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

Unveiling the mechanisms of Fe(III)-loaded chitosan composite (CTS-Fe) in enhancing anaerobic digestion of waste activated sludge

Anaerobic digestion (AD) of waste activated sludge (WAS) is usually limited by the low generation efficiency of methane. Fe(III)-loaded chitosan composite (CTS-Fe) have been reported to effectively enhanced the digestion of WAS, but its role in promoting anaerobic sludge digestion remains unclear. In present study, the effects of CTS-Fe on the hydrolysis and methanogenesis stages of WAS anaerobic digestion were investigated. The addition of CTS-Fe increased methane production potential by 8%-23% under the tested conditions with the addition of 5-20 g/L CTS-Fe. Besides, the results demonstrate that the addition of CTS-Fe could effectively promote the hydrolysis of WAS, evidenced by lower protein or polysaccharides concentration, higher soluble organic carbon in rector adding CTS-Fe, as well as the increased activity of extracellular hydrolase with higher CTS-Fe concentration. Meanwhile, the enrichment of Clostridia abundance (iron-reducing bacteria (IRBs)) was observed in CTS-Fe adding reactor (8.9%-13.8%), which was higher than that in the control reactor (7.9%). The observation further suggesting the acceleration of hydrolysis through dissimilatory iron reduction (DIR) process, thus providing abundant substrates for methanogenesis. However, the presence of CTS-Fe was inhibited the acetoclastic and hydrogenotrophic methanogenesis process, which could be ascribed to the Fe(III) act as electron acceptor coupled to methane for anaerobic oxidation. Furthermore, coenzyme F420 activity in the CTS-Fe added reactor was 34.9% lower than in the blank, also abundance of microorganisms involved in hydrogenotrophic methanogenesis was decreased. Results from this study could provide theoretical support for the practical applications of CTS-Fe.

Microbial methane cycling in a landfill on a decadal time scale

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.

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.

Oleate Impacts on Acetoclastic and Hydrogenotrophic Methanogenesis under Mesophilic and Thermophilic Conditions

This study investigated oleate inhibition concentration on mesophilic and thermophilic sludge by utilizing acetate and H2/CO2 (80:20, v/v) as substrate, respectively. In addition, another batch experiment was carried out to explore the influence of oleate loads (mM-oleate/g-VS) on methane production. Generally, the mesophilic anaerobic system was more stable than the thermophilic system, which embodied higher microbial abundance, higher methane yield, and higher oleate tolerance. Furthermore, this study provides a possible methanogenic pathway impacted by oleate under mesophilic and thermophilic conditions according to functional microbial composition. Lastly, this paper provides noticeable and avoidable oleate concentrations and loads under different experimental conditions as a guide for future anaerobic bioreactors of lipidic waste biodegradation.

Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions

During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.

Patterns of syntrophic interactions in methanogenic conversion of propionate

Methanogenesis is central to anaerobic digestion processes. The conversion of propionate as a key intermediate for methanogenesis requires syntrophic interactions between bacterial and archaeal partners. In this study, a series of methanogenic enrichments with propionate as the sole substrate were developed to identify microbial populations specifically involved in syntrophic propionate conversion. These rigorously controlled propionate enrichments exhibited functional stability with consistent propionate conversion and methane production; yet, the methanogenic microbial communities experienced substantial temporal dynamics, which has important implications on the understanding of mechanisms involved in microbial community assembly in anaerobic digestion. Syntrophobacter was identified as the most abundant and consistent bacterial partner in syntrophic propionate conversion regardless of the origin of the source culture, the concentration of propionate, or the temporal dynamics of the culture. In contrast, the methanogen partners involved in syntrophic propionate conversion lacked consistency, as the dominant methanogens varied as a function of process condition and temporal dynamics. Methanoculleus populations were specifically enriched as the syntrophic partner at inhibitory levels of propionate, likely due to the ability to function under unfavorable environmental conditions. Syntrophic propionate conversion was carried out exclusively via transformation of propionate into acetate and hydrogen in enrichments established in this study. Microbial populations highly tolerant of elevated propionate, represented by Syntrophobacter and Methanoculleus, are of great significance in understanding methanogenic activities during process perturbations when propionate accumulation is frequently encountered. Key points • Syntrophobacter was the most consistent bacterial partner in propionate metabolism. • Diverse hydrogenotrophic methanogen populations could serve as syntrophic partners. • Methanoculleus emerged as a methanogen partner tolerant of elevated propionate.

Understanding methane emission from stored animal manure: A review to guide model development

National inventories of methane (CH₄ ) emission from manure management are based on guidelines from the Intergovernmental Panel on Climate Change using country-specific emission factors. These calculations must be simple and, consequently, the effects of management practices and environmental conditions are only crudely represented in the calculations. The intention of this review is to develop a detailed understanding necessary for developing accurate models for calculating CH₄ emission from liquid manure, with particular focus on the microbiological conversion of organic matter to CH₄ . Themes discussed are (a) the liquid manure environment; (b) methane production processes from a modeling perspective; (c) development and adaptation of methanogenic communities; (d) mass and electron conservation; (e) steps limiting CH₄ production; (f) inhibition of methanogens; (g) temperature effects on CH₄ production; and (h) limits of existing estimation approaches. We conclude that a model must include calculation of microbial response to variations in manure temperature, substrate availability and age, and management system, because these variables substantially affect CH₄ production. Methane production can be reduced by manipulating key variables through management procedures, and the effects may be taken into account by including a microbial component in the model. When developing new calculation procedures, it is important to include reasonably accurate algorithms of microbial adaptation. This review presents concepts for these calculations and ideas for how these may be carried out. A need for better quantification of hydrolysis kinetics is identified, and the importance of short- and long-term microbial adaptation is highlighted.

High-rate blackwater anaerobic digestion under septic tank conditions with the amendment of biosolids-derived biochar synthesized at different temperatures

Septic tanks have been widely used for blackwater treatment in developing countries, while high-rate septic tanks with improved methane recovery are yet to be achieved. This study investigated biosolids-derived biochar (synthesized at 300℃, 425℃, and 550℃) as an additive for developing high-rate septic tanks. The experiments were conducted with anaerobic bioreactors operated with synthetic blackwater under septic tank conditions. All biochar amended reactors demonstrated a steady increase in daily methane production for increasing OLR from 0.08 to 3 g COD/L/d. The control reactor showed significant process disturbances at OLRs ≥ 2 g COD/L/d with an accumulation of volatile fatty acids followed by pH drop. At OLR of 3 g COD/L/d, the daily methane production from biochar amended reactors was ~ 4.3 times higher than the control (300 vs. 70 mL per day). Biochar addition established a robust microbiome consisted of a higher abundance of hydrogenotrophic and acetoclastic methanogens and hydrogen-producing fermentative bacteria.

Thermophilic biogas production from microalgae-bacteria aggregates: biogas yield, community variation and energy balance

Biogas production through anaerobic mesophilic digestion is the most straightforward biofuel production route integrated into microalgae-bacteria wastewater treatment plants. Improvement of this biofuel route without adding pretreatment units is possible through the temperature increase. This paper presents a comprehensive evaluation of the transitory effect of different temperatures (35 °C and 55 °C) and hydraulic retention times (HRT) of 15 and 30 d on the long-term methane production using non-pretreated microalgae-bacteria aggregates as a feedstock. The thermophilic transition from mesophilic inoculum adapted to microalgae-bacteria aggregate increased 1.7-fold the methane production (0.41 m³CH₄ kgVS^-1) at HRT of 30 d. A substantial decrease in the microbial community's diversity present in the anaerobic reactor was observed when thermophilic conditions were applied, explaining the long adaptation period needed. The increase of the operative temperature condition promotes changes in the dominance pathway of methanogenesis from hydrogenotrophic to acetolactic. The energy balance assessment showed a positive net energy ratio when the digester was operated at an HRT of 30 d. A maximum net energy ratio of 1.5 was achieved at mesophilic temperature. This study demonstrated, based on experimental data, that microalgal digestion with an HRT of 30 d favors energy self-sustainability in microalgal wastewater treatment plants.

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Evidence of thermophilic waste decomposition at a landfill exhibiting elevated temperature regions

There have been several reports of landfills exhibiting temperatures as high as 80 to 100 °C. This observation has motivated researchers to understand the causes of the elevated temperatures and to develop predictive models of landfill temperature. The objective of this research was to characterize the methanogenic activity of microbial communities that were derived from landfill samples excavated from a section of a landfill exhibiting gas well temperatures above 55 °C. Specific objectives were to: (1) determine the upper temperature limit for methane production; (2) evaluate the kinetics of methane generation when landfill-derived microcosms are incubated above and below their excavation temperature and derive a temperature inhibition function; and (3) evaluate microbial community shifts in response to temperature perturbations. Landfill microcosms were derived from 57 excavated landfill samples and incubated within ±2.5 °C of their excavation temperature between 42.5 °C and 87.5 °C. Results showed an optimum temperature for methane generation of ~57 °C and a 95% reduction in methane yield at ~72 °C. When select cultures were perturbed between 5 °C below and 15 °C above their in-situ temperature, both the rate and maximum methane production decreased as incubation temperature increased. Microbial community characterization using 16S rRNA amplicon sequencing suggests that thermophilic methanogenic activity can be attributed to methanogens of the genus Methanothermobacter. This study demonstrated that from a microbiological standpoint, landfills may maintain active methanogenic processes while experiencing temperatures in the thermophilic regime (<72 °C).

Sugarcane vinasse extreme thermophilic digestion: a glimpse on biogas free management

The high temperature in which sugarcane vinasse (SV) is generated (~ 90 °C) and the positive effect of higher temperatures in biochemical reactions have motivated the evaluation of SV anaerobic digestion (AD) under extreme temperature conditions. Two-stage (acidogenic/methanogenic) and single-stage (methanogenic) AD of SV were evaluated under 70 °C in structured-bed reactors. The extreme temperature was beneficial to the acidogenic step of the two-stage AD process. The methane production, however, was hindered at 70 °C. The VMP of the single and two-stage reactors accounted, respectively, for only 13% and 7% of the production rate reported in sugarcane vinasse AD at 55 °C. At 70 °C, the main genera responsible for methane production was Methanothermobacter and the acetoclastic methanogenesis did not occur, resulting in acetic acid build up (15,800 mg L^-1). These results brought a new perspective for sugarcane vinasse management, with acetic acid production alternatively to methanization. In this perspective, two-stage process would be composed of acidogenic and acetogenic reactors, and beyond acetate, hydrogen and other soluble compounds could be recovered in a complete biorefinery process.

Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes

The properties of digestates generated through anaerobic digestion are influenced by interactions between the digester microbial communities, feedstock properties and digester operating conditions. This study investigated the effect of varying initial feedstock carbon to nitrogen (C/N) ratios on digestate microbiota and predicted abundance of genes encoding lignocellulolytic activity. The C/N ratio had a significant impact on the digestate microbiome. Feedstocks with intermediate C/N ratio (20–27) (where higher biomethane potential was observed) showed higher relative abundance of archaea compared to feedstocks with C/N ratios at 17 and 34. Within microbial networks, four microbial clusters and eight connector microorganisms changed significantly with the C/N ratio (P &lt; 0.05). Feedstocks with C/N &lt; 23 were richer in organisms from the family Thermotogaceae and genus Caldicoprobacter and enhanced potential for degradation of maltose, galactomannans, melobiose and lactose. This study provides new insights into how anaerobic digestion conditions relate to the structure and functional potential of digester microbial communities, which may be relevant to both digester performance and subsequent utilization of digestates for composting or amending soil.

Simultaneous H2S mitigation and methanization enhancement of chicken manure through the introduction of the micro-aeration approach

The impact on H₂S alleviation and methane yield enhancement after submitting the anaerobic digestion of chicken manure to a finite amount of air was investigated. The largest reduction in the H₂S biogas content (58% lower) occurred when air intensity of 30 ml/g VS_in was injected into the reactors. Consequently, a maximum methane yield (335 mL-g VS_in^-1), which was 77% higher than the control, was concurrently achieved. Slight sulfate accumulation (<330 mg L^-1) was observed inside the micro-aerated digesters with higher air intensities, suggesting a suppression of sulfide inhibition. Bacterial diversity/richness was enhanced in these digesters while the relative abundance of Methanocelleus increased by 36%. The most important contributing factor to enhancement was the synergistic effect resulting from increments in the hydrolysis rate and the suppression of sulfide inhibition. The results highlighted the potential of in situ H₂S mitigation with the added benefit of methane yield enhancement.

Biogas Production from Oil Palm Empty Fruit Bunches and Palm Oil Decanter Cake using Solid-State Anaerobic co-Digestion

Oil palm empty fruit bunches (EFB) and palm oil decanter cake (DC) were used to investigate biogas production by using solid-state anaerobic co-digestion (SS-AcoD) with 15% total solid (TS) content. Solid state anaerobic digestion (SS-AD) using substrate to inoculum (S:I) ratio of 3:1, methane yields of 353.0 mL-CH4/g-VS and 101.5 mL-CH4/g-VS were respectively achieved from mono-digestion of EFB without oil palm ash (OPA) addition and of DC with 10% OPA addition under mesophilic conditions 35 °C. By adding 5% OPA to SS-AD using 3:1 S:I ratio under thermophilic conditions (55 °C), mono-digestion of EFB and DC provided methane yields of 365.0 and 160.3 mL-CH4/g-VS, respectively. Furthermore, SS-AcoD of EFB:DC at 1:1 mixing ratio (volatile solid, VS basis), corresponding to carbon to nitrogen (C:N) ratio of 32, gathering with S:I ratio of 3:1 and 5% ash addition, synergistic effect is observed together with similar methane yields of 414.4 and 399.3 mL-CH4/g-VS, achieved under 35 °C and 55 °C, respectively. According to first order kinetic analysis under synergistic condition, methane production rate from thermophilic operation is 5 times higher than that from mesophilic operation. Therefore, SS-AcoD could be potentially beneficial to generate biogas from EFB and DC.

Air-side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome

Air-side stripping without a prior solid-liquid phase separation step is a feasible and promising process to control ammonia concentration in thermophilic digesters. During the process, part of the anaerobic biomass is exposed to high temperature, high pH and aerobic conditions. However, there are no studies assessing the effects of those harsh conditions on the microbial communities of thermophilic digesters. To fill this knowledge gap, the microbiomes of two thermophilic digesters (55°C), fed with a mixture of pig manure and nitrogen-rich co-substrates, were investigated under different organic loading rates (OLR: 1.1-5.2 g COD l-1  day-1 ), ammonia concentrations (0.2-1.5 g free ammonia nitrogen l-1 ) and stripping frequencies (3-5 times per week). The bacterial communities were dominated by Firmicutes and Bacteroidetes phyla, while the predominant methanogens were Methanosarcina sp archaea. Increasing co-substrate fraction, OLR and free ammonia nitrogen (FAN) favoured the presence of genera Ruminiclostridium, Clostridium and Tepidimicrobium and of hydrogenotrophic methanogens, mainly Methanoculleus archaea. The data indicated that the use of air-side stripping did not adversely affect thermophilic microbial communities, but indirectly modulated them by controlling FAN concentrations in the digester. These results demonstrate the viability at microbial community level of air side-stream stripping process as an adequate technology for the ammonia control during anaerobic co-digestion of nitrogen-rich substrates.

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.

Impact of seasonal temperature transition, alkalinity and other abiotic factors on the persistence of viruses in swine and dairy manures

Animal manures are a valued source of nutrients for crop production. They frequently do, however, contain zoonotic pathogens including a wide range of viruses. Ideally, manures would be treated prior to land application, reducing the burden of zoonotic viruses, and thus the potential for transmission to adjacent water resources or crops intended for human or animal consumption. In the present study, manure was obtained from four dairy and three swine farms. The manure was incubated anaerobically in the laboratory for 28 weeks at temperatures ranging from 4 to 25 °C, and multiple physical and chemical parameters were monitored. The abundance of various DNA and RNA viruses was measured throughout the incubation by amplifying virus-specific gene targets. A combination of statistical analyses were applied to identify whether the viruses are significantly impacted by temperature transition or affected by other abiotic factors. Temperature had no effect on the persistence of any of the viruses studied. An increase in pH of the manures during the incubation was significantly (P < 0.05) associated with decreased persistence, suggesting that pH manipulation during storage could reduce the abundance of viruses.

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer

Food processing facilities often use antimicrobial quaternary ammonium compound (QAC) sanitizers to maintain cleanliness. These QACs can end up in wastewaters used as feedstock for anaerobic digestion. The aim of this study was to measure the effect of QAC contamination on biogas production and structure of microbial communities in thermophilic digester sludge. Methane production and biogas quality data were analyzed in batch anaerobic digesters containing QAC at 0, 15, 50, 100 and 150mg/L. Increasing sanitizer concentration in the bioreactors negatively impacted methane production rate and biogas quality. Microbial community composition data was obtained through 16S rRNA gene sequencing from the QAC-contaminated sludges. Sequencing data showed no significant restructuring of the bacterial communities. However, significant restructuring was observed within the archaeal communities as QAC concentration increased. Further studies to confirm these effects on a larger scale and with a longer retention time are necessary.

Identifying methanogen community structures and their correlations with performance parameters in four full-scale anaerobic sludge digesters

Four full-scale mesophilic anaerobic digesters treating waste sludge were monitored to characterize methanogen communities and their relationship with process parameters. The performance of the four digesters were dissimilar with the average chemical oxygen demand removal efficiencies between 24 and 45% and differing pH. Real-time quantitative PCR showed that archaeal 16S rRNA gene concentration ([ARC]) and, more pronouncedly, its ratio to bacterial counterpart ([ARC]/[BAC]) correlated positively with the performance parameters, including the lipid removal efficiency. Pyrosequencing identified 12 methanogen genera, of which Methanolinea, Methansaeta, and Methanospirillum collectively accounted for 79.2% of total archaeal reads. However, Methanoculleus, a numerically minor (1.9±2.6%) taxa, was the most promising biomarker for positive performance, while Methanoregula was abundant in samples with poor performance. These results could be useful for the control and management of anaerobic sludge digestion.

Dairy Manure Total Solid Levels Impact CH Flux and Abundance of Methanogenic Archaeal Communities

Stored liquid dairy manures are methane (CH) emission hotspots because of the large amount of slurry volatile solids (VS) converted into CH by methanogens under anaerobic conditions. Our research has indicated that a reduction of total solids (TS) of slurries before storage can reduce CH emissions. In the current study, methanogen abundance was characterized in tanks with different CH emissions. Using mesoscale slurry storage facilities equipped for continuous gaseous emission monitoring, we stored dairy slurries having TS from 9.5 to 0.3% for up to 6 mo. Samples were taken after Day 30 and Day 120 of the storage (20 May-16 Nov. 2010) from the upper and bottom layers of the slurries. Methanogenic communities were studied by targeting the gene encoding the α subunit methyl-coenzyme M reductase (), which catalyzes the final step of methanogenesis. Interestingly, mean abundances of methanogens increased by ∼8 and 23% at the top and bottom sections, respectively, as slurry TS decreased from 9.5 to 0.3%. Cumulative CH emissions, however, decreased by ∼70% as slurry TS decreased from 9.5 to 0.3%. Nevertheless, compared with Day 30 of storage, mean abundances of methanogens were relatively higher at Day 120 (up to 19%), consistent with an increase in the cumulative CH emissions. Polymerase chain reaction denaturing gel electrophoresis analysis indicated a low methanogen diversity, with most bands sequenced closely related to the genus (>95% amino acid sequence similarity), the hydrogenotrophic methanogens. Results suggest that available carbon substrate and not methanogen abundance may be limiting cumulative CH emissions at reduced TS levels of dairy slurries.

High-rate, High Temperature Acetotrophic Methanogenesis Governed by a Three Population Consortium in Anaerobic Bioreactors

A combination of acetate oxidation and acetoclastic methanogenesis has been previously identified to enable high-rate methanogenesis at high temperatures (55 to 65°C), but this capability had not been linked to any key organisms. This study combined RNA–stable isotope probing on ¹³C-labelled acetate and 16S amplicon sequencing to identify the active micro-organisms involved in high-rate methanogenesis. Active biomass was harvested from three bench-scale thermophilic bioreactors treating waste activated sludge at 55, 60 and 65°C, and fed with ¹³-C labelled and ¹²C-unlabelled acetate. Acetate uptake and cumulative methane production were determined and kinetic parameters were estimated using model-based analysis. Pyrosequencing performed on ¹³C- enriched samples indicated that organisms accumulating labelled carbon were Coprothermobacter (all temperatures between 55 and 65°C), acetoclastic Methanosarcina (55 to 60°C) and hydrogenotrophic Methanothermobacter (60 to 65°C). The increased relative abundance of Coprothermobacter with increased temperature corresponding with a shift to syntrophic acetate oxidation identified this as a potentially key oxidiser. Methanosarcina likely acts as both a hydrogen utilising and acetoclastic methanogen at 55°C, and is replaced by Methanothermobacter as a hydrogen utiliser at higher temperatures.

Optimization and microbial community analysis for production of biogas from solid waste residues of palm oil mill industry by solid-state anaerobic digestion

This study investigated the improvement of biogas production from solid-state anaerobic digestion (SS-AD) of oil palm biomass by optimizing of total solids (TS) contents, feedstock to inoculum (F:I) ratios and carbon to nitrogen (C:N) ratios. Highest methane yield from EFB, OPF and OPT of 358, 280 and 324m(3)CH4ton(-1)VS, respectively, was achieved at TS content of 16%, C:N ratio of 30:1 and F:I ratio of 2:1. The main contribution to methane from biomass was the degradation of cellulose and hemicellulose. The highest methane production of 72m(3)CH4ton(-1) biomass was achieved from EFB. Bacteria community structure in SS-AD process of oil palm biomass was dominated by Ruminococcus sp. and Clostridium sp., while archaea community was dominated by Methanoculleus sp. Oil palm biomass has great potential for methane production via SS-AD.

Effects of sludge inoculum and organic feedstock on active microbial communities and methane yield during anaerobic digestion

Anaerobic digestion (AD) is a widespread microbial technology used to treat organic waste and recover energy in the form of methane ("biogas"). While most AD systems have been designed to treat a single input, mixtures of digester sludge and solid organic waste are emerging as a means to improve efficiency and methane yield. We examined laboratory anaerobic cultures of AD sludge from two sources amended with food waste, xylose, and xylan at mesophilic temperatures, and with cellulose at meso- and thermophilic temperatures, to determine whether and how the inoculum and substrate affect biogas yield and community composition. All substrate and inoculum combinations yielded methane, with food waste most productive by mass. Pyrosequencing of transcribed bacterial and archaeal 16S rRNA showed that community composition varied across substrates and inocula, with differing ratios of hydrogenotrophic/acetoclastic methanogenic archaea associated with syntrophic partners. While communities did not cluster by either inoculum or substrate, additional sequencing of the bacterial 16S rRNA gene in the source sludge revealed that the bacterial communities were influenced by their inoculum. These results suggest that complete and efficient AD systems could potentially be assembled from different microbial inocula and consist of taxonomically diverse communities that nevertheless perform similar functions.

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

Sequestration of CO₂ in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO₂ building up and also for the in situ potential bioconversion of stored CO₂ to methane. However, the information on these functional microbial communities and the impact of CO₂ storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO₂-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO₂. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO₂ injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO₂ injection and, if so, demonstrated the potential for microbial fixation and conversion of CO₂ into methane in subsurface oil reservoirs.

Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters

The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD.

Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants

The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed significant similarities. The absence of genes for a putative ammonium uptake system may indicate that M. bourgensis MS2(T) is adapted to environments rich in ammonium/ammonia. Specific genes featuring predicted functions in the context of osmolyte production were detected in the genome of M. bourgensis MS2(T). Mapping of metagenome sequences derived from a production-scale biogas plant revealed that M. bourgensis MS2(T) almost completely comprises the genetic information of dominant methanogens present in the biogas reactor analyzed. Hence, availability of the M. bourgensis MS2(T) genome sequence may be valuable regarding further research addressing the performance of Methanoculleus species in agricultural biogas plants.

Substrate induced emergence of different active bacterial and archaeal assemblages during biomethane production

This study analyzed the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose or xylan) by barcoded 454 pyrosequencing of the bacterial and archaeal 16S rRNA genes in the DNA and RNA. The number of operational taxonomic units at 97% similarity for bacteria and archaea ranged from 162-261 and 31-166, respectively. Principal coordinates analysis and Venn diagram revealed that there were significant differences in the microbial community structure between the active members transforming each substrate and the inoculum. The active bacterial populations detected were those required for the hydrolysis of the amended substrate. The active archaeal populations were methanogens but the ratio of Methanosarcinales and Methanomicrobiales varied between the cultures. Overall, results of this study showed that a subset of the populations became active and altered in relative abundance during methane production according to the amended substrate.