Oxidation of methane in boreal forest soils: a comparison of seven measures

Methane oxidation rates were measured in boreal forest soils using seven techniques that provide a range of information on soil CH₄ oxidation. These include: (a) short-term static chamber experiments with a free-air (1.7 ppm CH₄) headspace, (b) estimating CH₄ oxidation rates from soil CH₄ distributions and (c)²²²Rn-calibrated flux measurements, (d) day-long static chamber experiments with free-air and amended (+20 to 2000 PPM CH₄) headspaces, (e) jar experiments on soil core sections using free-air and (f) amended (+500 ppm CH₄) headspaces, and (g) jar experiments on core sections involving tracer additions of¹⁴CH₄. Short-term unamended chamber measurements,²²²Rn-calibrated flux measurements, and soil CH₄ distributions show independently that the soils are capable of oxidizing atmospheric CH₄ at rates ranging to < 2 mg m^–2 d^–1. Jar experiments with free-air headspaces and soil CH₄ profiles show that CH₄ oxidation occurs to a soil depth of 60 cm and is maximum in the 10 to 20 cm zone. Jar experiments and chamber measurements with free-air headspaces show that CH₄ oxidation occurs at low (< 0.9 ppm) thresholds. The¹⁴CH₄-amended jar experiments show the distribution of end products of CH₄ oxidation; 60% is transformed to CO₂ and the remainder is incorporated in biomass. Chamber and jar experiments under amended atmospheres show that these soils have a high capacity for CH₄ oxidation and indicate potential CH₄ oxidation rates as high as 867 mg m^–2 d^–1. Methane oxidation in moist soils modulates CH₄ emission and can serve as a negative feedback on atmospheric CH₄ increases.     

Aggregation-dependent turnover of flagellar adhesion molecules in chlamydomonas gametes

Previous studies on flagellar adhesion in chlamydomonas (Snell, W. and S. Roseman. 1979. J. Biol. Chem. 254:10820-10829.) have shown that as gametes adhere to flagella isolated from gametes of the opposite mating type, the adhsiveness of the added flagella but not of the gametes is lost. The studies reported here show that the addition of protein synthesis inhibitors (cycloheximide [CH] or anisomycin) to the medium of such cell- flagella mixtures causes the cells to lose their adhesiveness. This loss, however, occurs only after the cells have interacted with 4-8 flagella/cell and does not occur if the cells are kept in CH (7 h) without aggregating. The availability of an impotent (imp) mating type plus (MT(+)) mutant (provided by U.W. Goodenough), which adheres but is unable to undergo the fusion that normally follows adhesion, made it possible to determine whether a similar loss of adhesiveness occurs in mixtures of matting type minus (mt(-)) and imp mt(+) gametes. In the absence of inhibitor, mt(-) and imp mt(+) gametes adhered to each other (without fusing) for several hours; however, in the presence of CH or anisomycin, the gametes began to de-adhere 35 min after mixing, and, by 90 min, 100 percent of the cells were single again. This effect was reversible, and the rapid turnover of cells were single again. This effect was reversible, and the rapid turnover of molecules involved in adhesion occurred only during adhesion inasmuch as gametes pretreated for 4 h with CH were able to aggregate in CH for the same length of time as nonpretreated cells aggregated in CH. By the addition of CH at various times after the mt(-) and imp mt(+) gametes were mixed, measurements were made of the “pool size” of the molecules involved in adhesion. The pool reached a minimum after 25 min of aggregation, rapidly increased for the next 25 min, and then leveled off at the premixing level. These results suggest that flagellar adhesion in chlamydomonas causes modification of surface molecules (receptors, ligands), which brings about their inactivation and stimulates their replacement.     

Anaerobic mineralization of marine sediment organic matter: Rates and the role of anaerobic processes in the oceanic carbon economy

Abstract

This paper addresses three related questions: (1) What factors control the efficiency of carbon burial in sediments? (2) Are rates of anaerobic organic matter degradation intrinsically lower than aerobic rates? (3) How important are anaerobic processes in the global marine sediment carbon economy?

Carbon burial efficiency (the ratio of the carbon burial rate and the carbon flux to the sediment surface) was estimated from literature data for a range of environments and was shown to be a function of sedimentation rate. No difference independent of sedimentation rate was found between aerobic and anaerobic sediments.

A review of recent microcosm and laboratory studies shows that anaerobic rates are not intrinsically lower than aerobic rates; fresh organic matter degrades at similar rates under oxic and anoxic conditions. Aerobic decomposition rates near the sediment surface are typically greater than anaerobic rates at depth because the most labile carbon is consumed before it can be buried in the anoxic zone.

A model approach was taken in estimating the importance of anaerobic processes in the global marine sediment economy, instead of extrapolating measured rates as done previously. The result, 150 Tg C yr^?1, is two to nine times lower than previous estimates. This rate is about 9% of the global aerobic carbon oxidation rate and is about equal to the rate of long‐term carbon burial. The importance of anaerobic processes in marine sediments lies in their role in determining the amount of carbon preserved, not in the amount of carbon remineralized overall.     

Hydrogen production by methanogens under low-hydrogen conditions

Hydrogen production was studied in four species of methanogens (Methanothermobacter marburgensis, Methanosaeta thermophila, Methanosarcina barkeri, and Methanosaeta concilii) under conditions of low (sub-nanomolar) ambient hydrogen concentration using a specially designed culture apparatus. Transient hydrogen production was observed and quantified for each species studied. Methane was excluded as the electron source, as was all organic material added during growth of the cultures (acetate, yeast extract, peptone). Hydrogen production showed a strong temperature dependence, and production ceased at temperatures below the growth range of the organisms. Addition of polysulfides to the cultures greatly decreased hydrogen production. The addition of bromoethanesulfonic acid had little influence on hydrogen production. These experiments demonstrate that some methanogens produce excess reducing equivalents during growth and convert them to hydrogen when the ambient hydrogen concentration becomes low. The lack of sustained hydrogen production by the cultures in the presence of methane provides evidence against "reverse methanogenesis" as the mechanism for anaerobic methane oxidation.     

A culture apparatus for maintaining H2 at sub-nanomolar concentrations

We devised a microbial culture apparatus capable of maintaining sub-nanomolar H2 concentrations. This apparatus provides a method for study of interspecies hydrogen transfer by externally fulfilling the thermodynamic requirement for low H2 concentrations, thereby obviating the need for use of cocultures to study some forms of metabolism. The culture vessel is constructed of glass and operates by sparging a liquid culture with purified gases, thereby removing H2 as it is produced. We used the culture apparatus to decouple a syntrophic association in an ethanol-consuming, methanogenic enrichment culture, allowing ethanol oxidation to dominate methane production. We also used the culture apparatus to grow pure cultures of the ethanol-oxidizing, proton-reducing Pelobacter acetylenicus (WoAcy 1), and to study the bioenergetics of growth.     

Characterization of dental pulp stem/stromal cells of Huntington monkey tooth germs

Background

Activation by extracellular ligands of G protein-coupled (GPCRs) and tyrosine kinase receptors (RTKs), results in the generation of second messengers that in turn control specific cell functions. Further, modulation/amplification or inhibition of the initial signalling events, depend on the recruitment onto the plasma membrane of soluble protein effectors. High throughput methodologies to monitor quantitatively second messenger production, have been developed over the last years and are largely used to screen chemical libraries for drug development. On the contrary, no such high throughput methods are yet available for the other aspect of GPCRs regulation, i.e. protein translocation to the plasma membrane, despite the enormous interest of this phenomenon for the modulation of receptor downstream functions. Indeed, to date, the experimental procedures available are either inadequate or complex and expensive.

Results

Here we describe the development of a novel conceptual approach to the study of cytosolic proteins translocation to the inner surface of the plasma membrane. The basis of the technique consists in: i) generating chimeras between the protein of interests and the calcium (Ca²⁺)-sensitive, luminescent photo-protein, aequorin and ii) taking advantage of the large Ca²⁺ concentration [Ca²⁺] difference between bulk cytosolic and the sub-plasma membrane rim.

Conclusion

This approach, that keeps unaffected the translocation properties of the signalling protein, can in principle be applied to any protein that, upon activation, moves from the cytosol to the plasma membrane. Thus, not only the modulation of GPCRs and RTKs can be investigated in this way, but that of all other proteins that can be recruited to the plasma membrane also independently of receptor activation. Moreover, its automated version, which can provide information about the kinetics and concentration-dependence of the process, is also applicable to high throughput screening of drugs affecting the translocation process.     

Private specificities can dominate the humoral response to self-antigens in patients with cryptogenic fibrosing alveolitis

Background  

The pathogenetic mechanisms that underlie the interstitial lung disease cryptogenic fibrosing alveolitis (CFA) may involve an immunological reaction to unidentified antigens in the lung, resulting in tissue damage.     

Rapid Methane Oxidation in a Landfill Cover Soil

Methane oxidation rates observed in a topsoil covering a retired landfill are the highest reported (45 g m⁻² day⁻¹) for any environment. This microbial community had the capacity to rapidly oxidize CH₄ at concentrations ranging from <1 ppm (microliters per liter) (first-order rate constant [k] = −0.54 h⁻¹) to >10⁴ ppm (k = −2.37 h⁻¹). The physiological characteristics of a methanotroph isolated from the soil (characteristics determined in aqueous medium) and the natural population, however, were similar to those of other natural populations and cultures: the Q₁₀ and optimum temperature were 1.9 and 31°C, respectively, the apparent half-saturation constant was 2.5 to 9.3 μM, and 19 to 69% of oxidized CH₄ was assimilated into biomass. The CH₄ oxidation rate of this soil under waterlogged (41% [wt/vol] H₂O) conditions, 6.1 mg liter⁻¹ day⁻¹, was near rates reported for lake sediment and much lower than the rate of 116 mg liter⁻¹ day⁻¹ in the same soil under moist (11% H₂O) conditions. Since there are no large physiological differences between this microbial community and other CH₄ oxidizers, we attribute the high CH₄ oxidation rate in moist soil to enhanced CH₄ transport to the microorganisms; gas-phase molecular diffusion is 10⁴-fold faster than aqueous diffusion. These high CH₄ oxidation rates in moist soil have implications that are important in global climate change. Soil CH₄ oxidation could become a negative feedback to atmospheric CH₄ increases (and warming) in areas that are presently waterlogged but are projected to undergo a reduction in summer soil moisture.     

New perspectives on anaerobic methane oxidation

Anaerobic methane oxidation is a globally important but poorly understood process. Four lines of evidence have recently improved our understanding of this process. First, studies of recent marine sediments indicate that a consortium of methanogens and sulphate-reducing bacteria are responsible for anaerobic methane oxidation; a mechanism of 'reverse methanogenesis' was proposed, based on the principle of interspecies hydrogen transfer. Second, studies of known methanogens under low hydrogen and high methane conditions were unable to induce methane oxidation, indicating that 'reverse methanogenesis' is not a widespread process in methanogens. Third, lipid biomarker studies detected isotopically depleted archaeal and bacterial biomarkers from marine methane vents, and indicate that Archaea are the primary consumers of methane. Finally, phylogenetic studies indicate that only specific groups of Archaea and SRB are involved in methane oxidation. This review integrates results from these recent studies to constrain the responsible mechanisms.     

Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the pantherine lineage of Felidae

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among 17 Felidae species, notably 15 in the previously described pantherine lineage. The polymerase chain reaction (PCR) was used to generate sequences of 358 base pairs of the mitochondrial 12S RNA gene and 289 base pairs of the cytochrome b protein coding gene. DNA sequences were compared within and between 17 felid and five nonfelid carnivore species. Evolutionary trees were constructed using phenetic, cladistic, and maximum likelihood algorithms. The combined results suggested several phylogenetic relationships including (1) the recognition of a recently evolved monophyletic genus Panthera consisting of Panthera leo, P. pardus, P. onca, P. uncia, P. tigris, and Neofelis nebulosa; (2) the recent common ancestry of Acinonyx jubatus, the African cheetah, and Puma concolor, the American puma; and (3) two golden cat species, Profelis temmincki and Profelis aurata, are not sister species, and the latter is strongly associated with Caracal caracal. These data add to the growing database of vertebrate mtDNA sequences and, given the relatively recent divergence among the felids represented here (1-10 Myr), allow 12S and cytochrome b sequence evolution to be addressed over a time scale different from those addressed in most work on vertebrate mtDNA.