454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

The microbial community of 21 full-scale biogas reactors was examined using 454 pyrosequencing of 16S rRNA gene sequences. These reactors included seven (six mesophilic and one thermophilic) digesting sewage sludge (SS) and 14 (ten mesophilic and four thermophilic) codigesting (CD) various combinations of wastes from slaughterhouses, restaurants, households, etc. The pyrosequencing generated more than 160,000 sequences representing 11 phyla, 23 classes, and 95 genera of Bacteria and Archaea. The bacterial community was always both more abundant and more diverse than the archaeal community. At the phylum level, the foremost populations in the SS reactors included Actinobacteria, Proteobacteria, Chloroflexi, Spirochetes, and Euryarchaeota, while Firmicutes was the most prevalent in the CD reactors. The main bacterial class in all reactors was Clostridia. Acetoclastic methanogens were detected in the SS, but not in the CD reactors. Their absence suggests that methane formation from acetate takes place mainly via syntrophic acetate oxidation in the CD reactors. A principal component analysis of the communities at genus level revealed three clusters: SS reactors, mesophilic CD reactors (including one thermophilic CD and one SS), and thermophilic CD reactors. Thus, the microbial composition was mainly governed by the substrate differences and the process temperature.

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.

Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing

BACKGROUND

Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion.

RESULTS

In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester.

CONCLUSIONS

In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.

Potential of Biological Processes to Eliminate Antibiotics in Livestock Manure: An Overview

Simple Summary

Beside their use to treat infections, antibiotics are used excessively as growth promoting factors in livestock industry. Animals discharge in their feces and urine between 70%–90% of the antibiotic administrated unchanged or in active metabolites. Because livestock manure is re-applied to land as a fertilizer, concerns are growing over spread of antibiotics in water and soil. Development of antibiotic resistant bacteria is a major risk. This paper reviewed the potential of anaerobic digestion to degrade antibiotics in livestock manure. Anaerobic digestion can degrade manure-laden antibiotic to various extents depending on the concentration and class of antibiotic, bioreactor operating conditions, type of feedstock and inoculum sources.

Abstract

Degrading antibiotics discharged in the livestock manure in a well-controlled bioprocess contributes to a more sustainable and environment-friendly livestock breeding. Although most antibiotics remain stable during manure storage, anaerobic digestion can degrade and remove them to various extents depending on the concentration and class of antibiotic, bioreactor operating conditions, type of feedstock and inoculum sources. Generally, antibiotics are degraded during composting > anaerobic digestion > manure storage > soil. Manure matrix variation influences extraction, quantification, and degradation of antibiotics, but it has not been well investigated. Fractioning of manure-laden antibiotics into liquid and solid phases and its effects on their anaerobic degradation and the contribution of abiotic (physical and chemical) versus biotic degradation mechanisms need to be quantified for various manures, antibiotics types, reactor designs and temperature of operations. More research is required to determine the kinetics of antibiotics’ metabolites degradation during anaerobic digestion. Further investigations are required to assess the degradation of antibiotics during psychrophilic anaerobic digestion.

A Review of the Processes, Parameters, and Optimization of Anaerobic Digestion

Anaerobic digestion is a technology that has been used by humans for centuries. Anaerobic digestion is considered to be a useful tool that can generate renewable energy and significant research interest has arisen recently. The underlying theory of anaerobic digestion has been established for decades; however, a great deal of current research is directed towards the optimization of anaerobic digestion under diverse digestion conditions. This review provides a summary of the processes underlying anaerobic digestion, commonly-utilized measurements of anaerobic sludge, operating parameters of anaerobic digesters, and methods of acceleration and optimization used to improve process efficiency. Recent developments in addition to older research are considered to provide a general but comprehensive summary of accumulated knowledge in the theory of anaerobic digestion, as well as considerations in the efficient operation of digesters. We have determined that the numerous factors pertinent to the design and operation of batch-based anaerobic digesters must each be considered to ensure the maximum efficiency and cost-effectiveness of a digester provided its respective operating conditions.

Crop Residue Burning in India: Policy Challenges and Potential Solutions

India, the second largest agro-based economy with year-round crop cultivation, generates a large amount of agricultural waste, including crop residues. In the absence of adequate sustainable management practices, approximately 92 seems a very small number of metric tons of crop waste is burned every year in India, causing excessive particulate matter emissions and air pollution. Crop residue burning has become a major environmental problem causing health issues as well as contributing to global warming. Composting, biochar production and mechanization are a few effective sustainable techniques that can help to curtail the issue while retaining the nutrients present in the crop residue in the soil. The government of India has attempted to curtail this problem, through numerous measures and campaigns designed to promote sustainable management methods such as converting crop residue into energy. However, the alarming rise of air pollution levels caused by crop residue burning in the city of Delhi and other northern areas in India observed in recent years, especially in and after the year of 2015, suggest that the issues is not yet under control. The solution to crop residue burning lies in the effective implementation of sustainable management practices with Government interventions and policies. This manuscript addresses the underlying technical as well as policy issues that has prevented India from achieving a long-lasting solution and also potential solutions that have been overlooked. However, effective implementation of these techniques also requires us to look at other socioeconomic aspects that had not been considered. This manuscript also discusses some of the policy considerations and functionality based on the analyses and current practices. The agricultural waste sector can benefit immensely from some of the examples from other waste sectors such as the municipal solid waste (MSW) and wastewater management where collection, segregation, recycling and disposal are institutionalized to secure an operational system. Active stakeholder involvement including education and empowerment of farmers along with technical solutions and product manufacturing can also assist tremendously. Even though the issue of crop residue burning touches many sectors, such as environment, agriculture, economy, social aspects, education, and energy, the past governmental efforts mainly revolved around agriculture and energy. This sectorial thinking is another barrier that needs to be broken. The government of India as well as governments of other developing countries can benefit from the emerging concept of nexus thinking in managing environmental resources. Nexus thinking promotes a higher-level integration and higher level of stakeholder involvement that goes beyond the disciplinary boundaries, providing a supporting platform to solve issues such as crop residue burning.

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.

Microbial anaerobic digestion (bio-digesters) as an approach to the decontamination of animal wastes in pollution control and the generation of renewable energy

With an ever increasing population rate; a vast array of biomass wastes rich in organic and inorganic nutrients as well as pathogenic microorganisms will result from the diversified human, industrial and agricultural activities. Anaerobic digestion is applauded as one of the best ways to properly handle and manage these wastes. Animal wastes have been recognized as suitable substrates for anaerobic digestion process, a natural biological process in which complex organic materials are broken down into simpler molecules in the absence of oxygen by the concerted activities of four sets of metabolically linked microorganisms. This process occurs in an airtight chamber (biodigester) via four stages represented by hydrolytic, acidogenic, acetogenic and methanogenic microorganisms. The microbial population and structure can be identified by the combined use of culture-based, microscopic and molecular techniques. Overall, the process is affected by bio-digester design, operational factors and manure characteristics. The purpose of anaerobic digestion is the production of a renewable energy source (biogas) and an odor free nutrient-rich fertilizer. Conversely, if animal wastes are accidentally found in the environment, it can cause a drastic chain of environmental and public health complications.

Biogas production from co-digestion of corn stover and chicken manure under anaerobic wet, hemi-solid, and solid state conditions

Corn stover (CS) and chicken manure (CM) are ubiquitous agricultural wastes at low cost and have the potential to achieve a nutrient-balance when mixed together to produce biomethane via anaerobic digestion (AD). The main objective of this work was to investigate methane production at different CS to CM ratios and to evaluate the process stability under wet (W-AD), hemi-solid state (HSS-AD) and solid state (SS-AD) conditions. Results showed that synergistic effects were found when mixing two substrates at CS:CM ratios of 3:1 and 1:1 (on volatile solid basis). The highest methane yield of 218.8 mL/g VS added was achieved in W-AD at CS:CM ratio of 3:1. In SS-AD, the highest volumetric methane productivity of 14.2L methane/L reactor volume was found at CS:CM of 1:1. The results of this work provide useful information to improve the efficiency and stability of co-digestion of CS and CM under different AD conditions.

Management strategies for anaerobic digestate of organic fraction of municipal solid waste: Current status and future prospects

Anaerobic digestion has emerged as the preferred treatment for organic fraction of municipal solid waste. Digestate management strategies are devised not only for safe disposal but also to increase the value and marketability. Regulations and standards for digestate management are framed to address the pollution concerns, conserve vulnerable zones, prevent communicable diseases, and to educate on digestate storage and applications. Regulations and the desired end uses are the main drivers for the enhancement of digestate through pretreatment, in vessel cleaning, and post-digestion treatment technologies for solid and liquid fractions of digestate. The current management practice involves utilization of digestate for land application either as fertilizer or soil improver. Prospects are bright for alternative usage such as microalgal cultivation, biofuel and bioethanol production. Presently, the focus of optimization of the anaerobic digestion process is directed only towards enhancing biogas yield, ignoring the quality of digestate produced. A paradigm shift is needed in the approach from 'biogas optimization' to 'integrated biogas-digestate optimization'.

Methodologies to assess biodegradation of bioplastics during aerobic composting and anaerobic digestion: A review

Bioplastics are emerging on the market as sustainable materials which rise to the challenge to improve the lifecycle of plastics from the perspective of the circular economy. The article aims at providing a critical insight of research studies carried out in the last 20 years on the degradation of bioplastics under aerobic composting and anaerobic digestion conditions. It mainly focuses on the various and different methodologies which have been proposed and developed to monitor the process of biodegradation of several bioplastic materials: CO₂ and CH₄ measurements, mass loss and disintegration degree, spectroscopy, visual analysis and scanning electron microscopy. Moreover, across the wide range of studies, the process conditions of the experimental setup, such as temperature, test duration and waste composition, often vary from author to author and in accordance with the international standard followed for the test. The different approaches, in terms of process conditions and monitoring methodologies, are pointed out in the review and highlighted to find significant correlations between the results obtained and the experimental procedures. These observed correlations allow critical considerations to be reached about the efficiency of the methodologies and the influence of the main abiotic factors on the process of biodegradation of bioplastics.

Environmental impact of biogas: A short review of current knowledge

The social acceptance of biogas is often hampered by environmental and health concerns. In this study, the current knowledge about the impact of biogas technology is presented and discussed. The survey reports the emission rate estimates of the main greenhouse gases (GHG), namely CO₂, CH₄ and N₂O, according to several case studies conducted over the world. Direct emissions of gaseous pollutants are then discussed, with a focus on nitrogen oxides (NO_x); evidences of the importance of suitable biomass and digestate storages are also reported. The current knowledge on the environmental impact induced by final use of digestate is critically discussed, considering both soil fertility and nitrogen release into atmosphere and groundwater; several case studies are reported, showing the importance of NH₃ emissions with regards to secondary aerosol formation. The biogas upgrading to biomethane is also included in the study: with this regard, the methane slip in the off-gas can significantly reduce the environmental benefits.

Programmed iron oxide nanoparticles disintegration in anaerobic digesters boosts biogas production

A novel concept of dosing iron ions using Fe3O4 engineered nanoparticles is used to improve biogas production in anaerobic digestion processes. Since small nanoparticles are unstable, they can be designed to provide ions in a controlled manner, and the highest ever reported improvement of biogas production is obtained. The nanoparticles evolution during operation is followed by an array of spectroscopic techniques.

Towards a carbon-negative sustainable bio-based economy

The bio-based economy relies on sustainable, plant-derived resources for fuels, chemicals, materials, food and feed rather than on the evanescent usage of fossil resources. The cornerstone of this economy is the biorefinery, in which renewable resources are intelligently converted to a plethora of products, maximizing the valorization of the feedstocks. Innovation is a prerequisite to move a fossil-based economy toward sustainable alternatives, and the viability of the bio-based economy depends on the integration between plant (green) and industrial (white) biotechnology. Green biotechnology deals with primary production through the improvement of biomass crops, while white biotechnology deals with the conversion of biomass into products and energy. Waste streams are minimized during these processes or partly converted to biogas, which can be used to power the processing pipeline. The sustainability of this economy is guaranteed by a third technology pillar that uses thermochemical conversion to valorize waste streams and fix residual carbon as biochar in the soil, hence creating a carbon-negative cycle. These three different multidisciplinary pillars interact through the value chain of the bio-based economy.

Technologies for Biogas Upgrading to Biomethane: A Review

The environmental impacts and high long-term costs of poor waste disposal have pushed the industry to realize the potential of turning this problem into an economic and sustainable initiative. Anaerobic digestion and the production of biogas can provide an efficient means of meeting several objectives concerning energy, environmental, and waste management policy. Biogas contains methane (60%) and carbon dioxide (40%) as its principal constituent. Excluding methane, other gasses contained in biogas are considered as contaminants. Removal of these impurities, especially carbon dioxide, will increase the biogas quality for further use. Integrating biological processes into the bio-refinery that effectively consume carbon dioxide will become increasingly important. Such process integration could significantly improve the sustainability of the overall bio-refinery process. The biogas upgrading by utilization of carbon dioxide rather than removal of it is a suitable strategy in this direction. The present work is a critical review that summarizes state-of-the-art technologies for biogas upgrading with particular attention to the emerging biological methanation processes. It also discusses the future perspectives for overcoming the challenges associated with upgradation. While biogas offers a good substitution for fossil fuels, it still not a perfect solution for global greenhouse gas emissions and further research still needs to be conducted.

Biological Pretreatment Strategies for Second-Generation Lignocellulosic Resources to Enhance Biogas Production

With regard to social and environmental sustainability, second-generation biofuel and biogas production from lignocellulosic material provides considerable potential, since lignocellulose represents an inexhaustible, ubiquitous natural resource, and is therefore one important step towards independence from fossil fuel combustion. However, the highly heterogeneous structure and recalcitrant nature of lignocellulose restricts its commercial utilization in biogas plants. Improvements therefore rely on effective pretreatment methods to overcome structural impediments, thus facilitating the accessibility and digestibility of (ligno)cellulosic substrates during anaerobic digestion. While chemical and physical pretreatment strategies exhibit inherent drawbacks including the formation of inhibitory products, biological pretreatment is increasingly being advocated as an environmentally friendly process with low energy input, low disposal costs, and milder operating conditions. Nevertheless, the promising potential of biological pretreatment techniques is not yet fully exploited. Hence, we intended to provide a detailed insight into currently applied pretreatment techniques, with a special focus on biological ones for downstream processing of lignocellulosic biomass in anaerobic digestion.

Genome-Centric Metatranscriptomics Analysis Reveals the Role of Hydrochar in Anaerobic Digestion of Waste Activated Sludge

Anaerobic digestion (AD) of waste activated sludge (WAS) has been widely used, while it poses problems including low methane yield and production rate. Hydrochar is produced by hydrothermal liquefaction of biomass; however, little is known about the role of hydrochar in promoting AD of WAS. The present study showed that hydrochar increased the methane production rate by 30.8% and yield by 31.4% of hydrothermal pretreated dewatered WAS. Hydrochar increased the methane production rate and yield by enhancing the acidification and methanogenesis processes. Genomic-centric metatranscriptomics were used to identify the metabolic activities and transcriptomic response of individual metagenome-assembled genomes that were enriched by hydrochar. Although Methanosarcina sp. FDU0106 had been shown unable to used H₂, it had the complete pathway for the reduction of CO₂ to methane. Syntrophomonas sp. FDU0164 expressed genes for extracellular electron transfer via electrically pili, suggesting that Syntrophomonas sp. FDU0164 and Methanosarcina sp. FDU0106 were exchanging electrons via direct interspecies electron transfer. The expression of pili was decreased, indicating that hydrochar could replace its roles. Additionally, Firmicutes sp. FDU0048, Proteiniphilum sp. FDU0082, and Aminobacterium mobile FDU0089 were related to the degradation of organics, which could be related to the enhanced methane yield.

Relating Anaerobic Digestion Microbial Community and Process Function

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Effects and optimization of the use of biochar in anaerobic digestion of food wastes

The addition of various amounts of biochar to anaerobic digestion of food wastes at different ratios of inoculum to substrate (ISR) was investigated to evaluate the effect of biochar as a functional additive and to optimize the additive dosage of biochar. The biochar treatments at ISR 2, 1, and 0.8 shortened the lag phase of digestion by -20.0%-10.9%, 43.3%-54.4%, and 36.3%-54.0%, and raised the maximum methane production rate by 100%-275%, 100%-133.3%, and 33.3%-100%, respectively, compared to control without biochar. Biochar also enhanced the degradation rate of dissolved organics and volatile fatty acids. Furthermore, the amount of biochar with best effectiveness at ISR = 2, 1, and 0.8 was 2.5, 0.625, and 0.5 g g(-1)-waste, respectively. Therefore, the effectiveness of biochar depended on the additive amount of biochar and at the same time the inoculum amount, implying a complementary role of abiotic biochar to biotic inoculum.

Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome

Mixed communities of microbes play important roles in health, the environment, agriculture, and biotechnology. While tapping the combined activities of organisms within microbiomes may allow the utilization of a wider range of substrates in preference to the use of pure cultures for biomanufacturing, harnessing the metabolism of these mixed cultures remains a major challenge. Here, we predicted metabolic functions of bacteria in a microbiome that produces medium-chain fatty acids from a renewable feedstock. Our findings lay the foundation for efforts to begin addressing how to engineer and control microbiomes for improved biomanufacturing, how to build synthetic mixtures of microbes that produce valuable chemicals from renewable resources, and how to better understand the microbial communities that contribute to health, agriculture, and the environment.

Biomanufacturing from renewable feedstocks can offset fossil fuel-based chemical production. One potential biomanufacturing strategy is production of medium-chain fatty acids (MCFA) from organic feedstocks using either pure cultures or microbiomes. While the set of microbes in a microbiome can often metabolize organic materials of greater diversity than a single species can and while the role of specific species may be known, knowledge of the carbon and energy flow within and between organisms in MCFA-producing microbiomes is only now starting to emerge. Here, we integrated metagenomic, metatranscriptomic, and thermodynamic analyses to predict and characterize the metabolic network of an anaerobic microbiome producing MCFA from organic matter derived from lignocellulosic ethanol fermentation conversion residue. A total of 37 high-quality (>80% complete, <10% contamination) metagenome-assembled genomes (MAGs) were recovered from the microbiome, and metabolic reconstruction of the 10 most abundant MAGs was performed. Metabolic reconstruction combined with metatranscriptomic analysis predicted that organisms affiliated with Lactobacillus and Coriobacteriaceae would degrade carbohydrates and ferment sugars to lactate and acetate. Lachnospiraceae- and Eubacteriaceae-affiliated organisms were predicted to transform these fermentation products to MCFA. Thermodynamic analyses identified conditions under which H₂ is expected to be either produced or consumed, suggesting a potential role of H₂ partial pressure in MCFA production. From an integrated systems analysis perspective, we propose that MCFA production could be improved if microbiomes were engineered to use homofermentative instead of heterofermentative Lactobacillus and if MCFA-producing organisms were engineered to preferentially use a thioesterase instead of a coenzyme A (CoA) transferase as the terminal enzyme in reverse β-oxidation.

IMPORTANCE Mixed communities of microbes play important roles in health, the environment, agriculture, and biotechnology. While tapping the combined activities of organisms within microbiomes may allow the utilization of a wider range of substrates in preference to the use of pure cultures for biomanufacturing, harnessing the metabolism of these mixed cultures remains a major challenge. Here, we predicted metabolic functions of bacteria in a microbiome that produces medium-chain fatty acids from a renewable feedstock. Our findings lay the foundation for efforts to begin addressing how to engineer and control microbiomes for improved biomanufacturing, how to build synthetic mixtures of microbes that produce valuable chemicals from renewable resources, and how to better understand the microbial communities that contribute to health, agriculture, and the environment.

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Biomethane Production From Lignocellulose: Biomass Recalcitrance and Its Impacts on Anaerobic Digestion

Anaerobic digestion using lignocellulosic material as the substrate is a cost-effective strategy for biomethane production, which provides great potential to convert biomass into renewable energy. However, the recalcitrance of native lignocellulosic biomass makes it resistant to microbial hydrolysis, which reduces the bioconversion efficiency of organic matter into biogas. Therefore, it is necessary to critically investigate the correlation between lignocellulose characteristics and bioconversion efficiency. Accordingly, this review comprehensively summarizes the anaerobic digestion process and rate-limiting step, structural and compositional properties of lignocellulosic biomass, recalcitrance and inhibitors of lignocellulose and their major effects on anaerobic digestion for biomethane production. Moreover, various type of pretreatment strategies applied to lignocellulosic biomass was discussed in detail, which would contribution to cell wall degradation and improvement of biomethane yields. In the view of current knowledge, high energy input and cost requirements are the main limitations of these pretreatment methods. In addition to optimization of fermentation process, further studies should focus much more on key structural influence factors of biomass recalcitrance and anaerobic digestion efficiency, which will contribute to improvement of biomethane production from lignocellulose.

Hormesis-Like Effects of Tetrabromobisphenol A on Anaerobic Digestion: Responses of Metabolic Activity and Microbial Community

Tetrabromobisphenol A (TBBPA) has extensive applications in various fields; its release into ecosystems and the potential toxic effects on organisms are becoming major concerns. Here, we investigated the effects of TBBPA on anaerobic digestion, whose process is closely related to the carbon cycles under anaerobic conditions. The results revealed that TBBPA exhibited dose-dependent hormesis-like effects on methane production from glucose, i.e., the presence of 0.1 mg/L TBBPA increased the methane production rate by 8.79%, but 1.0-4.0 mg/L TBBPA caused 3.45-28.98% of decrement. We found that TBBPA was bound by the tyrosine-like proteins of the extracellular polymeric substances of anaerobes and induced the increase of reactive oxygen species, whose slight accumulation stimulated the metabolism activities but high accumulation increased the apoptosis of anaerobes. Owing to the differences between individual anaerobes in tolerance, TBBPA at 0.1 mg/L stimulated the acidogenesis and hydrogenotrophic methanogenesis, whereas higher levels (i.e., 1.0-4.0 mg/L) severely restrained all of the processes of acidogenesis, acetogenesis, and methanogenesis. Along with the accumulation of bisphenol A (BPA) produced from TBBPA by Longilinea sp. and Pseudomonas sp., the methanogenic pathway was partly shifted from acetate-dependent to hydrogen-dependent direction, and the activities of carbon monoxide dehydrogenase and acetyl-CoA decarbonylase/synthase were inhibited, while acetate kinase and F420 were hormetically affected. These findings elucidated the mechanism of anaerobic syntrophic consortium responses to TBBPA, supplementing the potential environmental risks of brominated flame retardants.

Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems

Anaerobic digestion (AD) is a microbial process widely used to treat organic wastes. While the microbes involved in digestion of municipal sludge are increasingly well characterized, the taxonomic and functional compositions of AD digesters treating industrial wastewater have been understudied. This study examined metagenomes from a biogas-producing digester treating municipal sludge in Shek Wu Hui (SWH), Hong Kong and an industrial wastewater digester in Guangzhou (GZ), China, and compared their taxonomic composition and reconstructed biochemical pathways. Genes encoding carbohydrate metabolism and protein metabolism functions were overrepresented in GZ, while genes encoding functions related to fatty acids, lipids and isoprenoids were overrepresented in SWH, reflecting the plants' feedstocks. Mapping of genera to functions in each community indicated that both digesters had a high level of functional redundancy, and a more even distribution of genera in GZ suggested that it was more functionally stable. While fermentation in both samples was dominated by Clostridia, SWH had an overrepresentation of Proteobacteria, including syntrophic acetogens, reflecting its more complex substrate. Considering the growing importance of biogas as an alternative fuel source, a detailed mechanistic understanding of AD is important and this report will be a basis for further study of industrial wastewater AD.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Gene Removal in Anaerobic Digestion of Swine Manure

This study employed high-throughput quantitative PCR and 16S rRNA sequencing to evaluate the effect of temperature and residual antibiotics on the dynamics of antibiotic resistance genes (ARGs) and microbial communities during anaerobic digestion of swine manure. The abundances of total ARGs and 16S rRNA genes significantly decreased in all of four treatments (25°C, 37°C, and 37°C with 50 mg of wet weight antibiotics of body weight, and 55°C). The abundances of most ARG types were significantly correlated with those of the 16S rRNA gene and transposase gene (P < 0.01). However, the abundances of total ARGs at 55°C were much higher than those of other treatments. Meanwhile, the microbial communities at 55°C, where the Streptococcus pathogen remained at a relatively high abundance and cellulose degraders and hydrogen producers, such as Ethanoligenens and Coprococcus bacteria, increased, were markedly different from those of other treatments. Redundancy analysis indicates that temperature, pH, and the genus Streptococcus had the highest explanation for ARG variation among experimental factors, chemical properties, and representative genera, respectively. Network analysis further showed that the genus Streptococcus contributed greatly to the higher ARG abundance at 55°C. The moderate antibiotic residue only caused a slight and transitory inhibition for microbially diverse populations and promotion for ARG abundance, probably due to the degradation of antibiotics and microbial adaptability. Our results clarify the cooperativity of gene transfer-related items on ARG variation and intensively prove that higher temperature cannot always achieve better ARG removal in anaerobic digestion unless pathogens and gene transfer elements are more efficiently inhibited.IMPORTANCE Antibiotic resistance genes (ARGs) are frequently detected with high abundance in manure-applied soils. Anaerobic digestion is one of widely used processes for animal waste treatment. Thus, it is critical to understand the potential of anaerobic digestion to attenuate ARGs. Although some previous studies recommended thermophilic digestion for ARG removal, they did not get sufficient evidence to support this view. The antibiotics applied to animals are mostly excreted through feces and urine because of incomplete metabolism. It is indispensable to know whether residual antibiotics in manure will hinder ARG attenuation in anaerobic digesters. The significance of our research is in comprehensively understanding the evolution and mechanism of ARGs in anaerobic digestion of swine manure affected by temperature and residual antibiotics, which will allow the development of an ARG elimination strategy before their release into the environment.