Selective inhibition of reactions involved in methanogenesis and fatty acid production on rice roots

Tylosin in anaerobic reactors: degradation kinetics, effects on methane production and on the microbial community

Tylosin eliminated in animal waste, during therapeutic treatment, can be efficiently removed in anaerobic systems. The present study investigated the influence of tylosin concentration and assessed its degradation kinetics and the microorganisms involved in each stage of its anaerobic digestion (hydrolysis/acidogenesis; acetogenesis; methanogenesis). The results showed a stimulating effect on methane production with increasing tylosin concentration in the poultry litter up to 80 mg kg-1 tylosin (232.9 NL CH4 kg SV-1). As for tylosin degradation, greater removal of antibiotics was observed in the methanogenic phase (88%), followed by acetogenic (84%) and hydrolytic/acidogenic (76%) phases. The higher rate of tylosin degradation obtained in the methanogenic step, is mainly related to the co-metabolic effect exerted by the presence of acetate and its degradation by acetoclastic methanogens. Indeed, metagenomic analyses suggested a syntrophic action between archaea of ​​the genus Methanobacterium, and bacteria such as Clostridium and Flexilinea, which seemed decisive for tylosin degradation.

Stability of ex situ biological methanation of H2/CO2 with a mixed microbial culture in a pilot scale bubble column reactor

Biological methanation is a promising technology for gas and carbon valorisation. Therefore, process stability is required to allow its scale up and development. A pilot scale bubble column reactor was used for ex situ biological methanation with Mixed Microbial Culture (MMC). A 16S rRNA high throughput sequencing analysis revealed the MMC reached a stable composition with 50-60% Methanobacterium in closed liquid mode, a robust genus adapted to large scale constraints. Class MBA03 was identified as an indicator of process stability. Methanogenic genera moved toward 50% of Methanothermobacter when intensifying the process, and proteolytic activity was identified while 94% of H₂/CO₂ was converted into methane at 4NL.L^-1.d^-1. This study gives clarifications on the origin of volatile fatty acids (VFA) apparitions. Acetate and propionate accumulated when methanogenic activity weakened due to nutritive deficiency, and when P_H2 reached 0.7 bar. The MMC withstood a storage period of 34d at room temperature indicating its suitability for industrial constraints.

A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals

Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.

Syntrophic propionate-oxidizing bacteria in methanogenic systems

The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.

Physiological Effects of 2-Bromoethanesulfonate on Hydrogenotrophic Pure and Mixed Cultures

Mixed or pure cultures can be used for biomethanation of hydrogen. Sodium 2-bromoethanesulfonate (BES) is an inhibitor of methanogenesis used to investigate competing reactions like homoacetogenesis in mixed cultures. To understand the effect of BES on the hydrogenotrophic metabolism in a biomethanation process, anaerobic granules from a wastewater treatment plant, a hydrogenotrophic enrichment culture, and pure cultures of Methanococcus maripaludis and Methanobacterium formicicum were incubated under H₂/CO₂ headspace in the presence or absence of BES, and the turnover of H₂, CO₂, CH₄, formate and acetate was analyzed. Anaerobic granules produced the highest amount of formate after 24 h of incubation in the presence of BES. Treating the enrichment culture with BES led to the accumulation of formate. M. maripaludis produced more formate than M. formicicum when treated with BES. The non-inhibited methanogenic communities produced small amounts of formate whereas the pure cultures did not. The highest amount of acetate was produced by the anaerobic granules concomitantly with formate consumption. These results indicate that formate is an important intermediate of hydrogenotrophic metabolism accumulating upon methanogenesis inhibition.

Elucidating degradation properties, microbial community, and mechanism of microplastics in sewage sludge under different terminal electron acceptors conditions

This study is designed to investigate the roles of five key terminal electron acceptors (TEAs): O₂, NO₃^-, Fe³⁺, SO₄^2-, and CH₂O, typically existing in the sludge on the degradation rates and pathways of three representative MPs: polylactic acid (PLA), polyvinyl chloride (PVC), and polyhydroxyalkanoate (PHA). The results revealed that approximately 51.46 ∼ 52.70% of PHA was degraded within 43 days, despite PLA and PVC being degraded insignificantly. Different TEAs significantly affected the end-products of PHA. The production rate of acetate gradually decreased from 90.48, 42.67, 38.30, and 17.56 to 3.30% when the TEAs were tested with CH₂O, O₂, SO₄^2-, NO₃^- and Fe³⁺, respectively. The main functional bacteria involved in the PHA degradation were hydrolysis bacteria Burkholderiaceae and homo-acetogenic bacteria Clostridiacea, which accounted for 0.83% and 18.91% of the microbes. The current investigation could help improve understanding of MPs degradation pathways and mechanisms and minimize their risks in practice.

Archaea inhibition: Strategies for the enhancement of volatile fatty acids production from microalgae

In the present study, anaerobic sludge was subjected to thermal and chemical pretreatments to favour VFAs production from a protein-rich waste (i.e. microalgae biomass). Sludge pretreatments have been previously used in hydrogen production; however, information about how they can affect VFAs production from microalgae is still lacking. Thermal pretreatment was studied at: (i) 80 °C for 10 and 30 min; (ii) 120 °C for 10 and 30 min; and (iii) 100 °C for 20 min. 2-bromoethanesulfonate (BES) at 10 mM and 30 mM was used as chemical pretreatment. Besides, a combination of both pretreatment methods (80 °C and 120 °C at 10 mM and 30 mM BES) was also tested. Thermal pretreatment increased organic matter conversions into VFAs (up to 71% COD-VFAs/COD_in) when compared to control values (40% in the untreated anaerobic sludge). Acetic acid was the most abundant VFAs at high temperatures (120 °C) and when BES was employed (up to 60% and 40%, respectively, in terms of COD). On the other hand, propionic acid was the most abundant product at low temperatures and in the untreated anaerobic sludge (up to 60% in terms of COD). This research work might set guidelines in order to choose a suitable sludge pretreatment for VFAs production from microalgae.

A conceptual method to simultaneously inhibit methane and hydrogen sulfide production in sewers: The carbon metabolic pathway and microbial community shift

In this study, the impact of COD/SO₄^2- ratio in sewage on methane and hydrogen sulfide production in sewer biofilms was investigated by using three identical lab-scale gravity sewer systems. The results showed that the COD/SO₄^2- played a key role in the competition between methanogenic archaea (MA) and sulfate reducing bacteria (SRB). Both the lowest methane and hydrogen sulfide production were obtained at COD/SO₄^2- ratio of 6. The carbon transformation revealed that the activity of both MA and SRB was inhibited at this COD/SO₄^2- ratio. Methanosarcina and Methanobacterium were the two dominant MA, while Desulfonema, Desulfotomaculum and Desulfovibrio were the dominant SRB in this case. The specific SRB activity measured by batch tests proved that acetate was mainly degraded by the MA, while propionate was the preferred substrate for the SRB.

Improvement of caproic acid production in a Clostridium kluyveri H068 and Methanogen 166 co-culture fermentation system

The aim of this study was to develop a bioprocess capable of producing caproic acid using a binary fermentation system consisting of Clostridium kluyveri H068 and Methanogen 166 which could then be applied to the brewing of Chinese strong flavor liquor. We initially explored the mechanism by which the Methanogen 166 strain facilitates caproic acid accumulation, revealing its ability to convert accumulated H₂ that is produced by C. kluyveri H068 into methane, thereby eliminating the hydrogen-mediated feedback inhibition that normally constrains C. kluyveri H068 and thus enhancing caproic acid production. In addition, laboratory experiments were conducted to optimize this binary fermentation system, allowing us to determine that the optimum conditions for caproic acid production are a mixed inoculum size of 10% with a C. kluyveri H588/Methanogen 166 inoculation ratio of 2:1 (v/v), a sodium acetate concentration of 20 g/L, a 4% ethanol content (v/v), and a yeast extract concentration of 10 g/L. We further scaled this optimized condition up to use in a 1000 L fermenter and the obtained caproic acid broth was subjected to pit-entry fermentation. Our results demonstrated that this pit-entry fermentation approach was an efficient means of improving the quality of Chinese strong flavor liquor.

Enzyme- and gene-based approaches for developing methanogen-specific compounds to control ruminant methane emissions: a review

Methane emissions from ruminants are of worldwide concern due to their potential to adversely affect climate patterns. Methane emissions can be mitigated in several ways, including dietary manipulation, the use of alternative hydrogen sinks, and by the direct inhibition of methanogens. In the present review, we summarise and emphasise studies where defined chemically synthesised compounds have been used to mitigate ruminant methane emissions by direct targeting of methanogens and discuss the future potential of such inhibitors. We also discuss experiments, where methanogen-specific enzymes and pure cultures of methanobacterial species have been used to aid development of inhibitors. Application of certain compounds can result in dramatic reductions of methane emissions from ruminant livestock, demonstrating ‘proof of principle’ of chemical inhibitors of methanogenesis. More recently, genome sequencing of rumen methanogens has enabled an in-depth analysis of the enzymatic pathways required for methane formation. Chemogenomic methods, similar to those used in the fight against cancer and infectious diseases, can now be used to specifically target a pathway or enzyme in rumen methanogens. However, few rumen methanogen enzymes have been structurally or biochemically characterised. Any compound, whether natural or man-made, that is used as a mitigation strategy will need to be non-toxic to the host animal (and humans), cost-effective, environmentally friendly, and not accumulate in host tissues or milk products. Chemically synthesised inhibitors offer potentially significant advantages, including high levels of sustained inhibition, the ability to be easily and rapidly produced for global markets, and have the potential to be incorporated into slow-release vehicles for grazing animals.

Simultaneous anaerobic transformation of tetrachloroethene and carbon tetrachloride in a continuous flow column

Tetrachloroethene (PCE) and carbon tetrachloride (CT) were simultaneously transformed in a packed column that was bioaugmented with the Evanite culture (EV). The data presented here have been obtained over a period of 1930days. Initially the column was continuously fed synthetic groundwater with PCE (0.1mM), sulfate (SO4(2-)) (0.2mM) and formate (2.1mM) or lactate (1.1mM), but not CT. In these early stages of the study the effluent H2 concentrations ranged from 7 to 19nM, and PCE was transformed to ethene (ETH) (81 to 85%) and vinyl chloride (VC) (11 to 17%), and SO4(2-) was completely reduced when using either lactate or formate as electron donors. SO4(2-) reduction occurred concurrently with cis-DCE and VC dehalogenation. Formate was a more effective substrate for promoting dehalogenation based on electron donor utilization efficiency. Simultaneous PCE and CT tests found CT (0.015mM) was completely transformed with 20% observed as chloroform (CF) and trace amounts of chloromethane (CM) and dichloromethane (DCM), but no methane (CH4) or carbon disulfide (CS2). PCE transformation to ETH improved with CT addition in response to increases in H2 concentrations to 160nM that resulted from acetate formation being inhibited by either CT or CF. Lactate fermentation was negatively impacted after CT transformation tests, with propionate accumulating, and H2 concentrations being reduced to below 1nM. Under these conditions both SO4(2-) reduction and dehalogenation were negatively impacted, with sulfate reduction not occurring and PCE being transformed to cis-dichloroethene (c-DCE) (52%) and VC (41%). Upon switching to formate, H2 concentrations increased to 40nM, and complete SO4(2-) reduction was achieved, while PCE was transformed to ETH (98%) and VC (1%), with no acetate detected. Throughout the study PCE dehalogenation to ethene was positively correlated with the effluent H2 concentrations.

Improving volatile fatty acids production by exploiting the residual substrates in post-fermented sludge: Protease catalysis of refractory protein

The real cause to the low yield of volatile fatty acids (VFAs), from inhibition or low biodegradation, is uncertain in sludge anaerobic fermentation. In this study, poor biodegradability of proteins and fast decrease of the indigenous hydrolase activity in the residual post-fermented sludge were found to be the major reasons. With the addition of trypsin or alkaline protease in residual post-fermented sludge after primary alkaline fermentation, degradation efficiency of refractory protein increased by 33.6% and 34.8%, respectively. Accordingly, the VFAs yields were improved by 69.7% and 106.1%, respectively. Furthermore, the activities of added trypsin and alkaline protease could maintain at 13.52 U/mL and 19.11 U/mL in the alkaline fermentation process. This study demonstrated that exploiting the refractory proteins in residual post-fermented sludge by protease addition seems to be a very promising way for improving VFAs yield of conventional alkaline fermentations with waste activated sludge.

Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH₃F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH₃F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH₃F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH₃F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH₃F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.

Methanogenic Archaea and oral infections - ways to unravel the black box

Archaea, organisms that make up the third domain of cellular life are members of the human oral microflora. They are strikingly less diverse than oral bacteria and appear to be relatively rare with respect to their numerical abundance. Since they have been exclusively found in association with oral infections such as periodontitis and apical periodontitis and given their unique physiology and energy metabolism, it is highly plausible that they are more than just secondary colonizers of infected areas, but instead are actively involved in the overall poly-microbial infection process. Conversely, it is a highly challenging task to clearly demonstrate their possible active participation – mostly due to the difficulty to grow them in routine microbiology laboratories. This current review points out the importance for understanding the medical impact of methanogens and aims at devising strategies for elucidating the true function of archaea in the oral ecosystem.

Composition of archaeal community in a paddy field as affected by rice cultivar and N fertilizer

Methanogenesis in paddy fields is significantly influenced by environmental and field management factors such as rice cultivar and nitrogenous fertilizer. However, it has been unclear whether such effects are reflected in the structure of methanogenic archaeal populations. In the present study, molecular analyses including cloning and sequencing and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of archaeal 16S rRNA genes were used to characterize the methanogenic archaeal assemblages and to identify the effect of environmental variables including rice cultivar and N fertilizer on archaeal community compositions in a Chinese paddy field soil. The correlation between methanogenic archaeal composition and environmental variables was explored by correspondence analysis. The results showed that the spatial or niche factor (rice roots versus rhizosphere, surface, and the deeper layer soils) had the greatest influence on the archaeal community composition. There was an obvious enrichment or selection of hydrogenotrophic as opposed to acetoclastic methanogens by rice roots. The archaeal community also changed, though slightly, between the rhizosphere and bulk soils and between the surface soil and the deeper layer soil. However, rice cultivar and N fertilizer appear to have an effect only on methanogens tightly associated with rice roots.

Role of the methylcitrate cycle in propionate metabolism and detoxification in Mycobacterium smegmatis

Catabolism of odd-chain-length fatty acids yields acetyl-CoA and propionyl-CoA. A common pathway of propionyl-CoA metabolism in micro-organisms is the methylcitrate cycle, which includes the dedicated enzymes methylcitrate synthase (MCS), methylcitrate dehydratase (MCD) and methylisocitrate lyase (MCL). The methylcitrate cycle is essential for propionate metabolism in Mycobacterium tuberculosis. Unusually, M. tuberculosis lacks an MCL orthologue and this activity is provided instead by two isoforms of the glyoxylate cycle enzyme isocitrate lyase (ICL1 and ICL2). These bifunctional (ICL/MCL) enzymes are jointly required for propionate metabolism and for growth and survival in mice. In contrast, the non-pathogenic species Mycobacterium smegmatis encodes a canonical MCL enzyme in addition to ICL1 and ICL2. The M. smegmatis gene encoding MCL (prpB) is clustered with genes encoding MCS (prpC) and MCD (prpD). Here we show that deletion of the M. smegmatis prpDBC locus reduced but did not eliminate MCL activity in cell-free extracts. The residual MCL activity was abolished by deletion of icl1 and icl2 in the DeltaprpDBC background, suggesting that these genes encode bifunctional ICL/MCL enzymes. A DeltaprpB Deltaicl1 Deltaicl2 mutant was unable to grow on propionate or mixtures of propionate and glucose. We hypothesize that incomplete propionyl-CoA metabolism might cause toxic metabolites to accumulate. Consistent with this idea, deletion of prpC and prpD in the DeltaprpB Deltaicl1 Deltaicl2 background paradoxically restored growth on propionate-containing media. These observations suggest that the marked attenuation of ICL1/ICL2-deficient M. tuberculosis in mice could be due to the accumulation of toxic propionyl-CoA metabolites, rather than inability to utilize fatty acids per se.

Biohydrogen production in granular up-flow anaerobic sludge blanket (UASB) reactors with mixed cultures under hyper-thermophilic temperature (70 degrees C)

Hyper-thermophilic hydrogen production without methane was demonstrated for the first time in granular up-flow anaerobic sludge blanket (UASB) system fed with glucose using mixed cultures. The maximum hydrogen yield in this study was 2.47 +/- 0.15 mol H2/mol glucose. This high yield has never been previously reported in mixed culture systems and it was likely due to more favorable thermodynamic conditions at hyper-thermophilic temperatures. Different start-up strategies (bromoethanosulfonate (BES) addition and flow recycle) were evaluated. BES addition during start-up prevented the establishment of methanogenic cultures in granules. Flow recycle was important to achieve higher hydrogen yield through enriching better hydrogen-producing organisms and reduced the start-up period as well. This study indicated UASB system was a promising system for hydrogen production.

Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment

Methyl fluoride is frequently used to specifically inhibit acetoclastic methanogenesis, thus allowing determination of the relative contribution of acetate versus H2/CO2 to total CH4 production in natural environments. However, the effect of the inhibitor on growth of the target archaeal population has not yet been studied. Therefore, we incubated rice roots as an environmental model system under anoxic conditions in the presence and absence of CH3F, measured the activity and Gibbs free energy (DeltaG) of CH4 production, and determined the abundance of individual archaeal populations by using a combination of quantitative (real-time) PCR and analysis of terminal restriction fragment length polymorphism targeting the 16S rRNA gene. It was shown that CH3F specifically inhibited not only acetoclastic methanogenic activity but also the proliferation of Methanosarcina spp, which were the prevalent acetoclastic methanogens in our environmental model system. Therefore, inhibition experiments with CH3F seem to be a suitable method for quantifying acetoclastic CH4 production. It is furthermore shown that the growth and final population size of methanogens were consistent with energetic conditions that at least covered the maintenance requirements of the population.

Trophic interactions in the methanogenic microbial community of low-temperature terrestrial ecosystems

The formation of methane in various ecosystems is due to the functioning of an anaerobic community, which combines trophically different groups of microorganisms. The methanogenic microbial community is a complex biological system, which responds to low temperatures by changes in its trophic structure resulting in redistributing matter flows. The enhanced activity of homoacetogenic bacteria at low temperature plays a significant role in this redistribution. Due to their relatively high growth rates and metabolic versatility, homoacetogens can successfully compete with fermenting bacteria and hydrogenotrophic methanogenic archaea for common substrates. The concentration of hydrogen is an important regulatory factor in the psychroactive methanogenic community. At low temperature methanogenic archaea possessing a higher affinity for hydrogen than homoacetogens provide for interspecies H2 transport in syntrophic reactions of fatty acid decomposition. The formation of a balanced community at low temperature is a longtime process. Cold terrestrial ecosystems are dominated by psychroactive (psychrotolerant) microorganisms, which can grow over a wide range of ambient temperatures.

Pathway of CH4 formation in anoxic rice field soil and rice roots determined by 13C-stable isotope fractionation

In anoxic rice fields methane is produced by either reduction of CO2 or cleavage of acetate. We measured the delta 13C-values of CH4 and CO2, acetate and organic carbon during time course experiments with anoxic methanogenic soil and root samples and used these values to calculate the fractions of CH4 (and acetate) produced from CO2 reduction. Comparison with radiotracer and/or inhibitor studies constrained the kinetic fractionation factors used for calculation. The fractionation factors for the conversion of CO2 to CH4 and of acetate to CH4 were on the order of alpha = 1.07 (epsilon = -70%) and epsilon > or = - 20%, respectively. The pathway of CH4 production changed with time of anoxic incubation. Anoxic slurries of rice field soil first produced CH4 predominantly (>50%) from CO2, then predominantly (>80%) from acetate and finally (after about one month) according to the theoretically expected ratio (33% CO2 and 67% acetate). Anoxic rice roots, on the other hand, initially produced CH4 exclusively from CO2, followed by contribution of acetate of about 40-60%. Rice roots also produced acetate that partially originated (< or = 1 30%) from reduction of CO2 as determined by calculation of isotopic fractionation using fractionation factors from the literature. The results demonstrate that there is quite some variability in pathways of CH4 production, and also indicate that isotopic fractionation factors may be different in different habitats and change with time.