Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1

A proteome-wide protein-protein interaction (PPI) network of Methanobrevibacter ruminantium M1 (MRU), a predominant rumen methanogen, was constructed from its metabolic genes using a gene neighborhood algorithm and then compared with closely related rumen methanogens Using proteome-wide PPI approach, we constructed network encompassed 2194 edges and 637 nodes interacting with 634 genes. Network quality and robustness of functional modules were assessed with gene ontology terms. A structure-function-metabolism mapping for each protein has been carried out with efforts to extract experimental PPI concomitant information from the literature. The results of our study revealed that some topological properties of its network were robust for sharing homologous protein interactions across heterotrophic and hydrogenotrophic methanogens. MRU proteome has shown to establish many PPI sub-networks for associated metabolic subsystems required to survive in the rumen environment. MRU genome found to share interacting proteins from its PPI network involved in specific metabolic subsystems distinct to heterotrophic and hydrogenotrophic methanogens. Across these proteomes, the interacting proteins from differential PPI networks were shared in common for the biosynthesis of amino acids, nucleosides, and nucleotides and energy metabolism in which more fractions of protein pairs shared with Methanosarcina acetivorans. Our comparative study expedites our knowledge to understand a complex proteome network associated with typical metabolic subsystems of MRU and to improve its genome-scale reconstruction in the future.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

Thermophilic anaerobic digestion of livestock waste: the effect of ammonia

Ammonia concentrations of 4 g N/l or more inhibited thermophilic digestion of cattle manure. A stable digestion of cattle manure could be maintained with ammonia concentrations up to 6 g N/l after 6 months of operation. However, the methane yield was reduced and the concentration of volatile fatty acids increased from 1 to 3 g/l as acetate, compared to controls with an ammonia concentration of 2.5 g N/l. The temporary strong inhibition following an one-step increase in ammonia concentration was reduced by applying a gradual increase. The specific methanogenic activity of ammonia-inhibited reactors (6 g N/l) with acetate or hydrogen as substrate was reduced by 73 and 52%, respectively. Tests of ammonia toxicity on the acetate- and hydrogen-utilizing populations showed a higher sensitivity of the aceticlastic compared to the hydrogenotrophic methanogens; the specific growth rate for the aceticlastic methanogens was halved at ammonia concentrations of 3.5 g N/l, compared to 7 g N/l for the hydrogenotrophic methanogens. Correspondence to: B. K. Ahring     

滨海湿地甲烷产生途径和产甲烷菌研究进展

滨海湿地在全球碳循环中起着重要的作用,其甲烷排放量占全球海洋甲烷排放的75%.本文综述了滨海湿地主要甲烷产生途径、产甲烷菌种类及其影响因子.滨海湿地SO₄^2-含量丰富,乙酸发酵和H₂/CO₂途径产甲烷受抑制,乙酸营养型和氢营养型产甲烷菌丰度较低;而利用甲胺类等“非竞争性”底物的C1甲基化合物歧化途径不受硫酸还原菌竞争底物的限制,兼性营养型产甲烷菌成为产甲烷优势菌.盐度与SO₄^2-含量和植被类型密切相关,影响竞争性电子和产甲烷底物的种类和含量,对甲烷产生途径和产甲烷菌群落结构有重要影响.目前,滨海湿地产甲烷菌群落结构、甲烷产生途径的关键控制因素尚需明确,其对甲烷排放的影响有待进一步研究.     

Substrate Availability,pH, and Temperature Influence Methanogenesis and Mild Steel Corrosion

Solid deposits of corroded pipelines in the Niger Delta were analyzed both chemically and microbiologically. The addition of substrate, especially acetate, significantly stimulated the methane production ranging from 0.85 to 1.60 mmole compared with 0.65 mmole of the control. Acetotrophic and hydrogenotrophic methanogens had their optimal methane production and corrosion rate at pH 5.5. All three types of methanogens produced the most methane at 37°C. Methane production by methanogens correlated strongly with corrosion rate. Pyrosequencing surveys show dominance of acetotrophic, hydrogenotrophic, and methylotrophic methanogens in the samples with no significant presence of sulfate-reducing bacteria (SRB), most likely due to the presence of the biocide, tetrakis-hydroxymethyl phosphonium sulfate. Our study shows that methanogens were one possible cause of pipeline failures in samples from the Niger Delta without the syntrophic association with SRB.     

Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil

Methane emission from paddy fields may be reduced by the addition of electron acceptors to stimulate microbial populations competitive to methanogens. We have studied the effects of ferrihydrite and gypsum (CaSO(4). 2H(2)O) amendment on methanogenesis and population dynamics of methanogens after flooding of Italian rice field soil slurries. Changes in methanogen community structure were followed by archaeal small subunit (SSU) ribosomal DNA (rDNA)- and rRNA-based terminal restriction fragment length polymorphism analysis and by quantitative SSU rRNA hybridization probing. Under ferrihydrite amendment, acetate was consumed efficiently (<60 microM) and a rapid but incomplete inhibition of methanogenesis occurred after 3 days. In contrast to unamended controls, the dynamics of Methanosarcina populations were largely suppressed as indicated by rDNA and rRNA analysis. However, the low acetate availability was still sufficient for activation of Methanosaeta spp., as indicated by a strong increase of SSU rRNA but not of relative rDNA frequencies. Unexpectedly, rRNA amounts of the novel rice cluster I (RC-I) methanogens increased significantly, while methanogenesis was low, which may be indicative of transient energy conservation coupled to Fe(III) reduction by these methanogens. Under gypsum addition, hydrogen was rapidly consumed to low levels ( approximately 0.4 Pa), indicating the presence of a competitive population of hydrogenotrophic sulfate-reducing bacteria (SRB). This was paralleled by a suppressed activity of the hydrogenotrophic RC-I methanogens as indicated by the lowest SSU rRNA quantities detected in all experiments. Full inhibition of methanogenesis only became apparent when acetate was depleted to nonpermissive thresholds (<5 microM) after 10 days. Apparently, a competitive, acetotrophic population of SRB was not present initially, and hence, acetotrophic methanosarcinal populations were less suppressed than under ferrihydrite amendment. In conclusion, although methane production was inhibited effectively under both mitigation regimens, different methanogenic populations were either suppressed or stimulated, which demonstrates that functionally similar disturbances of an ecosystem may result in distinct responses of the populations involved.     

Anaerobic microbial counts of different potential anaerobic inocula

Sludges of various origin were analysed on the basis of microbial counts of anaerobes in order to investigate potential and alternative sources for inoculating anaerobic digestors. Sludges from neutralization and oil and fat separation tanks of a sugar cane factory, and from a stabilisation pond of a purified terephthalic-acid-producing plant were found to be adequate potential inocula. Activated sludges were found to have both hydrogenotrophic and acetoclastic methanogens and obligate hydrogen-producing acetogens (OHPA). In all sludges tested, hydrogenotrophic methanogens were the dominant strict anaerobes. The ratio between most probable number counts of acetoclastic methanogens and OPHA seems to be different between dispersed sludges and granular sludges. Correspondence to: J. P. Guyot     

Competitive exclusion and coexistence of pathogens in a homosexually-transmitted disease model

A sexually-transmitted disease model for two strains of pathogen in a one-sex, heterogeneously-mixing population has been studied completely by Jiang and Chai in (J Math Biol 56:373-390, 2008). In this paper, we give a analysis for a SIS STD with two competing strains, where populations are divided into three differential groups based on their susceptibility to two distinct pathogenic strains. We investigate the existence and stability of the boundary equilibria that characterizes competitive exclusion of the two competing strains; we also investigate the existence and stability of the positive coexistence equilibrium, which characterizes the possibility of coexistence of the two strains. We obtain sufficient and necessary conditions for the existence and global stability about these equilibria under some assumptions. We verify that there is a strong connection between the stability of the boundary equilibria and the existence of the coexistence equilibrium, that is, there exists a unique coexistence equilibrium if and only if the boundary equilibria both exist and have the same stability, the coexistence equilibrium is globally stable or unstable if and only if the two boundary equilibria are both unstable or both stable.     

Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane

Hydrogenotrophic methanogens can use gaseous substrates, such as H₂ and CO₂, in CH₄ production. H₂ gas is used to reduce CO₂. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH₄ production from CO₂ and H₂. CO₂ and H₂ were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5–5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH₄ production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp., restricted the development of acetoclastic methanogens in the acidic CH₄ production process. The results show that acidic operation of a CH₄ production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens.     

Research of population with impulsive perturbations based on dynamics of a neutral delay equation and ecological quality system

This paper studies the global behaviors of a nonlinear autonomous neutral delay differential population model with impulsive perturbation. This model may be suitable for describing the dynamics of population with long larval and short adult phases. It is shown that the system may have global stability of the extinction and positive equilibria, or grow without being bounded under some conditions.     

Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes

ABSTRACT: BACKGROUND: Buffering to achieve pH control is crucial for successful trichloroethene (TCE) anaerobic bioremediation. Bicarbonate (HCO3-) is the natural buffer in groundwater and the buffer of choice in the laboratory and at contaminated sites undergoing biological treatment with organohalide respiring microorganisms. However, HCO3- also serves as the electron acceptor for hydrogenotrophic methanogens and hydrogenotrophic homoacetogens, two microbial groups competing with organohalide respirers for hydrogen (H2). We studied the effect of HCO3- as a buffering agent and the effect of HCO3--consuming reactions in a range of concentrations (2.5-30 mM) with an initial pH of 7.5 in H2-fed TCE reductively dechlorinating communities containing Dehalococcoides, hydrogenotrophic methanogens, and hydrogenotrophic homoacetogens. RESULTS: Rate differences in TCE dechlorination were observed as a result of added varying HCO3- concentrations due to H2-fed electrons channeled towards methanogenesis and homoacetogenesis and pH increases (up to 8.7) from biological HCO3- consumption. Significantly faster dechlorination rates were noted at all HCO3- concentrations tested when the pH buffering was improved by providing 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) as an additional buffer. Electron balances and quantitative PCR revealed that methanogenesis was the main electron sink when the initial HCO3- concentrations were 2.5 and 5 mM, while homoacetogenesis was the dominant process and sink when 10 and 30 mM HCO3- were provided initially. CONCLUSIONS: Our study reveals that HCO3- is an important variable for bioremediation of chloroethenes as it has a prominent role as an electron acceptor for methanogenesis and homoacetogenesis. It also illustrates the changes in rates and extent of reductive dechlorination resulting from the combined effect of electron donor competition stimulated by HCO3- and the changes in pH exerted by methanogens and homoacetogens.     

Stable Carbon Isotope Fractionation by Methylotrophic Methanogenic Archaea

In natural environments methane is usually produced by aceticlastic and hydrogenotrophic methanogenic archaea. However, some methanogens can use C₁ compounds such as methanol as the substrate. To determine the contributions of individual substrates to methane production, the stable-isotope values of the substrates and the released methane are often used. Additional information can be obtained by using selective inhibitors (e.g., methyl fluoride, a selective inhibitor of acetoclastic methanogenesis). We studied stable carbon isotope fractionation during the conversion of methanol to methane in Methanosarcina acetivorans, Methanosarcina barkeri, and Methanolobus zinderi and generally found large fractionation factors (−83‰ to −72‰). We further tested whether methyl fluoride impairs methylotrophic methanogenesis. Our experiments showed that even though a slight inhibition occurred, the carbon isotope fractionation was not affected. Therefore, the production of isotopically light methane observed in the presence of methyl fluoride may be due to the strong fractionation by methylotrophic methanogens and not only by hydrogenotrophic methanogens as previously assumed.     

Adaption of microbial community during the start-up stage of a thermophilic anaerobic digester treating food waste

A successful start-up enables acceleration of anaerobic digestion (AD) into steady state. The microbial community influences the AD performance during the start-up. To investigate how microbial communities changed during the start-up, microbial dynamics was analyzed via high-throughput sequencing in this study. The results confirmed that the AD was started up within 25 d. Thermophilic methanogens and bacterial members functioning in hydrolysis, acidogenesis, and syntrophic oxidation became predominant during the start-up stage, reflecting a quick adaption of microorganisms to operating conditions. Such predominance also indicated the great contribution of these members to the fast start-up of AD. Redundancy analysis confirmed that the bacterial abundance significantly correlated with AD conditions. The stable ratio of hydrogenotrophic methanogens to aceticlastic methanogens is also important to maintain the stability of the AD process. This work will be helpful to understand the contribution of microbial community to the start-up of AD.     

Methanosarcina as the dominant aceticlastic methanogens during mesophilic anaerobic digestion of putrescible waste

Taking into account isotope ¹³C value a mathematical model was developed to describe the dynamics of methanogenic population during mesophilic anaerobic digestion of putrescible solid waste and waste imitating Chinese municipal solid waste. Three groups of methanogens were considered in the model including unified hydrogenotrophic methanogens and two aceticlastic methanogens Methanosaeta sp. and Methanosarcina sp. It was assumed that Methanosaeta sp. and Methanosarcina sp. are inhibited by high volatile fatty acids concentration. The total organic and inorganic carbon concentrations, methane production, methane and carbon dioxide partial pressures as well as the isotope ¹³C incorporation in PSW and CMSW were used for the model calibration and validation. The model showed that in spite of the high initial biomass concentration of Methanosaeta sp. Methanosarcina sp. became the dominant aceticlastic methanogens in the system. This prediction was confirmed by FISH. It is concluded that Methanosarcina sp. forming multicellular aggregates may resist to inhibition by volatile fatty acids (VFAs) because a slow diffusion rate of the acids limits the VFA concentrations inside the Methanosarcina sp. aggregates.     

The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review

Among different conversion processes for biomass, biological anaerobic digestion is one of the most economic ways to produce biogas from various biomass substrates. In addition to hydrolysis of polymeric substances, the activity and performance of the methanogenic bacteria is of paramount importance during methanogenesis. The aim of this paper is primarily to review the recent literature about the occurrence of both acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of particulate biomass to methane (not wastewater treatment), while this review does not cover the activity of the acetate oxidizing bacteria. Both acetotrophic and hydrogenotrophic methanogens are essential for the last step of methanogenesis, but the reports about their roles during this phase of the process are very limited. Despite, some conclusions can still be drawn. At low concentrations of acetate, normally filamentous Methanosaeta species dominate, e.g., often observed in sewage sludge. Apparently, high concentrations of toxic ionic agents, like ammonia, hydrogen sulfide (H₂S) and volatile fatty acids (VFA), inhibit preferably Methanosaetaceae and especially allow the growth of Methanosarcina species consisting of irregular cell clumps, e.g., in cattle manure. Thermophilic conditions can favour rod like or coccoid hydrogenotrophic methanogens. Thermophilic Methanosarcina species were also observed, but not thermophilic Methanosaetae. Other environmental factors could favour hydrogentrophic bacteria, e.g., short or low retention times in a biomass reactor. However, no general rules regarding process parameters could be derivated at the moment, which favours hydrogenotrophic methanogens. Presumably, it depends only on the hydrogen concentration, which is generally not mentioned in the literature.     

Quantitative analysis of the trophic groups with a fluorescence in situ hybridization (FISH) and the competitive kinetics of a propionate enriched anaerobic culture

An anaerobic culture had been enriched with propionate, which was a critical compound inhibiting the total anaerobic process when significantly accumulated. In addition, the distribution of the trophic groups was investigated using the tool of fluorescence in situ hybridization with 16S rRNA targeted oligonucleotide probes to understand the bacterial communication. Then the kinetic constants in the competitive inhibition models were obtained. The ratio of the methanogens was increased as the culture was enriched, whereas that of the acidogens was decreased. The sum of the acetoclastic and hydrogenotrophic methanogens was 34% and the methanogens was 50% at the 68^th day. Approximately 16% of the cells detected by DAPI staining were unknown. The degradation of ethanol is thermodynamically more favorable. However, the substrate affinity to propionate was presumably higher than to ethanol since the culture had been acclimated to the propionate-rich environment. Ethanol and acetate did not show any inhibition effect on the methane fermentation of propionate.     

Diversity of rumen microbiota using metagenome sequencing and methane yield in Indian sheep fed on straw and concentrate diet

An in vivo study aiming to investigate the rumen methanogens community structure was conducted in Mandya sheep fed on straw and concentrate diet. The ruminal fluid samples were collected and processed for unravelling the rumen microbiota and methanogens diversity. Further, the daily enteric methane emission and methane yield was also quantified using the SF₆ tracer technique. Results indicated that the Bacteroidetes (～57%) and Firmicutes (25%) were two prominent affiliates of the bacterial community. Archaea represented about 2.5% of the ruminal microbiota. Methanobacteriales affiliated methanogens were the most prevalent in sheep rumen. The study inveterate that the ruminal archaea community in sheep is composed of 9 genera and 18 species. Methanobrevibacter represented the largest genus of the archaeome, while methylotrophs genera constituted only 13% of the community. Methanobrevibacter gottschalkii was the prominent methanogen, and Methaobrevibacter ruminantium distributed at a lower frequency (～2.5%). Among Methanomassiliicoccales, Group 12 sp. ISO4-H5 constituted the most considerable fraction (～11%). KEGG reference pathway for methane metabolism indicated the formation of methane through hydrogenotrophic and methylotrophic pathways, whereas the acetoclastic pathway was not functional in sheep. The enteric methane emission and methane yield was 19.7 g/d and 20.8 g/kg DMI, respectively. Various species of Methanobrevibacter were differently correlated, and the distribution of hydrogenotrophic methanogens mainly explained the variability in methane yield between the individual sheep. It can be inferred from the study that the hydrogenotrophic methanogens dominate the rumen archaeal community in sheep and methylotrophic/aceticlastic methanogens represent a minor fraction of the community. Further studies are warranted for establishing the metabolic association between the prevalent hydrogenotrophs and methylotrophs to identify the key reaction for reducing methane emission.     

Global Stability for Delay SIR and SEIR Epidemic Models with Nonlinear Incidence Rate

In this paper, based on SIR and SEIR epidemic models with a general nonlinear incidence rate, we incorporate time delays into the ordinary differential equation models. In particular, we consider two delay differential equation models in which delays are caused (i) by the latency of the infection in a vector, and (ii) by the latent period in an infected host. By constructing suitable Lyapunov functionals and using the Lyapunov–LaSalle invariance principle, we prove the global stability of the endemic equilibrium and the disease-free equilibrium for time delays of any length in each model. Our results show that the global properties of equilibria also only depend on the basic reproductive number and that the latent period in a vector does not affect the stability, but the latent period in an infected host plays a positive role to control disease development.     

Modeling and analysis of a predator-prey model with disease in the prey

A system of retarded functional differential equations is proposed as a predator-prey model with disease in the prey. Mathematical analyses of the model equations with regard to invariance of non-negativity, boundedness of solutions, nature of equilibria, permanence and global stability are analyzed. If the coefficient in conversing prey into predator k=k(0) is constant (independent of delay tau;, gestation period), we show that positive equilibrium is locally asymptotically stable when time delay tau; is suitable small, while a loss of stability by a Hopf bifurcation can occur as the delay increases. If k=k(0)e(-dtau;) (d is the death rate of predator), numerical simulation suggests that time delay has both destabilizing and stabilizing effects, that is, positive equilibrium, if it exists, will become stable again for large time delay. A concluding discussion is then presented.