Metabolite recycling and bidirectional C fluxes: Revolutionizing our view on microbial C cycling in soils

NASA Astrophysics Data System (ADS)

Dippold, M. A.; Apostel, C.; Kuzyakov, Y.

2016-12-01

Biogeochemists' view on microbial C transformation in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the anabolism. However, life in a C limited environment as challenging as soil requires microbial adaptation strategies at all levels of metabolism. By coupling of position-specific labeling of core metabolites with compound-specific isotope analysis we demonstrated that catabolic oxidation of these metabolites exists in parallel to reductive, energy consuming pathways, reducing them for anabolic purposes. Up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in the citric acid cycle. Furthermore, position-specific labeling of rather `cost-intensive' biomass compounds such as fatty acids revealed that intact recycling of metabolites is a crucial microbial adaptation to C scarcity in soils. Both processes are unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. To understand how microorganisms catalyze the biogeochemical fluxes in soil, a profound understanding of their metabolic adaptation strategies such as recycling or switching between bidirectional fluxes is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

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. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Designing and Creating a Synthetic Omega Oxidation Pathway in Saccharomyces cerevisiae Enables Production of Medium-Chain α, ω-Dicarboxylic Acids

PubMed Central

Han, Li; Peng, Yanfeng; Zhang, Yuangyuan; Chen, Wujiu; Lin, Yuping; Wang, Qinhong

2017-01-01

Medium-chain (C8–C14) α, ω-dicarboxylic acids (α, ω-DCAs), which have numerous applications as raw materials for producing various commodities and polymers in chemical industry, are mainly produced from chemical or microbial conversion of petroleum-derived alkanes or plant-derived fatty acids at present. Recently, significant attention has been gained to microbial production of medium-chain α, ω-DCAs from simple renewable sugars. Here, we designed and created a synthetic omega oxidation pathway in Saccharomyces cerevisiae to produce C10 and C12 α, ω-DCAs from renewable sugars and fatty acids by introducing a heterogeneous cytochrome P450 CYP94C1 and cytochrome reductase ATR1. Furthermore, the deletion of fatty acyl-CoA synthetase genes FAA1 and FAA4 increased the production of medium-chain α, ω-DCAs from 4.690 ± 0.088 mg/L to 12.177 ± 0.420 mg/L and enabled the production of C14 and C16 α, ω-DCAs at low percentage. But blocking β-oxidation pathway by deleting fatty-acyl coenzyme A oxidase gene POX1 and overexpressing different thioesterase genes had no significant impact on the production and the composition of α, ω-dicarboxylic acids. Overall, our study indicated the potential of microbial production of medium-chain α, ω-DCAs from renewable feedstocks using engineered yeast. PMID:29163455

Comparison of different two-pathway models for describing the combined effect of DO and nitrite on the nitrous oxide production by ammonia-oxidizing bacteria.

PubMed

Lang, Longqi; Pocquet, Mathieu; Ni, Bing-Jie; Yuan, Zhiguo; Spérandio, Mathieu

2017-02-01

The aim of this work is to compare the capability of two recently proposed two-pathway models for predicting nitrous oxide (N 2 O) production by ammonia-oxidizing bacteria (AOB) for varying ranges of dissolved oxygen (DO) and nitrite. The first model includes the electron carriers whereas the second model is based on direct coupling of electron donors and acceptors. Simulations are confronted to extensive sets of experiments (43 batches) from different studies with three different microbial systems. Despite their different mathematical structures, both models could well and similarly describe the combined effect of DO and nitrite on N 2 O production rate and emission factor. The model-predicted contributions for nitrifier denitrification pathway and hydroxylamine pathway also matched well with the available isotopic measurements. Based on sensitivity analysis, calibration procedures are described and discussed for facilitating the future use of those models.

Assessment of anti-oxidant activity of plant extracts using microbial test systems.

PubMed

Oktyabrsky, O; Vysochina, G; Muzyka, N; Samoilova, Z; Kukushkina, T; Smirnova, G

2009-04-01

To evaluate the anti-oxidant properties of extracts from 20 medicinal herbs growing in western Siberia using microbial test systems and different in vitro methods. In vivo anti-oxidant activity of extracts was evaluated for their capacity to protect bacteria, Escherichia coli, against bacteriostatic and bactericidal effects of H(2)O(2) and menadione, and action on anti-oxidant gene expression. In vitro anti-oxidant activity has been examined by a number of methods including: the 1,1-diphenyl-2-picrylhydrazyl radical (DPPH(*))-scavenging assay, chelating activity and capacity to protect plasmid DNA against oxidative damage. In addition, total polyphenol content was determined. The extracts of Fragaria vesca, Rosa majalis, Pentaphylloides fruticosa, Alchemilla vulgaris and Pulmonaria mollis possessed the highest levels of anti-oxidant activity in vivo and in vitro. The protective properties were more closely related to the DPPH(*) radical-scavenging activity, tannin content and action on anti-oxidant gene expression than to other parameters. The extracts of medicinal plants may have anti-oxidant effects on bacteria simultaneously through several different pathways, including direct inhibition of reactive oxygen species, iron chelation and anti-oxidant genes induction. Using microbial test systems, we revealed herbs that may be used as potential sources of natural anti-oxidants.

Iron Transformation Pathways and Redox Micro-Environments in Seafloor Sulfide-Mineral Deposits: Spatially Resolved Fe XAS and δ(57/54)Fe Observations.

PubMed

Toner, Brandy M; Rouxel, Olivier J; Santelli, Cara M; Bach, Wolfgang; Edwards, Katrina J

2016-01-01

Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50'N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffraction (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ(57)Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. These micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits.

Microbial methane from in situ biodegradation of coal and shale: A review and reevaluation of hydrogen and carbon isotope signatures

USGS Publications Warehouse

Vinson, David S.; Blair, Neal E.; Martini, Anna M.; Larter, Steve; Orem, William H.; McIntosh, Jennifer C.

2017-01-01

Stable carbon and hydrogen isotope signatures of methane, water, and inorganic carbon are widely utilized in natural gas systems for distinguishing microbial and thermogenic methane and for delineating methanogenic pathways (acetoclastic, hydrogenotrophic, and/or methylotrophic methanogenesis). Recent studies of coal and shale gas systems have characterized in situ microbial communities and provided stable isotope data (δD-CH4, δD-H2O, δ13C-CH4, and δ13C-CO2) from a wider range of environments than available previously. Here we review the principal biogenic methane-yielding pathways in coal beds and shales and the isotope effects imparted on methane, document the uncertainties and inconsistencies in established isotopic fingerprinting techniques, and identify the knowledge gaps in understanding the subsurface processes that govern H and C isotope signatures of biogenic methane. We also compare established isotopic interpretations with recent microbial community characterization techniques, which reveal additional inconsistencies in the interpretation of microbial metabolic pathways in coal beds and shales. Collectively, the re-assessed data show that widely-utilized isotopic fingerprinting techniques neglect important complications in coal beds and shales.Isotopic fingerprinting techniques that combine δ13C-CH4 with δD-CH4 and/or δ13C-CO2have significant limitations: (1) The consistent ~ 160‰ offset between δD-H2O and δD-CH4 could imply that hydrogenotrophic methanogenesis is the dominant metabolic pathway in microbial gas systems. However, hydrogen isotopes can equilibrate between methane precursors and coexisting water, yielding a similar apparent H isotope signal as hydrogenotrophic methanogenesis, regardless of the actual methane formation pathway. (2) Non-methanogenic processes such as sulfate reduction, Fe oxide reduction, inputs of thermogenic methane, anaerobic methane oxidation, and/or formation water interaction can cause the apparent carbon isotope fractionation between δ13C-CH4 and δ13C-CO2(α13CCO2-CH4) to differ from the true methanogenic fractionation, complicating interpretation of methanogenic pathways. (3) Where little-fractionating non-methanogenic bacterial processes compete with highly-fractionating methanogenesis, the mass balance between CH4 and CO2 is affected. This has implications for δ13C values and provides an alternative interpretation for net C isotope signatures than solely the pathways used by active methanogens. (4) While most of the reviewed values of δD-H2O - δD-CH4 and α13CCO2-CH4 are apparently consistent with hydrogenotrophic methanogenesis as the dominant pathway in coal beds and shales, recent microbial community characterization techniques suggest a possible role for acetoclastic or methylotrophic methanogenesis in some basins.

Nitrous oxide fluxes and soil oxygen dynamics of soil treated with cow urine

USDA-ARS?s Scientific Manuscript database

Ruminant urine deposition onto pastures creates hot-spots where emissions of nitrous oxide (N2O) are produced by aerobic and anaerobic microbial pathways. However, limited measurements of in situ soil oxygen (O2)-N2O relationships hinder the prediction of N2O emissions from urine-affected soil. This...

Comparative metagenomic analysis of the microbial communities in the surroundings of Iheya north and Iheya ridge hydrothermal fields reveals insights into the survival strategy of microorganisms in deep-sea environments

NASA Astrophysics Data System (ADS)

Wang, Hai-liang; Sun, Li

2018-04-01

In this study, metagenomic analysis was performed to investigate the taxonomic compositions and metabolic profiles of the microbial communities inhabiting the sediments in the surroundings of Iheya North and Iheya Ridge hydrothermal fields. The microbial communities in four different samples were found to be dominated by bacteria and, to a much lesser extent, archaea belonging to the phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Deinococcus-Thermus, and Nitrospirae, which play important roles in the cycling of carbon, nitrogen, and sulfur. All four microbial communities (i) contained chemoautotrophs and heterotrophs, the former probably fixed CO2 via various carbon fixation pathways, and the latter may degrade organic matters using nitrate and sulfate as electron acceptors, (ii) exhibited an abundance of DNA repair genes and bacterial sulfur oxidation mediated by reverse sulfate reduction, and (iii) harbored bacteria and archaea involved in anaerobic methane oxidation via intra-aerobic denitrification and reverse methanogenesis, which were found for the first time in hydrothermal areas. Furthermore, genes involved in DNA repair, reductive acetyl-CoA pathway, and ammonia metabolism were possibly affected by distance to the vent fields. These findings facilitate our understanding of the strategies of the microbial communities to adapt to the environments in deep sea areas associated with hydrothermal vents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toner, Brandy M.; Rouxel, Olivier J.; Santelli, Cara M.

Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50'N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffractionmore » (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ 57Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. Lastly, these micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits.« less

Microbial Fe biomineralization in mafic and ultramafic rocks

NASA Astrophysics Data System (ADS)

Templeton, A. S.; Mayhew, L.; McCollom, T.; Trainor, T.

2011-12-01

Fluid-filled microfractures within mafic and ultramafic rocks, such as basalt and peridotite, may be one of the most ubiquitous microbial habitats on the modern and ancient earth. In seafloor and subseafloor systems, one of the dominant energy sources is the oxidation of Fe by numerous potential oxidants under aerobic to anaerobic conditions. In particular, the oxidation of Fe may be directly catalyzed by microbial organisms, or result in the production of molecular hydrogen which can then fuel diverse lithotrophic metabolisms. However, it remains challenging to identify the dominant metabolic activities and unravel the microscale biogeochemical processes occuring within such rock-hosted systems. We are investigating the mechanisms of solid-state Fe-oxidation and biomineralization in basalt, olivine, pyroxenes and basalts, in the presence and absence of microbial organisms that can thrive across the full stability range of water. In this talk we will present synchrotron-based x-ray scattering and spectroscopic analyses of Fe speciation within secondary minerals formed during microbially-mediated vs. abiotic water-rock interactions. Determining the valence state and mineralogy of Fe-bearing phases is critical for determining the water-rock reaction pathways and identifying potential biominerals that may form; therefore, we will highlight new approaches for identifying key Fe transformations within complex geological media. In addition, many of our experimental studies involve the growth of lithotrophic biofilms on well-characterized mineral surfaces in order to determine the chemistry of the microbe-mineral interface during progressive electron-transfer reactions. By coupling x-ray spectroscopy, x-ray diffraction, and electron-microscopy measurements, we will also contrast the evolution of mineral surfaces that undergo microbially-mediated oxidative alteration against minerals surfaces that produce H2 to sustain anaerobic microbial communities.

Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, M.; Lamminmäki, T.; Itävaara, M.

2015-08-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is great but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. The great sequencing depth revealed that up to 95 and 99 % of the bacterial and archaeal communities, respectively, were composed of only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3 and 6 fold more bacterial and archaeal taxa. Several clusters of co-occurring rare taxa were identified, which correlated significantly with physicochemical parameters, such as salinity, concentration of inorganic or organic carbon, sulphur, pH and depth. The metabolic properties of the microbial communities were predicted using PICRUSt. The rough prediction showed that the metabolic pathways included commonly fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier conditions on Earth, but could also be induced again if changes in their living conditions occur. In this study only the rare taxa correlated with any physicochemical parameters. Thus these microorganisms can respond to environmental change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock environments.

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

PubMed Central

2012-01-01

Background The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status. Results Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. Conclusions This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis. PMID:23013615

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

NASA Astrophysics Data System (ADS)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

Microbial degradation of [C14C]polystyrene and 1,3-diphenylbutane.

PubMed

Sielicki, M; Focht, D D; Martin, J P

1978-07-01

Microbial degradation of [beta-14C]polystyrene and 1,3-diphenylbutane, a compound structurally representing the smallest repeating unit of styrene (dimer), was investigated in soil and liquid enrichment cultures. Degradation rates in soil, as determined by 14CO2 evolution from applied [14C]polystyrene, varied from 1.5 to 3.0% for a 4-month period. Although relatively low, these percentages were 15 to 30 times greater than values previously reported. Enrichment cultures, containing 1,3-diphenylbutane as the only carbon souce, were used to determine the mechanisms of microbial oxidation of the polymer chain ends. Metabolism of 1,3-diphenylbutane appeared to involve the attack by a monooxygenease to form 2-phenyl-4-hydroxyphenylbutane followed by a further oxidation and subsequent fission of the benzene ring to yield 4-phenylvaleric acid and an unidentified 5-carbon fragment via the classic meta-fission pathway. Phenylacetic acid was probably formed from 4-phenylvaleric acid by subsequent beta-oxidation of the side chain, methyl-oxidation and decarboxylation. An initial examination of the population of microorganisms in the diphenylbutane enrichment cultures indicated that these oxidative reactions are carried out by common soil microorganism of the genera Bacillus, Pseudomonas, Micrococcus, and Nocardia.

Iron Transformation Pathways and Redox Micro-Environments in Seafloor Sulfide-Mineral Deposits: Spatially Resolved Fe XAS and δ57/54Fe Observations

PubMed Central

Toner, Brandy M.; Rouxel, Olivier J.; Santelli, Cara M.; Bach, Wolfgang; Edwards, Katrina J.

2016-01-01

Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50′N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffraction (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ57Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. These micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits. PMID:27242685

Iron transformation pathways and redox micro-environments in seafloor sulfide-mineral deposits: Spatially resolved Fe XAS and δ 57/54Fe observations

DOE PAGES

Toner, Brandy M.; Rouxel, Olivier J.; Santelli, Cara M.; ...

2016-05-10

Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50'N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffractionmore » (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ 57Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. Lastly, these micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Tfaily, Malak M.; Crump, Alex R.

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically-bound (i.e., mineral and microbial) OC at terrestrial-aquatic interfaces. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in directmore » conflict with the concept of ‘priming’—that inputs of water-soluble and thermodynamically-favorable terrestrial OC protects bound-OC from oxidation. Based on our results, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.« less

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions.

PubMed

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, Paul M.

2000-01-01

 The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, P.M.

2000-01-01

The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

PubMed Central

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

Microbial fuel cells

DOEpatents

Nealson, Kenneth H; Pirbazari, Massoud; Hsu, Lewis

2013-04-09

A microbial fuel cell includes an anode compartment with an anode and an anode biocatalyst and a cathode compartment with a cathode and a cathode biocatalyst, with a membrane positioned between the anode compartment and the cathode compartment, and an electrical pathway between the anode and the cathode. The anode biocatalyst is capable of catalyzing oxidation of an organic substance, and the cathode biocatalyst is capable of catalyzing reduction of an inorganic substance. The reduced organic substance can form a precipitate, thereby removing the inorganic substance from solution. In some cases, the anode biocatalyst is capable of catalyzing oxidation of an inorganic substance, and the cathode biocatalyst is capable of catalyzing reduction of an organic or inorganic substance.

Nitric Oxide Production by the Human Intestinal Microbiota by Dissimilatory Nitrate Reduction to Ammonium

PubMed Central

Vermeiren, Joan; Van de Wiele, Tom; Verstraete, Willy; Boeckx, Pascal; Boon, Nico

2009-01-01

The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. 15N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells. PMID:19888436

Nitric oxide production by the human intestinal microbiota by dissimilatory nitrate reduction to ammonium.

PubMed

Vermeiren, Joan; Van de Wiele, Tom; Verstraete, Willy; Boeckx, Pascal; Boon, Nico

2009-01-01

The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. (15)N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells.

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

PubMed

Palomo, Alejandro; Jane Fowler, S; Gülay, Arda; Rasmussen, Simon; Sicheritz-Ponten, Thomas; Smets, Barth F

2016-11-01

Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.

Isotope signatures of N₂O in a mixed microbial population system: constraints on N₂O producing pathways in wastewater treatment.

PubMed

Wunderlin, Pascal; Lehmann, Moritz F; Siegrist, Hansruedi; Tuzson, Béla; Joss, Adriano; Emmenegger, Lukas; Mohn, Joachim

2013-02-05

We present measurements of site preference (SP) and bulk (15)N/(14)N ratios (δ(15)N(bulk)(N2O)) of nitrous oxide (N(2)O) by quantum cascade laser absorption spectroscopy (QCLAS) as a powerful tool to investigate N(2)O production pathways in biological wastewater treatment. QCLAS enables high-precision N(2)O isotopomer analysis in real time. This allowed us to trace short-term fluctuations in SP and δ(15)N(bulk)(N2O) and, hence, microbial transformation pathways during individual batch experiments with activated sludge from a pilot-scale facility treating municipal wastewater. On the basis of previous work with microbial pure cultures, we demonstrate that N(2)O emitted during ammonia (NH(4)(+)) oxidation with a SP of -5.8 to 5.6 ‰ derives mostly from nitrite (NO(2)(-)) reduction (e.g., nitrifier denitrification), with a minor contribution from hydroxylamine (NH(2)OH) oxidation at the beginning of the experiments. SP of N(2)O produced under anoxic conditions was always positive (1.2 to 26.1 ‰), and SP values at the high end of this spectrum (24.9 to 26.1 ‰) are indicative of N(2)O reductase activity. The measured δ(15)N(bulk)(N2O) at the initiation of the NH(4)(+) oxidation experiments ranged between -42.3 and -57.6 ‰ (corresponding to a nitrogen isotope effect Δδ(15)N = δ(15)N(substrate) - δ(15)N(bulk)(N2O) of 43.5 to 58.8 ‰), which is considerably higher than under denitrifying conditions (δ(15)N(bulk)(N2O) 2.4 to -17 ‰; Δδ(15)N = 0.1 to 19.5 ‰). During the course of all NH(4)(+) oxidation and nitrate (NO(3)(-)) reduction experiments, δ(15)N(bulk)(N2O) increased significantly, indicating net (15)N enrichment in the dissolved inorganic nitrogen substrates (NH(4)(+), NO(3)(-)) and transfer into the N(2)O pool. The decrease in δ(15)N(bulk)(N2O) during NO(2)(-) and NH(2)OH oxidation experiments is best explained by inverse fractionation during the oxidation of NO(2)(-) to NO(3)(-).

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

PubMed Central

Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin

2010-01-01

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs. PMID:20333304

The Response of Nitrifying Bacteria to Treatments of N-Serve and Roundup in Continuous-Flow Soil Columns

DTIC Science & Technology

1988-07-15

Science Society of America, Inc. Atlas , R. V. and R. Bartha . 1987. Microbial Ecology : Fundamentale and Applications, 2nd Edition. Benjamin/Cuynmings...Thompson and Troeh, 1978). However, many nutrient cycling pathways are mediated by only a few genera of bacteria ( Atlas and Bartha , 1987). So...mole of ammonium and nitrite oxidized, respectively ( Atlas and Bartha , 1987). Therefore, large amounts of substrate must be oxidized to provide

¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells.

PubMed

Luo, Shuai; Guo, Weihua; Nealson, Kenneth H; Feng, Xueyang; He, Zhen

2016-02-12

Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.

pH-dependent ammonia removal pathways in microbial fuel cell system.

PubMed

Kim, Taeyoung; An, Junyeong; Lee, Hyeryeong; Jang, Jae Kyung; Chang, In Seop

2016-09-01

In this work, ammonia removal paths in microbial fuel cells (MFCs) under different initial pH conditions (pH 7.0, 8.0, and 8.6) were investigated. At a neutral pH condition (pH 7.0), MFC used an electrical energy of 27.4% and removed 23.3% of total ammonia by electrochemical pathway for 192h. At the identical pH condition, 36.1% of the total ammonia was also removed by the biological path suspected to be biological ammonia oxidation process (e.g., Anammox). With the initial pH increased, the electrochemical removal efficiency decreased to less than 5.0%, while the biological removal efficiency highly increased to 61.8%. In this study, a neutral pH should be maintained in the anode to utilize MFCs for ammonia recovery via electrochemical pathways from wastewater stream. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reversal of β-oxidative pathways for the microbial production of chemicals and polymer building blocks.

PubMed

Kallscheuer, Nicolai; Polen, Tino; Bott, Michael; Marienhagen, Jan

2017-07-01

β-Oxidation is the ubiquitous metabolic strategy to break down fatty acids. In the course of this four-step process, two carbon atoms are liberated per cycle from the fatty acid chain in the form of acetyl-CoA. However, typical β-oxidative strategies are not restricted to monocarboxylic (fatty) acid degradation only, but can also be involved in the utilization of aromatic compounds, amino acids and dicarboxylic acids. Each enzymatic step of a typical β-oxidation cycle is reversible, offering the possibility to also take advantage of reversed metabolic pathways for applied purposes. In such cases, 3-oxoacyl-CoA thiolases, which catalyze the final chain-shortening step in the catabolic direction, mediate the condensation of an acyl-CoA starter molecule with acetyl-CoA in the anabolic direction. Subsequently, the carbonyl-group at C3 is stepwise reduced and dehydrated yielding a chain-elongated product. In the last years, several β-oxidation pathways have been studied in detail and reversal of these pathways already proved to be a promising strategy for the production of chemicals and polymer building blocks in several industrially relevant microorganisms. This review covers recent advancements in this field and discusses constraints and bottlenecks of this metabolic strategy in comparison to alternative production pathways. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Combining position-specific 13C labeling with compound-specific isotope analysis: first steps towards soil fluxomics

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Kuzyakov, Yakov

2015-04-01

Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino sugar 13C analysis showed that oxidizing catabolic pathways and anabolic pathways, i.e. building-up new cellular compounds, occurred in soils simultaneously. This involved an intensive C recycling within the microorganisms that was observed not only for cytosolic compounds but also for cell wall polymers. Fungal metabolism and fluxes were slower than bacterial intracellular C recycling and turnover. Furthermore, position-specific labeling of glutamate and subsequent 13C analysis of microbial phospholipid fatty acids (PLFA) revealed starvation pathways, which were only active in specific microbial groups in soils. These studies revealed that position-specific labeling enables the reconstruction of metabolic pathways of LMWOS within diverse microbial communities in complex media such as soil. Processes occurring simultaneously in soil i.e. 1) within individual, reversible metabolic pathways and 2) in various microbial groups could be traced by position-specific labeling in soils in situ. Tracing these pathways and understanding their regulating factors are crucial for soil C fluxomics, the extremely complex network of transformations towards mineralization versus the formation of microbial biomass compounds. Quantitative models to assess microbial group specific metabolic networks can be generated and parameterized by this approach. The submolecular knowledge of transformation steps and biochemical pathways in soils and their regulating factors is essential for understanding C cycling and long-term C storage in soils.

Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

PubMed

Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

2014-10-01

Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recent advances in mathematical modeling of nitrous oxides emissions from wastewater treatment processes.

PubMed

Ni, Bing-Jie; Yuan, Zhiguo

2015-12-15

Nitrous oxide (N2O) can be emitted from wastewater treatment contributing to its greenhouse gas footprint significantly. Mathematical modeling of N2O emissions is of great importance toward the understanding and reduction of the environmental impact of wastewater treatment systems. This article reviews the current status of the modeling of N2O emissions from wastewater treatment. The existing mathematical models describing all the known microbial pathways for N2O production are reviewed and discussed. These included N2O production by ammonia-oxidizing bacteria (AOB) through the hydroxylamine oxidation pathway and the AOB denitrification pathway, N2O production by heterotrophic denitrifiers through the denitrification pathway, and the integration of these pathways in single N2O models. The calibration and validation of these models using lab-scale and full-scale experimental data is also reviewed. We conclude that the mathematical modeling of N2O production, while is still being enhanced supported by new knowledge development, has reached a maturity that facilitates the estimation of site-specific N2O emissions and the development of mitigation strategies for a wastewater treatment plant taking into the specific design and operational conditions of the plant. Copyright © 2015 Elsevier Ltd. All rights reserved.

Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes: OC Oxidation Processes Across Vegetation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Tfaily, Malak M.; Crump, Alex R.

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically-bound (i.e., mineral and microbial) OC at terrestrial-aquatic interfaces. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in directmore » conflict with the concept of ‘priming’—that inputs of water-soluble and thermodynamically-favorable terrestrial OC protects bound-OC from oxidation. Based on our results, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.« less

Biological Oxidation of Fe(II) in Reduced Nontronite Coupled with Nitrate Reduction by Pseudogulbenkiania sp. Strain 2002

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Linduo; Dong, Hailiang; Kukkadapu, Ravi K.

Nitrate contamination in soils, sediments, and water bodies is a significant issue. Although much is known about nitrate degradation in these environments, especially via microbial pathways, a complete understanding of all degradation processes, especially in clay mineral-rich soils, is still lacking. The objective of this study was to study the potential of removing nitrate contaminant using structural Fe(II) in clay mineral nontronite. Specifically, the coupled processes of microbial oxidation of Fe(II) in microbially reduced nontronite (NAu-2) and nitrate reduction by Pseudogulbenkiania species strain 2002 was investigated. Bio-oxidation experiments were conducted in bicarbonate-buffered medium under both growth and nongrowth conditions. Themore » extents of Fe(II) oxidation and nitrate reduction were measured by wet chemical methods. X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), and 57Fe-Mössbauer spectroscopy were used to observe mineralogical changes associated with Fe(III) reduction and Fe(II) oxidation in nontronite. The bio-oxidation extent under growth and nongrowth conditions reached 93% and 57%, respectively. Over the same time period, nitrate was completely reduced under both conditions to nitrogen gas (N2), via an intermediate product nitrite. Magnetite was a mineral product of nitrate-dependent Fe(II) oxidation, as evidenced by XRD data and TEM diffraction patterns. The results of this study highlight the importance of iron-bearing clay minerals in the global nitrogen cycle with potential applications in nitrate removal in soils.« less

Microbial models of mammalian metabolism: production of novel alpha-diketone metabolites of warfarin and phenprocoumon using Aspergillus niger.

PubMed

Rizzo, J D; Davis, P J

1988-12-01

1. The coumarin anticoagulants warfarin and phenprocoumon were metabolized by Aspergillus niger via oxidative ring cleavage to yield the corresponding alpha-diketone metabolites. 2. Structural identification was based upon physical, spectral, and chromatographic comparisons of isolated metabolites and synthetic standards generated by the oxidative cleavage of warfarin or phenprocoumon with pyridinium chlorochromate. 3. This pathway of metabolism has been previously observed for coumarin anticoagulants in mammalian systems.

The Soil Microbial Response to a Massive Natural Gas Leak

NASA Astrophysics Data System (ADS)

Tavormina, P. L.; Newman, S.; Shen, L.; Connon, S. A.; Okumura, M.; Orphan, V. J.

2016-12-01

The 2015/2016 gas leak in the Porter Ranch community (Southern California) was the largest natural gas leak in US history. While considerable attention has focused on the amount of methane released to the atmosphere and the effects of other gas components on human well-being, less attention has been given to the response of soil microbes to this event. These microbes represent natural pathways for utilization of C1 compounds in soils and, possibly, untapped potential to remediate natural and anthropogenic gas emissions. We monitored onsite and background soil methane concentrations and microbial communities during and following the Porter Ranch gas leak. Soil core samples (25cm depth, collected twice monthly beginning in January 2016) were preserved for DNA, RNA, microscopic, stable isotope probing, and chromatographic methods. Simultaneously to coring, gas from soil pore spaces was collected for cavity ringdown spectroscopy to measure carbon dioxide, methane and ethane concentrations, and estimate corresponding isotopic values in carbon dioxide and methane. By pairing these measurements with high throughput sequencing, transcript analysis, and cultivation, we demonstrate discrete shifts in the total microbial community in surface (0 - 5 cm) and deep (20 - 25 cm) soils. Importantly, we find that methane consumption likely occurred in surface soils during and following the leak. The lineages most significantly correlated with elevated methane from the leak event were five orders of magnitude more abundant near the leak event in space and time, indicating a microbial bloom. These lineages are previously unrecognized members of Sphingomonadaceae, and they encode at least two biochemical pathways for methane oxidation. Cultivation of the first representative of this group now allows more detailed investigation into its capacity for microbially-mediated soil methane oxidation and mitigation.

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa.

PubMed

Muratova, Anna; Dubrovskaya, Ekaterina; Golubev, Sergey; Grinev, Vyacheslav; Chernyshova, Marina; Turkovskaya, Olga

2015-09-01

We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere. Copyright © 2015 Elsevier GmbH. All rights reserved.

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.

PubMed

Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G; De Francisci, Davide; Valle, Giorgio; Angelidaki, Irini

2016-01-01

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Host heme oxygenase-1: Friend or foe in tackling pathogens?

PubMed

Singh, Nisha; Ahmad, Zeeshan; Baid, Navin; Kumar, Ashwani

2018-05-14

Infectious diseases are a major challenge in management of human health worldwide. Recent literature suggests that host immune system could be modulated to ameliorate the pathogenesis of infectious disease. Heme oxygenase (HMOX1) is a key regulator of cellular signaling and it could be modulated using pharmacological reagents. HMOX1 is a cytoprotective enzyme that degrades heme to generate carbon monoxide (CO), biliverdin, and molecular iron. CO and biliverdin (or bilirubin derived from it) can restrict the growth of a few pathogens. Both of these also induce antioxidant pathways and anti-inflammatory pathways. On the other hand, molecular iron can induce proinflammatory pathway besides making the cellular environment oxidative in nature. Since microbial infections often induce oxidative stress in host cells/tissues, role of HMOX1 has been analyzed in the pathogenesis of number of infections. In this review, we have described the role of HMOX1 in pathogenesis of bacterial infections caused by Mycobacterium species, Salmonella and in microbial sepsis. We have also provided a succinct overview of the role of HMOX1 in parasitic infections such as malaria and leishmaniasis. In the end, we have also elaborated the role of HMOX1 in viral infections such as AIDS, hepatitis, dengue, and influenza. © 2018 IUBMB Life, 2018. © 2018 International Union of Biochemistry and Molecular Biology.

Biosynthesis and engineering of kaempferol in Saccharomyces cerevisiae.

PubMed

Duan, Lijin; Ding, Wentao; Liu, Xiaonan; Cheng, Xiaozhi; Cai, Jing; Hua, Erbing; Jiang, Huifeng

2017-09-26

Kaempferol is a flavonol with broad bioactivity of anti-oxidant, anti-cancer, anti-diabetic, anti-microbial, cardio-protective and anti-asthma. Microbial synthesis of kaempferol is a promising strategy because of the low content in primary plant source. In this study, the biosynthesis pathway of kaempferol was constructed in the budding yeast Saccharomyces cerevisiae to produce kaempferol de novo, and several biological measures were taken for high production. Firstly, a high efficient flavonol synthases (FLS) from Populus deltoides was introduced into the biosynthetic pathway of kaempferol. Secondly, a S. cerevisiae recombinant was constructed for de novo synthesis of kaempferol, which generated about 6.97 mg/L kaempferol from glucose. To further promote kaempferol production, the acetyl-CoA biosynthetic pathway was overexpressed and p-coumarate was supplied as substrate, which improved kaempferol titer by about 23 and 120%, respectively. Finally, a fed-batch process was developed for better kaempferol fermentation performance, and the production reached 66.29 mg/L in 40 h. The titer of kaempferol in our engineered yeast is 2.5 times of the highest reported titer. Our study provides a possible strategy to produce kaempferol using microbial cell factory.

Novel Allylic Oxidation of α-Cedrene to sec-Cedrenol by a Rhodococcus Strain

PubMed Central

Takigawa, Hirofumi; Kubota, Hiromi; Sonohara, Hiroshi; Okuda, Mitsuyoshi; Tanaka, Shigeyoshi; Fujikura, Yoshiaki; Ito, Susumu

1993-01-01

A bacterial strain, designated KSM-7358, that can use α-cedrene for growth was isolated. The strain was identified as a member of the genus Rhodococcus and catalyzed the novel allylic oxidation of α-cedrene regiospecifically to produce (R)-10-hydroxycedrene (sec-cedrenol) with a very high yield. α-Curcumene was also produced as a possible metabolite of sec-cedrenol. A possible pathway for the microbial conversion of α-cedrene to sec-cedrenol and α-curcumene is proposed. PMID:16348930

13C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells

PubMed Central

Luo, Shuai; Guo, Weihua; H. Nealson, Kenneth; Feng, Xueyang; He, Zhen

2016-01-01

Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and 13C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the 13C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that 13C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms. PMID:26868848

Bioturbation and Manganese Cycling in Hemipelagic Sediments

NASA Astrophysics Data System (ADS)

Aller, R. C.

1990-06-01

The activities of infaunal macrobenthos have major influences on the types, rates and distributions of diagenetic reactions involving manganese in relatively carbon-rich deep-sea and nearshore sediments. In some non-sulphidic hemipelagic deposits of the eastern equatorial Pacific (Panama Basin) biogenic reworking drives internal cycles of manganese, which can apparently account for up to ca. 100% of organic carbon oxidation and reduction of O2 supplied (diffusively) to the sea floor. Heterotrophic (carbon-based) manganese reduction is stimulated by simultaneous mixing of reactive organic matter and manganese oxide into suboxic-anoxic deposits. In sulphidic sediments, biogenic reworking must also enhance a lithotrophic pathway (sulphur-based) pathway of manganese reduction by promoting contact of manganese oxides and iron sulphides. Particle reworking dramatically alters the balance between aerobic and anaerobic decomposition pathways, promoting the utilization of O2 in the reoxidaton of reduced metabolites rather than direct oxidation of carbon. Irrigated burrows create microenvironments, which increase manganese reduction-oxidation and deplete Mn2+ from deeper pore waters. This may increase net Mn2+ production rates by removal of metabolites and potential co-precipitants with Mn2+. The occurrence and geometry of manganese oxide encrusted biogenic structures imply specific adaptations of infauna to manganese based microbial activity in hemipelagic sediments like the Panama Basin.

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

PubMed Central

Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

2015-01-01

ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System

PubMed Central

Bai, Yaohui; Liu, Ruiping; Liang, Jinsong; Qu, Jiuhui

2013-01-01

While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic) and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ∼1011 prokaryotes per gram) in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90%) dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn2+ and As3+, might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water. PMID:23593378

Integrated metagenomic and physiochemical analyses to evaluate the potential role of microbes in the sand filter of a drinking water treatment system.

PubMed

Bai, Yaohui; Liu, Ruiping; Liang, Jinsong; Qu, Jiuhui

2013-01-01

While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic) and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ≈ 10(11) prokaryotes per gram) in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90%) dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn(2+) and As(3+), might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

PubMed Central

Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.; Paša-Tolić, Ljiljana; Hallam, Steven J.

2014-01-01

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand. PMID:25053816

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

PubMed

Hawley, Alyse K; Brewer, Heather M; Norbeck, Angela D; Paša-Tolić, Ljiljana; Hallam, Steven J

2014-08-05

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1

PubMed Central

Chu, Cui-Wei; Liu, Bin; Li, Na; Yao, Shi-Gang; Cheng, Dan; Zhao, Jia-Dong; Qiu, Ji-Guo; Yan, Xin; He, Jian

2017-01-01

ABSTRACT Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C—S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C—S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD+ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis. IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C—S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism. PMID:28939603

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1.

PubMed

Chu, Cui-Wei; Liu, Bin; Li, Na; Yao, Shi-Gang; Cheng, Dan; Zhao, Jia-Dong; Qiu, Ji-Guo; Yan, Xin; He, Qin; He, Jian

2017-12-01

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S -acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum , alkanesulfonate monooxygenase from Pseudomonas savastanoi , and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC , was located 7,129 bp downstream of tmoAB , and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD + as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis. IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N -deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S -acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism. Copyright © 2017 American Society for Microbiology.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

PubMed

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-08-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules.

PubMed

Ishii, Satoshi; Song, Yanjun; Rathnayake, Lashitha; Tumendelger, Azzaya; Satoh, Hisashi; Toyoda, Sakae; Yoshida, Naohiro; Okabe, Satoshi

2014-10-01

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments.

PubMed

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-11-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration--a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments

PubMed Central

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-01-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration—a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder. PMID:25871933

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens

PubMed Central

Levar, Caleb E; Hoffman, Colleen L; Dunshee, Aubrey J; Toner, Brandy M; Bond, Daniel R

2017-01-01

Geobacter sulfurreducens uses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of –0.10 V vs the standard hydrogen electrode, whereas the ImcH-dependent pathway operates only above this value. Here, we provide evidence that G. sulfurreducens also requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)-(oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors. Freshly precipitated Fe(III)-(oxyhydr)oxides could not be reduced by mutants lacking the high-potential pathway. Aging these minerals by autoclaving did not change their powder X-ray diffraction pattern, but restored reduction by mutants lacking the high-potential pathway. Mutants lacking the low-potential, CbcL-dependent pathway had higher growth yields with both soluble and insoluble Fe(III). Together, these data suggest that the ImcH-dependent pathway exists to harvest additional energy when conditions permit, and CbcL switches on to allow respiration closer to thermodynamic equilibrium conditions. With evidence of multiple pathways within a single organism, the study of extracellular respiration should consider not only the crystal structure or solubility of a mineral electron acceptor, but rather the redox potential, as this variable determines the energetic reward affecting reduction rates, extents, and final microbial growth yields in the environment. PMID:28045456

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

PubMed Central

Landry, Zachary; Swan, Brandon K.; Herndl, Gerhard J.; Stepanauskas, Ramunas

2017-01-01

ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. PMID:28420738

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products.

PubMed

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-11-04

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism.

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

PubMed Central

Kozlowski, Jessica A; Stieglmeier, Michaela; Schleper, Christa; Klotz, Martin G; Stein, Lisa Y

2016-01-01

Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76T exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196T. In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions. PMID:26882267

Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier.

PubMed

Hoyles, Lesley; Snelling, Tom; Umlai, Umm-Kulthum; Nicholson, Jeremy K; Carding, Simon R; Glen, Robert C; McArthur, Simon

2018-03-21

Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbiome influences the gut-brain axis: modification of autonomic/sensorimotor connections, immune activation, and neuroendocrine pathway regulation. We hypothesised interactions between circulating gut-derived microbial metabolites, and the blood-brain barrier (BBB) also contribute to the gut-brain axis. Propionate, produced from dietary substrates by colonic bacteria, stimulates intestinal gluconeogenesis and is associated with reduced stress behaviours, but its potential endocrine role has not been addressed. After demonstrating expression of the propionate receptor FFAR3 on human brain endothelium, we examined the impact of a physiologically relevant propionate concentration (1 μM) on BBB properties in vitro. Propionate inhibited pathways associated with non-specific microbial infections via a CD14-dependent mechanism, suppressed expression of LRP-1 and protected the BBB from oxidative stress via NRF2 (NFE2L2) signalling. Together, these results suggest gut-derived microbial metabolites interact with the BBB, representing a fourth facet of the gut-brain axis that warrants further attention.

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH.

PubMed

Percak-Dennett, E; He, S; Converse, B; Konishi, H; Xu, H; Corcoran, A; Noguera, D; Chan, C; Bhattacharyya, A; Borch, T; Boyd, E; Roden, E E

2017-09-01

Pyrite (FeS 2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO 2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals. © 2017 John Wiley & Sons Ltd.

Microbial production of the aromatic building-blocks (S)-styrene oxide and (R)-1,2-phenylethanediol from renewable resources.

PubMed

McKenna, Rebekah; Pugh, Shawn; Thompson, Brian; Nielsen, David R

2013-12-01

(S)-Styrene oxide and (R)-1,2-phenylethanediol are chiral aromatic molecular building blocks used commonly as precursors to pharmaceuticals and other specialty chemicals. Two pathways have been engineered in Escherichia coli for their individual biosynthesis directly from glucose. The novel pathways each constitute extensions of the previously engineered styrene pathway, developed by co-expressing either styrene monooxygenase (SMO) or styrene dioxygenase (SDO) to convert styrene to (S)-styrene oxide and (R)-1,2-phenylethanediol, respectively. StyAB from Pseudomonas putida S12 was determined to be the most effective SMO. SDO activity was achieved using NahAaAbAcAd of Pseudomonas sp. NCIB 9816-4, a naphthalene dioxygenase with known broad substrate specificity. Production of phenylalanine, the precursor to both pathways, was systematically enhanced through a number of mutations, most notably via deletion of tyrA and over-expression of tktA. As a result, (R)-1,2-phenylethanediol reached titers as high as 1.23 g/L, and at 1.32 g/L (S)-styrene oxide titers already approach their toxicity limit. As with other aromatics, product toxicity was strongly correlated with a model of membrane accumulation and disruption. This study additionally demonstrates that greater flux through the styrene pathway can be achieved if its toxicity is addressed, as achieved in this case by reacting styrene to less toxic products. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of different nitrous oxide production models with four continuous long-term wastewater treatment process data series.

PubMed

Spérandio, Mathieu; Pocquet, Mathieu; Guo, Lisha; Ni, Bing-Jie; Vanrolleghem, Peter A; Yuan, Zhiguo

2016-03-01

Five activated sludge models describing N2O production by ammonium oxidising bacteria (AOB) were compared to four different long-term process data sets. Each model considers one of the two known N2O production pathways by AOB, namely the AOB denitrification pathway and the hydroxylamine oxidation pathway, with specific kinetic expressions. Satisfactory calibration could be obtained in most cases, but none of the models was able to describe all the N2O data obtained in the different systems with a similar parameter set. Variability of the parameters can be related to difficulties related to undescribed local concentration heterogeneities, physiological adaptation of micro-organisms, a microbial population switch, or regulation between multiple AOB pathways. This variability could be due to a dependence of the N2O production pathways on the nitrite (or free nitrous acid-FNA) concentrations and other operational conditions in different systems. This work gives an overview of the potentialities and limits of single AOB pathway models. Indicating in which condition each single pathway model is likely to explain the experimental observations, this work will also facilitate future work on models in which the two main N2O pathways active in AOB are represented together.

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources.

PubMed

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe(2+) ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD(+) through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats.

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources

PubMed Central

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe2+ ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD+ through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats. PMID:26500609

Flat laminated microbial mat communities

NASA Astrophysics Data System (ADS)

Franks, Jonathan; Stolz, John F.

2009-10-01

Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River Estuary

NASA Astrophysics Data System (ADS)

Hines, David E.; Lisa, Jessica A.; Song, Bongkeun; Tobias, Craig R.; Borrett, Stuart R.

2012-06-01

Estuaries serve important ecological and economic functions including habitat provision and the removal of nutrients. Eutrophication can overwhelm the nutrient removal capacity of estuaries and poses a widely recognized threat to the health and function of these ecosystems. Denitrification and anaerobic ammonium oxidation (anammox) are microbial processes responsible for the removal of fixed nitrogen and diminish the effects of eutrophication. Both of these microbial removal processes can be influenced by direct inputs of dissolved inorganic nitrogen substrates or supported by microbial interactions with other nitrogen transforming pathways such as nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The coupling of nitrogen removal pathways to other transformation pathways facilitates the removal of some forms of inorganic nitrogen; however, differentiating between direct and coupled nitrogen removal is difficult. Network modeling provides a tool to examine interactions among microbial nitrogen cycling processes and to determine the within-system history of nitrogen involved in denitrification and anammox. To examine the coupling of nitrogen cycling processes, we built a nitrogen budget mass balance network model in two adjacent 1 cm3 sections of bottom water and sediment in the oligohaline portion of the Cape Fear River Estuary, NC, USA. Pathway, flow, and environ ecological network analyses were conducted to characterize the organization of nitrogen flow in the estuary and to estimate the coupling of nitrification to denitrification and of nitrification and DNRA to anammox. Centrality analysis indicated NH4+ is the most important form of nitrogen involved in removal processes. The model analysis further suggested that direct denitrification and coupled nitrification-denitrification had similar contributions to nitrogen removal while direct anammox was dominant to coupled forms of anammox. Finally, results also indicated that partial nitrification-anammox may play an important role in anammox nitrogen removal in the Cape Fear River Estuary.

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap.

PubMed

Zhang, Xian; Niu, Jiaojiao; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-01-19

Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate.

PubMed

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-01-01

CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs.

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate

PubMed Central

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M.; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-01-01

CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs. PMID:27047478

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

NASA Astrophysics Data System (ADS)

Keiluweit, Marco; Bougoure, Jeremy J.; Zeglin, Lydia H.; Myrold, David D.; Weber, Peter K.; Pett-Ridge, Jennifer; Kleber, Markus; Nico, Peter S.

2012-10-01

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of 13C- and 15N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of 15N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.

Variations in microbial carbon sources and cycling in the deep continental subsurface

NASA Astrophysics Data System (ADS)

Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood; Wilkie, Kenna; Kieft, Thomas L.; Magnabosco, Cara; Lau, Maggie C. Y.; Pullin, Michael J.; Hendrickson, Sarah B.; Wommack, K. Eric; Sakowski, Eric G.; van Heerden, Esta; Kuloyo, Olukayode; Linage, Borja; Borgonie, Gaetan; Onstott, Tullis C.

2016-01-01

Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3 km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied. In the shallower boreholes at circa 1 kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05 kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34 kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples. In the samples collected from >3 kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼-24‰ and 0‰, respectively. The dominant CO2-fixation pathways were 3-HP/4-HB cycle > acetyl-CoA pathway > reductive pentose phosphate cycle.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

PubMed Central

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-01-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration. PMID:28350393

Metaproteomics of aquatic microbial communities in a deep and stratified estuary.

PubMed

Colatriano, David; Ramachandran, Arthi; Yergeau, Etienne; Maranger, Roxane; Gélinas, Yves; Walsh, David A

2015-10-01

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

2012 Gordon Research Conference on Mutagenesis - Formal Schedule and Speaker/Poster Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demple, Bruce

2012-08-24

The delicate balance among cellular pathways that control mutagenic changes in DNA will be the focus of the 2012 Mutagenesis Gordon Research Conference. Mutagenesis is essential for evolution, while genetic stability maintains cellular functions in all organisms from microbes to metazoans. Different systems handle DNA lesions at various times of the cell cycle and in different places within the nucleus, and inappropriate actions can lead to mutations. While mutation in humans is closely linked to disease, notably cancers, mutational systems can also be beneficial. The conference will highlight topics of beneficial mutagenesis, including full establishment of the immune system, cellmore » survival mechanisms, and evolution and adaptation in microbial systems. Equal prominence will be given to detrimental mutation processes, especially those involved in driving cancer, neurological diseases, premature aging, and other threats to human health. Provisional session titles include Branching Pathways in Mutagenesis; Oxidative Stress and Endogenous DNA Damage; DNA Maintenance Pathways; Recombination, Good and Bad; Problematic DNA Structures; Localized Mutagenesis; Hypermutation in the Microbial World; and Mutation and Disease.« less

Denitrification: an important pathway for nitrous oxide production in tropical mangrove sediments (Goa, India).

PubMed

Fernandes, Sheryl Oliveira; Bharathi, P A Loka; Bonin, Patricia C; Michotey, Valérie D

2010-01-01

Net nitrous oxide production and denitrification activity were measured in two mangrove ecosystems of Goa, India. The relatively pristine site Tuvem was compared to Divar, which is prone to high nutrient input. Stratified sampling at 2-cm intervals within the 0- to 10-cm depth range showed that N2O production at both the locations decreased with depth. Elevated denitrification activity at Divar resulted in maximum production of up to 1.95 nmol N2O-N g(-1) h(-1) at 2 to 4 cm, which was three times higher than at Tuvem. Detailed investigations to understand the major pathway contributing to N2O production performed at Tuvem showed that incomplete denitrification was responsible for up to 43 to 93% of N2O production. Nitrous oxide production rates closely correlated to nitrite concentration (n = 15; r = -0.47; p < 0.05) and denitrifier abundance (r = 0.55; p < 0.05), suggesting that nitrite utilization by microbial activity leads to N2O production. Nitrous oxide production through nitrification was below detection, affirming that denitrification is the major pathway responsible for production of the greenhouse gas. Net N2O production in these mangrove systems are comparatively higher than those reported from other natural estuarine sediments and therefore warrant mitigation measures.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-11-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

PubMed Central

Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

2015-01-01

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems. PMID:25575307

Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation.

PubMed

Jamieson, James; Prommer, Henning; Kaksonen, Anna H; Sun, Jing; Siade, Adam J; Yusov, Anna; Bostick, Benjamin

2018-05-15

Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.

2014-08-05

Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components formore » nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.« less

Surveying N2O-producing pathways in bacteria.

PubMed

Stein, Lisa Y

2011-01-01

Nitrous oxide (N(2)O) is produced by bacteria as an intermediate of both dissimilatory and detoxification pathways under a range of oxygen levels, although the majority of N(2)O is released in suboxic to anoxic environments. N(2)O production under physiologically relevant conditions appears to require the reduction of nitric oxide (NO) produced from the oxidation of hydroxylamine (nitrification), reduction of nitrite (denitrification), or by host cells of pathogenic bacteria. In a single bacterial isolate, N(2)O-producing pathways can be complex, overlapping, involve multiple enzymes with the same function, and require multiple layers of regulatory machinery. This overview discusses how to identify known N(2)O-producing inventory and regulatory sequences within bacterial genome sequences and basic physiological approaches for investigating the function of that inventory. A multitude of review articles have been published on individual enzymes, pathways, regulation, and environmental significance of N(2)O-production encompassing a large diversity of bacterial isolates. The combination of next-generation deep sequencing platforms, emerging proteomics technologies, and basic microbial physiology can be used to expand what is known about N(2)O-producing pathways in individual bacterial species to discover novel inventory and unifying features of pathways. A combination of approaches is required to understand and generalize the function and control of N(2)O production across a range of temporal and spatial scales within natural and host environments. Copyright © 2011 Elsevier Inc. All rights reserved.

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

PubMed

Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

2017-10-03

In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

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 detailed understanding of the vertical and longitudinal distribution of microbial taxa throughout CP. These studies will provide insight into the operation of the microbial Fe redox cycle, demonstrating how genomic properties relate to and control geochemical conditions with depth and distance in a Fe-rich, neutral pH geothermal environment.

Surface-oxidized cobalt phosphide used as high efficient electrocatalyst in activated carbon air-cathode microbial fuel cell

NASA Astrophysics Data System (ADS)

Yang, Tingting; Wang, Zhong; Li, Kexun; Liu, Yi; Liu, Di; Wang, Junjie

2017-09-01

Herein, we report a simplistic method to fabricate the surface-oxidized cobalt phosphide (CoP) nanocrystals (NCs), which is used as electrocatalyst for oxygen reduction reaction (ORR) in microbial fuel cell (MFC) for the first time. The corallite-like CoP NCs are successfully prepared by a hydrothermal reaction following a phosphating treatment in N2 atmosphere. When used as an ORR catalyst, cobalt phosphide shows comparable onset potential, inferior resistance, as well as a small Tafel slope with long-term stability in neutral media. The maximum power density of MFC embellished with 10% CoP reached 1914.4 ± 59.7 mW m-2, which is 108.5% higher than the control. The four-electron pathway, observed by the RDE, plays a crucial role in electrochemical catalytic activity. In addition, material characterizations indicate that the surface oxide layer (CoOx) around the metallic CoP core is important and beneficial for ORR. Accordingly, it can be expected that the as-synthesized CoP will be a promising candidate of the non-precious metal ORR electrocatalysts for electrochemical energy applications.

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

PubMed

Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

2014-09-01

Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products

PubMed Central

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-01-01

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism. PMID:26530351

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Electron acceptor redox potential globally regulates transcriptomic profiling in Shewanella decolorationis S12

NASA Astrophysics Data System (ADS)

Lian, Yingli; Yang, Yonggang; Guo, Jun; Wang, Yan; Li, Xiaojing; Fang, Yun; Gan, Lixia; Xu, Meiying

2016-08-01

Electron acceptor redox potential (EARP) was presumed to be a determining factor for microbial metabolism in many natural and engineered processes. However, little is known about the potentially global effects of EARP on bacteria. In this study, we compared the physiological and transcriptomic properties of Shewanella decolorationis S12 respiring with different EARPs in microbial electrochemical systems to avoid the effects caused by the other physicochemical properties of real electron acceptor. Results showed that the metabolic activities of strain S12 were nonlinear responses to EARP. The tricarboxylic acid cycle for central carbon metabolism was down-regulated while glyoxylate shunt was up-regulated at 0.8 V compared to 0.2 and -0.2 V, which suggested that EARP is an important but not the only determinant for metabolic pathways of strain S12. Moreover, few cytochrome c genes were differentially expressed at different EARPs. The energy intensive flagella assembly and assimilatory sulfur metabolism pathways were significantly enriched at 0.8 V, which suggested strain S12 had stronger electrokinesis behavior and oxidative stress-response at high EARP. This study provides the first global information of EARP regulations on microbial metabolism, which will be helpful for understanding microorganism respiration.

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

PubMed Central

Brazelton, William J.; Nelson, Bridget; Schrenk, Matthew O.

2012-01-01

Ultramafic rocks in the Earth’s mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). In order to assess the potential for microbial H2 utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H2-oxidizers. Both sites also yielded metagenomic evidence for microbial H2 production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood–Ljungdahl pathway. In general, our results point to H2-oxidizing Betaproteobacteria thriving in shallow, oxic–anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H2-powered primary production in serpentinite-hosted subsurface habitats. PMID:22232619

Metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.

PubMed

Brazelton, William J; Nelson, Bridget; Schrenk, Matthew O

2012-01-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H(2)). In order to assess the potential for microbial H(2) utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H(2)-oxidizers. Both sites also yielded metagenomic evidence for microbial H(2) production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood-Ljungdahl pathway. In general, our results point to H(2)-oxidizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H(2)-powered primary production in serpentinite-hosted subsurface habitats.

Interferon-inducible effector mechanisms in cell-autonomous immunity

PubMed Central

MacMicking, John D.

2014-01-01

Interferons (IFNs) induce the expression of hundreds of genes as part of an elaborate antimicrobial programme designed to combat infection in all nucleated cells — a process termed cell-autonomous immunity. As described in this Review, recent genomic and subgenomic analyses have begun to assign functional properties to novel IFN-inducible effector proteins that restrict bacteria, protozoa and viruses in different subcellular compartments and at different stages of the pathogen life cycle. Several newly described host defence factors also participate in canonical oxidative and autophagic pathways by spatially coordinating their activities to enhance microbial killing. Together, these IFN-induced effector networks help to confer vertebrate host resistance to a vast and complex microbial world. PMID:22531325

Year-round N2O production by benthic NOx reduction in a monomictic south-alpine lake

NASA Astrophysics Data System (ADS)

Freymond, C. V.; Wenk, C. B.; Frame, C. H.; Lehmann, M. F.

2013-12-01

Nitrous oxide (N2O) is a potent greenhouse gas, generated through microbial nitrogen (N) turnover processes, such as nitrification, nitrifier denitrification, and denitrification. Previous studies quantifying natural sources have mainly focused on soils and the ocean, but the potential role of terrestrial water bodies in the global N2O budget has been widely neglected. Furthermore, the biogeochemical controls on the production rates and the microbial pathways that produce benthic N2O in lakes are essentially unknown. In this study, benthic N2O fluxes and the contributions of the microbial pathways that produce N2O were assessed using 15N label flow-through sediment incubations in the eutrophic, monomictic south basin of Lake Lugano in Switzerland. The sediments were a significant source of N2O throughout the year, with production rates ranging between 140 and 2605 nmol N2O h-1 m-2, and the highest observed rates coinciding with periods of water column stratification and stably anoxic conditions in the overlying bottom water. Nitrate (NO3-) reduction via denitrification was found to be the major N2O production pathway in the sediments under both oxygen-depleted and oxygen-replete conditions in the overlying water, while ammonium oxidation did not contribute significantly to the benthic N2O flux. A marked portion (up to 15%) of the total NO3- consumed by denitrification was reduced only to N2O, without complete denitrification to N2. These fluxes were highest when the bottom water had stabilized to a low-oxygen state, in contrast with the notion that stable anoxia is particularly conducive to complete denitrification without accumulation of N2O. This study provides evidence that lake sediments are a significant source of N2O to the overlying water and may produce large N2O fluxes to the atmosphere during seasonal mixing events.

γ–Butyrobetaine is a pro-atherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO

PubMed Central

Koeth, Robert A.; Levison, Bruce S.; Culley, Miranda K.; Buffa, Jennifer A.; Wang, Zeneng; Gregory, Jill C.; Org, Elin; Wu, Yuping; Li, Lin; Smith, Jonathan D.; Wilson Tang, W. H.; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2014-01-01

Summary L- Carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ~1000-fold higher than the formation of TMA. Moreover, we show γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, and like dietary L-carnitine, in a gut microbiota-dependent manner is converted into TMA and TMAO, and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal distinct taxa are associated with the production of γBB versus TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine versus γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine versus γBB, respectively. PMID:25440057

A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dietrich, Jeffrey; Yoshikuni, Yasuo; Fisher, Karl

2009-11-30

Production of fine heterologus pathways in microbial hosts is frequently hindered by insufficient knowledge of the native metabolic pathway and its cognate enzymes; often the pathway is unresolved and enzymes lack detailed characterization. An alternative paradigm to using native pathways is de novo pathway design using well-characterized, substrate-promiscuous enzymes. We demonstrate this concept using P450BM3 from Bacillus megaterium. Using a computer model, we illustrate how key P450BM3 activ site mutations enable binding of non-native substrate amorphadiene, incorporating these mutations into P450BM3 enabled the selective oxidation of amorphadiene arteminsinic-11s,12-epoxide, at titers of 250 mg L"1 in E. coli. We also demonstratemore » high-yeilding, selective transformations to dihydroartemisinic acid, the immediate precursor to the high value anti-malarial drug artemisinin.« less

Sulfur geochemistry and microbial sulfate reduction during low-temperature alteration of uplifted lower oceanic crust: Insights from ODP Hole 735B

USGS Publications Warehouse

Alford, Susan E.; Alt, Jeffrey C.; Shanks, Wayne C.

2011-01-01

Sulfide petrography plus whole rock contents and isotope ratios of sulfur were measured in a 1.5 km section of oceanic gabbros in order to understand the geochemistry of sulfur cycling during low-temperature seawater alteration of the lower oceanic crust, and to test whether microbial effects may be present. Most samples have low SO4/ΣS values (≤ 0.15), have retained igneous globules of pyrrhotite ± chalcopyrite ± pentlandite, and host secondary aggregates of pyrrhotite and pyrite laths in smectite ± iron-oxyhydroxide ± magnetite ± calcite pseudomorphs of olivine and clinopyroxene. Compared to fresh gabbro containing 100–1800 ppm sulfur our data indicate an overall addition of sulfide to the lower crust. Selection of samples altered only at temperatures ≤ 110 °C constrains microbial sulfate reduction as the only viable mechanism for the observed sulfide addition, which may have been enabled by the production of H2 from oxidation of associated olivine and pyroxene. The wide range in δ34Ssulfide values (− 1.5 to + 16.3‰) and variable additions of sulfide are explained by variable εsulfate-sulfide under open system pathways, with a possible progression into closed system pathways. Some samples underwent oxidation related to seawater penetration along permeable fault horizons and have lost sulfur, have high SO4/ΣS (≥ 0.46) and variable δ34Ssulfide (0.7 to 16.9‰). Negative δ34Ssulfate–δ34Ssulfide values for the majority of samples indicate kinetic isotope fractionation during oxidation of sulfide minerals. Depth trends in sulfide–sulfur contents and sulfide mineral assemblages indicate a late-stage downward penetration of seawater into the lower 1 km of Hole 735B. Our results show that under appropriate temperature conditions, a subsurface biosphere can persist in the lower oceanic crust and alter its geochemistry.

Complete and simultaneous removal of ammonium and m-cresol in a nitrifying sequencing batch reactor.

PubMed

Zepeda, Alejandro; Ben-Youssef, Chérif; Rincón, Susana; Cuervo-López, Flor; Gómez, Jorge

2013-06-01

The kinetic behavior, oxidizing ability and tolerance to m-cresol of a nitrifying sludge exposed to different initial concentrations of m-cresol (0-150 mg C L(-1)) were evaluated in a sequencing batch reactor fed with 50 mg NH4 (+)-N L(-1) and operated during 4 months. Complete removal of ammonium and m-cresol was achieved independently of the initial concentration of aromatic compound in all the assays. Up to 25 mg m-cresol-C L(-1) (C/N ratio of 0.5), the nitrifying yield (Y-NO3 (-)) was 0.86 ± 0.05, indicating that the nitrate was the main product of the process; no biomass growth was detected. From 50 to 150 mg m-cresol-C L(-1) (1.0 ≤ C/N ≤ 3.0), simultaneous microbial growth and partial ammonium-to-nitrate conversion were obtained, reaching a maximum microbial total protein concentration of 0.763 g L(-1) (247 % of its initial value) and the lowest Y-NO3 (-) 0.53 ± 0.01 at 150 mg m-cresol-C L(-1). m-Cresol induced a significant decrease in the values of both specific rates of ammonium and nitrite oxidation, being the ammonium oxidation pathway the mainly inhibited. The nitrifying sludge was able to completely oxidize up to 150 mg m-cresol-C L(-1) by SBR cycle, reaching a maximum specific removal rate of 6.45 g m-cresol g(-1) microbial protein-N h(-1). The number of SBR cycles allowed a metabolic adaptation of the nitrifying consortium since nitrification inhibition decreased and faster oxidation of m-cresol took place throughout the cycles.

A mathematical model for regulating monomer composition of the microbially synthesized polyhydroxyalkanoate copolymers.

PubMed

Xu, Jun; Guo, Baohua; Zhang, Zengmin; Wu, Qiong; Zhou, Quan; Chen, Jinchun; Chen, Guoqiang; Li, Guodong

2005-06-30

A mathematical model is proposed for predicting the copolymer composition of the microbially synthesized polyhydroxyalkanoate (PHA) copolymers. Based on the biochemical reactions involved in the precursor formation and polymerization pathways, the model correlates the copolymer composition with the cultivation conditions, the enzyme levels and selectivity, and the metabolic pathways. It suggests the following points: (1) in the case of a sole carbon source, the copolymer composition depends mainly on the topology of the metabolic pathways and the selectivity of both the enzymes involved in the precursor formation and the polymerization route; (2) the copolymer composition can be varied in a wide range via alteration of the flux ratio of different types of monomers channeled from two or more independent and simultaneous pathways; (3) the enzymes which should be over-expressed or inhibited to obtain the desired copolymer composition can be predicted. For example, inhibition of the beta-oxidation pathway will increase the content of the monomer units with longer chain length. To test the model, various experiments were envisaged by varying cultivation time, concentration and chain length of the sole carbon source, and molar ratio of the cosubstrates. The predictions from the model agree well with the experimental results. Therefore, the proposed model will be useful in predicting the PHA copolymer composition under different biochemical reaction conditions. In other words, it can provide a guide for the synthesis of desired PHA copolymers.

C1 Metabolism in Corynebacterium glutamicum: an Endogenous Pathway for Oxidation of Methanol to Carbon Dioxide

PubMed Central

Witthoff, Sabrina; Mühlroth, Alice

2013-01-01

Methanol is considered an interesting carbon source in “bio-based” microbial production processes. Since Corynebacterium glutamicum is an important host in industrial biotechnology, in particular for amino acid production, we performed studies of the response of this organism to methanol. The C. glutamicum wild type was able to convert 13C-labeled methanol to 13CO2. Analysis of global gene expression in the presence of methanol revealed several genes of ethanol catabolism to be upregulated, indicating that some of the corresponding enzymes are involved in methanol oxidation. Indeed, a mutant lacking the alcohol dehydrogenase gene adhA showed a 62% reduced methanol consumption rate, indicating that AdhA is mainly responsible for methanol oxidation to formaldehyde. Further studies revealed that oxidation of formaldehyde to formate is catalyzed predominantly by two enzymes, the acetaldehyde dehydrogenase Ald and the mycothiol-dependent formaldehyde dehydrogenase AdhE. The Δald ΔadhE and Δald ΔmshC deletion mutants were severely impaired in their ability to oxidize formaldehyde, but residual methanol oxidation to CO2 was still possible. The oxidation of formate to CO2 is catalyzed by the formate dehydrogenase FdhF, recently identified by us. Similar to the case with ethanol, methanol catabolism is subject to carbon catabolite repression in the presence of glucose and is dependent on the transcriptional regulator RamA, which was previously shown to be essential for expression of adhA and ald. In conclusion, we were able to show that C. glutamicum possesses an endogenous pathway for methanol oxidation to CO2 and to identify the enzymes and a transcriptional regulator involved in this pathway. PMID:24014532

Nitrifier-induced denitrification is an important source of soil nitrous oxide and can be inhibited by a nitrification inhibitor 3,4-dimethylpyrazole phosphate.

PubMed

Shi, Xiuzhen; Hu, Hang-Wei; Zhu-Barker, Xia; Hayden, Helen; Wang, Juntao; Suter, Helen; Chen, Deli; He, Ji-Zheng

2017-12-01

Soil ecosystem represents the largest contributor to global nitrous oxide (N 2 O) production, which is regulated by a wide variety of microbial communities in multiple biological pathways. A mechanistic understanding of these N 2 O production biological pathways in complex soil environment is essential for improving model performance and developing innovative mitigation strategies. Here, combined approaches of the 15 N- 18 O labelling technique, transcriptome analysis, and Illumina MiSeq sequencing were used to identify the relative contributions of four N 2 O pathways including nitrification, nitrifier-induced denitrification (nitrifier denitrification and nitrification-coupled denitrification) and heterotrophic denitrification in six soils (alkaline vs. acid soils). In alkaline soils, nitrification and nitrifier-induced denitrification were the dominant pathways of N 2 O production, and application of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) significantly reduced the N 2 O production from these pathways; this is probably due to the observed reduction in the expression of the amoA gene in ammonia-oxidizing bacteria (AOB) in the DMPP-amended treatments. In acid soils, however, heterotrophic denitrification was the main source for N 2 O production, and was not impacted by the application of DMPP. Our results provide robust evidence that the nitrification inhibitor DMPP can inhibit the N 2 O production from nitrifier-induced denitrification, a potential significant source of N 2 O production in agricultural soils. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories.

PubMed

Zhao, Chunhua; Zhao, Qiuwei; Li, Yin; Zhang, Yanping

2017-06-24

The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron.

PubMed

Castelle, Cindy J; Roger, Magali; Bauzan, Marielle; Brugna, Myriam; Lignon, Sabrina; Nimtz, Manfred; Golyshina, Olga V; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne

2015-08-01

The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse ('uphill') electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma. Copyright © 2015 Elsevier B.V. All rights reserved.

Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment.

PubMed

Chao, Yuanqing; Ma, Liping; Yang, Ying; Ju, Feng; Zhang, Xu-Xiang; Wu, Wei-Min; Zhang, Tong

2013-12-19

The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to Alphaproteobacteria in TW. Further functional analysis indicated the basic metabolic functions of microorganisms in TW did not vary considerably. However, protective functions, i.e. glutathione synthesis genes in 'oxidative stress' and 'detoxification' subsystems, significantly increased, revealing the surviving bacteria may have higher chlorine resistance. Similar results were also found in glutathione metabolism pathway, which identified the major reaction for glutathione synthesis and supported more genes for glutathione metabolism existed in TW. This metagenomic study largely enhanced our knowledge about the influences of treatment processes, especially chlorination, on bacterial community structure and protective functions (e.g. glutathione metabolism) in ecosystems of DWTPs.

Isotope Effects Associated with N2O Production By Fungal and Bacterial Nitric Oxide Reductases: Implications for Tracing Microbial Production Pathways

NASA Astrophysics Data System (ADS)

Ostrom, N. E.; Yang, H.; Gandhi, H.; Hegg, E. L.

2014-12-01

Site preference (SP), the difference in δ15N between the central (α) and outer (β) N atoms in N2O, has emerged as a conservative tracer of microbial N2O production. The key advantages of SP relative to bulk isotopes are (1) that it is independent of the isotope composition of the substrates of nitrification and denitrification and (2) has not been shown to exhibit fractionation during production. In pure microbial culture distinct SP values for N2O production from bacterial denitrification, including nitrifier-denitrification (-10 to 0 ‰), relative to hydroxylamine oxidation and fungal denitrification (33-37 ‰) provide a promising basis to resolve production pathways. In this study, we determined the δ15N, δ18O, δ15Nα, and δ15Nβ of N2O generated by purified fungal (P450nor) and bacterial nitric oxide reductases. The isotope values were used to calculate SP values, enrichment factors (e), and kinetic isotope effects (KIEs). Both O and Nα displayed normal isotope effects during enzymatic NO reduction by the P450nor with e values of -25.7‰ (KIE = 1.0264) and -12.6‰ (KIE = 1.0127), respectively. However, bulk nitrogen (average δ15N of Nα and Nβ) and Nβ exhibited inverse isotope effects with e values of 14.0‰ (KIE = 0.9862) and 36.1‰ (KIE = 0.9651), respectively. The observed inverse isotope effect in δ15Nβ is consistent with reversible binding of the first NO in the P450nor reaction mechanism. Experiments with bacterial nitric oxide reductase are ongoing, however, preliminary data indicates a inverse isotope effect in the α and β positions and a normal isotope effect in δ18O. In contrast to the constant SP observed during N2O production observed in microbial cultures, the SP measured for purified P450nor was not constant, increasing from ~15‰ to ~29‰ during the course of the reaction. Our results clearly indicate that fractionation of SP during N2O production by P450nor is not zero, and that SP values higher and lower than the proposed end member value of 37‰ can be expected during fungal denitrification. The observation in pure microbial culture of constant SP can only be reconciled if the rate of nitrite and NO reduction are the same (thereby maintaining a steady NO concentration in the cell), and, further, that the magnitude of the P450nor NO binding constant (Kd) maintains the extent of the reaction (1-f) at 65%.

Bloom of a denitrifying methanotroph, "Candidatus Methylomirabilis limnetica", in a deep stratified lake.

PubMed

Graf, Jon S; Mayr, Magdalena J; Marchant, Hannah K; Tienken, Daniela; Hach, Philipp F; Brand, Andreas; Schubert, Carsten J; Kuypers, Marcel M M; Milucka, Jana

2018-05-28

Methanotrophic bacteria represent an important biological filter regulating methane emissions into the atmosphere. Planktonic methanotrophic communities in freshwater lakes are typically dominated by aerobic gamma-proteobacteria, with a contribution from alpha-proteobacterial methanotrophs and the NC10 bacteria. The NC10 clade encompasses methanotrophs related to "Candidatus Methylomirabilis oxyfera", which oxidize methane using a unique pathway of denitrification that tentatively produces N 2 and O 2 from nitric oxide (NO). Here we describe a new species of the NC10 clade, "Ca. Methylomirabilis limnetica", which dominated the planktonic microbial community in the anoxic depths of the deep stratified Lake Zug in two consecutive years, comprising up to 27% of the total bacterial population. Gene transcripts assigned to "Ca. M. limnetica" constituted up to one third of all metatranscriptomic sequences in situ. The reconstructed genome encoded a complete pathway for methane oxidation, and an incomplete denitrification pathway, including two putative nitric oxide dismutase genes. The genome of "Ca. M. limnetica" exhibited features possibly related to genome streamlining (i.e. less redundancy of key metabolic genes) and adaptation to its planktonic habitat (i.e. gas vesicle genes). We speculate that "Ca. M. limnetica" temporarily bloomed in the lake during non-steady-state conditions suggesting a niche for NC10 in the lacustrine methane and nitrogen cycle. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Complete nitrification by Nitrospira bacteria

PubMed Central

Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia; Bulaev, Alexandr; Kirkegaard, Rasmus H.; von Bergen, Martin; Rattei, Thomas; Bendinger, Bernd; Nielsen, Per H.; Wagner, Michael

2016-01-01

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered as a two-step process catalyzed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes both the pathways for ammonia and nitrite oxidation, which are concomitantly expressed during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities. PMID:26610024

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

PubMed Central

Xie, Wei; Wang, Fengping; Guo, Lei; Chen, Zeling; Sievert, Stefan M; Meng, Jun; Huang, Guangrui; Li, Yuxin; Yan, Qingyu; Wu, Shan; Wang, Xin; Chen, Shangwu; He, Guangyuan; Xiao, Xiang; Xu, Anlong

2011-01-01

Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production. PMID:20927138

Self-assembly of biomorphic carbon/sulfur microstructures in sulfidic environments

PubMed Central

Cosmidis, Julie; Templeton, Alexis S.

2016-01-01

In natural and laboratory-based environments experiencing sustained counter fluxes of sulfide and oxidants, elemental sulfur (S0)—a key intermediate in the sulfur cycle—can commonly accumulate. S0 is frequently invoked as a biomineralization product generated by enzymatic oxidation of hydrogen sulfide and polysulfides. Here we show the formation of S0 encapsulated in nanometre to micrometre-scale tubular and spherical organic structures that self-assemble in sulfide gradient environments in the absence of any direct biological activity. The morphology and composition of these carbon/sulfur microstructures so closely resemble microbial cellular and extracellular structures that new caution must be applied to the interpretation of putative microbial biosignatures in the fossil record. These reactions between sulfide and organic matter have important implications for our understanding of S0 mineralization processes and sulfur interactions with organic carbon in the environment. They furthermore provide a new pathway for the synthesis of carbon-sulfur nanocomposites for energy storage technologies. PMID:27628108

Self-assembly of biomorphic carbon/sulfur microstructures in sulfidic environments

NASA Astrophysics Data System (ADS)

Cosmidis, Julie; Templeton, Alexis S.

2016-09-01

In natural and laboratory-based environments experiencing sustained counter fluxes of sulfide and oxidants, elemental sulfur (S0)--a key intermediate in the sulfur cycle--can commonly accumulate. S0 is frequently invoked as a biomineralization product generated by enzymatic oxidation of hydrogen sulfide and polysulfides. Here we show the formation of S0 encapsulated in nanometre to micrometre-scale tubular and spherical organic structures that self-assemble in sulfide gradient environments in the absence of any direct biological activity. The morphology and composition of these carbon/sulfur microstructures so closely resemble microbial cellular and extracellular structures that new caution must be applied to the interpretation of putative microbial biosignatures in the fossil record. These reactions between sulfide and organic matter have important implications for our understanding of S0 mineralization processes and sulfur interactions with organic carbon in the environment. They furthermore provide a new pathway for the synthesis of carbon-sulfur nanocomposites for energy storage technologies.

Source Tracking of Nitrous Oxide using A Quantum Cascade ...

EPA Pesticide Factsheets

Nitrous oxide is an important greenhouse gas and ozone depleting substance. Nitrification and denitrification are two major biological pathways that are responsible for soil emissions of N2O. However, source tracking of in-situ or laboratory N2O production is still challenging to soil scientists. The objective of this study was to introduce the use of a new technology, quantum cascade laser (QCL) spectroscopy, which allows for significantly improved accuracy and precision to continuously measure real-time N2O for source tracking. This data provides important emission inventory information to air quality and atmospheric chemistry models. The task demonstrated that QCL spectroscopy can measure the flux of nitrous oxide at ambient and well as elevated concentrations in real time. The fractionation of the nitrous oxide produced by microbial processing of nitrate can be measured and characterized as isotopic signatures related to the nitrifying or denitrifying state of the microbial communities. This has important implications for monitoring trace gases in the atmosphere. The data produced by this system will provide clients including the air quality and climate change communities with needed information on the sources and strengths of N2O emissions for modeling and research into mitigation strategies to reduce overall GHG emissions in agricultural systems.

[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.

Monoterpenol Oxidative Metabolism: Role in Plant Adaptation and Potential Applications

PubMed Central

Ilc, Tina; Parage, Claire; Boachon, Benoît; Navrot, Nicolas; Werck-Reichhart, Danièle

2016-01-01

Plants use monoterpenols as precursors for the production of functionally and structurally diverse molecules, which are key players in interactions with other organisms such as pollinators, flower visitors, herbivores, fungal, or microbial pathogens. For humans, many of these monoterpenol derivatives are economically important because of their pharmaceutical, nutraceutical, flavor, or fragrance applications. The biosynthesis of these derivatives is to a large extent catalyzed by enzymes from the cytochrome P450 superfamily. Here we review the knowledge on monoterpenol oxidative metabolism in plants with special focus on recent elucidations of oxidation steps leading to diverse linalool and geraniol derivatives. We evaluate the common features between oxidation pathways of these two monoterpenols, such as involvement of the CYP76 family, and highlight the differences. Finally, we discuss the missing steps and other open questions in the biosynthesis of oxygenated monoterpenol derivatives. PMID:27200002

Source identification of nitrous oxide on autotrophic partial nitrification in a granular sludge reactor.

PubMed

Rathnayake, R M L D; Song, Y; Tumendelger, A; Oshiki, M; Ishii, S; Satoh, H; Toyoda, S; Yoshida, N; Okabe, S

2013-12-01

Emission of nitrous oxide (N2O) during biological wastewater treatment is of growing concern since N2O is a major stratospheric ozone-depleting substance and an important greenhouse gas. The emission of N2O from a lab-scale granular sequencing batch reactor (SBR) for partial nitrification (PN) treating synthetic wastewater without organic carbon was therefore determined in this study, because PN process is known to produce more N2O than conventional nitrification processes. The average N2O emission rate from the SBR was 0.32 ± 0.17 mg-N L(-1) h(-1), corresponding to the average emission of N2O of 0.8 ± 0.4% of the incoming nitrogen load (1.5 ± 0.8% of the converted NH4(+)). Analysis of dynamic concentration profiles during one cycle of the SBR operation demonstrated that N2O concentration in off-gas was the highest just after starting aeration whereas N2O concentration in effluent was gradually increased in the initial 40 min of the aeration period and was decreased thereafter. Isotopomer analysis was conducted to identify the main N2O production pathway in the reactor during one cycle. The hydroxylamine (NH2OH) oxidation pathway accounted for 65% of the total N2O production in the initial phase during one cycle, whereas contribution of the NO2(-) reduction pathway to N2O production was comparable with that of the NH2OH oxidation pathway in the latter phase. In addition, spatial distributions of bacteria and their activities in single microbial granules taken from the reactor were determined with microsensors and by in situ hybridization. Partial nitrification occurred mainly in the oxic surface layer of the granules and ammonia-oxidizing bacteria were abundant in this layer. N2O production was also found mainly in the oxic surface layer. Based on these results, although N2O was produced mainly via NH2OH oxidation pathway in the autotrophic partial nitrification reactor, N2O production mechanisms were complex and could involve multiple N2O production pathways. Copyright © 2013 Elsevier Ltd. All rights reserved.

A microbial model of mammalian metabolism: biotransformation of 4,5-dimethoxyl-canthin-6-one using Cunninghamella blakesleeana CGMCC 3.970.

PubMed

Fan, Hong-Xia; Zhou, Zheng-Qun; Peng, Jun; Wu, Bao-Jian; Chen, He-Ru; Bao, Xue-Feng; Mu, Zhen-Qiang; Jiao, Wei-Hua; Yao, Xin-Sheng; Gao, Hao

2017-04-01

1. A filamentous fungus, Cunninghamella blakesleeana CGMCC 3.970, was applied as a microbial system to mimic mammalian metabolism of 4,5-dimethoxyl-canthin-6-one (1). Compound 1 belongs to canthin-6-one type alkaloids, which is a major bioactive constituent of a traditional Chinese medicine (the stems of Picrasma quassioides). 2. After 72 h of incubation in potato dextrose broth, 1 was metabolized to seven metabolites as follows: 4-methoxyl-5-hydroxyl-canthin-6-one (M1), 4-hydroxyl-5-methoxyl-canthin-6-one (M2), canthin-6-one (M3), canthin-6-one N-oxide (M4), 10-hydroxyl-4,5-dimethoxyl-canthin-6-one (M5), 1-methoxycarbonl-β-carboline (M6), and 4-methoxyl-5-O-β-D-glucopyranosyl-canthin-6-one (M7). 3. The structures of metabolites were determined using spectroscopic analyses, chemical methods, and comparison of NMR data with those of known compounds. Among them, M7 was a new compound. 4. The metabolic pathways of 1 were proposed, and the metabolic processes involved phase I (O-demethylation, dehydroxylation, demethoxylation, N-oxidation, hydroxylation, and oxidative ring cleavage) and phase II (glycosylation) reactions. 5. This was the first research on microbial transformation of canthin-6-one alkaloid, which could be a useful microbial model for producing the mammalian phase I and phase II metabolites of canthin-6-one alkaloids. 6. 1, M1-M5, and M7 are canthin-6-one alkaloids, whereas M6 belongs to β-carboline type alkaloids. The strain of Cunninghamella blakesleeana can supply an approach to transform canthin-6-one type alkaloids into β-carboline type alkaloids.

Mechanisms and pathways of aniline elimination from aquatic environments.

PubMed Central

Lyons, C D; Katz, S; Bartha, R

1984-01-01

The fate of aniline, a representative of arylamine pollutants derived from the manufacture of dyes, coal liquefaction, and pesticide degradation, was comprehensively evaluated by use of unpolluted and polluted pond water as model environments. Evaporation plus autoxidation proved to be minor elimination mechanisms, removing ca. 1% of the added aniline per day. Instantaneous binding to humic components of a 0.1% sewage sludge inoculum removed 4%. Biodegradation of aniline in pond water was accelerated by the sewage sludge inoculum. A substantial portion of the degraded aniline carbon was mineralized to CO2 within a 1-week period, and microbial biomass was formed as a result of aniline utilization. Biodegradation was clearly the most significant removal mechanism of polluting aniline from pond water. A gas chromatographic-mass spectrometric analysis of biodegradation intermediates revealed that the major pathway of aniline biodegradation in pond water involved oxidative deamination to catechol, which was further metabolized through cis,cis-muconic, beta-ketoadipic, levulinic, and succinic acid intermediates to CO2. Minor biodegradation pathways involved reversible acylation to acetanilide and formanilide, whereas N-oxidation resulted in small amounts of oligomeric condensation products. PMID:6497369

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

PubMed

Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

2016-01-15

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management. Copyright © 2015 Elsevier B.V. All rights reserved.

Early diagenesis in the sediments of the Congo deep-sea fan dominated by massive terrigenous deposits: Part III - Sulfate- and methane- based microbial processes

NASA Astrophysics Data System (ADS)

Pastor, L.; Toffin, L.; Decker, C.; Olu, K.; Cathalot, C.; Lesongeur, F.; Caprais, J.-C.; Bessette, S.; Brandily, C.; Taillefert, M.; Rabouille, C.

2017-08-01

Geochemical profiles (SO42-, H2S, CH4, δ13CH4) and phylogenetic diversity of Archaea and Bacteria from two oceanographic cruises dedicated to the lobes sediments of the Congo deep-sea fan are presented in this paper. In this area, organic-rich turbidites reach 5000 m and allow the establishment of patchy cold-seep-like habitats including microbial mats, reduced sediments, and vesicomyid bivalves assemblages. These bivalves live in endosymbiosis with sulfur-oxidizing bacteria and use sulfides to perform chemosynthesis. In these habitats, unlike classical abyssal sediments, anoxic processes are dominant. Total oxygen uptake fluxes and methane fluxes measured with benthic chambers are in the same range as those of active cold-seep environments, and oxygen is mainly used for reoxidation of reduced compounds, especially in bacterial mats and reduced sediments. High concentrations of methane and sulfate co-exist in the upper 20 cm of sediments, and evidence indicates that sulfate-reducing microorganisms and methanogens co-occur in the shallow layers of these sediments. Simultaneously, anaerobic oxidation of methane (AOM) with sulfate as the electron acceptor is evidenced by the presence of ANMEs (ANaerobic MEthanotroph). Dissolved sulfide produced through the reduction of sulfate is reoxidized through several pathways depending on the habitat. These pathways include vesicomyid bivalves uptake (adults or juveniles in the bacterial mats habitats), reoxidation by oxygen or iron phases within the reduced sediment, or reoxidation by microbial mats. Sulfide uptake rates by vesicomyids measured in sulfide-rich sea water (90±18 mmol S m-2 d-1) were similar to sulfide production rates obtained by modelling the sulfate profile with different bioirrigation constants, highlighting the major control of vesicomyids on sulfur cycle in their habitats.

The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.

PubMed

Vieira, A; Ribera-Guardia, A; Marques, R; Barreto Crespo, M T; Oehmen, A; Carvalho, G

2018-06-02

The emission of the greenhouse gas nitrous oxide (N 2 O) can occur during biological nutrient removal. Denitrifying enhanced biological phosphorus removal (d-EBPR) systems are an efficient means of removing phosphate and nitrogen, performed by denitrifying polyphosphate-accumulating organisms (d-PAOs). The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO 3 - ), nitrite (NO 2 - ), and N 2 O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. Reverse transcriptase-qPCR (RT-qPCR) and high-throughput sequencing, combined with chemical analysis, were used to study gene expression, microbial diversity, and denitrification kinetics. The potential for N 2 O production was greater than the potential for its reduction in most tests. A strong correlation was observed between the N 2 O reduction rate and the relative gene expression of nitrous oxide reductase per nitrite reductase (nosZ/(nirS + nirK)), suggesting that the expression of denitrifying marker genes is a strong predictor of the N 2 O reduction rate. The d-EBPR community maintained a core population with low variations throughout the study. Furthermore, phylogenetic analyses of the studied marker genes revealed that the organisms actively involved in denitrification were closely related to Thauera sp., Candidatus Accumulibacter phosphatis, and Candidatus Competibacter denitrificans. Moreover, Competibacter-related OTUs seem to be important contributors to the N 2 O reduction capacity of the system, likely scavenging the N 2 O produced by other organisms. Overall, this study contributes to a better understanding of the microbial biochemistry and the genetics involving biological denitrification removal, important to minimize N 2 O emissions in wastewater treatment plants.

Effect of chromium (VI) on the multiple nitrogen removal pathways and microbial community of aerobic granular sludge.

PubMed

Zheng, Xiao-Ying; Lu, Dan; Wang, Ming-Yang; Chen, Wei; Zhou, Gan; Zhang, Yuan

2017-06-12

The frequent appearance of Cr(VI) significantly impacts the microbial metabolism in wastewater. In this study, long-term effects of Cr(VI) on microbial community, nitrogen removal pathways and mechanism of aerobic granular sludge (AGS) were investigated. AGS had strong resistance ability to 1.0 mg/L Cr(VI). 3.0 mg/L Cr(VI) increased the heterotrophic-specific ammonia uptake rate (HSAUR) and heterotrophic-specific nitrate uptake rate (HSNUR) transiently, whereas 5.0 mg/L Cr(VI) sharply decreased the specific ammonia uptake rate (SAUR), specific nitrate uptake rate (SNUR) and simultaneous nitrification denitrification rate (SNDR). It was found that Cr (VI) has a greater inhibitory effect on autotrophic nitrification (ASAUR), and the maximal inhibition rate (IR) was 139.19%. Besides, the inhibition of Cr (VI) on nitrogen removal process belongs to non-competitive inhibition. Cr(VI) had a weaker negative impact on heterotrophic bacteria compared with that on autotrophic bacteria. Denaturing gradient gel electrophoresis analyses suggest that Acidovorax sp., flavobacterium sp., uncultured soil bacterium, uncultured nitrosospira sp., uncultured prokaryote, uncultured β-proteobacterium and uncultured pseudomonas sp. were the dominant species. The inhibition of Cr(VI) on nitrite-oxidizing bacteria was the strongest, followed by ammonia-oxidizing bacteria and denitrifying bacteria. Linear correlations between bacterial count and biomass-specific uptake rate were observed when the Cr(VI) concentration exceeded 3 mg/L. This study revealed the effect of Cr(VI) on nitrification is more serious than that on denitrification. Autotrophic and heterotrophic nitrification, heterotrophic denitrification and simultaneous nitrification denitrification played a significant role on nitrogen removal under Cr(VI) stress.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla withmore » no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.« less

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

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin

PubMed Central

Sharrar, Allison M.; Flood, Beverly E.; Bailey, Jake V.; Jones, Daniel S.; Biddanda, Bopaiah A.; Ruberg, Steven A.; Marcus, Daniel N.; Dick, Gregory J.

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea. PMID:28533768

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

PubMed

Sharrar, Allison M; Flood, Beverly E; Bailey, Jake V; Jones, Daniel S; Biddanda, Bopaiah A; Ruberg, Steven A; Marcus, Daniel N; Dick, Gregory J

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H 2 -based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H 2 oxidation via Ni-Fe hydrogenases, and the use of O 2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction ( sat, apr , and dsr ) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea.

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

USDA-ARS?s Scientific Manuscript database

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 ...

Origin of sulfur for elemental sulfur concentration in salt dome cap rocks, Gulf Coast Basin, USA

NASA Astrophysics Data System (ADS)

Hill, J. M.; Kyle, R.; Loyd, S. J.

2017-12-01

Calcite cap rocks of the Boling and Main Pass salt domes contain large elemental sulfur accumulations. Isotopic and petrographic data indicate complex histories of cap rock paragenesis for both domes. Whereas paragenetic complexity is in part due to the open nature of these hydrodynamic systems, a comprehensive understanding of elemental sulfur sources and concentration mechanisms is lacking. Large ranges in traditional sulfur isotope compositions (δ34S) among oxidized and reduced sulfur-bearing phases has led some to infer that microbial sulfate reduction and/or influx of sulfide-rich formation waters occurred during calcite cap rock formation. Ultimately, traditional sulfur isotope analyses alone cannot distinguish among local microbial or exogenous sulfur sources. Recently, multiple sulfur isotope (32S, 33S, 34S, 36S) studies reveal small, but measurable differences in mass-dependent behavior of microbial and abiogenic processes. To distinguish between the proposed sulfur sources, multiple-sulfur-isotope analyses have been performed on native sulfur from the Boling and Main Pass cap rocks. Similarities or deviations from equilibrium relationships indicate which pathways were responsible for native sulfur precipitation. Pathway determination provides insight into Gulf Coast cap rock development and potentially highlights the conditions that led to anomalous sulfur enrichment in Boling and Main Pass Domes.

Proteome analysis of Aspergillus flavus isolate-specific responses to oxidative stress in relationship to aflatoxin production capability.

PubMed

Fountain, Jake C; Koh, Jin; Yang, Liming; Pandey, Manish K; Nayak, Spurthi N; Bajaj, Prasad; Zhuang, Wei-Jian; Chen, Zhi-Yuan; Kemerait, Robert C; Lee, R Dewey; Chen, Sixue; Varshney, Rajeev K; Guo, Baozhu

2018-02-21

Aspergillus flavus is an opportunistic pathogen of plants such as maize and peanut under conducive conditions such as drought stress resulting in significant aflatoxin production. Drought-associated oxidative stress also exacerbates aflatoxin production by A. flavus. The objectives of this study were to use proteomics to provide insights into the pathogen responses to H 2 O 2 -derived oxidative stress, and to identify potential biomarkers and targets for host resistance breeding. Three isolates, AF13, NRRL3357, and K54A with high, moderate, and no aflatoxin production, were cultured in medium supplemented with varying levels of H 2 O 2 , and examined using an iTRAQ (Isobaric Tags for Relative and Absolute Quantification) approach. Overall, 1,173 proteins were identified and 220 were differentially expressed (DEPs). Observed DEPs encompassed metabolic pathways including antioxidants, carbohydrates, pathogenicity, and secondary metabolism. Increased lytic enzyme, secondary metabolite, and developmental pathway expression in AF13 was correlated with oxidative stress tolerance, likely assisting in plant infection and microbial competition. Elevated expression of energy and cellular component production in NRRL3357 and K54A implies a focus on oxidative damage remediation. These trends explain isolate-to-isolate variation in oxidative stress tolerance and provide insights into mechanisms relevant to host plant interactions under drought stress allowing for more targeted efforts in host resistance research.

Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems.

PubMed

Chandran, Kartik; Stein, Lisa Y; Klotz, Martin G; van Loosdrecht, Mark C M

2011-12-01

Chemolithoautotrophic AOB (ammonia-oxidizing bacteria) form a crucial component in microbial nitrogen cycling in both natural and engineered systems. Under specific conditions, including transitions from anoxic to oxic conditions and/or excessive ammonia loading, and the presence of high nitrite (NO₂⁻) concentrations, these bacteria are also documented to produce nitric oxide (NO) and nitrous oxide (N₂O) gases. Essentially, ammonia oxidation in the presence of non-limiting substrate concentrations (ammonia and O₂) is associated with N₂O production. An exceptional scenario that leads to such conditions is the periodical switch between anoxic and oxic conditions, which is rather common in engineered nitrogen-removal systems. In particular, the recovery from, rather than imposition of, anoxic conditions has been demonstrated to result in N₂O production. However, applied engineering perspectives, so far, have largely ignored the contribution of nitrification to N₂O emissions in greenhouse gas inventories from wastewater-treatment plants. Recent field-scale measurements have revealed that nitrification-related N₂O emissions are generally far higher than emissions assigned to heterotrophic denitrification. In the present paper, the metabolic pathways, which could potentially contribute to NO and N₂O production by AOB have been conceptually reconstructed under conditions especially relevant to engineered nitrogen-removal systems. Taken together, the reconstructed pathways, field- and laboratory-scale results suggest that engineering designs that achieve low effluent aqueous nitrogen concentrations also minimize gaseous nitrogen emissions.

Microbial utilization of low molecular weight organic substrates in soil depends on their carbon oxidation state

NASA Astrophysics Data System (ADS)

Gunina, Anna; Smith, Andrew; Jones, Davey; Kuzyakov, Yakov

2017-04-01

Removal of low molecular weight organic substances (LMWOS), originating from plants and microorganisms, from soil solution is regulated by microbial uptake. In addition to the concentration of LMWOS in soil solution, the chemical properties of each substance (e.g. C oxidation state, number of C atoms, number of -COOH groups) can affect their uptake and subsequent partitioning of C within the soil microbial community. The aim of this study was to trace the initial fate of three dominant classes of LMWOS in soil (sugars, carboxylic and amino acids), including their removal from solution and utilization by microorganisms, and to reveal the effect of substance chemical properties on these processes. Soil solution, spiked at natural abundance levels with 14C-labelled glucose, fructose, malate, succinate, formate, alanine or glycine, was added to the soil and 14C was traced in the dissolved organic carbon (DOC), CO2, cytosol and soil organic carbon (SOC) over 24 hours. The half-life time of all LMWOS in the DOC (T1 /2-solution) varied between 0.6-5.0 min showing extremely fast initial uptake of LMWOS. The T1 /2-solution of substances was dependent on C oxidation state, indicating that less oxidized organic substances (with C oxidation state "0") were retained longer in soil solution than oxidized substances. The LMWOS-C T1 /2-fast, characterizing the half-life time of 14C in the fast mineralization pool, ranged between 30 and 80 min, with the T1 /2-fast of carboxylic acids (malic acid) being the fastest and the T1 /2-fast of amino acids (glycine) being the slowest. An absence of correlation between T1 /2-fast and either C oxidation state, number of C atoms, or number of -COOH groups suggests that intercellular metabolic pathways are more important for LMWOS transformation in soil than their basic chemical properties. The CO2 release during LMWOS mineralization accounted for 20-90% of 14C applied. Mineralization of LMWOS was the least for sugars and the greatest for carboxylic (formic) acids, whereas the 14C incorporations into cytosol and SOC were opposite. The portion of LMWOS mineralized to CO2 increased with their C oxidation state corresponding to the decrease of C incorporated into the cytosol and SOC pools. The ratio of 14C incorporated into cytosol to 14C incorporated into CO2 pool ranged between 0.03 and 1.19, being the lowest for carboxylic acids and highest for sugars, and decreased with substances C oxidation state. Thus, the C oxidation state is one of the crucial parameter of LMWOS determining their partitioning between two main C fluxes: mineralization and microbial stabilization/immobilization. Our data suggests that the uptake of common LMWOS from soil solution by microorganisms and final LMWOS-C partitioning within microbial biomass may be possible to predict from the physicochemical properties of the substance.

The history of aerobic ammonia oxidizers: from the first discoveries to today.

PubMed

Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

2014-07-01

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

PubMed Central

Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

2014-01-01

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

Metal availability and the expanding network of microbial metabolisms in the Archaean eon

NASA Astrophysics Data System (ADS)

Moore, Eli K.; Jelen, Benjamin I.; Giovannelli, Donato; Raanan, Hagai; Falkowski, Paul G.

2017-09-01

Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron-sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.

Formation of toxic 2-nonyl-p-benzoquinones from α-tertiary 4-nonylphenol isomers during microbial metabolism of technical nonylphenol.

PubMed

Gabriel, Frédéric L P; Mora, Mauricio Arrieta; Kolvenbach, Boris A; Corvini, Philippe F X; Kohler, Hans-Peter E

2012-06-05

In many environmental compartments, microbial degradation of α-quaternary nonylphenols proceeds along an ipso-substitution pathway. It has been reported that technical nonylphenol contains, besides α-quaternary nonylphenols, minor amounts of various α-H, α-methyl substituted tertiary isomers. Here, we show that potentially toxic metabolites of such minor components are formed during ipso-degradation of technical nonylphenol by Sphingobium xenophagum Bayram, a strain isolated from activated sewage sludge. Small but significant amounts of nonylphenols were converted to the corresponding nonylhydroquinones, which in the presence of air oxygen oxidized to the corresponding nonyl-p-benzoquinones-yielding a complex mixture of potentially toxic metabolites. Through reduction with ascorbic acid and subsequent analysis by gas chromatography-mass spectrometry, we were able to characterize this unique metabolic fingerprint and to show that its components originated for the most part from α-tertiary nonylphenol isomers. Furthermore, our results indicate that the metabolites mixture also contained several α, β-dehydrogenated derivatives of nonyl-p-benzoquinones that originated by hydroxylation induced rearrangement, and subsequent ring and side chain oxidation from α-tertiary nonylphenol isomers. We predict that in nonylphenol polluted natural systems, in which microbial ipso-degradation is prominent, 2-alkylquinone metabolites will be produced and will contribute to the overall toxicity of the remaining material.

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization.

PubMed

Orellana, Luis H; Chee-Sanford, Joanne C; Sanford, Robert A; Löffler, Frank E; Konstantinidis, Konstantinos T

2017-11-03

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for better understanding nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points across one year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), with similar cropping histories. Although microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural water-based ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. Importance Even though the impact of agricultural management on the microbial community structure has already been recognized, understanding of the dynamics of individual microbial populations and what functions each population encodes are limited. Yet, this information is important for better understanding nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year-round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic compared to their marine counterparts previously studied. Copyright © 2017 American Society for Microbiology.

Microbes: Agents of Isotopic Change

NASA Astrophysics Data System (ADS)

Fogel, M. L.

2012-12-01

Microbes drive many of the important oxidation and reduction reactions on Earth; digest almost all forms of organic matter; and can serve as both primary and secondary producers. Because of their versatile biochemistry and physiology, they impart unique isotopic signatures to organic and inorganic materials, which have proven to be key measurements for understanding elemental cycling now and throughout Earth's history. Understanding microbial isotope fractionations in laboratory experiments has been important for interpreting isotopic patterns measured in natural settings. In fact, the pairing of simple experiment with natural observation has been the pathway for interpreting the fingerprint of microbial processes in ancient sediments and rocks. Examples of how key experiments have explained stable isotope fractionations by microbes and advanced the field of microbial ecology will be presented. Learning the isotopic signatures of Earth's microbes is a valuable exercise for predicting what isotopic signatures could be displayed by possible extant or extinct extraterrestrial life. Given the potential for discovery on Mars, Enceladus, and other solar system bodies, new methods and techniques for pinpointing what is unique about microbial isotope signatures is particularly relevant.

Microbial oceanography of anoxic oxygen minimum zones.

PubMed

Ulloa, Osvaldo; Canfield, Donald E; DeLong, Edward F; Letelier, Ricardo M; Stewart, Frank J

2012-10-02

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

Microbial oceanography of anoxic oxygen minimum zones

PubMed Central

Ulloa, Osvaldo; Canfield, Donald E.; DeLong, Edward F.; Letelier, Ricardo M.; Stewart, Frank J.

2012-01-01

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N2) and nitrous oxide (N2O) gases. Anaerobic microbial processes, including the two pathways of N2 production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two “end points” represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future. PMID:22967509

Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.

PubMed

Dhamankar, Himanshu; Prather, Kristala L J

2011-08-01

The dwindling nature of petroleum and other fossil reserves has provided impetus towards microbial synthesis of fuels and value added chemicals from biomass-derived sugars as a renewable resource. Microbes have naturally evolved enzymes and pathways that can convert biomass into hundreds of unique chemical structures, a property that can be effectively exploited for their engineering into Microbial Chemical Factories (MCFs). De novo pathway engineering facilitates expansion of the repertoire of microbially synthesized compounds beyond natural products. In this review, we visit some recent successes in such novel pathway engineering and optimization, with particular emphasis on the selection and engineering of pathway enzymes and balancing of their accessory cofactors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Divergence of macrophage phagocytic and antimicrobial programs in leprosy.

PubMed

Montoya, Dennis; Cruz, Daniel; Teles, Rosane M B; Lee, Delphine J; Ochoa, Maria Teresa; Krutzik, Stephan R; Chun, Rene; Schenk, Mirjam; Zhang, Xiaoran; Ferguson, Benjamin G; Burdick, Anne E; Sarno, Euzenir N; Rea, Thomas H; Hewison, Martin; Adams, John S; Cheng, Genhong; Modlin, Robert L

2009-10-22

Effective innate immunity against many microbial pathogens requires macrophage programs that upregulate phagocytosis and direct antimicrobial pathways, two functions generally assumed to be coordinately regulated. We investigated the regulation of these key functions in human blood-derived macrophages. Interleukin-10 (IL-10) induced the phagocytic pathway, including the C-type lectin CD209 and scavenger receptors, resulting in phagocytosis of mycobacteria and oxidized low-density lipoprotein. IL-15 induced the vitamin D-dependent antimicrobial pathway and CD209, yet the cells were less phagocytic. The differential regulation of macrophage functional programs was confirmed by analysis of leprosy lesions: the macrophage phagocytosis pathway was prominent in the clinically progressive, multibacillary form of the disease, whereas the vitamin D-dependent antimicrobial pathway predominated in the self-limited form and in patients undergoing reversal reactions from the multibacillary to the self-limited form. These data indicate that macrophage programs for phagocytosis and antimicrobial responses are distinct and differentially regulated in innate immunity to bacterial infections.

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2013-09-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2012-12-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2013-09-07

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated withmore » microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).« less

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

PubMed Central

Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.

2016-01-01

ABSTRACT Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community. PMID:27235442

Microbial utilization of low molecular weight organics in soil depends on the substances properties

NASA Astrophysics Data System (ADS)

Gunina, Anna

2016-04-01

Utilization of low molecular weight organic substances (LMWOS) in soil is regulated by microbial uptake from solution and following incorporation of into specific cell cycles. Various chemical properties of LMWOS, namely oxidation state, number of carbon (C) atoms, number of carboxylic (-COOH) groups, can affect their uptake from soil solution and further microbial utilization. The aim of the study was to trace the initial fate (including the uptake from soil solution and utilization by microorganisms) of three main classes of LMWOS, having contrast properties - sugars, carboxylic and amino acids. Top 10 cm of mineral soil were collected under Silver birch stands within the Bangor DIVERSE experiment, UK. Soil solution was extracted by centrifugation at 4000 rpm during 15 min. Soil was spiked with 14C glucose or fructose; malic, succinic or formic acids; alanine or glycine. No additional non-labeled LMWOS were added. 14C was traced in the dissolved organic matter (DOM), CO2, cytosol and soil organic matter (SOM) during one day. To estimate half-life times (T1 /2)of LMWOS in soil solution and in SOM pools, the single and double first order kinetic equations were fitted to the uptake and mineralization dynamics, respectively. The LMWOS T1 /2in DOM pool varied between 0.6-5 min, with the highest T1 /2for sugars (3.7 min) and the lowest for carboxylic acids (0.6-1.4 min). Thus, initial uptake of LMWOS is not a limiting step of microbial utilization. The T1 /2 of carboxylic and amino acids in DOM were closely related with oxidation state, showing that reduced substances remain in soil solution longer, than oxidized. The initial T1 /2 of LMWOS in SOM ranged between 30-80 min, with the longest T1 /2 for amino acids (50-80 min) and the shortest for carboxylic acids (30-48 min). These T1 /2values were in one-two orders of magnitude higher than LMWOS T1 /2 in soil solution, pointing that LMWOS mineralization occur with a delay after the uptake. Absence of correlations between LMWOS T1 /2 in SOM with C oxidation state, number of C atoms or number of -COOH groups in LMWOS demonstrates that intercellular metabolic pathways are more important. Mineralization of LMWOS amounted for 20-90% of total applied amount. Maximum mineralization was found for carboxylic acids and minimum for sugars, whereas 14C incorporation into cytosol and SOM pools followed the opposite trend. There were close positive correlation between the portion of mineralized C and substance oxidation state, but negative with the amount of C incorporated into the cytosol and SOM pools. This shows that substance properties affect the final partitioning of LMWOS-C between mineralized and utilized pools. Thus, initial uptake of LMWOS from soil solution and final partitioning of LMWOS-C between the mineralized and microbially utilized pools are related to their chemical properties. In contrast, LMWOS mineralization dynamics is regulated by intercellular metabolization pathways.

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

PubMed Central

Laverock, B.; Kitidis, V.; Tait, K.; Gilbert, J. A.; Osborn, A. M.; Widdicombe, S.

2013-01-01

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms. PMID:23980243

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics

PubMed Central

Balkema, Cherel; Sorokin, Dimitry Y.

2017-01-01

ABSTRACT Thiocyanate (N=C−S−) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ54-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation. PMID:29285524

Tírez lake as a terrestrial analog of Europa.

PubMed

Prieto-Ballesteros, Olga; Rodríguez, Nuria; Kargel, Jeffrey S; Kessler, Carola González; Amils, Ricardo; Remolar, David Fernández

2003-01-01

Tírez Lake (La Mancha, central Spain) is proposed as a terrestrial analogue of Europa's ocean. The proposal is based on the comparison of the hydrogeochemistry of Tírez Lake with the geochemical features of the alteration mineralogy of meteoritic precursors and with Galileo's Near Infrared Mapping Spectrometer data on Europa's surface. To validate the astrobiological potential of Tírez Lake as an analog of Europa, different hydrogeochemical, mineral, and microbial analyses were performed. Experimental and theoretical modeling helped to understand the crystallization pathways that may occur in Europa's crust. Calculations about the oxidation state of the hypothetical Europan ocean were estimated to support the sulfate-rich neutral liquid model as the origin of Europa's observed hydrated minerals and to facilitate their comparison with Tírez's hydrogeochemistry. Hydrogeochemical and mineralogical analyses showed that Tírez waters corresponded to Mg-Na-SO(4)-Cl brines with epsomite, hexahydrite, and halite as end members. A preliminary microbial ecology characterization identified two different microbial domains: a photosynthetically sustained community represented by planktonic/benthonic forms and microbial mat communities, and a subsurficial anaerobic realm in which chemolithotrophy predominates. Fluorescence in situ hybridization has been used to characterize the prokaryotic diversity of the system. The subsurficial community seemed to be dominated by sulfate-reducing bacteria and methanogens. Frozen Tírez brines were analyzed by Fourier-transform infrared techniques providing spectra similar to those reported previously using pure components and to the Galileo spectral data. Calorimetric measurements of Tírez brines showed pathways and phase metastability for magnesium sulfate and sodium chloride crystallization that may aid in understanding the processes involved in the formation of Europa's icy crust. The use of fluorescence hybridization techniques for microbial detection and characterization in hypersaline environments makes this methodology strongly advisable for future Europa astrobiological missions.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE PAGES

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.; ...

2016-01-22

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

2016-01-01

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents.

PubMed

Crovadore, Julien; Soljan, Vice; Calmin, Gautier; Chablais, Romain; Cochard, Bastien; Lefort, François

2017-10-01

Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.

Ammonium removal pathways and microbial community in GAC-sand dual media filter in drinking water treatment.

PubMed

Feng, Shuo; Xie, Shuguang; Zhang, Xiaojian; Yang, Zhiyu; Ding, Wei; Liao, Xiaobin; Liu, Yuanyuan; Chen, Chao

2012-01-01

A GAC-sand dual media filter (GSF) was devised as an alternative solution for drinking water treatment plant to tackle the raw water polluted by ammonium in place of expensive ozone-GAC processes or bio-pretreatments. The ammonium removal pathways and microbial community in the GSFs were investigated. The concentrations of ammonium, nitrite and nitrate nitrogen were monitored along the filter. Total inorganic nitrogen (TIN) loss occurred during the filtration. For 1 mg ammonium removal, the TIN loss was as high as 0.35 mg, DO consumption was 3.06 mg, and alkalinity consumption was 5.55 mg. It was assumed that both nitrification and denitrification processes occur in the filters to fit the TIN loss and low DO consumption. During the filtration, nitritation, nitrification and nitritation-anaerobic ammonium oxidation processes probably occur, while traditional nitrification and denitrification and simultaneous nitrification and denitrification processes may occur. In the GSFs, Nitrosomonas and Nitrospira are likely to be involved in nitrification processes, while Novosphingobium, Comamonadaceae and Oxalobacteraceae may be involved in denitrification processes.

Metal Transport, Heavy Metal Speciation and Microbial Fixation Through Fluvial Subenvironments, Lower Coeur D'Alene River Valley, Idaho

NASA Astrophysics Data System (ADS)

Hooper, R. L.; Mahoney, J. B.

2001-12-01

The lower Coeur d'Alene River Valley of northern Idaho is the site of extensive lead and zinc contamination resulting from both direct riverine tailings disposal and flood remobilization of contaminated sediments derived from the Coeur d'Alene mining district upstream. Variations in the hydrologic regime, redox conditions, porosity/permeability, organic content and microbial activity results in complicated metal transport pathways. Documentation of these pathways is a prerequisite to effective remediation, and requires accurate analysis of lateral and vertical variations. An analytical approach combining sequential extraction, electron microscopy, and microanalysis provides a comprehensive assessment of particulate speciation in this complex hydrologic system. Rigorously controlled sample preparation and a new sequential extraction protocol provide unprecedented insight into the role of metal sequestration in fluvial subenvironments. Four subenvironments were investigated: bedload, overbank (levee), marsh, and lacustrine. Periodic floods remobilize primary ore minerals and secondary minerals from upstream tailings (primarily oxyhydroxides, sulfides and carbonates). The bedload in the lower valley is a reducing environment and acts as a sink for detrital carbonates and sulfides moving downstream. In addition, authigenic/biogenic Fe, Pb and Zn sulfides and phosphates are common in bedload sediments near the sediment/water interface. Flood redistribution of oxide, sulfide and carbonate phases results in periodic contaminant recharge generating a complex system of metal dissolution, mobilization, migration and precipitation. In levee environments, authigenic sulfides from flood scouring are quickly oxidized resulting in development of oxide coated grain surfaces. Stability of detrital minerals on the levee is variable depending on sediment permeability, grain size and mineralogy resulting in a complex stratigraphy of oxide zones mottled with zones dominated by detrital and authigenic carbonate and sulfide phases. Marshes subjected to periodic subaerial exposure/flooding are even more complex and dominated by authigenic and biogenic mineralization. Lacustrine environments are dominated by nanocrystalline inorganic and biogenic sulfide minerals in the upper third of the contaminated sediment column with increasing amounts of silt sized detrital sulfides (especially sphalerite) closer to the premining surface. In pH-neutral subenvironments within the wetlands and lateral lakes of the lower Coeur d'Alene River Valley, microbial fixation plays a critical role in sequestering metals. Complex metal oxyhydroxide phases provided via flood recharge to river edge, marsh and lacustrine environments rapidly dissolve upon encountering anoxic conditions. Microbial activity is extremely effective in removing heavy metals from the water column, producing a nanocrystalline biofilm substrate characterized by ZnS (sphalerite) and non-stoichiometric PbS, FeS, and mixed metal sulfides. These solid phases are inherently unstable, and the sequestered metals become readily available through changes in redox or pH conditions, particularly dam-controlled annual fluctuations in base level, or during removal by bottom-feeding aquatic water fowl. The recognition of the inherent complexity and instability of microbially produced sulfidic material in a pH-neutral environment has important implications for remediation efforts utilizing wetland filtration methods.

Hydrothermal Synthesis of Nanostructured Manganese Oxide as Cathodic Catalyst in a Microbial Fuel Cell Fed with Leachate

PubMed Central

Haoran, Yuan; Lifang, Deng; Tao, Lu; Yong, Chen

2014-01-01

Much effort has been devoted to the synthesis of novel nanostructured MnO2 materials because of their unique properties and potential applications as cathode catalyst in Microbial fuel cell. Hybrid MnO2 nanostructures were fabricated by a simple hydrothermal method in this study. Their crystal structures, morphology, and electrochemical characters were carried out by FESEM, N2-adsorption-desorption, and CV, indicating that the hydrothermally synthesized MnO2 (HSM) was structured by nanorods of high aspect ratio and multivalve nanoflowers and more positive than the naturally synthesized MnO2 (NSM), accompanied by a noticeable increase in oxygen reduction peak current. When the HSM was employed as the cathode catalyst in air-cathode MFC which fed with leachate, a maximum power density of 119.07 mW/m2 was delivered, 64.68% higher than that with the NSM as cathode catalyst. Furthermore, the HSM via a 4-e pathway, but the NSM via a 2-e pathway in alkaline solution, and as 4-e pathway is a more efficient oxygen reduction reaction, the HSM was more positive than NSM. Our study provides useful information on facile preparation of cost-effective cathodic catalyst in air-cathode MFC for wastewater treatment. PMID:24723824

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

PubMed Central

Ionescu, Danny; Siebert, Christian; Polerecky, Lubos; Munwes, Yaniv Y.; Lott, Christian; Häusler, Stefan; Bižić-Ionescu, Mina; Quast, Christian; Peplies, Jörg; Glöckner, Frank Oliver; Ramette, Alban; Rödiger, Tino; Dittmar, Thorsten; Oren, Aharon; Geyer, Stefan; Stärk, Hans-Joachim; Sauter, Martin; Licha, Tobias; Laronne, Jonathan B.; de Beer, Dirk

2012-01-01

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit. PMID:22679498

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

[Microbial denitrogenation of fuel oil].

PubMed

Li, Shan-shan; Ma, Ting; Li, Guo-qiang; Liang, Feng-lai; Liu, Ru-lin

2006-12-01

The amount of organic nitrides contained in fuel oil is smaller than the one of organic sulfur compounds, but the existence of them is enough to affect the invariability of oil product greatly , and has a big effect on the color of oil. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing the catalyzing rate of the catalyst and increasing process costs. Further more, some nitrogen organic compounds possess mutagenic and toxic activities. The combustion of these contaminants form nitrogen oxides (NOx), releasing of which to the air will cause the formation of acid rain and hence to air pollution. The classical hydroprocessing methods of nitrogen removal are costly and complicated, so the scientists are more and more interested in microbial denitrogenation. The aspects as follows are introduced, including the aromatic nitrogen compounds of fuel oil, the varieties of denitrogenation techincs, the classes of microbial denitrogenation and its biochemical pathways, molecular genetics developments of carbazole-degradative genes, and our opinion of the research direction in the future.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

DOE PAGES

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; ...

2015-07-22

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla withmore » no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.« less

Trimethylamine N-Oxide: The Good, the Bad and the Unknown.

PubMed

Velasquez, Manuel T; Ramezani, Ali; Manal, Alotaibi; Raj, Dominic S

2016-11-08

Trimethylamine N -oxide (TMAO) is a small colorless amine oxide generated from choline, betaine, and carnitine by gut microbial metabolism. It accumulates in the tissue of marine animals in high concentrations and protects against the protein-destabilizing effects of urea. Plasma level of TMAO is determined by a number of factors including diet, gut microbial flora and liver flavin monooxygenase activity. In humans, a positive correlation between elevated plasma levels of TMAO and an increased risk for major adverse cardiovascular events and death is reported. The atherogenic effect of TMAO is attributed to alterations in cholesterol and bile acid metabolism, activation of inflammatory pathways and promotion foam cell formation. TMAO levels increase with decreasing levels of kidney function and is associated with mortality in patients with chronic kidney disease. A number of therapeutic strategies are being explored to reduce TMAO levels, including use of oral broad spectrum antibiotics, promoting the growth of bacteria that utilize TMAO as substrate and the development of target-specific molecules with varying level of success. Despite the accumulating evidence, it is questioned whether TMAO is the mediator of a bystander in the disease process. Thus, it is important to undertake studies examining the cellular signaling in physiology and pathological states in order to establish the role of TMAO in health and disease in humans.

Mechanisms and pathways of aniline elimination from aquatic environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyons, C.D.; Katz, S.; Bartha, R.

1984-09-01

The fate of aniline, a representative of arylamine pollutants derived from the manufacture of dyes, coal liquefaction, and pesticide degradation, was comprehensively evaluated by use of unpolluted and polluted pond water as model environments. Evaporation plus autoxidation proved to be minor elimination mechanisms, removing ca. 1% of the added aniline per day. Instantaneous binding to humic components of a 0.1% sewage sludge inoculum removed 4%. Biodegradation of aniline in pond water was accelerated by the sewage sludge inoculum. A substantial portion of the degraded aniline carbon was mineralized to CO/sub 2/ within a 1-week period, and microbial biomass was formedmore » as a result of analine utilization. Biodegradation was clearly the most significant removal mechanism of polluting aniline from pond water. A gas chromatographic-mass spectrometric analysis of biodegradation intermediates revealed that the major pathway of aniline biodegradation in pond water involved oxidative deamination to catechol, which was further metabolized through cis,cis-muconic, beta-ketoadipic, levulinic, and succinic acid intermediates to CO/sub 2/. Minor biodegradation pathways involved reversible acylation to acetanilide and formanilide, whereas N-oxidation resulted in small amounts of oligomeric condensation products. 36 references, 4 figures, 3 tables.« less

Neutrophil-mediated oxidative burst and host defense are controlled by a Vav-PLCγ2 signaling axis in mice

PubMed Central

Graham, Daniel B.; Robertson, Charles M.; Bautista, Jhoanne; Mascarenhas, Francesca; Diacovo, M. Julia; Montgrain, Vivianne; Lam, Siu Kit; Cremasco, Viviana; Dunne, W. Michael; Faccio, Roberta; Coopersmith, Craig M.; Swat, Wojciech

2007-01-01

Oxidative burst, a critical antimicrobial mechanism of neutrophils, involves the rapid generation and release of reactive oxygen intermediates (ROIs) by the NADPH oxidase complex. Genetic mutations in an NADPH oxidase subunit, gp91 (also referred to as NOX2), are associated with chronic granulomatous disease (CGD), which is characterized by recurrent and life-threatening microbial infections. To combat such infections, ROIs are produced by neutrophils after stimulation by integrin-dependent adhesion to the ECM in conjunction with stimulation from inflammatory mediators, or microbial components containing pathogen-associated molecular patterns. In this report, we provide genetic evidence that both the Vav family of Rho GTPase guanine nucleotide exchange factors (GEFs) and phospholipase C–γ2 (PLC-γ2) are critical mediators of adhesion-dependent ROI production by neutrophils in mice. We also demonstrated that Vav was critically required for neutrophil-dependent host defense against systemic infection by Staphylococcus aureus and Pseudomonas aeruginosa, 2 common pathogens associated with fatal cases of hospital-acquired pneumonia. We identified a molecular pathway in which Vav GEFs linked integrin-mediated signaling with PLC-γ2 activation, release of intracellular Ca2+ cations, and generation of diacylglycerol to control assembly of the NADPH oxidase complex and ROI production by neutrophils. Taken together, our data indicate that integrin-dependent signals generated during neutrophil adhesion contribute to the activation of NADPH oxidase by a variety of distinct effector pathways, all of which require Vav. PMID:17932569

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

NASA Astrophysics Data System (ADS)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

The Role of Thaumarchaeota in N2O generation in an unconfined basalt-sandstone aquifer system, Western Victoria (Australia)

NASA Astrophysics Data System (ADS)

Moreau, J. W.; Hepburn, E.

2015-12-01

The mechanisms by which nitrous oxide is produced and transformed in groundwater are poorly understood. Here we used GC-MS and nitrogen and oxygen isotope analyses to quantify nitrate, ammonia and nitrous oxide levels in nitrate-contaminated aquifers in the Newer Volcanics province of Western Victoria. Quantitative polymerase chain reaction (Q-PCR), and phylogenetic analyses of functional nitrogen-cycling and 16S rRNA genes, of whole community microbial DNA from groundwater samples obtained from different depths within different aquifers with low-flow pumping revealed nitrate, ammonia and nitrous oxide levels of up to ~40 mg/L, up to ~0.85 mg/L, and up to ~770 nM, respectively in several groundwater samples. Delta 15N and delta 18O values ranged from -2.68‰ to 68.19‰ and -3.37‰ to 26.83‰, respectively. Nitrate and nitrous oxide concentrations decreased with depth in the unconfined aquifer, while TOC generally increased. Higher ammonia levels were observed in more heavily ferruginized sandstones. Increaased nitrate and nitrous oxide levels were found within the principal basaltic aquifers. Q-PCR results showed variable concentrations of nir, nar, nos and amo genes associated with different redox transformations along the nitrification and denitrification pathways, indicating potential nitrous oxide formation via both pathways within different depths in the aquifer. 16S rRNA gene analyses implicated an important role for the Thaumarchaeota in groundwater nitrogen cycling.

HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function.

PubMed

Guard, B C; Suchodolski, J S

2016-06-01

Recent molecular studies have revealed a complex microbiota in the dog intestine. Convincing evidence has been reported linking changes in microbial communities to acute and chronic gastrointestinal inflammation, especially in canine inflammatory bowel disease (IBD). The most common microbial changes observed in intestinal inflammation are decreases in the bacterial phyla Firmicutes (i.e., Lachnospiraceae, Ruminococcaceae, and ) and Bacteroidetes, with concurrent increases in Proteobacteria (i.e., ). Due to the important role of microbial-derived metabolites for host health, it is important to elucidate the metabolic consequences of gastrointestinal dysbiosis and physiological pathways implicated in specific disease phenotypes. Metagenomic studies have used shotgun sequencing of DNA as well as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to characterize functional changes in the bacterial metagenome in gastrointestinal disease. Furthermore, wide-scale and untargeted measurements of metabolic products derived by the host and the microbiota in intestinal samples allow a better understanding of the functional alterations that occur in gastrointestinal disease. For example, changes in bile acid metabolism and tryptophan catabolism recently have been reported in humans and dogs. Also, metabolites associated with the pentose phosphate pathway were significantly altered in chronic gastrointestinal inflammation and indicate the presence of oxidative stress in dogs with IBD. This review focuses on the advancements made in canine metagenomics and metabolomics and their implications in understanding gastrointestinal disease as well as the development of better treatment approaches.

Following Carbon Isotopes from Methane to Molecules

NASA Astrophysics Data System (ADS)

Freeman, K. H.

2017-12-01

Continuous-flow methods introduced by Hayes (Matthews and Hayes, 1978; Freeman et al., 1990; Hayes et al., 1990) for compound-specific isotope analyses (CSIA) transformed how we study the origins and fates of organic compounds. This analytical revolution launched several decades of research in which researchers connect individual molecular structures to diverse environmental and climate processes affecting their isotopic profiles. Among the first applications, and one of the more dramatic isotopically, was tracing the flow of natural methane into cellular carbon and cellular biochemical constituents. Microbial oxidation of methane can be tracked by strongly 13C-depleted organic carbon in early Earth sedimentary environments, in marine and lake-derived biomarkers in oils, and in modern organisms and their environments. These signatures constrain microbial carbon cycling and inform our understanding of ocean redox. The measurement of molecular isotopes has jumped forward once again, and it is now possible to determine isotope abundances at specific positions within increasingly complex organic structures. In addition, recent analytical developments have lowered sample sensitivity limits of CSIA to picomole levels. These new tools have opened new ways to measure methane carbon in the natural environment and within biochemical pathways. This talk will highlight how molecular isotope methods enable us to follow the fate of methane carbon in complex environments and along diverse metabolic pathways, from trace fluids to specific carbon positions within microbial biomarkers.

Microbial degradation and toxicity of hexahydro-1,3,5-trinitro-1,3,5-triazine.

PubMed

Khan, Muhammad Imran; Lee, Jaejin; Park, Joonhong

2012-10-01

In the present work, current knowledge on the potential fate, microbial degradation, and toxicity of hexahydro- 1,3,5-trinitro-1,3,5-triazine (RDX) was thoroughly reviewed, focusing on the toxicological assessment of a variety of potential RDX degradation pathways in bacteria and fungi. The present review on microbial degradation pathways and toxicities of degradation intermediates suggests that, among aerobic RDX degradation pathways, the one via denitration may be preferred in a toxicological perspective, and that among anaerobic pathways, those forming 4- nitro-2,4-diazabutanal (NDAB) via ring cleavage of 1-nitroso- 3,5-dinitro-1,3,5-triazinane (MNX) may be toxicologically advantageous owing to its potential mineralization under partial or complete anoxic conditions. These findings provide important information on RDX-degrading microbial pathways, toxicologically most suitable to be stimulated in contaminated fields.

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

PubMed Central

Manzoor, Shahid; Bongcam-Rudloff, Erik; Schnürer, Anna; Müller, Bettina

2016-01-01

Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle. PMID:27851830

Isotopomeric characterization of nitrous oxide produced by reaction of enzymes extracted from nitrifying and denitrifying bacteria

NASA Astrophysics Data System (ADS)

Yamazaki, T.; Hozuki, T.; Arai, K.; Toyoda, S.; Koba, K.; Fujiwara, T.; Yoshida, N.

2014-05-01

Nitrous oxide (N2O) is a potent greenhouse gas and produced in denitrification and nitrification by various microorganisms. Site preference (SP) of 15N in N2O, which is defined as the difference in the natural abundance of isotopomers 14N15NO and 15N14NO relative to 14N14NO, has been reported to be a useful tool to quantitatively distinguish N2O production pathways. To determine representative SP values for each microbial process, we firstly measured SP of N2O produced in the enzyme reaction of hydroxylamine oxidoreductase (HAO) purified from two species of ammonia oxidizing bacteria (AOB), Nitrosomonas europaea and Nitrosococcus oceani, and that of nitric oxide reductase (NOR) from Paracoccus denitrificans. The SP value for NOR reaction (-5.9 ± 2.1‰) showed nearly the same value as that reported for N2O produced by P. denitrificans in pure culture. In contrast, SP value for HAO reaction (36.3 ± 2.3‰) was a little higher than the values reported for N2O produced by AOB in aerobic pure culture. Using the SP values obtained by HAO and NOR reactions, we calculated relative contribution of the nitrite (NO2-) reduction (which is followed by NO reduction) to N2O production by N. oceani incubated under different O2 availability. Our calculations revealed that previous in vivo studies might have underestimated the SP value for the NH2OH oxidation pathway possibly due to a small contribution of NO2- reduction pathway. Further evaluation of isotopomer signatures of N2O using common enzymes of other processes related to N2O would improve the isotopomer analysis of N2O in various environments.

Isotopomeric characterization of nitrous oxide produced by reaction of enzymes extracted from nitrifying and denitrifying bacteria

NASA Astrophysics Data System (ADS)

Yamazaki, T.; Hozuki, T.; Arai, K.; Toyoda, S.; Koba, K.; Fujiwara, T.; Yoshida, N.

2013-10-01

Nitrous oxide (N2O) is a potent greenhouse gas and produced in denitrification and nitrification in environmental nitrogen cycle by various microorganism. Site preference (SP) of 15N in N2O, which is defined as the difference in the natural abundance of isotopomers 14N15NO and 15N14NO relative to 14N14NO, has been reported to be a useful tool to quantitatively distinguish N2O production pathway. To determine representative SP value for each microbial process, we firstly measured SP of N2O produced in the enzyme reaction of hydroxylamine oxidoreductase (HAO) purified from two species of ammonia oxidizing bacteria (AOB), Nitrosomonas europaea and Nitrosococcus oceani, and that of nitric oxide reductase (NOR) from Paracoccus denitrificans, respectively. The SP value for NOR reaction (-5.9 ± 2.1‰) showed nearly the same value as that reported for N2O produced by P. denitrificans in pure culture. In contrast, SP value for HAO reaction (36.3 ± 2.3‰) was a little higher than the values reported for N2O produced by AOB in aerobic pure culture. Using the SP values obtained by HAO and NOR reactions, we calculated relative contribution of the nitrite (NO2-) reduction (which is followed by NO reduction) to N2O production by N. oceani incubated under different O2 availability. Our calculations revealed that previous in vivo studies might have underestimated the SP value for NH2OH oxidation pathway possibly due to a small contribution of NO2- reduction pathway. Further evaluation of isotopomer signatures of N2O using common enzymes of other processes related to N2O would improve the isotopomer analysis of N2O in various environments.

Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes*

PubMed Central

Nam, Young-Woo; Nihira, Takanori; Arakawa, Takatoshi; Saito, Yuka; Kitaoka, Motomitsu; Nakai, Hiroyuki; Fushinobu, Shinya

2015-01-01

The microbial oxidative cellulose degradation system is attracting significant research attention after the recent discovery of lytic polysaccharide mono-oxygenases. A primary product of the oxidative and hydrolytic cellulose degradation system is cellobionic acid (CbA), the aldonic acid form of cellobiose. We previously demonstrated that the intracellular enzyme belonging to glycoside hydrolase family 94 from cellulolytic fungus and bacterium is cellobionic acid phosphorylase (CBAP), which catalyzes reversible phosphorolysis of CbA into glucose 1-phosphate and gluconic acid (GlcA). In this report, we describe the biochemical characterization and the three-dimensional structure of CBAP from the marine cellulolytic bacterium Saccharophagus degradans. Structures of ligand-free and complex forms with CbA, GlcA, and a synthetic disaccharide product from glucuronic acid were determined at resolutions of up to 1.6 Å. The active site is located near the dimer interface. At subsite +1, the carboxylate group of GlcA and CbA is recognized by Arg-609 and Lys-613. Additionally, one residue from the neighboring protomer (Gln-190) is involved in the carboxylate recognition of GlcA. A mutational analysis indicated that these residues are critical for the binding and catalysis of the aldonic and uronic acid acceptors GlcA and glucuronic acid. Structural and sequence comparisons with other glycoside hydrolase family 94 phosphorylases revealed that CBAPs have a unique subsite +1 with a distinct amino acid residue conservation pattern at this site. This study provides molecular insight into the energetically efficient metabolic pathway of oxidized sugars that links the oxidative cellulolytic pathway to the glycolytic and pentose phosphate pathways in cellulolytic microbes. PMID:26041776

Systematic engineering of the central metabolism in Escherichia coli for effective production of n-butanol.

PubMed

Saini, Mukesh; Li, Si-Yu; Wang, Ze Win; Chiang, Chung-Jen; Chao, Yun-Peng

2016-01-01

Microbes have been extensively explored for production of environment-friendly fuels and chemicals. The microbial fermentation pathways leading to these commodities usually involve many redox reactions. This makes the fermentative production of highly reduced products challenging, because there is a limited NADH output from glucose catabolism. Microbial production of n-butanol apparently represents one typical example. In this study, we addressed the issue by adjustment of the intracellular redox state in Escherichia coli. This was initiated with strain BuT-8 which carries the clostridial CoA-dependent synthetic pathway. Three metabolite nodes in the central metabolism of the strain were targeted for engineering. First, the pyruvate node was manipulated by enhancement of pyruvate decarboxylation in the oxidative pathway. Subsequently, the pentose phosphate (PP) pathway was amplified at the glucose-6-phosphate (G6P) node. The pathway for G6P isomerization was further blocked to force the glycolytic flux through the PP pathway. It resulted in a growth defect, and the cell growth was later recovered by limiting the tricarboxylic acid cycle at the acetyl-CoA node. Finally, the resulting strain exhibited a high NADH level and enabled production of 6.1 g/L n-butanol with a yield of 0.31 g/g-glucose and a productivity of 0.21 g/L/h. The production efficiency of fermentative products in microbes strongly depends on the intracellular redox state. This work illustrates the flexibility of pyruvate, G6P, and acetyl-CoA nodes at the junction of the central metabolism for engineering. In principle, high production of reduced products of interest can be achieved by individual or coordinated modulation of these metabolite nodes.

Analysis of the coexisting pathways for NO and N2O formation in Chernozem using the (15)N-tracer SimKIM-Advanced model.

PubMed

Stange, Claus Florian; Spott, Oliver; Russow, Rolf

2013-01-01

The nitrogen (N) cycle consists of a variety of microbial processes. These processes often occur simultaneously in soils, but respond differently to local environmental conditions due to process-specific biochemical restrictions (e.g. oxygen levels). Hence, soil nitrogen cycling (e.g. soil N gas production through nitrification and denitrification) is individually affected through these processes, resulting in the complex and highly dynamic behaviour of total soil N turnover. The development and application of methods that facilitate the quantification of individual contributions of coexisting processes is a fundamental prerequisite for (i) understanding the dynamics of soil N turnover and (ii) implementing these processes in ecosystem models. To explain the unexpected results of the triplet tracer experiment (TTE) of Russow et al. (Role of nitrite and nitric oxide in the processes of nitrification and denitrification in soil: results from (15)N tracer experiments. Soil Biol Biochem. 2009;41:785-795) the existing SimKIM model was extended to the SimKIM-Advanced model through the addition of three separate nitrite subpools associated with ammonia oxidation, oxidation of organic nitrogen (Norg), and denitrification, respectively. For the TTE, individual treatments with (15)N ammonium, (15)N nitrate, and (15)N nitrite were conducted under oxic, hypoxic, and anoxic conditions, respectively, to clarify the role of nitric oxide as a denitrification intermediate during N2O formation. Using a split nitrite pool, this analysis model explains the observed differences in the (15)N enrichments in nitric oxide (NO) and nitrous oxide (N2O) which occurred in dependence on different oxygen concentrations. The change from oxic over hypoxic to anoxic conditions only marginally increased the NO and N2O release rates (1.3-fold). The analysis using the model revealed that, under oxic and hypoxic conditions, Norg-based N2O production was the dominant pathway, contributing to 90 and 50 % of the total soil N2O release. Under anoxic conditions, denitrification was the dominant process for soil N2O release. The relative contribution of Norg to the total soil NO release was small. Ammonia oxidation served as the major pathway of soil NO release under oxic and hypoxic conditions, while denitrification was dominant under anoxic conditions. The model parameters for soil with moderate soil organic matter (SOM) content were not scalable to an additional data set for soil with higher SOM content, indicating a strong influence of SOM content on microbial N turnover. Thus, parameter estimation had to be re-calculated for these conditions, highlighting the necessity of individual soil-dependent parameter estimations.

Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor.

PubMed

Ali, Muhammad; Rathnayake, Rathnayake M L D; Zhang, Lei; Ishii, Satoshi; Kindaichi, Tomonori; Satoh, Hisashi; Toyoda, Sakae; Yoshida, Naohiro; Okabe, Satoshi

2016-10-01

Nitrous oxide (N2O) production pathway in a signal-stage nitritation-anammox sequencing batch reactor (SBR) was investigated based on a multilateral approach including real-time N2O monitoring, N2O isotopic composition analysis, and in-situ analyses of spatial distribution of N2O production rate and microbial populations in granular biomass. N2O emission rate was high in the initial phase of the operation cycle and gradually decreased with decreasing NH4(+) concentration. The average emission of N2O was 0.98 ± 0.42% and 1.35 ± 0.72% of the incoming nitrogen load and removed nitrogen, respectively. The N2O isotopic composition analysis revealed that N2O was produced via NH2OH oxidation and NO2(-) reduction pathways equally, although there is an unknown influence from N2O reduction and/or anammox N2O production. However, the N2O isotopomer analysis could not discriminate the relative contribution of nitrifier denitrification and heterotrophic denitrification in the NO2(-) reduction pathway. Various in-situ techniques (e.g. microsensor measurements and FISH (fluorescent in-situ hybridization) analysis) were therefore applied to further identify N2O producers. Microsensor measurements revealed that approximately 70% of N2O was produced in the oxic surface zone, where nitrifiers were predominantly localized. Thus, NH2OH oxidation and NO2 reduction by nitrifiers (nitrifier-denitrification) could be responsible for the N2O production in the oxic zone. The rest of N2O (ca. 30%) was produced in the anammox bacteria-dominated anoxic zone, probably suggesting that NO2(-) reduction by coexisting putative heterotrophic denitrifiers and some other unknown pathway(s) including the possibility of anammox process account for the anaerobic N2O production. Further study is required to identify the anaerobic N2O production pathways. Our multilateral approach can be useful to quantitatively examine the relative contributions of N2O production pathways. Good understanding of the key N2O production pathways is essential to establish a strategy to mitigate N2O emission from biological nitrogen removal processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Hypersaline Microbial Mat Lipid Biomarkers

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

2002-01-01

Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

PubMed

Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

2017-08-24

Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

Integrating 'omic' data and biogeochemical modeling: the key to understanding the microbial regulation of matter cycling in soil

NASA Astrophysics Data System (ADS)

Pagel, Holger; Kandeler, Ellen; Seifert, Jana; Camarinha-Silva, Amélia; Kügler, Philipp; Rennert, Thilo; Poll, Christian; Streck, Thilo

2016-04-01

Matter cycling in soils and associated soil functions are intrinsically controlled by microbial dynamics. It is therefore crucial to consider functional traits of microorganisms in biogeochemical models. Tremendous advances in 'omic' methods provide a plethora of data on physiology, metabolic capabilities and ecological life strategies of microorganisms in soil. Combined with isotopic techniques, biochemical pathways and transformations can be identified and quantified. Such data have been, however, rarely used to improve the mechanistic representation of microbial dynamics in soil organic matter models. It is the goal of the Young Investigator Group SoilReg to address this challenge. Our general approach is to tightly integrate experiments and biochemical modeling. NextGen sequencing will be applied to identify key functional groups. Active microbial groups will be quantified by measurements of functional genes and by stable isotope probing methods of DNA and proteins. Based on this information a biogeochemical model that couples a mechanistic representation of microbial dynamics with physicochemical processes will be set up and calibrated. Sensitivity and stability analyses of the model as well as scenario simulations will reveal the importance of intrinsic and extrinsic controls of organic matter turnover. We will demonstrate our concept and present first results of two case studies on pesticide degradation and methane oxidation.

Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.

PubMed

Ding, Jing; Lu, Yong-Ze; Fu, Liang; Ding, Zhao-Wei; Mu, Yang; Cheng, Shuk H; Zeng, Raymond J

2017-03-01

Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils.

PubMed

Sutton, Nora B; Langenhoff, Alette A M; Lasso, Daniel Hidalgo; van der Zaan, Bas; van Gaans, Pauline; Maphosa, Farai; Smidt, Hauke; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-03-01

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Microbial synthesis of medium-chain chemicals from renewables.

PubMed

Sarria, Stephen; Kruyer, Nicholas S; Peralta-Yahya, Pamela

2017-12-01

Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the metabolic engineer; instead, fatty acid synthesis and reversed β-oxidation are manipulated to synthesize medium-chain chemical precursors. Even so, chain lengths remain difficult to control, which means that purification must be used to obtain the desired products, titers of which are typically low and rarely exceed milligrams per liter. By engineering the substrate specificity and activity of the pathway enzymes that generate the fatty acyl intermediates and chain-tailoring enzymes, researchers can boost the type and yield of medium-chain chemicals. Development of technologies to both manipulate chain-tailoring enzymes and to assay for products promises to enable the generation of g/L yields of medium-chain chemicals.

Microbial ecology of soda lakes: investigating sulfur and nitrogen cycling at Mono Lake, CA, USA

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Phillips, A. A.; Wells, M.; Bao, R.; Fullerton, K. M.; Stamps, B. W.; Speth, D. R.; Johnson, H.; Sessions, A. L.

2017-12-01

Soda lakes represent unique ecosystems characterized by extremes of pH, salinity and distinct geochemical cycling. Despite these extreme conditions, soda lakes are important repositories of biological adaptation and have a highly functional microbial system. We investigated the biogeochemical cycling of sulfur and nitrogen compounds in Mono Lake, California, located east of the Sierra Nevada mountains. Mono lake is characterized by hyperalkaline, hypersaline and high sulfate concentrations and can enter prolonged periods of meromixis due to freshwater inflow. Typically, the microbial sulfur cycle is highly active in soda lakes with both oxidation and reduction of sulfur compounds. However, the biological sulfur cycle is connected to many other main elemental cycles such as carbon, nitrogen and metals. Here we investigated the interaction between sulfur and nitrogen cycling in Mono lake using a combination of molecular, isotopic, and geochemical observations to explore the links between microbial phylogenetic composition and functionality. Metagenomic and 16S rRNA gene amplicon sequencing were determined at two locations and five depths in May 2017. 16S rRNA gene amplicon sequencing analysis revealed organisms capable of both sulfur and nitrogen cycling. The relative abundance and distribution of functional genes (dsrA, soxAB, nifH, etc) were also determined. These genetic markers indicate the potential in situ relevance of specific carbon, nitrogen, and sulfur pathways in the water column prior to the transition to meromictic stratification. However, genes for sulfide oxidation, denitrification, and ammonification were present. Genome binning guided by the most abundant dsrA sequences, GC content, and abundance with depth identified a Thioalkalivibrio paradoxus bin containing genes capable of sulfur oxidation, denitrification, and nitrate reduction. The presence of a large number of sulfur and nitrogen cycling genes associated with Thioalkalivibrio paradoxus suggests thiosulfate oxidation may be coupled to nitrate reduction despite the extremely low level of nitrate in Mono Lake. Our results illustrate the centrality of living organisms in both shaping and responding to geochemical cycles, as well as future directions for exploring coupled biogeochemical cycles in Mono Lake.

Fluctuation Analysis of Redox Potential to Distinguish Microbial Fe(II) Oxidation.

PubMed

Enright, A M L; Ferris, F G

2016-11-01

We developed a novel method for distinguishing abiotic and biological iron oxidation in liquid media using oxidation-reduction (redox) potential time series data. The instrument and processing algorithm were tested by immersing the tip of a Pt electrode with an Ag-AgCl reference electrode into an active iron-oxidizing biofilm in a groundwater discharge zone, as well as in two abiotic systems: a killed sample and a chemical control from the same site. We used detrended fluctuation analysis to characterize average root mean square fluctuation behavior, which was distinct in the live system. The calculated α value scaling exponents determined by detrended fluctuation analysis were significantly different at p < 0.001. This indicates that time series of electrode response data may be used to distinguish live and abiotic chemical reaction pathways. Due to the simplicity, portability, and small size, it may be suitable for characterization of extraterrestrial environments where water has been observed, such as Mars and Europa. Key Words: Oxidation-reduction potential-Detrended fluctuation analysis-Iron-oxidizing bacteria. Astrobiology 16, 846-852.

Isotopic Monitoring of N2O Emissions from Wastewater Treatment: Evidence for N2O Production Associated with Anammox Metabolism?

NASA Astrophysics Data System (ADS)

Harris, E. J.; Wunderlin, P.; Joss, A.; Emmenegger, L.; Kipf, M.; Wolf, B.; Mohn, J.

2015-12-01

Microbial production is the major source of N2O, the strongest greenhouse gas produced within the nitrogen cycle, and the most important stratospheric ozone destructant released in the 21st century. Wastewater treatment is an important and growing source of N2O, with best estimates predicting N2O emissions from this sector will have increased by >25% by 2020. Novel treatment employing partial nitritation-anammox, rather than traditional nitrification-denitrification, has the potential to achieve a neutral carbon footprint due to increased biogas production - if N2O production accounts for <0.5-1% of total nitrogen turnover. As a further motivation for this research, microbial pathways identified from wastewater treatment can be applied to our understanding of N cycling in the natural environment. This study presents the first online isotopic measurements of offgas N2O from a partial-nitritation anammox reactor 1. The measured N2O isotopic composition - in particular the N2O isotopic site preference (SP = δ15Nα - δ15Nβ) - was used to understand N2O production pathways in the reactor. When N2O emissions peaked due to high dissolved oxygen concentrations, low SP showed that N2O was produced primarily via nitrifier denitrification by ammonia oxidizing bacteria (AOBs). N2O production by AOBs via NH2OH oxidation, in contrast, did not appear to be important under any conditions. Over the majority of the one-month measurement period, the measured SP was much higher than expected following our current understanding of N2O production pathways 2. SP reached 41‰ during normal operating conditions and achieved a maximum of 45‰ when nitrite was added under anoxic conditions. These results could be explained by unexpectedly strong heterotrophic N2O reduction despite low dissolved organic matter concentrations, or by an incomplete understanding of isotopic fractionation during N2O production from NH2OH oxidation by AOBs - however the explanation most consistent with all results is a previously unknown N2O production pathway associated with anammox metabolism. Harris et al. (2015) Water Res., 83: 258-270. Wunderlin et al. (2013) Env. Sci. Tech., 47: 1339-1348.

Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

PubMed

Yu, Ping; Chen, Xingge; Li, Peng

2017-09-01

Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Soil Fluxomics: Disentangling Microbial Group Specific Metabolism by Modeling of 13C-Incorporation into PLFAs

NASA Astrophysics Data System (ADS)

Apostel, C.; Kuzyakov, Y.; Dippold, M. A.

2016-12-01

Soils are the largest terrestrial C sinks and microorganisms are the most important drivers of organic matter (OM) dynamics in soils: C allocation to ana- or catabolism in microbial cells is the decisive step, whether C gets oxidized to CO2 or whether it is allocated to microbial biomass, which, after cell death can be stabilized in soils. The metabolic parameter describing the ratio between the two fluxes is the carbon use efficiency (CUE), which can be assessed by position-specific labeling followed by metabolic flux modelling. However, to disentangle the single microbial groups' contribution to the bulk soil CUE, a tracing of individual groups metabolism is necessary. We assessed short-term (3 and 10 days) transformations of monosaccharides by adding position-specifically 13C labeled glucose to soil in a field experiment. Incorporation of 13C in the microbial PLFAs enabled us to distinguish individual microbial groups metabolic fluxes and compare their C-utilization efficiency using a quantitative C-flux model. The position-specific pattern in PLFAs revealed two sets of microorganisms: one metabolized glucose mainly by glycolysis and the other mainly by the pentose-phosphate pathway, which results in a higher CUE. Both of those sets included prokaryotic as well as eukaryotic microorganisms. This demonstrates that phylogenetic grouping is not decisive for the metabolic behavior of a microbial group and that the contribution of individual group members to the soil C fluxes cannot be concluded from their phylogeny.

Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

PubMed Central

Peng, Qiannan; Jiang, Shuaiming; Chen, Jieling; Ma, Chenchen; Huo, Dongxue; Shao, Yuyu; Zhang, Jiachao

2018-01-01

Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing tropical microbial resources. PMID:29559966

Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chourey, Karuna; Nissen, Silke; Vishnivetskaya, T.

2013-01-01

High performance mass spectrometry instrumentation coupled with improved protein extraction techniques enable metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e., 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e., Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences in protein expression between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected up-gradient of the EVO injection points. In particular,more » proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate (PHB) granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of a Dechloromonas sp. was highly expressed suggesting active nitrous oxide (N2O) respiration. c-type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that metal reduction has not commenced 4 days post EVO delivery. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique for complementing nucleic acid-based approaches.« less

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

PubMed

Dyksma, Stefan; Bischof, Kerstin; Fuchs, Bernhard M; Hoffmann, Katy; Meier, Dimitri; Meyerdierks, Anke; Pjevac, Petra; Probandt, David; Richter, Michael; Stepanauskas, Ramunas; Mußmann, Marc

2016-08-01

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.

Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

NASA Astrophysics Data System (ADS)

Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

2014-12-01

Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine oxidoreductase (HAO) were abundant and more similar to known anammox HAO genes than those used in aerobic ammonia oxidation. The elevated levels of anammox transcripts suggest that anammox may play a significant role in nitrogen cycling within groundwater systems.

Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides.

PubMed

Kondo, Katsuhito; Okamoto, Akihiro; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-07-07

In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79.

PubMed

Sedlacek, Christopher J; Nielsen, Susanne; Greis, Kenneth D; Haffey, Wendy D; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J; Bollmann, Annette

2016-08-01

Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The life cycle of iron Fe(III) oxide: impact of fungi and bacteria

NASA Astrophysics Data System (ADS)

Bonneville, Steeve

2014-05-01

Iron oxides are ubiquitous reactive constituents of soils, sediments and aquifers. They exhibit vast surface areas which bind a large array of trace metals, nutrients and organic molecules hence controlling their mobility/reactivity in the subsurface. In this context, understanding the "life cycle" of iron oxide in soils is paramount to many biogeochemical processes. Soils environments are notorious for their extreme heterogeneity and variability of chemical, physical conditions and biological agents at play. Here, we present studies investigating the role of two biological agents driving iron oxide dynamics in soils, root-associated fungi (mycorrhiza) and bacteria. Mycorrhiza filaments (hypha) grow preferentially around, and on the surface of nutrient-rich minerals, making mineral-fungi contact zones, hot-spots of chemical alteration in soils. However, because of the microscopic nature of hyphae (only ~ 5 µm wide for up to 1 mm long) and their tendency to strongly adhere to mineral surface, in situ observations of this interfacial micro-environment are scarce. In a microcosm, ectomycorrhiza (Paxillus involutus) was grown symbiotically with a pine tree (Pinus sylvestris) in the presence of freshly-cleaved biotite under humid, yet undersaturated, conditions typical of soils. Using spatially-resolved ion milling technique (FIB), transmission electron microscopy and spectroscopy (TEM/STEM-EDS), synchrotron based X-ray microscopy (STXM), we were able to quantify the speciation of Fe at the biotite-hypha interface. The results shows that substantial oxidation of biotite structural-Fe(II) into Fe(III) subdomains occurs at the contact zone between mycorrhiza and biotite. Once formed, iron(III) oxides can reductively dissolve under suboxic conditions via several abiotic and microbial pathways. In particular, they serve as terminal electron acceptors for the oxidation of organic matter by iron reducing bacteria. We aimed here to understand the role of Fe(III) mineral properties, in particular the influence of solubility, in the kinetics of microbial iron reduction. We used the facultative anaerobic gram-positive bacterium Shewanella putrefaciens as model iron reducing bacterium, with several ferrihydrite, hematite, goethite or lepidocrocite as electron acceptor, and lactate as electron donor. Maximum microbial Fe(III) reduction rates and solubility of Fe(III) phases were found to positively correlated in a Linear Free Energy Relationship suggesting a rate limitation by the electron transfer between iron reductases and a Fe(III) center, or by the subsequent desorption of Fe2+ from the iron oxide mineral surface.

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

NASA Astrophysics Data System (ADS)

Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

2016-07-01

Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

Redox metabolites signal polymicrobial biofilm development via the NapA oxidative stress cascade in Aspergillus

PubMed Central

Zheng, He; Kim, Jaekuk; Liew, Mathew; Yan, John K.; Herrera, Oscar; Bok, JinWoo; Kelleher, Neil L.; Keller, Nancy P.; Wang, Yun

2014-01-01

Summary Background Filamentous fungi and bacteria form mixed-species biofilms in nature and diverse clinical contexts. They secrete a wealth of redox-active small molecule secondary metabolites, which are traditionally viewed as toxins that inhibit growth of competing microbes. Results Here we report that these “toxins” can act as interspecies signals, affecting filamentous fungal development via oxidative stress regulation. Specifically, in co-culture biofilms, Pseudomonas aeruginosa phenazine-derived metabolites differentially modulated Aspergillus fumigatus development, shifting from weak vegetative growth to induced asexual sporulation (conidiation) along a decreasing phenazine gradient. The A. fumigatus morphological shift correlated with the production of phenazine radicals and concomitant reactive oxygen species (ROS) production generated by phenazine redox cycling. Phenazine conidiation signaling was conserved in the genetic model A. nidulans, and mediated by NapA, a homolog of AP-1-like bZIP transcription factor, which is essential for the response to oxidative stress in humans, yeast, and filamentous fungi. Expression profiling showed phenazine treatment induced a NapA-dependent response of the global oxidative stress metabolome including the thioredoxin, glutathione and NADPH-oxidase systems. Conidiation induction in A. nidulans by another microbial redox-active secondary metabolite, gliotoxin, also required NapA. Conclusions This work highlights that microbial redox metabolites are key signals for sporulation in filamentous fungi, which are communicated through an evolutionarily conserved eukaryotic stress response pathway. It provides a foundation for interspecies signaling in environmental and clinical biofilms involving bacteria and filamentous fungi. PMID:25532893

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

PubMed Central

Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

2016-01-01

Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil.

PubMed

Soares, Johnny R; Cassman, Noriko A; Kielak, Anna M; Pijl, Agata; Carmo, Janaína B; Lourenço, Kesia S; Laanbroek, Hendrikus J; Cantarella, Heitor; Kuramae, Eiko E

2016-07-27

Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Rheological Enhancement of Pork Myofibrillar Protein-Lipid Emulsion Composite Gels via Glucose Oxidase Oxidation/Transglutaminase Cross-Linking Pathway.

PubMed

Wang, Xu; Xiong, Youling L; Sato, Hiroaki

2017-09-27

Porcine myofibrillar protein (MP) was modified with glucose oxidase (GluOx)-iron that produces hydroxyl radicals then subjected to microbial transglutaminase (TGase) cross-linking in 0.6 M NaCl at 4 °C. The resulting aggregation and gel formation of MP were examined. The GluOx-mediated oxidation promoted the formation of both soluble and insoluble protein aggregates via disulfide bonds and occlusions of hydrophobic groups. The subsequent TGase treatment converted protein aggregates into highly cross-linked polymers. MP-lipid emulsion composite gels formed with such polymers exhibited markedly enhanced gelling capacity: up to 4.4-fold increases in gel firmness and 3.5-fold increases in gel elasticity over nontreated protein. Microstructural examination showed small oil droplets dispersed in a densely packed gel matrix when MP was oxidatively modified, and the TGase treatment further contributed to such packing. The enzymatic GluOx oxidation/TGase treatment shows promise to improve the textural properties of emulsified meat products.

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.

PubMed

Pan, Yao; Abell, Guy C J; Bodelier, Paul L E; Meima-Franke, Marion; Sessitsch, Angela; Bodrossy, Levente

2014-08-01

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.

PubMed

Fortunato, Caroline S; Huber, Julie A

2016-08-01

The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched (13)C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE PAGES

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG; ...

2012-11-29

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center.

PubMed

Anantharaman, Karthik; Breier, John A; Dick, Gregory J

2016-01-01

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.

From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

2015-12-01

Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations. Quantitative models to assess microbial group specific metabolic pathways can be generated and parameterized by this approach. The knowledge of submolecular C transformation steps and its regulating factors is essential for understanding C cycling and long-term C storage in soils.

Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney

PubMed Central

Li, Jiangtao; Cui, Jiamei; Yang, Qunhui; Cui, Guojie; Wei, Bingbing; Wu, Zijun; Wang, Yong; Zhou, Huaiyang

2017-01-01

When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting. PMID:28785251

Quantitative X-ray photoelectron spectroscopy-based depth profiling of bioleached arsenopyrite surface by Acidithiobacillus ferrooxidans

NASA Astrophysics Data System (ADS)

Zhu, Tingting; Lu, Xiancai; Liu, Huan; Li, Juan; Zhu, Xiangyu; Lu, Jianjun; Wang, Rucheng

2014-02-01

In supergene environments, microbial activities significantly enhance sulfide oxidation and result in the release of heavy metals, causing serious contamination of soils and waters. As the most commonly encountered arsenic mineral in nature, arsenopyrite (FeAsS) accounts for arsenic contaminants in various environments. In order to investigate the geochemical behavior of arsenic during microbial oxidation of arsenopyrite, (2 3 0) surfaces of arsenopyrite slices were characterized after acidic (pH 2.00) and oxidative decomposition with or without an acidophilic microorganism Acidithiobacillus ferrooxidans. The morphology as well as chemical and elemental depth profiles of the oxidized arsenopyrite surface were investigated by scanning electron microscopy and X-ray photoelectron spectroscopy. With the mediation of bacteria, cell-shaped and acicular pits were observed on the reacted arsenopyrite surface, and the concentration of released arsenic species in solution was 50 times as high as that of the abiotic reaction after 10 days reaction. Fine-scale XPS depth profiles of the reacted arsenopyrite surfaces after both microbial and abiotic oxidation provided insights into the changes in chemical states of the elements in arsenopyrite surface layers. Within the 450 nm surface layer of abiotically oxidized arsenopyrite, Fe(III)-oxides appeared and gradually increased towards the surface, and detectable sulfite and monovalent arsenic appeared above 50 nm. In comparison, higher contents of ferric sulfate, sulfite, and arsenite were found in the surface layer of approximately 3 μm of the microbially oxidized arsenopyrite. Intermediates, such as Fe(III)-AsS and S0, were detectable in the presence of bacteria. Changes of oxidative species derived from XPS depth profiles show the oxidation sequence is Fe > As = S in abiotic oxidation, and Fe > S > As in microbial oxidation. Based on these results, a possible reaction path of microbial oxidation was proposed in a concept model.

Mechanism and toxicity research of benzalkonium chloride oxidation in aqueous solution by H2O2/Fe(2+) process.

PubMed

Zhang, Qian; Xia, Yu-Feng; Hong, Jun-Ming

2016-09-01

As widely used disinfectants, the pollution caused by benzalkonium chloride (BAC) has attracted a lot of attention in recent years. Since it is not suitable for biodegradation, BAC was degraded firstly by Fenton advanced oxidation technologies (AOTs) in this research to enhance the biodegradability of the pollutions. The result revealed that the optimal molar ratio of H2O2/Fe(2+) for BAC degradation was 10:1, and the COD removal rate was 32 %. To clarify the pathway of degradation, the technique of GC-MS was implemented herein to identify intermediates and the toxicity of those BAC intermediates were also novelty tested through microbial fuel cells (MFC). The findings indicated that ten transformation products including benzyl dimethyl amine and dodecane were formed during the H2O2/Fe(2+) processes, which means the degradation pathway of BAC was initiated both on the hydrophobic (alkyl chain) and hydrophilic (benzyl and ammonium moiety) region of the surfactant. The toxicity of BAC before and after treated by Fenton process was monitored through MFC system. The electricity generation was improved 337 % after BAC was treated by H2O2/Fe(2+) oxidation processes which indicated that the toxicity of those intermediates were much lower than BAC. The mechanism and toxicity research in this paper could provide the in-depth understanding to the pathway of BAC degradation and proved the possibility of AOTs for the pretreatment of a biodegradation process.

Microbial mineral colonization across a subsurface redox transition zone

DOE PAGES

Converse, Brandon J.; McKinley, James P.; Resch, Charles T.; ...

2015-08-28

Here our study employed 16S rRNA gene amplicon pyrosequencing to examine the hypothesis that chemolithotrophic Fe(II)-oxidizing bacteria (FeOB) would preferentially colonize the Fe(II)-bearing mineral biotite compared to quartz sand when the minerals were incubated in situ within a subsurface redox transition zone (RTZ) at the Hanford 300 Area site in Richland, WA, USA. The work was motivated by the recently documented presence of neutral-pH chemolithotrophic FeOB capable of oxidizing structural Fe(II) in primary silicate and secondary phyllosilicate minerals in 300 Area sediments and groundwater (Benzine et al., 2013). Sterilized portions of sand+biotite or sand alone were incubated in situ formore » 5 months within a multilevel sampling (MLS) apparatus that spanned a ca. 2-m interval across the RTZ in two separate groundwater wells. Parallel MLS measurements of aqueous geochemical species were performed prior to deployment of the minerals. Contrary to expectations, the 16S rRNA gene libraries showed no significant difference in microbial communities that colonized the sand+biotite vs. sand-only deployments. Both mineral-associated and groundwater communities were dominated by heterotrophic taxa, with organisms from the Pseudomonadaceae accounting for up to 70% of all reads from the colonized minerals. These results are consistent with previous results indicating the capacity for heterotrophic metabolism (including anaerobic metabolism below the RTZ) as well as the predominance of heterotrophic taxa within 300 Area sediments and groundwater. Although heterotrophic organisms clearly dominated the colonized minerals, several putative lithotrophic (NH 4 +, H 2, Fe(II), and HS - oxidizing) taxa were detected in significant abundance above and within the RTZ. Such organisms may play a role in the coupling of anaerobic microbial metabolism to oxidative pathways with attendant impacts on elemental cycling and redox-sensitive contaminant behavior in the vicinity of the RTZ.« less

A Novel Uncultured Bacterium of the Family Gallionellaceae: Description and Genome Reconstruction Based on the Metagenomic Analysis of Microbial Community in Acid Mine Drainage.

PubMed

Kadnikov, V V; Ivasenko, D A; Beletsky, A V; Mardanov, A V; Danilova, E V; Pimenov, N V; Karnachuk, O V; Ravin, N V

2016-07-01

Drainage waters at the metal mining areas often have low pH and high content of dissolved metals due to oxidation of sulfide minerals. Extreme conditions limit microbial diversity in- such ecosystems. A drainage water microbial community (6.5'C, pH 2.65) in an open pit at the Sherlovaya Gora polymetallic open-cast mine (Transbaikal region, Eastern Siberia, Russia) was studied using metagenomic techniques. Metagenome sequencing provided information for taxonomic and functional characterization of the micro- bial community. The majority of microorganisms belonged to a single uncultured lineage representing a new Betaproteobacteria species of the genus Gallionella. While no.acidophiles are known among the cultured members of the family Gallionellaceae, similar 16S rRNA gene sequences were detected in acid mine drain- ages. Bacteria ofthe genera Thiobacillus, Acidobacterium, Acidisphaera, and Acidithiobacillus,-which are com- mon in acid mine drainage environments, were the minor components of the community. Metagenomic data were -used to determine the almost complete (-3.4 Mb) composite genome of the new bacterial. lineage desig- nated Candidatus Gallionella acididurans ShG14-8. Genome analysis revealed that Fe(II) oxidation probably involved the cytochromes localized on the outer membrane of the cell. The electron transport chain included NADH dehydrogenase, a cytochrome bc1 complex, an alternative complex III, and cytochrome oxidases of the bd, cbb3, and bo3 types. Oxidation of reduced sulfur compounds probably involved the Sox system, sul- fide-quinone oxidoreductase, adenyl sulfate reductase, and sulfate adenyltransferase. The genes required for autotrophic carbon assimilation via the Calvin cycle were present, while no pathway for nitrogen fixation was revealed. High numbers of RND metal transporters and P type ATPases were probably responsible for resis- tance to heavy metals. The new microorganism was an aerobic chemolithoautotroph of the group of psychrotolerant iron- and sulfur-oxidizing acidophiles of the family Gallionellaceae, which are common in acid mine drainages.

Preserved Filamentous Microbial Biosignatures in the Brick Flat Gossan, Iron Mountain, California

PubMed Central

Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A.

2015-01-01

Abstract A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater as tentative possibilities. Key Words: Geobiology—Biosignatures—Filaments—Mars—Microbial fossils. Astrobiology 15, 637–668. PMID:26247371

Autotrophic and heterotrophic nitrification-anoxic denitrification dominated the anoxic/oxic sewage treatment process during optimization for higher loading rate and energy savings.

PubMed

Zhang, Xueyu; Zheng, Shaokui; Zhang, Hangyu; Duan, Shoupeng

2018-04-30

This study clarified the dominant nitrogen (N)-transformation pathway and the key ammonia-oxidizing microbial species at three loading levels during optimization of the anoxic/oxic (A/O) process for sewage treatment. Comprehensive N-transformation activity analysis showed that ammonia oxidization was performed predominantly by aerobic chemolithotrophic and heterotrophic ammonia oxidization, whereas N 2 production was performed primarily by anoxic denitrification in the anoxic unit. The abundances of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria, and anaerobic AOB in activated sludge reflected their activities on the basis of high-throughput sequencing data. AOB amoA gene clone libraries revealed that the predominant AOB species in sludge samples shifted from Nitrosomonas europaea (61% at the normal loading level) to Nitrosomonas oligotropha (58% and 81% at the two higher loading levels). Following isolation and sequencing, the predominant culturable heterotrophic AOB in sludge shifted from Agrobacterium tumefaciens (42% at the normal loading level) to Acinetobacter johnsonii (52% at the highest loading level). Copyright © 2018 Elsevier Ltd. All rights reserved.

Nitrous oxide (N2O) emission from aquaculture: a review.

PubMed

Hu, Zhen; Lee, Jae Woo; Chandran, Kartik; Kim, Sungpyo; Khanal, Samir Kumar

2012-06-19

Nitrous oxide (N(2)O) is an important greenhouse gas (GHG) which has a global warming potential 310 times that of carbon dioxide (CO(2)) over a hundred year lifespan. N(2)O is generated during microbial nitrification and denitrification, which are common in aquaculture systems. To date, few studies have been conducted to quantify N(2)O emission from aquaculture. Additionally, very little is known with respect to the microbial pathways through which N(2)O is formed in aquaculture systems. This review suggests that aquaculture can be an important anthropogenic source of N(2)O emission. The global N(2)O-N emission from aquaculture in 2009 is estimated to be 9.30 × 10(10) g, and will increase to 3.83 × 10(11)g which could account for 5.72% of anthropogenic N(2)O-N emission by 2030 if the aquaculture industry continues to increase at the present annual growth rate (about 7.10%). The possible mechanisms and various factors affecting N(2)O production are summarized, and two possible methods to minimize N(2)O emission, namely aquaponic and biofloc technology aquaculture, are also discussed. The paper concludes with future research directions.

Biodegradation of 3-methyldiphenylether (MDE) by Hydrogenophaga atypical strain QY7-2 and cloning of the methy-oxidation gene mdeABCD

NASA Astrophysics Data System (ADS)

Yang, Qian; Cai, Shu; Dong, Shaowei; Chen, Lulu; Chen, Jifei; Cai, Tianming

2016-12-01

3-Methyldiphenylether (MDE) is an important alkyl-substituted diphenyl ether compound that is widely used as an intermediate in the synthesis of pyrethroid insecticides. An efficient MDE-degrading strain QY7-2, identified as Hydrogenophaga atypical, was isolated from activated sludge for the first time. Strain QY7-2 can utilize MDE as the sole carbon and energy source and completely mineralize MDE. The degradation pathway of MDE was proposed in the strain through metabolites identification. A gene cluster involving in methy-oxidation of MDE was cloned from QY7-2 and expressed in Escherichia coli BL21 (DE3), and the products were purified by SDS-PAGE. The specific activities of the recombinant enzymes MdeAB, MdeC and MdeD were 113.8 ± 3.5, 274.5 ± 6.2 and 673.4 ± 8.7 nmol min-1 mg-1, respectively. These results provide the biochemical and genetic foundation of microbial degradation pathway of MDE and benefit the bioremediation of MDE-contaminated environments.

Biodegradation of 3-methyldiphenylether (MDE) by Hydrogenophaga atypical strain QY7-2 and cloning of the methy-oxidation gene mdeABCD

PubMed Central

Yang, Qian; Cai, Shu; Dong, Shaowei; Chen, Lulu; Chen, Jifei; Cai, Tianming

2016-01-01

3-Methyldiphenylether (MDE) is an important alkyl-substituted diphenyl ether compound that is widely used as an intermediate in the synthesis of pyrethroid insecticides. An efficient MDE-degrading strain QY7-2, identified as Hydrogenophaga atypical, was isolated from activated sludge for the first time. Strain QY7-2 can utilize MDE as the sole carbon and energy source and completely mineralize MDE. The degradation pathway of MDE was proposed in the strain through metabolites identification. A gene cluster involving in methy-oxidation of MDE was cloned from QY7-2 and expressed in Escherichia coli BL21 (DE3), and the products were purified by SDS-PAGE. The specific activities of the recombinant enzymes MdeAB, MdeC and MdeD were 113.8 ± 3.5, 274.5 ± 6.2 and 673.4 ± 8.7 nmol min−1 mg−1, respectively. These results provide the biochemical and genetic foundation of microbial degradation pathway of MDE and benefit the bioremediation of MDE-contaminated environments. PMID:27995977

Redox and Chemical Activities of the Hemes in the Sulfur Oxidation Pathway Enzyme SoxAX*

PubMed Central

Bradley, Justin M.; Marritt, Sophie J.; Kihlken, Margaret A.; Haynes, Kate; Hemmings, Andrew M.; Berks, Ben C.; Cheesman, Myles R.; Butt, Julea N.

2012-01-01

SoxAX enzymes couple disulfide bond formation to the reduction of cytochrome c in the first step of the phylogenetically widespread Sox microbial sulfur oxidation pathway. Rhodovulum sulfidophilum SoxAX contains three hemes. An electrochemical cell compatible with magnetic circular dichroism at near infrared wavelengths has been developed to resolve redox and chemical properties of the SoxAX hemes. In combination with potentiometric titrations monitored by electronic absorbance and EPR, this method defines midpoint potentials (Em) at pH 7.0 of approximately +210, −340, and −400 mV for the His/Met, His/Cys−, and active site His/CysS−-ligated heme, respectively. Exposing SoxAX to S2O42−, a substrate analog with Em ∼−450 mV, but not Eu(II) complexed with diethylene triamine pentaacetic acid (Em ∼−1140 mV), allows cyanide to displace the cysteine persulfide (CysS−) ligand to the active site heme. This provides the first evidence for the dissociation of CysS− that has been proposed as a key event in SoxAX catalysis. PMID:23060437

Sequential batch thermophilic solid-state anaerobic digestion of lignocellulosic biomass via recirculating digestate as inoculum - Part II: Microbial diversity and succession.

PubMed

Lin, Long; Yu, Zhongtang; Li, Yebo

2017-10-01

This study aimed to investigate the effect of recirculation of digestate as inoculum on the microbial communities in thermophilic solid-state anaerobic digestion (SS-AD) of yard trimmings. The SS-AD consisted of 4 consecutive runs (30days/run), with digestate from the previous run being used as the inoculum of the subsequent run. Bacterial and archaeal communities (day 0, 4, 8, 12, 20, and 30) were examined using Illumina sequencing of 16S rRNA genes. The results revealed substantial microbial succession toward increased diversity until run 3. The proportions of Firmicutes that contained cellulolytic bacteria doubled, which might explain the concomitantly increased cellulose degradation and volatile fatty acids (VFAs). Clostridia and Thermotogae appeared to correlate with VFAs. The VFA accumulation likely induced dynamic shifts of methanogens, particularly to hydrogenotrophic Methanothermobacter, implying that non-acetoclastic oxidative pathway dominated during the steady-state thermophilic SS-AD. This study suggested that recirculating SS-AD digestate might be an effective way for inoculation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial communities involved in methane production from hydrocarbons in oil sands tailings.

PubMed

Siddique, Tariq; Penner, Tara; Klassen, Jonathan; Nesbø, Camilla; Foght, Julia M

2012-09-04

Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Pilot scale application of nanosized iron oxides as electron acceptors for bioremediation

NASA Astrophysics Data System (ADS)

Bosch, Julian; Fritzsche, Andreas; Frank-Fahle, Beatrice; Lüders, Tilmann; Höss, Sebastian; Eisenmann, Heinrich; Held, Thomas; Totsche, Kai U.; Meckenstock, Rainer U.

2014-05-01

Microbial reduction of ferric iron is a major biogeochemical process in groundwater aquifer ecosystems and often associated with the degradation of organic contaminants, as bacteria couple iron reduction to the oxidation reduced carbon like e.g. BTEX. Yet in general the low bioavailability of natural iron oxides limits microbial reduction rates. However, nanosized iron oxides have an unequally enhanced bioavailability and reactivity compared to their respective bulk, macro-sized, and more crystalline materials. At the same time, nanosized iron oxides can be produced in stable colloidal suspensions, permitting efficient injections into contaminated aquifers. We examined the reactivity of nanosized synthetic colloidal iron oxides in microbial iron reduction. Application of colloidal nanoparticles led to a strong and sustainable enhancement of microbial reaction rates in batch experiments and sediment columns. Toluene oxidation was increased five-fold as compared to bulk, non-colloidal ferrihydrite as electron acceptor. Furthermore, we developed a unique approach for custom-tailoring the subsurface mobility of these particles after being injected into a contaminant plume. In a field pilot application, we injected 18 m3 of an iron oxide nanoparticle solution into a BTEX contaminated aquifer with a maximum excess pressure as low as 0.2 bar. The applied suspension showed a superior subsurface mobility, creating a reactive zone of 4 m height (corresponding to the height of the confined aquifer) and 6 m in diameter. Subsequent monitoring of BTEX, microbial BTEX degradation metabolites, ferrous iron generation, stable isotopes fractionation, microbial populations, and methanogenesis demonstrated the strong impact of our approach. Mathematic processed X-ray diffractograms and FTIR spectra provided a semi-quantitatively estimate of the long-term fate of the iron oxide colloids in the aquifer. Potential environmental risks of the injection itself were monitored with ecotoxicological investigations. Our data suggest that the injection of ferric iron nanoparticles as electron acceptors into contaminated aquifers for the enhancement of microbial contaminant degradation might develop into a novel bioremediation strategy.

Study of the role of anaerobic metabolism in succinate production by Enterobacter aerogenes.

PubMed

Tajima, Yoshinori; Kaida, Kenichi; Hayakawa, Atsushi; Fukui, Keita; Nishio, Yousuke; Hashiguchi, Kenichi; Fudou, Ryosuke; Matsui, Kazuhiko; Usuda, Yoshihiro; Sode, Koji

2014-09-01

Succinate is a core biochemical building block; optimizing succinate production from biomass by microbial fermentation is a focus of basic and applied biotechnology research. Lowering pH in anaerobic succinate fermentation culture is a cost-effective and environmentally friendly approach to reducing the use of sub-raw materials such as alkali, which are needed for neutralization. To evaluate the potential of bacteria-based succinate fermentation under weak acidic (pH <6.2) and anaerobic conditions, we characterized the anaerobic metabolism of Enterobacter aerogenes AJ110637, which rapidly assimilates glucose at pH 5.0. Based on the profile of anaerobic products, we constructed single-gene knockout mutants to eliminate the main anaerobic metabolic pathways involved in NADH re-oxidation. These single-gene knockout studies showed that the ethanol synthesis pathway serves as the dominant NADH re-oxidation pathway in this organism. To generate a metabolically engineered strain for succinate production, we eliminated ethanol formation and introduced a heterogeneous carboxylation enzyme, yielding E. aerogenes strain ΔadhE/PCK. The strain produced succinate from glucose with a 60.5% yield (grams of succinate produced per gram of glucose consumed) at pH <6.2 and anaerobic conditions. Thus, we showed the potential of bacteria-based succinate fermentation under weak acidic conditions.

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

USGS Publications Warehouse

Bargar, J.R.; Fuller, C.C.; Marcus, M.A.; Brearley, A.J.; Perez De la Rosa, M.; Webb, S.M.; Caldwell, W.A.

2009-01-01

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 ?? 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-?? 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 Mn oxides 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. ?? 2008 Elsevier Ltd.

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.

Applications of Graphene-Modified Electrodes in Microbial Fuel Cells

PubMed Central

Yu, Fei; Wang, Chengxian; Ma, Jie

2016-01-01

Graphene-modified materials have captured increasing attention for energy applications due to their superior physical and chemical properties, which can significantly enhance the electricity generation performance of microbial fuel cells (MFC). In this review, several typical synthesis methods of graphene-modified electrodes, such as graphite oxide reduction methods, self-assembly methods, and chemical vapor deposition, are summarized. According to the different functions of the graphene-modified materials in the MFC anode and cathode chambers, a series of design concepts for MFC electrodes are assembled, e.g., enhancing the biocompatibility and improving the extracellular electron transfer efficiency for anode electrodes and increasing the active sites and strengthening the reduction pathway for cathode electrodes. In spite of the challenges of MFC electrodes, graphene-modified electrodes are promising for MFC development to address the reduction in efficiency brought about by organic waste by converting it into electrical energy. PMID:28773929

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Johnson, Tim; Fredrickson, James K.

The hyporheic corridor (HC) is a critical component of riverine ecosystems that encompasses the river-11 groundwater continuum. The mixing of groundwater (GW) with river water (RW) in the HC can 12 stimulate biogeochemical activity, and here we (i) propose a novel thermodynamic mechanism 13 underlying this phenomenon, and (ii) reveal broader impacts on dissolved organic carbon (DOC) 14 biogeochemistry and microbial ecology. We show that thermodynamically-favorable DOC 15 accumulates in GW despite decreases in DOC concentration along subsurface flow paths, and that RW 16 contains less thermodynamically-favorable DOC, but at higher concentrations. This indicates that DOC 17 in GW ismore » protected from microbial oxidation by low total energy contained within the DOC pool, while 18 RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-19 RW mixing overcomes these protection mechanisms and stimulates respiration. Mixing models 20 coupled with time-lapse electrical resistance tomography revealed that stimulated respiration leads 21 to tipping points in spatiotemporal dynamics of DOC across the HC. Further, shifts in DOC speciation 22 and biochemical pathways were associated with shifts in microbiome composition, highlighting 23 feedbacks among hydrology, DOC biochemistry, and microbial ecology. These results reveal that 24 previously unrecognized thermodynamic-based mechanisms regulated by GW-RW mixing can strongly 25 influence biogeochemical and microbial dynamics in riverine ecosystems.« less

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

DOE PAGES

Stegen, James C.; Johnson, Tim; Fredrickson, James K.; ...

2018-02-08

The hyporheic corridor (HC) is a critical component of riverine ecosystems that encompasses the river-11 groundwater continuum. The mixing of groundwater (GW) with river water (RW) in the HC can 12 stimulate biogeochemical activity, and here we (i) propose a novel thermodynamic mechanism 13 underlying this phenomenon, and (ii) reveal broader impacts on dissolved organic carbon (DOC) 14 biogeochemistry and microbial ecology. We show that thermodynamically-favorable DOC 15 accumulates in GW despite decreases in DOC concentration along subsurface flow paths, and that RW 16 contains less thermodynamically-favorable DOC, but at higher concentrations. This indicates that DOC 17 in GW ismore » protected from microbial oxidation by low total energy contained within the DOC pool, while 18 RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-19 RW mixing overcomes these protection mechanisms and stimulates respiration. Mixing models 20 coupled with time-lapse electrical resistance tomography revealed that stimulated respiration leads 21 to tipping points in spatiotemporal dynamics of DOC across the HC. Further, shifts in DOC speciation 22 and biochemical pathways were associated with shifts in microbiome composition, highlighting 23 feedbacks among hydrology, DOC biochemistry, and microbial ecology. These results reveal that 24 previously unrecognized thermodynamic-based mechanisms regulated by GW-RW mixing can strongly 25 influence biogeochemical and microbial dynamics in riverine ecosystems.« less

Low Stress Mechanical Properties of Plasma-Treated Cotton Fabric Subjected to Zinc Oxide-Anti-Microbial Treatment.

PubMed

Kan, Chi-Wai; Lam, Yin-Ling

2013-01-22

Cotton fabrics are highly popular because of their excellent properties such as regeneration, bio-degradation, softness, affinity to skin and hygroscopic properties. When in contact with the human body, cotton fabrics offer an ideal environment for microbial growth due to their ability to retain oxygen, moisture and warmth, as well as nutrients from spillages and body sweat. Therefore, an anti-microbial coating formulation (Microfresh and Microban together with zinc oxide as catalyst) was developed for cotton fabrics to improve treatment effectiveness. In addition, plasma technology was employed in the study which roughened the surface of the materials, improving the loading of zinc oxides on the surface. In this study, the low stress mechanical properties of plasma pre-treated and/or anti-microbial-treated cotton fabric were studied. The overall results show that the specimens had improved bending properties when zinc oxides were added in the anti-microbial coating recipe. Also, without plasma pre-treatment, anti-microbial-treatment of cotton fabric had a positive effect only on tensile resilience, shear stress at 0.5° and compressional energy, while plasma-treated specimens had better overall tensile properties even after anti-microbial treatment.

Low Stress Mechanical Properties of Plasma-Treated Cotton Fabric Subjected to Zinc Oxide-Anti-Microbial Treatment

PubMed Central

Kan, Chi-Wai; Lam, Yin-Ling

2013-01-01

Cotton fabrics are highly popular because of their excellent properties such as regeneration, bio-degradation, softness, affinity to skin and hygroscopic properties. When in contact with the human body, cotton fabrics offer an ideal environment for microbial growth due to their ability to retain oxygen, moisture and warmth, as well as nutrients from spillages and body sweat. Therefore, an anti-microbial coating formulation (Microfresh and Microban together with zinc oxide as catalyst) was developed for cotton fabrics to improve treatment effectiveness. In addition, plasma technology was employed in the study which roughened the surface of the materials, improving the loading of zinc oxides on the surface. In this study, the low stress mechanical properties of plasma pre-treated and/or anti-microbial-treated cotton fabric were studied. The overall results show that the specimens had improved bending properties when zinc oxides were added in the anti-microbial coating recipe. Also, without plasma pre-treatment, anti-microbial-treatment of cotton fabric had a positive effect only on tensile resilience, shear stress at 0.5° and compressional energy, while plasma-treated specimens had better overall tensile properties even after anti-microbial treatment. PMID:28809311

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Coupling electrokinetics with microbial biodegradation enhances the removal of cycloparaffinic hydrocarbons in soils.

PubMed

Yuan, Ye; Guo, Shuhai; Li, Fengmei; Wu, Bo; Yang, Xuelian; Li, Xuan

2016-12-15

An innovative approach that couples electrokinetics with microbial degradation to breakdown cycloparaffinic hydrocarbons in soils is described. Soils were spiked with cyclododecane, used as a model pollutant, at approximately 1000mgkg -1 . A mixture of petroleum-utilizing bacteria was added to achieve about 10 6 -10 7 CFUg -1 . Then, three treatments were applied for 25 days: (1) no electric field, control; (2) a constant voltage gradient of 1.3Vcm -1 in one direction; and (3) the same electric field, but with periodical switching of polarity. The degradation pathway of cyclododecane was not changed by the electric field, but the dynamic processes were remarkably enhanced, especially when the electric field was periodically switched. After 25 days, 79.9% and 87.0% of the cyclododecane was degraded in tests 2 and 3, respectively; both much higher than the 61.5% degraded in test 1. Analysis of the intermediate products strongly indicated that the competitive advantage of the electric field was the increase in ring-breaking of cyclododecane, resulting in greater concentrations of linear substances that were more susceptible to microbial attack, that is, β-oxidation. The conditions near the cathode were more favorable for the growth and metabolism of microorganisms, which also enhanced β-oxidation of the linear alkanoic acids. Therefore, when the electric field polarity was periodically switched, the functions of both the anode and cathode electrodes were applied across the whole soil cell, further increasing the degradation efficiency. Copyright © 2016 Elsevier B.V. All rights reserved.

Plant effects on soil denitrification - a review of potential mechanisms

NASA Astrophysics Data System (ADS)

Malique, Francois; Butterbach-Bahl, Klaus; Dannenmann, Michael

2017-04-01

Denitrification is a microbial process occurring in soils, both producing and consuming the potent greenhouse gas nitrous oxide (NO), competing for nitrate with plants and hydrological leaching pathways, removing nutrients and reactive nitrogen from the biosphere, and closing the global nitrogen cycle. Despite its obvious importance, denitrification remained among the least well quantified biogeochemical processes in soils. This is due to enormous methodological difficulties involved in the direct quantification of soil microbial denitrification rates (mainly with regard to the terminal product N2) and the denitrification nitrogen gas product ratios (NO:N2O:N2), Plants may affect denitrification through a myriad of mechanisms such as e.g., competition for nitrate and water, through oxygen consumption, by regulating litter quality and changing soil pH, and via the exudation of labile carbon or secondary plant compounds involved in shaping the rhizospheric microbial community. However, plant effects on denitrification so far hardly were quantified so that the actual extent of plant control on denitrification is largely unknown. Here, we summarize the current knowledge on mechanisms how plants can affect denitrification rates and N gas product ratios in soils at temporal scales from hours to days and years. We review earlier research to quantify plant effects on denitrification as well as critically discuss the limited methods currently available to quantify plant-soil-denitrifier interactions. Finally, we provide pointers to use plants as tools to manage denitrification, e.g. to improve N use efficiency in agricultural ecosystems and to minimize soil nitrous oxide emissions.

Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

PubMed

Pirie, Christopher M; De Mey, Marjan; Jones Prather, Kristala L; Ajikumar, Parayil Kumaran

2013-04-19

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor.

PubMed

Zhang, Xiaojing; Zhang, Nan; Fu, Haoqiang; Chen, Tao; Liu, Sa; Zheng, Shuhua; Zhang, Jie

2017-11-01

In this study, a membrane bioreactor (MBR) was adopted for completely autotrophic nitrogen removal over nitrite (CANON) process. Zinc oxide nanoparticles (ZnO NPs) was step-wise increased to analyze the influence on nitrogen removal, microbial activity and microbial communities. Finally ZnO NPs was removed to study its recovery capability. The bioactivities of ammonia-oxidizing bacteria (AOB), anaerobic ammonia-oxidizing bacteria (AAOB) and nitrite-oxidizing bacteria (NOB) were detected by batch experiments. Results showed that the ZnO NPs with low concentration (≤5mgL -1 ) was profitable for nitrogen removal while the high concentration performed inhibition, and it lowered the abundance of both AOB and NOB while enhanced that of AAOB. ZnO NPs with high concentration (≥10mgL -1 ) suppressed both AOB and AAOB, and long-term exposure within ZnO NPs led to microbial diversity decrease. The inhibition threshold of ZnO NPs on CANON process was 10mgL -1 , and the profitable concentration was 1mgL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

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. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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 utilization of dissolved Fe(II) as an energy source is not likely to take place.

Combination of microbial oxidation and biogenic schwertmannite immobilization: A potential remediation for highly arsenic-contaminated soil.

PubMed

Yang, Zhihui; Wu, Zijian; Liao, Yingping; Liao, Qi; Yang, Weichun; Chai, Liyuan

2017-08-01

Here, a novel strategy that combines microbial oxidation by As(III)-oxidizing bacterium and biogenic schwertmannite (Bio-SCH) immobilization was first proposed and applied for treating the highly arsenic-contaminated soil. Brevibacterium sp. YZ-1 isolated from a highly As-contaminated soil was used to oxidize As(III) in contaminated soils. Under optimum culture condition for microbial oxidation, 92.3% of water-soluble As(III) and 84.4% of NaHCO 3 -extractable As(III) in soils were removed. Bio-SCH synthesized through the oxidation of ferrous sulfate by Acidithiobacillus ferrooxidans immobilize As(V) in the contaminated soil effectively. Consequently, the combination of microbial oxidation and Bio-SCH immobilization performed better in treating the highly As-contaminated soil with immobilization efficiencies of 99.3% and 82.6% for water-soluble and NaHCO 3 -extractable total As, respectively. Thus, the combination can be considered as a green remediation strategy for developing a novel and valuable solution for As-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

PubMed Central

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2016-01-01

Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. PMID:26023869

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

USDA-ARS?s Scientific Manuscript database

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...

Preserved Filamentous Microbial Biosignatures in the Brick Flat Gossan, Iron Mountain, California.

PubMed

Williams, Amy J; Sumner, Dawn Y; Alpers, Charles N; Karunatillake, Suniti; Hofmann, Beda A

2015-08-01

A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater as tentative possibilities.

Preserved filamentous microbial biosignatures in the Brick Flat gossan, Iron Mountain, California

USGS Publications Warehouse

Williams, Amy J.; Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A

2015-01-01

A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater astentative possibilities.

Oxidative shielding or oxidative stress?

PubMed

Naviaux, Robert K

2012-09-01

In this review I report evidence that the mainstream field of oxidative damage biology has been running fast in the wrong direction for more than 50 years. Reactive oxygen species (ROS) and chronic oxidative changes in membrane lipids and proteins found in many chronic diseases are not the result of accidental damage. Instead, these changes are the result of a highly evolved, stereotyped, and protein-catalyzed "oxidative shielding" response that all eukaryotes adopt when placed in a chemically or microbially hostile environment. The machinery of oxidative shielding evolved from pathways of innate immunity designed to protect the cell from attack and limit the spread of infection. Both oxidative and reductive stress trigger oxidative shielding. In the cases in which it has been studied explicitly, functional and metabolic defects occur in the cell before the increase in ROS and oxidative changes. ROS are the response to disease, not the cause. Therefore, it is not the oxidative changes that should be targeted for therapy, but rather the metabolic conditions that create them. This fresh perspective is relevant to diseases that range from autism, type 1 diabetes, type 2 diabetes, cancer, heart disease, schizophrenia, Parkinson's disease, and Alzheimer disease. Research efforts need to be redirected. Oxidative shielding is protective and is a misguided target for therapy. Identification of the causal chemistry and environmental factors that trigger innate immunity and metabolic memory that initiate and sustain oxidative shielding is paramount for human health.

Nitrite oxidation in the Namibian oxygen minimum zone.

PubMed

Füssel, Jessika; Lam, Phyllis; Lavik, Gaute; Jensen, Marlene M; Holtappels, Moritz; Günter, Marcel; Kuypers, Marcel M M

2012-06-01

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in (15)N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (≤372 nM NO(2)(-) d(-1)) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ~9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO(3)(-) was re-oxidized back to NO(3)(-) via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.

Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage ▿ †

PubMed Central

Huang, Li-Nan; Zhou, Wen-Hua; Hallberg, Kevin B.; Wan, Cai-Yun; Li, Jie; Shu, Wen-Sheng

2011-01-01

Analysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings. Although Acidithiobacillus ferrooxidans and Leptospirillum spp. were consistently present in the acidic tailings, acidophilic archaea, mostly Ferroplasma acidiphilum, were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage. PMID:21705549

Environmental Genomic Analysis of Stratified Microbial Communities and Climate Active Gases in the Subarctic Pacific Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Wright, J.; Hallam, S.; Merzouk, A.; Tortell, P.

2008-12-01

Oxygen minimum zones (OMZs) are areas of low dissolved oxygen concentrations that play a major role in biogeochemical cycling within the world's oceans. They are major sinks for nitrogen and sources for the greenhouse gases carbon dioxide and nitrous oxide. Therefore, microbial mediated biological activity associated with these systems directly impacts ocean productivity and global climate balance. There is increasing evidence that ocean warming trends will decrease dissolved oxygen concentrations within the coastal and interior regions of the subarctic Pacific, causing an expansion of the hypoxic boundary layer. This expansion will have a direct effect on coastal benthic ecosystems and the productivity of marine fisheries due to habitat loss and changes in nutrient cycling. In order to understand the potential implications of these transitions, we are performing environmental genomic analyses of indigenous microbial communities found in coastal and open ocean OMZs in the subarctic Pacific Ocean in relation to dissolved gas and nutrient concentrations. In addition to identifying and describing the key microbial players and biochemical pathways contributing to carbon, nitrogen and sulfur metabolism within the subarctic Pacific Ocean, this work provides a solid comparative genomic foundation for understanding the biogeochemical processes at work in marine OMZs around the globe.

Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.

PubMed

Chourey, Karuna; Nissen, Silke; Vishnivetskaya, Tatiana; Shah, Manesh; Pfiffner, Susan; Hettich, Robert L; Löffler, Frank E

2013-10-01

High-performance MS instrumentation coupled with improved protein extraction techniques enables metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e. 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e. Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and the Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected upgradient of the EVO injection points. In particular, proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of Dechloromonas spp. was highly abundant, suggesting active nitrous oxide (N2 O) respiration. c-Type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that uranium reduction has not commenced 4 days post EVO amendment. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique as a monitoring tool and for complementing nucleic acid-based approaches. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

PubMed Central

Anantharaman, Karthik; Breier, John A; Dick, Gregory J

2016-01-01

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic ‘bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy. PMID:26046257

In situ analysis of oxygen consumption and diffusive transport in high-temperature acidic iron-oxide microbial mats.

PubMed

Bernstein, Hans C; Beam, Jacob P; Kozubal, Mark A; Carlson, Ross P; Inskeep, William P

2013-08-01

The role of dissolved oxygen as a principal electron acceptor for microbial metabolism was investigated within Fe(III)-oxide microbial mats that form in acidic geothermal springs of Yellowstone National Park (USA). Specific goals of the study were to measure and model dissolved oxygen profiles within high-temperature (65-75°C) acidic (pH = 2.7-3.8) Fe(III)-oxide microbial mats, and correlate the abundance of aerobic, iron-oxidizing Metallosphaera yellowstonensis organisms and mRNA gene expression levels to Fe(II)-oxidizing habitats shown to consume oxygen. In situ oxygen microprofiles were obtained perpendicular to the direction of convective flow across the aqueous phase/Fe(III)-oxide microbial mat interface using oxygen microsensors. Dissolved oxygen concentrations dropped from ∼ 50-60 μM in the bulk-fluid/mat surface to below detection (< 0.3 μM) at a depth of ∼ 700 μm (∼ 10% of the total mat depth). Net areal oxygen fluxes into the microbial mats were estimated to range from 1.4-1.6 × 10(-4)  μmol cm(-2)  s(-1) . Dimensionless parameters were used to model dissolved oxygen profiles and establish that mass transfer rates limit the oxygen consumption. A zone of higher dissolved oxygen at the mat surface promotes Fe(III)-oxide biomineralization, which was supported using molecular analysis of Metallosphaera yellowstonensis 16S rRNA gene copy numbers and mRNA expression of haem Cu oxidases (FoxA) associated with Fe(II)-oxidation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

PubMed

Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

2017-02-01

The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L -1 ) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L -1 . The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L -1 NiO NPs at the phyla, class and genus levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tuning constitutive and pathological inflammation in the gut via the interaction of dietary nitrate and polyphenols with host microbiome.

PubMed

Rocha, Bárbara S; Nunes, Carla; Laranjinha, João

2016-12-01

Chronic inflammation is currently recognized as a critical process in modern-era epidemics such as diabetes, obesity and neurodegeneration. However, little attention is paid to the constitutive inflammatory pathways that operate in the gut and that are mandatory for local welfare and the prevention of such multi-organic diseases. Hence, the digestive system, while posing as a barrier between the external environment and the host, is crucial for the balance between constitutive and pathological inflammatory events. Gut microbiome, a recently discovered organ, is now known to govern the interaction between exogenous agents and the host with ensued impact on local and systemic homeostasis. Whereas gut microbiota may be modulated by a myriad of factors, diet constitutes one of its major determinants. Thus, dietary compounds that influence microbial flora may thereby impact on inflammatory pathways. One such example is the redox environment in the gut lumen which is highly dependent on the local generation of nitric oxide along the nitrate-nitrite-nitric oxide pathway and that is further enhanced by simultaneous consumption of polyphenols. In this paper, different pathways encompassing the interaction of dietary nitrate and polyphenols with gut microbiota will be presented and discussed in connection with local and systemic inflammatory events. Furthermore, it will be discussed how these interactive cycles (nitrate-polyphenols-microbiome) may pose as novel strategies to tackle inflammatory diseases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Iron oxide nanoparticles in geomicrobiology: from biogeochemistry to bioremediation.

PubMed

Braunschweig, Juliane; Bosch, Julian; Meckenstock, Rainer U

2013-09-25

Iron oxides are important constituents of soils and sediments and microbial iron reduction is considered to be a significant anaerobic respiration process in the subsurface, however low microbial reduction rates of macroparticulate Fe oxides in laboratory studies led to an underestimation of the role of Fe oxides in the global Fe redox cycle. Recent studies show the high potential of nano-sized Fe oxides in the environment as, for example, electron acceptor for microbial respiration, electron shuttle between different microorganisms, and scavenger for heavy metals. Biotic and abiotic reactivity of iron macroparticles differ significantly from nano-sized Fe oxides, which are usually much more reactive. Factors such as particle size, solubility, ferrous iron, crystal structure, and organic molecules were identified to influence the reactivity. This review discusses factors influencing the microbial reactivity of Fe oxides. It highlights the differences between natural and synthetic Fe oxides especially regarding the presence of organic molecules such as humic acids and natural organic matter. Attention is given to the transport behavior of Fe oxides in laboratory systems and in the environment, because of the high affinity of different contaminants to Fe oxide surfaces and associated co-transport of pollutants. The high reactivity of Fe oxides and their potential as adsorbents for different pollutants are discussed with respect to application and development of remediation technologies. Copyright © 2013. Published by Elsevier B.V.

Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

PubMed

Sauder, Laura A; Ross, Ashley A; Neufeld, Josh D

2016-04-01

Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir.

PubMed

Pan, Pan; Hong, Bo; Mbadinga, Serge Maurice; Wang, Li-Ying; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-09-01

Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe 3 O 4 ), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe 3 O 4 ) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, β-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe 3 O 4 ) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/β-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of β-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.

Two-Step Oxidation of Refractory Gold Concentrates with Different Microbial Communities.

PubMed

Wang, Guo-Hua; Xie, Jian-Ping; Li, Shou-Peng; Guo, Yu-Jie; Pan, Ying; Wu, Haiyan; Liu, Xin-Xing

2016-11-28

Bio-oxidation is an effective technology for treatment of refractory gold concentrates. However, the unsatisfactory oxidation rate and long residence time, which cause a lower cyanide leaching rate and gold recovery, are key factors that restrict the application of traditional bio-oxidation technology. In this study, the oxidation rate of refractory gold concentrates and the adaption of microorganisms were analyzed to evaluate a newly developed two-step pretreatment process, which includes a high temperature chemical oxidation step and a subsequent bio-oxidation step. The oxidation rate and recovery rate of gold were improved significantly after the two-step process. The results showed that the highest oxidation rate of sulfide sulfur could reach to 99.01 % with an extreme thermophile microbial community when the pulp density was 5%. Accordingly, the recovery rate of gold was elevated to 92.51%. Meanwhile, the results revealed that moderate thermophiles performed better than acidophilic mesophiles and extreme thermophiles, whose oxidation rates declined drastically when the pulp density was increased to 10% and 15%. The oxidation rates of sulfide sulfur with moderate thermophiles were 93.94% and 65.73% when the pulp density was increased to 10% and 15%, respectively. All these results indicated that the two-step pretreatment increased the oxidation rate of refractory gold concentrates and is a potential technology to pretreat the refractory sample. Meanwhile, owing to the sensitivity of the microbial community under different pulp density levels, the optimization of microbial community in bio-oxidation is necessary in industry.

Reactive Oxygen Species-Producing Myeloid Cells Act as a Bone Marrow Niche for Sterile Inflammation-Induced Reactive Granulopoiesis.

PubMed

Zhu, Haiyan; Kwak, Hyun-Jeong; Liu, Peng; Bajrami, Besnik; Xu, Yuanfu; Park, Shin-Young; Nombela-Arrieta, Cesar; Mondal, Subhanjan; Kambara, Hiroto; Yu, Hongbo; Chai, Li; Silberstein, Leslie E; Cheng, Tao; Luo, Hongbo R

2017-04-01

Both microbial infection and sterile inflammation augment bone marrow (BM) neutrophil production, but whether the induced accelerated granulopoiesis is mediated by a common pathway and the nature of such a pathway are poorly defined. We recently established that BM myeloid cell-derived reactive oxygen species (ROS) externally regulate myeloid progenitor proliferation and differentiation in bacteria-elicited emergency granulopoiesis. In this article, we show that BM ROS levels are also elevated during sterile inflammation. Similar to in microbial infection, ROS were mainly generated by the phagocytic NADPH oxidase in Gr1 + myeloid cells. The myeloid cells and their ROS were uniformly distributed in the BM when visualized by multiphoton intravital microscopy, and ROS production was both required and sufficient for sterile inflammation-elicited reactive granulopoiesis. Elevated granulopoiesis was mediated by ROS-induced phosphatase and tensin homolog oxidation and deactivation, leading to upregulated PtdIns(3,4,5)P3 signaling and increased progenitor cell proliferation. Collectively, these results demonstrate that, although infection-induced emergency granulopoiesis and sterile inflammation-elicited reactive granulopoiesis are triggered by different stimuli and are mediated by distinct upstream signals, the pathways converge to NADPH oxidase-dependent ROS production by BM myeloid cells. Thus, BM Gr1 + myeloid cells represent a key hematopoietic niche that supports accelerated granulopoiesis in infective and sterile inflammation. This niche may be an excellent target in various immune-mediated pathologies or immune reconstitution after BM transplantation. Copyright © 2017 by The American Association of Immunologists, Inc.

Reactive oxygen species-producing myeloid cells act as a bone marrow niche for sterile inflammation-induced reactive granulopoiesis

PubMed Central

Zhu, Haiyan; Kwak, Hyun-Jeong; Liu, Peng; Bajrami, Besnik; Xu, Yuanfu; Park, Shin-Young; Nombela-Arrieta, Cesar; Mondal, Subhanjan; Kambara, Hiroto; Yu, Hongbo; Chai, Li; Silberstein, Leslie E.; Cheng, Tao; Luo, Hongbo R.

2017-01-01

Summary Both microbial infection and sterile inflammation augment bone marrow (BM) neutrophil production, but whether the induced accelerated granulopoiesis is mediated by a common pathway and the nature of such a pathway are poorly defined. We recently established that BM myeloid cell-derived reactive oxygen species (ROS) externally regulate myeloid progenitor proliferation and differentiation in bacteria-elicited emergency granulopoiesis. Here we show that BM ROS levels are also elevated during sterile inflammation. Similar to in microbial infection, ROS were mainly generated by the phagocytic NADPH oxidase in Gr1+ myeloid cells. The myeloid cells and their ROS were uniformly distributed in the BM when visualized by multi-photon intravital microscopy, and ROS production was both required and sufficient for sterile inflammation-elicited reactive granulopoiesis. Elevated granulopoiesis was mediated by ROS-induced PTEN oxidation and deactivation leading to upregulated PtdIns(3,4,5)P3 signaling and increased progenitor cell proliferation. Collectively, these results demonstrate that although infection-induced emergency granulopoiesis and sterile inflammation-elicited reactive granulopoiesis are triggered by different stimuli and are mediated by distinct upstream signals, the pathways converge to NADPH oxidase-dependent ROS production by BM myeloid cells. Thus, BM Gr1+ myeloid cells represent a key hematopoietic niche that supports accelerated granulopoiesis in both infective and sterile inflammation. This niche may be an excellent target in various immune-mediated pathologies or immune reconstitution after BM transplantation. PMID:28235862

Fungal oxidative dissolution of the Mn(II)-bearing mineral rhodochrosite and the role of metabolites in manganese oxide formation.

PubMed

Tang, Yuanzhi; Zeiner, Carolyn A; Santelli, Cara M; Hansel, Colleen M

2013-04-01

Microbially mediated oxidation of Mn(II) to Mn(III/IV) oxides influences the cycling of metals and remineralization of carbon. Despite the prevalence of Mn(II)-bearing minerals in nature, little is known regarding the ability of microbes to oxidize mineral-hosted Mn(II). Here, we explored oxidation of the Mn(II)-bearing mineral rhodochrosite (MnCO3 ) and characteristics of ensuing Mn oxides by six Mn(II)-oxidizing Ascomycete fungi. All fungal species substantially enhanced rhodochrosite dissolution and surface modification. Mineral-hosted Mn(II) was oxidized resulting in formation of Mn(III/IV) oxides that were all similar to δ-MnO2 but varied in morphology and distribution in relation to cellular structures and the MnCO3 surface. For four fungi, Mn(II) oxidation occurred along hyphae, likely mediated by cell wall-associated proteins. For two species, Mn(II) oxidation occurred via reaction with fungal-derived superoxide produced at hyphal tips. This pathway ultimately resulted in structurally unique Mn oxide clusters formed at substantial distances from any cellular structure. Taken together, findings for these two fungi strongly point to a role for fungal-derived organic molecules in Mn(III) complexation and Mn oxide templation. Overall, this study illustrates the importance of fungi in rhodochrosite dissolution, extends the relevance of biogenic superoxide-based Mn(II) oxidation and highlights the potential role of mycogenic exudates in directing mineral precipitation. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

PubMed Central

Graves, Christopher J.; Makrides, Elizabeth J.; Schmidt, Victor T.; Giblin, Anne E.; Cardon, Zoe G.

2016-01-01

ABSTRACT Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. IMPORTANCE In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. PMID:26944843

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.

PubMed

Graves, Christopher J; Makrides, Elizabeth J; Schmidt, Victor T; Giblin, Anne E; Cardon, Zoe G; Rand, David M

2016-05-01

Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. Copyright © 2016 Graves et al.

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

PubMed

Escudero, Lorena; Oetiker, Nia; Gallardo, Karem; Tebes-Cayo, Cinthya; Guajardo, Mariela; Nuñez, Claudia; Davis-Belmar, Carol; Pueyo, J J; Chong Díaz, Guillermo; Demergasso, Cecilia

2018-05-10

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

PubMed Central

Jia, Yangyang; Wilkins, David; Lu, Hongyuan; Cai, Mingwei

2015-01-01

Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions. PMID:26712547

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marinemore » mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.« less

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Genome Informed Trait-Based Models

NASA Astrophysics Data System (ADS)

Karaoz, U.; Cheng, Y.; Bouskill, N.; Tang, J.; Beller, H. R.; Brodie, E.; Riley, W. J.

2013-12-01

Trait-based approaches are powerful tools for representing microbial communities across both spatial and temporal scales within ecosystem models. Trait-based models (TBMs) represent the diversity of microbial taxa as stochastic assemblages with a distribution of traits constrained by trade-offs between these traits. Such representation with its built-in stochasticity allows the elucidation of the interactions between the microbes and their environment by reducing the complexity of microbial community diversity into a limited number of functional ';guilds' and letting them emerge across spatio-temporal scales. From the biogeochemical/ecosystem modeling perspective, the emergent properties of the microbial community could be directly translated into predictions of biogeochemical reaction rates and microbial biomass. The accuracy of TBMs depends on the identification of key traits of the microbial community members and on the parameterization of these traits. Current approaches to inform TBM parameterization are empirical (i.e., based on literature surveys). Advances in omic technologies (such as genomics, metagenomics, metatranscriptomics, and metaproteomics) pave the way to better-initialize models that can be constrained in a generic or site-specific fashion. Here we describe the coupling of metagenomic data to the development of a TBM representing the dynamics of metabolic guilds from an organic carbon stimulated groundwater microbial community. Illumina paired-end metagenomic data were collected from the community as it transitioned successively through electron-accepting conditions (nitrate-, sulfate-, and Fe(III)-reducing), and used to inform estimates of growth rates and the distribution of metabolic pathways (i.e., aerobic and anaerobic oxidation, fermentation) across a spatially resolved TBM. We use this model to evaluate the emergence of different metabolisms and predict rates of biogeochemical processes over time. We compare our results to observational outputs.

The vent microbiome: patterns and drivers

NASA Astrophysics Data System (ADS)

Pachiadaki, M.

2015-12-01

Microbial processes within deep-sea hydrothermal vents affect the global biogeochemical cycles. Still, there are significant gaps in our understanding of the microbiology and the biogeochemistry of deep-sea hydrothermal systems. Vents differ in temperature, host rock composition and fluid chemistry; factors that are hypothesized to shape the distribution of the microbial communities, their metabolic capabilities and their activities. Using large-scale single cell genomics, we obtained insights into the genomic content of several linkages of a diffuse flow vent. The genomes show high metabolic versatility. Sulfur oxidation appears to be predominant but there is the potential of using a variety of e- donors and acceptors to obtain energy. To further assess the ecological importance of the vent auto- and heterotrophs, the global biogeography of the analyzed lineages will be investigated by fragment recruitment of metagenomes produced from the same site as well as other hydrothermal systems. Metatranscriptomic and metaproteomic data will be integrated to examine the expression of the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production. The comparative analysis of the key players and associated pathways among various vent sites that differ in physicochemical characteristics is anticipated to decipher the patterns and drivers of the global dispersion and the local diversification of the vent microbiome.

Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

NASA Astrophysics Data System (ADS)

Andre, B. J.; Rajaram, H.; Silverstein, J.

2010-12-01

Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction diffusion model at the scale of a single rock is developed incorporating the proposed kinetic rate expressions. Simulations of initiation, washout and AMD flows are discussed to gain a better understanding of the role of porosity, effective diffusivity and reactive surface area in generating AMD. Simulations indicate that flow boundary conditions control generation of acid rock drainage as porosity increases.

Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp.

PubMed

He, Yi; Wang, Bin; Chen, Wanping; Cox, Russell J; He, Jingren; Chen, Fusheng

High throughput genome sequencing has revealed a multitude of potential secondary metabolites biosynthetic pathways that remain cryptic. Pathway reconstruction coupled with genetic engineering via heterologous expression enables discovery of novel compounds, elucidation of biosynthetic pathways, and optimization of product yields. Apart from Escherichia coli and yeast, fungi, especially Aspergillus spp., are well known and efficient heterologous hosts. This review summarizes recent advances in heterologous expression of microbial secondary metabolite biosynthesis in Aspergillus spp. We also discuss the technological challenges and successes in regard to heterologous host selection and DNA assembly behind the reconstruction of microbial secondary metabolite biosynthesis. Copyright © 2018 Elsevier Inc. All rights reserved.

Anaerobic Biodegradation of Ethylene Glycol within Hydraulic Fracturing Fluid

NASA Astrophysics Data System (ADS)

Heyob, K. M.; Mouser, P. J.

2014-12-01

Ethylene glycol (EG) is a commonly used organic additive in hydraulic fracturing fluids used for shale gas recovery. Under aerobic conditions, this compound readily biodegrades to acetate and CO2 or is oxidized through the glycerate pathway. In the absence of oxygen, organisms within genera Desulfovibrio, Acetobacterium, and others can transform EG to acetaldehyde, a flammable and suspected carcinogenic compound. Acetaldehyde can then be enzymatically degraded to ethanol or acetate and CO2. However, little is known on how EG degrades in the presence of other organic additives, particularly under anaerobic conditions representative of deep groundwater aquifers. To better understand the fate and attenuation of glycols within hydraulic fracturing fluids we are assessing their biodegradation potential and pathways in batch anaerobic microcosm treatments. Crushed Berea sandstone was inoculated with groundwater and incubated with either EG or a synthetic fracturing fluid (SFF) containing EG formulations. We tracked changes in dissolved organic carbon (DOC), EG, and its transformation products over several months. Approximately 41% of bulk DOC in SFF is degraded within 21 days, with 58% DOC still remaining after 63 days. By comparison, this same SFF degrades by 70% within 25 days when inoculated with sediment-groundwater microbial communities, suggesting that bulk DOC degradation occurs at a slower rate and to a lesser extent with bedrock. Aerobic biodegradation of EG occurs rapidly (3-7 days); however anaerobic degradation of EG is much slower, requiring several weeks for substantial DOC loss to be observed. Ongoing experiments are tracking the degradation pathways of EG alone and in the presence of SFF, with preliminary data showing incomplete glycol transformation within the complex hydraulic fracturing fluid mixture. This research will help to elucidate rates, processes, and pathways for EG biodegradation and identify key microbial taxa involved in its degradation.

Identification of novel potential acetate-oxidizing bacteria in an acetate-fed methanogenic chemostat based on DNA stable isotope probing.

PubMed

Wang, Hui-Zhong; Gou, Min; Yi, Yue; Xia, Zi-Yuan; Tang, Yue-Qin

2018-05-11

Acetate is a significant intermediate of anaerobic fermentation. There are two pathways for converting acetate to CH 4 and CO 2 : acetoclastic methanogenesis by acetoclastic methanogens, and syntrophic acetate oxidation by acetate-oxidizing bacteria (AOB) and hydrogenotrophic methanogens. Detailed investigations of syntrophic acetate-oxidizing bacteria (SAOB) should contribute to the elucidation of the microbial mechanisms of methanogenesis. In this study, we investigated the major phylogenetic groups of acetate-utilizing bacteria (AUB) in a mesophilic methanogenic chemostat fed with acetate as the sole carbon source by using DNA stable isotope probing (SIP) technology. The results indicated that acetoclastic methanogenesis and acetate oxidization/hydrogenotrophic methanogenesis coexisted in the mesophilic chemostat fed with acetate, operated at a dilution rate of 0.1 d -1 . OTU Ace13(9-17) (KU869530), Ace13(9-4) (KU667241), and Ace13(9-23) (KU667236), assigned to the phyla Firmicutes and Bacteroidetes, were probably potential SAOB in the chemostat, which needs further investigation. Species in the phyla Proteobacteria, Deferribacteres, Acidobacteria, Spirochaetes and Actinobacteria were probably capable of utilizing acetate for their growth. Methanoculleus was likely to be the preferred hydrogenotrophic methanogen for syntrophy with AOB in the chemostat.

Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels.

PubMed

Cheon, Seungwoo; Kim, Hye Mi; Gustavsson, Martin; Lee, Sang Yup

2016-12-01

As climate change has become one of the major global risks, our heavy dependence on petroleum-derived fuels has received much public attention. To solve such problems, production of sustainable fuels has been intensively studied over the past years. Thanks to recent advances in synthetic biology and metabolic engineering technologies, bio-based platforms for advanced biofuels production have been developed using various microorganisms. The strategies for production of advanced biofuels have converged upon four major metabolic routes: the 2-ketoacid pathway, the fatty acid synthesis (FAS) pathway, the isoprenoid pathway, and the reverse β-oxidation pathway. Additionally, the polyketide synthesis pathway has recently been attracting interest as a promising alternative biofuel production route. In this article, recent trends in advanced biofuels production are reviewed by categorizing them into three types of advanced biofuels: alcohols, biodiesel and jet fuel, and gasoline. Focus is given on the strategies of employing synthetic biology and metabolic engineering for the development of microbial strains producing advanced fuels. Finally, the prospects for future advances needed to achieve much more efficient bio-based production of advanced biofuels are discussed, focusing on designing advanced biofuel production pathways coupled with screening, modifying, and creating novel enzymes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

PubMed

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

Use It or Lose It: Advances in Our Understanding of Terrestrial Nitrogen Retention and Loss (Invited)

NASA Astrophysics Data System (ADS)

Silver, W. L.; Yang, W. H.

2013-12-01

Understanding of the terrestrial nitrogen (N) cycle has grown over the last decade to include a variety of pathways that have the potential to either retain N in the ecosystem or result in losses to the atmosphere or groundwater. Early work has described the mechanics of these N transformations, but the relevance of these processes to ecosystem, regional, or global scale N cycling has not been well quantified. In this study, we review advances in our understanding of the terrestrial N cycle, and focus on three pathways with particular relevance to N retention and loss: dissimilatory nitrate and nitrite reduction to ammonium (DNRA), anaerobic ammonium oxidation (annamox), and anaerobic ammonium oxidation coupled to iron reduction (Feammox). We discuss the role of these processes in the microbial N economy (sensu Burgin et al. 2011) of the terrestrial N cycle, the environmental and ecological constraints, and relationships with other key biogeochemical cycles. We also discuss recent advances in analytical approaches that have improved our ability to detect these and related N fluxes in terrestrial ecosystems. Finally, we present a scaling exercise that identifies the potential importance of these pathways for N retention and loss across a range of spatial and temporal scales, and discuss their significance in terms of N limitation to net primary productivity, N leaching to groundwater, and the release of reactive N gases to the atmosphere.

Mercury methylation in mine wastes collected from abandoned mercury mines in the USA

USGS Publications Warehouse

Gray, J.E.; Hines, M.E.; Biester, H.; Lasorsa, B.K.; ,

2003-01-01

Speciation and transformation of Hg was studied in mine wastes collected from abandoned Hg mines at McDermitt, Nevada, and Terlingua, Texas, to evaluate formation of methyl-Hg, which is highly toxic. In these mine wastes, we measured total Hg and methyl-Hg contents, identified various Hg compounds using a pyrolysis technique, and determined rates of Hg methylation and methyl-Hg demethylation using isotopic-tracer methods. Mine wastes contain total Hg contents as high as 14000 ??g/g and methyl-Hg concentrations as high as 88 ng/g. Mine wastes were found to contain variable amounts of cinnabar, metacinnabar, Hg salts, Hg0, and Hg0 and Hg2+ sorbed onto matrix particulates. Samples with Hg0 and matrix-sorbed Hg generally contained significant methyl-Hg contents. Similarly, samples containing Hg0 compounds generally produced significant Hg methylation rates, as much as 26%/day. Samples containing mostly cinnabar showed little or no Hg methylation. Mine wastes with high methyl-Hg contents generally showed low methyl-Hg demethylation, suggesting that Hg methylation was dominant. Methyl-Hg demethylation was by both oxidative and microbial pathways. The correspondence of mine wastes containing Hg0 compounds and measured Hg methylation suggests that Hg0 oxidizes to Hg2+, which is subsequently bioavailable for microbial Hg methylation.

Natural attenuation process via microbial oxidation of arsenic in a high Andean watershed.

PubMed

Leiva, Eduardo D; Rámila, Consuelo d P; Vargas, Ignacio T; Escauriaza, Cristian R; Bonilla, Carlos A; Pizarro, Gonzalo E; Regan, John M; Pasten, Pablo A

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and < 310 mm annual rainfall), which are conditions that have rarely been studied. Our model system was the upper Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

PubMed Central

Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R.

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons. PMID:26417542

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

PubMed

Spain, Anne M; Elshahed, Mostafa S; Najar, Fares Z; Krumholz, Lee R

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring's source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

Borneol Dehydrogenase from Pseudomonas sp. Strain TCU-HL1 Catalyzes the Oxidation of (+)-Borneol and Its Isomers to Camphor

PubMed Central

Tsang, Hoi-Lung; Huang, Jui-Lin; Lin, Yu-Hsuan; Huang, Kai-Fa; Lu, Pei-Luen; Lin, Guang-Huey; Khine, Aye Aye; Hu, Anren

2016-01-01

ABSTRACT Most plant-produced monoterpenes can be degraded by soil microorganisms. Borneol is a plant terpene that is widely used in traditional Chinese medicine. Neither microbial borneol dehydrogenase (BDH) nor a microbial borneol degradation pathway has been reported previously. One borneol-degrading strain, Pseudomonas sp. strain TCU-HL1, was isolated by our group. Its genome was sequenced and annotated. The genome of TCU-HL1 consists of a 6.2-Mbp circular chromosome and one circular plasmid, pTHL1 (12.6 kbp). Our results suggest that borneol is first converted into camphor by BDH in TCU-HL1 and is further decomposed through a camphor degradation pathway. The recombinant BDH was produced in the form of inclusion bodies. The apparent Km values of refolded recombinant BDH for (+)-borneol and (−)-borneol were 0.20 ± 0.01 and 0.16 ± 0.01 mM, respectively, and the kcat values for (+)-borneol and (−)-borneol were 0.75 ± 0.01 and 0.53 ± 0.01 s−1, respectively. Two plant BDH genes have been reported previously. The kcat and kcat/Km values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. IMPORTANCE The degradation of borneol in a soil microorganism through a camphor degradation pathway is reported in this study. We also report a microbial borneol dehydrogenase. The kcat and kcat/Km values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. The indigenous borneol- and camphor-degrading strain isolated, Pseudomonas sp. strain TCU-HL1, reminds us of the time 100 years ago when Taiwan was the major producer of natural camphor in the world. PMID:27542933

Investigating the hydrological origins of Blood Falls - geomicrobiological insights into a briny subglacial Antarctic aquifer

NASA Astrophysics Data System (ADS)

Mikucki, J.; Tulaczyk, S. M.; Purcell, A. M.; Dachwald, B.; Lyons, W. B.; Welch, K. A.; Auken, E.; Dugan, H. A.; Walter, J. I.; Pettit, E. C.; Doran, P. T.; Virginia, R. A.; Schamper, C.; Foley, N.; Feldmann, M.; Espe, C.; Ghosh, D.; Francke, G.

2015-12-01

Subglacial waters tend to accumulate solutes from extensive rock-water interactions, which, when released to the surface, can provide nutrients to surface ecosystems providing a 'hot spot' for microbial communities. Blood Falls, an iron-rich, saline feature at the terminus of Taylor Glacier in the McMurdo Dry Valleys, Antarctica is a well-studied subglacial discharge. Here we present an overview of geophysical surveys, thermomechanical drilling exploration and geomicrobiological analyses of the Blood Falls system. A helicopter-borne transient electromagnetic system (SkyTEM) flown over the Taylor Glacier revealed a surprisingly extensive subglacial aquifer and indicates that Blood Falls may be the only surface manifestation of this extensive briny groundwater. Ground-based temperature sensing and GPR data combined with the helicopter-borne TEM data enabled targeted drilling into the englacial conduit that delivers brine to the surface. During the 2014-15 austral summer field season, we used a novel ice-melting drill (the IceMole) to collect englacial brine for geomicrobiological analyses. Results from previously collected outflow and more recent samples indicate that the brine harbors a metabolically active microbial community that persists, despite cold, dark isolation. Isotope geochemistry and molecular analysis of functional genes from BF suggested that a catalytic or 'cryptic' sulfur cycle was linked to iron reduction. Recent metagenomic analysis confirms the presence of numerous genes involved in oxidative and reductive sulfur transformations. Metagenomic and metabolic activity data also indicate that subglacial dark CO2 fixation occurs via various pathways. Genes encoding key steps in CO2 fixation pathways including the Calvin Benson Basham and Wood Ljungdahl pathway were present and brine samples showed measureable uptake of 14C-labeled bicarbonate. These results support the notion that, like the deep subsurface, subglacial environments are chemosynthetic, deriving energy in part by cycling iron and sulfur compounds. Collectively our interdisciplinary dataset indicates that subsurface brines are widespread in the Taylor Valley polar desert and this previously unknown groundwater network likely supports unique microbial life.

The Extent of Fermentative Transformation of Phenolic Compounds in the Bioanode Controls Exoelectrogenic Activity in a Microbial Electrolysis Cell

DOE PAGES

Zeng, Xiaofei; Collins, Maya; Borole, Abhijeet P.; ...

2016-11-27

Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived streams and to promote water reuse in biofuel production. Thus, a thorough understanding of the fate of phenolic compounds in bioanodes is urgently needed. The present study investigated the biotransformation of three structurally similar phenolic compounds (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA), and their individual contribution to exoelectrogenesis in a microbial electrolysis cell (MEC) bioanode. Fermentation of SA resulted in themore » highest exoelectrogenic activity among the three compounds tested, with 50% of the electron equivalents converted to current, compared to 12 and 9% for VA and HBA, respectively. The biotransformation of SA, VA and HBA was initiated by demethylation and decarboxylation reactions common to all three compounds, resulting in their corresponding hydroxylated analogs. SA was transformed to pyrogallol (1,2,3-trihydroxybenzene), whose aromatic ring was then cleaved via a phloroglucinol pathway, resulting in acetate production, which was then used in exoelectrogenesis. In contrast, more than 80% of VA and HBA was converted to catechol (1,2-dihydroxybenzene) and phenol (hydroxybenzene) as their respective dead-end products. The persistence of catechol and phenol is explained by the fact that the phloroglucinol pathway does not apply to di- or mono-hydroxylated benzenes. Previously reported, alternative ring-cleaving pathways were either absent in the bioanode microbial community or unfavorable due to high energy-demand reactions. With the exception of acetate oxidation, all biotransformation steps in the bioanode occurred via fermentation, independently of exoelectrogenesis. Therefore, the observed exoelectrogenic activity in batch runs conducted with SA, VA and HBA was controlled by the extent of fermentative transformation of the three phenolic compounds in the bioanode, which is related to the number and position of the methoxy and hydroxyl substituents.« less

Metagenomic and Clumped Isotopologue Evidence for Microbial Methanogenesis in the Zambales Ophiolite

NASA Astrophysics Data System (ADS)

Woycheese, K. M.; Meyer-Dombard, D. R.; Cardace, D.; Arcilla, C. A.; Ono, S.

2017-12-01

Active serpentinization occurring in the Zambales Ophiolite Range in the Philippines results in ultrabasic (pH > 10) fluid springs high in dissolved hydrogen and methane. Concentrations of dissolved gases varies between the springs; H2 ranges from 16-20% and CH4 by 8-12% by volume. Hydrogen gas is generated by serpentinization, but the provenance of methane is unknown and thought to be thermogenically derived based on a previously-reported δDCH4 values from the Los Fuegos Eternos gas seep1. Here, we present metagenomic and 13CH3D clumped isotopologue evidence for hydrogenotropic and acetoclastic methanogenesis in fluid springs and sediments collected from Manleluag Spring Protected Landscape, Mangatarem, Pangasinan, the Philippines. Methane gas collected from two springs was analyzed on a tunable infrared laser direct absorption spectroscopy (TILDAS) at the Massachusetts Institute of Technology to determine the equilibration temperature of methane. Stable isotope analysis of methane C and H indicate δ13C vs. PDB ratios near -14‰ and δD vs. SMOW ratios near -367‰. The Δ13CH3D approximately -1.0‰ vs. stochastic distribution, which is "anticlumped" (i.e. values <0‰, at which temperature cannot be expressed) and indicative of microbial methanogenesis2. Shotgun metagenomic sequencing analysis of fluids and sediments from Manleluag reveals an abundance of methanogenesis-related genes. Universal methanogenesis genes encoding methyl-coenzyme M reductase (mcr) and heterodisulfide reductase (hdr) are detected in spring fluids and sediments. Genes encoding key steps of both hydrogenotrophic and acetoclastic methanogenesis are present. Universal methane oxidation genes methanol dehydrogenase (mdh) and methane monooxygenase (mmo) are present but less abundant than methanogenesis genes, and not found in all sampling locations. Carbon assimilation genes detected in fluid and sediment metagenomes indicate that the ribulose monophosphate pathway is the predominant methane oxidation mechanism utilized by methanotrophs. This work indicates that the source of microbial methane in Zambales may be very complex and likely involves multiple metabolic pathways. 1. Abrajano et al. (1988). Chem. Geol. 71: 211-222. 2. Wang et al. (2015). Science. 348(6233): 428-431.

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

RETRACTED: Aerobic degradation of 4-nitroaniline (4-NA) via novel degradation intermediates by Rhodococcus sp. strain FK48.

PubMed

Khan, Fazlurrahman; Pandey, Janmejay; Vikram, Surendra; Pal, Deepika; Cameotra, Swaranjit Singh

2013-06-15

An aerobic strain, Rhodococcus sp. strain FK48, capable of growing on 4-nitroaniline (4-NA) as the sole source of carbon, nitrogen, and energy has been isolated from enrichment cultures originating from contaminated soil samples. During growth studies with non- induced cells of FK48 catalyzed sequential denitrification (release of NO₂ substituent) and deamination (release of NH₂ substituent) of 4-NA. However, none of the degradation intermediates could be identified with growth studies. During resting cell studies, 4-NA-induced cells of strain FK48 transformed 4-NA via a previously unknown pathway which involved oxidative hydroxylation leading to formation of 4-aminophenol (4-AP). Subsequent degradation involved oxidated deamination of 4-AP and formation of 1,2,4-benzenetriol (BT) as the major identified terminal aromatic intermediate. Identification of these intermediates was ascertained by HPLC, and GC-MS analyses of the culture supernatants. 4-NA-induced cells of strain FK48 showed positive activity for 1,2,4-benzenetriol dioxygenase in spectrophotometric assay. This is the first conclusive study on aerobic microbial degradation of 4-NA and elucidation of corresponding metabolic pathway. Copyright © 2013 Elsevier B.V. All rights reserved.

Purification, crystallization and X-ray diffraction analysis of a novel ring-cleaving enzyme (BoxC{sub C}) from Burkholderia xenovorans LB400

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bains, Jasleen; Boulanger, Martin J., E-mail: mboulang@uvic.ca

2008-05-01

Preliminary X-ray diffraction studies of a novel ring-cleaving enzyme from B. xenovorans LB400 encoded by the benzoate-oxidation (box) pathway. The assimilation of aromatic compounds by microbial species requires specialized enzymes to cleave the thermodynamically stable ring. In the recently discovered benzoate-oxidation (box) pathway in Burkholderia xenovorans LB400, this is accomplished by a novel dihydrodiol lyase (BoxC{sub C}). Sequence analysis suggests that BoxC{sub C} is part of the crotonase superfamily but includes an additional uncharacterized region of approximately 115 residues that is predicted to mediate ring cleavage. Processing of X-ray diffraction data to 1.5 Å resolution revealed that BoxC{sub C} crystallizedmore » with two molecules in the asymmetric unit of the P2{sub 1}2{sub 1}2{sub 1} space group, with a solvent content of 47% and a Matthews coefficient of 2.32 Å{sup 3} Da{sup −1}. Selenomethionine BoxC{sub C} has been purified and crystals are currently being refined for anomalous dispersion studies.« less

Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates

USGS Publications Warehouse

Roger, Jennifer Roberts; Bennett, Philip C.

2004-01-01

Microorganisms play an important role in the weathering of silicate minerals in many subsurface environments, but an unanswered question is whether the mineral plays an important role in the microbial ecology. Silicate minerals often contain nutrients necessary for microbial growth, but whether the microbial community benefits from their release during weathering is unclear. In this study, we used field and laboratory approaches to investigate microbial interactions with minerals and glasses containing beneficial nutrients and metals. Field experiments from a petroleum-contaminated aquifer, where silicate weathering is substantially accelerated in the contaminated zone, revealed that phosphorus (P) and iron (Fe)-bearing silicate glasses were preferentially colonized and weathered, while glasses without these elements were typically barren of colonizing microorganisms, corroborating previous studies using feldspars. In laboratory studies, we investigated microbial weathering of silicates and the release of nutrients using a model ligand-promoted pathway. A metal-chelating organic ligand 3,4 dihydroxybenzoic acid (3,4 DHBA) was used as a source of chelated ferric iron, and a carbon source, to investigate mineral weathering rate and microbial metabolism.In the investigated aquifer, we hypothesize that microbes produce organic ligands to chelate metals, particularly Fe, for metabolic processes and also form stable complexes with Al and occasionally with Si. Further, the concentration of these ligands is apparently sufficient near an attached microorganism to destroy the silicate framework while releasing the nutrient of interest. In microcosms containing silicates and glasses with trace phosphate mineral inclusions, microbial biomass increased, indicating that the microbial community can use silicate-bound phosphate inclusions. The addition of a native microbial consortium to microcosms containing silicates or glasses with iron oxide inclusions correlated to accelerated weathering and release of Si into solution as well as the accelerated degradation of the model substrate 3,4 DHBA. We propose that silicate-bound P and Fe inclusions are bioavailable, and microorganisms may use organic ligands to dissolve the silicate matrix and access these otherwise limiting nutrients.

Nitrite oxidation in the Namibian oxygen minimum zone

PubMed Central

Füssel, Jessika; Lam, Phyllis; Lavik, Gaute; Jensen, Marlene M; Holtappels, Moritz; Günter, Marcel; Kuypers, Marcel MM

2012-01-01

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in 15N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO2− d−1) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO3− was re-oxidized back to NO3− via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways. PMID:22170426

Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates

PubMed Central

Steele, Joshua A.; Ziebis, Wiebke; Scheller, Silvan; Case, David; Reynard, Linda M.; Orphan, Victoria J.

2017-01-01

ABSTRACT Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH3D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH3D procedure and the well-established 14CH4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH3D method were directly and consistently proportional to 14C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method. IMPORTANCE Microbial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH3D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH3D procedure with the well-established 14C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH3D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH3D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics. PMID:28861523

Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates.

PubMed

Marlow, Jeffrey J; Steele, Joshua A; Ziebis, Wiebke; Scheller, Silvan; Case, David; Reynard, Linda M; Orphan, Victoria J

2017-01-01

Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH 3 D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH 3 D procedure and the well-established 14 CH 4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH 3 D method were directly and consistently proportional to 14 C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method. IMPORTANCE Microbial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH 3 D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH 3 D procedure with the well-established 14 C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH 3 D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH 3 D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics.

Hydrogen Isotope Fractionation during the Biodegradation of 1,2-Dichloroethane: Potential for Pathway Identification Using a Multi-element (C, Cl, and H) Isotope Approach.

PubMed

Palau, Jordi; Shouakar-Stash, Orfan; Hatijah Mortan, Siti; Yu, Rong; Rosell, Monica; Marco-Urrea, Ernest; Freedman, David L; Aravena, Ramon; Soler, Albert; Hunkeler, Daniel

2017-09-19

Even though multi-element isotope fractionation patterns provide crucial information with which to identify contaminant degradation pathways in the field, those involving hydrogen are still lacking for many halogenated groundwater contaminants and degradation pathways. This study investigates for the first time hydrogen isotope fractionation during both aerobic and anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) using five microbial cultures. Transformation-associated isotope fractionation values (ε bulk H ) were -115 ± 18‰ (aerobic C-H bond oxidation), -34 ± 4‰ and -38 ± 4‰ (aerobic C-Cl bond cleavage via hydrolytic dehalogenation), and -57 ± 3‰ and -77 ± 9‰ (anaerobic C-Cl bond cleavage via reductive dihaloelimination). The dual-element C-H isotope approach (Λ C-H = Δδ 2 H/Δδ 13 C ≈ ε bulk H /ε bulk C , where Δδ 2 H and Δδ 13 C are changes in isotope ratios during degradation) resulted in clearly different Λ C-H values: 28 ± 4 (oxidation), 0.7 ± 0.1 and 0.9 ± 0.1 (hydrolytic dehalogenation), and 1.76 ± 0.05 and 3.5 ± 0.1 (dihaloelimination). This result highlights the potential of this approach to identify 1,2-DCA degradation pathways in the field. In addition, distinct trends were also observed in a multi- (i.e., Δδ 2 H versus Δδ 37 Cl versus Δδ 13 C) isotope plot, which opens further possibilities for pathway identification in future field studies. This is crucial information to understand the mechanisms controlling natural attenuation of 1,2-DCA and to design appropriate strategies to enhance biodegradation.

Superoxide Production by a Manganese-Oxidizing Bacterium Facilitates Iodide Oxidation

PubMed Central

Li, Hsiu-Ping; Daniel, Benjamin; Creeley, Danielle; Grandbois, Russell; Zhang, Saijin; Xu, Chen; Ho, Yi-Fang; Schwehr, Kathy A.; Kaplan, Daniel I.; Santschi, Peter H.; Hansel, Colleen M.

2014-01-01

The release of radioactive iodine (i.e., iodine-129 and iodine-131) from nuclear reprocessing facilities is a potential threat to human health. The fate and transport of iodine are determined primarily by its redox status, but processes that affect iodine oxidation states in the environment are poorly characterized. Given the difficulty in removing electrons from iodide (I−), naturally occurring iodide oxidation processes require strong oxidants, such as Mn oxides or microbial enzymes. In this study, we examine iodide oxidation by a marine bacterium, Roseobacter sp. AzwK-3b, which promotes Mn(II) oxidation by catalyzing the production of extracellular superoxide (O2−). In the absence of Mn2+, Roseobacter sp. AzwK-3b cultures oxidized ∼90% of the provided iodide (10 μM) within 6 days, whereas in the presence of Mn(II), iodide oxidation occurred only after Mn(IV) formation ceased. Iodide oxidation was not observed during incubations in spent medium or with whole cells under anaerobic conditions or following heat treatment (boiling). Furthermore, iodide oxidation was significantly inhibited in the presence of superoxide dismutase and diphenylene iodonium (a general inhibitor of NADH oxidoreductases). In contrast, the addition of exogenous NADH enhanced iodide oxidation. Taken together, the results indicate that iodide oxidation was mediated primarily by extracellular superoxide generated by Roseobacter sp. AzwK-3b and not by the Mn oxides formed by this organism. Considering that extracellular superoxide formation is a widespread phenomenon among marine and terrestrial bacteria, this could represent an important pathway for iodide oxidation in some environments. PMID:24561582

Superoxide production by a manganese-oxidizing bacterium facilitates iodide oxidation.

PubMed

Li, Hsiu-Ping; Daniel, Benjamin; Creeley, Danielle; Grandbois, Russell; Zhang, Saijin; Xu, Chen; Ho, Yi-Fang; Schwehr, Kathy A; Kaplan, Daniel I; Santschi, Peter H; Hansel, Colleen M; Yeager, Chris M

2014-05-01

The release of radioactive iodine (i.e., iodine-129 and iodine-131) from nuclear reprocessing facilities is a potential threat to human health. The fate and transport of iodine are determined primarily by its redox status, but processes that affect iodine oxidation states in the environment are poorly characterized. Given the difficulty in removing electrons from iodide (I(-)), naturally occurring iodide oxidation processes require strong oxidants, such as Mn oxides or microbial enzymes. In this study, we examine iodide oxidation by a marine bacterium, Roseobacter sp. AzwK-3b, which promotes Mn(II) oxidation by catalyzing the production of extracellular superoxide (O2(-)). In the absence of Mn(2+), Roseobacter sp. AzwK-3b cultures oxidized ∼90% of the provided iodide (10 μM) within 6 days, whereas in the presence of Mn(II), iodide oxidation occurred only after Mn(IV) formation ceased. Iodide oxidation was not observed during incubations in spent medium or with whole cells under anaerobic conditions or following heat treatment (boiling). Furthermore, iodide oxidation was significantly inhibited in the presence of superoxide dismutase and diphenylene iodonium (a general inhibitor of NADH oxidoreductases). In contrast, the addition of exogenous NADH enhanced iodide oxidation. Taken together, the results indicate that iodide oxidation was mediated primarily by extracellular superoxide generated by Roseobacter sp. AzwK-3b and not by the Mn oxides formed by this organism. Considering that extracellular superoxide formation is a widespread phenomenon among marine and terrestrial bacteria, this could represent an important pathway for iodide oxidation in some environments.

Biodegradation of organic matter and anodic microbial communities analysis in sediment microbial fuel cells with/without Fe(III) oxide addition.

PubMed

Xu, Xun; Zhao, Qingliang; Wu, Mingsong; Ding, Jing; Zhang, Weixian

2017-02-01

To enhance the biodegradation of organic matter in sediment microbial fuel cell (SMFC), Fe(III) oxide, as an alternative electron acceptor, was added into the sediment. Results showed that the SMFC with Fe(III) oxide addition obtained higher removal efficiencies for organics than the SMFC without Fe(III) oxide addition and open circuit bioreactor, and produced a maximum power density (P max ) of 87.85mW/m 2 with a corresponding maximum voltage (V max ) of 0.664V. The alteration of UV-254 and specific ultraviolet absorbance (SUVA) also demonstrated the organic matter in sediments can be effectively removed. High-throughput sequencing of anodic microbial communities indicated that bacteria from the genus Geobacter were predominantly detected (21.23%) in the biofilm formed on the anode of SMFCs, while Pseudomonas was the most predominant genus (18.12%) in the presence of Fe(III) oxide. Additionally, compared with the open circuit bioreactor, more electrogenic bacteria attached to the biofilm of anode in SMFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation

NASA Astrophysics Data System (ADS)

Jerez, Carlos A.

The microbial solubilization of metals using chemolithoautotrophic microorganisms has successfully been used in industrial processes called biomining to extract metals such as copper, gold, uranium and others. The most studied leaching bacteria are from the genus Acidithiobacillus belonging to the Gram-negative γ-proteobacteria. Acidithiobacillus spp. obtain their energy from the oxidation of ferrous iron, elemental sulfur, or partially oxidized sulfur compounds. Other thermophilic archaeons capable of oxidizing sulfur and iron (II) have also been known for many years, and they are mainly from the genera Sulfolobus, Acidianus, Metallosphaera and Sulfurisphaera. Recently, some mesophilic iron (II)-oxidizing archaeons such as Ferroplasma acidiphilium and F. acidarmanus belonging to the Thermoplasmales have also been isolated and characterized. Recent studies of microorganisms consider them in their consortia, integrating fundamental biological knowledge with metagenomics, metaproteomics, and other data to obtain a global picture of how a microbial community functions. The understanding of microbial growth and activities in oxidizing metal ions will be useful for improving applied microbial biotechnologies such as biomining, bioshrouding, biomonitoring and bioremediation of metals in acidic environments.

Cobalamin Protection against Oxidative Stress in the Acidophilic Iron-oxidizing Bacterium Leptospirillum Group II CF-1

PubMed Central

Ferrer, Alonso; Rivera, Javier; Zapata, Claudia; Norambuena, Javiera; Sandoval, Álvaro; Chávez, Renato; Orellana, Omar; Levicán, Gloria

2016-01-01

Members of the genus Leptospirillum are aerobic iron-oxidizing bacteria belonging to the phylum Nitrospira. They are important members of microbial communities that catalyze the biomining of sulfidic ores, thereby solubilizing metal ions. These microorganisms live under extremely acidic and metal-loaded environments and thus must tolerate high concentrations of reactive oxygen species (ROS). Cobalamin (vitamin B12) is a cobalt-containing tetrapyrrole cofactor involved in intramolecular rearrangement reactions and has recently been suggested to be an intracellular antioxidant. In this work, we investigated the effect of the exogenous addition of cobalamin on oxidative stress parameters in Leptospirillum group II strain CF-1. Our results revealed that the external supplementation of cobalamin reduces the levels of intracellular ROSs and the damage to biomolecules, and also stimulates the growth and survival of cells exposed to oxidative stress exerted by ferric ion, hydrogen peroxide, chromate and diamide. Furthermore, exposure of strain CF-1 to oxidative stress elicitors resulted in the transcriptional activation of the cbiA gene encoding CbiA of the cobalamin biosynthetic pathway. Altogether, these data suggest that cobalamin plays an important role in redox protection of Leptospirillum strain CF-1, supporting survival of this microorganism under extremely oxidative environmental conditions. Understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help to develop strategies to make biomining processes more effective. PMID:27242761

Cobalamin Protection against Oxidative Stress in the Acidophilic Iron-oxidizing Bacterium Leptospirillum Group II CF-1.

PubMed

Ferrer, Alonso; Rivera, Javier; Zapata, Claudia; Norambuena, Javiera; Sandoval, Álvaro; Chávez, Renato; Orellana, Omar; Levicán, Gloria

2016-01-01

Members of the genus Leptospirillum are aerobic iron-oxidizing bacteria belonging to the phylum Nitrospira. They are important members of microbial communities that catalyze the biomining of sulfidic ores, thereby solubilizing metal ions. These microorganisms live under extremely acidic and metal-loaded environments and thus must tolerate high concentrations of reactive oxygen species (ROS). Cobalamin (vitamin B12) is a cobalt-containing tetrapyrrole cofactor involved in intramolecular rearrangement reactions and has recently been suggested to be an intracellular antioxidant. In this work, we investigated the effect of the exogenous addition of cobalamin on oxidative stress parameters in Leptospirillum group II strain CF-1. Our results revealed that the external supplementation of cobalamin reduces the levels of intracellular ROSs and the damage to biomolecules, and also stimulates the growth and survival of cells exposed to oxidative stress exerted by ferric ion, hydrogen peroxide, chromate and diamide. Furthermore, exposure of strain CF-1 to oxidative stress elicitors resulted in the transcriptional activation of the cbiA gene encoding CbiA of the cobalamin biosynthetic pathway. Altogether, these data suggest that cobalamin plays an important role in redox protection of Leptospirillum strain CF-1, supporting survival of this microorganism under extremely oxidative environmental conditions. Understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help to develop strategies to make biomining processes more effective.

Vestiges of Submarine Serpentinization Recorded in the Microbiology of Continental Ophiolite Complexes

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Sabuda, M.; Brazelton, W. J.; Twing, K. I.

2017-12-01

The study of serpentinization-influenced microbial ecosystems at and below the seafloor has accelerated in recent years with multidisciplinary drilling expeditions to the Atlantis Massif (X357), Southwest Indian Ridge (X360) and Mariana Forearc (X366). In parallel, a number of studies have surveyed serpentinizing systems in ophiolite complexes which host a range of geologic histories, geochemical characteristics, fluid pathways, and consequently microbiology. As ophiolite complexes originate as seafloor materials, it is likely that a microbiological record of seafloor serpentinization processes is maintained through the emplacement and weathering of continental serpentinites. This hypothesis was evaluated through a global comparison of continental serpentinite springs and groundwater, ranging from highly brackish (saline) to freshwater. One of the most saline sites, known as the Coast Range Ophiolite Microbial Observatory (CROMO), was used as a point-of-comparison to marine serpentinizing systems, such as the Lost City Hydrothermal Field. Although there was little taxonomic overlap between microbial populations in marine and terrestrial systems, both communities harbored an abundance of genes involved in sulfur metabolism, including sulfide oxidation, thiosulfate disproportionation, and sulfate reduction. The phylogeny of key genes involved in these metabolic processes was evaluated relative to published studies and compared between sites. Together, these data provide insights into both the functioning of microbial communities in modern-day serpentinizing systems, and the transport processes that disperse microorganisms between marine and terrestrial serpentinites.

Integration of metagenomic and stable carbon isotope evidence reveals the extent and mechanisms of carbon dioxide fixation in high-temperature microbial communities

DOE PAGES

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.; ...

2017-02-03

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although themore » contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.« less

Quantifying manganese and nitrogen cycle coupling in manganese-rich, organic carbon-starved marine sediments: Examples from the Clarion-Clipperton fracture zone

NASA Astrophysics Data System (ADS)

Mogollón, José M.; Mewes, Konstantin; Kasten, Sabine

2016-07-01

Extensive deep-sea sedimentary areas are characterized by low organic carbon contents and thus harbor suboxic sedimentary environments where secondary (autotrophic) redox cycling becomes important for microbial metabolic processes. Simulation results for three stations in the Eastern Equatorial Pacific with low organic carbon content (<0.5 dry wt %) and low sedimentation rates (10-1-100 mm ky-1) show that ammonium generated during organic matter degradation may act as a reducing agent for manganese oxides below the oxic zone. Likewise, at these sedimentary depths, dissolved reduced manganese may act as a reducing agent for oxidized nitrogen species. These manganese-coupled transformations provide a suboxic conversion pathway of ammonium and nitrate to dinitrogen. These manganese-nitrogen interactions further explain the presence and production of dissolved reduced manganese (up to tens of μM concentration) in sediments with high nitrate (>20 μM) concentrations.

Zero-valent sulphur is a key intermediate in marine methane oxidation.

PubMed

Milucka, Jana; Ferdelman, Timothy G; Polerecky, Lubos; Franzke, Daniela; Wegener, Gunter; Schmid, Markus; Lieberwirth, Ingo; Wagner, Michael; Widdel, Friedrich; Kuypers, Marcel M M

2012-11-22

Emissions of methane, a potent greenhouse gas, from marine sediments are controlled by anaerobic oxidation of methane coupled primarily to sulphate reduction (AOM). Sulphate-coupled AOM is believed to be mediated by a consortium of methanotrophic archaea (ANME) and sulphate-reducing Deltaproteobacteria but the underlying mechanism has not yet been resolved. Here we show that zero-valent sulphur compounds (S(0)) are formed during AOM through a new pathway for dissimilatory sulphate reduction performed by the methanotrophic archaea. Hence, AOM might not be an obligate syntrophic process but may be carried out by the ANME alone. Furthermore, we show that the produced S(0)--in the form of disulphide--is disproportionated by the Deltaproteobacteria associated with the ANME. Our observations expand the diversity of known microbially mediated sulphur transformations and have significant implications for our understanding of the biogeochemical carbon and sulphur cycles.

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.

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats.

PubMed

Mobberley, Jennifer M; Khodadad, Christina L M; Foster, Jamie S

2013-11-01

Thrombolites are unlaminated carbonate deposits formed by the metabolic activities of microbial mats and can serve as potential models for understanding the molecular mechanisms underlying the formation of lithifying communities. To assess the metabolic complexity of these ecosystems, high throughput DNA sequencing of a thrombolitic mat metagenome was coupled with phenotypic microarray analysis. Functional protein analysis of the thrombolite community metagenome delineated several of the major metabolic pathways that influence carbonate mineralization including cyanobacterial photosynthesis, sulfate reduction, sulfide oxidation, and aerobic heterotrophy. Spatial profiling of metabolite utilization within the thrombolite-forming microbial mats suggested that the top 5 mm contained a more metabolically diverse and active community than the deeper within the mat. This study provides evidence that despite the lack of mineral layering within the clotted thrombolite structure there is a vertical gradient of metabolic activity within the thrombolitic mat community. This metagenomic profiling also serves as a foundation for examining the active role individual functional groups of microbes play in coordinating metabolisms that lead to mineralization.

A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications.

PubMed

Leng, Ling; Yang, Peixian; Singh, Shubham; Zhuang, Huichuan; Xu, Linji; Chen, Wen-Hsing; Dolfing, Jan; Li, Dong; Zhang, Yan; Zeng, Huiping; Chu, Wei; Lee, Po-Heng

2018-01-01

The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China

PubMed Central

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73–0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41–95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs. PMID:26761709

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

PubMed

Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

2014-11-01

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

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.

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

PubMed Central

Berlemont, Renaud; Martiny, Adam C.; Martiny, Jennifer B. H.

2015-01-01

Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems. PMID:26231641

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

PubMed Central

Sierra-García, Isabel Natalia; Correa Alvarez, Javier; Pantaroto de Vasconcellos, Suzan; Pereira de Souza, Anete; dos Santos Neto, Eugenio Vaz; de Oliveira, Valéria Maia

2014-01-01

Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs. PMID:24587220

Decomposition of complex microbial behaviors into resource-based stress responses

PubMed Central

Carlson, Ross P.

2009-01-01

Motivation: Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies. Results: Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost–benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized simultaneously in different combinations to adapt to diverse conditions. Contact: rossc@biofilms.montana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19008248

Effects of Drought Manipulation on Soil Nitrogen Cycling: A Meta-Analysis

NASA Astrophysics Data System (ADS)

Homyak, Peter M.; Allison, Steven D.; Huxman, Travis E.; Goulden, Michael L.; Treseder, Kathleen K.

2017-12-01

Many regions on Earth are expected to become drier with climate change, which may impact nitrogen (N) cycling rates and availability. We used a meta-analytical approach on the results of field experiments that reduced precipitation and measured N supply (i.e., indices of N mineralization), soil microbial biomass, inorganic N pools (ammonium (NH4+) and nitrate (NO3-)), and nitrous oxide (N2O) emissions. We hypothesized that N supply and N2O emissions would be relatively insensitive to precipitation reduction and that reducing precipitation would increase extractable NH4+ and NO3- concentrations because microbial processes continue, whereas plant N uptake diminishes with drought. In support of this hypothesis, extractable NH4+ increased by 25% overall with precipitation reduction; NH4+ also increased significantly with increasing magnitude of precipitation reduction. In contrast, N supply and extractable NO3- did not change and N2O emissions decreased with reduced precipitation. Across studies microbial biomass appeared unchanged, yet from the diversity of studies, it was clear that proportionally smaller precipitation reductions increased microbial biomass, whereas larger proportional reductions in rainfall reduced microbial biomass; there was a positive intercept (P = 0.005) and a significant negative slope (P = 0.0002) for the regression of microbial biomass versus % precipitation reduction (LnR = -0.009 × (% precipitation reduction) + 0.4021). Our analyses imply that relative to other N variables, N supply is less sensitive to reduced precipitation, whereas processes producing N2O decline. Drought intensity and duration, through sustained N supply, may control how much N becomes vulnerable to loss via hydrologic and gaseous pathways upon rewetting dry soils.

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

PubMed Central

Ren, Min; Zhang, Zhufeng; Wang, Xuelian; Zhou, Zhiwei; Chen, Dong; Zeng, Hui; Zhao, Shumiao; Chen, Lingling; Hu, Yuanliang; Zhang, Changyi; Liang, Yunxiang; She, Qunxin; Zhang, Yi; Peng, Nan

2018-01-01

Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin. PMID:29593680

Physical and Biological Carbon Isotope Fractionation in Methane During Gas-Push-Pull-Tests

NASA Astrophysics Data System (ADS)

Gonzalez-Gil, G.; Schroth, M. H.; Gomez, K.; Zeyer, J.

2005-12-01

Stable isotope analyses have become a common tool to assess microbially-mediated processes in subsurface environments. We investigated if stable carbon isotope analysis can be used as a tool to complement gas push-pull tests (GPPTs), a novel technique that was recently developed and tested for the in-situ quantification of CH4 oxidation in soils. During a GPPT a gas mixture containing CH4, O2 and nonreactive tracer gases is injected into the soil, where CH4 is oxidized by indigenous microorganisms. Thereafter, a blend of injected gas mixture and soil air is extracted from the same location, and CH4 oxidation is quantified from an analysis of extracted CH4 and tracer gases. To assess the magnitude of physical isotope fractionation due to molecular diffusion during GPPTs, we conducted laboratory experiments in the absence of microbial activity in a 1m-high, 1m-diameter tank filled with dry sand. During the GPPTs' extraction phase, the isotopic composition of methane was analyzed. Results indicated strong carbon isotope fractionation (>20 per mil) during GPPTs. To assess the combined effect of physical and biological isotope fractionation, numerical simulations of GPPTs were conducted in which microbial CH4 isotope fractionation was simulated using first-order rate constants and microbial kinetic isotope fractionation factors previously reported for methane oxidation in landfill environments. Results of these simulations indicated that for small CH4 oxidation rates, overall isotope fractionation in CH4 is dominated by physical fractionation. Conversely, for high CH4 oxidation rates, overall fractionation is dominated by biological fractionation. Thus, CH4 isotope fractionation data alone from a single GPPT cannot be used to assess microbial CH4 oxidation. However, biological fractionation may be quantified if physical fractionation due to diffusion is known. This can be achieved by conducting two sequential GPPTs, with microbial activity being inhibited in the second test.

Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

PubMed

Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

2016-06-27

Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO 3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

Global biogeography of microbial nitrogen-cycling traits in soil

NASA Astrophysics Data System (ADS)

Nelson, M.; Martiny, A.; Martiny, J. B. H.

2016-12-01

Microorganisms drive much of the Earth's nitrogen (N) cycle. However, despite their importance, many ecosystem models do not explicitly consider microbial communities and their functions. One obstacle in doing this is that we lack a complete understanding of the role that microbes play in biogeochemical processes. To address this challenge we used metagenomics to assess various N cycling traits of soil microorganisms in samples from around the globe. As measurable characteristics of an organism, traits can be used to quantify the role of microbes in ecosystem processes. Using 365 publically available soil metagenomes, we characterized the biogeography of microbial N cycling traits, defined as the abundance and composition of eight N pathways. We found strong biogeographic patterns in the frequency of N pathway traits; however, our models explained much less variation in taxonomic composition across sites. Focusing on individual N pathways, we identified the prominent taxa harboring these pathways. In addition, we found an unexpectedly high frequency of Bacteria encoding the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a little studied N cycle process in soils. Finally, across all N pathways, phylogenetic analysis revealed that some phyla seem to be N cycle generalists (i.e delta-Proteobacteria), with the potential to carry out many N transformations, whereas others seem to be specialists (i.e. Cyanobacteria). As the most comprehensive map to date of the global distribution of microbial N traits, this study provides a springboard for further investigation of the prominent players in N cycling in soils. Overall, biogeographic patterns of traits can provide a foundation for understanding how microbial diversity impacts ecosystem processes and ultimately predicting how this diversity may shift in the face of global change.

Boosting methane generation by co-digestion of sludge with fruit and vegetable waste: Internal environment of digester and methanogenic pathway.

PubMed

Di Maria, Francesco; Barratta, Martino

2015-09-01

The effects of anaerobic co-digestion of waste-mixed sludge with fruit and vegetable waste (FVW) on the methane generation of a mesophilic digester was investigated. Organic loading rates (OLR) were 1.46kgVS/m(3)day, 2.1kgVS/m(3)day and 2.8kgVS/m(3)day. Increase in the OLR due to FVW co-digestion caused modification of the internal environment of the digester, mainly in terms of N-NH4 (mg/L). Corresponding microbial populations were investigated by metagenomic high-throughput sequencing. Maximum specific bio-methane generation of 435 NLCH4 per kgVS feed was achieved for an OLR of 2.1kgVS/m(3)day, which corresponded to a biomethane generation per kgVS removed of about 1700 NLCH4. In these conditions the methanogenic pathway was dominated by aceticlastic Methanosaeta and hydrogenotrophic/aceticlastic Methanoscarcinae. Ammonia concentration in the digester resulted a key parameter for enhancing syntrophic acetate oxidation, enabling a balanced aceticlastic and hydrogenotrophic/aceticlastic methanogenic pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms.

PubMed

Araújo, Ademir Sérgio Ferreira; Lima, Luciano Moura; Santos, Vilma Maria; Schmidt, Radomir

2016-10-01

Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.

Pathways and mechanisms for removal of dissolved organic carbon from leaf leachate in streams

Treesearch

Clifford N. Dahm

1981-01-01

Removal of dissolved organic carbon (DOC) from water resulting from adsorption and microbial uptake was examined to determine the importance of biotic and abiotic pathways. Physical–chemical adsorption to components of the stream sediment or water and biotic assimilation associated with the microbial population was determined in recirculating chambers utilizing...

Microbial removal of no.sub.x from gases

DOEpatents

Sublette, Kerry L.

1991-01-01

Disclosed is a process by which a gas containing nitric oxide is contacted with an anaerobic microbial culture of denitrifying bacteria to effect the chemical reduction of the nitric oxide to elemental nitrogen. The process is particularly suited to the removal of nitric oxide from flue gas streams and gas streams from nitric acid plants. Thiobacillus dentrificians as well as other bacteria are disclosed for use in the process.

Assessment of the performance of SMFCs in the bioremediation of PAHs in contaminated marine sediments under different redox conditions and analysis of the associated microbial communities.

PubMed

Hamdan, Hamdan Z; Salam, Darine A; Hari, Ananda Rao; Semerjian, Lucy; Saikaly, Pascal

2017-01-01

The biodegradation of naphthalene, 2-methylnaphthalene and phenanthrene was evaluated in marine sediment microbial fuel cells (SMFCs) under different biodegradation conditions, including sulfate reduction as a major biodegradation pathway, employment of anode as terminal electron acceptor (TEA) under inhibited sulfate reducing bacteria activity, and combined sulfate and anode usage as electron acceptors. A significant removal of naphthalene and 2-methylnaphthalene was observed at early stages of incubation in all treatments and was attributed to their high volatility. In the case of phenanthrene, a significant removal (93.83±1.68%) was measured in the closed circuit SMFCs with the anode acting as the main TEA and under combined anode and sulfate reduction conditions (88.51±1.3%). A much lower removal (40.37±3.24%) was achieved in the open circuit SMFCs operating with sulfate reduction as a major biodegradation pathway. Analysis of the anodic bacterial community using 16S rRNA gene pyrosequencing revealed the enrichment of genera with potential exoelectrogenic capability, namely Geoalkalibacter and Desulfuromonas, on the anode of the closed circuit SMFCs under inhibited SRB activity, while they were not detected on the anode of open circuit SMFCs. These results demonstrate the role of the anode in enhancing PAHs biodegradation in contaminated marine sediments and suggest a higher system efficiency in the absence of competition between microbial redox processes (under SRB inhibition), namely due to the anode enrichment with exoelectrogenic bacteria, which is a more energetically favorable mechanism for PAHs oxidation than sulfate. Copyright © 2016. Published by Elsevier B.V.

Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas.

PubMed

Marlow, Jeffrey J; Kumar, Amit; Enalls, Brandon C; Reynard, Linda M; Tuross, Noreen; Stephanopoulos, Gregory; Girguis, Peter

2018-06-01

Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy-rich, yet the most efficient methane-activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by-products at a comparable rate and in near-stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost-effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep-sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep-sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full-scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane-oxidizing, sulfide-generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane-dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth-based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane-activating microbial communities using a low-mass and sediment-free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use. © 2018 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals Inc.

Harnessing a methane‐fueled, sediment‐free mixed microbial community for utilization of distributed sources of natural gas

PubMed Central

Marlow, Jeffrey J.; Kumar, Amit; Enalls, Brandon C.; Reynard, Linda M.; Tuross, Noreen

2018-01-01

Abstract Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy‐rich, yet the most efficient methane‐activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by‐products at a comparable rate and in near‐stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost‐effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep‐sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep‐sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full‐scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane‐oxidizing, sulfide‐generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane‐dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth‐based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane‐activating microbial communities using a low‐mass and sediment‐free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use. PMID:29460958

Anaerobic degradation of 1,1,2,2-tetrachloroethane and association with microbial communities in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland : laboratory experiments and comparisons to field data

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.; Kirshtein, Julie D.; Jones, Elizabeth J.

2003-01-01

Defining biodegradation rates and processes is a critical part of assessing the feasibility of monitored natural attenuation as a remediation method for ground water containing organic contaminants. During 1998?2001, the U.S. Geological Survey conducted a microbial study at a freshwater tidal wetland along the West Branch Canal Creek, Aberdeen Proving Ground, Maryland, as part of an investigation of natural attenuation of chlorinated volatile organic compounds (VOCs) in the wetland sediments. Geochemical analyses and molecular biology techniques were used to investigate factors controlling anaerobic degradation of 1,1,2,2-tetrachloroethane (TeCA), and to characterize the microbial communities that potentially are important in its degradation. Rapid TeCA and daughter product degradation observed in laboratory experiments and estimated with field data confirm that natural attenuation is a feasible remediation method at this site. The diverse microbial community that seems to be involved in TeCA degradation in the wetland sediments varies with changing spatial and seasonal conditions, allowing continued effective natural attenuation throughout the year. Rates of TeCA degradation in anaerobic microcosm experiments conducted with wetland sediment collected from two different sites (WB23 and WB30) and during three different seasons (March?April 1999, July?August 1999, and October?November 2000) showed little spatial variability but high seasonal variability. Initial first-order degradation rate constants for TeCA ranged from 0.10?0.01 to 0.16?0.05 per day (half-lives of 4.3 to 6.9 days) for March?April 1999 and October?November 2000 microcosms incubated at 19 degrees Celsius, whereas lower rate constants of 0 ? 0.03 and 0.06 ? 0.03 per day were obtained in July?August 1999 microcosms incubated at 19 degrees Celsius. Microbial community profiles showed that low microbial biomass and microbial diversity in the summer, possibly due to competition for nutrients by the wetland vegetation, could account for these unexpectedly low degradation rates. In microcosms incubated at 5 degrees Celsius, about 50 percent of the initial TeCA in solution was converted to daughter products within a 35-day incubation period, indicating that biodegradation in the wetland sediments can continue during cold winter temperatures. Initial pathways of TeCA degradation were the same in the wetland sediment microcosms regardless of the season or sediment collection site, the reduction-oxidation conditions, and the previous exposure of the sediment to contamination. Immediate and simultaneous dichloroelimination and hydrogenolysis, producing 1,2-dichloro-ethene (12DCE) and 1,1,2-trichloroethane (112TCA), respectively, were the initial TeCA degradation pathways in all live microcosm experiments. The production and degradation of vinyl chloride (VC), which is the most toxic of the TeCA daughter compounds, was affected by spatial and seasonal variability, reduction-oxidation condition, and pre-exposure of the wetland sediment. TeCA-amended microcosms constructed with WB30 sediment showed approximately twice as much VC production as those constructed with WB23 sediment. Results of 112TCA-amended microcosms indicated that the greater production of VC in the WB30 sediment resulted from a greater predominance of the 112TCA dichloro-elimination pathway in these sediments. VC degradation also was substantially higher in microcosms constructed with WB30 sediment than those constructed with WB23 sediment, resulting in lower VC concentrations at the end of WB30 microcosms. Enrichment experiments in which microcosm slurry was amended with high initial VC concentrations showed that the spatial difference in VC degradation was negligible after prolonged incubation under methanogenic conditions. Inhibition of methanogenic activity in microcosms by addition of sulfate or of 2-bromoethanesulfonic acid inhibited production and degradation of VC. Inhibition of methanogenesis b

Electrodes as Terminal Electron Acceptors in Anaerobic Ammonium Oxidation

NASA Astrophysics Data System (ADS)

Ruiz-Urigüen, M.; Jaffe, P. R.

2017-12-01

Anaerobic ammonium (NH4+) oxidation under iron (Fe) reducing conditions is a microbial- mediated process known as Feammox. This is a novel pathway in the nitrogen cycle, and a key process for alleviating NH4+ accumulation in anoxic soils, wetlands, and wastewater. Acidimicrobiaceae-bacterium A6, phylum Actinobacteria, are one type of autotrophic bacteria linked to this process. The Feammox-bacteria obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, iron oxides are the TEAs. However, in this study we show that electrodes in Microbial Electrolysis Cells (MECs) or electrodes set in the field can be used as TEAs by Feammox-bacteria. The potential difference between electrodes is the driving force for electron transfer, making the reaction energetically feasible. Our results show that MECs containing Feammox cultures can remove NH4+ up to 3.5 mg/L in less than 4 hours, compared to an average of 9 mg/L in 2 weeks when cultured under traditional conditions. Concomitantly, MECs produce an average current of 30.5 A/m3 whilst dead bacteria produced low (<2.7 A/m3) or no current. Furthermore, we have measured that A6 biomass increased from 5E4 cells/ml to 9.77E5 cells/ml in 2 weeks of operation, indicating the feasibility of growing A6 in MECs. Results from the electrodes in the field show higher percentage of electrogenic bacteria, including Acidimicrobiaceae-bacterium, on the more reducing electrode, compared to the more oxidized one. Our initial results also suggest that electrodes contained more Actinobacteria when compared to bulk soil. Electrodes as TEAs enhance electrogenic bacteria recovery and culturing. The use of MECs for the productions of Feammox-bacteria eliminates the dependence of Fe, a finite electron acceptor, therefore, allowing for continuous NH4+ removal. Finally, Fe-free Feammox-bacteria can be applied to reduce other metals of environmental concern; therefore, opening the range of possible application of Feammox-bacteria.

Physiological and Chemical Investigations into Microbial Degradation of Synthetic Poly(cis-1,4-isoprene)

PubMed Central

Bode, Helge B.; Zeeck, Axel; Plückhahn, Kirsten; Jendrossek, Dieter

2000-01-01

Streptomyces coelicolor 1A and Pseudomonas citronellolis were able to degrade synthetic high-molecular-weight poly(cis-1,4-isoprene) and vulcanized natural rubber. Growth on the polymers was poor but significantly greater than that of the nondegrading strain Streptomyces lividans 1326 (control). Measurement of the molecular weight distribution of the polymer before and after degradation showed a time-dependent increase in low-molecular-weight polymer molecules for S. coelicolor 1A and P. citronellolis, whereas the molecular weight distribution for the control (S. lividans 1326) remained almost constant. Three degradation products were isolated from the culture fluid of S. coelicolor 1A grown on vulcanized rubber and were identified as (6Z)-2,6-dimethyl-10-oxo-undec-6-enoic acid, (5Z)-6-methyl-undec-5-ene-2,9-dione, and (5Z,9Z)-6,10-dimethyl-pentadec-5,9-diene-2,13-dione. An oxidative pathway from poly(cis-1,4-isoprene) to methyl-branched diketones is proposed. It includes (i) oxidation of an aldehyde intermediate to a carboxylic acid, (ii) one cycle of β-oxidation, (iii) oxidation of the conjugated double bond resulting in a β-keto acid, and (iv) decarboxylation. PMID:10966376

Coastal eutrophication thresholds: a matter of sediment microbial processes.

PubMed

Lehtoranta, Jouni; Ekholm, Petri; Pitkänen, Heikki

2009-09-01

In marine sediments, the major anaerobic mineralization processes are Fe(III) oxide reduction and sulfate reduction. In this article, we propose that the two alternative microbial mineralization pathways in sediments exert decisively different impacts on aquatic ecosystems. In systems where iron reduction dominates in the recently deposited sediment layers, the fraction of Fe(III) oxides that is dissolved to Fe(II) upon reduction will ultimately be transported to the oxic layer, where it will be reoxidized. Phosphorus, which is released from Fe(III) oxides and decomposing organic matter from the sediment, will be largely trapped by this newly formed Fe(III) oxide layer. Consequently, there are low concentrations of phosphorus in near-bottom and productive water layers and primary production tends to be limited by phosphorus (State 1). By contrast, in systems where sulfate reduction dominates, Fe(III) oxides are reduced by sulfides. This chemical reduction leads to the formation and permanent burial of iron as solid iron sulfides that are unable to capture phosphorus. In addition, the cycling of iron is blocked, and phosphorus is released to overlying water. Owing to the enrichment of phosphorus in water, the nitrogen : phosphorus ratio is lowered and nitrogen tends to limit algal growth, giving an advantage to nitrogen-fixing blue-green algae (State 2). A major factor causing a shift from State 1 to State 2 is an increase in the flux of labile organic carbon to the bottom sediments; upon accelerating eutrophication a critical point will be reached when the availability of Fe(III) oxides in sediments will be exhausted and sulfate reduction will become dominant. Because the reserves of Fe(III) oxides are replenished only slowly, reversal to State 1 may markedly exceed the time needed to reduce the flux of organic carbon to the sediment. A key factor affecting the sensitivity of a coastal system to such a regime shift is formed by the hydrodynamic alterations that decrease the transport of O2 to the near-bottom water, e.g., due to variations in salinity and temperature stratification.

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 changes in the abundance of different organisms that occupy these microenvironments. The relative consumption of oxygen by different members of Fe(II)-oxidizing mat communities has implications for autotroph-heterotroph associations and the dynamic micromorphology of active Fe(III)-oxide terraces.

Constraining pathways of microbial mediation for carbonate concretions of the Miocene Monterey Formation using carbonate-associated sulfate

NASA Astrophysics Data System (ADS)

Loyd, Sean J.; Berelson, William M.; Lyons, Timothy W.; Hammond, Douglas E.; Corsetti, Frank A.

2012-02-01

Carbonate concretions can form as a result of organic matter degradation within sediments. However, the ability to determine specific processes and timing relationships to particular concretions has remained elusive. Previously employed proxies (e.g., carbon and oxygen isotopes) cannot uniquely distinguish among diagenetic alkalinity sources generated by microbial oxidation of organic matter using oxygen, nitrate, metal oxides, and sulfate as electron acceptors, in addition to degradation by thermal decarboxylation. Here, we employ concentrations of carbonate-associated sulfate (CAS) and δ 34S CAS (along with more traditional approaches) to determine the specific nature of concretion authigenesis within the Miocene Monterey Formation. Integrated geochemical analyses reveal that at least three specific organo-diagenetic reaction pathways can be tied to concretion formation and that these reactions are largely sample-site specific. One calcitic concretion from the Phosphatic Shale Member at Naples Beach yields δ 34S CAS values near Miocene seawater sulfate (˜+22‰ VCDT), abundant CAS (ca. 1000 ppm), depleted δ 13C carb (˜-11‰ VPDB), and very low concentrations of Fe (ca. 700 ppm) and Mn (ca. 15 ppm)—characteristics most consistent with shallow formation in association with organic matter degradation by nitrate, iron-oxides and/or minor sulfate reduction. Cemented concretionary layers of the Phosphatic Shale Member at Shell Beach display elevated δ 34S CAS (up to ˜+37‰), CAS concentrations of ˜600 ppm, mildly depleted δ 13C carb (˜-6‰), moderate amounts of Mn (ca. 250 ppm), and relatively low Fe (ca. 1700 ppm), indicative of formation in sediments dominated by sulfate reduction. Finally, concretions within a siliceous host at Montaña de Oro and Naples Beach show minimal CAS concentrations, positive δ 13C values, and the highest concentrations of Fe (ca. 11,300 ppm) and Mn (ca. 440 ppm), consistent with formation in sediments experiencing methanogenesis in a highly reducing environment. This study highlights the promise in combining CAS analysis with more traditional techniques to differentiate among diagenetic reactions as preserved in the geologic record and shows potential for unraveling subsurface biospheric processes in ancient samples with a high degree of specificity.

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...

Pathway and Molecular Mechanisms for Malachite Green Biodegradation in Exiguobacterium sp. MG2

PubMed Central

Wang, Ji’ai; Gao, Feng; Liu, Zhongzhong; Qiao, Min; Niu, Xuemei; Zhang, Ke-Qin; Huang, Xiaowei

2012-01-01

Malachite green (MG), N-methylated diaminotriphenylmethane, is one of the most common dyes in textile industry and has also been used as an effective antifungal agent. However, due to its negative impact on the environment and carcinogenic effects to mammalian cells, there is a significant interest in developing microbial agents to degrade this type of recalcitrant molecules. Here, an Exiguobacterium sp. MG2 was isolated from a river in Yunnan Province of China as one of the best malachite green degraders. This strain had a high decolorization capability even at the concentration of 2500 mg/l and maintained its stable activity within the pH range from 5.0 to 9.0. High-pressure liquid chromatography, liquid chromatography-mass spectrometry and gas chromatography–mass spectrometry were employed to detect the catabolic pathway of MG. Six intermediate products were identified and a potential biodegradation pathway was proposed. This pathway involves a series of reactions of N-demethylation, reduction, benzene ring-removal, and oxidation, which eventually converted N-methylated diaminotriphenylmethane into N, N-dimethylaniline that is the key precursor to MG. Furthermore, our molecular biology experiments suggested that both triphenylmethane reductase gene tmr and cytochrome P450 participated in MG degradation, consistent with their roles in the proposed pathway. Collectively, our investigation is the first report on a biodegradation pathway of triphenylmethane dye MG in bacteria. PMID:23251629

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

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.

Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a

PubMed Central

Luo, Quan; Hiessl, Sebastian; Poehlein, Anja; Daniel, Rolf

2014-01-01

The complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid–AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity. PMID:24747905

Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems

PubMed Central

Bradford, Lauren; Huang, Sichao; Szalay, Anna; Leix, Carmen; Weissbach, Max; Táncsics, András; Drewes, Jörg E.

2016-01-01

ABSTRACT It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic “Candidatus Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to “Ca. Methylomirabilis oxyfera” and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from “Ca. Methylomirabilis oxyfera” and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g−1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. IMPORTANCE NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium “Ca. Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future. PMID:27986721

Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems.

PubMed

Zhu, Baoli; Bradford, Lauren; Huang, Sichao; Szalay, Anna; Leix, Carmen; Weissbach, Max; Táncsics, András; Drewes, Jörg E; Lueders, Tillmann

2017-02-15

It has recently been suggested that oxygenic dismutation of NO into N 2 and O 2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O 2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 10 7 to 5.2 × 10 10 copies · g -1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. NO dismutation into N 2 and O 2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium "Ca Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future. Copyright © 2017 American Society for Microbiology.

CoMn2O4-supported functionalized carbon nanotube: efficient catalyst for oxygen reduction in microbial fuel cells

NASA Astrophysics Data System (ADS)

Zhu, Nengwu; Lu, Yu; Liu, Bowen; Zhang, Taiping; Huang, Jianjian; Shi, Chaohong; Wu, Pingxiao; Dang, Zhi; Wang, Ruixin

2017-10-01

Recently, the synthesis of nonprecious metal catalysts with low cost and high oxygen reduction reaction (ORR) efficiency is paid much attention in field of microbial fuel cells (MFCs). Transition metal oxides (AMn2O4, A = Co、Ni, and Zn) supported on carbon materials such as graphene and carbon nanotube exhibit stronger electroconductivity and more active sites comparing to bare AMn2O4. Herein, we demonstrate an easy operating Hummer's method to functionalize carbon nanotubes (CNTs) with poly (diallyldimethylammonium chloride) in order to achieve effective loading of CoMn2O4 nanoparticles, named CoMn2O4/PDDA-CNTs (CMODT). After solvothermal treatment, nanoscale CoMn2O4 particles ( 80 nm) were successfully attached on the noncovalent functionalized carbon nanotube. Results show that such composites possess an outstanding electrocatalytic activity towards ORR comparable to the commercial Pt/C catalyst in neutral media. Electrochemical detections as cyclic voltammogram (CV) and rotating ring-disk electrode tests (RRDE) showed that the potential of oxygen reduction peak of 30% CMODT was at - 0.3 V (vs Ag/AgCl), onset potential was at + 0.4 V. Among them, 30% CMODT composite appeared the best candidate of oxygen reduction via 3.9 electron transfer pathway. When 30% CMODT composite was utilized as cathode catalyst in air cathode MFC, the reactor obtained 1020 mW m-2 of the highest maximum power density and 0.781 V of open circuit voltage. The excellent activity and low cost (0.2 g-1) of the hybrid materials demonstrate the potential of transition metal oxide/carbon as effective cathode ORR catalyst for microbial fuel cells. [Figure not available: see fulltext.

Pathways for arsenic from sediments to groundwater to streams: Biogeochemical processes in the Inner Coastal Plain, New Jersey, USA

USGS Publications Warehouse

Barringer, Julia L.; Mumford, Adam; Young, Lily Y.; Reilly, Pamela A.; Bonin, Jennifer L.; Rosman, Robert

2010-01-01

The Cretaceous and Tertiary sediments that underlie the Inner Coastal Plain of New Jersey contain the arsenic-rich mineral glauconite. Streambed sediments in two Inner Coastal Plain streams (Crosswicks and Raccoon Creeks) that traverse these glauconitic deposits are enriched in arsenic (15–25 mg/kg), and groundwater discharging to the streams contains elevated levels of arsenic (>80 μg/L at a site on Crosswicks Creek) with arsenite generally the dominant species. Low dissolved oxygen, low or undetectable levels of nitrate and sulfate, detectable sulfide concentrations, and high concentrations of iron and dissolved organic carbon (DOC) in the groundwater indicate that reducing environments are present beneath the streambeds and that microbial activity, fueled by the DOC, is involved in releasing arsenic and iron from the geologic materials. In groundwater with the highest arsenic concentrations at Crosswicks Creek, arsenic respiratory reductase gene (arrA) indicated the presence of arsenic-reducing microbes. From extracted DNA, 16s rRNA gene sequences indicate the microbial community may include arsenic-reducing bacteria that have not yet been described. Once in the stream, iron is oxidized and precipitates as hydroxide coatings on the sediments. Arsenite also is oxidized and co-precipitates with or is sorbed to the iron hydroxides. Consequently, dissolved arsenic concentrations are lower in streamwater than in the groundwater, but the arsenic contributed by groundwater becomes part of the arsenic load in the stream when sediments are suspended during high flow. A strong positive relation between concentrations of arsenic and DOC in the groundwater samples indicates that any process—natural or anthropogenic—that increases the organic carbon concentration in the groundwater could stimulate microbial activity and thus increase the amount of arsenic that is released from the geologic materials.

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 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.

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia.

PubMed

Carlson, Ross P; Beck, Ashley E; Phalak, Poonam; Fields, Matthew W; Gedeon, Tomas; Hanley, Luke; Harcombe, William R; Henson, Michael A; Heys, Jeffrey J

2018-04-17

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Colloidal Nanomolybdenum Influence upon the Antioxidative Reaction of Chickpea Plants ( Cicer arietinum L.)

NASA Astrophysics Data System (ADS)

Taran, Nataliya; Batsmanova, Ludmila; Kosyk, Oksana; Smirnov, Oleksandr; Kovalenko, Mariia; Honchar, Liubov; Okanenko, Alexander

2016-10-01

The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops. The purpose of the study was a comparative evaluation of presowing treatment with nanomolybdenum and microbiological preparation impact upon the development of adaptive responses in chickpea plants. Oxidative processes did not develop in all variants of the experiment but in variants treated with microbial preparation, and joint action of microbial and nanopreparations even declined, as evidenced by the reduction of thiobarbituric acid reactive substances in photosynthetic tissues by 15 %. The activity of superoxide dismutase increased (by 15 %) in variant "nanomolybdenum" and joint action "microbial + nanomolybdenum," but it decreased by 20 % in variants with microbial preparation treatment. The same dependence was observed in changes of catalase activity. Antioxidant status factor, which takes into account the ratio of antioxidant to pro-oxidant, was the highest in variants with joint action of microbial preparation and nanomolybdenum (0.7), the lowest in variants with microbial treatment only (0.1). Thus, the results show that the action of nanoparticles of molybdenum activated antioxidant enzymes and decreased oxidative processes, thus promoting adaptation of plants.

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

DOE PAGES

Beam, Jacob P.; Bernstein, Hans C.; Jay, Zackary J.; ...

2016-02-15

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) inmore » 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.« less

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

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.

Evidence for biological nitrification inhibition in Brachiaria pastures

PubMed Central

Subbarao, G. V.; Nakahara, K.; Hurtado, M. P.; Ono, H.; Moreta, D. E.; Salcedo, A. F.; Yoshihashi, A. T.; Ishikawa, T.; Ishitani, M.; Ohnishi-Kameyama, M.; Yoshida, M.; Rondon, M.; Rao, I. M.; Lascano, C. E.; Berry, W. L.; Ito, O.

2009-01-01

Nitrification, a key process in the global nitrogen cycle that generates nitrate through microbial activity, may enhance losses of fertilizer nitrogen by leaching and denitrification. Certain plants can suppress soil-nitrification by releasing inhibitors from roots, a phenomenon termed biological nitrification inhibition (BNI). Here, we report the discovery of an effective nitrification inhibitor in the root-exudates of the tropical forage grass Brachiaria humidicola (Rendle) Schweick. Named “brachialactone,” this inhibitor is a recently discovered cyclic diterpene with a unique 5-8-5-membered ring system and a γ-lactone ring. It contributed 60–90% of the inhibitory activity released from the roots of this tropical grass. Unlike nitrapyrin (a synthetic nitrification inhibitor), which affects only the ammonia monooxygenase (AMO) pathway, brachialactone appears to block both AMO and hydroxylamine oxidoreductase enzymatic pathways in Nitrosomonas. Release of this inhibitor is a regulated plant function, triggered and sustained by the availability of ammonium (NH4+) in the root environment. Brachialactone release is restricted to those roots that are directly exposed to NH4+. Within 3 years of establishment, Brachiaria pastures have suppressed soil nitrifier populations (determined as amoA genes; ammonia-oxidizing bacteria and ammonia-oxidizing archaea), along with nitrification and nitrous oxide emissions. These findings provide direct evidence for the existence and active regulation of a nitrification inhibitor (or inhibitors) release from tropical pasture root systems. Exploiting the BNI function could become a powerful strategy toward the development of low-nitrifying agronomic systems, benefiting both agriculture and the environment. PMID:19805171

Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages

PubMed Central

León-Zayas, Rosa; Novotny, Mark; Podell, Sheila; Shepard, Charles M.; Berkenpas, Eric; Nikolenko, Sergey; Pevzner, Pavel; Lasken, Roger S.

2015-01-01

Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments. PMID:26386059

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

PubMed Central

Han, Ruyang; Karaoz, Ulas; Lim, HsiaoChien; Brodie, Eoin L.

2013-01-01

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H2 cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments. PMID:23064329

Strategies for microbial synthesis of high-value phytochemicals

NASA Astrophysics Data System (ADS)

Li, Sijin; Li, Yanran; Smolke, Christina D.

2018-03-01

Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit low abundance in nature. Recent demonstrations of industrial-scale production of phytochemicals in yeast have shown that microbial production of these high-value chemicals is a promising alternative to sourcing these molecules from native plant hosts. However, a number of challenges remain in the broader application of this approach, including the limited knowledge of plant secondary metabolism and the inefficient reconstitution of plant metabolic pathways in microbial hosts. In this Review, we discuss recent strategies to achieve microbial biosynthesis of complex phytochemicals, including strategies to: (1) reconstruct plant biosynthetic pathways that have not been fully elucidated by mining enzymes from native and non-native hosts or by enzyme engineering; (2) enhance plant enzyme activity, specifically cytochrome P450 activity, by improving efficiency, selectivity, expression or electron transfer; and (3) enhance overall reaction efficiency of multi-enzyme pathways by dynamic control, compartmentalization or optimization with the host's metabolism. We also highlight remaining challenges to — and future opportunities of — this approach.

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

PubMed

Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

2018-02-06

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beam, Jake; Bernstein, Hans C.; Jay, Z.

Iron oxide microbial mats are ubiquitous geobiological features on Earth and occur in extant acidic hot springs of Yellowstone National Park (YNP), WY, USA, and form as a result of microbial processes. The relative contribution of different organisms to the development of these mat ecosystems is of specific interest. We hypothesized that chemolithoautotrophic organisms contribute to the early development and production of Fe(III)-oxide mats, which could support later-colonizing heterotrophic microorganisms. Sterile glass slides were incubated in the outflow channels of two acidic geothermal springs in YNP, and spatiotemporal changes in Fe(III)-oxide accretion and abundance of relevant community members were measured.more » Lithoautotrophic Hydrogenobaculum spp. were first colonizers and the most abundant taxa identified during early successional stages (7 – 40 days). Populations of M. yellowstonensis colonized after ~ 7 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized after 30 days, and emerge as the dominant functional guild in mature iron oxide mats (1 – 2 cm thick) that form after 70 – 120 days. First-order rate constants of iron oxide accretion ranged from 0.05 – 0.046 day-1, and reflected the absolute amount of iron accreted. Micro- and macroscale microterracettes were identified during iron oxide mat development, and suggest that the mass transfer of oxygen limits microbial growth. This was also demonstrated using microelectrode measurements of oxygen as a function of mat depth, which showed steep gradients in oxygen from the aqueous mat interface to ~ 1 mm. The formation and succession of amorphous Fe(III)-oxide mat communities follows a predictable pattern of distinct stages and growth. The successional stages and microbial signatures observed in these extant Fe(III)-oxide mat communities may be relevant to other past or present Fe(III)-oxide mineralizing systems.« less

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 abundance and expression of total bacteria (targeting 16S rRNA), fungi (targeting ITS) and the nosZ genes in the soil communities. Thus, this study demonstrates potential impact of antibiotic contaminated manure on microbial communities responsible for agricultural N2O emissions.

Identification of Antimony- and Arsenic-Oxidizing Bacteria Associated with Antimony Mine Tailing

PubMed Central

Hamamura, Natsuko; Fukushima, Koh; Itai, Takaaki

2013-01-01

Antimony (Sb) is a naturally occurring toxic element commonly associated with arsenic (As) in the environment and both elements have similar chemistry and toxicity. Increasing numbers of studies have focused on microbial As transformations, while microbial Sb interactions are still not well understood. To gain insight into microbial roles in the geochemical cycling of Sb and As, soils from Sb mine tailing were examined for the presence of Sb- and As-oxidizing bacteria. After aerobic enrichment culturing with AsIII (10 mM) or SbIII (100 μM), pure cultures of Pseudomonas- and Stenotrophomonas-related isolates with SbIII oxidation activities and a Sinorhizobium-related isolate capable of AsIII oxidation were obtained. The AsIII-oxidizing Sinorhizobium isolate possessed the aerobic arsenite oxidase gene (aioA), the expression of which was induced in the presence of AsIII or SbIII. However, no SbIII oxidation activity was detected from the Sinorhizobium-related isolate, suggesting the involvement of different mechanisms for Sb and As oxidation. These results demonstrate that indigenous microorganisms associated with Sb mine soils are capable of Sb and As oxidation, and potentially contribute to the speciation and mobility of Sb and As in situ. PMID:23666539

Formation of methane and nitrous oxide in plants

NASA Astrophysics Data System (ADS)

Keppler, Frank; Lenhart, Katharina

2017-04-01

Methane, the second important anthropogenic greenhouse gas after carbon dioxide, is the most abundant reduced organic compound in the atmosphere and plays a central role in atmospheric chemistry. The global atmospheric methane budget is determined by many natural and anthropogenic terrestrial and aquatic surface sources, balanced primarily by one major sink (hydroxyl radicals) in the atmosphere. Natural sources of atmospheric methane in the biosphere have until recently been attributed to originate solely from strictly anaerobic microbial processes in wetland soils and rice paddies, the intestines of termites and ruminants, human and agricultural waste, and from biomass burning, fossil fuel mining and geological sources including mud volcanoes and seeps. However, recent studies suggested that terrestrial vegetation, fungi and mammals may also produce methane without the help of methanogens and under aerobic conditions (e.g. Keppler et al. 2009, Wang et al. 2013). These novel sources have been termed "aerobic methane production" to distinguish them from the well-known anaerobic methane production pathway. Nitrous oxide is another important greenhouse gas and major source of ozone-depleting nitric oxide. About two thirds of nitrous oxide emissions are considered to originate from anthropogenic and natural terrestrial sources, and are almost exclusively related to microbial processes in soils and sediments. However, the global nitrous oxide budget still has major uncertainties since it is unclear if all major sources have been identified but also the emission estimates of the know sources and stratospheric sink are afflicted with high uncertainties. Plants contribute, although not yet quantified, to nitrous oxide emissions either indirectly as conduits of soil derived nitrous oxide (Pihlatie et al. 2005), or directly via generation of nitrous oxide in leaves (Dean & Harper 1986) or on the leaf surface induced by UV irradiation (Bruhn et al. 2014). Moreover, lichens and mosses, so called cryptogamic covers, were recently identified to release substantial amounts of nitrous oxide (Lenhart et al. 2015). In this presentation we will give a brief overview of recent observations of aerobic methane formation and nitrous oxide emissions from terrestrial vegetation. Furthermore, we will present new results from laboratory incubation experiments that provide further insights into the formation of methane and nitrous oxide from plants. References: Bruhn, D. et al.: Leaf surface wax is a source of plant methane formation under UV radiation and in the presence of oxygen. Plant Biology 16, 512-516, 2014. Chang, C. et al.: Nitrous Oxide Emission through Plants. Soil Science Society of America Journal 62, 35-38, 1998. Dean, J. V., Harper, J. E.: Nitric oxide and nitrous oxide production by soybean and winged bean during the in vivo nitrate reductase assay. Plant Physiology 82, 718-723, 1986. Keppler, F., Boros, M., Frankenberg, C., Lelieveld, J., McLeod, A., Pirttilä, A. M., Röckmann, T., Schnitzler, J.: Methane formation in aerobic environments, Environmental Chemistry, 6, 459-465, 2009. Lenhart, K. et al.: Nitrous oxide and methane emissions from cryptogamic covers. Global Change Biology 21, 3889-3900, 2015. Pihlatie, M., Ambus, P., Rinne, J., Pilegaard, K., Vesala, T.: Plant-mediated nitrous oxide emissions from beech (Fagus sylvatica) leaves. New Phytologist 168, 93-98, 2005. Wang, Z.-P., Chang, S. X., Chen, H., Han, X.-G.: Widespread non-microbial methane production by organic compounds and the impact of environmental stresses, Earth-Science Reviews, 127, 193-202, 2013.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

[Effect of temperature on the rate of oxidation of pyrrhotite-rich sulfide ore flotation concentrate and the structure of the acidophilic chemolithoautotrophic microbial community].

PubMed

Moshchanetskii, P V; Pivovarova, T A; Belyi, A V; Kondrat'eva, T F

2014-01-01

Oxidation of flotation concentrate of a pyrrhotite-rich sulfide ore by acidophilic chemolithoautotrophic microbial communities at 35, 40, and 45 degrees C was investigated. According to the physicochemical parameters of the liquid phase of the pulp, as well as the results of analysis of the solid residue after biooxidation and cyanidation, the community developed at 40 degrees C exhibited the highest rate of oxidation. The degree of gold recovery at 35, 40, and 45 degrees C was 89.34, 94.59, and 83.25%, respectively. At 40 degrees C, the highest number of microbial cells (6.01 x 10(9) cells/mL) was observed. While temperature had very little effect on the species composition of microbial communities, except for the absence of Leptospirillum ferriphilum at 35 degrees C, the shares of individual species in the communities varied with temperature. Relatively high numbers of Sulfobacillus thermosulfidooxidans, the organism oxidizing iron and elemental sulfur at higher rates than other acidophilic chemolithotrophic species, were observed at 40 degrees C.

Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run.

PubMed

Grettenberger, Christen L; Pearce, Alexandra R; Bibby, Kyle J; Jones, Daniel S; Burgos, William D; Macalady, Jennifer L

2017-04-01

Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens , a species that is associated with high rates of Fe(II) oxidation in laboratory studies. IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121-1123, 1970, https://doi.org/10.1126/science.167.3921.1121). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens , a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation. Copyright © 2017 American Society for Microbiology.

Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation

PubMed Central

van Lingen, Henk J.; Plugge, Caroline M.; Fadel, James G.; Kebreab, Ermias; Bannink, André; Dijkstra, Jan

2016-01-01

Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered. The aim of this study was to quantify the control of PH2 on reaction rates of specific fermentation pathways, methanogenesis and NADH oxidation in rumen microbes. The control of PH2 was quantified using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. Unity FT was calculated for all glucose fermentation pathways considered, indicating no inhibition of PH2 on the production of a specific type of VFA (e.g., acetate, propionate and butyrate) in the rumen. For NADH oxidation without ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity to zero for different NAD+ to NADH ratios and pH of 6.2 and 7.0, which indicates thermodynamic control of PH2. For NADH oxidation with ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity at pH of 7.0 only. For the acetate to propionate conversion, FT increased from 0.65 to unity with increasing PH2, which indicates thermodynamic control. For propionate to acetate and butyrate to acetate conversions, FT decreased to zero below the rumen range of PH2, indicating full thermodynamic suppression. For methanogenesis by archaea without cytochromes, FT differed from unity only below the rumen range of PH2, indicating no thermodynamic control. This theoretical investigation shows that thermodynamic control of PH2 on individual VFA produced and associated yield of hydrogen and methane cannot be explained without considering NADH oxidation. PMID:27783615

NF-κB/Rel Proteins and the Humoral Immune Responses of Drosophila melanogaster

PubMed Central

Ganesan, Sandhya; Aggarwal, Kamna; Paquette, Nicholas; Silverman, Neal

2011-01-01

Nuclear Factor-κB (NF-κB)/Rel transcription factors form an integral part of innate immune defenses and are conserved throughout the animal kingdom. Studying the function, mechanism of activation and regulation of these factors is crucial for understanding host responses to microbial infections. The fruit fly Drosophila melanogaster has proved to be a valuable model system to study these evolutionarily conserved NF-κB mediated immune responses. Drosophila combats pathogens through humoral and cellular immune responses. These humoral responses are well characterized and are marked by the robust production of a battery of anti-microbial peptides. Two NF-κB signaling pathways, the Toll and the IMD pathways, are responsible for the induction of these antimicrobial peptides. Signal transduction in these pathways is strikingly similar to that in mammalian TLR pathways. In this chapter, we discuss in detail the molecular mechanisms of microbial recognition, signal transduction and NF-κB regulation, in both the Toll and the IMD pathways. Similarities and differences relative to their mammalian counterparts are discussed, and recent advances in our understanding of the intricate regulatory networks in these NF-κB signaling pathways are also highlighted. PMID:20852987

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

The effect of coal bed dewatering and partial oxidation on biogenic methane potential

USGS Publications Warehouse

Jones, Elizabeth J.P.; Harris, Steve H.; Barnhart, Elliott P.; Orem, William H.; Clark, Arthur C.; Corum, Margo D.; Kirshtein, Julie D.; Varonka, Matthew S.; Voytek, Mary A.

2013-01-01

Coal formation dewatering at a site in the Powder River Basin was associated with enhanced potential for secondary biogenic methane determined by using a bioassay. We hypothesized that dewatering can stimulate microbial activity and increase the bioavailability of coal. We analyzed one dewatered and two water-saturated coals to examine possible ways in which dewatering influences coal bed natural gas biogenesis by looking at differences with respect to the native coal microbial community, coal-methane organic intermediates, and residual coal oxidation potential. Microbial biomass did not increase in response to dewatering. Small Subunit rRNA sequences retrieved from all coals sampled represented members from genera known to be aerobic, anaerobic and facultatively anaerobic. A Bray Curtis similarity analysis indicated that the microbial communities in water-saturated coals were more similar to each other than to the dewatered coal, suggesting an effect of dewatering. There was a higher incidence of long chain and volatile fatty acid intermediates in incubations of the dewatered coal compared to the water-saturated coals, and this could either be due to differences in microbial enzymatic activities or to chemical oxidation of the coal associated with O2 exposure. Dilute H2O2 treatment of two fractions of structural coal (kerogen and bitumen + kerogen) was used as a proxy for chemical oxidation by O2. The dewatered coal had a low residual oxidation potential compared to the water-saturated coals. Oxidation with 5% H2O2 did increase the bioavailability of structural coal, and the increase in residual oxidation potential in the water saturated coals was approximately equivalent to the higher methanogenic potential measured in the dewatered coal. Evidence from this study supports the idea that coal bed dewatering could stimulate biogenic methanogenesis through partial oxidation of the structural organics in coal once anaerobic conditions are restored.

Acetogenic microbial degradation of vinyl chloride

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

2000-01-01

Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C- acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries, respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and humic acids- reducing conditions.Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C-acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and humic acids-reducing conditions.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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. Aftermore » 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.« less

Tools of pathway reconstruction and production of economically relevant plant secondary metabolites in recombinant microorganisms.

PubMed

Dziggel, Clarissa; Schäfer, Holger; Wink, Michael

2017-01-01

Plant secondary metabolites exhibit a variety of biological activities and therefore serve as valuable therapeutics or flavoring compounds. However, the small amounts isolated from plants often cannot meet market demands. This led to the exploration of other, more profitable methods for their production, including plant cell culture systems, chemical synthesis and biotechnological production in microbial hosts. The biotechnological production can be pursued by reconstructing metabolic pathways in selected microbial systems. But due to their complexity, most of these pathways are not completely understood and require the expression of a multitude of genes in a foreign organism. Recently, next generation sequencing data and advances in gene silencing in plants allowed the elucidation of some biosynthetic pathways in more detail. Thus, the de novo production of some natural products, including morphine, strictosidine, artemisinin, taxol ® and resveratrol, in extensively engineered microbial hosts has become feasible. This review highlights the reconstruction of these pathways, missing pieces and novel techniques employed. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

PubMed Central

Xue, Kai; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy; Robertson, Philip G.; Schmidt, Thomas M.

2013-01-01

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3− concentration and denitrification genes, NH4+ concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes. PMID:23241975

Role of Ergothioneine in Microbial Physiology and Pathogenesis.

PubMed

Cumming, Bridgette M; Chinta, Krishna C; Reddy, Vineel P; Steyn, Adrie J C

2018-02-20

L-ergothioneine is synthesized in actinomycetes, cyanobacteria, methylobacteria, and some fungi. In contrast to other low-molecular-weight redox buffers, glutathione and mycothiol, ergothioneine is primarily present as a thione rather than a thiol at physiological pH, which makes it resistant to autoxidation. Ergothioneine regulates microbial physiology and enables the survival of microbes under stressful conditions encountered in their natural environments. In particular, ergothioneine enables pathogenic microbes, such as Mycobacterium tuberculosis (Mtb), to withstand hostile environments within the host to establish infection. Recent Advances: Ergothioneine has been reported to maintain bioenergetic homeostasis in Mtb and protect Mtb against oxidative stresses, thereby enhancing the virulence of Mtb in a mouse model. Furthermore, ergothioneine augments the resistance of Mtb to current frontline anti-TB drugs. Recently, an opportunistic fungus, Aspergillus fumigatus, which infects immunocompromised individuals, has been found to produce ergothioneine, which is important in conidial health and germination, and contributes to the fungal resistance against redox stresses. The molecular mechanisms of the functions of ergothioneine in microbial physiology and pathogenesis are poorly understood. It is currently not known if ergothioneine is used in detoxification or antioxidant enzymatic pathways. As ergothioneine is involved in bioenergetic and redox homeostasis and antibiotic susceptibility of Mtb, it is of utmost importance to advance our understanding of these mechanisms. A clear understanding of the role of ergothioneine in microbes will advance our knowledge of how this thione enhances microbial virulence and resistance to the host's defense mechanisms to avoid complete eradication. Antioxid. Redox Signal. 28, 431-444.

Fractionation of carbon and hydrogen isotopes by methane-oxidizing bacteria

USGS Publications Warehouse

Coleman, D.D.; Risatti, J.B.; Schoell, M.

1981-01-01

Carbon isotopic analysis of methane has become a popular technique in the exploration for oil and gas because it can be used to differentiate between thermogenic and microbial gas and can sometimes be used for gas-source rock correlations. Methane-oxidizing bacteria, however, can significantly change the carbon isotopic composition of methane; the origin of gas that has been partially oxidized by these bacteria could therefore be misinterpreted. We cultured methane-oxidizing bacteria at two different temperatures and monitored the carbon and hydrogen isotopic compositions of the residual methane. The residual methane was enriched in both 13C and D. For both isotopic species, the enrichment at equivalent levels of conversion was greater at 26??C than at 11.5??C. The change in ??D relative to the change in ??13C was independent of temperature within the range studied. One culture exhibited a change in the fractionation pattern for carbon (but not for hydrogen) midway through the experiment, suggesting that bacterial oxidation of methane may occur via more than one pathway. The change in the ??D value for the residual methane was from 8 to 14 times greater than the change in the ??13C value, indicating that combined carbon and hydrogen isotopic analysis may be an effective way of identifying methane which has been subjected to partial oxidation by bacteria. ?? 1981.

Modeling central metabolism and energy biosynthesis across microbial life

DOE PAGES

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal; ...

2016-08-08

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Modeling central metabolism and energy biosynthesis across microbial life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Modeling central metabolism and energy biosynthesis across microbial life.

PubMed

Edirisinghe, Janaka N; Weisenhorn, Pamela; Conrad, Neal; Xia, Fangfang; Overbeek, Ross; Stevens, Rick L; Henry, Christopher S

2016-08-08

Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. To overcome this challenge, we developed methods and tools ( http://coremodels.mcs.anl.gov ) to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of model organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. We predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.

Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

PubMed Central

Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph; Qureshi, Tabish M.; Lige, Bao; Derrick, Anne M.; Agbo, Eddy C.; Sriram, Ganesh

2013-01-01

Synthetic biology enables metabolic engineering of industrial microbes to synthesize value-added molecules. In this, a major challenge is the efficient redirection of carbon to the desired metabolic pathways. Pinpointing strategies toward this goal requires an in-depth investigation of the metabolic landscape of the organism, particularly primary metabolism, to identify precursor and cofactor availability for the target compound. The potent antimalarial therapeutic artemisinin and its precursors are promising candidate molecules for production in microbial hosts. Recent advances have demonstrated the production of artemisinin precursors in engineered yeast strains as an alternative to extraction from plants. We report the application of in silico and in vivo metabolic pathway analyses to identify metabolic engineering targets to improve the yield of the direct artemisinin precursor dihydroartemisinic acid (DHA) in yeast. First, in silico extreme pathway (ExPa) analysis identified NADPH-malic enzyme and the oxidative pentose phosphate pathway (PPP) as mechanisms to meet NADPH demand for DHA synthesis. Next, we compared key DHA-synthesizing ExPas to the metabolic flux distributions obtained from in vivo 13C metabolic flux analysis of a DHA-synthesizing strain. This comparison revealed that knocking out ethanol synthesis and overexpressing glucose-6-phosphate dehydrogenase in the oxidative PPP (gene YNL241C) or the NADPH-malic enzyme ME2 (YKL029C) are vital steps toward overproducing DHA. Finally, we employed in silico flux balance analysis and minimization of metabolic adjustment on a yeast genome-scale model to identify gene knockouts for improving DHA yields. The best strategy involved knockout of an oxaloacetate transporter (YKL120W) and an aspartate aminotransferase (YKL106W), and was predicted to improve DHA yields by 70-fold. Collectively, our work elucidates multiple non-trivial metabolic engineering strategies for improving DHA yield in yeast. PMID:23898325

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 microbially to carbon dioxide. Microbial methane oxidation is a biogeochemical process that limits the release of methane, a greenhouse gas from anaerobic environments. Anaerobic methane oxidation plays an important role in marine sediments. Similar processes may take place in deep subsurface and thus fuel the deep microbial community. Organisms or consortia responsible for anaerobic methane oxidation have not yet been cultured, although diverse aerobic methanotrophs have been isolated from a variety of underground niches. The presence of aerobic methanotrophs in the anoxic subsurface remains to be explained. The presence of methane in the deep subsurface have been shown all over the world. The flux of gases between the deep subsurface and the atmosphere is driven by the concentration gradient from depth to the atmosphere. However, methane is consumed by methanotrophs on the way of its evolution in oxidized environments and is transformed to organic form, available for further microbial processing. When the impact of subsurface environments to global warming is estimated, it is necessary to take into account the activity of methane-producing Archaea and methane-oxidizing biofilters in groundwater. Microbial production and oxidation of methane is involved in the carbon cycle in the deep subsurface environments.

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

Improving Microbial Genome Annotations in an Integrated Database Context

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

PubMed

He, Tianliang; Li, Hongyun; Zhang, Xiaobo

2017-07-11

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival. Copyright © 2017 He et al.

Global microbialization of coral reefs.

PubMed

Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

2016-04-25

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

Textural and mineralogical characteristics of microbial fossils associated with modern and ancient iron (oxyhydr)oxides: terrestrial analogue for sediments in Gale Crater.

PubMed

Potter-McIntyre, Sally L; Chan, Marjorie A; McPherson, Brian J

2014-01-01

Iron (oxyhydr)oxide microbial mats in modern to ∼100 ka tufa terraces are present in a cold spring system along Ten Mile Graben, southeastern Utah, USA. Mats exhibit morphological, chemical, and textural biosignatures and show diagenetic changes that occur over millennial scales. The Jurassic Brushy Basin Member of the Morrison Formation in the Four Corners region of the USA also exhibits comparable microbial fossils and iron (oxyhydr)oxide biosignatures in the lacustrine unit. Both the modern spring system and Brushy Basin Member represent alkaline, saline, groundwater-fed systems and preserve diatoms and other similar algal forms with cellular elaboration. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se, P) are associated with microbial fossils in modern and ancient iron (oxyhydr)oxides and may be potential markers for biosignatures. The presence of ferrihydrite in ∼100 ka fossil microbial mats and Jurassic rocks suggests that this thermodynamically unstable mineral may also be a potential biomarker. One of the most extensive sedimentary records on Mars is exposed in Gale Crater and consists of non-acidic clays and sulfates possibly of lacustrine origin. These terrestrial iron (oxyhydr)oxide examples are a valuable analogue because of similar iron- and clay-rich host rock compositions and will help (1) understand diagenetic processes in a non-acidic, saline lacustrine environment such as the sedimentary rocks in Gale Crater, (2) document specific biomediated textures, (3) demonstrate how biomediated textures might persist or respond to diagenesis over time, and (4) provide a ground truth library of textures to explore and compare in extraterrestrial iron (oxyhydr)oxides, where future explorations hope to detect past evidence of life.

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.

PubMed

MacGregor, Barbara J; Biddle, Jennifer F; Harbort, Christopher; Matthysse, Ann G; Teske, Andreas

2013-09-01

A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability. © 2013.

Filamentous hydrous ferric oxide biosignatures in a pipeline carrying acid mine drainage at Iron Mountain Mine, California

USGS Publications Warehouse

Williams, Amy J.; Alpers, Charles N.; Sumner, Dawn Y.; Campbell, Kate M.

2017-01-01

A pipeline carrying acidic mine effluent at Iron Mountain, CA, developed Fe(III)-rich precipitate caused by oxidation of Fe(II)aq. The native microbial community in the pipe included filamentous microbes. The pipe scale consisted of microbial filaments, and schwertmannite (ferric oxyhydroxysulfate, FOHS) mineral spheres and filaments. FOHS filaments contained central lumina with diameters similar to those of microbial filaments. FOHS filament geometry, the geochemical environment, and the presence of filamentous microbes suggest that FOHS filaments are mineralized microbial filaments. This formation of textural biosignatures provides the basis for a conceptual model for the development and preservation of biosignatures in other environments.

Biological Superoxide In Manganese Oxide Formation

NASA Astrophysics Data System (ADS)

Hansel, C.; Learman, D.; Zeiner, C.; Santelli, C. M.

2011-12-01

Manganese (Mn) oxides are among the strongest sorbents and oxidants within the environment, controlling the fate and transport of numerous elements and the degradation of recalcitrant carbon. Both bacteria and fungi mediate the oxidation of Mn(II) to Mn(III/IV) oxides but the genetic and biochemical mechanisms responsible remain poorly understood. Furthermore, the physiological basis for microbial Mn(II) oxidation remains an enigma. We have recently reported that a common marine bacterium (Roseobacter sp. AzwK-3b) oxidizes Mn(II) via reaction with extracellular superoxide (O2-) produced during exponential growth. Here we expand this superoxide-mediated Mn(II) oxidation pathway to fungi, introducing a surprising homology between prokaryotic and eukaryotic metal redox processes. For instance, Stibella aciculosa, a common soil Ascomycete filamentous fungus, precipitates Mn oxides at the base of asexual reproductive structures (synnemata) used to support conidia (Figure 1). This distribution is a consequence of localized production of superoxide (and it's dismutation product hydrogen peroxide, H2O2), leading to abiotic oxidation of Mn(II) by superoxide. Disruption of NADPH oxidase activity using the oxidoreductase inhibitor DPI leads to diminished cell differentiation and subsequent Mn(II) oxidation inhibition. Addition of Cu(II) (an effective superoxide scavenger) leads to a concentration dependent decrease in Mn oxide formation. We predict that due to the widespread production of extracellular superoxide within the fungal and likely bacterial kingdoms, biological superoxide may be an important contributor to the cycling of Mn, as well as other metals (e.g., Hg, Fe). Current and future explorations of the genes and proteins involved in superoxide production and Mn(II) oxidation will ideally lend insight into the physiological and biochemical basis for these processes.

Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway.

PubMed

Yan, Jinyong; Yan, Yunjun; Madzak, Catherine; Han, Bingnan

2017-02-01

Microbial production routes, notably whole-cell lipase-mediated biotransformation and fatty-acids-derived biosynthesis, offer new opportunities for synthesizing biodiesel. They compare favorably to immobilized lipase and chemically catalyzed processes. Genetically modified whole-cell lipase-mediated in vitro route, together with in vivo and ex vivo microbial biosynthesis routes, constitutes emerging and rapidly developing research areas for effective production of biodiesel. This review presents recent advances in customizing microorganisms for producing biodiesel, via genetic engineering of lipases and metabolic engineering (including system regulation) of fatty-acids-derived pathways. Microbial hosts used include Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Aspergillus oryzae. These microbial cells can be genetically modified to produce lipases under different forms: intracellularly expressed, secreted or surface-displayed. They can be metabolically redesigned and systematically regulated to obtain balanced biodiesel-producing cells, as highlighted in this study. Such genetically or metabolically modified microbial cells can support not only in vitro biotransformation of various common oil feedstocks to biodiesel, but also de novo biosynthesis of biodiesel from glucose, glycerol or even cellulosic biomass. We believe that the genetically tractable oleaginous yeast Yarrowia lipolytica could be developed to an effective biodiesel-producing microbial cell factory. For this purpose, we propose several engineered pathways, based on lipase and wax ester synthase, in this promising oleaginous host.

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

NASA Astrophysics Data System (ADS)

Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

2013-07-01

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations) was nearly constant (250 μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (⩾38 μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of ΣNH3, NO2- and NO3- of the stream water. The δ15N value of ΣNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial ΣNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of ΣNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of ΣNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

Fossilization of Iron-Oxidizing Bacteria at Hydrothermal Vents: a Useful Biosignature on Mars?

NASA Astrophysics Data System (ADS)

Leveille, R. J.; Lui, S.

2009-05-01

Iron oxidizing bacteria are ubiquitous in marine and terrestrial environments on Earth, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Putative microfossils of iron oxidizing bacteria have been found in jaspers as old as 490Ma and microbial iron oxidation may be an ancient metabolic pathway. In order to investigate the usefulness of mineralized iron oxidizing bacteria as a biosignature, we have examined mineral samples collected from relict hydrothermal systems along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic, neutrophilic iron oxidizing bacteria, isolated from Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and oxygen concentration (5 percent) in a controlled bioreactor system. Both natural samples and experimental products were examined with a combination of variable pressure scanning electron microscopy (SEM), field emission gun SEM, and in some cases by preparing samples with a focused ion beam (FIB) milling system. Natural seafloor samples display abundant filamentous forms often resembling, in both size and shape, the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Generally, these filamentous features are 1-5 microns in diameter and up to several microns in length. Some samples consist entirely of low- density, porous masses of silica encrusted filamentous forms. Presumably, these masses were formed by a rapid precipitation by the influx of silica-rich fluids into a microbial mat dominated by bacteria with filamentous morphologies. The presence of rare, amorphous (unmineralized) filamentous matter rich in C and Fe suggests that these bacteria were iron oxidizers. There is no evidence that sulfur oxidizers were present. Filamentous features sectioned by FIB milling show internal material within semi-hollow tubular-like features. Silica encrustations also show pseudo-concentric growth bands. In the bioreactor cultures, constant conditions led to abundant microbial growth and formation of an iron oxyhydroxide precipitate, either in direct association with the cells or within the growth medium. This suggests that not all of the iron precipitation is biogenic in origin. Cells typically show a filamentous morphology reminiscent of the mineral-encrusted forms observed in the natural samples. Continuing work includes high-resolution TEM observations of cultured organisms, examination of 2-year long in situ seafloor incubation experiments, and bioreactor silicification experiments in order to better understand the roles of iron and silica in the fossilization process. Microaerophilic iron oxidation could have existed on the early Earth in environments containing small amounts of oxygen produced either by locally concentrated photosynthetic microorganisms (e.g., cyanobacteria) or abiotically, as proposed for the subsurface of the Fe-dominated Rio Tinto (Spain) basin system. By analogy, similar subsurface or near-surface microaerophilic environments could have existed on Mars in the past. The distinctive morphologies and mineralization patterns of iron oxidizing bacteria could be a useful biosignature to search for on Mars. Deposits and biogenic features similar to those described here could theoretically be identified on Mars with existing imaging and analytical technologies. Therefore, future missions to Mars should target ancient hydrothermal systems, some of which have been putatively identified already.

Flume experiments elucidate relationships between microbial genetics, nitrogen species and hydraulics in controlling nitrous oxide production in the hyporheic zone

NASA Astrophysics Data System (ADS)

Quick, A. M.; Farrell, T. B.; Reeder, W. J.; Feris, K. P.; Tonina, D.; Benner, S. G.

2014-12-01

The hyporheic zone is a potentially important producer of nitrous oxide, a powerful greenhouse gas. The location and magnitude of nitrous oxide generation within the hyporheic zone involves complex interactions between multiple nitrogen species, redox conditions, microbial communities, and hydraulics. To better understand nitrous oxide generation and emissions from streams, we conducted large-scale flume experiments in which we monitored pore waters along hyporheic flow paths within stream dune structures. Measured dissolved oxygen, ammonia, nitrate, nitrite, and dissolved nitrous oxide showed distinct spatial relationships reflecting redox changes along flow paths. Denitrifying genes (nosZ, nirS, and nirK), determined using qPCR, were spatially associated with abundances of nitrogen species. Using residence times along a flow path, clear trends in oxygen conditions, genes encoding for microbial catalysis, and nitrogen species were observed. Hotspots of targeted genes correlated with hotspots for conversion of nitrogen species, including nitrous oxide production and conversion to dinitrogen. Trends were apparent regardless of dune size, allowing for the possibility to apply observed relationships to multiple streambed morphologies. Relating streambed morphology and loading of nitrogen species allows for prediction of nitrous oxide production in the hyporheic zone.

Functional ecology of an Antarctic Dry Valley

PubMed Central

Chan, Yuki; Van Nostrand, Joy D.; Zhou, Jizhong; Pointing, Stephen B.

2013-01-01

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution. PMID:23671121

Functional ecology of an Antarctic Dry Valley.

PubMed

Chan, Yuki; Van Nostrand, Joy D; Zhou, Jizhong; Pointing, Stephen B; Farrell, Roberta L

2013-05-28

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.

A microbial-mineralization approach for syntheses of iron oxides with a high specific surface area.

PubMed

Yagita, Naoki; Oaki, Yuya; Imai, Hiroaki

2013-04-02

Of minerals and microbes: A microbial-mineralization-inspired approach was used to facilitate the syntheses of iron oxides with a high specific surface area, such as 253 m(2)g(-1) for maghemite (γ-Fe(2)O(3)) and 148 m(2)g(-1) for hematite (α-Fe(2)O(3)). These iron oxides can be applied to electrode material of lithium-ion batteries, adsorbents, and catalysts. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production.

PubMed

George, Kevin W; Chen, Amy; Jain, Aakriti; Batth, Tanveer S; Baidoo, Edward E K; Wang, George; Adams, Paul D; Petzold, Christopher J; Keasling, Jay D; Lee, Taek Soon

2014-08-01

The ability to rapidly assess and optimize heterologous pathway function is critical for effective metabolic engineering. Here, we develop a systematic approach to pathway analysis based on correlations between targeted proteins and metabolites and apply it to the microbial production of isopentenol, a promising biofuel. Starting with a seven-gene pathway, we performed a correlation analysis to reduce pathway complexity and identified two pathway proteins as the primary determinants of efficient isopentenol production. Aided by the targeted quantification of relevant pathway intermediates, we constructed and subsequently validated a conceptual model of isopentenol pathway function. Informed by our analysis, we assembled a strain which produced isopentenol at a titer 1.5 g/L, or 46% of theoretical yield. Our engineering approach allowed us to accurately identify bottlenecks and determine appropriate pathway balance. Paired with high-throughput cloning techniques and analytics, this strategy should prove useful for the analysis and optimization of increasingly complex heterologous pathways. © 2014 Wiley Periodicals, Inc.

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

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.

Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration

PubMed Central

Wing, Boswell A.; Halevy, Itay

2014-01-01

We present a quantitative model for sulfur isotope fractionation accompanying bacterial and archaeal dissimilatory sulfate respiration. By incorporating independently available biochemical data, the model can reproduce a large number of recent experimental fractionation measurements with only three free parameters: (i) the sulfur isotope selectivity of sulfate uptake into the cytoplasm, (ii) the ratio of reduced to oxidized electron carriers supporting the respiration pathway, and (iii) the ratio of in vitro to in vivo levels of respiratory enzyme activity. Fractionation is influenced by all steps in the dissimilatory pathway, which means that environmental sulfate and sulfide levels control sulfur isotope fractionation through the proximate influence of intracellular metabolites. Although sulfur isotope fractionation is a phenotypic trait that appears to be strain specific, we show that it converges on near-thermodynamic behavior, even at micromolar sulfate levels, as long as intracellular sulfate reduction rates are low enough (<<1 fmol H2S⋅cell−1⋅d−1). PMID:25362045

Long-term bio-H2 and bio-CH4 production from food waste in a continuous two-stage system: Energy efficiency and conversion pathways.

PubMed

Algapani, Dalal E; Qiao, Wei; di Pumpo, Francesca; Bianchi, David; Wandera, Simon M; Adani, Fabrizio; Dong, Renjie

2018-01-01

Anaerobic digestion is a well-established technology for treating organic waste, but it is still under challenge for food waste due to process stability problems. In this work, continuous H 2 and CH 4 production from canteen food waste (FW) in a two-stage system were successfully established by optimizing process parameters. The optimal hydraulic retention time was 5d for H 2 and 15d for CH 4 . Overall, around 59% of the total COD in FW was converted into H 2 (4%) and into CH 4 (55%). The fluctuations of FW characteristics did not significantly affect process performance. From the energy point view, the H 2 reactor contributed much less than the methane reactor to total energy balance, but it played a key role in maintaining the stability of anaerobic treatment of food waste. Microbial characterization indicated that methane formation was through syntrophic acetate oxidation combined with hydrogenotrophic methanogenesis pathway. Copyright © 2017. Published by Elsevier Ltd.

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Jia; McCalley, Carmody K.; Frolking, Steve

Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesismore » (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 4 (δ 13C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

DOE PAGES

Deng, Jia; McCalley, Carmody K.; Frolking, Steve; ...

2017-06-13

Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesismore » (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 4 (δ 13C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less

Oxidants at the Surface of Mars: A Review in Light of Recent Exploration Results.

PubMed

Lasne, J; Noblet, A; Szopa, C; Navarro-González, R; Cabane, M; Poch, O; Stalport, F; François, P; Atreya, S K; Coll, P

2016-12-01

In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith. As several exploration missions currently focus on the detection of organics on Mars (or will do so in the near future), knowledge of the oxidative state of the surface is fundamental. It will allow for determination of the capability of organics to survive on a geological timescale, the most favorable places to seek them, and the best methods to process the samples collected at the surface. With this aim, we review the main oxidants assumed to be present on Mars, their possible formation pathways, and those laboratory studies in which their reactivity with organics under Mars-like conditions has been evaluated. Among the oxidants assumed to be present on Mars, only four have been detected so far: perchlorate ions (ClO 4 - ) in salts, hydrogen peroxide (H 2 O 2 ) in the atmosphere, and clays and metal oxides composing surface minerals. Clays have been suggested as catalysts for the oxidation of organics but are treated as oxidants in the following to keep the structure of this article straightforward. This work provides an insight into the oxidizing potential of the surface of Mars and an estimate of the stability of organic matter in an oxidizing environment. Key Words: Mars surface-Astrobiology-Oxidant-Chemical reactions. Astrobiology 16, 977-996.

Assessing microbial utilization of free versus sorbed Alanine by using position-specific 13C labeling and 13C-PLFA analysis

NASA Astrophysics Data System (ADS)

Herschbach, Jennifer; Apostel, Carolin; Spielvogel, Sandra; Kuzyakov, Yakov; Dippold, Michaela

2016-04-01

Microbial utilization is a key transformation process of soil organic matter (SOM). Sorption of low molecular weight organic substances (LMWOS) to soil mineral surfaces blocks or delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil science, combined with 13C-phospholipid fatty acid (PLFA) analysis, to assess microbial utilization of sorbed and non-sorbed Alanine in soil. Alanine has various functional groups enabling different sorption mechanisms via its positive charge (e.g. to clay minerals by cation exchange), as well as via its negative charge (e.g. to iron oxides by ligand exchange). To assess changes in the transformation pathways caused by sorption, we added uniformly and position-specifically 13C and 14C labeled Alanine to the Ap of a loamy Luvisol in a short-term (10 days) incubation experiment. To allow for sorption of the tracer solution to an aliquot of this soil, microbial activity was minimized in this subsample by sterilizing the soil by γ-radiation. After shaking, the remaining solutions were filtered and the non-sorbed Alanine was removed with Millipore water and then added to non-sterilized soil. For the free Alanine treatment, solutions with Alanine of similar amount and isotopic composition were prepared, added to the soil and incubated as well. The respired CO2 was trapped in NaOH and its 14C-activity was determined at increasing times intervals. Microbial utilization of Alanine's individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Sorption to soil minerals delayed respiration to CO2 and reduced initial respiration rate by 80%. Irrespective of sorption, the highest amount was respired from the carboxylic position (C-1), whereas the amino-bound (C-2) and the methylic position (C-3) were preferentially incorporated into PLFA of microorganisms due to the basic microbial metabolism of C3 molecules in glycolysis. Reconstruction of microbial transformation pathways showed that the C-2 position of Alanine was lost as CO2 faster than its C-3 position regardless of whether the molecule was used ana- or catabolically. The highest incorporations of all positions in PLFA were accomplished by Gram negatives. Free Alanine was preferentially used by highly competitive prokaryotes, while sorbed Alanine was preferred by filamentous microorganisms. In detail, the free living osmotrophic Gram negative bacteria utilize more easily accessible dissolved substances. The utilization of sorbed substances are achieved by less mobile microorganisms, e.g. eukaryotic fungi and Actinomycetes, which form biofilms. None of these findings could have been achieved without the position-specific labeling approach, therefore this method will strongly improve our understanding of stabilization processes and soil C fluxes.

Methane oxidation and abundance of methane oxidizers in tropical agricultural soil (vertisol) in response to CuO and ZnO nanoparticles contamination.

PubMed

Mohanty, Santosh Ranjan; Rajput, Parul; Kollah, Bharati; Chourasiya, Dipanti; Tiwari, Archana; Singh, Muneshwar; Rao, A Subba

2014-06-01

There is worldwide concern over the increase use of nanoparticles (NPs) and their ecotoxicological effect. It is not known if the annual production of tons of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding the NPs particularly the metal oxide (CuO, ZnO) on CH4 oxidation activity in vertisol and the abundance of heterotrophs, methane oxidizers, and ammonium oxidizers. Soil samples collected from the agricultural field located at Madhya Pradesh, India, were incubated with either CuO and ZnO NPs or ionic heavy metals (CuCl2, ZnCl2) separately at 0, 10, and 20 μg g(-1) soil. CH4 oxidation activity in the soil samples was estimated at 60 and 100 % moisture holding capacity (MHC) in order to link soil moisture regime with impact of NPs. NPs amended to soil were highly toxic for the microbial-mediated CH4 oxidation, compared with the ionic form. The trend of inhibition was Zn 20 > Zn 10 > Cu 20 > Cu 10. NPs delayed the lag phase of CH4 oxidation to a maximum of 4-fold and also decreased the apparent rate constant k up to 50 % over control. ANOVA and Pearson correlation analysis (α = 0.01) revealed significant impact of NPs on the CH4 oxidation activity and microbial abundance (p < 0.0001, and high F statistics). Principal component analysis (PCA) revealed that PC1 (metal concentration) rendered 76.06 % of the total variance, while 18.17 % of variance accounted by second component (MHC). Biplot indicated negative impact of NPs on CH4 oxidation and microbial abundance. Our result also confirmed that higher soil moisture regime alleviates toxicity of NPs and opens new avenues of research to manage ecotoxicity and environmental hazard of NPs.

Microbial metabolism in soil at low temperatures: Mechanisms unraveled by position-specific 13C labeling

NASA Astrophysics Data System (ADS)

Bore, Ezekiel

2016-04-01

Microbial transformation of organic substances in soil is the most important process of the C cycle. Most of the current studies base their information about transformation of organic substances on incubation studies under laboratory conditions and thus, we have a profound knowledge on SOM transformations at ambient temperatures. However, metabolic pathway activities at low temperature are not well understood, despite the fact that the processes are relevant for many soils globally and seasonally. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5, -5 -20 oC. Soils were sampled after 1, 3 and 10 days and additionally after 30 days for samples at -20 °C. The 13C from individual molecule position was quantifed in respired CO2, bulk soil, extractable organic C and extractable microbial biomass by chloroform fumigation extraction (CFE) and cell membranes of microbial communities classified by 13C phospholipid fatty acid (PLFA) analysis. 13CO2 released showed a dominance of the flux from C-1 position at 5 °C. Consequently, at 5 °C, pentose phosphate pathway activity is a dominant metabolic pathway of glucose metabolization. In contrast to -5 °C and -20 oC, metabolic behaviors completely switched towards a preferential respiration of the glucose C-4 position. With decreasing temperature, microorganism strongly shifted towards metabolization of glucose via glycolysis which indicates a switch to cellular maintenance. High recoveries of 13C in extractable microbial biomass at -5 °C indicates optimal growth condition for the microorganisms. PLFA analysis showed high incorporation of 13C into Gram negative bacteria at 5 °C but decreased with temperature. Gram positive bacteria out-competed Gram negatives with decreasing temperature. This study revealed a remarkable microbial activity at temperatures below 0 °C, differing significantly from that at ambient temperatures. These metabolic pathways, can be unraveled based on position-specific labeling.

Temporal variation of nitrogen balance within constructed wetlands treating slightly polluted water using a stable nitrogen isotope experiment.

PubMed

Zhang, Wanguang; Lei, Qiongye; Li, Zhengkui; Han, Huayang

2016-02-01

Slightly polluted water has become one of the main sources of nitrogen contaminants in recent years, for which constructed wetlands (CW) is a typical and efficient treatment. However, the knowledge about contribution of individual nitrogen removal pathways and nitrogen balance in constructed wetlands is still limited. In this study, a stable-isotope-addition experiment was performed in laboratory-scale constructed wetlands treating slightly polluted water to determine quantitative contribution of different pathways and temporal variation of nitrogen balance using Na(15)NO3 as tracer. Microbial conversion and substrate retention were found to be the dominant pathways in nitrogen removal contributing 24.4-79.9 and 8.9-70.7 %, respectively, while plant contributed only 4.6-11.1 % through direct assimilation but promoted the efficiency of other pathways. In addition, microbial conversion became the major way to remove N whereas nitrogen retained in substrate at first was gradually released to be utilized by microbes and plants over time. The findings indicated that N2 emission representing microbial conversion was not only the major but also permanent nitrogen removal process, thus keeping a high efficiency of microbial conversion is important for stable and efficient nitrogen removal in constructed wetlands.

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.

PubMed

Lu, Xiao-Ming; Chen, Chang; Zheng, Tian-Ling

2017-05-01

Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.

Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.

PubMed

Scholten, Johannes C M; Culley, David E; Nie, Lei; Munn, Kyle J; Chow, Lely; Brockman, Fred J; Zhang, Weiwen

2007-06-29

The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.

Semi-continuous methane production from undiluted brown algae using a halophilic marine microbial community.

PubMed

Miura, Toyokazu; Kita, Akihisa; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nakashimada, Yutaka

2016-01-01

Acclimated marine sediment-derived culture was used for semi-continuous methane production from materials equivalent to raw brown algae, without dilution of salinity and without nutrient supply, under 3 consecutive conditions of varying organic loading rates (OLRs) and hydraulic retention time (HRT). Methane production was stable at 2.0gVS/kg/day (39-day HRT); however, it became unstable at 2.9gVS/kg/day (28-day HRT) due to acetate and propionate accumulation. OLR subsequently decreased to 1.7gVS/kg/day (46-day HRT), stabilizing methane production beyond steady state. Methane yield was above 300mL/g VS at all OLRs. These results indicated that the acclimated marine sediment culture was able to produce methane semi-continuously from raw brown algae without dilution and nutrient supply under steady state. Microbial community analysis suggested that hydrogenotrophic methanogens predominated among archaea during unstable methane production, implying a partial shift of the methanogenic pathway from acetoclastic methanogenesis to acetate oxidation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of temperature and substrate concentration on degradation rates of acetate, propionate and hydrogen and their links to microbial community structure.

PubMed

Zhao, Jing; Westerholm, Maria; Qiao, Wei; Yin, Dongmin; Bi, Shaojie; Jiang, Mengmeng; Dong, Renjie

2018-05-01

The present study investigates the conversion of acetate, propionate and hydrogen consumption linked to the microbial community structure and related to temperature and substrate concentration. Biogas reactors were continuously fed with coffee powder (20 g-COD/L) or acetate (20, 40, and 60 g-COD/L) and operated for 193 days at 37 °C or 55 °C conditions. Starting HRT was 23 days which was then reduced to 7 days. The kinetics of acetate and propionate degradation and hydrogen consumption rates were measured in batch assays. At HRT 7 days, the degradation rate of propionate was higher in thermophilic batches, while acetate degradation rate was higher at mesophilic conditions. The gaseous hydrogen consumption in acetate reactors increased proportionally with temperature and substrate concentration, while the dissolved hydrogen was not affected. The relative high abundance of hydrogentrophic methanogens indicated that the methanogenesis was directed towards the syntrophic acetate oxidation pathway at high acetate concentration and high temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

NASA Astrophysics Data System (ADS)

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

C. Doc Richardson; Nancy W. Hinman; Jill R. Scott

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compoundsmore » associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.« less

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.

PubMed

Reitschuler, Christoph; Spötl, Christoph; Hofmann, Katrin; Wagner, Andreas O; Illmer, Paul

2016-04-01

(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

NASA Astrophysics Data System (ADS)

Stief, P.

2013-12-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

NASA Astrophysics Data System (ADS)

Stief, P.

2013-07-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments often is enhanced even more than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies revealed that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

NASA Astrophysics Data System (ADS)

Richardson, C. Doc; Hinman, Nancy W.; Scott, Jill R.

2013-10-01

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compounds associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.

Textural and Mineralogical Characteristics of Microbial Fossils Associated with Modern and Ancient Iron (Oxyhydr)Oxides: Terrestrial Analogue for Sediments in Gale Crater

PubMed Central

Chan, Marjorie A.; McPherson, Brian J.

2014-01-01

Abstract Iron (oxyhydr)oxide microbial mats in modern to ∼100 ka tufa terraces are present in a cold spring system along Ten Mile Graben, southeastern Utah, USA. Mats exhibit morphological, chemical, and textural biosignatures and show diagenetic changes that occur over millennial scales. The Jurassic Brushy Basin Member of the Morrison Formation in the Four Corners region of the USA also exhibits comparable microbial fossils and iron (oxyhydr)oxide biosignatures in the lacustrine unit. Both the modern spring system and Brushy Basin Member represent alkaline, saline, groundwater-fed systems and preserve diatoms and other similar algal forms with cellular elaboration. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se, P) are associated with microbial fossils in modern and ancient iron (oxyhydr)oxides and may be potential markers for biosignatures. The presence of ferrihydrite in ∼100 ka fossil microbial mats and Jurassic rocks suggests that this thermodynamically unstable mineral may also be a potential biomarker. One of the most extensive sedimentary records on Mars is exposed in Gale Crater and consists of non-acidic clays and sulfates possibly of lacustrine origin. These terrestrial iron (oxyhydr)oxide examples are a valuable analogue because of similar iron- and clay-rich host rock compositions and will help (1) understand diagenetic processes in a non-acidic, saline lacustrine environment such as the sedimentary rocks in Gale Crater, (2) document specific biomediated textures, (3) demonstrate how biomediated textures might persist or respond to diagenesis over time, and (4) provide a ground truth library of textures to explore and compare in extraterrestrial iron (oxyhydr)oxides, where future explorations hope to detect past evidence of life. Key Words: Biogeochemistry—Mars—Biosignatures—Diagenesis—Iron oxides. Astrobiology 14, 1–14. PMID:24380534

Nitrous oxide emissions and denitrification rates: A blueprint for smart management and remediation of agricultural landscapes.

NASA Astrophysics Data System (ADS)

Tomasek, A.; Hondzo, M.; Kozarek, J. L.

2015-12-01

Anthropogenic activities have greatly altered the global nitrogen cycle, especially in the agriculturally dominated Midwest, with severe consequences on human and aquatic health. Complete microbial denitrification can be viewed as a nitrogen sink, converting soluble nitrate into inert nitrogen gas. This research aims to quantify and correlate the driving parameters in microbial denitrification and explore the relationship to the abundance of denitrifying genes and the microbial communities at these sites. Denitrifying genes for each step in the denitrification process have been quantified. Data from a field site in Southern Minnesota has been collected throughout the season for two years enabling investigation into the temporal variability of denitrification. Data was collected at two cross-sections across the channel to determine the effect of bank location and moisture content on denitrification. Data were collected in an experimental basin in the summer of 2015 to determine the effect of flooding and benthic organic matter content and quality on microbial denitrification and nitrous oxide production. Four sediment types were investigated in three different flood regimes. After each raising or lowering of the water level, soil cores were taken to determine soil characteristics, the potential denitrification using the denitrification enzyme activity method, nitrous oxide production using a static core method, and the denitrifying gene abundance. Chambers were also deployed over each soil amendment in each flood regime to determine the nitrous oxide production over time. Results from these studies will convey a more complete explanation of denitrification and nitrous oxide production under varying environmental conditions. By determining the driving parameters for microbial denitrification, denitrification hot spots and hot moments can be created and enhanced. One potential consequence of increased denitrification is the possibility of incomplete denitrification resulting in the release of nitrous oxide, a greenhouse gas with 300 times the warming potential of carbon dioxide. The investigation of nitrous oxide emissions and correlation to denitrification rates will facilitate smart management and remediation efforts of agricultural landscapes.

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

PubMed

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-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation.

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-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation. PMID:26244346

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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. Aftermore » 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.« less

Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input.

PubMed

Xu, Xi-jun; Chen, Chuan; Wang, Ai-jie; Yu, Hao; Zhou, Xu; Guo, Hong-liang; Yuan, Ye; Lee, Duu-jong; Zhou, Jizhong; Ren, Nan-qi

2014-08-15

Limited-oxygen mediated synergistic relationships between sulfate-reducing bacteria (SRB), nitrate-reducing bacteria (NRB) and sulfide-oxidizing bacteria (SOB, including nitrate-reducing, sulfide-oxidizing bacteria NR-SOB) were predicted to simultaneously remove contaminants of nitrate, sulfate and high COD, and eliminate sulfide generation. A lab-scale experiment was conducted to examine the impact of limited oxygen on these oxy-anions degradation, sulfide oxidation and associated microbial functional responses. In all scenarios tested, the reduction of both nitrate and sulfate was almost complete. When limited-oxygen was fed into bioreactors, S(0) formation was significantly improved up to ∼ 70%. GeoChip 4.0, a functional gene microarray, was used to determine the microbial gene diversity and functional potential for nitrate and sulfate reduction, and sulfide oxidation. The diversity of the microbial community in bioreactors was increased with the feeding of limited oxygen. Whereas the intensities of the functional genes involved in sulfate reduction did not show a significant difference, the abundance of the detected denitrification genes decreased in limited oxygen samples. More importantly, sulfide-oxidizing bacteria may alter their populations/genes in response to limited oxygen potentially to function more effectively in sulfide oxidation, especially to elemental sulfur. The genes fccA/fccB from nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB), such as Paracoccus denitrificans, Thiobacillus denitrificans, Beggiatoa sp., Thiomicrospira sp., and Thioalkalivibrio sp., were more abundant under limited-oxygen condition. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Quantification of nitrous oxide (N2O) emissions and soluble microbial product (SMP) production by a modified AOB-NOB-N2O-SMP model.

PubMed

Kim, MinJeong; Wu, Guangxue; Yoo, ChangKyoo

2017-03-01

A modified AOB-NOB-N 2 O-SMP model able to quantify nitrous oxide (N 2 O) emissions and soluble microbial product (SMP) production during wastewater treatment is proposed. The modified AOB-NOB-N 2 O-SMP model takes into account: (1) two-step nitrification by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), (2) N 2 O production by AOB denitrification under oxygen-limited conditions and (3) SMP production by microbial growth and endogenous respiration. Validity of the modified model is demonstrated by comparing the simulation results with experimental data from lab-scale sequencing batch reactors (SBRs). To reliably implement the modified model, a model calibration that adjusts model parameters to fit the model outputs to the experimental data is conducted. The results of this study showed that the modeling accuracy of the modified AOB-NOB-N 2 O-SMP model increases by 19.7% (NH 4 ), 51.0% (NO 2 ), 57.8% (N 2 O) and 16.7% (SMP) compared to the conventional model which does not consider the two-step nitrification and SMP production by microbial endogenous respiration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Distinguishing Indigenous from Contaminating Microorganisms in Rock Samples from a Deep Au Mine in South Africa

NASA Technical Reports Server (NTRS)

Onstott, T. C.; Moser, D. P.; Fredrickson, J. K.; Pfiffner, S. M.; Phelps, T. J.; White, D. C.; Peacock, A.; Balkwill, D.; Hoover, R. B.; Krumholz, L.;

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

PubMed

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

TBK1-targeted suppression of TRIF-dependent signaling pathway of Toll-like receptors by 6-shogaol, an active component of ginger.

PubMed

Park, Se-Jeong; Lee, Mi-Young; Son, Bu-Soon; Youn, Hyung-Sun

2009-07-01

Toll-like receptors (TLRs) are primary sensors that detect a wide variety of microbial components involving induction of innate immune responses. After recognition of microbial components, TLRs trigger the activation of myeloid differential factor 88 (MyD88) and Toll-interleukin-1 (IL-1) receptor domain-containing adapter inducing interferon-beta (TRIF)-dependent downstream signaling pathways. 6-Shoagol, an active ingredient of ginger, inhibits the MyD88-dependent signaling pathway by inhibiting inhibitor-kappaB kinase activity. Inhibitor-kappaB kinase is a key kinase in nuclear factor kappaB (NF-kappaB) activation. However, it is not known whether 6-shogaol inhibits the TRIF-dependent signaling pathway. Our goal was to identify the molecular target of 6-shogaol in the TRIF-dependent pathway of TLRs. 6-Shogaol inhibited the activation of interferon-regulatory factor 3 (IRF3) induced by lipopolysaccharide (LPS) and by polyriboinosinic polyribocytidylic acid (poly[I:C]), overexpression of TRIF, TANK-binding kinase1 (TBK1), and IRF3. Furthermore, 6-shogaol inhibited TBK1 activity in vitro. Together, these results suggest that 6-shogaol inhibits the TRIF-dependent signaling pathway of TLRs by targeting TBK1, and, they imply that 6-shogaol can modulate TLR-derived immune/inflammatory target gene expression induced by microbial infection.

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

PubMed

Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

2016-08-01

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

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

The triple isotopes of oxygen (Δ17O' = δ17O'-0.528 × δ18O' using logarithmic deltas) can trace the oxygen sources of sulfate produced during sulfide oxidation, an important biogeochemical process on Earth's surface and possibly also on Mars [1]. δ18OSO4 compositions are determined by the isotopic selectivity of the mechanism(s) responsible for their changes, and the δ18O value of the reactants (O2 vs. H2O). The relative proportional importance and contribution of each of those sources and mechanisms, as well as their associated isotopic fractionations, are not well understood. We are investigating the use of Δ 17O as a quantitative and qualitative tracer for the different processes and oxygen sources involved in sulfate production. Δ17O signatures are distinct fingerprints of these reservoirs, independent of fractionation factors that can be ambiguous. We conducted controlled abiotic and biotic (Acidithiobacillus ferrooxidans, A.f.) laboratory experiments in which water was spiked with 18O, allowing us to quantify the sources of sulfate oxygen and therefore the processes attending sulfate formation. Results of this Δ17O tracer study show that A.f. microbes initiate pyrite S-oxidation within hours of exposure, and that sulfate is produced from ~90% atmospheric oxygen. This initial lag-phase (< 3 days) is characterized by subtle and multiple changes in oxygen source and contribution that is likely due to the adjustment of the microbial metabolism from S to Fe2+-oxidation. A more detailed understanding of the microbial mechanisms and behavior in the initial lag-phase will aid in the understanding of the ecological conditions required for microbial populations to establish and survive. An exponential phase of growth, facilitated by microbial Fe2+-oxidation, follows. The source of sulfate rapidly switches to abiotic sulfide oxidation during exponential growth and the source of oxygen switches from atmospheric O2 to nearly ~100% water. Pending acquisition of 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.

Oxidants at the Surface of Mars: A Review in Light of Recent Exploration Results

NASA Astrophysics Data System (ADS)

Lasne, J.; Noblet, A.; Szopa, C.; Navarro-González, R.; Cabane, M.; Poch, O.; Stalport, F.; François, P.; Atreya, S. K.; Coll, P.

2016-12-01

In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith. As several exploration missions currently focus on the detection of organics on Mars (or will do so in the near future), knowledge of the oxidative state of the surface is fundamental. It will allow for determination of the capability of organics to survive on a geological timescale, the most favorable places to seek them, and the best methods to process the samples collected at the surface. With this aim, we review the main oxidants assumed to be present on Mars, their possible formation pathways, and those laboratory studies in which their reactivity with organics under Mars-like conditions has been evaluated. Among the oxidants assumed to be present on Mars, only four have been detected so far: perchlorate ions (ClO4-) in salts, hydrogen peroxide (H2O2) in the atmosphere, and clays and metal oxides composing surface minerals. Clays have been suggested as catalysts for the oxidation of organics but are treated as oxidants in the following to keep the structure of this article straightforward. This work provides an insight into the oxidizing potential of the surface of Mars and an estimate of the stability of organic matter in an oxidizing environment.

Oncoidal granular iron formation in the Mesoarchaean Pongola Supergroup, southern Africa: Textural and geochemical evidence for biological activity during iron deposition.

PubMed

Smith, A J B; Beukes, N J; Gutzmer, J; Czaja, A D; Johnson, C M; Nhleko, N

2017-11-01

We document the discovery of the first granular iron formation (GIF) of Archaean age and present textural and geochemical results that suggest these formed through microbial iron oxidation. The GIF occurs in the Nconga Formation of the ca. 3.0-2.8 Ga Pongola Supergroup in South Africa and Swaziland. It is interbedded with oxide and silicate facies micritic iron formation (MIF). There is a strong textural control on iron mineralization in the GIF not observed in the associated MIF. The GIF is marked by oncoids with chert cores surrounded by magnetite and calcite rims. These rims show laminated domal textures, similar in appearance to microstromatolites. The GIF is enriched in silica and depleted in Fe relative to the interbedded MIF. Very low Al and trace element contents in the GIF indicate that chemically precipitated chert was reworked above wave base into granules in an environment devoid of siliciclastic input. Microbially mediated iron precipitation resulted in the formation of irregular, domal rims around the chert granules. During storm surges, oncoids were transported and deposited in deeper water environments. Textural features, along with positive δ 56 Fe values in magnetite, suggest that iron precipitation occurred through incomplete oxidation of hydrothermal Fe 2+ by iron-oxidizing bacteria. The initial Fe 3+ -oxyhydroxide precipitates were then post-depositionally transformed to magnetite. Comparison of the Fe isotope compositions of the oncoidal GIF with those reported for the interbedded deeper water iron formation (IF) illustrates that the Fe 2+ pathways and sources for these units were distinct. It is suggested that the deeper water IF was deposited from the evolved margin of a buoyant Fe 2+ aq -rich hydrothermal plume distal to its source. In contrast, oncolitic magnetite rims of chert granules were sourced from ambient Fe 2+ aq -depleted shallow ocean water beyond the plume. © 2017 John Wiley & Sons Ltd.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

PubMed Central

Pjevac, Petra; Meier, Dimitri V.; Markert, Stephanie; Hentschker, Christian; Schweder, Thomas; Becher, Dörte; Gruber-Vodicka, Harald R.; Richter, Michael; Bach, Wolfgang; Amann, Rudolf; Meyerdierks, Anke

2018-01-01

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys. PMID:29696004

Promotion of Iron Oxide Reduction and Extracellular Electron Transfer in Shewanella oneidensis by DMSO

PubMed Central

Cheng, Yuan-Yuan; Li, Bing-Bing; Li, Dao-Bo; Chen, Jie-Jie; Li, Wen-Wei; Tong, Zhong-Hua; Wu, Chao; Yu, Han-Qing

2013-01-01

The dissimilatory metal reducing bacterium Shewanella oneidensis MR-1, known for its capacity of reducing iron and manganese oxides, has great environmental impacts. The iron oxides reducing process is affected by the coexistence of alternative electron acceptors in the environment, while investigation into it is limited so far. In this work, the impact of dimethyl sulphoxide (DMSO), a ubiquitous chemical in marine environment, on the reduction of hydrous ferric oxide (HFO) by S. oneidensis MR-1 was investigated. Results show that DMSO promoted HFO reduction by both wild type and ΔdmsE, but had no effect on the HFO reduction by ΔdmsB, indicating that such a promotion was dependent on the DMSO respiration. With the DMSO dosing, the levels of extracellular flavins and omcA expression were significantly increased in WT and further increased in ΔdmsE. Bioelectrochemical analysis show that DMSO also promoted the extracellular electron transfer of WT and ΔdmsE. These results demonstrate that DMSO could stimulate the HFO reduction through metabolic and genetic regulation in S. oneidensis MR-1, rather than compete for electrons with HFO. This may provide a potential respiratory pathway to enhance the microbial electron flows for environmental and engineering applications. PMID:24244312

Microbial oxidative sulfur metabolism: biochemical evidence of the membrane-bound heterodisulfide reductase-like complex of the bacterium Aquifex aeolicus.

PubMed

Boughanemi, Souhela; Lyonnet, Jordan; Infossi, Pascale; Bauzan, Marielle; Kosta, Artémis; Lignon, Sabrina; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne

2016-08-01

The Hdr (heterodisulfide reductase)-like enzyme is predicted, from gene transcript profiling experiments previously published, to be essential in oxidative sulfur metabolism in a number of bacteria and archaea. Nevertheless, no biochemical and physicochemical data are available so far about this enzyme. Genes coding for it were identified in Aquifex aeolicus, a Gram-negative, hyperthermophilic, chemolithoautotrophic and microaerophilic bacterium that uses inorganic sulfur compounds as electron donor to grow. We provide biochemical evidence that this Hdr-like enzyme is present in this sulfur-oxidizing prokaryote (cultivated with thiosulfate or elemental sulfur). We demonstrate, by immunolocalization and cell fractionation, that Hdr-like enzyme is associated, presumably monotopically, with the membrane fraction. We show by co-immunoprecipitation assay or partial purification, that the Hdr proteins form a stable complex composed of at least five subunits, HdrA, HdrB1, HdrB2, HdrC1 and HdrC2, present in two forms of high molecular mass on native gel (∼240 and 450 kDa). These studies allow us to propose a revised model for dissimilatory sulfur oxidation pathways in A. aeolicus, with Hdr predicted to generate sulfite. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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 spp.). However, only a small proportion of the cells in the mat reside within the sheaths. Most are located on or around the sheaths, which provide a physical framework for the community. Preliminary results from FISH experiments on the iron-rich spring samples show some similarities, including an abundance of Betaproteobacteria. Enrichment and isolation experiments are being performed to identify the iron-oxidizing organisms. Iron-oxidizers have been enriched from all sites. In some cultures it has been difficult to isolate the iron-oxidizing organisms from a non-iron-oxidizing heterotroph, possibly indicating co-dependence. Knowledge of the microbial community structure and the metabolic activities of key members will enable us to better understand the processes and chemical conditions which generate iron oxide deposits found in the geologic record on Earth and possibly extraterrestrial habitats.

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

NASA Astrophysics Data System (ADS)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (<60 °C), Fe-rich and H2S-depleted hydrothermal fluids yielded δ56Fe values near +0.1‰, indistinguishable from basalt values. Suspended particles in the vent fluids and FeOx deposits recovered nearby active vents yielded systematically positive δ56Fe values. The enrichment in heavy Fe isotopes between +1.05‰ and +1.43‰ relative to Fe(II) in vent fluids suggest partial oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where they form, and are less sensitive to abiotic versus biotic origins. It follows that FeOx deposits at Loihi Seamount provides important modern analogues for ancient seafloor Fe-rich deposits allowing for testing hypotheses about the biogeochemical cycling of Fe isotopes on early Earth.

Possibilities for extremophilic microorganisms in microbial electrochemical systems

PubMed Central

Dopson, Mark; Ni, Gaofeng; Sleutels, Tom HJA

2015-01-01

Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems. PMID:26474966

Aerobic Microbial Respiration in Oceanic Oxygen Minimum Zones

NASA Astrophysics Data System (ADS)

Kalvelage, Tim; Lavik, Gaute; Jensen, Marlene M.; Revsbech, Niels Peter; Schunck, Harald; Loescher, Carolin; Desai, Dhwani K.; LaRoche, Julie; Schmitz-Streit, Ruth; Kuypers, Marcel M. M.

2014-05-01

In the oxygen minimum zones (OMZs) of the tropical oceans, sluggish ventilation combined with strong microbial respiration of sinking organic matter results in the depletion of oxygen (O2). When O2 concentrations drop below ~5 µmol/L, organic matter is generally assumed to be respired with nitrate, ultimately leading to the loss of fixed inorganic nitrogen via anammox and denitrification. However, direct measurements of microbial O2 consumption at low O2 levels are - apart from a single experiment conducted in the OMZ off Peru - so far lacking. At the same time, consistently observed active aerobic ammonium and nitrite oxidation at non-detectable O2 concentrations (<1 µmol/L) in all major OMZs, suggests aerobic microorganisms, likely including heterotrophs, to be well adapted to near-anoxic conditions. Consequently, microaerobic (≤5 µmol/L) remineralization of organic matter, and thus release of ammonium, in low- O2 environments might be significantly underestimated at present. Here we present extensive measurements of microbial O2 consumption in OMZ waters, combined with highly sensitive O2 (STOX) measurements and meta-omic functional gene analyses. Short-term incubation experiments with labelled O2 (18-18O2) carried out in the Namibian and Peruvian OMZ, revealed persistent aerobic microbial activity at depths with non-detectable concentrations of O2 (≤50 nmol/L). In accordance, examination of metagenomes and metatranscriptomes from Chilean and Peruvian OMZ waters identified genes encoding for terminal respiratory oxidases with high O2 affinities as well as their expression by diverse microbial communities. Oxygen consumption was particularly enhanced near the upper OMZ boundaries and could mostly (~80%) be assigned to heterotrophic microbial activity. Compared to previously identified anaerobic microbial processes, microaerobic organic matter respiration was the dominant remineralization pathway and source of ammonium (~90%) in the upper Namibian and Peruvian OMZ. Our results reconcile so-far existing mismatches between ammonium sources and sinks in OMZs, and may help to improve biogeochemical modelling of the effects of future ocean de-oxygenation on aerobic and anaerobic organic matter remineralization in these zones.

Synthetic Biology of Polyhydroxyalkanoates (PHA).

PubMed

Meng, De-Chuan; Chen, Guo-Qiang

Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers. This was achieved by engineering the genome of Pseudomonas putida or Pseudomonas entomophiles to weaken the β-oxidation and in situ fatty acid synthesis pathways, so that a fatty acid fed to the bacteria maintains its original chain length and structures when incorporated into the PHA chains. The engineered bacterium allows functional groups in a fatty acid to be introduced into PHA, forming functional PHA, which, upon grafting, generates endless PHA variety. Recombinant Escherichia coli also succeeded in producing efficiently poly(3-hydroxypropionate) or P3HP, the strongest member of PHA. Synthesis pathways of P3HP and its copolymer P3HB3HP of 3-hydroxybutyrate and 3-hydroxypropionate were assembled respectively to allow their synthesis from glucose. CRISPRi was also successfully used to manipulate simultaneously multiple genes and control metabolic flux in E. coli to obtain a series of copolymer P3HB4HB of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB). The bacterial shapes were successfully engineered for enhanced PHA accumulation.

Cellular and molecular engineering of yeast Saccharomyces cerevisiae for advanced biobutanol production.

PubMed

Kuroda, Kouichi; Ueda, Mitsuyoshi

2016-02-01

Butanol is an attractive alternative energy fuel owing to several advantages over ethanol. Among the microbial hosts for biobutanol production, yeast Saccharomyces cerevisiae has a great potential as a microbial host due to its powerful genetic tools, a history of successful industrial use, and its inherent tolerance to higher alcohols. Butanol production by S. cerevisiae was first attempted by transferring the 1-butanol-producing metabolic pathway from native microorganisms or using the endogenous Ehrlich pathway for isobutanol synthesis. Utilizing alternative enzymes with higher activity, eliminating competitive pathways, and maintaining cofactor balance achieved significant improvements in butanol production. Meeting future challenges, such as enhancing butanol tolerance and implementing a comprehensive strategy by high-throughput screening, would further elevate the biobutanol-producing ability of S. cerevisiae toward an ideal microbial cell factory exhibiting high productivity of biobutanol. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Inactivation of conserved genes induces microbial aversion, drug detoxification, and innate immunity in C.elegans

PubMed Central

Melo, Justine A.; Ruvkun, Gary

2012-01-01

Summary The nematode C. elegans consumes benign bacteria such as E. coli and is repelled by pathogens and toxins. Here we show that RNAi and toxin-mediated disruption of core cellular activities, including translation, respiration, and protein turnover, stimulates behavioral avoidance of attractive E. coli. RNAi of such essential processes also induces expression of detoxification and innate immune response genes in the absence of toxins or pathogens. Disruption of core processes in non-neuronal tissues can stimulate aversion behavior, revealing a neuroendocrine axis of control. Microbial avoidance requires serotonergic and Jnk kinase signaling. We propose that surveillance pathways oversee critical cellular activities to detect pathogens, many of which deploy toxins and virulence factors to disrupt these same host pathways. Variation in cellular surveillance and endocrine pathways controlling behavior, detoxification and immunity selected by past toxin or microbial interactions could underlie aberrant responses to foods, medicines, and microbes. PMID:22500807

Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

PubMed

Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

2016-09-01

A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Microbial diversity and community structure in an antimony-rich tailings dump.

PubMed

Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

2016-09-01

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation.

PubMed

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-11-17

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation

PubMed Central

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-01-01

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES. PMID:26573014

[Acclimatization and characteristics of microbial community in sulphate-dependent anaerobic methane oxidation].

PubMed

Xi, Jing-Ru; Liu, Su-Qin; Li, Lin; Liu, Jun-Xin

2014-12-01

The greenhouse effect of methane is 26 times worse than that of carbon dioxide, and wastewater containing high concentrations of sulfate is harmful to water, soil and plants. Therefore, anaerobic oxidation of methane driven by sulfate is one of the effective ways for methane reduction. In this paper, with sulfate as the electron accepter, a microbial consortium capable of oxidating methane under anaerobic condition was cultured. The diversity and characteristics of bacterial and archaeal community were investigated by PCR-DGGE, and phylogenetic analysis of the dominant microorganisms was also carried out. The DGGE fingerprints showed that microbial community structure changed distinctly, and the abundance of methane-oxidizing archea and sulfate-reducing bacteria increased in the acclimatization system added sulfate. After acclimatization, the bacterial diversity increased, while archaea diversity decreased slightly. The representative bands in the DGGE profiles were excised and sequenced. Results indicated that the dominant species in the acclimatization system were Spirochaetes, Desulfuromonadales, Methanosarcinales, Methanosaeta. Methane converted into carbon dioxide while sulfate transformed into hydrogen sulfide and sulfur in the process of anaerobic methane oxidation accompanied by sulphate reduction.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA.

PubMed

Edwardson, Christian F; Hollibaugh, James T

2017-10-01

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.

Microbial content of household dust associated with exhaled NO in asthmatic children.

EPA Science Inventory

Exhaled nitric oxide (eNO) is increasingly used as a non-invasive measure of airway inflammation. Despite this, little information exists regarding the potential effects of indoor microbial components on eNO. We determined the influence of microbial contaminants in house dust and...

Abundance and Distribution of Diagnostic Carbon Fixation Genes in a Deep-Sea Hydrothermal Gradient Ecosystem

NASA Astrophysics Data System (ADS)

Blumenfeld, H. N.; Kelley, D. S.; Girguis, P. R.; Schrenk, M. O.

2010-12-01

The walls of deep-sea hydrothermal vent chimneys sustain steep thermal and chemical gradients resulting from the mixing of hot (350°C+) hydrothermal fluids with cold, oxygenated seawater. The chemical disequilibrium generated from this process has the potential to drive numerous chemolithoautotrophic metabolisms, many of which have been demonstrated to be operative in microbial pure cultures. In addition to the well-known Calvin Cycle, at least five additional pathways have been discovered including the Reverse Tricarboxylic Acid Cycle (rTCA), the Reductive Acetyl-CoA pathway, and the 3-hydroxyproprionate pathway. Most of the newly discovered pathways have been found in thermophilic and hyperthermophilic Bacteria and Archaea, which are the well represented in microbial diversity studies of hydrothermal chimney walls. However, to date, little is known about the environmental controls that impact various carbon fixation pathways. The overlap of limited microbial diversity with distinct habitat conditions in hydrothermal chimney walls provides an ideal setting to explore these relationships. Hydrothermal chimney walls from multiple structures recovered from the Juan de Fuca Ridge in the northeastern Pacific were sub-sampled and analyzed using PCR-based assays. Earlier work showed elevated microbial abundances in the outer portions of mature chimney walls, with varying ratios of Archaea to Bacteria from the outer to inner portions of the chimneys. Common phylotypes identified in these regions included Epsilonproteobacteria, Gammaproteobacteria, and Desulfurococcales. Total genomic DNA was extracted from mineralogically distinct niches within these structures and queried for genes coding key regulatory enzymes for each of the well studied carbon fixation pathways. Preliminary results show the occurrence of genes representing rTCA cycle (aclB) and methyl coenzyme A reductase (mcrA) - a proxy for the Reductive Acetyl-CoA Pathway within interior portion of mature hydrothermal chimneys. Ongoing analyses are aimed at quantifying the abundances of these diagnostic carbon fixation genes within the hydrothermal chimney gradients. These data are being compared to a broad array of contextual data to provide insight into the environmental and biological controls that may impact the distribution of the various carbon fixation pathways. Application of genomic approaches to the hydrothermal chimney ecosystem will provide insight into the microbial ecology of such structures and refine our ability to measure autotrophy in hydrothermal habitats sustained by chemical energy.

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea.

PubMed

Wu, Yuzhi; Qiu, Jian-Wen; Qian, Pei-Yuan; Wang, Yong

2018-05-01

In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.

Microbial Preference for Soil Organic Carbon Changes Along Redox Gradients as a Function of the Energetic Cost of Respiration

NASA Astrophysics Data System (ADS)

Naughton, H.; Keiluweit, M.; Fendorf, S. E.; Farrant, D. N.

2016-12-01

Soil organic carbon (SOC) chemistry is known to impact carbon preservation via mineral associations and physical protection, which chemically or physically block SOC from microbial enzymatic access for decomposition. However, SOC decay models that include these processes do not reliably predict SOC dynamics. We propose that the energetics of respiration additionally regulate SOC cycling. Specifically, organic carbon will only be respired if the available electron acceptors yield enough energy for microbial growth when metabolically coupled to the SOC. To test this hypothesis, we constructed dual pore domain reactors in which water flows normal to a column of packed soil, allowing oxygen to diffuse from the upper channel through the soil and establish a redox gradient. With increasing depth into the soil column, the soil experiences a typical redox profile indicative of anaerobic respiration processes: after oxygen is consumed, nitrate, Mn, Fe, and sulfate serve as electron acceptors. We measure porewater and effluent for nitrate, sulfate, Fe(II) and Mn(II) and take microsensor profiles of dissolved oxygen and H2S to characterize the redox gradient and respiration pathways. To this we couple incubations of solid material at each depth post-experiment and quantify CO2 and CH4 production to assess respiration potential along the redox gradient. Porewater SOC chemistry is analyzed via spectroscopy and mass spectrometry to interpret SOC oxidation state and composition and thus test thermodynamic predictions on SOC stability given the available redox acceptors at a given depth in the reactor. Within 0.5 cm of the soil surface, oxygen concentrations drop below detection and signs of anaerobic respiration (Fe(II) production, loss of nitrate) initiate while respiration rates drops precipitously. More oxidized SOC is preferentially utilized with progression along the redox gradient, supporting thermodynamic predictions. This work highlights the potential of SOC chemistry within specific redox metabolic zones of soils and sediments to drive carbon utilization. An improved understanding on organic carbon utliization is critical to predict SOC dynamics under changing hydrology (e.g. saltwater intrusion, permafrost melting), temperature, and other factors impacting microbial respiration energetics.

Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

2014-12-01

The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass pool suggests a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems.

Nano-structured manganese oxide as a cathodic catalyst for enhanced oxygen reduction in a microbial fuel cell fed with a synthetic wastewater.

PubMed

Liu, Xian-Wei; Sun, Xue-Fei; Huang, Yu-Xi; Sheng, Guo-Ping; Zhou, Kang; Zeng, Raymond J; Dong, Fang; Wang, Shu-Guang; Xu, An-Wu; Tong, Zhong-Hua; Yu, Han-Qing

2010-10-01

Microbial fuel cells (MFCs) provide new opportunities for the simultaneous wastewater treatment and electricity generation. Enhanced oxygen reduction capacity of cost-effective metal-based catalysts in an air cathode is essential for the scale-up and commercialization of MFCs in the field of wastewater treatment. We demonstrated that a nano-structured MnO(x) material, prepared by an electrochemically deposition method, could be an effective catalyst for oxygen reduction in an MFC to generate electricity with the maximum power density of 772.8 mW/m(3) and remove organics when the MFC was fed with an acetate-laden synthetic wastewater. The nano-structured MnO(x) with the controllable size and morphology could be readily obtained with the electrochemical deposition method. Both morphology and manganese oxidation state of the nano-scale catalyst were largely dependent on the electrochemical preparation process, and they governed its catalytic activity and the cathodic oxygen reduction performance of the MFC accordingly. Furthermore, cyclic voltammetry (CV) performed on each nano-structured material suggests that the MnO(x) nanorods had an electrochemical activity towards oxygen reduction reaction via a four-electron pathway in a neutral pH solution. This work provides useful information on the facile preparation of cost-effective cathodic catalysts in a controllable way for the single-chamber air-cathode MFC for wastewater treatment. Copyright © 2010 Elsevier Ltd. All rights reserved.

Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.

PubMed

León-Zayas, Rosa; Novotny, Mark; Podell, Sheila; Shepard, Charles M; Berkenpas, Eric; Nikolenko, Sergey; Pevzner, Pavel; Lasken, Roger S; Bartlett, Douglas H

2015-12-01

Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Effect of Trichoderma viride biofertilizer on ammonia volatilization from an alkaline soil in Northern China.

PubMed

Wang, Xia; Xu, Shengjun; Wu, Shanghua; Feng, Shugeng; Bai, Zhihui; Zhuang, Guoqiang; Zhuang, Xuliang

2018-04-01

Ammonia (NH 3 ) volatilization is one of the primary pathways of nitrogen (N) loss from soils after chemical fertilizer is applied, especially from the alkaline soils in Northern China, which results in lower efficiency for chemical fertilizers. Therefore, we conducted an incubation experiment using an alkaline soil from Tianjin (pH8.37-8.43) to evaluate the suppression effect of Trichoderma viride (T. viride) biofertilizer on NH 3 volatilization, and compared the differences in microbial community structure among all samples. The results showed that viable T. viride biofertilizer (T) decreased NH 3 volatilization by 42.21% compared with conventional fertilizer ((CK), urea), while nonviable T. viride biofertilizer (TS) decreased NH 3 volatilization by 32.42%. NH 3 volatilization was significantly higher in CK and sweet potato starch wastewater (SPSW) treatments during the peak period. T. viride biofertilizer also improved the transfer of ammonium from soil to sweet sorghum. Plant dry weights increased 91.23% and 61.08% for T and TS, respectively, compared to CK. Moreover, T. viride biofertilizer enhanced nitrification by increasing the abundance of ammonium-oxidizing archaea (AOA) and ammonium-oxidizing bacteria (AOB). The results of high-throughput sequencing indicated that the microbial community structure and composition were significantly changed by the application of T. viride biofertilizer. This study demonstrated the immense potential of T. viride biofertilizer in reducing NH 3 volatilization from alkaline soil and simultaneously improving the utilization of fertilizer N by sweet sorghum. Copyright © 2017. Published by Elsevier B.V.

Prevalence of the Ancient Wood-Ljungdahl Pathway in a Subseafloor Olivine Community

NASA Astrophysics Data System (ADS)

Smith, A. R.; Mueller, R.; Fisk, M. R.; Mason, O. U.; Popa, R.; Kieft, B.; Colwell, F. S.

2018-05-01

The ancient Wood-Ljungdahl pathway used for biosynthesis and energy generation was found to be the predominant metabolic pathway in a microbial community from olivine grains incubated in the Juan de Fuca subseafloor aquifer.

The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa

NASA Astrophysics Data System (ADS)

Russell, Michael J.; Murray, Alison E.; Hand, Kevin P.

2017-12-01

Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs - relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts - could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as "electron disposal units" for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes.

Substrate scope of a dehydrogenase from Sphingomonas species A1 and its potential application in the synthesis of rare sugars and sugar derivatives.

PubMed

Beer, Barbara; Pick, André; Döring, Manuel; Lommes, Petra; Sieber, Volker

2018-07-01

Rare sugars and sugar derivatives that can be obtained from abundant sugars are of great interest to biochemical and pharmaceutical research. Here, we describe the substrate scope of a short-chain dehydrogenase/reductase from Sphingomonas species A1 (SpsADH) in the oxidation of aldonates and polyols. The resulting products are rare uronic acids and rare sugars respectively. We provide insight into the substrate recognition of SpsADH using kinetic analyses, which show that the configuration of the hydroxyl groups adjacent to the oxidized carbon is crucial for substrate recognition. Furthermore, the specificity is demonstrated by the oxidation of d-sorbitol leading to l-gulose as sole product instead of a mixture of d-glucose and l-gulose. Finally, we applied the enzyme to the synthesis of l-gulose from d-sorbitol in an in vitro system using a NADH oxidase for cofactor recycling. This study shows the usefulness of exploring the substrate scope of enzymes to find new enzymatic reaction pathways from renewable resources to value-added compounds. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Abiotic Nitrous Oxide Production in Natural and Artificial Seawater

NASA Astrophysics Data System (ADS)

Ochoa, H.; Stanton, C. L.; Cavazos, A. R.; Ostrom, N. E.; Glass, J. B.

2014-12-01

The ocean contributes approximately one third of global sources of nitrous oxide (N2O) to the atmosphere. While nitrification is thought to be the dominant pathway for marine N2O production, mechanisms remain unresolved. Previous studies have carried the implicit assumption that marine N2O originates directly from enzymatic sources. However, abiotic production of N2O is possible via chemical reactions between nitrogenous intermediates and redox active trace metals in seawater. In this study, we investigated N2O production and isotopic composition in treatments with and without added hydroxylamine (NH2OH) and nitric oxide (NO), intermediates in microbial oxidation of ammonia to nitrite, and Fe(III). Addition of substrates to sterile artificial seawater was compared with filtered and unfiltered seawater from Sapelo Island, coastal Georgia, USA. N2O production was observed immediately after addition of Fe(III) in the presence of NH2OH at pH 8 in sterile artificial seawater. Highest N2O production was observed in the presence of Fe(III), NO, and NH2OH. The isotopomer site preference of abiotically produced N2O was consistent with previous studies (31 ± 2 ‰). Higher abiotic N2O production was observed in sterile artificial seawater (salinity: 35 ppt) than filtered Sapelo Island seawater (salinity: 25 ppt) whereas diluted sterile artificial seawater (18 ppt) showed lowest N2O production, suggesting that higher salinity promotes enhanced abiotic N2O production. Addition of Fe(III) to unfiltered Sapelo Island seawater stimulated N2O production. The presence of ammonia-oxidizing archaea (AOA), which lack known N2O producing enzymes, in Sapelo Island seawater was confirmed by successful amplification of the archaeal amoA gene, whereas ammonia-oxidizing bacteria (AOB), which contain N2O-producing enzymes were undetected. Given the few Fe-containing proteins present in AOA, it is likely that Fe(III) addition promoted N2O production via an abiotic vs. enzymatic N2O mechanism. Overall, this study suggests that abiotic N2O production may be occurring in marine environments where microbial ammonia oxidation occurs in the presence of elevated Fe and/or other redox-active metals, such as coastal areas, oxygen minimum zones, and near the sediment-water interface.

Expanding the product profile of a microbial alkane biosynthetic pathway.

PubMed

Harger, Matthew; Zheng, Lei; Moon, Austin; Ager, Casey; An, Ju Hye; Choe, Chris; Lai, Yi-Ling; Mo, Benjamin; Zong, David; Smith, Matthew D; Egbert, Robert G; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

2013-01-18

Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.

Perturbation Experiments: Approaches for Metabolic Pathway Analysis in Bioreactors.

PubMed

Weiner, Michael; Tröndle, Julia; Albermann, Christoph; Sprenger, Georg A; Weuster-Botz, Dirk

2016-01-01

In the last decades, targeted metabolic engineering of microbial cells has become one of the major tools in bioprocess design and optimization. For successful application, a detailed knowledge is necessary about the relevant metabolic pathways and their regulation inside the cells. Since in vitro experiments cannot display process conditions and behavior properly, process data about the cells' metabolic state have to be collected in vivo. For this purpose, special techniques and methods are necessary. Therefore, most techniques enabling in vivo characterization of metabolic pathways rely on perturbation experiments, which can be divided into dynamic and steady-state approaches. To avoid any process disturbance, approaches which enable perturbation of cell metabolism in parallel to the continuing production process are reasonable. Furthermore, the fast dynamics of microbial production processes amplifies the need of parallelized data generation. These points motivate the development of a parallelized approach for multiple metabolic perturbation experiments outside the operating production reactor. An appropriate approach for in vivo characterization of metabolic pathways is presented and applied exemplarily to a microbial L-phenylalanine production process on a 15 L-scale.

Metabolic capability and in situ activity of microorganisms in an oil reservoir.

PubMed

Liu, Yi-Fan; Galzerani, Daniela Domingos; Mbadinga, Serge Maurice; Zaramela, Livia S; Gu, Ji-Dong; Mu, Bo-Zhong; Zengler, Karsten

2018-01-05

Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.

Role of Ergothioneine in Microbial Physiology and Pathogenesis

PubMed Central

Cumming, Bridgette M.; Chinta, Krishna C.; Reddy, Vineel P.

2018-01-01

Abstract Significance: L-ergothioneine is synthesized in actinomycetes, cyanobacteria, methylobacteria, and some fungi. In contrast to other low-molecular-weight redox buffers, glutathione and mycothiol, ergothioneine is primarily present as a thione rather than a thiol at physiological pH, which makes it resistant to autoxidation. Ergothioneine regulates microbial physiology and enables the survival of microbes under stressful conditions encountered in their natural environments. In particular, ergothioneine enables pathogenic microbes, such as Mycobacterium tuberculosis (Mtb), to withstand hostile environments within the host to establish infection. Recent Advances: Ergothioneine has been reported to maintain bioenergetic homeostasis in Mtb and protect Mtb against oxidative stresses, thereby enhancing the virulence of Mtb in a mouse model. Furthermore, ergothioneine augments the resistance of Mtb to current frontline anti-TB drugs. Recently, an opportunistic fungus, Aspergillus fumigatus, which infects immunocompromised individuals, has been found to produce ergothioneine, which is important in conidial health and germination, and contributes to the fungal resistance against redox stresses. Critical Issues: The molecular mechanisms of the functions of ergothioneine in microbial physiology and pathogenesis are poorly understood. It is currently not known if ergothioneine is used in detoxification or antioxidant enzymatic pathways. As ergothioneine is involved in bioenergetic and redox homeostasis and antibiotic susceptibility of Mtb, it is of utmost importance to advance our understanding of these mechanisms. Future Directions: A clear understanding of the role of ergothioneine in microbes will advance our knowledge of how this thione enhances microbial virulence and resistance to the host's defense mechanisms to avoid complete eradication. Antioxid. Redox Signal. 28, 431–444. PMID:28791878

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Detecting volatile compounds from Kraft lignin degradation in the headspace of microbial cultures by selected ion flow tube mass spectrometry (SIFT-MS).

PubMed

Gibson, Andrew; Malek, Lada; Dekker, Robert F H; Ross, Brian

2015-05-01

Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was used to quantify methanol and other volatile compounds in the headspace of one bacterial and 12 fungal lignin-degrading microbial cultures. Cultures were grown in 250 mL Erlenmeyer flasks capped with aluminum foil containing 40 mL of nutrient media using Kraft lignin (0.3% w/v) as the sole carbon source. Analysis was done using SIFT-MS with H3O(+) and NO(+) precursors. Product ions were identified with multiple ion mode (MIM). Full scan (FS) mode was used to identify other compounds of interest. Absidia cylindrospora, Ischnoderma resinosum and Pholiota aurivella increased headspace methanol concentration by 136 ppb, 1196 ppb and 278 ppb, respectively, while Flammulina velutipes and Laetiporus sulphureus decreased concentration below ambient levels. F. velutipes and L. sulphureus were found to produce products of methanol oxidation (formaldehyde and formic acid) and were likely metabolizing methanol. Some additional unidentified compounds generated by the fungal cultures are intriguing and will require further study. SIFT-MS can be used to quantify methanol and other volatile compounds in the headspace of microbial cultures and has the potential to be a rapid, sensitive, non-invasive tool useful in elucidating the mechanisms of lignin degradative pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Factors that control the stable carbon isotopic composition of methane produced in an anoxic marine sediment

NASA Technical Reports Server (NTRS)

Alperin, M. J.; Blair, Neal E.; Albert, D. B.; Hoehler, T. M.; Martens, C. S.

1993-01-01

The carbon isotopic composition of methane produced in anoxic marine sediment is controlled by four factors: (1) the pathway of methane formation, (2) the isotopic composition of the methanogenic precursors, (3) the isotope fractionation factors for methane production, and (4) the isotope fractionation associated with methane oxidation. The importance of each factor was evaluated by monitoring stable carbon isotope ratios in methane produced by a sediment microcosm. Methane did not accumulate during the initial 42-day period when sediment contained sulfate, indicating little methane production from 'noncompetitive' substrates. Following sulfate depletion, methane accumulation proceeded in three distinct phases. First, CO2 reduction was the dominant methanogenic pathway and the isotopic composition of the methane produced ranged from -80 to -94 per thousand. The acetate concentration increased during this phase, suggesting that acetoclastic methanogenic bacteria were unable to keep pace with acetate production. Second, acetate fermentation became the dominant methanogenic pathway as bacteria responded to elevated acetate concentrations. The methane produced during this phase was progressively enriched in C-13, reaching a maximum delta(C-13) value of -42 per thousand. Third, the acetate pool experienced a precipitous decline from greater than 5 mM to less than 20 micro-M and methane production was again dominated by CO2 reduction. The delta(C-13) of methane produced during this final phase ranged from -46 to -58 per thousand. Methane oxidation concurrent with methane production was detected throughout the period of methane accumulation, at rates equivalent to 1 to 8 percent of the gross methane production rate. Thus methane oxidation was too slow to have significantly modified the isotopic signature of methane. A comparison of microcosm and field data suggests that similar microbial interactions may control seasonal variability in the isotopic composition of methane emitted from undisturbed Cape Lookout Bight sediment.

Gaining electricity from in situ oxidation of hydrogen produced by fermentative cellulose degradation.

PubMed

Niessen, J; Schröder, U; Harnisch, F; Scholz, F

2005-01-01

To exploit the fermentative hydrogen generation and direct hydrogen oxidation for the generation of electric current from the degradation of cellulose. Utilizing the metabolic activity of the mesophilic anaerobe Clostridium cellulolyticum and the thermophilic Clostridium thermocellum we show that electricity generation is possible from cellulose fermentation. The current generation is based on an in situ oxidation of microbially synthesized hydrogen at platinum-poly(tetrafluoroaniline) (Pt-PTFA) composite electrodes. Current densities of 130 mA l(-1) (with 3 g cellulose per litre medium) were achieved in poised potential experiments under batch and semi-batch conditions. The presented results show that electricity generation is possible by the in situ oxidation of hydrogen, product of the anaerobic degradation of cellulose by cellulolytic bacteria. For the first time, it is shown that an insoluble complex carbohydrate like cellulose can be used for electricity generation in a microbial fuel cell. The concept represents a first step to the utilization of macromolecular biomass components for microbial electricity generation.

Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

PubMed

Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

2016-03-01

Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enhancement of electricity production by graphene oxide in soil microbial fuel cells and plant microbial fuel cells.

PubMed

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.

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

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

PubMed Central

Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

2008-01-01

The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

Geobiology: A Conceptual Framework for Understanding Earth's Surface

NASA Astrophysics Data System (ADS)

Sumner, D. Y.

2016-12-01

A topic of study becomes a new field when it provides a useful conceptual framework for understanding suites of important processes. Geobiology integrates microbial biology with Earth sciences in a way that allows us to ask - and answer - deeper questions about Earth and the life on it. Recent studies of the oxidation of Earth's surface exemplify the impact of Geobiology as a new field. For decades, scientists have understood that Earth's surface was oxidized by photosynthesis. Geochemical records indicate dramatic redox changes both globally, e.g. the loss of MIF sulfur signatures due to formation of an ozone layer, and locally, as preserved in sedimentary rocks. However, these records depend critically on the dynamics of both the global biosphere and local microbial ecology. For example, an increase in global redox due to photosynthetic iron oxidation has different biogeochemical implications than an increase from oxygenic photosynthesis; O2 reacts very differently with organic matter and minerals than iron oxyhydroxides do, influencing microbial ecology as well as potential geochemical signatures in sedimentary rocks. Thus, studies of modern microbial communities provide insights into the interactions among metabolisms and geochemical gradients that have shaped Earth's redox history. For example, the ability of cyanobacteria to create O2 oases in benthic mats and soils on land provides a new framework for evaluating redox-sensitive elemental fluxes to the ocean. Similarly, genomic studies of Cyanobacteria have revealed close relatives, Melainabacteria, that are mostly obligate anaerobes. The evolutionary relationships between these two groups, as preserved in their genomes, reflect important microbial processes that led to oxidation of Earth's surface. By combining insights from microbial biology and sedimentary geochemistry, geobiologists will develop significantly more accurate models of the interactions between life and Earth.

Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

2015-12-01

Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

PubMed

Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

2012-12-01

Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

Biogeochemistry of Fe(II) oxidation in a photosynthetic microbial mat: Implications for Precambrian Fe(II) oxidation

NASA Astrophysics Data System (ADS)

Trouwborst, Robert E.; Johnston, Anne; Koch, Gretchen; Luther, George W.; Pierson, Beverly K.

2007-10-01

We studied the role of microbial photosynthesis in the oxidation of Fe(II) to Fe(III) in a high Fe(II) and high Mn(II) hot spring devoid of sulfide and atmospheric oxygen in the source waters. In situ light and dark microelectrode measurements of Fe(II), Mn(II) and O 2 were made in the microbial mat consisting of cyanobacteria and anoxygenic photosynthetic Chloroflexus sp. We show that Fe(II) oxidation occurred when the mat was exposed to varying intensities of sunlight but not near infrared light. We did not observe any Mn(II) oxidation under any light or dark condition over the pH range 5-7. We observed the impact of oxygenic photosynthesis on Fe(II) oxidation, distinct from the influence of atmospheric O 2 and anoxygenic photosynthesis. In situ Fe(II) oxidation rates in the mats and cell suspensions exposed to light are consistent with abiotic oxidation by O 2. The oxidation of Fe(II) to form primary Fe(III) phases contributed to banded iron-formations (BIFs) during the Precambrian. Both oxygenic photosynthesis, which produces O 2 as an oxidizing waste product, and anoxygenic photosynthesis in which Fe(II) is used to fix CO 2 have been proposed as Fe(II) oxidation mechanisms. Although we do not know the specific mechanisms responsible for all Precambrian Fe(II) oxidation, we assessed the relative importance of both mechanisms in this modern hot spring environment. In this environment, cyanobacterial oxygen production accounted for all the observed Fe(II) oxidation. The rate data indicate that a modest population of cyanobacteria could have mediated sufficient Fe(II) oxidation for some BIFs.

Impact of organic carbon and nutrients mobilized during chemical oxidation on subsequent bioremediation of a diesel-contaminated soil.

PubMed

Sutton, Nora B; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-02-01

Remediation with in situ chemical oxidation (ISCO) impacts soil organic matter (SOM) and the microbial community, with deleterious effects on the latter being a major hurdle to coupling ISCO with in situ bioremediation (ISB). We investigate treatment of a diesel-contaminated soil with Fenton's reagent and modified Fenton's reagent coupled with a subsequent bioremediation phase of 187d, both with and without nutrient amendment. Chemical oxidation mobilized SOM into the liquid phase, producing dissolved organic carbon (DOC) concentrations 8-16 times higher than the untreated field sample. Higher aqueous concentrations of nitrogen and phosphorous species were also observed following oxidation; NH4(+) increased 14-172 times. During the bioremediation phase, dissolved carbon and nutrient species were utilized for microbial growth-yielding DOC concentrations similar to field sample levels within 56d of incubation. In the absence of nutrient amendment, the highest microbial respiration rates were correlated with higher availability of nitrogen and phosphorus species mobilized by oxidation. Significant diesel degradation was only observed following nutrient amendment, implying that nutrients mobilized by chemical oxidation can increase microbial activity but are insufficient for bioremediation. While all bioremediation occurred in the first 28d of incubation in the biotic control microcosm with nutrient amendment, biodegradation continued throughout 187d of incubation following chemical oxidation, suggesting that chemical treatment also affects the desorption of organic contaminants from SOM. Overall, results indicate that biodegradation of DOC, as an alternative substrate to diesel, and biological utilization of mobilized nutrients have implications for the success of coupled ISCO and ISB treatments. Copyright © 2013 Elsevier Ltd. All rights reserved.

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

Lack of electricity production by Pelobacter carbinolicus indicates that the capacity for Fe(III) oxide reduction does not necessarily confer electron transfer ability to fuel cell anodes.

PubMed

Richter, Hanno; Lanthier, Martin; Nevin, Kelly P; Lovley, Derek R

2007-08-01

The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize ethanol, suggesting that P. carbinolicus grew in the fuel cell by converting ethanol to hydrogen and acetate, which G. sulfurreducens oxidized with electron transfer to the anode. Up to 83% of the electrons available in ethanol were recovered as electricity and in the metabolic intermediate acetate. Hydrogen consumption by G. sulfurreducens was important for ethanol metabolism by P. carbinolicus. Confocal microscopy and analysis of 16S rRNA genes revealed that half of the cells growing on the anode surface were P. carbinolicus, but there was a nearly equal number of planktonic cells of P. carbinolicus. In contrast, G. sulfurreducens was primarily attached to the anode. P. carbinolicus represents the first Fe(III) oxide-reducing microorganism found to be unable to produce current in a microbial fuel cell, providing the first suggestion that the mechanisms for extracellular electron transfer to Fe(III) oxides and fuel cell anodes may be different.

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

USGS Publications Warehouse

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

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)–H2SO4 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 μmol/L/h whereas Sb(III) oxidized at 0.03–0.05 μmol/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 μmol/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.

Electron microscopy study of microbial mat in the North Fiji basin hydrothermal vent

NASA Astrophysics Data System (ADS)

Park, H.; Kim, J. W.; Lee, J. W.

2017-12-01

Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that the hydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. In the present study multiline of analytical methods (X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM)) were utilized to investigate the mineralogy/chemistry of microbe-mineral interaction in hydrothermal microbial mat. Microbial mat samples were recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602. XRD analysis showed that red-colored microbial mat contains Fe-oxides and Fe-oxyhydroxides. Various morphologies of minerals in the red-colored microbial mat observed by SEM are mainly showed sheath shaped, resembled with Leptothrix microbial structure, stalks shaped, similar with Marioprofundus microbial structure and globule shaped microbial structures. They are also detected with DNA analysis. The cross sectional observation of microbial structures encrusted with Fe-oxide and Fe-oxyhydroxide at a nano scale by Transmission Electron Microscopy (TEM) and Focused Ion Beam (FIB) technique was developed to verify the structural/biogeochemical properties in the microbe-mineral interaction. Systematic nano-scale measurements on the biomineralization in the microbial mat leads the understandings of biogeochemical environments around the hydrothermal vent.

Novel Strategy for Tracking the Microbial Degradation of Azo Dyes with Different Polarities in Living Cells.

PubMed

Liu, Fei; Xu, Meiying; Chen, Xingjuan; Yang, Yonggang; Wang, Haiji; Sun, Guoping

2015-10-06

Direct visualization evidence is important for understanding the microbial degradation mechanisms. To track the microbial degradation pathways of azo dyes with different polar characterizations, sensors based on the fluorescence resonance energy transfer (FRET) from 1,8-naphthalimide to azo dyes were synthesized, in which the quenched fluorescence will recover when the azo bond was cleaved. In living cells, the sensor-tracking experiment showed that the low polarity and hydrophobic azo dye can be taken up into the cells and reduced inside the cells, whereas the high polarity and hydrophilic azo dye can be reduced only outside the cells because of the selective permeability of the cell membranes. These results indicated that there were two different bacterial degradation pathways available for different polarity azo dyes. To our knowledge, no fluorescent sensor has yet been designed for illuminating the microbial degradation mechanisms of organic pollutants with different characteristics.

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

PubMed

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

2014-12-01

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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.