Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.     

Protonmotive force-driven synthesis of ATP during methane formation from molecular hydrogen and formaldehyde or carbon dioxide in Methanosarcina barkeri

Abstract Methane formation from formaldehyde and H₂ or from carbon dioxide and H₂, as performed by cell suspensions of Methanosarcina barkeri , was coupled to ATP synthesis. In correspondence with this, methane formation was inhibited by N , N '-dicyclohexylcarbodiimide (DCCD), which at the same time, caused a decrease of the intracellular ATP concentration but only a slow decrease of the membrane potential. Addition of the uncoupler tetrachlorosalicylanilide (TCS) led to a relief of the inhibition of methane formation from CH₂O + H₂, but not from CO₂+ H₂.     

The carbon and hydrogen stable isotope composition of bacteriogenic methane: A laboratory study using a landfill inoculum

Anaerobic bacterial degradation of landfill waste produces a globally significant source of the greenhouse gas methane. Stable isotopic measurements of methane [δ^I3C(CH₄) and δD(CH₄)] can often fingerprint different sources of methane (natural vs. anthro‐pogenic) and help identify the bacterial processes involved in methane production. Landfill microbial communities are complex and diverse, and hence so too is the biogeochem‐istry of methane formation. To investigate the influence of (l) the methane formation pathway (acetoclastic methanogenesis and CO₂ reduction), and (2) SD of water on the stable isotopic composition of landfill methane, two model butyrate‐degrading landfill systems were established. The systems were inoculated with domestic refuse from a landfill and incubated in the laboratory for 92 days. Both systems were identical except δD of water initially added to system 2 was 118% heavier than system 1. Between days 39 and 72 the systems were resupplemented with butyrate. Production of CH₄ and CO₂ and changes in volatile fatty acid concentration confirmed that active methanogenic populations had been established. CH₄ became ¹³C enriched in both incubations with time. Interpreting changes in acetate, butyrate, and propionate concentration during incubation is complicated, but these observations and other information suggest that the dominant methanogenic substrate changed front CO₂/H₂ to acetate as the experiment progressed. This is also consistent with the observed ¹³C enrichment of CH₄, as ¹³C discrimination during methane production from acetate is less than from CO₂. In contrast, δD(CH₄) remained relatively constant, suggesting that this measurement may not provide a reliable basis for distinguishing between CH₄ from CO₂ reduction and acetoclastic methanogenesis, as has previously been suggested.     

Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils

Vegetable oils are used to increase energy density of dairy cow diets, although they can provoke changes in rumen bacteria populations and have repercussions on the biohydrogenation process. The aim of this study was to evaluate the effect of two sources of dietary lipids: soybean oil (SO, an unsaturated source) and hydrogenated palm oil (HPO, a saturated source) on bacterial populations and the fatty acid profile of ruminal digesta. Three non-lactating Holstein cows fitted with ruminal cannulae were used in a 3×3 Latin square design with three periods consisting of 21 days. Dietary treatments consisted of a basal diet (Control, no fat supplement) and the basal diet supplemented with SO (2.7% of dry matter (DM)) or HPO (2.7% of DM). Ruminal digesta pH, NH₃–N and volatile fatty acids were not affected by dietary treatments. Compared with control and HPO, total bacteria measured as copies of 16S ribosomal DNA/ml by quantitative PCR was decreased (P<0.05) by SO. Fibrobacter succinogenes, Butyrivibrio proteoclasticus and Anaerovibrio lipolytica loads were not affected by dietary treatments. In contrast, compared with control, load of Prevotella bryantii was increased (P<0.05) with HPO diet. Compared with control and SO, HPO decreased (P<0.05) C18:2 cis n-6 in ruminal digesta. Contents of C15:0 iso, C18:11 trans-11 and C18:2 cis-9, trans-11 were increased (P<0.05) in ruminal digesta by SO compared with control and HPO. In conclusion, supplementation of SO or HPO do not affect ruminal fermentation parameters, whereas HPO can increase load of ruminal P. bryantii. Also, results observed in our targeted bacteria may have depended on the saturation degree of dietary oils.     

Effect of plant secondary compounds on in vitro methane,ammonia production and ruminal protozoa population

Aims

The objective of this study was to evaluate the potential of secondary plant metabolites from 38 sources to serve as antimethanogenic additives in ruminant diets. The effect of leaf tannins from these different plant sources on rumen fermentation, protozoal populations and methanogenesis was also studied.

Methods and Results

Samples (200 mg dry matter, DM) were incubated without and with polyethylene glycol (PEG)‐6000 (400 mg DM) as a tannin binder during 24‐h incubation in the in vitro Hohenheim gas system. In the leaf samples, total phenol (g kg^?1 DM) was maximum in Pimenta officinalis (312) followed by Oenothera lamarckiana (185) and Lawsonia inermis (105). Of the 38 samples, condensed tannins exceeded 4·0 g kg^?1 in only Alpinia galanga (7·50), Cinnamomum verum (4·58), Pelargonium graveolens (18·7) and Pimenta officinalis (23·2) and were not detected in seven samples. When the bioactivity of the leaf samples was assessed using the tannin bioassay, the percentage increase in the amount of gas produced during incubation of samples with the tannin‐binding agent PEG‐6000 over the amount produced during incubation without the tannin binder ranged from nil (zero) to 367%, with the highest being recorded with A. galanga leaves. The ratio of methane reduction per ml of total gas reduction was maximum with Rauvolfia serpentina (131·8) leaves, followed by Indigofera tinctoria (16·8) and Withania somnifera (10·2) leaves. Total and differential protozoal counts increased with added PEG in twenty‐two samples, maximum being in Pimenta officinalis. Increased accumulation of total volatile fatty acids during incubation with added PEG‐6000 was recorded, and the values ranged from zero to 61%. However, the increase was significant in only 11 of the 38 tannin sources tested indicating noninterference of tannin on in vitro fermentation of carbohydrates by the majority of samples tested. Conversely, in 26 of 38 plant sources, the leaf tannins reduced N‐digestibility as evidenced by increased accumulation of NH₃‐N with added PEG.

Conclusions

Our study unequivocally demonstrated that plants containing secondary metabolites such as Rauvolfia serpentine, Indigofera tinctoria and Withania somnifera have great potential to suppress methanogenesis with minimal adverse effect of feedstuff fermentation.

Significance and Impact of the Study

It was established that methanogenesis was not essentially related to the density of protozoa population in vitro. The tannins contained in these plants could be of interest in the development of new additives in ruminant nutrition.     

Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane

Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.     

Stability and reactivity of liposome‐encapsulated formate dehydrogenase and cofactor system in carbon dioxide gas‐liquid flow

Formate dehydrogenase from Candida boidinii (CbFDH) is potentially applicable in reduction of CO₂ through oxidation of cofactor NADH into NAD⁺. For this, the CbFDH activity needs to be maintained under practical reaction conditions, such as CO₂ gas‐liquid flow. In this work, CbFDH and cofactor were encapsulated in liposomes and the liposomal enzymes were characterized in an external loop airlift bubble column. The airlift was operated at 45°C with N₂ or CO₂ as gas phase at the superficial gas velocity U_G of 2.0 or 3.0 cm/s. The activities of liposomal CbFDH/cofactor systems were highly stable in the airlift regardless of the type of gas phase because liposome membranes prevented interactions of the encapsulated enzyme and cofactor molecules with the gas‐liquid interface of bubbles. On the other hand, free CbFDH was deactivated in the airlift especially at high U_G with CO₂ bubbles. The liposomal CbFDH/NADH could catalyze reduction of CO₂ in the airlift giving the fractional oxidation of the liposomal NADH of 23% at the reaction time of 360 min. The cofactor was kept inside liposomes during the reaction operation with less than 10% of leakage. All of the results obtained demonstrate that the liposomal CbFDH/NADH functions as a stable catalyst for reduction of CO₂ in the airlift. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Oxygen depletion and carbon dioxide and methane production in waters of the Pantanal wetland of Brazil

This study examines dissolved O₂, CO₂ and CH₄ in waters of the Pantanal, a vast savanna floodplain in Brazil. Measurements are presented for 540 samples from throughout the region, ranging from areas of sheet flooding to sluggish marsh streams to the major rivers of the region. Dissolved O₂ is often strongly depleted, particularly in waters filled with emergent vascular plants, which are the most extensive aquatic environment of the region. Median O₂ concentrations were 35 M for vegetated waters, 116 M for the Paraguay River, 95 M for tributary rivers, and 165 M for open lakes (atmospheric equilibrium, 230–290 M). Airwater diffusive fluxes were calculated from dissolved gas concentrations for representative vegetated floodplain waters, based on data collected over the course of an annual cycle. These fluxes reveal about twice as much CO₂ evasion as can be accounted for by invasion of O₂ (overall means in nmol cm^-2 s^-1: O₂ 0.18, CO₂ 0.34, and CH₄ 0.017). Methanogenesis is estimated to account for ca. 20% of the total heterotrophic metabolism in the water column and sediments, with the remainder likely due mostly to aerobic respiration. Anaerobic respiration is limited by the low concentrations of alternate electron acceptors. We hypothesize that O₂ transported through the stems of emergent plants is consumed in aerobic respiration by plant tissues or microorganisms, producing CO₂ that preferentially dissolves into the water, and thus explaining most of the excess CO₂ evasion. This hypothesis is supported by measurements of gases in submersed stems of emergent plants.     

Effect of disodium fumarate on microbial abundance,ruminal fermentation and methane emission in goats under different forage : concentrate ratios

This study investigated the effects of disodium fumarate (DF) on methane emission, ruminal fermentation and microbial abundance in goats under different forage (F) : concentrate (C) ratios and fed according to maintenance requirements. Four ruminally fistulated, castrated male goats were used in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and the main factors being the F : C ratios (41 : 59 or 58 : 42) and DF supplementation (0 or 10 g/day). DF reduced methane production (P < 0.05) on average by 11.9%, irrespective of the F : C ratio. The concentrations of total volatile fatty acids, acetate and propionate were greater in the rumen of goats supplemented with DF (P < 0.05), whereas the abundance of methanogens was lower (P < 0.05). In high-forage diets, the abundance of Selenomonas ruminantium, a fumarate-reducing bacterium, was greater in the rumen of goats supplemented with DF. The abundance of fungi, protozoa, Ruminococus flavefaciens and Fibrobacter succinogenes were not affected by the addition of DF. Variable F : C ratios affected the abundance of methanogens, fungi and R. flavefaciens (P < 0.05), but did not affect methane emission. The result implied that DF had a beneficial effect on the in vivo rumen fermentation of the goats fed diets with different F : C ratios and that this effect were not a direct action on anaerobic fungi, protozoa and fibrolytic bacteria, the generally recognized fiber-degrading and hydrogen-producing microorganisms, but due to the stimulation of fumarate-reducing bacteria and the depression of methanogens.     

Decomposition of carbon-bearing compounds and their influence on methane formation in a lignite incubation experiment

Carbon-bearing compounds (glucose, sodium acetate, methanol, yeast extract, and nutrient broth) were added in different proportions to cultures to stimulate methanogenesis in a lignite incubation experiment. Their addition significantly influenced the isotopic composition of methane generated during the fermentation of lignite. Glucose was degraded mainly in the first 2 weeks of incubation, when the atmospheric air was present in the headspace and used for biomass growth. Sodium acetate, methanol, and, presumably, lignite were decomposed in the next phase, in which anaerobic conditions occurred. The simultaneous decomposition of sodium acetate and methanol (as single substrates or as a mixture) with lignite resulted in the formation of methane with δ¹³C(CH₄) values typical for methyl-type fermentation. The identification of decomposed compounds in the mixture of sodium acetate and methanol was accomplished via isotopic analysis of carbon and hydrogen in the methane. The δ²H(CH₄) values in the case of methanol biodegradation were characterized by a negative trend over time, in contrast to a positive trend observed when sodium acetate decomposed. This observation may help to identify a very good tracer for the determination of methane precursors during methyl-type fermentation.     

The effect of vascular plants on carbon turnover and methane emissions from a tundra wetland

This paper investigates how vascular plants affect carbon flow and the formation and emission of the greenhouse gas methane (CH₄) in an arctic wet tundra ecosystem in NE Greenland. We present a field experiment where we studied, in particular, how species‐specific root exudation patterns affect the availability of acetate, a hypothesized precursor of CH₄ formation. We found significantly higher acetate formation rates in the root vicinity of Eriophorum scheuchzeri compared with another dominating sedge in the wetland, i.e. Dupontia psilosantha. Furthermore a shading treatment, which reduced net photosynthesis, resulted in significantly decreased formation rates of acetate. We also found that the potential CH₄ production of the peat profile was highly positively correlated to the concentration of acetate at the respective depths, whereas it was negatively correlated to the concentration of total dissolved organic carbon. This suggests that acetate is a substrate of importance to the methanogens in the studied ecosystem and that acetate concentration in this case can serve as a predictor of substrate quality. To further investigate the importance of acetate as a predecessor to CH₄, we brought an intact peat‐plant monolith system collected at the field site in NE Greenland to the laboratory, sealed it hermetically and studied the decomposition of ¹⁴C‐labelled acetate injected at the depth of methanogenic activity. After 4 h, ¹⁴CH₄ emission from the monolith could be observed. In conclusion, allocation of recently fixed carbon to the roots of certain species of vascular plants affects substrate quality and influence CH₄ formation.     

Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis

Stable isotope probing (SIP) allows the isolation of nucleic acids from targeted metabolically active organisms in environmental samples. In previous studies, DNA-SIP has been performed with the one-carbon growth substrates methane and methanol to study methylotrophic organisms. The methylotrophs that incorporated the labelled substrate were identified with polymerase chain reaction and sequencing of 16S rRNA and 'functional genes' for methanotrophs (mxaF, pmoA, mmoX). In this study, a SIP experiment was performed using a forest soil sample incubated with (13)CH(4), and the (13)C-DNA was purified and cloned into a bacterial artificial chromosome (BAC) plasmid. A library of 2300 clones was generated and most of the clones contained inserts between 10 and 30 kb. The library was probed for key methylotrophy genes and a 15.2 kb clone containing a pmoCAB operon, encoding particulate methane monooxygenase, was identified and sequenced. Analysis of the pmoA sequence suggested that the clone was most similar to that of a Methylocystis sp. previously detected in this forest soil. Twelve other open reading frames were identified on the clone, including the gene encoding beta-ribofuranosylaminobenzene 5'-phosphate synthase, which is involved in the biosynthesis of the 'archaeal' C(1)-carrier, tetrahydromethanopterin, which is also found in methylotrophs. This study demonstrates that relatively large DNA fragments from uncultivated organisms can be readily isolated using DNA-SIP, and cloned into a vector for metagenomic analysis.     

Contribution of 13C-NMR spectroscopy to the elucidation of pathways of propionate formation and degradation in methanogenic environments

Propionate is an important intermediate in the anaerobic degradation of complex organic matter to methane and carbon dioxide. The metabolism of propionate-forming and propionate-degrading bacteria is reviewed here. Propionate is formed during fermentation of polysaccharides, proteins and fats. The study of the fate of 13C-labelled compounds by nuclear magnetic resonance (NMR) spectroscopy has contributed together with other techniques to the present knowledge of the metabolic routes which lead to propionate formation from these substrates. Since propionate oxidation under methanogenic conditions is thermodynamically difficult, propionate often accumulates when the rates of its formation and degradation are unbalanced. Bacteria which are able to degrade propionate to the methanogenic substrates acetate and hydrogen can only perform this reaction when the methanogens consume acetate and hydrogen efficiently. As a consequence, propionate can only be degraded by obligatory syntrophic consortia of microorganisms. NMR techniques were used to study the degradation of propionate by defined and less defined cultures of these syntrophic consortia. Different types of side-reactions were reported, like the reductive carboxylation to butyrate and the reductive acetylation to higher fatty acids.     

Reconstructing long‐term changes (150 years) in the carbon cycle of a clear‐water lake based on the stable carbon isotope composition (δ13C) of chironomid and cladoceran subfossil remains

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Characterization of a thermally stable and organic solvent-adaptative NAD+ -dependent formate dehydrogenase from Bacillus sp. F1

Aims: To characterize a robust NAD⁺‐dependent formate dehydrogenase firstly obtained from a nonmethylotroph, Bacillus sp. F1. Methods and Results: The Bacillus sp. F1 NAD⁺‐dependent formate dehydrogenase (BacFDH) gene was cloned by TAIL‐PCR and heterologous expressed in Escherichia coli. BacFDH was stable at temperatures below 55°C, and the half‐life at 60°C was determined as 52·9 min. This enzyme also showed a broad pH stability and retained more than 80% of the activities after incubating in buffers with different pH ranging from 4·5 to 10·5 for 1 h. The activity of BacFDH was significantly enhanced by some metal ions. Moreover, BacFDH exhibited high tolerance to 20% dimethyl sulfoxide, 60% acetone, 10% methanol, 20% ethanol, 60% isopropanol and 20% n‐hexane. Like other FDHs, BacFDH displayed strict substrate specificity for formate. Conclusion: We isolated a robust formate dehydrogenase, designated as BacFDH, which showed excellent thermal stability, organic solvent stability and a broad pH stability. Significance and Impact of the Study: The multi‐aspect stability makes BacFDH a competitive candidate for coenzyme regeneration in practical applications of chiral chemicals and pharmaceuticals synthesis with a relatively low cost, especially for the catalysis performed in extreme pH conditions and organic solvents.     

The effect of sulfate and nitrate on methane formation in a freshwater sediment

A freshwater sediment from a ditch of a peat grassland near Zegveld (Province of Utrecht, The Netherlands) was investigated for its potential methanogenic and syntrophic activity and the influence of sulfate and nitrate on these potential activities. Methanogenesis started after a 10 days lagphase. After 35–40 days aceticlastic methanogens were sufficiently enriched to cause a net decrease of acetate. In the presence of sulfate methane formation was only slightly affected. The addition of nitrate led to an outcompetion of aceticlastic methanogens by nitrate reducers. When inorganic electron acceptors were absent, substrates like propionate and butyrate were converted by syntrophic methanogenic consortia. Addition of inorganic electron acceptors resulted in an outcompetition of the syntrophic propionate and butyrate degrading consortia by the sulfate and nitrate reducers.     

Determination of isotope fractionation factors and quantification of carbon flow by stable carbon isotope signatures in a methanogenic rice root model system

Methanogenic processes can be quantified by stable carbon isotopes, if necessary modeling parameters, especially fractionation factors, are known. Anoxically incubated rice roots are a model system with a dynamic microbial community and thus suitable to investigate principal geochemical processes in anoxic natural systems. Here we applied an inhibitor of acetoclastic methanogenesis (methyl fluoride), calculated the thermodynamics of the involved processes, and analyzed the carbon stable isotope signatures of CO₂, CH₄, propionate, acetate and the methyl carbon of acetate to characterize the carbon flow during anaerobic degradation of rice roots to the final products CO₂ and CH₄. Methyl fluoride inhibited acetoclastic methanogenesis and thus allowed to quantify the fractionation factor of CH₄ production from H₂/CO₂. Since our model system was not affected by H₂ gradients, the fractionation factor could alternatively be determined from the Gibbs free energies of hydrogenotrophic methanogenesis. The fractionation factor of acetoclastic methanogenesis was also experimentally determined. The data were used for successfully modeling the carbon flow. The model results were in agreement with the measured process data, but were sensitive to even small changes in the fractionation factor of hydrogenotrophic methanogenesis. Our study demonstrates that stable carbon isotope signatures are a proper tool to quantify carbon flow, if fractionation factors are determined precisely.     

Resource allocation to reproduction and soma in Drosophila: a stable isotope analysis of carbon from dietary sugar

Metabolic resources in adults of holometabolous insects may derive either from larval or adult feeding. In Drosophila melanogaster, reproduction and lifespan are differently affected by larval vs. adult resource availability, and it is unknown how larval vs. adult acquired nutrients are differentially allocated to somatic and reproductive function. Here we describe the allocation of carbon derived from dietary sugar in aging female D. melanogaster. Larval and adult flies were fed diets contrasting in sucrose (13)C/(12)C, from which we determined the extent to which carbon acquired at each stage contributed to adult somatic tissue and to egg manufacture. Dietary sugar is very important in egg provisioning; at every age, roughly one half of the carbon in eggs was derived from sugar, which turned over from predominantly larval to entirely adult dietary sources. Sucrose provided approximately 40% of total somatic carbon, of which adult dietary sucrose came to supply approximately 75%. Unlike in eggs, however, adult acquired sucrose did not entirely replace the somatic carbon from larvally acquired sucrose. Because carbon from larval sucrose appears to be fairly "replaceable", larval sucrose cannot be a limiting substrate in resource allocation between reproduction and lifespan.