Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter

The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics. Technical and chemical parameters indicated stable operation of the main fermenter but varying conditions for the open hydrolysis fermenter. Matching this, the microbiome in the hydrolysis fermenter has a higher dynamic than in the main fermenter. Metaproteomics-based microbiome analysis revealed a partial separation between early and common steps in carbohydrate degradation and primary fermentation in the hydrolysis fermenter but complex carbohydrate degradation, secondary fermentation, and methanogenesis in the main fermenter. Detailed metagenomics and metaproteomics characterization of the single metagenome-assembled genomes showed that the species focus on specific substrate niches and do not utilize their full genetic potential to degrade, for example, LCB. Overall, it seems that a separation of AD in a hydrolysis and a main fermenter does not improve the cleavage of complex substrates but significantly improves the overall process performance. In contrast, the remaining methanogenic activity in the hydrolysis fermenter may cause methane losses.

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.

Biomethane production and microbial strategies corresponding to high organic loading treatment for molasses wastewater in an upflow anaerobic filter reactor

Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. In this study, an upflow anaerobic filter (UAF) reactor was employed to establish a high organic loading treatment system for molasses wastewater and further investigated the microbial community dynamics in response to this stressful operation. The biogas production increased with an increase in total organic carbon (TOC) loading rate from 1.0 to 14 g/L/day, and then it decreased with further TOC loading rate addition until 16 g/L/day. The UAF reactor achieved a maximum biogas production of 6800 mL/L/day with a TOC removal efficiency of 66.5% at a TOC loading rate of 14 g/L/day. Further microbial analyses revealed that both the bacterial and archaeal communities developed multiple strategies to maintain stable operation of the reactor at high organic loading (e.g., Proteiniphilum and Defluviitoga maintained high abundances throughout the operation; Tissierella temporarily dominated the bacterial community at TOC loading rates of 8.0 to 14 g/L/day; and multi-trophic Methanosarcina shifted as the dominant methanogen at the TOC loading rates of 8.0 to 16 g/L/day). This study presents insights into a high organic loading molasses wastewater treatment system and the microbial flexibility in methane fermentation in response to process disturbances.

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.

Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum

An anaerobic bacterial strain, designated strain M3/9^T, was isolated from a laboratory-scale biogas fermenter fed with maize silage supplemented with 5 % wheat straw. Cells were straight, non-motile rods, which stained Gram-negative. Optimal growth occurred between 30 and 40°C, at pH 7.5-8.5, and up to 3.9 % (w/v) NaCl was tolerated. When grown on peptone from casein and soymeal, strain M3/9^T produced mainly acetic acid, ethanol, and isobutyric acid. The major cellular fatty acids of the novel strain were C_16 : 0 and C_16 : 0 DMA. The genome of strain M3/9^T is 3757  330 bp in size with a G+C content of 38.45 mol%. Phylogenetic analysis allocated strain M3/9^T within the family Lachnospiraceae with Clostridium colinum DSM 6011^T and Anaerotignum lactatifermentans DSM 14214^T being the most closely related species sharing 57.86 and 56.99% average amino acid identity and 16S rRNA gene sequence similarities of 91.58 and 91.26 %, respectively. Based on physiological, chemotaxonomic and genetic data, we propose the description of a novel species and genus Anaeropeptidivorans aminofermentans gen. nov., sp. nov., represented by the type strain M3/9^T (=DSM 100058^T=LMG 29527^T). In addition, an emended description of Clostridium colinum is provided.

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.

Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture

BACKGROUND

The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enriched communities.

RESULTS

By progressively shortening the hydraulic retention time (HRT) from 8 to 2 days with different temporal schemes in two bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing machine learning algorithms using 16S rRNA genes to predict n-caproate and n-caprylate productivities. Our dataset consisted of 14 and 40 samples from HRT of 8 and 2 days, respectively. Because of the size and balance of our dataset, we compared linear regression, support vector machine and random forest regression algorithms using the original and balanced datasets generated using synthetic minority oversampling. Further, we performed cross-validation to estimate model stability. The random forest regression was the best algorithm producing more consistent results with median of error rates below 8%. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter HRT. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.

CONCLUSIONS

Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterizing and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and microbial systems where community dynamics is linked to key functions. The general methodology used here can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites. Video Abstract.

Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome

Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m³ CH₄, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H₂-CO₂-converter, Methanothermobacter, always dominated in the thermophilic fermenters.

The challenges of monitoring and manipulating anaerobic microbial communities

Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum

Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.