Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane

Methane is the most abundant organic chemical in Earth's atmosphere, and its concentration is increasing with time, as a variety of independent measurements have shown. Photochemical reactions oxidize methane in the atmosphere; through these reactions, methane exerts strong influence over the chemistry of the troposphere and the stratosphere and many species including ozone, hydroxyl radicals, and carbon monoxide. Also, through its infrared absorption spectrum, methane is an important greenhouse gas in the climate system. We describe and enumerate key roles and reactions. Then we focus on two kinds of methane production: microbial and thermogenic. Microbial methanogenesis is described, and key organisms and substrates are identified along with their properties and habitats. Microbial methane oxidation limits the release of methane from certain methanogenic areas. Both aerobic and anaerobic oxidation are described here along with methods to measure rates of methane production and oxidation experimentally. Indicators of the origin of methane, including C and H isotopes, are reviewed. We identify and evaluate several constraints on the budget of atmospheric methane, its sources, sinks and residence time. From these constraints and other data on sources and sinks we construct a list of sources and sinks, identities, and sizes. The quasi-steady state (defined in the text) annual source (or sink) totals about 310(±60) × 1012 mol (500(±95) × 1012 g), but there are many remaining uncertainties in source and sink sizes and several types of data that could lead to stronger constraints and revised estimates in the future. It is particularly difficult to identify enough sources of radiocarbon-free methane.

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Biogeochemical aspects of atmospheric methane

This review shows that thermodynamic and kinetic constraints largely prevent large-scale methanogenesis in the open ocean water column. One example of open-ocean methanogenesis involves anoxic digestive tracts and fecal pellet microenvironments; methane released during fecal pellet disaggregation results in the mixed-layer methane maximum. However, the bulk of the methane in the ocean is added by coastal runoff, seeps, hydrothermal vents, decomposing hydrates, and mud volcanoes. Since methane is present in the open ocean at nanomolar concentrations, and since the flux to the atmosphere is small, the ultimate fate of ocean methane additions must be oxidation within the ocean. As indicated in the Introduction and highlighted in Table 3, sources of methane to the ocean water column are poorly quantified. There are only a small number of direct water column methane oxidation rates, so sinks are also poorly quantified. We know that methane oxidation rates are sensitive to ambient methane concentrations, but we have no information on reaction kinetics and only one report of the effect of pressure on methane oxidation. Our perspective on methane sources and the extent of methane oxidation has been changed dramatically by new techniques involving gene probes, determination of isotopically depleted biomarkers, and recent 14C-CH4 measurements showing that methane geochemistry in anoxic basins is dominated by seeps providing fossil methane. The role of anaerobic oxidation of methane has changed from a controversial curiosity to a major sink in anoxic basins and sediments. © 2007 American Chemical Society.

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Oceanic methane biogeochemistry.

Arsenic and selenium are readily metabolized by prokaryotes, par- ticipating in a full range of metabolic functions including as- similation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltrans- ferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its in- corporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaero- bic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in 76 Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

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Arsenic and selenium in microbial metabolism.

This review of anaerobic metabolism emphasizes aerobic oxidation, because the two processes cannot be separated in a complete treatment of the topic. It is process oriented and highlights the fascinating microorganisms that mediate anaerobic biogeochemistry. We begin this review with a brief discussion of CO 2 assimilation by autotrophs, the source of most of the reducing power on Earth, and then consider the biological processes that harness this potential energy. Energy liberation begins with the decomposition of organic macromolecules to relatively simple compounds, which are simplified further by fermentation. Methanogenesis is considered next because CH 4 is a product of acetate fermentation, and thus completes the catabolism of organic matter, particularly in the absence of inorganic electron acceptors. Finally, the organisms that use nitrogen, manganese, iron, and sulfur for terminal electron acceptors are considered in order of decreasing free-energy yield of the reactions.

Anaerobic Metabolism: Linkages to Trace Gases and Aerobic Processes

Addition of dimethylsulfide (DMS), dimethyldisulfide (DMDS), or methane thiol (MSH) to a diversity of anoxic aquatic sediments (eg, fresh water, estuarine, alkaline/hypersaline) stimulated methane production The yield of methane recovered from DMS was often 52 to 63%, although high concentrations of DMS (as well as MSH and DMDS) inhibited methanogenesis in some types of sediments Production of methane from these reduced methylated sulfur compounds was blocked by 2-bromoethanesulfonic acid Sulfate did not influence the metabolism of millimolar levels of DMS, DMDS, or MSH added to sediments However, when DMS was added at ∼2-μM levels as [14C]DMS, metabolism by sediments resulted in a 14CH4/14CO2 ratio of only 006 Addition of molybdate increased the ratio to 18, while 2-bromoethanesulfonic acid decreased it to 0, but did not block 14CO2 production These results indicate the methanogens and sulfate reducers compete for DMS when it is present at low concentrations; however, at high concentrations, DMS is a “noncompetitive” substrate for methanogens Metabolism of DMS by sediments resulted in the appearance of MSH as a transient intermediate A pure culture of an obligately methylotrophic estuarine methanogen was isolated which was capable of growth on DMS Metabolism of DMS by the culture also resulted in the transient appearance of MSH, but the organism could grow on neither MSH nor DMDS The culture metabolized [14C]-DMS to yield a 14CH4/14CO2 ratio of ∼28 Reduced methylated sulfur compounds represent a new class of substrates for methanogens and may be potential precursors of methane in a variety of aquatic habitats

Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen.

In vitro adherence of Lactobacillus species to vaginal epithelial cells.

An Arthrobacter sp. isolated from a glucose-sucrose agar plate was found to produce a neutral, extremely viscous, opalescent extracellular polymer. Growth, polymer production, and rheological properties and chemical composition of the isolated polymer were examined. The polymer was found to be substantially different from other arthrobacter polymers. Some unusual properties included irreversible loss of viscosity with high temperature and degradation of the polymer during fermentation and upon storage at 4 degrees C. Other characteristics included dependence on sucrose for polymer production, relative pH stability, increased viscosity with increased salt concentration, and pseudoplasticity. The polymer was found to be composed primarily (if not entirely) of d-fructose. The fructose content and other characteristics suggested that the polymer was a levan.

Production and Characterization of a Polymer from Arthrobacter sp

species (P.anaerobius, P.micros, P.parvulus, andP.productus) were produced inrabbits. Whenthese antisera were reacted against sonically disrupted cells andculture supernatant fluids inOuchterlony tests, linesofidentity were obtained among theantigens fromallthespecies anduninoculated culture medium. Whentheantisera were subsequently absorbed withthedehydrated culture mediumusedtogrow the peptostreptococci, allcross-reactions inheterologous antigen-antibody combinations wereeliminated, leaving onlyspecies-specific precipitin arcs.Theseabsorbed antisera, specific foreachPeptostreptococcus species byOuchterlony tests, were usedforrapid identification studies. Staphylococcus aureus-bearing protein A was sensitized witheachabsorbed antiserum. Thesereagents produced specific coagglutination reactions withsuspensions ofeachPeptostreptococcus reference strain andwith16clinical isolates. Nocross-reactions occurred withtheStreptococcus intermedius, Peptococcus magnus, or Peptococcus asaccharolyticus strains tested. Peptostreptococci (P.anaerobius, P.micros, P.parvulus, andP.productus) arecommonly present asnormalmicrobial flora inhumans. Theyareoften isolated fromwoundsandabscesses, pelvic inflammatory disease, empyema, peritonitis, puerperal fever, andsubacute bacterial endocarditis (10, 14). However, their significance ininfections isunclear because: (i) differentiation ofanaerobic gram-positive cocci hasbeencomplicated bytheabsence ofclear genus definitions andauniformly accepted classification schemeforspecies identification; (ii) specimens frominfected sites havecontained Peptostreptococcus species mixedwithother anaerobic organisms, causing difficulty indetermining their role inthedisease process; and(iii) arapid, reliable methodforidentifying these organisms isnotavailable. Conventional methods foridentifying anaerobicbacteria, including gas-liquid chromatographyandinoculation ofdifferential biochemical media, aretime-consuming andcostly. Inminiaturized substrate systems (15, 16)manyanaerobicgram-positive cocci growsopoorly that interpretations oftests aredifficult. Inaddition, gas-liquid chromatography ofcellular fatty acids (9, 18)differentiates someoftheanaerobic cocci, butthis information isinadequate foracomplete Peptostreptococcus differentiation. Because oftheproblems notedwithconventional methods, Staphylococcus protein Acoagglutination (SPAC)andOuchterlony double-diffusion precipitin tests wereselected forstudy as possible practical clinical procedures toidentify these organisms andtostudy their taxonomic relationships. Reference strains andclinical isolates wereidentified bybothserological and conventional differential biochemical tests and gas-liquid chromatography profiles. We found unique antigens andnocommongenusantigens amongthePeptostreptococcus

Anthony Catena

Papers

Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen.

In vitro adherence of Lactobacillus species to vaginal epithelial cells.

Production and Characterization of a Polymer from Arthrobacter sp

Antigenic Relationships andRapidIdentification of Peptostreptococcus Species