Effect of fruits and vegetables in the anaerobic digestion of food waste from university restaurant

The aim of this study was to evaluate the theoretical potential of methane production of the food waste generated by a university restaurant, as well as to verify the influence of the fruit and vegetable waste in the feeding composition of an anaerobic bioreactor treating this type of waste. Four feeding compositions combining three fractions of the food waste (fruit and vegetable fraction, soy protein and beans fraction, and rice fraction) at different concentrations were tested in anaerobic processes lasting 10 and 30 days. Additionally, a study of the theoretical potential of methane production from each fraction that composes the food waste was carried out, as well as the evaluation of the specific methanogenic activity of the anaerobic sludge. Despite its low theoretical potential of methane production (0.037 L_CH4/g), the presence of the fruit and vegetable mixture in three of the feeding compositions led to greater organic matter degradation (above 69%) and CH₄ yields (above 0.20 L_CH4/g_VS) in both periods tested, in comparison with the achieved by the feeding composition lacking this fraction. The results suggest that the presence of the fruit and vegetable mixture contributed with the supplementation of micro- and macroelements to the anaerobic sludge during the digestion of food waste.

Unveiling the characterization and development of prokaryotic community during the start-up and long-term operation of a pilot-scale anaerobic membrane bioreactor for the treatment of real municipal wastewater

The anaerobic membrane bioreactor (AnMBR) is a promising sustainable process and technology for the treatment of municipal wastewater from the perspective of carbon neutrality. In this study, a large pilot-scale AnMBR was constructed and the microbial community development of the anaerobic digested sludge in the AnMBR was determined during the treatment of municipal wastewater. The AnMBR system was conducted for 217 days during a long-term operation with the feed of real municipal wastewater. The characterization and dynamics of the microorganisms revealed that a stable prokaryotic community was gradually achieved. In the community of methane-producing archaea (or methanogens), the acetotrophic methanogen Methanosaeta was significantly enriched at an ambient temperature of 25 °C with an overwhelming relative abundance in the entire community. The abundance of Methanosaeta was even higher than the most abundant bacterial phyla Chloroflexi, Firmicutes, Proteobacteria and Bacteroidetes. This phenomenon is quite different from that found in other typical anaerobic systems. The massive enrichment of methanogens is the key to maintaining stable methane production in the treatment of municipal wastewater by the AnMBR. The interspecies cooperation of major functional bacterial groups including protein/carbohydrate/cellulose-degrading (genera Anaerovorax, Aminomonas, Levilinea, Flexilinea and Ruminococcus etc.), sulfate-reducing (Desulfovibrio and Desulfomicrobium etc.) and syntrophic (Syntrophorhabdus and Syntrophus etc.) bacteria with acetotrophic and hydrogenotrophic archaea enhances the stability of reactor operation and help to acclimate the entire prokaryotic community to the characteristics of real municipal wastewater.

A new approach to suppress methane emissions from rice cropping systems using ethephon

Rice is the main staple food for more than half of the world's population. Yet, rice cultivation is subjected to criticism because of its important role in methane (CH₄) emissions. Although several agronomic practices such as controlled irrigation and conservation tillage have been widely adopted to mitigate CH₄ emissions from rice cultivation, the benefits gained by these practices are highly dependent on site-specific soil and climate conditions, and often offset by yield reduction. The use of plant growth regulating compounds having the potential to increase the crop yield and mitigate CH₄ emissions may be an innovative approach to sustainable agriculture. Ethylene (C₂H₄), a plant growth regulator is known to have a strong inhibitory effect on methanogenesis. However, due to gaseous form and low water solubility, C₂H₄ has not been used to suppress methanogenesis in paddy fields. To develop C₂H₄ as a prospective soil amendment for reducing methane (CH₄) emissions, ethephon (2-Chloroethylphosphonic acid), a precursor of C₂H₄ was tested. We found that ethephon reduced CH₄ formation by 43%, similar to other well known methanogenic inhibitors (2-Bromoethanesulfonate, 2-Chlomoethanesulfonate, 2-Mercaptoethanesulfonate). However, ethephon rapidly hydrolyzed to C₂H₄ and methanogenic activity recuperated completely after C₂H₄ removal. To slow down the release of C₂H₄, ethephon was mixed with bio-degradable polymers such as cellulose acetate and applied to paddy soils. We found that compared with the control, the C₂H₄ release of ethephon slowed down to 90 days, and the CH₄ emissions were reduced by 90%. The application of ethephon at lower concentrations did not significantly alter bacterial communities, their relative abundance, and the abundance of methanotrophs, but it significantly reduced archaeal communities and the relative abundance and expression level of methanogens in paddy soils. Results suggest that cellulose acetate-mixed ethephon has great promise to suppress CH₄ emissions in rice paddies while ensuring sustainable yields.

Progress and Challenges in Archaeal Genetic Manipulation

Archaea inhabit a wide variety of habitats and are well-placed to provide insights into the origins of eukaryotes. In this primer, we examine the available model archaeal genetic systems. We consider the limitations and barriers involved in genetically modifying different archaeal species, the techniques and breakthroughs that have contributed to their tractability, and potential areas for future development.

Meconial Methanobrevibacter smithii suggests intrauterine methanogen colonization in preterm neonates

•

The first ever detection in the meconium of the methanogen M. smithii.

•

These data position M. smithii among the early inhabitants of the human gut.

•

These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.

To understand the dynamics of methanogens in the human intestinal microbiota, we investigated the presence of methanogens in meconium using a polyphasic approach including microscopy and PCR-sequencing in 33 meconium samples collected from 33 pre-term neonates, in accordance with current ethics regulation. In the presence of negative controls, 90.9% samples were real-time PCR-positive for methanogens and 69.7 % were PCR-sequencing positive, identified as Methanobrevibacter (M.) smithii. Further, auto-fluorescent analysis detected methanogens in the two meconium samples analyzed, with a morphology suggesting M. smithii. Multispacer Sequence Typing found M. smithii genotypes ST1 and ST2, previously described as intestinal microbiota inhabitants. C-section delivery and non-use of peripartum antibiotics significantly correlated with PCR-detection of methanogens in meconium. These data position M. smithii among the early inhabitants of the human gut, detectable immediately after birth and suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.

Sessile methanogens dominated cathodic biofilm: Distribution and network in physiological transitions

A mature cathodic biofilm plays the key role in biocathode electron transfer. The physiological transitions of it were of great interests as the sessile and dispersed (planktonic) work in a balance while it is still lack of understanding. In this study, an improved sampling method was used for detecting sessile, detached, and dispersed microorganisms. The results indicated a certain number of methanogens (82.6%) and its associated phyla (60%-90%) are immobilized as sessile biofilm. The Tax4Fun predicted a lower abundance of mobility associated genes and a significant enrichment (t-test, P = 0.003) of c-di-GMP in sessile biofilm. Overall, the microbial interaction and motility were predicted as two factors to affect the physiological transitions of cathodic biofilm. This finding could shed a light on the investigation of cathodic biofilm in a dynamic transition rather than a static community, playing a pivotal role in understanding the relation between specific property of biofilm.

Methanogen Abundance Thresholds Capable of Differentiating In Vitro Methane Production in Human Stool Samples

BACKGROUND

Intestinal methane (CH₄) gas production has been associated with a number of clinical conditions and may have important metabolic and physiological effects.

AIMS

In this study, taxonomic and functional gene analyses and in vitro CH₄ gas measurements were used to determine if molecular markers can potentially serve as clinical tests for colonic CH₄ production.

METHODS

We performed a cross-sectional study involving full stool samples collected from 33 healthy individuals. In vitro CH₄ gas measurements were obtained after 2-h incubation of stool samples and used to characterize samples as CH₄ positive (CH₄+) and CH₄ negative (CH₄-; n = 10 and 23, respectively). Next, we characterized the fecal microbiota through high-throughput DNA sequencing with a particular emphasis on archaeal phylum Euryarchaeota. Finally, qPCR analyses, targeting the mcrA gene, were done to determine the ability to differentiate CH₄+ versus CH₄- samples and to delineate major methanogen species associated with CH₄ production.

RESULTS

Methanobrevibacter was found to be the most abundant methane producer and its relative abundance provides a clear distinction between CH₄+ versus CH₄- samples. Its sequencing-based relative abundance detection threshold for CH₄ production was calculated to be 0.097%. The qPCR-based detection threshold separating CH₄+ versus CH₄- samples, based on mcrA gene copies, was 5.2 × 10⁵ copies/g.

CONCLUSION

Given the decreased time-burden placed on patients, a qPCR-based test on a fecal sample can become a valuable tool in clinical assessment of CH₄ producing status.

Detection of methanogens in peri-appendicular abscesses: Report of four cases

The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.

Mitigation of methane emission in a rice paddy field amended with biochar-based slow-release fertilizer

Despite improving soil quality and reducing nitrogen (N) loss in paddy soil, replacing chemical fertilizer with organic fertilizer would significantly accelerate greenhouse gas emission in terms of methane (CH₄). The application of slow-release fertilizer has been proposed an effective approach to control CH₄ emissions, in addition to reducing N loss. Yet, the understanding of CH₄ emissions from paddy fields with the additions of different fertilizers is still less known. Therefore, the effects of different fertilizer treatments, including chemical fertilizer treatment (CF), mixed chemical and organic fertilizer treatment (OF), biochar-based slow-release fertilizer treatment (SF), and no fertilizer control treatment (CK) on CH₄ emissions and methanogenic community structure in paddy soils were investigated through a field experiment. Results showed that slow-release fertilizer addition significantly decreased CH₄ emissions by 33.4%, during the whole rice growing season compared to those in OF. The cumulative CH₄ emissions were in a significantly positive relation to soil NH₄⁺-N. Slow-release fertilizer amendment decreased the relative abundances of Methanosarcina and Methanoregula and increased the relative abundances of hydrogenotrophic Methanocella and Rice Cluster I. Reduced CH₄ emissions with slow-release fertilizer amendment might be mainly attributed to the different forms of N in the fertilizer and available potassium (K) in the paddy soil. Our findings produce novel insights into the application of slow-release fertilizer in controlling CH₄ emissions from rice fields.

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

BACKGROUND

Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design.

RESULTS

We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail.

CONCLUSIONS

The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.

Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans

BACKGROUND

Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood.

RESULTS

We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH4 breath content 5-75 ppm) and low emitters (CH4 < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis.

CONCLUSIONS

This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.

Exploring the global vaginal microbiome and its impact on human health

Around the world, more than 175,000,000 women are diagnosed every year with gynaecological disease, in many cases contributing to high morbidity and mortality. For this reason, knowledge of the composition of the vaginal microbiome and its variations represents a real health challenge, as this is key to improving therapeutic management. This review traces the history of the poorly known vaginal microbiome and focuses on the latest findings concerning this ecosystem. Studies in the past decade have targeted complex bacterial communities within the vagina. However, due to the development of technology and the emergence of next generation sequencing (NGS), the exact definition of the vaginal microbiome has changed and can no longer be linked solely to the presence of bacteria. In order to reach a global view of the vaginal microbiome, it is essential to take into account all microorganisms that the vagina harbours, including fungi, viruses, archaea, and candidate phyla radiation. Although these communities represent only a minimal percentage of the vaginal microbiome, they may act as modifiers of its basic physiology and may play a key role in the maintenance of microbial communities, as well as metabolic and immune functions. Studies of the complex interactions between these different microorganisms have recently begun and are not yet fully understood. Results to date indicate that these microbial communities together constitute the first line of defence against infections. On the other hand, the slightest disturbance in this microbiome may lead to disease. For this reason, enhanced knowledge of these associations is critical to better identify predispositions to certain illnesses, which may open new therapeutic avenues. Currently however, only the tip of the iceberg is understood and current research on this ecosystem is revolutionising our knowledge and understanding of human health and disease.

Enhancing methane production from anaerobic digestion of waste activated sludge with addition of sodium lauroyl sarcosinate

In this study, sodium lauroyl sarcosinate (SLS) was used to promote anaerobic digestion of waste activated sludge for producing methane. It was found maximum cumulative methane production increased from 98.1 ± 3.1 to 166.0 ± 4.3 mL/g Volatile Suspended Solids (VSS) with dosage increasing from 0 (control) to 40 mg SLS/g TSS. But the addition of SLS (>10 mg SLS/g Total Suspended Solids (TSS)) resulted in prolonged lag phase time. Microbiological analysis showed that Syntrophobacter and Syntrophomonas both got enriched in reactors fed with SLS. Furthermore, hydrogenotrophic methanogens genus got more enrichment in contrast to acetoclastic methanogens. Mechanism analysis indicated that addition SLS could decrease surface tension, and promote release of organic matters as well as improve activities of hydrolytic enzymes. Besides, SLS could be nearly degraded completely within 3 days, and its degradation intermediates could be further transformed into methane gradually, thus enhancing methane production eventually.

Hyperthermophilic composting significantly decreases methane emissions: Insights into the microbial mechanism

Methane (CH₄) emissions from thermophilic composting (TC) are a substantial contributor to climate change. Hyperthermophilic composting (HTC) can influence CH₄-related microbial communities at temperatures up to 80 °C, and thus impact the CH₄ emissions during composting. This work investigated CH₄ emissions in sludge-derived HTC, and explored microbial community succession with quantitative PCR and high-throughput sequencing. Results demonstrated that HTC decreased CH₄ emissions by 52.5% compared with TC. In HTC, the CH₄ production potential and CH₄ oxidation potential were nearly 40% and 64.1% lower than that of TC, respectively. There was a reduction in the quantity of mcrA (3.7 × 10⁸ to 0 g^-1 TS) in HTC, which was more significant than the reduction in pmoA (2.0 × 10⁵ to 2.1 × 10⁴ g^-1 TS), and thus lead to reduce CH₄ emissions. It was found that the abundance of most methanogens and methanotrophs was inhibited in the hyperthermal environment, with a decline in Methanosarcina, Methanosaeta and Methanobrevibacter potentially being responsible for reducing the CH₄ emissions in HTC. This work provides important insight into mitigating CH₄ emissions in composting.

Effects of inhibitions by sodium ion and ammonia and different inocula on acetate-utilizing methanogenesis: Methanogenic activity and succession of methanogens

Acetate-fed anaerobic sequential batch experiments with four different inhibitory conditions (non-inhibitory (Lo), sodium-ion inhibitory (Na), ammonia inhibitory (Am), combined inhibitory (Hi)) were conducted using thirteen different inocula to investigate the inhibition effects by sodium-ion and ammonia and different inocula on acetate-utilizing methanogenesis and succession of methanogens. Sodium-ion and ammonia significantly extended lag-time λ and reduced specific-methanogenic-activity RCH4, and caused synergistic inhibition. The inhibition differed according to the initial methanogen community structures: the inhibition effects on λ and RCH4 were strongest ininocula with Methanosaeta concilii dominant and weakest in inocula with Methanoculleus bourgensis dominant. These inhibitory conditions determined the succession of methanogens: the most competitive methanogens were Methanosaeta concilii in Lo, Methanosarcina sp. in Na, Methanosarcina sp. and Methanoculleus bourgensis in Am, Methanoculleus bourgensis in Hi. This study provides valuable information for microbial management and optimization for AD processes treating wastewater that is rich in protein and/or salt.

Anaerobic co-digester microbiome during food waste valorization reveals Methanosaeta mediated methanogenesis with improved carbohydrate and lipid metabolism

This study determines the optimum food waste (FW) loading in an anaerobic digester for methane production. Interrelation between the degradation mechanism and microbial community composition was assessed through in-depth metabolic pathway analysis and gene quantification. Higher methane production and short lag phase were observed in the FW reactors with low substrate loadings (<4% v/v) while extended lag phase and incomplete substrate utilization were observed in the reactors fed with higher substrates (>6% v/v). The long-chain fatty acids (LCFAs) degradation was influenced by initial FW loading, and up to 99% LCFA degradation occurred at 4% FW reactor. The addition of 8 to 10% FW substrate inhibited methanogenesis due to the accumulation of volatile fatty acids (VFA) and low LCFA degradation. Under optimal conditions of substrate loading, Methanosaeta and Methanosarcina were abundant, indicating their role in methanogenesis and syntrophic acetogenesis, along with enhanced metabolic pathways specific for carbohydrate and lipid metabolism.

Hydrogen-driven microbial biogas upgrading: Advances, challenges and solutions

As a clean and renewable energy, biogas is an important alternative to fossil fuels. However, the high carbon dioxide (CO₂) content in biogas limits its value as a fuel. 'Biogas upgrading' is an advanced process which removes CO₂ from biogas, thereby converting biogas to biomethane, which has a higher commercial value. Microbial technologies offer a sustainable and cost-effective way to upgrade biogas, removing CO₂ using hydrogen (H₂) as electron donor, generated by surplus electricity from renewable wind or solar energy. Hydrogenotrophic methanogens can be applied to convert CO₂ with H₂ to methane (CH₄), or alternatively, homoacetogens can convert both CO₂ and H₂ into value-added chemicals. Here, we comprehensively review the current state of biogas generation and utilization, and describe the advances in biological, H₂-dependent biogas upgrading technologies, with particular attention to key challenges associated with the processes, e.g., metabolic limitations, low H₂ transfer rate, and finite CO₂ conversion rate. We also highlight several new strategies for overcoming technical barriers to achieve efficient CO₂ conversion, including process optimization to eliminate metabolic limitation, novel reactor designs to improve H₂ transfer rate and utilization efficiency, and employing advanced genetic engineering tools to generate more efficient microorganisms. The insights offered in this review will promote further exploration into microbial, H₂-driven biogas upgrading, towards addressing the global energy crisis and climate change associated with use of fossil fuels.

Prokaryotic Diversity and Metabolically Active Communities in Brines from Two Perennially Ice-Covered Antarctic Lakes

The genomic diversity of bacteria and archaea in brines (BC1, BC2, and BC3) from two adjacent and perennially frozen Antarctic lakes (L16 and L-2) in the Boulder Clay (BC) area was investigated together with the metabolically active fraction of both communities, by analyzing the bulk rRNA as a general marker of metabolic activity. Although similar bacterial and archaeal assemblages were observed at phylum level, differences were encountered when considering the distribution in species. Overall, the total bacterial communities were dominated by Bacteroidetes. A massive occurrence of flavobacterial sequences was observed within the metabolically active bacterial communities of the BC1 brine, whereas the active fractions in BC2 and BC3 strongly differed from the bulk communities being dominated by Betaproteobacteria (mainly Hydrogenophaga members). The BC lakes also hosted sequences of the most thermally tolerant archaea, also related to well-known hyperthermophiles. Interestingly, RNA sequences of the hyperthermophilic genus Ferroglobus were retrieved in all brine samples. Finally, a high abundance of the strictly anaerobic methanogens (such as Methanosarcina members) within the active community suggests that anoxic conditions might occur in the lake brines. Our findings indicate perennially ice-covered Antarctic lakes as plausible terrestrial candidates for the study of the potential for extant life on different bodies of our solar system.

Cow manure stabilizes anaerobic digestion of cocoa waste

Anaerobic digestion of a mono-feedstock often causes low methane yields and process instability. An effective strategy to overcome these barriers is co-digestion with animal manure. The obtained process improvement is often attributed to buffer capacity, nutrients, vitamins and trace metals, and microorganisms present in manure, but it remains unknown which factor plays the key role in digester performance. Here, we investigated anaerobic digestion of cocoa waste in four different treatments: mono-digestion, addition of synthetic nutrients, co-digestion with sterile cow manure, and co-digestion with raw cow manure. Co-digestion with raw manure resulted in the highest methane yield of 181 ± 39 L kg^-1 VS (volatile solids), similar to the co-digestion with sterile manure, i.e., 162 ± 52 L kg^-1 VS. The supplementation of synthetic nutrients to the anaerobic digestion of cocoa waste only temporarily increased methane yield, indicating that this will tackle a lack of nutrients in the short term, but has a limited long-term contribution to the stabilization of the process. Hence, because of the inability of synthetic nutrients to stabilize the digestion process and the similarity between the digesters fed sterile and raw manure, both at the physico-chemical and microbial level, the key contribution of manure co-digestion with cocoa seems to be the provision of buffering capacity.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

BACKGROUND

Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks.

RESULTS

The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa.

CONCLUSIONS

These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.

Interactions between methanotrophs and ammonia oxidizers modulate the response of in situ methane emissions to simulated climate change and its legacy in an acidic soil

Methane (CH₄) is one of the most important greenhouse gases which can be formed by methanogens and oxidized by methanotrophs, as well as ammonia oxidizers. Agricultural soils can be both a source and sink for atmospheric CH₄. However, it is unclear how climate change, will affect CH₄ emissions and the underlying functional guilds. In this field study, we determined the impact of simulated climate change (a warmer and drier condition) and its legacy effect on CH₄ emissions and the methanogenic and methanotrophic communities, as well as their relationships with ammonia oxidizers in an acidic soil with urea application. The climate change conditions were simulated in a greenhouse, and the legacy effect was simulated by removing the greenhouse after twelve months. Simulated climate change significantly decreased the in situ CH₄ emissions in the urea-treated soils while the legacy effect significantly decreased the in situ CH₄ emissions in the control plots, but had very little effect in the urea-treated soils. This indicates that the impact of simulated climate change and its legacy on CH₄ emissions was significantly modified by nitrogen fertilization. Methanotrophs were more sensitive than methanogens in response to simulated climate change and its legacy effect, especially in the urea treated soil. Significant negative correlations were observed between the abundances of ammonia oxidizers and methanotrophs. Additionally, results of partial least path modeling (PLS-PM) indicated that the interactions of methanogens and methanotrophs with ammonia oxidizing archaea (AOA) had significant positive relationships with in situ CH₄ emissions under the simulated climate change condition. Our work highlights the important role of AOA for CH₄ emissions under climate change conditions. Further research is needed to better understand this effect in other ecosystems.

Review: Methanogens and methane production in the digestive systems of nonruminant farm animals

The greenhouse gases (GHGs) derived from agriculture include carbon dioxide, nitrous oxide, and methane (CH₄). Of these GHGs, CH₄, in particular, constitutes a major component of the GHG emitted by the agricultural sector. Along with environmental concerns, CH₄ emission also leads to losses in gross energy intake with economic implications. While ruminants are considered the main source of CH₄ from agriculture, nonruminant animals also contribute substantially, and the CH₄ emission intensity of nonruminants remains comparable to that of ruminants. Means of mitigating CH₄ emissions from enteric fermentation have therefore been sought. Methane is produced by methanogens-archaeal microorganisms that inhabit the digestive tracts of animals and participate in fermentation processes. As the diversity of methanogen communities is thought to be responsible for the differences in CH₄ production among nonruminant animals, it is necessary to investigate the archaeal composition of specific animal species. Methanogens play an important role in energy metabolism and adipose tissue deposition in animals. Higher abundances of methanogens, along with their higher diversity, have been reported to contribute to lean phenotype in pigs. In particular, a greater abundance of Methanosphaera spp. and early dominance of Methanobrevibacter smithii have been reported to correlate with lower body fat formation in pigs. Besides the contribution of methanogens to the metabolic phenotype of their hosts, CH₄ release reduces the productivity that could be achieved through other hydrogen (H₂) disposal pathways. Enhanced participation of acetogenesis in H₂ disposal, leading to acetate formation, could be a more favorable direction for animal production and the environment. Better knowledge and understanding of the archaeal communities of the gastrointestinal tract (GIT), including their metabolism and interactions with other microorganisms, would thus allow the development of new strategies for inhibiting methanogens and shifting toward acetogenesis. There are a variety of approaches to inhibiting methanogens and mitigating methanogenesis in ruminants, which can find an application for nonruminants, such as nutritional changes through supplementation with biologically active compounds and management changes. We summarize the available reports and provide a comprehensive review of methanogens living in the GIT of various nonruminants, such as swine, horses, donkeys, rabbits, and poultry. This review will help in a better understanding of the populations and diversity of methanogens and the implications of their presence in nonruminant animals.

Inhibition mitigation of methanogenesis processes by conductive materials: A critical review

Methanogenesis can be promoted by the addition of conductive materials. Although stimulating effects of conductive materials on methane (CH₄) production has been extensively reported, the crucial roles on recovering methanogenic activities under inhibitory conditions have not been systematically discussed. This critical review presents the current findings on the effects of conductive materials in methanogenic systems under volatile fatty acids (VFAs), ammonia, sulfate, and nano-cytotoxicity stressed conditions. Conductive materials induce fast VFAs degradation, avoiding VFAs accumulation during anaerobic digestion. Under high ammonia concentrations, conductive materials may ensure sufficient energy conservation for methanogens to maintain intracellular pH and proton balance. When encountering the competition of sulfate-reducing bacteria, conductive materials can benefit electron competitive capability of methanogens, recovering CH₄ production activity. Conductive nanomaterials stimulate the excretion of extracellular polymeric substances, which can prevent cells from nano-cytotoxicity. Future perspectives about unraveling mitigation mechanisms induced by conductive materials in methanogenesis processes are further discussed.

Effects of biochar on methane emission from paddy soil: Focusing on DOM and microbial communities

Biochar can be used as a soil amendment. However, it generally possesses unique physicochemical properties and complex organics, which could affect soil methanogenesis. In this study，straw-based biochars obtained at 300 °C (BC300), 500 °C (BC500) and 700 °C (BC700) were added to the paddy soil. Compared with the blank group, BC300 significantly increased paddy soil methane emissions by about 38%. However, this promoting effect gradually disappeared with the increase of pyrolysis temperature, and the inhibition even appeared in the BC700 group with the methane reduction by 18.2%. This might be related to the organics released from biochar. Van Krevelen (VK) diagram showed that the aromaticity of BC700 and BC500 were significantly higher than BC300. Fluorescent analysis further revealed that BC300 increased the amount of degradable fluorescent organics in the soil, which could provide more substrate for methane production. Moreover, as pyrolysis temperature increased, the fluorescent organics released were more likely to be non-biodegradable humus. In addition, it was shown that BC700 could adsorb some inherent organics in the soil, and thus reduced the total organic content and inhibited soil methane emissions. Microbial analysis showed that methanogenesis had a positive correlation with the abundance of syntrophic bacteria (e.g. Desulfobacca and Clostridium) which had ability to further degrade various types of organics and provided substrates to the methanogens. This article provides a deeper understanding regarding for the effects of biochar on methane emission from paddy soil in terms of organics and microbial perspectives.

Quorum quenching altered microbial diversity and activity of anaerobic membrane bioreactor (AnMBR) and enhanced methane generation

A facultative bacterium Microbacterium sp. (QQ strain) was found significantly mitigated membrane biofouling and also increased methane production. It was found genera Nitrospira, norank-c-Bacterodetes vadinHA17, Trichococcus and family Anaerolineaceae were likely responsible for membrane biofouling. The presence of QQ strain increased the total abundance of fermentative and acetogenic genera by 0.61% and 379.61%, respectively, but had a minor effect on the abundance of methanogens. The increased methane production was likely due to the strengthened methanogenic activity and more available substrates. Homo-acetogenic Treponema was enriched (9.01%) in the presence of QQ strain suggesting that apart from hydrogenotrophic methanogenic pathway, extra CH₄ could be also produced from the additional acetate synthesized via homo-acetogenic pathway. This study advances knowledge about the effects of QQ strain on microbial communities, microbiota biofouling behavior and anaerobic fermentation process in AnMBRs.