Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes

Improved biohydrogen production by co-fermentation of corn straw and excess sludge: Insights into biochemical process, microbial community and metabolic genes

The global climate change mainly caused by fossil fuels combustion promotes that zero-carbon hydrogen production through eco-friendly methods has attracted attention in recent years. This investigation explored the biohydrogen production by co-fermentation of corn straw (CS) and excess sludge (ES), as well as comprehensively analyzed the internal mechanism. The results showed that the optimal ratio of CS to ES was 9:1 (TS) with the biohydrogen yield of 101.8 mL/g VS, which was higher than that from the mono-fermentation of CS by 1.0-fold. The pattern of volatile fatty acids (VFAs) indicated that the acetate was the most preponderant by-product in all fermentation systems during the biohydrogen production process, and its yield was improved by adding appropriate dosage of ES. In addition, the content of soluble COD (SCOD) was reduced as increasing ES, while concentration of NH4+-N showed an opposite tendency. Microbial community analysis revealed that the microbial composition in different samples showed a significant divergence. Trichococcus was the most dominant bacterial genus in the optimal ratio of 9:1 (CS/ES) fermentation system and its abundance was as high as 41.8%. The functional genes prediction found that the dominant metabolic genes and hydrogen-producing related genes had not been significantly increased in co-fermentation system (CS/ES = 9:1) compared to that in the mono-fermentation of CS, implying that enhancement of biohydrogen production by adding ES mainly relied on balancing nutrients and adjusting microbial community in this study. Further redundancy analysis (RDA) confirmed that biohydrogen yield was closely correlated with the enrichment of Trichococcus.

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

BACKGROUND

The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.

RESULTS

The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.

CONCLUSIONS

This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

Biomethane recovery through co-digestion of cheese whey and glycerol in a two-stage anaerobic fluidized bed reactor: Effect of temperature and organic loading rate on methanogenesis

Anaerobic digestion for CH₄ recovery in wastewater treatment has been carried out with different strategies to increase process efficiency, among which co-digestion and the two-stage process can be highlighted. In this context, this study aimed at evaluating the co-digestion of cheese whey and glycerol in a two-stage process using fluidized bed reactors, verifying the effect of increasing the organic loading rate (OLR) (2-20 g-COD.L^-1.d^-1) and temperature (thermophilic and mesophilic) in the second stage methanogenic reactor. The mesophilic methanogenic reactor (R-Meso) (mean temperature of 22 °C) was more tolerant to high OLR and its best performance was at 20 g-COD.L^-1.d^-1, resulting in methane yield (MY) and methane production (MPR) of 273 mL-CH₄.g-COD^-1 and 5.8 L-CH₄.L^-1.d^-1 (with 67% of CH₄), respectively. Through 16S rRNA gene massive sequencing analysis, a greater diversity of microorganisms was identified in R-Meso than in R-Thermo (second stage methanogenic reactor, 55 °C). Firmicutes was the phyla with higher relative abundance in R-Thermo, while in R-Meso the most abundant ones were Proteobacteria and Bacteroidetes. Regarding the Archaea domain, a predominance of hydrogenotrophic microorganisms could be observed, being the genera Methanothermobacter and Methanobacterium the most abundant in R-Thermo and R-Meso, respectively. The two-stage system composed with a thermophilic acidogenic reactor + R-Meso was more adequate for the co-digestion of cheese whey and glycerol than the single-stage process, promoting increases of up to 47% in the energetic yield (10.3 kJ.kg-COD^-1) and 14% in organic matter removal (90.5%).

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

BACKGROUND

The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle.

RESULTS

The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale.

CONCLUSIONS

Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.

Biological Aspects, Advancements and Techno-Economical Evaluation of Biological Methanation for the Recycling and Valorization of CO2

Nowadays, sustainable and renewable energy production is a global priority. Over the past decade, several Power-to-X (PtX) technologies have been proposed to store and convert the surplus of renewable energies into chemical bonds of chemicals produced by different processes. CO2 is a major contributor to climate change, yet it is also an undervalued source of carbon that could be recycled and represents an opportunity to generate renewable energy. In this context, PtX technologies would allow for CO2 valorization into renewable fuels while reducing greenhouse gas (GHG) emissions. With this work we want to provide an up-to-date overview of biomethanation as a PtX technology by considering the biological aspects and the main parameters affecting its application and scalability at an industrial level. Particular attention will be paid to the concept of CO2-streams valorization and to the integration of the process with renewable energies. Aspects related to new promising technologies such as in situ, ex situ, hybrid biomethanation and the concept of underground methanation will be discussed, also in connection with recent application cases. Furthermore, the technical and economic feasibility will be critically analyzed to highlight current options and limitations for implementing a sustainable process.

Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics

Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.

Engineering Cupriavidus necator DSM 545 for the one-step conversion of starchy waste into polyhydroxyalkanoates

Starch-rich by-products could be efficiently exploited for polyhydroxyalkanoates (PHAs) production. Unfortunately, Cupriavidus necator DSM 545, one of the most efficient PHAs producers, is not able to grow on starch. In this study, a recombinant amylolytic strain of C. necator DSM 545 was developed for the one-step PHAs production from starchy residues, such as broken rice and purple sweet potato waste. The glucodextranase G1d from Arthrobacter globiformis I42 and the α-amylase amyZ from Zunongwangia profunda SM-A87 were co-expressed into C. necator DSM 545. The recombinant C. necator DSM 545 #11, selected for its promising hydrolytic activity, produced high biomass levels with noteworthy PHAs titers: 5.78 and 3.65 g/L from broken rice and purple sweet potato waste, respectively. This is the first report on the engineering of C. necator DSM 545 for efficient amylase production and paves the way to the one-step conversion of starchy waste into PHAs.

Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches

Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms under anaerobic conditions. Methane gas, a beneficial by-product of the AD process, is a renewable energy source that can replace fossil fuels following purification. However, detailed functional roles and metabolic interactions between microbial populations involved in organic waste removal and methanogenesis are yet to be known. Recent metagenomic approaches based on advanced high-throughput sequencing techniques have enabled the exploration of holistic microbial taxonomy and functionality of complex microbial populations involved in the AD process. Gene-centric and genome-centric analyses based on metagenome-assembled genomes are a platform that can be used to study the composition of microbial communities and their roles during AD. This review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the AD process.

Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste

Bacterial community structure and dynamics in anaerobic digesters are primarily influenced by feedstock composition. It is therefore important to unveil microbial traits that explain microbiome variations in response to substrate changes. Here, gene and genome-centric metagenomics were used to examine microbiome dynamics in four laboratory-scale reactors, in which sewage sludge was co-digested with increasing amounts of food waste. A co-occurrence network revealed microbiome shifts in response to changes in substrate composition and concentration. Food waste concentration correlated with extracellular enzymes and metagenome-assembled genomes (MAGs) involved in the degradation of complex carbohydrates commonly found in fruits and plant cell walls as well as with the abundance of hydrolytic MAGs. A key role was attributed to Proteiniphillum for being the only bacteria that encoded the complete pectin degradation pathway. These results suggest that changes of feedstock composition establish new microbial niches for bacteria with the capacity to degrade newly added substrates.

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Two-Stage anaerobic digestion in agroindustrial waste treatment: A review

The anaerobic digestion is a process widely recognized as an interesting alternative for the treatment and stabilization of residual organic substrates. However, several technical limitations were observed based on the characteristics of the organic matter submitted to the process, such as the presence of high concentrations of soluble sugars or fats. The technology of anaerobic digestion in multiple stages is described as a viable option in the control of variables, optimizing the environmental conditions of the main microorganisms involved in the process, assuring high solid removal and methane production, besides allowing a higher energy yield through the generation of molecular fuel hydrogen. Several studies reviewed the process of anaerobic digestion in multiple stages in the treatment of food waste, although few report its use applied directly to agroindustrial residues. Thus, the present work aims to review the literature evaluating the scenario and viability of the multi-stage anaerobic digestion process applied to agroindustrial effluents. Effluents such as manipueira, vinasse, and dairy wastewater are substrates that present high yields when treated by AD processes with stage separation. The high concentration of easily fermentable sugars results in a high production of molecular hydrogen (co-product of the production of volatile acids in the acid phase) and methane (methanogenic phase). The great challenges related to the development of the sector are focused on the stability of the composition and yield of hydrogen in the acid phase, besides the problems resulting from the treatment of complex residues. Thus, the present study suggests that future works should focus on the technologies of new microorganisms and optimization of process parameters, providing maturation and scale-up of the two-stage anaerobic digestion technique.

Influence of biodegradable polybutylene succinate and non-biodegradable polyvinyl chloride microplastics on anammox sludge: Performance evaluation, suppression effect and metagenomic analysis

Microplastics (MPs) has been widely detected in wastewater treatment plants. However, there is a lack of research on its influence on anaerobic ammonia oxidation (anammox) process. Therefore, the effects of polybutylene succinate (PBS) and polyvinyl chloride (PVC) MPs on the nitrogen removal performance, microbial community and metabolites of anammox sludge were investigated. Results showed that PBS and PVC MPs reduced the nitrite removal efficiency of the anammox sludge, and PVC1 (0.1 g/L PVC) group was the most significant at 19.2 %. Fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS) spectra showed that PBS2 (0.5 g/L PBS) group increased the polysaccharide content in the anammox sludge. This may be because of the byproduct, which was produce during the biodegradation of PBS MPs, and decrease the agglomeration capacity of sludge, so as to increase the mass transfer. PBS2 group reduced the relative abundance of Methanosaeta (10.18 %) and the methane modules, and stimulated the anammox bacteria Ca. Brocadia (1.17 %) and the relative nitrogen metabolism modules. PVC2 group reduced the relative abundance of Ca. Brocadia (3.02 %), while was enriched Methanosaeta (2.1 %). Non-biodegradable PVC MPs was more harmful to anammox sludge, which would draw attention to the entry of PVC MPs into the anammox system.

Carbon migration and metagenomic characteristics during anaerobic digestion of rice straw

BACKGROUND

Considerable interest has been expressed in the development of anaerobic digestion (AD) of straw to solve the environmental problems caused by the dumping and burning of straw and to generate clean energy. However, the poor biodegradability of straw and the low efficiency of energy generation achieved during its AD are problematic. Studying the parameter changes involved in the process of AD is helpful for clarifying its micro-mechanisms and providing a theoretical basis for improving its efficiency. Currently, most research into process parameters has focused on gas production, methane content, pH, and volatile fatty acid (VFA) content; limited research has focused on carbon migration and functional gene changes during the AD of straw.

RESULTS

Carbon migration and changes in metagenomic characteristics during the AD of rice straw (RS) were investigated. Accumulated biogas production was 388.43 mL/g VS. Carbon in RS was consumed, and the amount of carbon decreased from 76.28 to 36.83 g (conversion rate 51.72%). The degree of hydrolysis rapidly increased during the first 5 days, and a large amount of carbon accumulated in the liquid phase before migrating into the gas phase. By the end of AD, the amount of carbon in the liquid and gas phases was 2.67 and 36.78 g, respectively. According to our metagenomic analysis, at the module level, the abundance of M00357, M00567, M00356, and M00563 (the modules related to the generation of methane) during AD were 51.23-65.43%, 13.96-26.88%, 16.44-22.98%, and 0.83-2.40%, respectively. Methyl-CoM, 5-methyl-5,6,7,8-tetrahydromethanopterin, and Acetyl-CoA were important intermediates.

CONCLUSIONS

Carbon was enriched in the liquid phase for the first 5 days and then gradually consumed, and most of the carbon was transferred to the gas phase by the end of AD. In this study, AD proceeded mainly via aceticlastic methanogenesis, which was indicated to be a dominant pathway in methane metabolism. Batch AD could be divided into three stages, including initiation (days 1-5), adaptation (days 6-20), and stabilization (days 21-50), according to biogas production performance, carbon migration, and metagenomic characteristics during AD.

Cheese whey fermentation into volatile fatty acids in an anaerobic sequencing batch reactor

The present research explored the optimization of volatile fatty acids (VFA) production from cheese whey in an anaerobic sequencing batch reactor (AnSBR). For that purpose, changes of solid and hydraulic retention times (SRT and HRT) were applied. Moreover, the experiments were coupled to metagenomic analyses by 16S rRNA sequencing. The results showed an enhancement of the process effectiveness at longer SRT and shorter HRT. The degree of acidification (DA) improved from 0.73 to 0.83 when increasing the SRT from 5 to 15 days. It also increased from 0.79 to 0.83 when lowering the HRT from 3 to 1 day. The acidification yield (Y_VFA/S) improved from 0.78 to 0.87 and from 0.86 to 0.90 g COD-VFA g COD-Lactose^-1 when increasing the SRT from 5 to 15 days and decreasing the HRT from 3 to 1 day, respectively. Hydrolytic bacteria dominated the microbial community at the shortest SRT, although they were replaced by acidogenic bacteria at longer SRT.

Dissecting methanogenesis for temperature-phased anaerobic digestion: Impact of temperature on community structure, correlation, and fate of methanogens

This study investigated the relationship between the temperature (35, 42, and 55 °C) used in temperature-phased anaerobic digestion (TPAD) and fate of methanogens between the two anaerobic digestion (AD) phases. Methanogens were profiled by using next generation sequencing (NGS) and droplet digital PCR approaches. The results showed that optimal combined temperatures for methane production were 55 °C during biological hydrolysis (BH) and 35 or 42 °C during AD. BH exhibited much lower archaeal population and was more susceptible to changes in temperature, compared to the AD phase. Additionally, we demonstrated, for the first time, that the BH step could affect the subsequent AD phase by altering AD methanogen composition and improve the stability of the process by enriching the rapidly growing Methanosarcina in the BH-AD process. These results are significant for understanding the mechanisms and stability of methane production in TPAD systems.

Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomass

Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.

An innovative multistage anaerobic hythane reactor (MAHR): Metabolic flux, thermodynamics and microbial functions

Biohythane production from wastewater via anaerobic fermentation currently relies on two-stage physically separated biohydrogen and biomethane reactors, which requires closed monitoring, the implementation of a control system, and cost-intensive, complex operation. Herein, an innovative multistage anaerobic hythane reactor (MAHR) was reported via integrating two-stage fermentation into one reactor. MAHR was constructed using an internal down-flow packed bed reactor and an external up-flow sludge blanket to enhance microbial enrichment and thermodynamic feasibility of the associated bioreactions. The performance of MAHR was investigated for 160 d based on biogas production, metabolic flux and microbial structure in comparison to a typical anaerobic high-rate reactor (up-flow anaerobic sludge blanket (UASB)). A biohythane production with an optimized hydrogen volume ratio (10-20%) and a high methane content (75-80%) was achieved in the hythane zone (M_H) and methane zone (M_M) in MAHR, respectively. In addition, MAHR showed a stronger capability to accommodate a high organic loading rate (120 g COD/L/d), and it enhanced the conversion of organics leading to a methane production rate 66% higher than UASB. Thermodynamic analysis suggested that hydrogen extraction in M_H significantly decreased the hydrogen partial pressure (<0.1% vol) which favored acetogenesis in M_M. Metabolic flux and microbial function analysis further supported the superior performance of MAHR over UASB, which was primarily attributed to enhanced acetogenesis and acetoclastic methanogenesis.

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

BACKGROUND

Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.

RESULTS

Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain.

CONCLUSIONS

The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

The Use of Lignin as a Microbial Carrier in the Co-Digestion of Cheese and Wafer Waste

The aim of the article was to present the effects of lignin grafted with polyvinylpyrrolidone (PVP) as a microbial carrier in anaerobic co-digestion (AcoD) of cheese (CE) and wafer waste (WF). Individual samples of waste cheese and wafers were also tested. The PVP modifier was used to improve the adhesive properties of the carrier surface. Lignin is a natural biopolymer which exhibits all the properties of a good carrier, including nontoxicity, biocompatibility, porosity, and thermal stability. Moreover, the analysis of the zeta potential of lignin and lignin combined with PVP showed their high electrokinetic stability within a wide pH range, that is, 4-11. The AcoD process was conducted under mesophilic conditions in a laboratory by means of anaerobic batch reactors. Monitoring with two standard parameters: pH and the VFA/TA ratio (volatile fatty acids-to-total alkalinity ratio) proved that the process was stable in all the samples tested. The high share of N-NH4+ in TKN (total Kjeldahl nitrogen), which exceeded 90% for WF+CE and CE at the last phases of the process, proved the effective conversion of nitrogen forms. The microbiological analyses showed that eubacteria proliferated intensively and the dehydrogenase activity increased in the samples containing the carrier, especially in the system with two co-substrates (WF+CE/lignin) and in the waste cheese sample (CE/lignin). The biogas production increased from 1102.00 m3 Mg-1 VS (volatile solids) to 1257.38 m3 Mg-1 VS in the WF+CE/lignin sample, and from 881.26 m3 Mg-1 VS to 989.65 m3 Mg-1 VS in the CE/lignin sample. The research results showed that the cell immobilization on lignin had very positive effect on the anaerobic digestion process.

Characterisation and microbial community analysis of lipid utilising microorganisms for biogas formation

In the anaerobic process, fat-oil-grease (FOG) is hydrolysed to long-chain fatty acids (LCFAs) and glycerol (GLYC), which are then used as substrates to produce biogas. The increase in FOG and LCFAs inhibits methanogenesis, and so far, most work investigating this inhibition has been carried out when FOG or LCFAs were used as co-substrates. In the current work, the inhibition of methanogenesis by FOG, LCFAs and GLYC was investigated when used as sole substrates. To gain more insight on the dynamics of this process, the change of microbial community was analysed using 16S rRNA gene amplicon sequencing. The results indicate that, as the concentrations of cooking olive oil (CO, which represents FOG) and LCFAs increase, methanogenesis is inhibited. For instance, at 0.01 g. L-1 of FOG, the rate of biogas formation was around 8 ml.L-1.day-1, and this decreased to <4 ml.L-1.day-1 at 40 g.L-1. Similar results were observed with the use of LCFAs. However, GLYC concentrations up to 100g.L-1 did not affect the rate of biogas formation. Acidic pH, temperature > = 45°C and NaCl > 3% led to a significant decrease in the rate of biogas formation. Microbial community analyses were carried out from samples from 3 different bioreactors (CO, OLEI and GLYC), on day 1, 5 and 15. In each bioreactor, microbial communities were dominated by Proteobacteria, Firmicutes and Bacteroidetes phyla. The most important families were Enterobacteriaceae, Pseudomonadaceae and Shewanellaceae (Proteobacteria phylum), Clostridiacea and Ruminococcaceae (Firmicutes) and Porphyromonadaceae and Bacteroidaceae (Bacteroidetes). In CO bioreactor, Proteobacteria bacteria decreased over time, while those of OLEI and GLYC bioreactors increased. A more pronounced increase in Bacteroidetes and Firmicutes were observed in CO bioreactor. The methanogenic archaea Methanobacteriaceae and Methanocorpusculaceae were identified. This analysis has shown that a set of microbial population is selected as a function of the substrate.

A Review of the Role of Critical Parameters in the Design and Operation of Biogas Production Plants

Many operating parameters, individually or together, may influence the performance of anaerobic digestion towards biogas or digestate yield and quality maximization. The most preferred method of optimizing an anaerobic digestion plant often relies on how carefully the crucial parameters, such as pH, temperature, organic loading rate, hydraulic retention time, and pressure, are chosen. There is a large amount of literature available on optimization of anaerobic digestion; however, given the continued development and implementation of innovative technologies, together with the introduction of increasingly complex systems, it is necessary to update present knowledge on process parameters and their role on operational ranges and flexibilities in real-life anaerobic digestion system. Accordingly, the present review discusses the importance of the selection of operational parameters in existing technologies and their impact on biogas yield. Notably, the four broad areas of feedstock utilization (substrate, inoculum, codigestion and pretreatment), process condition (pH, temperature, pressure, and reactor design), reactor control (HRT and OLR) and inhibition (Ammonia and VFAs) are covered in this review. In addition, particular emphasis is placed on the most recent innovations that have been or may be implemented in current or future biogas plants.

Microbial profiling during anaerobic digestion of cheese whey in reactors operated at different conditions

This study investigates the efficiency in methane production of lab-scale mesophilic (37 °C) and thermophilic (54 °C) continuous stirred tank reactors fed with cheese whey at different operational conditions. Results showed that whey mono-digestion was feasible at mesophilic conditions, while at thermophilic conditions frequent acidification incidents were recorded. The limited buffer capacity of the influent feedstock was responsible for the unstable anaerobic digestion process. The co-digestion of cheese whey with cattle manure maintained the pH levels higher than 7.0, and therefore, stable methane production rates were achieved without any significant accumulation of volatile fatty acids. An additional enhancement of the methane productivity was achieved by in-situ H₂ dispersion. Microbial community composition was investigated using high-throughput 16S rRNA gene amplicon sequencing and results were correlated with process parameters. Hydrogenotrophic methanogens were the dominant archaea during the whole experiment at mesophilic and thermophilic conditions.

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics

BACKGROUND

The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methane) or to produce high value-added compounds such as short-chain fatty acids (power-to-chemicals). Genome-centric metagenomics and metatranscriptomic analyses were performed to better understand the metabolic dynamics associated with H₂ injection in two different configurations of anaerobic digesters treating acidic wastes, specifically cheese manufacturing byproducts. These approaches revealed the key-genes involved in methanation and carbon fixation pathways at species level.

RESULTS

The biogas upgrading process in the single-stage configuration increased the CH₄ content by 7%. The dominant methanogenic species responsible for the upregulation of the hydrogenotrophic pathway in this reactor was Methanothermobacter wolfeii UC0008. In the two-stage configuration, H₂ injection induced an upregulation of CO₂ fixation pathways producing short-chain fatty acids, mainly acetate and butyrate. In this configuration, the abundant species Anaerobaculum hydrogeniformans UC0046 and Defluviitoga tunisiensis UC0050 primarily upregulated genes related to electron transport chains, suggesting putative syntrophisms with hydrogen scavenger microbes. Interestingly, Tepidanaerobacter acetatoxydans UC0018 did not act as an acetate-oxidizer in either reactor configurations, and instead regulated pathways involved in acetate production and uptake. A putative syntrophic association between Coprothermobacter proteolyticus UC0011 and M. wolfeii UC0008 was proposed in the two-stage reactor. In order to support the transcriptomic findings regarding the hydrogen utilization routes, an advanced bioconversion model was adapted for the simulation of the single- and two-stage reactor setups.

CONCLUSIONS

This is the first study investigating biogas reactor metatranscriptome dynamics following hydrogen injection for biomethanation and carbon fixation to short-chain fatty acids purposes. The same microbes showed different patterns of metabolic regulation in the two reactor configurations. It was observed an effect of the specialized acidogenic reactor on the overall microbial consortium composition and activity in the two-stage digester. There were also suggested the main species responsible for methanation, short-chain fatty acids production, and electron transport chain mechanisms, in both reactor configurations.