Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis

Eutrophication driven macrophyte-derived organic matter decomposition to methane emission relates to co-metabolism effect in freshwater sediments

Lakes and wetlands play pivotal roles in global organic matter storage, receiving significant inputs of organic material. However, the co-metabolic processes governing the decomposition of these organic materials and their impact on greenhouse gas emissions remain inadequately understood. This study aims to assess the effects of mixed decomposition involving macrophytes and cyanobacteria on carbon emissions. A series of microcosms was established to investigate the decomposition of macrophyte residues and algae over a period of 216 days. A two-component kinetic model was utilized to estimate methane (CH4) production rates. Gas isotope technology was employed to discern the contributions of CH4 produced by macrophyte residues or algae. Quantitative PCR and analysis of 16S rRNA gene amplicons were employed to assess changes in functional genes and microbial communities. There were significant differences in the cumulative carbon release from the decomposition of different plant types due to the addition of carbon sources. After adding algae, the cumulative emission of CH4 increased significantly. The δ13C-CH4 partitioning indicated that CH4 originated exclusively from the fresh organic carbon of macrophyte residues, while it shifted to algae source after adding algae. The synergistic effect of the mixed decomposition on the CH4 emissions was greater than the sum of the individual decompositions. The microbial community richness was higher in the single plant residue treatment compared to the mixed treatment with algae addition, while microbial evenness in the sediment increased steadily in each treatment. Our findings emphasize the pronounced co-metabolic effect observed during the mixed decomposition of macrophytes and cyanobacteria.

Micro-positive pressure significantly decreases greenhouse gas emissions by regulating archaeal community during industrial-scale dairy manure composting

In this study, the effects of micro-positive pressure formed by covering with a semipermeable membrane in the heating phase of dairy manure composting on greenhouse gas emissions and the mechanism of reducing methane emissions by the archaeal community were investigated. A large-scale experiment was conducted with semipermeable membrane-covered composting (SMC), forced aeration composting (FAC), and traditional static composting (TSC) groups. The results showed that the oxygen concentration and methanogen abundance were key factors in regulating methane emissions. In the heating phase of SMC, the micro-positive pressure could enhance the O2 utilization rate and heating rate, resulting in Methanobrevibacter and Methanobacterium greatly decreasing, and the abundance of mcrA decreased by 90.03%, while that of pmoA did not increase. Compared with FAC and TSC, the cumulative methane emissions in SMC decreased by 51.75% and 96.04%, respectively. Therefore, the micro-positive pressure could effectively reduce greenhouse gas emissions by inhibiting the growth of methanogens.

The evolving role of methanogenic archaea in mammalian microbiomes

Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.

Emission dynamics of greenhouse gases regulated by fluctuation of water level in river-connected wetland

The application of reservoirs in the upper reaches of rivers will change the hydrological rhythm of river-connected wetlands in the lower reaches, causing changes in the distribution of wetland vegetation. The differences of carbon and nitrogen sequestration and emission potential in different vegetations may lead to the dynamics of greenhouse gas emissions from wetlands during hydrological periods. For a wetland connected to the Yangzi River, China, the dynamic changes of vegetation and water areas were identified by remote sensing, and the water level, the emission fluxes of greenhouse gases and the functional bacteria of carbon and nitrogen in soil were measured in-situ. Compared with drought period, the area of phragmites zone in flooding period increased by 28.2%, while the areas of carex and phalaris zones decreased by 42.9%. The carbon and nitrogen accumulation in the soil of phragmites zone is the highest, while the cumulative amount of phalaris is the lowest. The emission fluxes of CH₄ and N₂O in mud/water and various vegetations were positively correlated with water level and reached the maximum during flooding period. Although the global warming potential of mud/water was highest than that of vegetations, carex zone had the highest warming potential among vegetation zones. CH₄ contributes 8-37 times as much as N₂O to global warming potential in the wetland. The increase of flooding time promoted the emissions of CH₄ and N₂O in the wetland. The anaerobic condition caused by flooding stimulated the activities of denitrifying and methanogenic bacteria, thus increasing the emission of greenhouse gases. The sequestrations and emissions of carbon and nitrogen regulated by a reservoir in the upstream suggest that the operation of water conservancies should be considered to alleviate the greenhouse gas emission from river-connected wetland.

Effects and microbial mechanisms of phosphogypsum and medical stone on organic matter degradation and methane emissions during swine manure composting

The degradation of organic matter (OM) and CH₄ emissions during composting greatly influence the composting efficiency and greenhouse effect. This study evaluated the effects of adding phosphogypsum (PPG) and medical stone (MS) on OM breakdown, CH₄ emissions, and their underlying mechanisms. MS accelerated the breakdown of OM in the early composting stage, whereas PPG increased it in the cooling and maturation periods. At the ending of composting, humification was also significantly promoted by PPG and MS (P < 0.05). Moreover, MS and PPG reduced CH₄ emissions by 27.64% and 23.12%, respectively, and significantly inhibited the activities of methanogens in terms of their abundance (mcrA) and composition (dominant genera such as Methanobrevibacter, Methanocorpusculum, and Methanothermus) (P < 0.05). Interestingly, MS enhanced the activity of enzymes and bacterial metabolism related to OM degradation in the early composting stage, whereas PPG promoted them during the cooling and maturity stages. MS and PPG inhibited the activities of enzymes related to CH₄ release during the cooling and maturity stages. Therefore, PPG and MS may have influenced OM degradation and CH₄ releases during composting via changes in bacterial metabolism and enzyme activity levels. PPG and MS could have altered the activities of methanogens to influence the transformation of carbon and CH₄ emissions according to network analysis and partial least-squares path modeling analysis. These findings provide insights at the molecular level into the effects of adding PPG and MS on OM degradation and CH₄ emissions during composting, thereby facilitating the application of PPG and MS in composting systems.

Prolonged acetogenic phase and biological succession during anaerobic digestion using swine manure

In recent years, global warming and the limitation of fossil fuels have been causing the governments of different countries to think about the search for more sustainable fuel sources. Biomethane (CH₄) has gained increasing attention in recent years as an alternative option for a sustainable source of energy. Biogas is generated during the anaerobic digestion of organic materials by the metabolism of complex microbial communities in the substrates that make up this digestion. The microbial community evaluation using 16S rDNA metabarcoding in a bench covered pond bioreactor using swine effluent revealed the dominant bacteria belonging to Firmicutes, Proteobacteria, and Bacteroidetes phyla. The methanogenic group was represented by the Euryarchaeota phylum. It was possible to observe that the relative frequency of the methanogenic archaea community decreased with the anaerobic digestion, indicating a biological succession stage. On the other hand, there was a predominant acetogenic diversity in this final stage. These data showed stabilization of biomethane production, although the microbial community of methanogens has drastically reduced in the late process.

An operative laboratory investigation of bioconversion route from waste coal to natural energy

Purpose

In the present research, the potential of reactivated consortium for the methane production consuming waste coal as a carbon source (1% w/v) in the modified media at mesophilic temperature (37 °C) was determined.

Methods

Media modification was conducted for the enhancement of methane production by selecting three different components from the two media, i.e., Methanosprillium sp. producing media (MSP) and methane-producing bacteria media (MPB). From MSP medium, C2H2NaO2 (sodium acetate), KH2PO4 (potassium dihydrogen the phosphate), and NaHCO3 (sodium bicarbonate) whereas from MPB medium; yeast extract, peptone, and NH4Cl (ammonium chloride) were selected in the range of 0.5–2.5 (g/l). Analytical assay, i.e., Fourier transform infrared spectroscopy (FTIR), gas chromatography mass spectrophotometry (GCMS), scanning electron microscopy (SEM), and energy dispersive X-ray (EDX) were conducted. Further, compatibility study and pathogenicity was performed.

Results

In the present study, reactivated consortia was used therefore key components of the media were modified. In case of MPB medium, 2 g/l of yeast extract, 2 g/l peptone, and 1 g/l NH4Cl showed the promising results; whereas for MSP medium, 1 g/l of KH2PO4, 0.5 g/l of NaHCO3, and 1.5 g/l of C2H2NaO2 were noted to be the suitable range for methane production. Analytical studies confirmed the presences of -OH and aliphatic groups which majorly belongs to alkane, alkene, and phenol derivative compounds whereas SEM and EDX studies delineated the active interaction of bacteria with coal particles and presences of carbon (C) as a major peak in untreated coal and absence of C peak in microbial treated coal. In addition, a compatibility study was performed and their successful results aid in the future approach of field implementation. Further, pathogenicity data indicated the non-virulent and non-toxic nature of the consortia.

Conclusions

The production of waste coal is one of the most problematic and common activities of the mining industry. They release toxic substances into the environment (water, air, and soil) and damage the local biodiversity. Therefore, the generation of biogenic methane from waste coal is an environmentally friendly approach to overcome this problem.

Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review

In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.

Severe cyanobacteria accumulation potentially induces methylotrophic methane producing pathway in eutrophic lakes

Although cyanobacteria blooms lead to an increase in methane (CH₄) emissions in eutrophic lakes have been intensively studied, the methane production pathways and driving mechanisms of the associated CH₄ emissions are still unclear. In this study, the hypereutrophic Lake Taihu, which has extreme cyanobacteria accumulation, was selected to test hypothesis of a potential methylotrophic CH₄ production pathway. Field observation displayed that the CH₄ emission flux from the area with cyanobacteria accumulation was 867.01 μg m^-2·min^-1, much higher than the flux of 3.44 μg m^-2·min^-1 in the non-cyanobacteria accumulation area. The corresponding abundance of methane-producing archaea (MPA) in the cyanobacteria-concentrated area was 77.33% higher than that in the non-concentrated area via RT-qPCR technologies. Synchronously, sediments from these areas were incubated in anaerobic bottles, and results exhibited the high CH₄ emission potential of the cyanobacteria concentrated area versus the non-concentrated area (1199.26 vs. 205.76 μmol/L) and more active biological processes (CO₂ emission, 2072.8 vs. -714.62 μmol/L). We also found evidence for the methylotrophic methane producing pathway, which contributed to the high CH₄ emission flux from the cyanobacteria accumulation area. Firstly, cyanobacteria decomposition provided the prerequisite of abundant methyl thioether substances, including DMS, DMDS, and DMTS. Results showed that the content of methyl thioethers increased with the biomass of cyanobacteria, and the released DMS, DMDS, and DMTS was up to 96.35, 3.22 and 13.61 μg/L, respectively, in the highly concentrated 25000 g/cm³ cyanobacteria treatment. Then, cyanobacteria decomposition created anaerobic microenvironments (DO 0.06 mg/L and Eh -304.8Mv) for methylotrophic methane production. Lastly, the relative abundance of Methanosarcinales was increased from 7.67% at the initial stage to 36.02% at the final stage within a sediment treatment with 10 mmol/L N(CH₃)₃. Quantitatively, the proportion of the methylotrophic methane production pathway was as high as 32.58%. This finding is crucial for accurately evaluating the methane emission flux, and evaluating future management strategies of eutrophic lakes.

Methane production and active microbial communities during anaerobic digestion of three commercial biodegradable coffee capsules under mesophilic and thermophilic conditions

Biodegradable plastics market is increasing these last decades, including for coffee capsules. Anaerobic digestion, as a potential end-of-life scenario for plastic waste, has to be investigated. For this purpose, mesophilic (38 °C) and thermophilic (58 °C) anaerobic digestion tests on three coffee capsules made up with biodegradable plastic (Beanarella®, Launay® or Tintoretto®) and spent coffee (control) were compared by their methane production and the microbial communities active during the process. Mesophilic biodegradation of the capsules was slow and did not reach completion after 100 days, methane production ranged between 67 and 127 NL (CH₄) kg^-1 (VS). Thermophilic anaerobic digestion resulted in a better biodegradation and reached completion around 100 days, methane productions were between 257 and 294 NL (CH₄) kg^-1 (VS). The microbial populations from the reactors fed with plastics versus spent coffee grounds were significantly different, under both the mesophilic and the thermophilic conditions. However, the different biodegradable plastics only had a small impact on the main microbial community composition at a similar operational temperature and sampling time. Interestingly, the genus Tepidimicrobium was identified as a potential key microorganisms involved in the thermophilic conversion of biodegradable plastic in methane.

Microbial mechanisms related to the effects of bamboo charcoal and bamboo vinegar on the degradation of organic matter and methane emissions during composting

In this study, functional microbial sequencing, quantitative PCR, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed to understand the microbial mechanisms related to the effects of bamboo charcoal (BC) and bamboo vinegar (BV) on the degradation of organic matter (OM) and methane (CH₄) emissions during composting. BC + BV resulted in the highest degradation of OM. BV was most effective treatment in controlling CH₄ emissions and it significantly reduced the abundance of the mcrA gene. Methanobrevibacter, Methanosarcina, and Methanocorpusculum were closely related to CH₄ emissions during the thermophilic composting period. PICRUSt analysis showed that BC and/or BV enhanced the metabolism associated with OM degradation and reduced CH₄ metabolism. Structural equation modeling indicated that BC + BV strongly promoted the metabolic activity of microorganisms, which had a positive effect on CH₄ emissions. Together these results suggest that BC + BV may be a suitable composting strategy if the aerobic conditions can be effectively improved during the thermophilic composting period.

The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau

Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.

Microbial community dynamics in anaerobic digesters treating conventional and vacuum toilet flushed blackwater

Decentralized wastewater treatment represents a promising sustainable option for future wastewater management. Blackwater collected from toilets contains high concentrations of organic matter, ideal for energy recovery using anaerobic digestion. Up-flow anaerobic sludge blanket (UASB) reactors treating conventional toilet (CT, 9 L water per flush) and vacuum toilet (VT, 1 L water per flush) blackwater with increments of loadings were successfully operated to steady state in three phases. The organic loading rates were maintained at comparable levels between the two reactors. The methanisation rates were 0.23-0.29 and 0.41-0.48 gCH₄-COD/gfeedCOD in the CT and VT reactors, and the COD removal rates were 72% and 89%, respectively. The enriched microbial consortia and the community dynamics under different loading phases were compared. The rank abundance distributions and alpha-diversity showed that archaeal communities were predominated by mono-enrichments in both CT and VT reactors, while bacterial communities showed lower diversity in the VT reactor. Through principal coordinates analysis (beta-diversity), clear divergences of archaeal and bacterial communities between the CT and VT reactors were revealed, and the archaeal community developed at a slower rate than the bacterial community. The enriched archaea were hydrogenotrophic methanogens, Methanolinea in the CT reactor (56.6%), and Methanogenium in the VT reactor (62.3%). The enriched bacteria were Porphyromonadaceae in both CT (15.9%) and VT (13.4%) reactors, sulfate-reducing bacteria in the CT reactor, and Fibrobacteraceae in the VT reactor (13.8%). Links between enriched consortia and ammonia stress were discussed. Isotope fraction analysis of the biogas showed a slight shift from acetoclastic methanogenesis to hydrogenotrophic methanogenesis. A closer look into the predicted metagenomic functional profiles showed agreeing results, where hydrogenotrophic methanogenesis and fhs gene abundances were higher in the VT reactor. We demonstrated that different blackwater types enriched different microbial consortia, probably due to ammonia concentrations and sulfate loadings, which should be taken into consideration for practical applications.

Characterization of microbial community and main functional groups of prokaryotes in thermophilic anaerobic co-digestion of food waste and paper waste

The thermophilic anaerobic co-digestion of food waste and paper waste was successfully operated with a 0% to 70% fraction of paper waste. The variation of functional microbial community was investigated by 16S rRNA gene analysis. The results indicated that the hydrolyzing bacterial community changed from carbohydrate/protein-degrading bacteria to cellulose-degrading bacteria when the paper waste ratio was higher than 50%. Significant changes in the taxon responsible for cellulose degradation were found depending on the paper waste fraction. Cellulose-degrading bacteria outcompeted lactic acid bacteria in the degradation of monosaccharide, resulting in a decline in the proportion of lactic acid bacteria and the absence of an accumulation of lactic acid. At high paper waste ratios, because the cellulose-degrading bacteria, such as Defluviitoga tunisiensis, were more likely to degrade monosaccharides directly to acetate and hydrogen rather than to propionate and butyrate, the abundance of syntrophs was reduced. The variation of those bacteria with high H₂-producing ability significantly influenced the proportion of hydrogenotrophic archaea. The change in the microbial community as the paper waste fraction increased was illustrated with regard to anaerobic degradation steps.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Activated carbon enhanced anaerobic digestion of food waste - Laboratory-scale and Pilot-scale operation

Effects of activated carbon (AC) supplementation on anaerobic digestion (AD) of food waste were elucidated in lab- and pilot-scales. Lab-scale AD was performed in 1 L and 8 L digesters, while pilot-scale AD was conducted in a 1000 L digester. Based on the optimal dose of 15 g AC per working volume derived from the 1 L digester, for the same AC dosage in the 8 L digester, an improved operation stability coupled with a higher methane yield was achieved even when digesters without AC supplementation failed after 59 days due to accumulation of substantial organic intermediates. At the same time, color removal from the liquid phase of the digestate was dramatically enhanced and the particle size of the digestate solids was increased by 53% through AC supplementation after running for 59 days. Pyrosequencing of 16S rRNA gene showed the abundance of predominant phyla Firmicutes, Elusimicrobia and Proteobacteria selectively enhanced by 1.7-fold, 2.9-fold and 2.1-fold, respectively. Pilot-scale digester without AC gave an average methane yield of 0.466 L⋅(gVS)^-1⋅d^-1 at a composition of 53-61% v/v methane. With AC augmentation, an increase of 41% in methane yield was achieved in the 1000 L digester under optimal organic loading rate (1.6 g VS_FW·L^-1·d^-1).

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box." We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester.

Overcoming organic and nitrogen overload in thermophilic anaerobic digestion of pig slurry by coupling a microbial electrolysis cell

The combination of the anaerobic digestion (AD) process with a microbial electrolysis cell (MEC) coupled to an ammonia stripping unit as a post-treatment was assessed both in series operation, to improve the quality of the effluent, and in loop configuration recirculating the effluent, to increase the AD robustness. The MEC allowed maintaining the chemical oxygen demand removal of the whole system of 46±5% despite the AD destabilization after doubling the organic and nitrogen loads, while recovering 40±3% of ammonia. The AD-MEC system, in loop configuration, helped to recover the AD (55% increase in methane productivity) and attained a more stable and robust operation. The microbial population assessment revealed an enhancement of AD methanogenic archaea numbers and a shift in eubacterial population. The AD-MEC combined system is a promising strategy for stabilizing AD against organic and nitrogen overloads, while improving the quality of the effluent and recovering nutrients for their reutilization.

Enhancing metaproteomics--The value of models and defined environmental microbial systems

Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.

Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals

The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation

Anaerobic digestion is a complex process involving hydrolysis, acidogenesis, acetogenesis and methanogenesis. The separation of the hydrogen-yielding (dark fermentation) and methane-yielding steps under controlled conditions permits the production of hydrogen and methane from biomass. The characterization of microbial communities developed in bioreactors is crucial for the understanding and optimization of fermentation processes. Previously we developed an effective system for hydrogen production based on long-term continuous microbial cultures grown on sugar beet molasses. Here, the acidic effluent from molasses fermentation was used as the substrate for methanogenesis in an upflow anaerobic sludge blanket bioreactor. This study focused on the molecular analysis of the methane-yielding community processing the non-gaseous products of molasses fermentation. The substrate for methanogenesis produces conditions that favor the hydrogenotrophic pathway of methane synthesis. Methane production results from syntrophic metabolism whose key process is hydrogen transfer between bacteria and methanogenic Archaea. High-throughput 454 pyrosequencing of total DNA isolated from the methanogenic microbial community and bioinformatic sequence analysis revealed that the domain Bacteria was dominated by Firmicutes (mainly Clostridia), Bacteroidetes, δ- and γ-Proteobacteria, Cloacimonetes and Spirochaetes. In the domain Archaea, the order Methanomicrobiales was predominant, with Methanoculleus as the most abundant genus. The second and third most abundant members of the Archaeal community were representatives of the Methanomassiliicoccales and the Methanosarcinales. Analysis of the methanogenic sludge by scanning electron microscopy with Energy Dispersive X-ray Spectroscopy and X-ray diffraction showed that it was composed of small highly heterogeneous mineral-rich granules. Mineral components of methanogenic granules probably modulate syntrophic metabolism and methanogenic pathways. A rough functional analysis from shotgun data of the metagenome demonstrated that our knowledge of methanogenesis is poor and/or the enzymes responsible for methane production are highly effective, since despite reasonably good sequencing coverage, the details of the functional potential of the microbial community appeared to be incomplete.

Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.

Pyrosequencing of mcrA and archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield.

Spatial and temporal variations of microbial community in a mixed plug-flow loop reactor fed with dairy manure

Mixed plug-flow loop reactor (MPFLR) has been widely adopted by the US dairy farms to convert cattle manure to biogas. However, the microbiome in MPFLR digesters remains unexplored. In this study, the microbiome in a MPFLR digester operated on a mega-dairy farm was examined thrice over a 2 month period. Within 23 days of retention time, 55-70% of total manure solid was digested. Except for a few minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of the digester and over time. Metagenomic analysis showed that although with some temporal variations, the bacterial community was rather stable spatially in the digester. The methanogenic community was also stable both spatially and temporally in the digester. Among methanogens, genus Methanosaeta dominated in the digester. Quantitative polymerase chain reaction (qPCR) analysis and metagenomic analysis yielded different relative abundance of individual genera of methanogens, especially for Methanobacterium, which was predominant based on qPCR analysis but undetectable by metagenomics. Collectively, the results showed that only small microbial and chemical gradients existed within the digester, and the digestion process occurred similarly throughout the MPFLR digester. The findings of this study may help improve the operation and design of this type of manure digesters.

Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study

In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester.

Methanogenic archaea diversity in Hanwoo (Bos taurus coreanae) rumen fluid, rectal dung, and barn floor manure using a culture-independent method based on mcrA gene sequences

The diversity of methanogenic archaea associated with Korean Hanwoo cattle was analyzed using mcrA gene sequences from samples of rumen fluid (RF), rectal dung (RD), and barn floor manure (BFM). The predominant species were Methanobrevibacter ruminantium in RF and BFM(63.6% and 62.4%, respectively) and Methanocorpusculum labreanum in RD (53.2%).

Microbial diversity and dynamics during methane production from municipal solid waste

The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and hemicellulose contents supported growth of larger methanogen populations that resulted in higher methane yield.

Metagenomic analysis of methanogen populations in three full-scale mesophilic anaerobic manure digesters operated on dairy farms in Vermont, USA

The microbial communities that produce biogas as a result of anaerobic digestion of manure remain poorly understood. Using next-generation sequencing, methanogen populations were investigated in three full scale mesophilic anaerobic digesters operated on dairy farms. A combined 50 246 non-chimeric sequence reads covering the V1-V3 hypervariable regions of the methanogen 16S rRNA gene were assigned to 307 species-level operational taxonomic units (OTUs). The Blue Spruce Farms (BSF) and Green Mountain Dairy (GMD) anaerobic digesters were found to have nearly identical methanogen profiles, with the overwhelming predominance of OTU 1 (98.5% and 99.7%, respectively), which showed 99.2% sequence identity to Methanosarcina thermophila. In contrast, methanogens from the Chaput Family Farms (CFF) anaerobic digester were more diverse, with five major OTUs belonging to four distinct phylogenetic groups (Methanomicrobiales, Methanosarcinales, Methanoplasmatales, and Methanobacteriales). Differences in management practices and years of operation were hypothesized as potential factors responsible for differences in the methanogen profiles.

Methanosarcina domination in anaerobic sequencing batch reactor at short hydraulic retention time

The Archaea population of anaerobic sequential batch reactor (ASBR) featuring cycle operations under varying hydraulic retention time (HRT) was evaluated for treating a dilute waste stream. Terminal-Restriction Length Polymorphism and clone libraries for both 16S rRNA gene and mcrA gene were employed to characterize the methanogenic community structure. Results revealed that a Methanosarcina dominated methanogenic community was successfully established when using an ASBR digester at short HRT. It was revealed that both 16S rRNA and mcrA clone library could not provide complete community structure, while combination of two different clone libraries could capture more archaea diversity. Thermodynamic calculations confirmed a preference for the observed population structure. The results both experimentally and theoretically confirmed that Methanosarcina dominance emphasizing ASBR's important role in treating low strength wastewater as Methanosarcina will be more adept at overcoming temperature and shock loadings experienced with treating this type of wastewater.

Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-(13)C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of (13)C into DNA was detectable at in situ acetate concentrations (~7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the (13)C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.

Characterization of a Methanogenic Community within an Algal Fed Anaerobic Digester

The microbial diversity and metabolic potential of a methanogenic consortium residing in a 3785-liter anaerobic digester, fed with wastewater algae, was analyzed using 454 pyrosequencing technology. DNA was extracted from anaerobic sludge material and used in metagenomic analysis through PCR amplification of the methyl-coenzyme M reductase α subunit (mcrA) gene using primer sets ML, MCR, and ME. The majority of annotated mcrA sequences were assigned taxonomically to the genera Methanosaeta in the order Methanosarcinales. Methanogens from the genus Methanosaeta are obligate acetotrophs, suggesting this genus plays a dominant role in methane production from the analyzed fermentation sample. Numerous analyzed sequences within the algae fed anaerobic digester were unclassified and could not be assigned taxonomically. Relative amplicon frequencies were determined for each primer set to determine the utility of each in pyrosequencing. Primer sets ML and MCR performed better quantitatively (representing the large majority of analyzed sequences) than primer set ME. However, each of these primer sets was shown to provide a quantitatively unique community structure, and thus they are of equal importance in mcrA metagenomic analysis.

The role of different methanogen groups evaluated by Real-Time qPCR as high-efficiency bioindicators of wet anaerobic co-digestion of organic waste

Methanogen populations and their domains are poorly understood; however, in recent years, research on this topic has emerged. The relevance of this field has also been enhanced by the growing economic interest in methanogen skills, particularly the production of methane from organic substrates. Management attention turned to anaerobic wastes digestion because the volume and environmental impact reductions. Methanogenesis is the biochemically limiting step of the process and the industrially interesting phase because it connects to the amount of biogas production. For this reason, several studies have evaluated the structure of methanogen communities during this process. Currently, it is clear that the methanogen load and diversity depend on the feeding characteristics and the process conditions, but not much data is available. In this study, we apply a Real-Time Polymerase Chain Reaction (RT-PCR) method based on mcrA target to evaluate, by specific probes, some subgroups of methanogens during the mesophilic anaerobic digestion process fed wastewater sludge and organic fraction of the municipal solid waste with two different pre-treatments. The obtained data showed the prevalence of Methanomicrobiales and significantly positive correlation between Methanosarcina and Methanosaetae and the biogas production rate (0.744 p < 0.01 and 0.641 p < 0.05). Methanosarcina detected levels are different during the process after the two pre-treatment of the input materials (T-test p < 0.05). Moreover, a role as diagnostic tool could be suggested in digestion optimisation.

Potential impact of process parameters upon the bacterial diversity in the mesophilic anaerobic digestion of beet silage

The impact of the process parameters hydraulic retention time (HRT), organic loading rate (OLR) and substrate upon bacterial diversity was analyzed. Therefore, a controlled anaerobic fermentation (1755 days) of beet silage, only initially inoculated with manure, was monitored by the amplified "ribosomal DNA" restriction analysis. More than 85% of detected operational taxonomic units (OTUs) could not be assigned to described Bacteria. In contrast to studies analyzing the digestion of energy crops in the presence of manure, Chloroflexi were detected, whereas Clostridia and Chloroflexi were identified as persistent groups. Both groups are known as potential hydrogen producers or users. Species distribution patterns for Firmicutes, Bacteroidetes, Synergistetes and Thermotogae were not clearly linked to process parameters. The presence of Planctomycetes, Actinobacteria and Alcaligenaceae was related to long HRTs and short OLRs, while Acidobacteria were governed by short HRTs and high OLRs, respectively. The impact of substrate variations on diversity was minute.