Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics

The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.

Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste

While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.

The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, Lachnospiraceae species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative Lachnospiraceae strain, Anaeropeptidivorans aminofermentans M3/9T was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9T possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9T was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9T and closely related Anaerotignum type strains, genome sequence comparisons were performed. M3/9T harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9T in other environments, large-scale fragment recruitments with the M3/9T genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter

Strain MD1^T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1^T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7-8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1^T are C_14:0 DMA and C_16:0. Strain MD1^T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1^T are Mobilitalea sibirica P3M-3^T and Anaerotaenia torta FH052^T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1^T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1^T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1^T=DSM 110715^T=JCM 39125^T) is proposed.

Gut Bacteria Shared by Children and Their Mothers Associate with Developmental Level and Social Deficits in Autism Spectrum Disorder

Gut microbiota may contribute to the pathogenesis and development of autism spectrum disorder. The maternal gut microbiota influences offspring gut microbial structure and composition.

The gut microbiota of autism spectrum disorder (ASD) children differs from that of children without ASD. The maternal gut microbiota impacts offspring gut microbiota. However, the relationship between the development of ASD and gut bacteria shared between children and their mothers remains elusive. Our study recruited 76 children with ASD and 47 age- and gender-matched children with typical development (TD), as well as the mothers of both groups, and investigated their gut microbiota using amplicon sequence variants (ASVs). The gut microbiota of ASD children was altered compared with that of children with TD, while no significant alterations were found in their mothers. We established 30 gut bacterial coabundance groups (CAGs) and found the relative abundances of CAG15 and CAG16 significantly decreased in ASD children. CAG15 showed a positive correlation with developmental level. The proportion of ASD children who shared either one of the two Lachnospiraceae ASVs from CAG15 with their mothers was significantly lower than that of children with TD. Moreover, we found that CAG12, CAG13, and CAG18 negatively correlated with the severity of social deficits in ASD children. ASD children who shared any one of the four (two Ruminococcaceae, one Lachnospiraceae, and one Collinsella) ASVs in CAG13 and CAG18 with their mothers showed a lower level of social deficits than ASD children that did not share those with their mothers. These data demonstrate that these shared gut bacteria in ASD children are associated with their developmental level and social deficits. This work provides a new direction toward understanding the role of the gut microbiota in the pathogenesis and development of ASD. (This study has been registered in the Chinese Clinical Trial Registry under number ChiCTR-RPC-16008139.)

IMPORTANCE Gut microbiota may contribute to the pathogenesis and development of autism spectrum disorder. The maternal gut microbiota influences offspring gut microbial structure and composition. However, the relationship between the clinical symptoms of autism spectrum disorder and the gut bacteria shared between children and their mothers is not yet known. In our study, the gut microbiota of children with autism spectrum disorder differed from that of children with typical development, but there were no differences in the gut microbiota of their mothers. More importantly, gut bacteria shared between children with autism spectrum disorder and their mothers were related to developmental disabilities and social deficits. Thus, our study suggests that these shared gut bacteria may play an important role in the development of autism spectrum disorder. This provides a new direction for future studies aiming to explore the role of the gut microbiota in autism spectrum disorder.

A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters

Genomic studies revealed the glycoside hydrolases of family 48 (GH48) as a powerful marker for the identification of truly cellulolytic bacteria. Here we report an improved method for detecting cellulolytic bacteria in lab-scale biogas fermenters by using GH48 genes as a molecular marker in DNA and RNA samples. We developed a mixture of primers for the specific amplification of a GH48 gene region in a broad range of bacteria. Additionally, we built a manually curated reference database containing GH48 gene sequences directly linked to the corresponding taxonomic information. Phylogenetic correlation analysis of GH48 to 16S rRNA gene sequences revealed that GH48 gene sequences with 94% identity belong with high confidence to the same genus. Applying this analysis, GH48 amplicon reads revealed that at mesophilic fermenter conditions, 50-99% of the OTUs appear to belong to novel taxa. In contrast, at thermophilic conditions, GH48 gene sequences from the genus Hungateiclostridium dominated with 60-91% relative abundance. The novel primer combinations enabled detection and relative quantification of a wide spectrum of GH48 genes in cellulolytic microbial communities. Deep phylogenetic correlation analysis and a simplified taxonomic identification with the novel database facilitate identification of cellulolytic organisms, including the detection of novel taxa in biogas fermenters.

Phenotypic characterization and comparative genome analysis of two strains of thermophilic, anaerobic, cellulolytic-xylanolytic bacterium Herbivorax saccincola

The genome sequences of thermophilic, anaerobic, and cellulolytic-xylanolytic bacterium Herbivorax saccincola strains A7 and GGR1 have recently been determined. Although both strains belong to the same species, A7 is alkaliphilic, non-endospore-forming, and ammonium-assimilating, whereas GGR1 is neutrophilic, endospore-forming, and weak-ammonium-assimilating. To better understand the phenotypic diversity among H. saccincola strains, the genome sequences of A7 and GGR1 were compared. A7 contained three additional genes showing similarity to an alkaline stress-associated ABC-transporter but lacked four endospore formation-associated genes, AUG58543 and AUG58618 (encoding SpoVT), AUG57258 (encoding SpoVS), and AUG58614 (encoding YdhD), all of which were present in GGR1. In addition, A7 contained key ammonia assimilation genes PQQ67145 and PQQ66619, encoding ornithine cyclodeaminase and arginase, respectively, which were absent in GGR1. There was no difference in the number and types of cellulosomal-scaffolding proteins and glycosyl hydrolases between the two strains. However, cellulase and xylanase enzymes from A7 demonstrated greater activity and stability at an alkaline pH compared with those from GGR1, and amino acid substitutions were identified in 11 glycosyl hydrolases from A7. This characterization though comparative genomic analysis provides useful information for understanding the genetic basis of the phenotypic differences between H. saccincola strains isolated from distinct areas and environments.

Creation of a functional hyperthermostable designer cellulosome

BACKGROUND

Renewable energy has become a field of high interest over the past decade, and production of biofuels from cellulosic substrates has a particularly high potential as an alternative source of energy. Industrial deconstruction of biomass, however, is an onerous, exothermic process, the cost of which could be decreased significantly by use of hyperthermophilic enzymes. An efficient way of breaking down cellulosic substrates can also be achieved by highly efficient enzymatic complexes called cellulosomes. The modular architecture of these multi-enzyme complexes results in substrate targeting and proximity-based synergy among the resident enzymes. However, cellulosomes have not been observed in hyperthermophilic bacteria.

RESULTS

Here, we report the design and function of a novel hyperthermostable "designer cellulosome" system, which is stable and active at 75 °C. Enzymes from Caldicellulosiruptor bescii, a highly cellulolytic hyperthermophilic anaerobic bacterium, were selected and successfully converted to the cellulosomal mode by grafting onto them divergent dockerin modules that can be inserted in a precise manner into a thermostable chimaeric scaffoldin by virtue of their matching cohesins. Three pairs of cohesins and dockerins, selected from thermophilic microbes, were examined for their stability at extreme temperatures and were determined stable at 75 °C for at least 72 h. The resultant hyperthermostable cellulosome complex exhibited the highest levels of enzymatic activity on microcrystalline cellulose at 75 °C, compared to those of previously reported designer cellulosome systems and the native cellulosome from Clostridium thermocellum.

CONCLUSION

The functional hyperthermophilic platform fulfills the appropriate physico-chemical properties required for exothermic processes. This system can thus be adapted for other types of thermostable enzyme systems and could serve as a basis for a variety of cellulolytic and non-cellulolytic industrial objectives at high temperatures.

Identification of parameters needed for optimal anaerobic co-digestion of chicken manure and corn stover

While studies have shown that anaerobic co-digestion of chicken manure (CM) and corn stover (CS) is an efficient method to treat these agricultural wastes, the microbial ecology of these systems and optimal parameters for the digestion process are yet to be determined. In this study, the effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion and microbial community structure were evaluated. Results demonstrated that both the highest cumulative methane yields and methane production rates were obtained from reactors with a CS : CM ratio of 1 : 1 during hemi-solid-state anaerobic digestion (HSS-AD). Cumulative methane yields and methane production rates were 24.8% and 42% lower in solid-state anaerobic digestion (SS-AD) reactors using the same CS : CM ratios. Analysis of microbial community structures revealed that cellulolytic bacteria and a diversity of syntrophic microorganisms capable of direct interspecies electron transfer (DIET) and hydrogen interspecies transfer (HIT) were enriched in the best-performing reactors. Methanosarcina species also dominated during HSS-AD, and their presence was positively correlated with methane production in the reactors.

The effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion performance and microbial community structure were evaluated in this study.

Variation in the Distribution of Hydrogen Producers from the Clostridiales Order in Biogas Reactors Depending on Different Input Substrates

With growing demand for clean and cheap energy resources, biogas production is emerging as an ideal solution, as it provides relatively cheap and clean energy, while also tackling the problematic production of excessive organic waste from crops and animal agriculture. Behind this process stands a variety of anaerobic microorganisms, which turn organic substrates into valuable biogas. The biogas itself is a mixture of gases, produced mostly as metabolic byproducts of the microorganisms, such as methane, hydrogen, or carbon dioxide. Hydrogen itself figures as a potent bio-fuel, however in many bioreactors it serves as the main substrate of methanogenesis, thus potentially limiting biogas yield. With help of modern sequencing techniques, we tried to evaluate the composition in eight bioreactors using different input materials, showing shifts in the microbial consortia depending on the substrate itself. In this paper, we provide insight on the occurrence of potentially harmful microorganisms such as Clostridium novyi and Clostridium septicum, as well as key genera in hydrogen production, such as Clostridium stercorarium, Mobilitalea sp., Herbinix sp., Herbivorax sp., and Acetivibrio sp.

Multidisciplinary involvement and potential of thermophiles

The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.

Addition of β-galactosidase boosts the xyloglucan degradation capability of endoglucanase Cel9D from Clostridium thermocellum

BACKGROUND

Increasing the efficiency of enzymatic biomass degradation is crucial for a more economically feasible conversion of abundantly available plant feedstock. Synergistic effects between the enzymes deployed in the hydrolysis of various hemicelluloses have been demonstrated, which can reduce process costs by lowering the amount of enzyme required for the reaction. Xyloglucan is the only major hemicellulose for which no such effects have been described yet.

RESULTS

We report the beneficial combination of two enzymes for the degradation of the hemicellulose xyloglucan. The addition of β-galactosidase Bga2B from Clostridium stercorarium to an in vitro hydrolysis reaction of a model xyloglucan substrate increased the enzymatic efficiency of endoglucanase Cel9D from Clostridium thermocellum to up to 22-fold. Furthermore, the total amount of enzyme required for high hydrolysis yields was lowered by nearly 80%. Increased yields were also observed when using a natural complex substrate-tamarind kernel powder.

CONCLUSION

The findings of this study may improve the valorization of feedstocks containing high-xyloglucan amounts. The combination of the endoglucanase Cel9D and the β-galactosidase Bga2B can be used to efficiently produce the heptasaccharide XXXG. The exploitation of one specific oligosaccharide may open up possibilities for the use as a prebiotic or platform chemical in additional reactions.

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.

Complete Genome Sequence of the Novel Cellulolytic, Anaerobic, Thermophilic Bacterium Herbivorax saccincola Type Strain GGR1, Isolated from a Lab Scale Biogas Reactor as Established by Illumina and Nanopore MinION Sequencing

The cellulolytic bacterium Herbivorax saccincola strain GGR1, which represents the type strain of this species, was isolated from the in vivo enriched cellulose-binding community of a lab scale thermophilic biogas reactor. Here, we report the complete genome sequence of H. saccincola GGR1^T, the first isolated member of the genus Herbivorax.

Analysis of a bio-electrochemical reactor containing carbon fiber textiles for the anaerobic digestion of tomato plant residues

A bio-electrochemical system packed with supporting material can promote anaerobic digestion for several types of organic waste. To expand the target organic matters of a BES, tomato plant residues (TPRs), generated year-round as agricultural and cellulosic waste, were treated using three methanogenic reactors: a continuous stirred tank reactor (CSTR), a carbon fiber textile (CFT) reactor, and a bio-electrochemical reactor (BER) including CFT with electrochemical regulation (BER + CFT). CFT had positive effects on methane fermentation and methanogen abundance. The microbial population stimulated by electrochemical regulation, including hydrogenotrophic methanogens, cellulose-degrading bacteria, and acetate-degrading bacteria, suppressed acetate accumulation, as evidenced by the low acetate concentration in the suspended fraction in the BER + CFT. These results indicated that the microbial community in the BER + CFT facilitated the efficient decomposition of TPR and its intermediates such as acetate to methane.