for CO, thereby preventing the development of a “CO runaway” atmosphere. Indeed, hydrogenogenic carboxydotrophy (CO + H2O → CO2 + H2) is an anaerobic metabolism that appears to be geographically widespread in hydrothermal microbial ecosystems, including those we have studied at hot springs in Uzon Caldera, Kamchatka, Russia. Carboxydotrophs have been isolated that can use CO as sole carbon and energy source in culture medium with headspace CO partial pressures ranging from ≤ 10-4 atm to ≥ 2 atm. In modern environments, this metabolism was thought to depend on CO supplied as a dissolved and free phase constituent of geothermal fluids. Recent dissolved and free phase gas measurements in Uzon hot springs, coupled with rate determinations of CO consumption in hot spring microbial mats, indicate that the supply of CO from volcanic gases is insufficient to meet the needs of the microbial communities in hot spring sediments. Instead, proximal biological production of CO by environmental microbial consortia must be invoked. The plausibility of widespread biogenic production of CO in natural microbial communities is supported by recent pure culture work that has shown small but ecologically significant CO production by certain methanogens and sulfate reducers. In the Archean, leakage to the atmosphere of even a small fraction of the biologically produced CO would have exceeded the volcanic outgassing flux. Biogenic CO production would also have diminished the biospheric sink for atmospheric CO. This would have had a major influence on the chemistry of the Archean atmosphere, possibly enabling CO concentrations to reach percent levels in the atmosphere. Elevated atmospheric CO concentrations in the Archean would have exerted significant pressures on the early biosphere. Futhermore, CO in the Archean atmosphere would have titrated OH radical, influencing the

  3. Chemolithotrophic perchlorate reduction linked to the oxidation of elemental sulfur.

    PubMed

    Ju, Xiumin; Field, Jim A; Sierra-Alvarez, Reyes; Salazar, Margarita; Bentley, Harold; Bentley, Richard

    2007-04-15

    Perchlorate (ClO(4)(-)) contamination of ground and surface water has been recently recognized as a widespread environmental problem. Biological methods offer promising perspectives of perchlorate remediation. Facultative anaerobic bacteria couple the oxidation of organic and inorganic electron-donating substrates to the reduction of perchlorate as a terminal electron acceptor, converting it completely to the benign end-product, chloride. Insoluble inorganic substrates are of interest for low maintenance bioreactor or permeable reactive barrier systems because they can provide a long-term supply of electron donor without generating organic residuals. The main objective of this research was to investigate the feasibility of utilizing elemental sulfur (S(0)) as an insoluble electron donor for the biological reduction of perchlorate. A chemolithotrophic enrichment culture derived from aerobic activated sludge was obtained which effectively coupled the oxidation of elemental sulfur to sulfate with the reduction of perchlorate to chloride and gained energy from the process for cell growth. The enrichment culture grew at a rate of 0.41 or 0.81 1/d in the absence and presence of added organic carbon for cell growth, respectively. The enrichment culture was also shown to carry out sulfur disproportionation to a limited extent as evidenced by the formation of sulfide and sulfate in the absence of added electron acceptor. When nitrate and perchlorate were added together, the two electron acceptors were removed simultaneously after an initial partial decrease in the nitrate concentration. PMID:17009322

  4. Synthesis of Cross-Linked DNA Containing Oxidized Abasic Site Analogues

    PubMed Central

    2015-01-01

    DNA interstrand cross-links are an important family of DNA damage that block replication and transcription. Recently, it was discovered that oxidized abasic sites react with the opposing strand of DNA to produce interstrand cross-links. Some of the cross-links between 2′-deoxyadenosine and the oxidized abasic sites, 5′-(2-phosphoryl-1,4-dioxobutane) (DOB) and the C4-hydroxylated abasic site (C4-AP), are formed reversibly. Chemical instability hinders biochemical, structural, and physicochemical characterization of these cross-linked duplexes. To overcome these limitations, we developed methods for preparing stabilized analogues of DOB and C4-AP cross-links via solid-phase oligonucleotide synthesis. Oligonucleotides of any sequence are attainable by synthesizing phosphoramidites in which the hydroxyl groups of the cross-linked product were orthogonally protected using photochemically labile and hydrazine labile groups. Selective unmasking of a single hydroxyl group precedes solid-phase synthesis of one arm of the cross-linked DNA. The method is compatible with commercially available phosphoramidites and other oligonucleotide synthesis reagents. Cross-linked duplexes containing as many as 54 nt were synthesized on solid-phase supports. Subsequent enzyme ligation of one cross-link product provided a 60 bp duplex, which is suitable for nucleotide excision repair studies. PMID:24949656

  5. Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.

    PubMed

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2010-01-01

    In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation. PMID:19826809

  6. Microbial pathways in colonic sulfur metabolism and links with health and disease

    PubMed Central

    Carbonero, Franck; Benefiel, Ann C.; Alizadeh-Ghamsari, Amir H.; Gaskins, H. Rex

    2012-01-01

    Sulfur is both crucial to life and a potential threat to health. While colonic sulfur metabolism mediated by eukaryotic cells is relatively well studied, much less is known about sulfur metabolism within gastrointestinal microbes. Sulfated compounds in the colon are either of inorganic (e.g., sulfates, sulfites) or organic (e.g., dietary amino acids and host mucins) origin. The most extensively studied of the microbes involved in colonic sulfur metabolism are the sulfate-reducing bacteria (SRB), which are common colonic inhabitants. Many other microbial pathways are likely to shape colonic sulfur metabolism as well as the composition and availability of sulfated compounds, and these interactions need to be examined in more detail. Hydrogen sulfide is the sulfur derivative that has attracted the most attention in the context of colonic health, and the extent to which it is detrimental or beneficial remains in debate. Several lines of evidence point to SRB or exogenous hydrogen sulfide as potential players in the etiology of intestinal disorders, inflammatory bowel diseases (IBDs) and colorectal cancer in particular. Generation of hydrogen sulfide via pathways other than dissimilatory sulfate reduction may be as, or more, important than those involving the SRB. We suggest here that a novel axis of research is to assess the effects of hydrogen sulfide in shaping colonic microbiome structure. Clearly, in-depth characterization of the microbial pathways involved in colonic sulfur metabolism is necessary for a better understanding of its contribution to colonic disorders and development of therapeutic strategies. PMID:23226130

  7. Applicability of anaerobic nitrate-dependent Fe(II) oxidation to microbial enhanced oil recovery (MEOR).

    PubMed

    Zhu, Hongbo; Carlson, Han K; Coates, John D

    2013-08-01

    Microbial processes that produce solid-phase minerals could be judiciously applied to modify rock porosity with subsequent alteration and improvement of floodwater sweep in petroleum reservoirs. However, there has been little investigation of the application of this to enhanced oil recovery (EOR). Here, we investigate a unique approach of altering reservoir petrology through the biogenesis of authigenic rock minerals. This process is mediated by anaerobic chemolithotrophic nitrate-dependent Fe(II)-oxidizing microorganisms that precipitate iron minerals from the metabolism of soluble ferrous iron (Fe(2+)) coupled to the reduction of nitrate. This mineral biogenesis can result in pore restriction and reduced pore throat diameter. Advantageously and unlike biomass plugs, these biominerals are not susceptible to pressure or thermal degradation. Furthermore, they do not require continual substrate addition for maintenance. Our studies demonstrate that the biogenesis of insoluble iron minerals in packed-bed columns results in effective hydrology alteration and homogenization of heterogeneous flowpaths upon stimulated microbial Fe(2+) biooxidation. We also demonstrate almost 100% improvement in oil recovery from hydrocarbon-saturated packed-bed columns as a result of this metabolism. These studies represent a novel departure from traditional microbial EOR approaches and indicate the potential for nitrate-dependent Fe(2+) biooxidation to improve volumetric sweep efficiency and enhance both the quality and quantity of oil recovered. PMID:23799785

  8. Identification of dityrosine cross-linked sites in oxidized human serum albumin.

    PubMed

    Annibal, Andrea; Colombo, Graziano; Milzani, Aldo; Dalle-Donne, Isabella; Fedorova, Maria; Hoffmann, Ralf

    2016-04-15

    Reactive oxygen species (ROS) can oxidize virtually all cellular components. In proteins cysteine, methionine, tryptophan, and tyrosine residues are most prone to oxidation and their oxidized forms are thus considered as biomarkers of oxidative protein damages. Ultraviolet radiation and some endogenous ROS can produce tyrosine radicals reacting with other tyrosine residues yielding intra- or intermolecular cross-links in proteins. These 3,3'-dityrosines can be quantified by their characteristic fluorescence, but analytical methods to identify the modification sites in proteins are still missing. Although mass spectrometry (MS) is routinely used to map other post-translational modifications, the analysis of dityrosines is challenged by simultaneous fragmentations of both cross-linked peptide chains producing complex tandem mass spectra. Additionally, the fragmentation patterns differ from linear peptides. Here, we studied the fragmentation behavior of dityrosine cross-linked peptides obtained by incubating three peptides (AAVYHHFISDGVR, TEVSSNHVLIYLDK, and LVAYYTLIGASGQR) with horseradish peroxidase in the presence of hydrogen peroxide. Homo- and hetero-dimerization via dityrosine was monitored by fluorescence spectroscopy and MS. The fragmentation characteristics of dityrosine-linked peptides were studied on an ESI-LTQ-Orbitrap-MS using collision induced dissociation, which allowed localizing the cross-linked positions and provided generic rules to identify this oxidative modification. When human serum albumin oxidized with 50-fold molar excess of HOCl in phosphate buffer saline was analyzed by nanoRPC-ESI-MS/MS, an automatic database search considering all possible (in-silico generated) tyrosine-containing peptides as dynamic modifications revealed four different types of oxidatively modified tyrosine residues including dityrosines linking ten different Tyr residues. The automatic database search was confirmed by manual interpretation of each tandem mass spectrum

  9. Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor

    PubMed Central

    Malkin, Sairah Y; Rao, Alexandra MF; Seitaj, Dorina; Vasquez-Cardenas, Diana; Zetsche, Eva-Maria; Hidalgo-Martinez, Silvia; Boschker, Henricus TS; Meysman, Filip JR

    2014-01-01

    Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution. PMID:24671086

  10. Metagenomic Assembly of the Dominant Zetaproteobacteria in an Iron-oxidizing Hydrothermal Microbial Mat

    NASA Astrophysics Data System (ADS)

    Moyer, C. L.; Fullerton, H.

    2013-12-01

    Iron is the fourth most abundant element in the Earth's crust and is potentially one of the most abundant energy sources on the earth as an electron donor for chemolithoautotrophic growth coupled to Fe(II) oxidation. Despite the rapid abiotic oxidation rate of iron, many microbes have adapted to feeding off this fleeting energy source. One such bacterial class is the Zetaproteobacteria. Iron-dominated microbial mat material was collected with a small-scale syringe sampler from Loihi Seamount, Hawaii. From this sample, gDNA was extracted and prepared for paired-end Illumina sequencing. Reconstruction of SSU rDNA genes using EMERGE allowed for comparison to previous SSU rDNA surveys. Clone libraries and qPCR show these microbial mats to be dominated by Zetaproteobacteria. Results from our in silico reconstruction confirm these initial findings. RDP classification of the EMERGE reconstructed sequences resulted in 44% of the community being identified as Zetaproteobacteria. The most abundant SSU rDNA has 99% similarity to Zeta OTU-2, and only a 94% similarity to M. ferrooxidans PV-1. Zeta OTU-2 has been shown to be the most cosmopolitan population in iron-dominated hydrothermal systems from across Pacific Ocean. Metagenomic assembly has resulted in many contigs with high identity to M. ferrooxidans as identified, by BLAST. However, with large differences in SSU rRNA similarity, M. ferrooxidans PV-1 is not an adequate reference. Current work is focusing on reconstruction of the dominant microbial mat member, without the use of a reference genome through an iterative assembly approach. The resulting 'pan-genome' will be compared to other Zetaproteobacteria (at the class level) and the functional ecology of this cosmopolitan microbial mat community member will be extrapolated. Thus far, we have detected multiple housekeeping genes involved in DNA replication, transcription and translation. The most abundant metabolic gene we have found is Aconitase, a key enzyme in the

  11. A grey box model of glucose fermentation and syntrophic oxidation in microbial fuel cells.

    PubMed

    de Los Ángeles Fernandez, Maria; de Los Ángeles Sanromán, Maria; Marks, Stanislaw; Makinia, Jacek; Gonzalez Del Campo, Araceli; Rodrigo, Manuel; Fernandez, Francisco Jesus

    2016-01-01

    In this work, the fermentative and oxidative processes taking place in a microbial fuel cell (MFC) fed with glucose were studied and modeled. The model accounting for the bioelectrochemical processes was based on ordinary, Monod-type differential equations. The model parameters were estimated using experimental results obtained from three H-type MFCs operated at open or closed circuits and fed with glucose or ethanol. The experimental results demonstrate that similar fermentation processes were carried out under open and closed circuit operation, with the most important fermentation products being ethanol (with a yield of 1.81molmol(-1) glucose) and lactic acid (with a yield of 1.36molmol(-1) glucose). A peak in the electricity generation was obtained when glucose and fermentation products coexisted in the liquid bulk. However, almost 90% of the electricity produced came from the oxidation of ethanol. PMID:26512864

  12. Synergetic interactions improve cobalt leaching from lithium cobalt oxide in microbial fuel cells.

    PubMed

    Huang, Liping; Li, Tianchi; Liu, Chuan; Quan, Xie; Chen, Lijie; Wang, Aijie; Chen, Guohua

    2013-01-01

    Cobalt leaching from lithium cobalt oxide is a promising reduction process for recovery of cobalt and recycle of spent lithium ion batteries, but suffers from consumption of large amount of reductants and energy, and generation of excess secondary polluted sludge. Thus, effective and environmental friendly processes are needed to improve the existing process limitations. Here we reported microbial fuel cells (MFCs) to effectively reduce Co(III) in lithium cobalt oxide with concomitant energy generation. There was a synergetic interaction in MFCs, leading to a more rapid Co(III) leaching at a rate 3.4 times the sum of rates by conventional chemical processes and no-acid controls. External resistor, solid/liquid ratio, solution conductivity, pH and temperature affected system performance. This study provides a new process for recovery of cobalt and recycle of spent lithium ion batteries with concomitant energy generation from MFCs. PMID:23211478

  13. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  14. Influence of sediment components on the immobilization of Zn during microbial Fe-(hydr)oxide reduction.

    PubMed

    Coby, Aaron J; Picardal, Flynn W

    2006-06-15

    The fate of Zn and other sorbed heavy metals during microbial reduction of iron oxides is different when comparing synthetic Fe-(hydr)oxides and natural sediments undergoing a similar degree of iron reduction. Batch experiments with the iron-reducing organism Shewanella putrefaciens were conducted to examine the effects of an aqueous complexant (nitrilotriacetic acid or NTA), two solid-phase complexants (kaolinite and montmorillonite), an electron carrier (anthraquinone disulfonic acid or AQDS), and a humic acid on the speciation of Zn during microbial reduction of synthetic goethite. Compared to systems containing only goethite and Zn, microbial Fe(III) reduction in the presence of clay resulted in up to a 50% reduction in Zn immobilization (insoluble in a 2 h 0.5 M HCl extraction) without affecting Fe(II) production. NTA (3 mM) increased Fe(II) production 2-fold and resulted in recovery of nearly 75% of Zn in the aqueous fraction. AQDS (50 microM) resulted in a 12.5% decrease in Fe(II) production and a 44% reduction in Zn immobilization. Humic acid additions resulted in up to a 25% decrease in Fe(II) production and 51% decrease in Zn immobilization. The results suggest that all the components examined here as either complexing agents or electron shuttles reduce the degree of Zn immobilization by limiting the availability of Zn for incorporation into newly formed biogenic minerals. These results have implications for the remediation of heavy metals in a variety of natural sediments. PMID:16830547

  15. Preliminary evaluation of a microbial fuel cell treating artificial dialysis wastewater using graphene oxide

    NASA Astrophysics Data System (ADS)

    Goto, Yuko; Yoshida, Naoko

    2016-02-01

    Artificial dialysis wastewater (ADWW) generally contains 800-2,200 mg L-1 of organic matter. Prior to its discharge to the sewage system, ADWW must be treated in order to reduce organic matter to less than 600 mg L-1. This study assesses the applicability of a microbial fuel cell (MFC) to the reduction of organic matter in ADWW as an alternative pre-treatment system to aeration. In the MFC, conductive floccular aggregates microbially produced from graphene oxide (GO-flocs) were applied as an anode material in the MFC. The GO-flocs were obtained by anaerobic incubation of graphene oxide (GO) with microorganisms in ADWW at 28 °C for a minimum of 10 days. During incubation, GO in the mixture was transformed into black conductive floccular aggregates having 0.12 mS cm-1, suggesting the microbial reduction of GO to the reduced form. The produced GO-flocs were then used as the anode material in a cylindrical MFC, which was filled with ADWW and covered with a floating, platinum (Pt)-coated carbon cathode. The MFC was polarized via an external resistance of 10 Ω and applied for 120 days by replacing half of the supernatant of the MFC with fresh ADWW, every 6-9 days. As a result, the MFC achieved a 128 mg L-1 d-1 chemical oxygen demand (CODCr) removal rate. For example, the MFC contained 1,500 mg-CODCr L-1 just after replacement, with this concentration being reduced to 1,000 mg-CODCr L-1 after 6-9 days of incubation. At the same time, the MFC showed an average power density of 28 mW m-2 and a maximum power density of 291 mW m-2. These results suggest that a MFC packed with GO-flocs can be used as an alternative biotreatment system, replacing the energy-intensive aeration process.

  16. Characterization of microbial communities removing nitrogen oxides from flue gas: the BioDeNOx process.

    PubMed

    Kumaraswamy, Rajkumari; van Dongen, Udo; Kuenen, J Gijs; Abma, Wiebe; van Loosdrecht, Mark C M; Muyzer, Gerard

    2005-10-01

    BioDeNOx is an integrated physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gases. In this process, the flue gas is purged through a scrubber containing a solution of Fe(II)EDTA2-, which binds the NOx to form an Fe(II)EDTA.NO2- complex. Subsequently, this complex is reduced in the bioreactor to dinitrogen by microbial denitrification. Fe(II)EDTA2-, which is oxidized to Fe(III)EDTA- by oxygen in the flue gas, is regenerated by microbial iron reduction. In this study, the microbial communities of both lab- and pilot-scale reactors were studied using culture-dependent and -independent approaches. A pure bacterial strain, KT-1, closely affiliated by 16S rRNA analysis to the gram-positive denitrifying bacterium Bacillus azotoformans, was obtained. DNA-DNA homology of the isolate with the type strain was 89%, indicating that strain KT-1 belongs to the species B. azotoformans. Strain KT-1 reduces Fe(II)EDTA.NO2- complex to N2 using ethanol, acetate, and Fe(II)EDTA2- as electron donors. It does not reduce Fe(III)EDTA-. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene fragments showed the presence of bacteria closely affiliated with members of the phylum Deferribacteres, an Fe(III)-reducing group of bacteria. Fluorescent in situ hybridization with oligonucleotide probes designed for strain KT-1 and members of the phylum Deferribacteres showed that the latter were more dominant in both reactors. PMID:16204556

  17. Characterization of Microbial Communities Removing Nitrogen Oxides from Flue Gas: the BioDeNOx Process

    PubMed Central

    Kumaraswamy, Rajkumari; van Dongen, Udo; Kuenen, J. Gijs; Abma, Wiebe; van Loosdrecht, Mark C. M.; Muyzer, Gerard

    2005-01-01

    BioDeNOx is an integrated physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gases. In this process, the flue gas is purged through a scrubber containing a solution of Fe(II)EDTA2−, which binds the NOx to form an Fe(II)EDTA·NO2− complex. Subsequently, this complex is reduced in the bioreactor to dinitrogen by microbial denitrification. Fe(II)EDTA2−, which is oxidized to Fe(III)EDTA− by oxygen in the flue gas, is regenerated by microbial iron reduction. In this study, the microbial communities of both lab- and pilot-scale reactors were studied using culture-dependent and -independent approaches. A pure bacterial strain, KT-1, closely affiliated by 16S rRNA analysis to the gram-positive denitrifying bacterium Bacillus azotoformans, was obtained. DNA-DNA homology of the isolate with the type strain was 89%, indicating that strain KT-1 belongs to the species B. azotoformans. Strain KT-1 reduces Fe(II)EDTA·NO2− complex to N2 using ethanol, acetate, and Fe(II)EDTA2− as electron donors. It does not reduce Fe(III)EDTA−. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene fragments showed the presence of bacteria closely affiliated with members of the phylum Deferribacteres, an Fe(III)-reducing group of bacteria. Fluorescent in situ hybridization with oligonucleotide probes designed for strain KT-1 and members of the phylum Deferribacteres showed that the latter were more dominant in both reactors. PMID:16204556

  18. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts

    PubMed Central

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0–3 mm, transitional zone (TZ) 3–7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98–0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86–113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem. PMID:27625645

  19. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts.

    PubMed

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0-3 mm, transitional zone (TZ) 3-7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98-0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86-113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem. PMID:27625645

  20. NATURAL ARSENIC CONTAMINATION OF HOLOCENE ALLUVIAL AQUIFERS BY LINKED TECTONIC, WEATHERING, AND MICROBIAL PROCESSES

    EPA Science Inventory

    Linked tectonic, geochemical, and biologic processes lead to natural arsenic contamination of groundwater in Holocene alluvial aquifers, which are the main threat to human health around the world. These groundwaters are commonly found a long distance from their ultimate source of...

  1. Heart disease link to fetal hypoxia and oxidative stress.

    PubMed

    Giussani, Dino A; Niu, Youguo; Herrera, Emilio A; Richter, Hans G; Camm, Emily J; Thakor, Avnesh S; Kane, Andrew D; Hansell, Jeremy A; Brain, Kirsty L; Skeffington, Katie L; Itani, Nozomi; Wooding, F B Peter; Cross, Christine M; Allison, Beth J

    2014-01-01

    The quality of the intrauterine environment interacts with our genetic makeup to shape the risk of developing disease in later life. Fetal chronic hypoxia is a common complication of pregnancy. This chapter reviews how fetal chronic hypoxia programmes cardiac and endothelial dysfunction in the offspring in adult life and discusses the mechanisms via which this may occur. Using an integrative approach in large and small animal models at the in vivo, isolated organ, cellular and molecular levels, our programmes of work have raised the hypothesis that oxidative stress in the fetal heart and vasculature underlies the mechanism via which prenatal hypoxia programmes cardiovascular dysfunction in later life. Developmental hypoxia independent of changes in maternal nutrition promotes fetal growth restriction and induces changes in the cardiovascular, metabolic and endocrine systems of the adult offspring, which are normally associated with disease states during ageing. Treatment with antioxidants of animal pregnancies complicated with reduced oxygen delivery to the fetus prevents the alterations in fetal growth, and the cardiovascular, metabolic and endocrine dysfunction in the fetal and adult offspring. The work reviewed offers both insight into mechanisms and possible therapeutic targets for clinical intervention against the early origin of cardiometabolic disease in pregnancy complicated by fetal chronic hypoxia. PMID:25015802

  2. Methanobactin and the Link between Copper and Bacterial Methane Oxidation.

    PubMed

    DiSpirito, Alan A; Semrau, Jeremy D; Murrell, J Colin; Gallagher, Warren H; Dennison, Christopher; Vuilleumier, Stéphane

    2016-06-01

    Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs. PMID:26984926

  3. A pan-Precambrian link between deglaciation and environmental oxidation

    USGS Publications Warehouse

    Raub, T.J.; Kirschvink, J.L.

    2007-01-01

    Despite a continuous increase in solar luminosity to the present, Earth’s glacial record appears to become more frequent, though less severe, over geological time. At least two of the three major Precambrian glacial intervals were exceptionally intense, with solid evidence for widespread sea ice on or near the equator, well within a “Snowball Earth” zone produced by ice-albedo runaway in energy-balance models. The end of the first unambiguously low-latitude glaciation, the early Paleoproterozoic Makganyene event, is associated intimately with the first solid evidence for global oxygenation, including the world’s largest sedimentary manganese deposit. Subsequent low-latitude deglaciations during the Cryogenian interval of the Neoproterozoic Era are also associated with progressive oxidation, and these young Precambrian ice ages coincide with the time when basal animal phyla were diversifying. However, specifically testing hypotheses of cause and effect between Earth’s Neoproterozoic biosphere and glaciation is complicated because large and rapid True Polar Wander events appear to punctuate Neoproterozoic time and may have episodically dominated earlier and later intervals as well, rendering geographic reconstruction and age correlation challenging except for an exceptionally well-defined global paleomagnetic database.

  4. Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction

    PubMed Central

    Hansel, Colleen M.; Zeiner, Carolyn A.; Santelli, Cara M.; Webb, Samuel M.

    2012-01-01

    Manganese (Mn) oxides are among the most reactive minerals within the environment, where they control the bioavailability of carbon, nutrients, and numerous metals. Although the ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides is scattered throughout the bacterial and fungal domains of life, the mechanism and physiological basis for Mn(II) oxidation remains an enigma. Here, we use a combination of compound-specific chemical assays, microspectroscopy, and electron microscopy to show that a common Ascomycete filamentous fungus, Stilbella aciculosa, oxidizes Mn(II) to Mn oxides by producing extracellular superoxide during cell differentiation. The reactive Mn oxide phase birnessite and the reactive oxygen species superoxide and hydrogen peroxide are colocalized at the base of asexual reproductive structures. Mn oxide formation is not observed in the presence of superoxide scavengers (e.g., Cu) and inhibitors of NADPH oxidases (e.g., diphenylene iodonium chloride), enzymes responsible for superoxide production and cell differentiation in fungi. Considering the recent identification of Mn(II) oxidation by NADH oxidase-based superoxide production by a common marine bacterium (Roseobacter sp.), these results introduce a surprising homology between some prokaryotic and eukaryotic organisms in the mechanisms responsible for Mn(II) oxidation, where oxidation appears to be a side reaction of extracellular superoxide production. Given the versatility of superoxide as a redox reactant and the widespread ability of fungi to produce superoxide, this microbial extracellular superoxide production may play a central role in the cycling and bioavailability of metals (e.g., Hg, Fe, Mn) and carbon in natural systems. PMID:22802654

  5. Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction

    SciTech Connect

    Hansel, C. M.; Zeiner, C. A.; Santelli, C. M.; Webb, S. M.

    2012-07-16

    Manganese (Mn) oxides are among the most reactive minerals within the environment, where they control the bioavailability of carbon, nutrients, and numerous metals. Although the ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides is scattered throughout the bacterial and fungal domains of life, the mechanism and physiological basis for Mn(II) oxidation remains an enigma. Here, we use a combination of compound-specific chemical assays, microspectroscopy, and electron microscopy to show that a common Ascomycete filamentous fungus, Stilbella aciculosa, oxidizes Mn(II) to Mn oxides by producing extracellular superoxide during cell differentiation. The reactive Mn oxide phase birnessite and the reactive oxygen species superoxide and hydrogen peroxide are colocalized at the base of asexual reproductive structures. Mn oxide formation is not observed in the presence of superoxide scavengers (e.g., Cu) and inhibitors of NADPH oxidases (e.g., diphenylene iodonium chloride), enzymes responsible for superoxide production and cell differentiation in fungi. Considering the recent identification of Mn(II) oxidation by NADH oxidase-based superoxide production by a common marine bacterium (Roseobacter sp.), these results introduce a surprising homology between some prokaryotic and eukaryotic organisms in the mechanisms responsible for Mn(II) oxidation, where oxidation appears to be a side reaction of extracellular superoxide production. Finally, given the versatility of superoxide as a redox reactant and the widespread ability of fungi to produce superoxide, this microbial extracellular superoxide production may play a central role in the cycling and bioavailability of metals (e.g., Hg, Fe, Mn) and carbon in natural systems.

  6. Microbiological aspects of ethylene oxide sterilization. II. Microbial resistance to ethylene oxide.

    PubMed

    Kereluk, K; Gammon, R A; Lloyd, R S

    1970-01-01

    The death rate kinetics of several sporeforming and nonsporeforming microorganisms, including radiation-resistant cocci, were determined by exposing them to a mixture of ethylene oxide and dichlorodifluoromethane (500 mg of ethylene oxide per liter, 30 to 50% relative humidity, and 54.4 C). Spore survivor curves obtained from tests of inoculated and exposed hygroscopic and nonhygroscopic carriers showed that the spores of Bacillus subtilis var. niger are more resistant to ethylene oxide than are spores of Clostridium sporogenes, B. stearothermophilus, and B. pumilus. The decimal reduction times (expressed as D values at 54.4 C-500 mg of ethylene oxide per liter) obtained under the test conditions for B. subtilis var. niger spores on hygroscopic and nonhygroscopic carriers exceeded the values obtained for the other organisms considered, both sporeformers and nonsporeformers. The decimal reduction times for the vegetative cells of the radiation-resistant organisms (Micrococcus radiodurans and two strains of Streptococcus faecalis) and the ATCC strain of S. faecalis demonstrated comparable resistance to ethylene oxide with the spores of C. sporogenes, B. stearothermophilus, and B. pumilus, but not those of B. subtilis var. niger. PMID:5415211

  7. In situ TEM tensile testing of carbon-linked graphene oxide nanosheets using a MEMS device

    NASA Astrophysics Data System (ADS)

    Cao, Changhong; Howe, Jane Y.; Perovic, Doug; Filleter, Tobin; Sun, Yu

    2016-07-01

    This paper reports in situ transmission electron microscopy (TEM) tensile testing of carbon-linked graphene oxide nanosheets using a monolithic TEM compatible microelectromechanical system device. The set-up allows direct on-chip nanosheet thickness mapping, high resolution electron beam linking of a pre-fractured nanosheet, and mechanical tensile testing of the nanosheet. This technique enables simultaneous mechanical and high energy electron beam characterization of 2D nanomaterials.

  8. In situ TEM tensile testing of carbon-linked graphene oxide nanosheets using a MEMS device.

    PubMed

    Cao, Changhong; Howe, Jane Y; Perovic, Doug; Filleter, Tobin; Sun, Yu

    2016-07-15

    This paper reports in situ transmission electron microscopy (TEM) tensile testing of carbon-linked graphene oxide nanosheets using a monolithic TEM compatible microelectromechanical system device. The set-up allows direct on-chip nanosheet thickness mapping, high resolution electron beam linking of a pre-fractured nanosheet, and mechanical tensile testing of the nanosheet. This technique enables simultaneous mechanical and high energy electron beam characterization of 2D nanomaterials. PMID:27256541

  9. Arsenite and ferrous iron oxidation linked to chemolithotrophic denitrification for the immobilization of arsenic in anoxic environments

    USGS Publications Warehouse

    Sun, W.; Sierra-Alvarez, R.; Milner, L.; Oremland, R.; Field, J.A.

    2009-01-01

    The objective of this study was to explore a bioremediation strategy based on injecting NO3- to support the anoxic oxidation of ferrous iron (Fe(II)) and arsenite (As(III)) in the subsurface as a means to immobilize As in the form of arsenate (As(V)) adsorbed onto biogenic ferric (Fe(III)) (hydr)oxides. Continuous flows and filled columns were used to simulate a natural anaerobic groundwater and sediment system with co-occurring As(III) and Fe(II) in the presence (column SF1) or absence (column SF2) of nitrate, respectively. During operation for 250 days, the average influent arsenic concentration of 567 ??g L-1 was reduced to 10.6 (??9.6) ??g L-1 in the effluent of column SF1. The cumulative removal of Fe(II) and As(III) in SF1 was 6.5 to 10-fold higher than that in SF2. Extraction and measurement of the mass of iron and arsenic immobilized on the sand packing of the columns were close to the iron and arsenic removed from the aqueous phase during column operation. The dominant speciation of the immobilized iron and arsenic was Fe(III) and As(V) in SF1, compared with Fe(II) and As(III) in SF2. The speciation was confirmed by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The results indicate that microbial oxidation of As(III) and Fe(II) linked to denitrification resulted in the enhanced immobilization of aqueous arsenic in anaerobic environments by forming Fe(III) (hydr)oxide coated sands with adsorbed As(V). ?? 2009 American Chemical Society.

  10. Advanced Experiment Analysis of controls on Microbial FE(III) Oxide Reduction

    SciTech Connect

    Roden, Eric E.; Urrutia, Matilde M.

    1999-06-01

    Understanding factors which control the long-term survival and activity of Fe(III)-reducing bacteria (FeRB) in subsurface sedimentary environments is important for predicting the ability of these organisms to serve as agents for bioremediation of organic and inorganic contaminants. This project seeks to refine our quantitative understanding of microbiological and geochemical controls on bacterial Fe(III) oxide reduction and growth of FeRB, using laboratory reactor systems which mimic to varying degrees the physical and chemical conditions of subsurface sedimentary environments. Methods for studying microbial Fe(III) oxide reduction and FeRB growth in experimental systems which incorporate advective aqueous phase flux are being developed for this purpose. These methodologies, together with an accumulating database on the kinetics of Fe(III) reduction and bacterial growth with various synthetic and natural Fe(III) oxide minerals, will be applicable to experimental and modeling studies of subsurface contaminant transformations directly coupled to or influenced by bacterial Fe(III) oxide reduction activity.

  11. Responses of oxidation rate and microbial communities to methane in simulated landfill cover soil microcosms.

    PubMed

    He, Ruo; Ruan, Aidong; Jiang, Chenjing; Shen, Dong-Sheng

    2008-10-01

    CH4 oxidation capacities and microbial community structures developed in response to the presence of CH4 were investigated in two types of landfill cover soil microcosms, waste soil (fine material in stabilized waste) and clay soil. CH4 emission fluxes were lower in the waste soil cover over the course of the experiment. After exposure to CH4 flow for 120 days, the waste soil developed CH4 oxidation capacity from 0.53 to 11.25-13.48micromol CH4gd.w.(-1)h(-1), which was ten times higher than the clay soil. The topsoils of the two soil covers were observed dried and inhibited CH4 oxidation. The maximum CH4 oxidation rate occurred at the depth of 10-20cm in the waste soil cover (the middle layer), whereas it took place mainly at the depth of 20-30cm in the clay soil cover (the bottom layer). The amounts of the phospholipid fatty acid (PLFA) biomarks 16:1omega8c and 18:1omega8c for type I and II methanotrophs, respectively, showed that type I methanotrophic bacteria predominated in the clay soil, while the type II methanotrophic bacteria were abundant in the waste soil, and the highest population in the middle layer. The results also indicated that a greater active methanotrophic community was developed in the waste soil relative to the clay soil. PMID:18294841

  12. Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

    DOEpatents

    Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

    2014-06-24

    The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

  13. Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation.

    PubMed

    Werner, Jeffrey J; Garcia, Marcelo L; Perkins, Sarah D; Yarasheski, Kevin E; Smith, Samuel R; Muegge, Brian D; Stadermann, Frank J; DeRito, Christopher M; Floss, Christine; Madsen, Eugene L; Gordon, Jeffrey I; Angenent, Largus T

    2014-06-01

    Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity. PMID:24657858

  14. Potential impact of microbial activity on the oxidant capacity and organic carbon budget in clouds.

    PubMed

    Vaïtilingom, Mickael; Deguillaume, Laurent; Vinatier, Virginie; Sancelme, Martine; Amato, Pierre; Chaumerliac, Nadine; Delort, Anne-Marie

    2013-01-01

    Within cloud water, microorganisms are metabolically active and, thus, are expected to contribute to the atmospheric chemistry. This article investigates the interactions between microorganisms and the reactive oxygenated species that are present in cloud water because these chemical compounds drive the oxidant capacity of the cloud system. Real cloud water samples with contrasting features (marine, continental, and urban) were taken from the puy de Dôme mountain (France). The samples exhibited a high microbial biodiversity and complex chemical composition. The media were incubated in the dark and subjected to UV radiation in specifically designed photo-bioreactors. The concentrations of H(2)O(2), organic compounds, and the ATP/ADP ratio were monitored during the incubation period. The microorganisms remained metabolically active in the presence of ()OH radicals that were photo-produced from H(2)O(2). This oxidant and major carbon compounds (formaldehyde and carboxylic acids) were biodegraded by the endogenous microflora. This work suggests that microorganisms could play a double role in atmospheric chemistry; first, they could directly metabolize organic carbon species, and second, they could reduce the available source of radicals through their oxidative metabolism. Consequently, molecules such as H(2)O(2) would no longer be available for photochemical or other chemical reactions, which would decrease the cloud oxidant capacity. PMID:23263871

  15. Potential impact of microbial activity on the oxidant capacity and organic carbon budget in clouds

    NASA Astrophysics Data System (ADS)

    Vaïtilingom, Mickael; Deguillaume, Laurent; Vinatier, Virginie; Sancelme, Martine; Amato, Pierre; Chaumerliac, Nadine; Delort, Anne-Marie

    2013-01-01

    Within cloud water, microorganisms are metabolically active and, thus, are expected to contribute to the atmospheric chemistry. This article investigates the interactions between microorganisms and the reactive oxygenated species that are present in cloud water because these chemical compounds drive the oxidant capacity of the cloud system. Real cloud water samples with contrasting features (marine, continental, and urban) were taken from the puy de Dôme mountain (France). The samples exhibited a high microbial biodiversity and complex chemical composition. The media were incubated in the dark and subjected to UV radiation in specifically designed photo-bioreactors. The concentrations of H2O2, organic compounds, and the ATP/ADP ratio were monitored during the incubation period. The microorganisms remained metabolically active in the presence of ●OH radicals that were photo-produced from H2O2. This oxidant and major carbon compounds (formaldehyde and carboxylic acids) were biodegraded by the endogenous microflora. This work suggests that microorganisms could play a double role in atmospheric chemistry; first, they could directly metabolize organic carbon species, and second, they could reduce the available source of radicals through their oxidative metabolism. Consequently, molecules such as H2O2 would no longer be available for photochemical or other chemical reactions, which would decrease the cloud oxidant capacity.

  16. Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

    SciTech Connect

    Orphan, Victoria Jeanne

    2014-11-26

    Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions between microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of

  17. Oxidation increases mucin polymer cross-links to stiffen airway mucus gels

    PubMed Central

    Yuan, Shaopeng; Hollinger, Martin; Lachowicz-Scroggins, Marrah E.; Kerr, Sheena C.; Dunican, Eleanor M.; Daniel, Brian M.; Ghosh, Sudakshina; Erzurum, Serpel C.; Willard, Belinda; Hazen, Stanley L.; Huang, Xiaozhu; Carrington, Stephen D.; Oscarson, Stefan; Fahy, John V.

    2015-01-01

    Airway mucus in cystic fibrosis (CF) is highly elastic, but the mechanism behind this pathology is unclear. We hypothesized that the biophysical properties of CF mucus are altered because of neutrophilic oxidative stress. Using confocal imaging, rheology, and biochemical measures of inflammation and oxidation, we found that CF airway mucus gels have a molecular architecture characterized by a core of mucin covered by a web of DNA and a rheological profile characterized by high elasticity that can be normalized by chemical reduction. We also found that high levels of reactive oxygen species in CF mucus correlated positively and significantly with high concentrations of the oxidized products of cysteine (disulfide cross-links). To directly determine whether oxidation can cross-link mucins to increase mucus elasticity, we exposed induced sputum from healthy subjects to oxidizing stimuli and found a marked and thiol-dependent increase in sputum elasticity. Targeting mucin disulfide cross-links using current thiol-amino structures such as N-acetylcysteine (NAC) requires high drug concentrations to have mucolytic effects. We therefore synthesized a thiol-carbohydrate structure (methyl 6-thio-6-deoxy-α-D-galactopyranoside) and found that it had stronger reducing activity than NAC and more potent and fast-acting mucolytic activity in CF sputum. Thus, oxidation arising from airway inflammation or environmental exposure contributes to pathologic mucus gel formation in the lung, which suggests that it can be targeted by thiol-modified carbohydrates. PMID:25717100

  18. Oxidation increases mucin polymer cross-links to stiffen airway mucus gels.

    PubMed

    Yuan, Shaopeng; Hollinger, Martin; Lachowicz-Scroggins, Marrah E; Kerr, Sheena C; Dunican, Eleanor M; Daniel, Brian M; Ghosh, Sudakshina; Erzurum, Serpel C; Willard, Belinda; Hazen, Stanley L; Huang, Xiaozhu; Carrington, Stephen D; Oscarson, Stefan; Fahy, John V

    2015-02-25

    Airway mucus in cystic fibrosis (CF) is highly elastic, but the mechanism behind this pathology is unclear. We hypothesized that the biophysical properties of CF mucus are altered because of neutrophilic oxidative stress. Using confocal imaging, rheology, and biochemical measures of inflammation and oxidation, we found that CF airway mucus gels have a molecular architecture characterized by a core of mucin covered by a web of DNA and a rheological profile characterized by high elasticity that can be normalized by chemical reduction. We also found that high levels of reactive oxygen species in CF mucus correlated positively and significantly with high concentrations of the oxidized products of cysteine (disulfide cross-links). To directly determine whether oxidation can cross-link mucins to increase mucus elasticity, we exposed induced sputum from healthy subjects to oxidizing stimuli and found a marked and thiol-dependent increase in sputum elasticity. Targeting mucin disulfide cross-links using current thiol-amino structures such as N-acetylcysteine (NAC) requires high drug concentrations to have mucolytic effects. We therefore synthesized a thiol-carbohydrate structure (methyl 6-thio-6-deoxy-α-D-galactopyranoside) and found that it had stronger reducing activity than NAC and more potent and fast-acting mucolytic activity in CF sputum. Thus, oxidation arising from airway inflammation or environmental exposure contributes to pathologic mucus gel formation in the lung, which suggests that it can be targeted by thiol-modified carbohydrates. PMID:25717100

  19. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents.

    PubMed

    Sutton, Nora B; Atashgahi, Siavash; van der Wal, Jurgen; Wijn, Geert; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H M

    2015-01-01

    In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR) to monitor the abundance of OHRB (Dehalococcoides mccartyi, Dehalobacter, Geobacter, and Desulfitobacterium) and reductive dehalogenase genes (rdh; tceA, vcrA, and bvcA) at a field location contaminated with chlorinated solvents prior to and following treatment with sodium persulfate. Natural attenuation of the contaminants tetrachloroethene (PCE) and trichloroethene (TCE) observed prior to ISCO was confirmed by the distribution of OHRB and rdh genes. In wells impacted by persulfate treatment, a 1 to 3 order of magnitude reduction in the abundances of OHRB and complete absence of rdh genes was observed 21 days after ISCO. Groundwater acidification (pH<3) and increase in the oxidation reduction potential (>500 mV) due to persulfate treatment were significant and contributed to disruption of the microbial community. In wells only mildly impacted by persulfate, a slight stimulation of the microbial community was observed, with more than 1 order of magnitude increase in the abundance of Geobacter and Desulfitobacterium 36 days after ISCO. After six months, regeneration of the OHRB community occurred, however, neither D. mccartyi nor any rdh genes were observed, indicating extended disruption of biological natural attenuation (NA) capacity following persulfate treatment. For full restoration of biological NA activity, additional time may prove sufficient; otherwise addition electron donor amendment or bioaugmentation may be required. PMID:24898385

  20. Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.

    PubMed

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3) NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A · m(-3) NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation. PMID:23717427

  1. Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

    PubMed Central

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M. Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m−3 NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m−3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation. PMID:23717427

  2. Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands

    PubMed Central

    Hu, Bao-lan; Shen, Li-dong; Lian, Xu; Zhu, Qun; Liu, Shuai; Huang, Qian; He, Zhan-fei; Geng, Sha; Cheng, Dong-qing; Lou, Li-ping; Xu, Xiang-yang; Zheng, Ping; He, Yun-feng

    2014-01-01

    The process of nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and shown to be mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera). Here, evidence for n-damo in three different freshwater wetlands located in southeastern China was obtained using stable isotope measurements, quantitative PCR assays, and 16S rRNA and particulate methane monooxygenase gene clone library analyses. Stable isotope experiments confirmed the occurrence of n-damo in the examined wetlands, and the potential n-damo rates ranged from 0.31 to 5.43 nmol CO2 per gram of dry soil per day at different depths of soil cores. A combined analysis of 16S rRNA and particulate methane monooxygenase genes demonstrated that M. oxyfera-like bacteria were mainly present in the deep soil with a maximum abundance of 3.2 × 107 gene copies per gram of dry soil. It is estimated that ∼0.51 g of CH4 m−2 per year could be linked to the n-damo process in the examined wetlands based on the measured potential n-damo rates. This study presents previously unidentified confirmation that the n-damo process is a previously overlooked microbial methane sink in wetlands, and n-damo has the potential to be a globally important methane sink due to increasing nitrogen pollution. PMID:24616523

  3. Oxidative stress modulates mitochondrial failure and cyclophilin D function in X-linked adrenoleukodystrophy

    PubMed Central

    López-Erauskin, Jone; Galino, Jorge; Bianchi, Patrizia; Fourcade, Stéphane; Andreu, Antoni L.; Ferrer, Isidre; Muñoz-Pinedo, Cristina

    2012-01-01

    A common process associated with oxidative stress and severe mitochondrial impairment is the opening of the mitochondrial permeability transition pore, as described in many neurodegenerative diseases. Thus, inhibition of mitochondrial permeability transition pore opening represents a potential target for inhibiting mitochondrial-driven cell death. Among the mitochondrial permeability transition pore components, cyclophilin D is the most studied and has been found increased under pathological conditions. Here, we have used in vitro and in vivo models of X-linked adrenoleukodystrophy to investigate the relationship between the mitochondrial permeability transition pore opening and redox homeostasis. X-linked adrenoleukodystrophy is a neurodegenerative condition caused by loss of function of the peroxisomal ABCD1 transporter, in which oxidative stress plays a pivotal role. In this study, we provide evidence of impaired mitochondrial metabolism in a peroxisomal disease, as fibroblasts in patients with X-linked adrenoleukodystrophy cannot survive when forced to rely on mitochondrial energy production, i.e. on incubation in galactose. Oxidative stress induced under galactose conditions leads to mitochondrial damage in the form of mitochondrial inner membrane potential dissipation, ATP drop and necrotic cell death, together with increased levels of oxidative modifications in cyclophilin D protein. Moreover, we show increased expression levels of cyclophilin D in the affected zones of brains in patients with adrenomyeloneuropathy, in spinal cord of a mouse model of X-linked adrenoleukodystrophy (Abcd1-null mice) and in fibroblasts from patients with X-linked adrenoleukodystrophy. Notably, treatment with antioxidants rescues mitochondrial damage markers in fibroblasts from patients with X-linked adrenoleukodystrophy, including cyclophilin D oxidative modifications, and reverses cyclophilin D induction in vitro and in vivo. These findings provide mechanistic insight into the

  4. The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

    PubMed Central

    Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Glazer, Brian T.; Krepski, Sean T.; Emerson, David

    2016-01-01

    Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe

  5. The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments.

    PubMed

    Chan, Clara S; McAllister, Sean M; Leavitt, Anna H; Glazer, Brian T; Krepski, Sean T; Emerson, David

    2016-01-01

    Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe

  6. Formation of single domain magnetite by green rust oxidation promoted by microbial anaerobic nitrate-dependent iron oxidation

    NASA Astrophysics Data System (ADS)

    Miot, Jennyfer; Li, Jinhua; Benzerara, Karim; Sougrati, Moulay Tahar; Ona-Nguema, Georges; Bernard, Sylvain; Jumas, Jean-Claude; Guyot, François

    2014-08-01

    Biomineralization of magnetite is a central geomicrobiological process that might have played a primordial role over Earth’s history, possibly leaving traces of life in the geological record or controlling trace metal(loid)s and organic pollutants mobility in modern environments. Magnetite biomineralization has been attributed to two main microbial pathways to date (namely magnetotactic bacteria and dissimilatory iron-reducing bacteria). Here, we uncover a new route of magnetite biomineralization involving the anaerobic nitrate-reducing iron(II) oxidizing bacterium Acidovorax sp. strain BoFeN1. Using transmission electron microscopy, scanning transmission X-ray microscopy, transmission Mössbauer spectroscopy and rock magnetic analyses, this strain is shown to promote the transformation of hydroxychloride green rust in equilibrium with dissolved Fe(II) to (1) periplasmic lepidocrocite (γ-FeOOH) and (2) extracellular magnetite, thus leading to strong redox heterogeneities at the nanometer scale. On the one hand, lepidocrocite was associated with protein moieties and exhibited an anisotropic texture, with the elongated axis parallel to the cell wall. On the other hand, magnetite crystals exhibited grain sizes and magnetic properties consistent with stable single domain particles. By comparison, abiotic controls led to a very slow (4 months vs. 2 days in BoFeN1 cultures) and incomplete oxidation of hydroxychloride green rust towards magnetite. As this abiotic magnetite exhibited the same size and magnetic properties (stable single domain particles) as magnetite produced in BoFeN1 cultures, only the co-occurrence of textured Fe(III)-oxides and magnetite, associated with the persistence of organic carbon molecules, might constitute valuable biosignatures to be looked for in the geological record. Our results furthermore contribute to a more complex picture of Fe redox cycling in the environment, providing an additional process of Fe(II)-bearing phase

  7. Microbial cycling, oxidative weathering, and the triple oxygen isotope consequences for marine sulfate

    NASA Astrophysics Data System (ADS)

    Johnston, D. T.; Cowie, B.; Turchyn, A. V.; Antler, G.; Gill, B. C.; Berelson, W.

    2015-12-01

    Microorganisms are responsible for most geochemical sulfur cycling in the ocean. On both modern and geological time scales, stable isotope ratios often serve as a mechanism to track conspicuous or coupled microbial processes, which in turn inform burial fluxes. The most common example of this approach is the use of sulfur isotopes in sulfate and sulfide (both aqueous and in mineral form) to track everything from rates of microbial processes through to the presence/absence of certain metabolic processes in a given environment. The use of oxygen isotope ratios in sulfate has developed in a similar fashion, providing complementary information to that of sulfur isotopes. Through our current work, we will extend the application of oxygen isotopes to include the trace stable oxygen isotope, 17O. These data are facilitated by a new laser F2 fluorination technique running at Harvard, and accompanied by the calibration of a suite of common sulfate standards. At first blush, 16O - 17O - 18O systematics should carry mass-dependent microbial fractionations with process-specific mass laws that are resolvable at the level of our analytical precision. We look to calibrate these biogeochemical effects through the integrated picture captured in marine pore water sulfate profiles, where the 18O/16O is known to evolve. In compliment, riverine sulfate (the sulfate input to the ocean) is an oxidative weathering product and is posited to carry a memory effect of tropospheric O2. Interestingly, the 17O/16O of that O2 carries a mass-independent signal reflecting the balance between stratospheric reactions and Earth surface biospheric fluxes. Through this presentation, we look to calibrate the controls on the balance between biospheric and atmospheric contributions to the marine sulfate reservoir. This is enabled by a series of isotope mass-balance models and with the ultimate goal of developing the geological triple oxygen isotope records of sulfate as a new environmental proxy for paleo

  8. Distribution of Microbial Arsenic Reduction, Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations

    PubMed Central

    Escudero, Lorena V.; Casamayor, Emilio O.; Chong, Guillermo; Pedrós-Alió, Carles; Demergasso, Cecilia

    2013-01-01

    The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations. PMID:24205341

  9. Ferrous iron removal promotes microbial reduction of crystalline iron(III) oxides

    SciTech Connect

    Roden, E.E.; Urrutia, M.M.

    1999-06-01

    Semicontinuous cultures were used to assess the effect of aqueous Fe(II) removal on the dissimilatory reduction of crystalline Fe(III) oxides by Shewanella alga strain BrY. Aqueous phase replacement in semicontinuous cultures resulted in a 2--3-fold increase in the cumulative amount of Fe(II) produced from synthetic goethite reduction over a 2-month incubation period, compared to parallel batch cultures. A more modest (maximum 30%) but significant stimulation of natural subsoil Fe(III) oxide reduction was observed. The extended Fe(III) reduction resulted from enhanced generation of aqueous Fe(II) which was periodically removed from the cultures. A concomitant stimulation of bacterial protein production was detected, which suggested that Fe(II) removal also promoted bacterial growth. A simulation model in which Fe(II) sorption to the solid-phase resulted in blockage of surface reduction sites captured the contrasting behavior of the batch vs semicontinuous Gt reduction systems. The findings indicate that elimination of Fe(II) via advective transport could play a significant role in governing the rate and extent of microbial Fe(III) oxide reduction in sedimentary environments.

  10. Quinone-mediated microbial synthesis of reduced graphene oxide with peroxidase-like activity.

    PubMed

    Liu, Guangfei; Zhang, Xin; Zhou, Jiti; Wang, Aijie; Wang, Jing; Jin, Ruofei; Lv, Hong

    2013-12-01

    The effects of different quinones on graphene oxide (GO) reduction by Shewanella oneidensis MR-1 and the peroxidase activity of the resultant reduced graphene oxide (QRGO) were studied. The presence of 100 μM anthraquinone-2-sulfonate (AQS), anthraquinone-2,6-disulfonate and 5-hydroxy-1,4-naphthoquinone could lead to 1.6-2.8-fold increase in GO reduction rate, whereas anthraquinone-2-carboxylate slowed down the reduction. The stimulating effects of AQS increased with the increase of its concentration (10-100 μM). The mediated effects were proved by direct GO reduction by microbially reduced AQS. The mediated reduction of GO to QRGO was characterized by UV-vis, XRD, FTIR, Raman spectra, XPS, TEM and AFM, respectively. The as-prepared QRGO possessed peroxidase-like activity, which could catalyze the oxidation of 3,3'5,5'-tetramethylbenzidine by H2O2, and followed Michealis-Menten kinetics. A colorimetric sensor for quantitative determination of glucose based on the peroxidase activity of QRGO was developed over a range of 1-120 μM with a detection limit of 1 μM. PMID:24140856

  11. The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia.

    PubMed

    Rawlings, Douglas E; Johnson, D Barrie

    2007-02-01

    Biomining, the use of micro-organisms to recover precious and base metals from mineral ores and concentrates, has developed into a successful and expanding area of biotechnology. While careful considerations are made in the design and engineering of biomining operations, microbiological aspects have been subjected to far less scrutiny and control. Biomining processes employ microbial consortia that are dominated by acidophilic, autotrophic iron- or sulfur-oxidizing prokaryotes. Mineral biooxidation takes place in highly aerated, continuous-flow, stirred-tank reactors or in irrigated dump or heap reactors, both of which provide an open, non-sterile environment. Continuous-flow, stirred tanks are characterized by homogeneous and constant growth conditions where the selection is for rapid growth, and consequently tank consortia tend to be dominated by two or three species of micro-organisms. In contrast, heap reactors provide highly heterogeneous growth environments that change with the age of the heap, and these tend to be colonized by a much greater variety of micro-organisms. Heap micro-organisms grow as biofilms that are not subject to washout and the major challenge is to provide sufficient biodiversity for optimum performance throughout the life of a heap. This review discusses theoretical and pragmatic aspects of assembling microbial consortia to process different mineral ores and concentrates, and the challenges for using constructed consortia in non-sterile industrial-scale operations. PMID:17259603

  12. Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

    NASA Astrophysics Data System (ADS)

    Patil, Rajendra; Gholap, Haribhau; Warule, Sambhaji; Banpurkar, Arun; Kulkarni, Gauri; Gade, Wasudeo

    2015-01-01

    The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet-visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications.

  13. Application of electrolysis to stimulate microbial reductive PCE dechlorination and oxidative VC biodegradation.

    PubMed

    Lohner, Svenja T; Tiehm, Andreas

    2009-09-15

    A novel approach was applied to stimulate biodegradation of chloroethenes bya coupled bioelectro-process. In a flow-through column system, microbial dechlorination of tetrachloroethene to cis-dichloroethene, vinyl chloride, and ethene was stimulated by hydrogen produced by water electrolysis. Dechlorinating bacteria (Dehalococcoides spp. and Desulfitobacterium spp.) and also methanogens and homoacetogens were detected in the anaerobic column. Simultaneously, oxidative biodegradation of lower chlorinated metabolites (vinyl chloride) was stimulated by electrolytic oxygen formation in the corresponding aerobic column. The process was stable for more than 100 days and an average removal of approximately 23 micromol/d PCE and 72 micromo/d vinyl chloride was obtained with a current density of 0.05 mA/cm2. Abiotic electrochemical degradation of the contaminants was not observed. Microbial dechlorination correlated with the current densities in the applied range of 0.01-0.05 mA/cm2. The results are promising for environmental applications, since with electrolysis hydrogen and oxygen can be supplied continuously to chloroethene degrading microorganisms, and the supply rates can be easily controlled by adjusting the electric current. PMID:19806748

  14. Microbiome-wide association studies link dynamic microbial consortia to disease.

    PubMed

    Gilbert, Jack A; Quinn, Robert A; Debelius, Justine; Xu, Zhenjiang Z; Morton, James; Garg, Neha; Jansson, Janet K; Dorrestein, Pieter C; Knight, Rob

    2016-07-01

    Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of its links with disease. In particular, time-series studies and multiple molecular perspectives are facilitating microbiome-wide association studies, which are analogous to genome-wide association studies. Early findings point to actionable outcomes of microbiome-wide association studies, although their clinical application has yet to be approved. An appreciation of the complexity of interactions among the microbiome and the host's diet, chemistry and health, as well as determining the frequency of observations that are needed to capture and integrate this dynamic interface, is paramount for developing precision diagnostics and therapies that are based on the microbiome. PMID:27383984

  15. New Aptes Cross-linked Polymers from Poly(ethylene oxide)s and Cyanuric Chloride for Lithium Batteries

    NASA Technical Reports Server (NTRS)

    Tigelaar, Dean M.; Meador, Mary Ann B.; Kinder, James D.; Bennett, William R.

    2005-01-01

    A new series of polymer electrolytes for use as membranes for lithium batteries are described. Electrolytes were made by polymerization between cyanuric chloride and diamino-terminated poly(ethylene oxide)s, followed by cross-linking via a sol-gel process. Thermal analysis and lithium conductivity of freestanding polymer films were studied. The effects of several variables on conductivity were investigated, such as length of backbone PEO chain, length of branching PEO chain, extent of branching, extent of cross-linking, salt content, and salt counterion. Polymer films with the highest percentage of PEO were found to be the most conductive, with a maximum lithium conductivity of 3.9 x 10(exp -5) S/cm at 25 C. Addition of plasticizer to the dry polymers increased conductivity by an order of magnitude.

  16. MICROBIAL RESPONSES TO IN SITU CHEMICAL OXIDATION, SIX-PHASE HEATING, AND STEAM INJECTION REMEDIATION TECHNOLOGIES IN GROUND WATER

    EPA Science Inventory

    The evaluation of microbial responses to three in situ source removal remedial technologies including permanganate-based in-situ chemical oxidation (ISCO), six-phase heating (SPH), and steam injection (SI) was performed at Cape Canaveral Air Station in Florida. The investigatio...

  17. Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

    PubMed

    Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

    2013-10-01

    The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. PMID:23673133

  18. Microbially mediated formation of a new REE enriched Mn-oxide, Ytterby mine, Sweden

    NASA Astrophysics Data System (ADS)

    Sjöberg, Susanne; Allard, Bert; Rattray, Jayne E.; Callac, Nolwenn; Skelton, Alasdair; Ivarsson, Magnus; Karlsson, Stefan; Sjöberg, Viktor; Dupraz, Christophe

    2016-04-01

    Characterization of a black substance seeping from fractured bedrock in a subterranean tunnel revealed a new, microbially mediated, secondary manganese oxide mineralisation, highly enriched in rare earth elements (REEs). This tunnel is dry and at shallow depth and was built to convert the former Ytterby mine, known for the discovery of yttrium (Y), scandium (Sc) and five rare earth elements, into a fuel deposit for the Swedish Armed Forces. As the type locality of these rare earth elements, the Ytterby mine gave its name to yttrium, ytterbium, erbium and terbium. Geochemical analysis shows that the substance is enriched in REEs with concentrations one to two orders of magnitude higher than the surrounding rocks. Elemental analysis and X-ray diffraction establish that the main component is a manganese oxide of the birnessite type (general formula: [Na,Ca]0.5[Mn(III),Mn(IV)]2O4xAq). There are also minor fractions of calcite, some other manganese oxides, feldspars, quartz and about 1% organic matter, but no iron oxides. Leaching studies (sequential and selective) were performed in order to establish how the minor components are associated with the matrix (in the lattice or merely adsorbed on the outer surface). It shows that the Ytterby birnessite contains about 1% REEs in the lattice, as well as calcium but no sodium. Formation of birnessite by manganese oxidizing bacteria is well-known (e.g. Tebo et al, 2004). Quantitative PCR shows that the total number of bacteria in the Ytterby substance is in the order 1010 cells per g substance while the water feeding the fracture has in the order of 106 cells per ml groundwater. qPCR data further confirm that manganese oxidizing microorganisms are present and that the abundance varies with the seasons. Analysis of the precipitated manganese using electron paramagnetic resonance spectroscopy shows that the substance is composed of two or more components, with one part having a biogenic signature. The occurrence of C31 to C35

  19. Investigation of an Iron-Oxidizing Microbial Mat Community Located near Aarhus, Denmark: Laboratory Studies

    PubMed Central

    Emerson, David; Revsbech, Niels Peter

    1994-01-01

    We constructed a small flow chamber in which suboxic medium containing 60 to 120 μM FeCl2 flowed up through a sample well into an aerated reservoir, thereby creating an suboxic-oxic interface similar to the physicochemical conditions that exist in natural iron seeps. When microbial mat material from the Marselisborg iron seep that contained up to 109 bacterial cells per cm3 (D. Emerson and N. P. Revsbech, Appl. Environ. Microbiol. 60:4022-4031, 1994) was placed in the sample well of the chamber, essentially all of the Fe2+ flowing through the sample well was oxidized at rates of up to 1,200 nmol of Fe2+ oxidized per h per cm3 of mat material. The oxidation rates of samples of the mat that were pasteurized prior to inoculation were only about 20 to 50% of the oxidation rates of unpasteurized samples. Sodium azide also significantly inhibited oxidation. These results suggest that at least 50% and up to 80% of the Fe oxidation in the chamber were actively mediated by the microbes in the mat. It also appeared that Fe stimulated the growth of the community since chambers fed with FeCl2 accumulated masses of either filamentous or particulate growth, both in the sample well and attached to the walls of the chamber. Control chambers that did not receive FeCl2 showed no sign of such growth. Furthermore, after 4 to 5 days the chambers fed with FeCl2 contained 35 to 75% more protein than chambers not supplemented with FeCl2. Leptothrix ochracea and, to a lesser extent, Gallionella spp. were responsible for the filamentous growth, and the sheaths and stalks, respectively, of these two organisms harbored large numbers of Fe-encrusted, nonappendaged unicellular bacteria. In chambers where particulate growth predominated, the unicellular bacteria alone appeared to be the primary agents of iron oxidation. These results provide the first clear evidence that the “iron bacteria” commonly found associated with neutral-pH iron seeps are responsible for most of the iron oxidation

  20. Development of Electroactive and Anaerobic Ammonium-Oxidizing (Anammox) Biofilms from Digestate in Microbial Fuel Cells.

    PubMed

    Di Domenico, Enea Gino; Petroni, Gianluca; Mancini, Daniele; Geri, Alberto; Di Palma, Luca; Ascenzioni, Fiorentina

    2015-01-01

    Microbial Fuel cells (MFCs) have been proposed for nutrient removal and energy recovery from different wastes. In this study the anaerobic digestate was used to feed H-type MFC reactors, one with a graphite anode preconditioned with Geobacter sulfurreducens and the other with an unconditioned graphite anode. The data demonstrate that the digestate acts as a carbon source, and even in the absence of anode preconditioning, electroactive bacteria colonise the anodic chamber, producing a maximum power density of 172.2 mW/m(2). The carbon content was also reduced by up to 60%, while anaerobic ammonium oxidation (anammox) bacteria, which were found in the anodic compartment of the reactors, contributed to nitrogen removal from the digestate. Overall, these results demonstrate that MFCs can be used to recover anammox bacteria from natural sources, and it may represent a promising bioremediation unit in anaerobic digestor plants for the simultaneous nitrogen removal and electricity generation using digestate as substrate. PMID:26273609

  1. Microbial oxidation of (-)-α-pinene to verbenol production by newly isolated strains.

    PubMed

    Rottava, Ieda; Cortina, Priscila F; Zanella, Camila A; Cansian, Rogerio L; Toniazzo, Geciane; Treichel, Helen; Antunes, Octavio A C; Oestreicher, Enrique G; de Oliveira, Debora

    2010-12-01

    Verbenol is a bicyclicbicycle secondary allylic alcohol, with pronounced camphor and mint flavor notes, mainly used as food flavoring. This compound is also used to control harmful insects, and hence has potential for using in agriculture, and is an intermediate in the synthesis of valuable perfume and medicinal substances. This work is focused on the microbial oxidation of (-)-α-pinene to verbenol production. To carry out the present study, 405 microorganisms were tested for their ability to bioconvert the substrate. From the isolated microorganisms, 193 were selected in the pre-screening using mineral medium for limonene degradation. At the screening step, 31 strains were able to convert (-)-α-pinene in verbenol. The highest concentration in verbenol from (-)-α-pinene was about 125.6 mg/L for yeast isolated from orange juice industrial residue. PMID:20526823

  2. Graphene oxide/carbon nanotube composite hydrogels-versatile materials for microbial fuel cell applications.

    PubMed

    Kumar, G Gnana; Hashmi, Saud; Karthikeyan, Chandrasekaran; GhavamiNejad, Amin; Vatankhah-Varnoosfaderani, Mohammad; Stadler, Florian J

    2014-11-01

    Carbonaceous nanocomposite hydrogels are prepared with an aid of a suspension polymerization method and are used as anodes in microbial fuel cells (MFCs). (Poly N-Isopropylacrylamide) (PNIPAM) hydrogels filled with electrically conductive carbonaceous nanomaterials exhibit significantly higher MFC efficiencies than the unfilled hydrogel. The observed morphological images clearly show the homogeneous dispersion of carbon nanotubes (CNTs) and graphene oxide (GO) in the PNIPAM matrix. The complex formation of CNTs and GO with NIPAM is evidenced from the structural characterizations. The effectual MFC performances are influenced by combining the materials of interest (GO and CNTs) and are attributed to the high surface area, number of active sites, and improved electron-transfer processes. The obtained higher MFC efficiencies associated with an excellent durability of the prepared hydrogels open up new possibilities for MFC anode applications. PMID:25228415

  3. Development of Electroactive and Anaerobic Ammonium-Oxidizing (Anammox) Biofilms from Digestate in Microbial Fuel Cells

    PubMed Central

    Di Domenico, Enea Gino; Petroni, Gianluca; Mancini, Daniele; Geri, Alberto; Palma, Luca Di; Ascenzioni, Fiorentina

    2015-01-01

    Microbial Fuel cells (MFCs) have been proposed for nutrient removal and energy recovery from different wastes. In this study the anaerobic digestate was used to feed H-type MFC reactors, one with a graphite anode preconditioned with Geobacter sulfurreducens and the other with an unconditioned graphite anode. The data demonstrate that the digestate acts as a carbon source, and even in the absence of anode preconditioning, electroactive bacteria colonise the anodic chamber, producing a maximum power density of 172.2 mW/m2. The carbon content was also reduced by up to 60%, while anaerobic ammonium oxidation (anammox) bacteria, which were found in the anodic compartment of the reactors, contributed to nitrogen removal from the digestate. Overall, these results demonstrate that MFCs can be used to recover anammox bacteria from natural sources, and it may represent a promising bioremediation unit in anaerobic digestor plants for the simultaneous nitrogen removal and electricity generation using digestate as substrate. PMID:26273609

  4. Iron isotope fractionation during microbial dissimilatory iron oxide reduction in simulated Archaean seawater.

    PubMed

    Percak-Dennett, E M; Beard, B L; Xu, H; Konishi, H; Johnson, C M; Roden, E E

    2011-05-01

    The largest Fe isotope excursion yet measured in marine sedimentary rocks occurs in shales, carbonates, and banded iron formations of Neoarchaean and Paleoproterozoic age. The results of field and laboratory studies suggest a potential role for microbial dissimilatory iron reduction (DIR) in producing this excursion. However, most experimental studies of Fe isotope fractionation during DIR have been conducted in simple geochemical systems, using pure Fe(III) oxide substrates that are not direct analogues to phases likely to have been present in Precambrian marine environments. In this study, Fe isotope fractionation was investigated during microbial reduction of an amorphous Fe(III) oxide-silica coprecipitate in anoxic, high-silica, low-sulphate artificial Archaean seawater at 30 °C to determine if such conditions alter the extent of reduction or isotopic fractionations relative to those observed in simple systems. The Fe(III)-Si coprecipitate was highly reducible (c. 80% reduction) in the presence of excess acetate. The coprecipitate did not undergo phase conversion (e.g. to green rust, magnetite or siderite) during reduction. Iron isotope fractionations suggest that rapid and near-complete isotope exchange took place among all Fe(II) and Fe(III) components, in contrast to previous work on goethite and hematite, where exchange was limited to the outer few atom layers of the substrate. Large quantities of low-δ(56)Fe Fe(II) (aqueous and solid phase) were produced during reduction of the Fe(III)-Si coprecipitate. These findings shed new light on DIR as a mechanism for producing Fe isotope variations observed in Neoarchaean and Paleoproterozoic marine sedimentary rocks. PMID:21504536

  5. Antibiotics and Manure Effects on Microbial Communities Responsible for Nitrous Oxide Emissions from Grasslands

    NASA Astrophysics Data System (ADS)

    Semedo, M.; Song, B.; Sparrer, T.; Crozier, C.; Tobias, C. R.; Phillips, R. L.

    2015-12-01

    Agroecosystems are major contributors of nitrous oxide (N2O) emissions. Denitrification and nitrification are the primary pathways of N2O emission in soils. However, there is uncertainty regarding the organisms responsible for N2O production. Bacteria were previously considered the only microbial N2O source, however, current studies indicate that fungi also produce N2O by denitrification. Denitrifying bacteria can be a source or sink of N2O depending on the presence and expression of nitrous oxide reductase genes (nosZ), encoding for the enzyme converting N2O to N2. Fungal denitrification may produce only N2O as an end product due to missing the nosZ gene. Animal manures applied to agricultural fields can transfer antibiotics to soils as a result of antibiotic use in the livestock industry. These antibiotics target mostly bacteria and may promote fungal growth. The growth inhibition of denitrifying bacteria may favor fungal denitrifiers potentially enhancing N2O emissions. Our objective is to examine the effects of antibiotic exposure and manure fertilization on the microbial communities responsible for N2 and N2O production in grasslands. Soil slurry incubations were conducted with tetracycline at different concentrations. A mesocosm experiment was also performed with soil cores exposed to tetracycline and cow manure. Production of N2O and N2 was measured using gas chromatography with electron capture detector (GC-ECD) and isotope ratio mass spectrometry (IRMS), respectively. Antibiotic inhibition of soil N2 production was found to be dose dependent, reaching up to 80% inhibition with 1g Kg-1 of tetracycline treatment, while N2O production was enhanced up to 8 times. These results suggest higher fungal denitrification with a concomitant decrease in bacterial denitrification after antibiotic exposure. We also found higher N2O fluxes in the soil mesocosms treated with manure plus tetracycline. Quantitative PCR (qPCR) will be conducted to examine the changes in

  6. Redox signalling directly regulates TDP-43 via cysteine oxidation and disulphide cross-linking.

    PubMed

    Cohen, Todd J; Hwang, Andrew W; Unger, Travis; Trojanowski, John Q; Lee, Virginia M Y

    2012-03-01

    TDP-43 is the major disease protein in ubiquitin-positive inclusions of amyotrophic lateral sclerosis and frontotemporal lobar degeneration (FTLD) characterized by TDP-43 pathology (FTLD-TDP). Accumulation of insoluble TDP-43 aggregates could impair normal TDP-43 functions and initiate disease progression. Thus, it is critical to define the signalling mechanisms regulating TDP-43 since this could open up new avenues for therapeutic interventions. Here, we have identified a redox-mediated signalling mechanism directly regulating TDP-43. Using in vitro and cell-based studies, we demonstrate that oxidative stress promotes TDP-43 cross-linking via cysteine oxidation and disulphide bond formation leading to decreased TDP-43 solubility. Biochemical analysis identified several cysteine residues located within and adjacent to the second RNA-recognition motif that contribute to both intra- and inter-molecular interactions, supporting TDP-43 as a target of redox signalling. Moreover, increased levels of cross-linked TDP-43 species are found in FTLD-TDP brains, indicating that aberrant TDP-43 cross-linking is a prominent pathological feature of this disease. Thus, TDP-43 is dynamically regulated by a redox regulatory switch that links oxidative stress to the modulation of TDP-43 and its downstream targets. PMID:22193716

  7. Redox signalling directly regulates TDP-43 via cysteine oxidation and disulphide cross-linking

    PubMed Central

    Cohen, Todd J; Hwang, Andrew W; Unger, Travis; Trojanowski, John Q; Lee, Virginia M Y

    2012-01-01

    TDP-43 is the major disease protein in ubiquitin-positive inclusions of amyotrophic lateral sclerosis and frontotemporal lobar degeneration (FTLD) characterized by TDP-43 pathology (FTLD-TDP). Accumulation of insoluble TDP-43 aggregates could impair normal TDP-43 functions and initiate disease progression. Thus, it is critical to define the signalling mechanisms regulating TDP-43 since this could open up new avenues for therapeutic interventions. Here, we have identified a redox-mediated signalling mechanism directly regulating TDP-43. Using in vitro and cell-based studies, we demonstrate that oxidative stress promotes TDP-43 cross-linking via cysteine oxidation and disulphide bond formation leading to decreased TDP-43 solubility. Biochemical analysis identified several cysteine residues located within and adjacent to the second RNA-recognition motif that contribute to both intra- and inter-molecular interactions, supporting TDP-43 as a target of redox signalling. Moreover, increased levels of cross-linked TDP-43 species are found in FTLD-TDP brains, indicating that aberrant TDP-43 cross-linking is a prominent pathological feature of this disease. Thus, TDP-43 is dynamically regulated by a redox regulatory switch that links oxidative stress to the modulation of TDP-43 and its downstream targets. PMID:22193716

  8. Iron Kinetics and Evolution of Microbial Populations in Low-pH, Ferrous Iron-Oxidizing Bioreactors.

    PubMed

    Jones, Rose M; Johnson, D Barrie

    2016-08-01

    Iron-rich, acidic wastewaters are commonplace pollutants associated with metal and coal mining. Continuous-flow bioreactors were commissioned and tested for their capacities to oxidize ferrous iron in synthetic and actual acid mine drainage waters using (initially) pure cultures of the recently described acidophilic, iron-oxidizing heterotrophic bacterium Acidithrix ferrooxidans grown in the presence of glucose and yeast extract. The bioreactors became rapidly colonized by this bacterium, which formed macroscopic streamer growths in the flowing waters. Over 97% of ferrous iron in pH 2.0-2.2 synthetic mine water was oxidized (at up to 225 mg L(-1) h(-1)) at dilution rates (D) of 0.6 h(-1). Rates of iron oxidation decreased with pH but were still significant, with influent liquors as low as pH 1.37. When fed with actual mine water, >90% of ferrous iron was oxidized at D values of 0.4 h(-1), and microbial communities within the bioreactors changed over time, with Atx. ferrooxidans becoming increasingly displaced by the autotrophic iron-oxidizing acidophiles Ferrovum myxofaciens, Acidithiobacillus ferrivorans, and Leptospirillum ferrooxidans (which were all indigenous to the mine water), although this did not have a negative impact on net ferrous-iron oxidation. The results confirmed the potential of using a heterotrophic acidophile to facilitate the rapid commissioning of iron-oxidizing bioreactors and illustrated how microbial communities within them can evolve without compromising the performances of the bioreactors. PMID:27377871

  9. [Analysis of microbial community structure at full-scale wastewater treatment plants by oxidation ditch].

    PubMed

    Guo, Yun; Yang, Dian-hai; Lu, Wen-jian

    2012-08-01

    The microbial populations of the oxidation ditch process at the full-scale municipal wastewater treatment plants (WWTP) in a city in north China were analyzed by fluorescent in situ hybridization (FISH). Fractions structure varieties and distribution characteristics of Accumulibacter as potential phosphorus accumulating organisms (PAOs), and Competibacter as potential glycogen accumulating organisms (GAOs) were quantified. The results indicated that Accumulibacter comprised around 2.0% +/- 0.6%, 3.4% +/- 0.6% and 3.5% +/- 1.2% of the total biomass in the anaerobic tank, anoxic zone and zone, respectively, while the corresponding values for Competibacter were 25.3% +/- 8.7%, 30.3% +/- 7.1% and 24.4% +/- 6.1%. Lower Accumulibacter fractions were found compared with previous full-scale reports (7%-22%), indicating low phosphorus removal efficiency in the oxidation ditch system. Statistical analysis indicated that the amount of PAOs was significantly higher in the anoxic zone and the aerobic zone compared with that in the anaerobic tank, while GAOs remained at the same level. PMID:23213894

  10. Simultaneous oxidation of arsenic and antimony at low and circumneutral pH, with and without microbial catalysis

    USGS Publications Warehouse

    Asta, M.P.; Kirk, Nordstrom D.; Blaine, McCleskey R.

    2012-01-01

    Arsenic and Sb are common mine-water pollutants and their toxicity and fate are strongly influenced by redox processes. In this study, simultaneous Fe(II), As(III) and Sb(III) oxidation experiments were conducted to obtain rates under laboratory conditions similar to those found in the field for mine waters of both low and circumneutral pH. Additional experiments were performed under abiotic sterile conditions to determine the biotic and abiotic contributions to the oxidation processes. The results showed that under abiotic conditions in aerated Fe(III)-H 2SO 4 solutions, Sb(III) oxidizes slightly faster than As(III). The oxidation rates of both elements were accelerated by increasing As(III), Sb(III), Fe(III), and Cl - concentrations in the presence of light. For unfiltered circumneutral water from the Giant Mine (Yellowknife, NWT, Canada), As(III) oxidized at 15-78??mol/L/h whereas Sb(III) oxidized at 0.03-0.05??mol/L/h during microbial exponential growth. In contrast, As(III) and Sb(III) oxidation rates of 0.01-0.03 and 0.01-0.02??mol/L/h, respectively, were obtained in experiments performed with acid unfiltered mine waters from the Iberian Pyritic Belt (SW Spain). These results suggest that the Fe(III) formed from microbial oxidation abiotically oxidized As(III) and Sb(III). After sterile filtration of both mine water samples, neither As(III), Sb(III), nor Fe(II) oxidation was observed. Hence, under the experimental conditions, bacteria were catalyzing As and Sb oxidation in the Giant Mine waters and Fe oxidation in the acid waters of the Iberian Pyrite Belt. ?? 2011 Elsevier Ltd.