Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters

An integrated review on the role of different biocatalysts, process parameters, bioreactor technologies and data-driven predictive models for upgrading biogas

As energy consumption and waste generation from human activities continue to rise, the technology of anaerobic digestion (AD), which converts waste into bioenergy, has gained popularity. Biogas produced from AD commonly contains 60 % CH4, 40 % CO2 and a minor fraction of impurities. Currently, several anaerobic reactors have been designed to upgrade the biogas with biomethane content above 90 %. This review summarizes the current trends in the biological upgradation of biogas from a bio-circular economy perspective to achieve sustainable energy goals. Examples of applications reporting the latest advancements in treating industrial effluents using high-rate anaerobic reactors have been mentioned. The integrated anaerobic-aerobic hybrid reactor offers a solution to the limitations of traditional methods in treating diverse effluents. A special focus on biological upgradation techniques such as in-situ, ex-situ, and hybrid mechanisms have been briefed. The key advantage of hybrid upgradation is its ability to address the pH rise during in-situ process. Additionally, the applications of artificial neural networks and optimization to upgrade biogas production have been discussed. The review concludes with future research directives with emphasis on the economic viability of the approaches.

Upscaling volatile fatty acids production: Demonstrating the reliability of anaerobic fermentation of food wastes from the lab towards industrial implementation

In recent years, the anaerobic fermentation (AF) of food waste (FW) has gained significant attention as a sustainable solution for waste valorization. However, the challenge of scaling up biotechnological processes for industrial applications remains a key barrier to commercialization. This investigation addressed this challenge by scaling up an auto-AF process from laboratory scale (4 L) to pilot (50 L) and demonstration scale in an industrial environment (250 L), using a lipid-rich FW (46.6 %, w/w) as the feedstock and endogenous microbiota as the inoculum. The applied operating conditions promoted the hydrolysis (>35 % volatile solids (VS) removal) and acidogenesis (>58 % of soluble chemical oxygen demand (sCOD) acidified) steps. As the reactor size for technology testing was increased, efficient mixing was crucial to ensure a proper homogenization of the fermentation broth. Lactic acid bacteria (LAB) prevailed in the endogenous microbiota, contributing to the enhanced hydrolysis and acidification efficiencies determined at all the scales. The minimal performance variations determined at different reactors' scales, along with the stability of the metabolite profiles, demonstrated the robustness and reliability of AF, opening the door to continue further industrialization.

Effects of tannin-tolerant lactic acid bacteria in combination with tannic acid on the fermentation quality, protease activity and bacterial community of stylo silage

BACKGROUND

Proteolysis during ensiling primarily occurs due to undesirable microbial and plant protease activities, which reduce the protein supply to ruminant livestock and cause a series of environmental problems. The objective of this study was to investigate the effects of the tannin-tolerant lactic acid bacterium strain Lactiplantibacillus plantarum 4 (LABLP4) in combination with tannic acid (TA) on protein preservation in stylo (Stylosanthes guianensis) silage. The stylos were either ensiled without additives (control) or treated with LABLP4 (106 colony-forming units per gram of fresh matter), 1% (fresh matter basis) TA, 2% TA, LABLP4 + 1% TA and LABLP4 + 2% TA. Fermentation quality, protein composition, protease activity and bacterial diversity were determined at 3, 7, 14 and 31 days of ensiling.

RESULTS

The combination of LABLP4 and TA decreased the pH, coliform bacteria count, non-protein nitrogen, ammonia-nitrogen (NH3-N) content and protease activities (P < 0.05) and increased the true protein content (P < 0.05) compared to the control. LABLP4 + TA led to a lower pH and NH3-N content than LABLP4 or TA alone (P < 0.05). On the last day (31 days) of ensiling, LABLP4 + TA increased the relative abundances of Firmicutes and Lactiplantibacillus (P < 0.05), except for the LABLP4 treatment, and decreased the relative abundance of Actinobacteria (P < 0.05).

CONCLUSION

The combination of tannin-tolerant LABLP4 and TA effectively improved the fermentation quality of stylo silage and reduced protein degradation by altering the bacterial community structure. © 2024 Society of Chemical Industry.

In Vitro Evaluation of Ruminal Digestibility, Fermentation Characteristics, and Bacterial Diversity of Kenaf Crop at Various Cutting Heights

The current study investigated the in vitro degradability, in vitro gas production, methane (CH4) production, and ruminal bacterial community of kenaf plants cut at different heights (130, 160, 190, 220, and 250 cm). These samples were subjected to an in vitro batch culture system using buffalo rumen fluid to measure gas and CH4 production at 3, 6, 9, 12, 24, 36, 48, and 72 h of incubation. Results reveal that crude protein (CP) concentration was the highest at the 220 cm height compared with the other heights. With the increase in height, gas and CH4 production decreased. However, the CH4 production at 190 cm was higher compared with the other plant heights. Dry matter degradation was higher at 190 cm and 220 cm, while ammonia-N and microbial CP were higher at the 220 cm height compared with the other heights. However, neutral detergent fiber degradation was the highest at the 130 cm height. Total volatile fatty acids, acetic acid, acetic acid/propane ratio, and pH value did not differ among the treatments, except for propionic acid, which was higher at the 130 cm and 160 cm heights. Overall, harvesting kenaf at plant heights of up to 220 cm was better in terms of its promising nutritional quality, improved dry matter degradation, and microbial CP contents.

Study of two approaches for the process water management from hydrothermal carbonization of swine manure: Anaerobic treatment and nutrient recovery

Hydrothermal carbonization (HTC) is a promising alternative to transform biomass waste into a solid carbonaceous material (hydrochar) and a process water with potential for material and energy recovery. In this study, two alternatives for process water treatment by conventional and acid-assisted HTC of swine manure are discussed. Process water from conventional HTC at 180 °C showed high biodegradability (55% COD removal) and methane production (∼290 mL STP CH4 g-1 CODadded) and the treatment in an upflow anaerobic sludge blanket reactor allowed obtaining a high methane production yield (1.3 L CH4 L-1 d-1) and COD removal (∼70%). The analysis of the microbiota showed a high concentration of Synergistota and Firmicutes phyla, with high degradation of organic nitrogen-containing organic compounds. Acid-assisted HTC proved to be a viable option for nutrient recovery (migration of 83% of the P to the process water), which allowed obtaining a solid salt by chemical precipitation with Mg(OH)2 (NPK of 4/4/0.4) and MgCl2 (NPK 8/17/0.5), with a negligible content of heavy metals. The characteristics of the precipitated solid complied with the requirements of European Regulation (2019)/1009 for fertilizers and amendments in agricultural soils, being a suitable alternative for the recycling of nutrients from wastes.

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Effects of Diets Combining Peanut Vine and Whole-Plant Corn Silage on Growth Performance, Meat Quality and Rumen Microbiota of Simmental Crossbred Cattle

Peanut vine is a typical peanut by-product and can be used as a quality roughage resource. Whole-plant corn silage is a commonly used roughage. However, few studies have investigated the effects of diets combining peanut vine and whole-plant corn silage on growth performance, antioxidant capacity, meat quality, rumen fermentation and microbiota of beef cattle. To investigate these effects, eighty Simmental crossbred cattle (body weight, 451.27 ± 10.38 kg) approximately 14 months old were randomly divided into four treatments for a 90-day feeding experiment. A one-way design method was used in this experiment. According to the roughage composition, the cattle were divided into a control treatment of 45% wheat straw and 55% whole-plant corn silage (WG), and three treatments of 25% peanut vine and 75% whole-plant corn silage (LPG), 45% peanut vine and 55% whole-plant corn silage (MPG), and 65% peanut vine and 35% whole-plant corn silage (HPG), and the concentrate was the same for all four treatment diets. The results showed that compared to the WG group, the MPG group experienced an increase in their average daily feed intake of 14%, an average daily gain of 32%, and an increase in SOD activity in the spleen of 33%; in the meat, dry matter content increased by 11%, crude protein by 9%, and ether extract content by 40%; in the rumen, the NH3-N content was reduced by 36%, the relative abundance of Firmicutes increased, and the relative abundance of Bacteroidetes decreased (p < 0.05). These results showed the composition of 45% peanut vine and 55% whole-plant corn silage in the roughage improved growth performance, antioxidant capacity, meat quality, rumen fermentation, and microbiota of beef cattle.

Lactic acid production from food waste at an anaerobic digestion biorefinery: effect of digestate recirculation and sucrose supplementation

Low lactic acid (LA) yields from direct food waste (FW) fermentation restrict this production pathway. However, nitrogen and other nutrients within FW digestate, in combination with sucrose supplementation, may enhance LA production and improve feasibility of fermentation. Therefore, this work aimed to improve LA fermentation from FWs by supplementing nitrogen (0-400 mgN·L-1) as NH4Cl or digestate and dosing sucrose (0-150 g·L-1) as a low-cost carbohydrate. Overall, NH4Cl and digestate led to similar improvements in the rate of LA formation (0.03 ± 0.02 and 0.04 ± 0.02 h-1 for NH4Cl and digestate, respectively), but NH4Cl also improved the final concentration, though effects varied between treatments (5.2 ± 4.6 g·L-1). While digestate altered the community composition and increased diversity, sucrose minimised community diversion from LA, promoted Lactobacillus growth at all dosages, and enhanced the final LA concentration from 25 to 30 g·L-1 to 59-68 g·L-1, depending on nitrogen dosage and source. Overall, the results highlighted the value of digestate as a nutrient source and sucrose as both community controller and means to enhance the LA concentration in future LA biorefinery concepts.

Efficient methane production from anaerobic co-digestion of poultry litter with wheat straw in daily sequencing batch reactor: Effects of carbon-to-nitrogen ratio, total solids, and hydraulic retention time

This study performed co-digestion of poultry litter (PL) with wheat straw in the daily anaerobic sequencing batch reactor considering operation parameters of carbon-to-nitrogen ratio (C/N, 11.6 to 28.4), total solids (TS, 2.6 to 9.4%), and hydraulic retention time (HRT, 7.6 to 24.4d). The inoculum with a diverse microbial community structure included 2% of methanogens (Methanosaeta) was chosen. Experimental performance by central composite design showed continuous methane production with the highest biogas production rate (BPR) obtained at C/N = 20, TS = 6%, and HRT = 7.6d, being (1.18 ± 0.14 L/L_R/d). A significant modified quadratic model (p < 0.0001) for predicting BPR was built (R²= 0.9724). The operation parameters and process stability both affected the release of nitrogen, phosphorus, and magnesium in the effluent. The results provided new support for the novel reactor operations for efficient bioenergy production from PL and agricultural wastes.

Effect of temperature and storage methods on liquid digestate: Focusing on the stability, phytotoxicity, and microbial community

Identifying the stability and phytotoxicity of liquid digestate (LD) is necessary for safe agricultural utilization. Storage temperature, method, and time are critical factors that affect the stability and phytotoxicity of LD. This study therefore aimed to explore the dynamics of stability, phytotoxicity, and microbial community of LD in cattle farms under different storage conditions. The results showed that the contents of solids, organic matter, nitrogen, and phosphorous decreased during storage and exhibited temperature dependency. Conversely, the seed germination index increased, which was negatively correlated with dissolved organic carbon and ammonium nitrogen and positively correlated with certain bacteria (Thermovirga and Fastidiosipila). Open storage and/or higher temperature were found to contribute to the stabilization efficiency and phytotoxicity disappearance of LD. Open storage of LD at 30 °C for 60 days and 20 °C for 90 days was safe for its agricultural utilization, while hermetic storage of LD at 30 °C for 120 days and 20 °C for 150 days was safe. However, for storage at 10 °C for 180 days, additional post-treatment is required.

Improving the quality of Napier grass silage with pyroligneous acid: Fermentation, aerobic stability, and microbial communities

The presence of undesirable microorganisms in silage always leads to poor fermentation quality and low aerobic stability. Pyroligneous acid (PA), a by-product of biochar production, is known to have strong antimicrobial and antioxidant activities. To investigate the effects of PA on fermentation characteristics, aerobic stability, and microbial communities, Napier grass was ensiled with or without 1 and 2% PA for 30 days and then aerobically stored for 5 days. The results showed that PA application decreased (P < 0.01) the pH value, ammonia nitrogen content, and number of undesirable microorganisms (coliform bacteria, yeasts, and molds) after 30 days of ensiling and 5 days of exposure to air. The temperature of the PA-treated group was stable during the 5-day aerobic test, which did not exceed room temperature more than 2°C. The addition of PA also enhanced the relative abundance of Lactobacillus and reduced that of Klebsiella and Kosakonia. The relative abundance of Candida was higher in PA-treated silage than in untreated silage. The addition of PA decreased the relative abundance of Kodamaea and increased that of Monascus after 5 days of exposure to air. The abundances of Cladosporium and Neurospora were relatively high in 2% PA-treated NG, while these genera were note observed in the control group. These results suggested that the addition of PA could improve fermentation characteristics and aerobic stability, and alter microbial communities of silage.

Cysteamine Supplementation In Vitro Remarkably Promoted Rumen Fermentation Efficiency towards Propionate Production via Prevotella Enrichment and Enhancing Antioxidant Capacity

Cysteamine (CS) is a vital antioxidant product and nutritional regulator that improves the productive performance of animals. A 2 × 4 factorial in vitro experiment was performed to determine the effect of the CS supplementation levels of 0, 20, 40, and 60 mg/g, based on substrate weight, on the ruminal fermentation, antioxidant capacity, and microorganisms of a high-forage substrate (HF, forage:corn meal = 7:3) in the Statistical Analysis System Institute. After 48 h of incubation, the in vitro dry matter disappearance and gas production in the LF group were higher when compared with a low-forage substrate (LF, forge hay:corn meal = 3:7), which was analyzed via the use of the MIXED procedure of the HF group, and these increased linearly with the increasing CS supplementation (p < 0.01). With regard to rumen fermentation, the pH and acetate were lower in the LF group compared to the HF group (p < 0.01). However, the ammonia N, microbial crude protein, total volatile fatty acids (VFA), and propionate in the LF group were greater than those in the HF group (p < 0.05). With the CS supplementation increasing, the pH, ammonia N, acetate, and A:P decreased linearly, while the microbial crude protein, total VFA, and propionate increased linearly (p < 0.01). Greater antioxidant capacity was observed in the LF group, and the increasing CS supplementation linearly increased the superoxide dismutase, catalase, glutathione peroxidase, total antioxidant capacity, glutathione, and glutathione reductase, while it decreased the malondialdehyde (p < 0.05). No difference occurred in the ruminal bacteria alpha diversity with the increasing CS supplementation, but it was higher in the LF group than in the HF group (p < 0.01). Based on the rumen bacterial community, a higher proportion of Bacteroidota, instead of Firmicutes, was in the LF group than in the HF group. Furthermore, increasing the CS supplementation linearly increased the relative abundance of Prevotella, norank_f_F082, and Prevotellaceae_UCG-001 under the two substrates (p < 0.05). Prevotella, norank_f_F082, and Prevotellaceae_UCG-001 were positively correlated with gas production, rumen fermentation, and antioxidant capacity in a Spearman correlation analysis (r > 0.31, p < 0.05). Overall, a CS supplementation of not less than 20 mg/g based on substrate weight enhanced the rumen fermentation and rumen antioxidant capacity of the fermentation system, and it guided the rumen fermentation towards glucogenic propionate by enriching the Prevotella in Bacteroidetes.

Characteristics of soil microbiota and organic carbon distribution in jackfruit plantation under different fertilization regimes

Manure amendment to improve soil organic carbon (SOC) content is an important strategy to sustain ecosystem health and crop production. Here, we utilize an 8-year field experiment to evaluate the impacts of organic and chemical fertilizers on SOC and its labile fractions as well as soil microbial and nematode communities in different soil depths of jackfruit (Artocarpus heterophyllus Lam.). Three treatments were designed in this study, including control with no amendment (CK), organic manure (OM), and chemical fertilizer (CF). Results showed that OM significantly increased the abundance of total nematodes, bacterivores, bacteria, and fungi as well as the value of nematode channel ratio (NCR) and maturity index (MI), but decreased plant-parasites and Shannon diversity (H′). Soil microbial and nematode communities in three soil depths were significantly altered by fertilizer application. Acidobacteria and Chloroflexi dominated the bacterial communities of OM soil, while Nitrospira was more prevalent in CF treatment. Organic manure application stimulated some functional groups of the bacterial community related to the C cycle and saprotroph-symbiotroph fungi, while some groups related to the nitrogen cycle, pathotroph-saprotroph-symbiotroph and pathotroph-saprotroph fungi were predominated in CF treatment. Furthermore, OM enhanced the soil pH, contents of total soil N, P, K, and SOC components, as well as jackfruit yield. Chemical fertilizers significantly affected available N, P, and K contents. The results of network analyses show that more significant co-occurrence relationships between SOC components and nematode feeding groups were found in CK and CF treatments. In contrast, SOC components were more related to microbial communities than to nematode in OM soils. Partial least-squares-path modeling (PLS-PM) revealed that fertilization had significant effects on jackfruit yield, which was composed of positive direct (73.6%) and indirect effects (fertilization → fungal community → yield). It was found that the long-term manure application strategy improves soil quality by increasing SOM, pH, and nutrient contents, and the increased microbivorous nematodes abundance enhanced the grazing pressure on microorganisms and concurrently promoted microbial-derived SOC turnover.

Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica

Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.

Effects of incineration leachate on anaerobic digestion of excess sludge and the related mechanisms

Anaerobic digestion (AD) refers to a reliable channel for energy recovery from organics. However, the digestion efficiency of excess sludge (ES) has been unsatisfactory since there are defects relating to ES hydrolysis. Therefore, this study explored a method to improve the anaerobic digestion of ES, which could simultaneously treat ES and incineration leachate, and revealed the potential mechanism of AD process. As the investigation was conducted on the influences exerted by incineration leachate on the four phases (i.e., solubilization, methanogenesis, acidogenesis and hydrolysis) of ES anaerobic digestion, and the effect mechanism. According to obtained results, adding appropriate amounts of incineration leachate could facilitate the steps of solubilization, hydrolysis, acidogenesis and methanogenesis of ES. The hydrolysis and acidogenesis efficiency in the leachate added digesters were 5.7%-17.1% and 13%-45% higher than that of the control digester, respectively. Meanwhile, cumulative methane yields (CMY) were 27-86 mL/gVS higher than that in the control digester. Besides, the sludge floc stability was reduced by the leachate with the decrease in the median particle size (MPS) and apparent activation energy (AAE) of the sludge. According to microbial community and diversity analysis, adding incineration leachate increased the relative abundance of hydrolytic-acidification bacteria in the digesters and the relative abundance of Methanosaeta and Methanosarcina. Thus, the digestive performance exhibited by the leachate participated system was improved. These mentioned findings may provide an approach for treating ES and incineration leachate in practical engineering.

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.

Key microbial clusters and environmental factors affecting the removal of antibiotics in an engineered anaerobic digestion system

To identify the key microbial clusters and influencing factors involved in antibiotic removal from engineered anaerobic digestion (AD) systems, the dynamic characteristics of antibiotics, physiochemical factors, microbial communities and functional genes were investigated by 16S rRNA and metagenome sequencing. The results showed that antibiotic removal occurred mainly in the first 21 days, and sulfonamides had the highest removal rate. The key microbial clusters related to the biodegradation of antibiotics consisted mainly of Firmicutes and Bacteroidetes. The key enzymes consisted of deaminases, peptidases, C-N ligases, decarboxylases and alkyl-aryl transferases. Structural equation modelling indicated that low concentrations of propionic acid promoted the biodegradation activities of key microbial clusters in the first 21 days, but their activities were inhibited by the accumulated propionic acid after 21 days. Thus, propionic acid should be regulated in engineered AD systems to prevent the adverse effect of acid inhibition on antibiotic-degrading bacteria.

Microbial characteristics in anaerobic membrane bioreactor treating domestic sewage: Effects of HRT and process performance

Two anaerobic membrane bioreactors (AnMBRs) equipped with different membrane pore size (0.4 or 0.05 µm) were operated at 25˚C and fed with domestic wastewater. The hydraulic retention time (HRT) of the reactors was shortened. The microbial communities of the two AnMBRs were investigated by 16S rRNA gene amplicon sequencing to see the effects of HRT. The predominant Archaea was an aceticlastic methanogen Methanosaeta. The composition of hydrogenotrophic methanogens changed with the HRTs: the population of Methanobacterium was higher for longer HRTs, whereas the population of unclassified Methanoregulaceae was higher for shorter HRTs. The Anaerolineae, Bacteroidia and Clostridia bacteria were dominant in both of the reactors, with a combined relative abundance of over 55%. The relative abundance of Anaerolineae was proportional to the biogas production performance. The change in the population of hydrogenotrophic methanogens or Anaerolineae can be used as an indicator for process monitoring. The sum of the relative abundance of Anaerolineae and Clostridia fluctuated slightly with changes in the HRT in both AnMBRs when the reactor was stably operated. The co-occurrence analysis revealed the relative abundance of the operational taxonomic units belonging to Anaerolineae and Clostridia was functionally equivalent during the treatment of real domestic sewage. A principal coordination analysis revealed that the changes in the microbial community in each reactor were consistent with the change of HRT. In addition, both the HRT and the stability of the process are important factors for maintaining microbial community structures.

Biomethane enhancement from corn straw using anaerobic digestion by-products as pretreatment agents: A highly effective and green strategy

The development of biogas projects feed by lignocellulosic biomass has been constrained by the high cost of pre- and post-treatment. In this study, a novel strategy for pretreatment by using two by-products, i.e., CO₂ and liquid digestate (LD), generated from anaerobic digestion (AD) was developed to overcome these shortcomings. Results showed that corn straw pretreated in LD pressurized under 1 Mpa CO₂ at 55 ℃ resulted in increased glucose and xylose contents and a 9.80% decrease in cellulose crystallinity. After 45 days of AD conversion, the methane yield increased by 50.97% compared with untreated straw. However, pretreatment in LD pressurized under 1 Mpa CO₂ at 170 ℃ produced 5-hydroxymethylfurfural and furfural, which led to a decrease in methane production from the straw in the subsequent AD conversion. The alteration of the microbial community in the pretreated slurry at 55 °C was another potential contributor to the enhanced performance of AD.

Biogas production from high solids digestion of Pennisetum purpureum x Pennisetum typhoideum: Suitable conditions and microbial communities

Effects of organic loading rates (OLRs), temperatures and effluent recirculation rates on biogas production from Giant Juncao Grass (GJG) using pilot-scale semi-continuously fed CSTRs were investigated. Thermophilic reactors could be stably operated at OLR up to 5.0 kg VS m^-3 d^-1, while damaged process stability was detected in mesophilic reactors at OLR of 4.0 kg VS m^-3 d^-1. Higher effluent recirculation rate (3:1) helped lessen negative effects of system being over-loaded, especially for mesophilic reactors. Microbial community analysis revealed that temperatures had the highest effect on bacterial community structure. Firmicutes were the dominant bacterial phyla found under high temperatures, while majority of archaea in all reactors belonged to the phylum Bathyarchaeota. Changes of microbial communities could partly explain system performance under different operating conditions. This study was the first to show GJG as a superior biogas feedstock to other energy crops thanks to its higher methane yields per planting area.

Comparison of anaerobic co-digestion of pig manure and sludge at different mixing ratios at thermophilic and mesophilic temperatures

The objective of this study is to assess the effects of the mixing ratio on the methane production and digestate dewaterability of co-digestion of pig manure (P) and sludge (S). Batch experiments were carried out at five different P/S mixing ratios at mesophilic and thermophilic temperatures. Compared to sludge anaerobic digestion, co-digestion of pig manure with sludge increased methane yield 83.0%-136.5% at mesophilic temperature and 31.3%-68.0% at thermophilic temperature. The normalized capillary suction time (NCST) and total solids (TS) of sediment (centrifugal dewatering) increased when pig manure proportion of substrate increased. The NCST at thermophilic temperatures (4.87-17.58 s g^-1-TSS) was higher than that at mesophilic temperatures (1.89-10.95 s g^-1-TSS). However, the TS of sediment was close at thermophilic and mesophilic temperatures. The results indicated that anaerobic co-digestion of pig manure and sludge at a proper mixing ratio (P/S = 2:1) provides a good choice for energy recovery and land utilization.

Aged landfill leachate enhances anaerobic digestion of waste activated sludge

Anaerobic digestion (AD) is considered as a sustainable pathway to recover energy from organic wastes, but the digestive efficiency for waste activated sludge (WAS) is not as expected due to the limitations in WAS hydrolysis. This study proposes an effective strategy to simultaneously treat WAS and landfill leachate, aiming to promote WAS hydrolysis and enhance organics converting to methane. The effects of landfill leachate on the four stages (i.e., solubilization, hydrolysis, acidogenesis, and methanogenesis) of AD of WAS, as well as the effect mechanisms were investigated. Results showed that adding appropriate amounts of landfill leachate could promote the steps of solubilization, hydrolysis and acidogenesis of WAS, but had no-effect on methanogenesis. The hydrolysis and acidogenesis efficiency in the leachate added digesters were 2.0%-8.4% and 35.2%-72.7% higher than the control digester. Mechanism studies indicated that humic acid (HA) contained in the leachate was conducive to the processes of both hydrolysis and acidogenesis, but detrimental to the methanogenesis. Effects of heavy metals (HMs) on AD of WAS was also dose-dependent. Digestive performance was inhibited by excessive HMs but promoted by moderate dosages. Humic acid and metal ions tend to interact to form complexes, and thus relieve their each inhibition effects. It is also found that the stability of sludge flocs was reduced by the leachate through reducing both apparent activation energy (AAE) and median particle size (MPS) of the sludge. Microbial community and diversity results revealed that the relative abundance of microbes responsible for hydrolysis and acidogenesis increased when landfill leachate was present. This research provides a more technically and economically feasible approach to co-treating and co-utilizing WAS and landfill leachate.

An anaerobic dynamic membrane bioreactor for enhancing sludge digestion: Impact of solids retention time on digestion efficacy

An anaerobic dynamic membrane bioreactor (AnDMBR), which enabled the decoupling of hydraulic retention time (HRT) and solids retention time (SRT), was used for enhancing sludge digestion, with the associated mechanisms elucidated. With the increase of SRT, the biogas production and sludge reduction rate were both enhanced. The specific biogas production and volatile solids (VS) reduction rate were improved to 0.79 L/g VS and 55.9% under SRT 50 d, respectively. Microbial community analysis revealed that Chloroflexi, which is capable of degrading metabolites and dead cells, was enriched at longer SRT. Further analysis showed that both acetoclastic and hydrogenotrophic methanogenesis contributed to the enhanced biogas production under higher SRT compared to the dominance of acetoclastic methanogenesis under lower SRT. The enhanced utilization of organic matter and acetate at longer SRT further confirmed the mechanisms. The results highlighted the potential of AnDMBR for high-efficient sludge digestion.

The potential and effects of saline-alkali alfalfa microbiota under salt stress on the fermentation quality and microbial

Background

The objective of this study was to evaluate the chemical compositions and microbial communities of salt-tolerant alfalfa silage. Salt-tolerant alfalfa was ensiled with no additive control, and cellulase for 30 and 60 to 90 days. In this study, the dry matter (DM) content of the raw material was 29.9% DM, and the crude protein (CP) content of the alfalfa was 21.9% CP.

Results

After 30 days of fermentation, the DM content with the cellulase treatment was reduced by 3.6%, and the CP content was reduced by 12.7%. After 60 days of fermentation, compared with alfalfa raw material, the DM content in the control group (CK) was reduced by 1%, the CP content was reduced by 9.5%, and the WSC (water-soluble carbohydrates) content was reduced by 22.6%. With the cellulase, the lactic acid content of the 30- and 60-day silages was 2.66% DM and 3.48% DM. The content of Firmicutes in salinized alfalfa raw material was less than 0.1% of the total bacterial content. Before and after ensiling, the microbes had similar composition at the phylum level, and were composed of Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria. The abundance of Pantoea was dominant in fresh alfalfa. In the absence of additives, after 30 days and 60 days of silage, the dominant lactic acid bacteria species became Lactococcus and Enterococcus.

Conclusions

The results showed that LAB (Lactobacillus, Lactococcus, Enterococcus, and Pediococcus) played a major role in the fermentation of saline alfalfa silage. It also can better preserve the nutrients of saline alfalfa silage. The use of cellulase enhances the reproduction of Lactobacillus. The fermentation time would also change the microbial community of silage fermentation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02213-2.

Effect of static magnetic field on microbial community during anaerobic digestion

Dairy wastewater is characterized by high concentration of organic compounds and is commonly used for energy production. Methods for enhancement of biogas production include application of magnetizers on the digester to induce static magnetic field (SMF). The study aimed at investigation of Bacteria and Archaea communities during anaerobic digestion of model dairy wastewater exposed to SMF. Magnetic field caused a significant increase in methane production to 373.2 mL/g VS compared to 200.2 mL/g VS in a control reactor and methane content to 56.8% compared to 49.1% in a control reactor. In both reactors, the biomass was dominated by Trichococcus sp. The relative abundance of lactic acid bacteria was of about 10% higher in the reactor exposed to SMF. This higher number of Lactobacillales resulted from a higher acetate production, which additionally caused enhanced growth of Methanosarcinacaea in the reactor exposed to SMF. SMF also stimulated the growth of hydrogenotrophic methanogens.

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

The Impact of Antimicrobial Substances on the Methanogenic Community during Methane Fermentation of Sewage Sludge and Cattle Slurry

This study showed the effect of amoxicillin (AMO), and oxytetracycline (OXY) at a concentration of 512 µg mL−1, and sulfamethoxazole (SMX), and metronidazole (MET) at a concentration of 1024 µg mL−1 on the efficiency of anaerobic digestion (AD) of sewage sludge (SS) and cattle slurry (CS). The production of biogas and methane (CH4) content, and the concentration of volatile fatty acids (VFAs) was analyzed in this study. Other determinations included the concentration of the mcrA gene, which catalyzes the methanogenesis, and analysis of MSC and MST gene concentration, characteristic of the families Methanosarcinaceae and Methanosaetaceae (Archaea). Both substrates differed in the composition of microbial communities, and in the sensitivity of these microorganisms to particular antimicrobial substances. Metronidazole inhibited SS fermentation to the greatest extent (sixfold decrease in biogas production and over 50% decrease in the content of CH4). The lowest concentrations of the mcrA gene (106 gD−1) were observed in CS and SS digestates with MET. A decline in the number of copies of the MSC and MST genes was noted in most of the digestate samples with antimicrobials supplementation. Due to selective pressure, antimicrobials led to a considerably lowered efficiency of the AD process and induced changes in the structure of methanogenic biodiversity.

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry

Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.

Response of Horticultural Soil Microbiota to Different Fertilization Practices

Environmentally friendly agricultural production necessitates manipulation of microbe-plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.

Waste to Energy: A Focus on the Impact of Substrate Type in Biogas Production

Anaerobic digestion is an efficient technology for a sustainable conversion of various organic wastes such as animal manure, municipal solid waste, agricultural residues and industrial waste into biogas. This technology offers a unique set of benefits, some of which include a good waste management technique, enhancement in the ecology of rural areas, improvement in health through a decrease of pathogens and optimization of the energy consumption of communities. The biogas produced through anaerobic digestion varies in composition, but it consists mainly of carbon dioxide methane together with a low quantity of trace gases. The variation in biogas composition are dependent on some factors namely the substrate type being digested, pH, operating temperature, organic loading rate, hydraulic retention time and digester design. However, the type of substrate used is of greater interest due to the direct dependency of microorganism activities on the nutritional composition of the substrate. Therefore, the aim of this review study is to provide a detailed analysis of the various types of organic wastes that have been used as a substrate for the sustainable production of biogas. Biogas formation from various substrates reported in the literature were investigated, an analysis and characterization of these substrates provided the pro and cons associated with each substrate. The findings obtained showed that the methane yield for all animal manure varied from 157 to 500 mL/gVS with goat and pig manure superseding the other animal manure whereas lignocellulose biomass varied from 160 to 212 mL/gVS. In addition, organic municipal solid waste and industrial waste showed methane yield in the ranges of 143–516 mL/gVS and 25–429 mL/gVS respectively. These variations in methane yield are primarily attributed to the nutritional composition of the various substrates.

Effects of intermittent mixing mode on solid state anaerobic digestion of agricultural wastes

This study investigated the effects of three different intermittent mixing modes (top, middle and bottom) on the performance of solid state anaerobic digestion (SS-AD) process of pig manure, corn stover and cucumber residues in a stirred tank reactor (STR). Results showed the cumulative methane yields of reactors had similar values (P > 0.05) except for the unmixed reactor (CK), which had a very low methane production. Reactors of top-mixed (T1) had shortest technical digestion time (T₈₀) and more stable physicochemical characteristics than the other treatments. These findings indicated the three mixing modes had almost no effect on the cumulative methane yields, but affected the digestion process. The main bacteria in T1 reactor was Clostridium_sensu_stricto_1. However, Caldicoprobacter accounted for a relatively large proportion of the bacteria in middle-mixed (T2) and bottom-mixed (T3) which was consistent with the later methane production than T1. Methanosarcina was the dominant archaea in T1 reactor. Methanoculleus and Methanosarcina were the main microorganisms in top and bottom area of T2 and T3 reactor. Acidogenic (top area) and methanogenic zones (bottom area) were formed in all reactors respectively, by combining the physicochemical properties and microorganisms. Overall, T1 showed more advantages for methane production during SS-AD.

Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR

Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.

Microbial community response to ammonia levels in hydrogen assisted biogas production and upgrading process

Biological conversion of carbon dioxide into methane using hydrogen derived from surplus renewable energy (wind power) as reducing power is a novel technology for biogas upgrading. High ammonia concentrations are toxic to the biogas upgrading process, however the mechanisms behind the inhibition as well as the microbial stress response in such unique upgrading system have never been reported. Thus, the effect of high ammonia concentrations on microbial community during hydrogen induced biogas upgrading process was evaluated here. The results showed that a change from aceticlastic pathway to hydrogenotrophic pathway occurred when ammonia level increased (1-7 g NH₄⁺-N L^-1). In addition, the bacteria, potentially syntrophic associated with hydrogenotrophic methanogens, were enriched at high ammonia concentrations. Moreover, growth of some bacteria (e.g., Halanaerobiaceaeen and Leucobacter) which were vulnerable to ammonia toxicity was restored upon hydrogen injection. Furthermore, hydrogen injection under high ammonia concentration could promote growth of some hydrolytic and fermentative bacteria.

Digestive performance of sludge with different crop straws in mesophilic anaerobic digestion

This study evaluated the digestive performance of excess sludge and different crop straws. Methane production, hydrolytic and acidogenic performance of different substrates were specially focused. Results showed that wheat straw presented the highest experimental biochemical methane potential (BMP, 462.5 mL/g VS_removal). Corn cob-added digester obtained the highest VS removal (68.8%) and the lowest methane content due to its high hemicellulose content. Kinetic studies showed that addition of crop straws could shorten the lag phase and accelerate the hydrolysis of substrates. 3DEEM results indicated that lignocellulosic compositions play important roles in sludge hydrolysis, while FE-SEM analysis showed that the lignocellulosic textures of different crop straws determine their hydrolytic performances. Microbial community and diversity results showed that the crop straws in sludge provided abundant nutrients and their unique structures supplied attachment points for microorganisms, which ensured the efficient operation of digestive process.

The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge

It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.

Molecular microbial ecology of stable versus failing rice straw anaerobic digesters

Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1  day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1  day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.

Spatial Variations of Bacterial Communities of an Anaerobic Lagoon-Type Biodigester Fed with Dairy Manure

Anaerobic digestion technology is being widely employed for sustainable management of organic wastes generated in animal farms, industries, etc. Nevertheless, biodigester microbiome is still considered a “black box” because it is regulated by different physico-chemical and operational factors. In this study, the bacterial diversity and composition in different sites of a full-scale lagoon type biodigester (23,000 m3) fed with dairy manure, viz., the influent, beginning, middle, final and effluent were analyzed. The biodigester registered a total of 1445 OTUs, which demonstrated the complex microbial ecosystem in it. Of them, only six OTUs were shared among all the different sampling points. The most abundant phyla belonged to Firmicutes, Proteobacteria, Latescibacteria and Thermotogae. The Simpson and Shannon index showed that the highest microbial diversity was observed in the beginning point of the biodigester, meanwhile, the lowest diversity was recorded in the middle. Based on the UniFrac distances, microbial communities with high similarity were recorded in the middle and final of the biodigester. It can be clearly observed that bacterial communities varied at the different points of the biodigester. However, based on metagenome predictions using PICRUSt, it was found that independent of the differences in taxonomy and location, bacterial communities maintained similar metabolic functions.

Ammonia stress on a resilient mesophilic anaerobic inoculum: Methane production, microbial community, and putative metabolic pathways

Short term inhibition tests, 16S rRNA tag sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), were employed to visualise the effects of increasing total ammoniacal nitrogen (TAN) concentration (3400-10166 ppm TAN) on microbial community structure and metabolic pathways for acetate degradation. The rate of methane production on acetate was significantly reduced by TAN concentrations above 6133 ppm; however, methane continued to be produced, even at 10166 ppm TAN (0.026 ± 0.0003 gCOD.gVS^-1_inoculum.day^-1). Hydrogenotrophic methanogenesis with syntrophic acetate oxidation (SAO) was identified as the dominant pathway for methane production. A shift towards SAO pathways at higher TAN concentrations and a decrease in the number of 'gene hits' for key genes in specific methanogenesis pathways was observed. Overall, the results highlighted potential for inhibition activity testing to be used together with PICRUSt, to estimate changes in microbial metabolism and to better understand microbial resilience in industrial AD facilities.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L_r^-1 d^-1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions.

Effects of Wilting and Lactobacillus plantarum Addition on the Fermentation Quality and Microbial Community of Moringa oleifera Leaf Silage

The objective of this study was to evaluate the effects of wilting and Lactobacillus plantarum (LP) addition on the silage fermentation quality and microbial community of Moringa oleifera Lam. leaf silage. Unwilted (direct-cut) or wilted M. oleifera leaves were prepared either with or without LP (1.0 × 10⁶ cfu/g) followed by either 60 or 120 days of ensiling, leading to eight treatment groups. The results showed that lactic acid was the dominant fermentation product, and no butyric acid was detected for any of the treatments. Higher acetic acid and propionic acid were detected during the fermentation of wilted silage compared to unwilted silage. Although NH₃-N content increased after wilting, the content was far below 10% of the dry matter (DM). In addition, higher pH was observed after 120 days of ensiling compared to 60 days. Wilting also influenced the bacterial community structure. Lactobacillus was the most dominant genus in unwilted samples while Enterobacteriales, Weissella, and Pantoea were the most dominant genera in wilted samples. Furthermore, the relative abundance of undesirable microorganisms was far below that of lactic acid bacteria in all treatments. In summary, wilting had significant effects on fermentation quality, and it was shown that M. oleifera leaves can undergo quality ensiling directly without the addition of LP.

Hydrogenotrophic Methanogenesis and Autotrophic Growth of Methanosarcina thermophila

Although Methanosarcinales are versatile concerning their methanogenic substrates, the ability of Methanosarcina thermophila to use carbon dioxide (CO2) for catabolic and anabolic metabolism was not proven until now. Here, we show that M. thermophila used CO2 to perform hydrogenotrophic methanogenesis in the presence as well as in the absence of methanol. During incubation with hydrogen, the methanogen utilized the substrates methanol and CO2 consecutively, resulting in a biphasic methane production. Growth exclusively from CO2 occurred slowly but reproducibly with concomitant production of biomass, verified by DNA quantification. Besides verification through multiple transfers into fresh medium, the identity of the culture was confirmed by 16s RNA sequencing, and the incorporation of carbon atoms from 13CO2 into 13CH4 molecules was measured to validate the obtained data. New insights into the physiology of M. thermophila can serve as reference for genomic analyses to link genes with metabolic features in uncultured organisms.

Modelling of an anaerobic plug-flow reactor. Process analysis and evaluation approaches with non-ideal mixing considerations

This study shows the implementation of the Anaerobic Digestion Model (ADM1) in an anaerobic plug-flow reactor (PFR) with two approaches based on the use of consecutive continuous stirred tank reactors (CSTR) connected in serie for considering non-ideal mixing. The two-region (TR) model splits each CSTR into two regions, while the particulate retention (PR) model adds a retention parameter. The models were calibrated and validated based on experimental data from a bench-scale reactor treating cow manure. The PFR conventional model slightly outperformed the non-ideal mixing approaches. However, the PR model showed an increase in biomass retention time treating high solid content substrate. Biogas production was not sensitive to variations of the mixing parameters. The liquid fraction content was better represented by the PR model than the PFR and TR models. The study shows how reactor modelling is useful for monitoring and supervising biogas plants.

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions

Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.

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.

Targeting Bacteria and Methanogens To Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure

Microbial communities in residual slurry left after removal of stored liquid dairy manure have been presumed to increase methane emission during new storage, but these microbes have not been studied. While actual manure storage tanks are filled gradually, pilot- and farm-scale studies on methane emissions from such systems often use a batch approach. In this study, six pilot-scale outdoor storage tanks with (10% and 20%) and without residual slurry were filled (gradually or in batch) with fresh dairy manure, and methane and methanogenic and bacterial communities were studied during 120 days of storage. Regardless of filling type, increased residual slurry levels resulted in higher abundance of methanogens and bacteria after 65 days of storage. However, stronger correlation between methanogen abundance and methane flux was observed in gradually filled tanks. Despite some variations in the diversity of methanogens or bacteria with the presence of residual slurry, core phylotypes were not impacted. In all samples, the phylum Firmicutes predominated (∼57 to 70%) bacteria: >90% were members of ClostridiaMethanocorpusculum dominated (∼57 to 88%) archaeal phylotypes, while Methanosarcina gradually increased with storage time. During peak flux of methane, Methanosarcina was the major player in methane production. The results suggest that increased levels of residual slurry have little impact on the dominant methanogenic or bacterial phylotypes, but large population sizes of these organisms may result in increased methane flux during the initial phases of storage.IMPORTANCE Methane is the major greenhouse gas emitted from stored liquid dairy manure. Residual slurry left after removal of stored manure from tanks has been implicated in increasing methane emissions in new storages, and well-adapted microbial communities in it are the drivers of the increase. Linking methane flux to the abundance, diversity, and activity of microbial communities in stored slurries with different levels of residual slurry can help to improve the mitigation strategy. Mesoscale and lab-scale studies conducted so far on methane flux from manure storage systems used batch-filled tanks, while the actual condition in many farms involves gradual filling. Hence, this study provides important information toward determining levels of residual slurry that result in significant reduction of well-adapted microbial communities prior to storage, thereby reducing methane emissions from manure storage tanks filled under farm conditions.