Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities

BACKGROUND

Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.

RESULTS

In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.

CONCLUSION

Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.

Decolorization and detoxification of Brilliant Crocein GR by a newly enriched thermophilic consortium

The environmental pollution caused by azo dyes at high temperatures has become an urgent problem. However, little attention has been paid to decolorizing azo dyes by thermophilic consortiums. In this study, a thermophilic bacterial consortium (BCGR-T) mainly composed of two genera, namely, Caldibacillus (70.90%) and Aeribacillus (17.63%) was first enriched, which can decolorize Brilliant Crocein GR (BCGR) at high temperatures (50-75 °C), pH values of 6∼8, dye concentrations (100-400 mg/L) and salinities (1-5%, w/v). The enzyme activity results showed that the azoreductase activity was nearly 8.8 times that of the control (p < 0.01), and the intracellular lignin peroxidase was also highly expressed with enzyme activity of 5.64 U (min-1 mg-1 protein) (p < 0.05), indicated that both azoreductase and intracellular lignin peroxidase played an important part in the decolorization process. Furthermore, seven new intermediate metabolic products, including aniline, phthalic acid, 2-carboxy benzaldehyde, phenylacetic acid, benzoic acid, toluene, and 4-methyl-hexanoic acid, were identified. In addition, functional genes related with the azo dye decolorization, such as those encoding the azoreductase, laccase, FMN reductase, NADPH-/NADH-quinone oxidoreductases and NADPH-/NADH dehydrogenases, catechol dioxygenase, homogentisate 1,2-dioxygenase, protocatechuate 3,4-dioxygenase, gentisate 1,2-dioxygenase, azobenzene reductase, naphthalene 1,2-dioxygenase, benzoate/toluate 1,2-dioxygenase, and anthranilate 1,2-dioxygenase and so on were found in the metagenome of the consortium BCGR-T. Finally, a new decolorization pathway of the thermophilic consortium BCGR-T was proposed. In addition, the phototoxicity of BCGR decreased after decolorization. Overall, the thermophilic consortium BCGR-T could be a promising candidate in the treatment of high concentration azo dye wastewater at high temperatures.

Understanding microbiome dynamics and functional responses during acidogenic fermentation of sucrose and sugarcane vinasse through metatranscriptomic analysis

Improving anaerobic digestion of sugarcane vinasse - a high-strength wastewater from ethanol distillation - is a subject of great interest, in view of the reduction of the pollutants and recovery of methane and valuable metabolites as byproducts. Through metatranscriptomic analysis, this study evaluated the active microbiome and metabolic pathways in a continuous acidogenic reactor: Stage 1S (control): 100% sucrose-based substrate (SBS); Stage 2SV (acclimation): 50% SBS and 50% vinasse; Stage 3V: 100% vinasse. Metatranscriptome obtained from each Stage was subjected to taxonomic and functional annotations. Under SBS feeding, pH dropped to pH 2.7 and biohydrogen production was observed. As vinasse was added, pH increased to 4.1-4.5, resulting in community structure and metabolite changes. In Stage 3V, biohydrogen production ceased, and propionate and acetate prevailed among the volatile fatty acids. Release of homoacetogenesis enzymes by Clostridium ljungdahlii and of uptake hydrogenase (EC 1.12.99.6) by Pectinatus frisingensis were linked to hydrogen consumption in Stages 2SV and 3V. Metabolic pathways of vinasse compounds, such as carbohydrates, malate, oxalate, glycerol, sulfate and phenol, were investigated in detail. In pyruvate metabolism, gene transcripts of oadA (oxaloacetate decarboxylase) and mdh (malate dehydrogenase), were upregulated in Stage 3V, being mostly attributed to P. frisingensis. Acetate formation from vinasse degradation was mainly attributed to Megasphaera and Clostridium, and propionate formation to P. frisingensis. Glycerol removal from vinasse exceeded 99%, and gene transcripts encoding for glpF (glycerol uptake facilitator protein), glpK (glycerol kinase) and glpABC (glycerol-3-phosphate dehydrogenase) were expressed mostly by Pectinatus and Prevotella. mRNA profiling showed that active bacteria and gene expression greatly changed when vinasse replaced sucrose, and Pectinatus was the main active bacterium degrading the searched compounds from vinasse. The identification of the main metabolic routes and the associated microorganisms achieved in this work contributes with valuable information to support further optimization of fermentation towards the desired metabolites.

Dual function of magnetic field in enhancing antibiotic wastewater treatment by an integrated photocatalysis and fluidized bed biofilm reactor (FBBR)

The integrated photocatalysis and fluidized bed biofilm reactor (FBBR) is an attractive wastewater treatment technique for managing wastewater containing antibiotics. However, the fast recombination of photoinduced charge and low microbial activity limit the degradation and mineralization efficiency for antibiotics. To address this, we attempt to introduce magnetic field (MF) to the integrated system with B-doped Bi3O4Cl as the photocatalysts to effectively improve removal and mineralization of ciprofloxacin (CIP). As a consequence, the degradation rate reaches 96% after 40 d in integrated system with MF. The biofilm inside the integrated system with MF carrier can mineralize the photocatalytic products, thereby increasing the total organic carbon (TOC) degradation rate by more than 32%. The electrochemical experiment indicates the Lorentz force generated by MF can accelerate charge separation, increasing the electron concentration. Simultaneously, the increased amounts of electrons lead to the generation of more ·OH and ·O2-. MF addition also results in increased biomass, increased biological respiratory activity, microbial community evolution and accelerated microbial metabolism, enabling more members to biodegrade photocatalytic intermediates. Therefore, applied MF is an efficient method to enhance CIP degradation and mineralization by the integrated system.

Effects of lysed sludge reflux point on ultrasound lysis-cryptic growth in anaerobic/aerobic (A/O) wastewater treatment: Sludge reduction, microbial community, and metabolism

Ultrasonication allows sludge reduction to be performed in situ during wastewater treatment, and the reflux point of the lysed sludge affects this performance. This study investigated the effects of reflux point (anaerobic stage, carbon/nitrogen (C/N) lowest stage, and aerobic stage) on sludge lysis-cryptic growth in an anaerobic/aerobic reactor and variations in the sludge and microbial community. The best reflux point occurred at the lowest C/N ratio stage, and a 50.96% reduction in excess sludge was achieved. The reflux of the lysed sludge to the aerobic stage reduced nitrogen and phosphorus removal. The reflux of the lysed sludge decreased the average sludge size, reaching 29.2 μm when reflux to the aerobic stage. Scanning electron microscopy showed that the sludge surface was unaffected by the reflux point. The Fourier-transform infrared spectrometry and X-ray photoelectron spectroscopy results showed that the most prominent variation in the intensity of the sludge functional groups occurred when the reflux was at the lowest C/N stage. The amount of extracellular polymeric substances decreased the most during reflux to the anaerobic stage. The sludge microbial communities varied with the reflux point, and the dominant phyla during reflux to the anaerobic, lowest C/N, and aerobic stages were Bacteroidetes, Firmicutes, and Bacteroidetes, respectively. Furthermore, the reflux point did not alter the metabolic pathway of sludge microorganisms but increased the number of enzymes in metabolic pathways.

Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis

Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H₂/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review

As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.

In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors

Background

Microbial-driven solubilization of lignocellulosic material is a natural mechanism that is exploited in anaerobic digesters (ADs) to produce biogas and other valuable bioproducts. Glycoside hydrolases (GHs) are the main enzymes that bacterial and archaeal populations use to break down complex polysaccharides in these reactors. Methodologies for rapidly screening the physical presence and types of GHs can provide information about their functional activities as well as the taxonomical diversity within AD systems but are largely unavailable. Targeted proteomic methods could potentially be used to provide snapshots of the GHs expressed by microbial consortia in ADs, giving valuable insights into the functional lignocellulolytic degradation diversity of a community. Such observations would be essential to evaluate the hydrolytic performance of a reactor or potential issues with it.

Results

As a proof of concept, we performed an in silico selection and evaluation of groups of tryptic peptides from five important GH families derived from a dataset of 1401 metagenome-assembled genomes (MAGs) in anaerobic digesters. Following empirical rules of peptide-based targeted proteomics, we selected groups of shared peptides among proteins within a GH family while at the same time being unique compared to all other background proteins. In particular, we were able to identify a tractable unique set of peptides that were sufficient to monitor the range of GH families. While a few thousand peptides would be needed for comprehensive characterization of the main GH families, we found that at least 50% of the proteins in these families (such as the key families) could be tracked with only 200 peptides. The unique peptides selected for groups of GHs were found to be sufficient for distinguishing enzyme specificity or microbial taxonomy. These in silico results demonstrate the presence of specific unique GH peptides even in a highly diverse and complex microbiome and reveal the potential for development of targeted metaproteomic approaches in ADs or lignocellulolytic microbiomes. Such an approach could be valuable for estimating molecular-level enzymatic capabilities and responses of microbial communities to different substrates or conditions, which is a critical need in either building or utilizing constructed communities or defined cultures for bio-production.

Conclusions

This in silico study demonstrates the peptide selection strategy for quantifying relevant groups of GH proteins in a complex anaerobic microbiome and encourages the development of targeted metaproteomic approaches in fermenters. The results revealed that targeted metaproteomics could be a feasible approach for the screening of cellulolytic enzyme capacities for a range of anaerobic microbiome fermenters and thus could assist in bioreactor evaluation and optimization.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02125-x.

Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases

BACKGROUND

Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited.

RESULTS

In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan).

CONCLUSIONS

We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.

Using Bacillus thuringiensis HM-311@hydroxyapatite@biochar beads to remediate Pb and Cd contaminated farmland soil

Cadmium (Cd) and lead (Pb) have become serious soil contaminants in China. In this work, we immobilized B. thuringiensis HM-311 (a heavy metal resistant strain) using vinegar residue biochar and hydroxyapatite (HAP) to form BtHM-311@HAP@biochar calcium alginate beads. In aqueous solution, the beads respectively reduced 1000 mg/L Pb²⁺ to 14.59 mg/L and 200 mg/L Cd²⁺ to 5.40 mg/L within 20 h. Furthermore, the results of pot experiment showed that the BtHM-311@HAP@biochar beads reduced the bioavailability of Pb and Cd in soil. The accumulation of Pb²⁺ in rice decreased by 39.97% in shoots and 46.40% in roots, while that of Cd²⁺ decreased by 34.59 and 44.9%, respectively. Similarly, the accumulation of Pb²⁺ in corn decreased by 40.86% in shoots and 51.34% in roots, while that of Cd²⁺ decreased by 41.28 and 42.91%, respectively. The beads also increased the microbial community diversity in the rhizosphere soil. These findings indicate that BtHM-311@HAP@biochar beads may be applicable for the bioremediation of Cd- and Pb-contaminated farmland soil.

An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures

The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.

Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA

Background

There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples.

Methods

Fecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination.

Results

The quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or -80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples.

Conclusion

Our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.

Dry anaerobic digestion of ammoniated straw: Performance and microbial characteristics

This paper explores the influence of the mixing ratio of ammoniated straw to biogas residue on the stability and methane yield of dry anaerobic digestion and analyzes the structure of the microbial community with digestion time. Five reactors containing ammoniated straw and swine manure biogas residue at ratios of 5:1, 4:2, 3:3, 2:4 and 1:5 (total solids) were constructed, and neither total ammonia nitrogen nor free ammonia nitrogen was inhibited. Three reactors produced gas successfully. The reactor with a ratio of 3:3 (R3-3) yielded the best methane production, with a cumulative methane production of 115.13 mL/(g·VS_added). Analysis of the R3-3 microbial community showed that bacteria were dominant species. Archaea, mainly Methanosarcina, played an important role in anaerobic digestion and methane production. Methanobacterium, with high acid tolerance, was positively related to total volatile fatty acids (TVFA), playing a key role in preventing the acidification of the anaerobic digestion system.

Effects of rice straw biochar on methanogenic bacteria and metabolic function in anaerobic digestion

Anaerobic digestion technology mitigates agricultural organic waste pollution, thereby alleviating the energy crisis. Biochar materials increase the utilisation rate of biomass resources and promote the enrichment and growth of microorganisms. Biochar is an effective exogenous additive that stabilises the anaerobic digestion, improves anaerobic digestion efficiency and gas production. Herein, biochar materials were prepared from rice straw utilising the sequencing batch anaerobic digestion process. The biochar microstructure was characterised by scanning electron microscopy (SEM) and Brunauer-Emmett-Teller (BET) analysis, and microbial succession and metabolic pathways were analysed using 16S rRNA sequencing to reveal the molecular mechanisms. Rice straw biochar addition increased gas production during anaerobic fermentation. SEM revealed that numerous cocci and microbacteria became agglomerated and attached to the surface and pores of biochar, which was revealed by BET analysis to be a good habitat for microorganisms. After anaerobic digestion, the specific surface area and total pore volume of biochar decreased. 16S rRNA gene sequencing showed that biochar affected the abundance of certain bacteria and archaea. Biochar had no obvious effect on the function of bacterial flora but inhibited carbohydrate metabolism by bacteria and glycan biosynthesis and metabolism by archaea in the anaerobic fermentation system while promoting lipid metabolism by archaea. Biochar addition inhibited acetic acid production in the anaerobic fermentation system and promoted methane production based on hydrogen and carbon dioxide levels.

Effect of wheat straw pretreated with liquid fraction of digestate from different substrates on anaerobic digestion performance and microbial community characteristics

The effects of liquid fraction of digestate (LFD) pretreatment on anaerobic digestion (AD) performance and microbial community characteristics were estimated. Prior to AD, LFD (LFD_SM, LFD_FW, and LFD_WS) collected separately from three continuously stirred tank reactors (CSTRs) using swine manure (SM), food waste (FW), and wheat straw (WS) as the mono-substrate was applied to pretreat WS. The results showed that AD with LFD pretreatment resulted in biomethane yields of 240.2-277.9 mL·gVS^-1, a 33.57%-54.54% improvement over the yield of the control, and also produced a time saving of 32.26%-46.77%. The pretreatment parameters were optimized for LFD pretreatment. The enhancement effect was in the order of LFD_FW > LFD_SM > LFD_WS. Simultaneously, the cellulose, hemicellulose and lignin contents in the WS and their characteristics (surface properties, crystallinity index, etc.) varied accordingly. The function of the microbial community was strengthened during the pretreatment stage, but the structure of the microbial community had a clear response to the LFD source substrates. Bacteroidetes was the most dominant phyla and was positively correlated with the hydrolysis rate. Consequently, the LFD from the different substrates used as pretreat agents could improve the AD performance of WS.

Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns

Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.

Microbial succession of lignocellulose degrading bacteria during composting of corn stalk

The discarding and burning of corn stalks in the fields after harvesting lead to environmental pollution and waste of resources. Composting is an effective way to disposal of the crop straws. Composting is a complex biochemical process and need a detail studied in cold region. Hence, the succession process of bacteria and Actinomycetes in the process of corn stalk composting in cold region was studied by 16SrRNA. Alpha diversity analysis showed that the detection results could represent the real situation. The bacterial community diversity from high to low was F50 > F90 > F0 > F10 > F20. The results of beta analysis showed that F20 and F50 had the most similar microbial structure at the phylum level, and the difference between F0 and F20 was the largest. The dominant microbes changed from Proteobacteria and Bacteroidetes in F0 in heating stage to Firmicutes and Proteobacteria, Actinobacteria and Firmicutes in F10 during early high temperature stage, and Actinobacteria, Proteobacteria and Bacteroidetes in cooling and post composting phases. Actinobacteria and Firmicutes were the dominant bacteria in the whole composting process. In the composting process, the microbial community was mainly involved in amino acid metabolism related to nitrogen transformation and carbohydrate metabolism related to lignocellulose degradation. Lignin and hemicellulose were mainly degraded in thermophilic stage. The conversion of nitrogen and degradation of cellulose occurred mainly in the early stages of composting. The research will be helpful to understand the biochemical process of composting in cold region.

Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches

Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.

Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.

Genome-centric investigation of anaerobic digestion using sustainable second and third generation substrates

Biogas production through co-digestion of second and third generation substrates is an environmentally sustainable approach. Green willow biomass, chicken manure waste and microalgae biomass substrates were combined in the anaerobic digestion experiments. Biochemical methane potential test showed that biogas yields of co-digestions were significantly higher compared to the yield when energy willow was the sole substrate. To scale up the experiment continuous stirred-tank reactors (CSRTs) are employed, digestion parameters are monitored. Furthermore, genome-centric metagenomics approach was employed to gain functional insight into the complex anaerobic decomposing process. This revealed the importance of Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes phyla as major bacterial participants, while Methanomicrobia and Methanobacteria represented the archaeal constituents of the communities. The bacterial phyla were shown to perform the carbohydrate hydrolysis. Among the representatives of long-chain carbohydrate hydrolysing microbes Bin_61: Clostridia is newly identified metagenome assembled genome (MAG) and Bin_13: DTU010 sp900018335 is common and abundant in all CSTRs. Methanogenesis was linked to the slow-growing members of the community, where hydrogenotrophic methanogen species Methanoculleus (Bin_10) and Methanobacterium (Bin_4) predominate. A sensitive balance between H₂ producers and consumers was shown to be critical for stable biomethane production and efficient waste biodegradation.

Methane production from green and woody biomass using short rotation willow genotypes for bioenergy generation

Short rotation plantations of willow genotypes, harvested in vegetative growth phases, were tested as an alternative biomass for methane production. The substrate characteristics, maximal methane yields (K) and highest methane production rates (µmax) were determined. Leaves and stems from diploid Energo (EN) and tetraploid (PP) plants, harvested in June were superior methane sources to woody tissue. This could be related to the lower lignin contents in green willow. Fermentation of pooled biomasses from tetraploid genotypes harvested in June-August was more efficient than methane production from diploid tissues. Microbial community analyses by 16S rRNA genes showed a dominance of the order Clostridiales. In field study, based on Energo plantation, the maximum in green biomass accumulation was in early month 9 of the vegetation period. A theoretical calculation showed similar or better energy potential per unit area for willow than in the case of maize silage. This study encourages the use of green willow biomass as feedstock in biomethanation processes due to its relatively low production costs and uncomplicated agricultural practice.

A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.

Wide-bound salt tolerance of the inocula from marine sediment and their specific microbial community

The microorganisms in marine sediment are promising candidates for the treatment of the saline wastes due to their property of salt tolerance. However, the knowledge about the microbial community and property of the marine sediments is still limited. In the present study, the salt tolerance of the microorganisms in the marine sediment that was collected from a marine fish farm was investigated by being used as inoculum for anaerobic digestion. The microbial communities were analyzed by high-throughput sequencing. The inoculum from the wastewater plant (IWTP) was taken as a control. The inoculum from the marine sediment (IMS) showed excellent capacity for anaerobic digestion at salinities of 0.3%-6%. Even at a salinity of 9%, the methane yield remained 60% of the highest yield. IMS provides promising microbial resources for the treatment of both fresh-water and saliferous organic wastes. While the IWTP was sensitive to salt, the methane yield decreased to 56% of the highest yield at the salinity of 3%. The bacterial taxonomic richness of IMS was about half of that in IWTP. Eighty-one genera were identified only in IWTP but not in IMS. The IMS possessed fewer bacterial members related to the nitrogen cycle than IWTP, but more members related to the sulfur cycle. The members of animal parasites or symbionts in IMS were significantly fewer than those in IWTP. The archaeal compositions of IMS and IWTP were different. The relative abundance of the unidentified archaea in IMS was much higher than that in IWTP with 12.52% vs 0.06% at phylum level. The findings of this work expand our understanding of the microorganisms in marine sediments and will promote the application of them in waste treatment.

Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill

Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.

Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes

Background

Volatile fatty acids (VFA) generated from ruminal fermentation by microorganisms provide up to 75% of total metabolizable energy in ruminants. Ruminal pH is an important factor affecting the profile and production of VFA by shifting the microbial community. However, how ruminal pH affects the microbial community and its relationship with expression of genes encoding carbohydrate-active enzyme (CAZyme) for fiber degradation and fermentation are not well investigated. To fill in this knowledge gap, six cannulated Holstein heifers were subjected to a continuous 10-day intraruminal infusion of distilled water or a dilute blend of hydrochloric and phosphoric acids to achieve a pH reduction of 0.5 units in a cross-over design. RNA-seq based transcriptome profiling was performed using total RNA extracted from ruminal liquid and solid fractions collected on day 9 of each period, respectively.

Results

Metatranscriptomic analyses identified 19 bacterial phyla with 156 genera, 3 archaeal genera, 11 protozoal genera, and 97 CAZyme transcripts in sampled ruminal contents. Within these, 4 bacteria phyla (Proteobacteria, Firmicutes, Bacteroidetes, and Spirochaetes), 2 archaeal genera (Candidatus methanomethylophilus and Methanobrevibacter), and 5 protozoal genera (Entodinium, Polyplastron, Isotricha, Eudiplodinium, and Eremoplastron) were considered as the core active microbes, and genes encoding for cellulase, endo-1,4-beta- xylanase, amylase, and alpha-N-arabinofuranosidase were the most abundant CAZyme transcripts distributed in the rumen. Rumen microbiota is not equally distributed throughout the liquid and solid phases of rumen contents, and ruminal pH significantly affect microbial ecosystem, especially for the liquid fraction. In total, 21 bacterial genera, 4 protozoal genera, and 6 genes encoding CAZyme were regulated by ruminal pH. Metabolic pathways participated in glycolysis, pyruvate fermentation to acetate, lactate, and propanoate were downregulated by low pH in the liquid fraction.

Conclusions

The ruminal microbiome changed the expression of transcripts for biochemical pathways of fiber degradation and VFA production in response to reduced pH, and at least a portion of the shifts in transcripts was associated with altered microbial community structure.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00092-6.

Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production

Complex microbiomes of pit mud (PM) play significant roles in imbuing flavors and qualities of Chinese strong-flavor liquor (CSFL) during fermentation. However, understanding both of the taxonomic and functional diversity of the whole microorganisms in PM still remain a major challenge. Here, PM microbiomes were investigated based on metagenomic sequencing, assembly and binning. Metagenomic data revealed that Euryarchaeota was the predominant phylum, followed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. For further functional exploration, 703 metagenome-assembled genomes (MAGs), including 304 novel strains, 197 novel species, and 94 novel genera were reconstructed. Three primary groups of Firmicutes (n = 406), Euryarchaeota (n = 130) and Bacteroidetes (n = 74), particularly genus of them Syntrophomonas, Thermacetogenium and Clostridium, methanogens (Methanobacterium, Methanoculleus, and Methanosarcina), Proteiniphilum and Prevotella, contained most of metabolic potential genes. Additionally, Chloroflexi was firstly reported to have potential to be involved in the caproic acid (CA) production. Bacteroidetes could be the key phylum to synthesize terpenes, and Armatimonadetes, Firmicutes, Ignavibacteriae and Verrucomicrobia may possess the same metabolic potential as well. Overall, this study will significantly improve our understanding of the diverse PM microbiome and help guide the future exploration of microbial resources for modifying PM fermentation processes.

New Insights into the Co-Occurrences of Glycoside Hydrolase Genes among Prokaryotic Genomes through Network Analysis

Glycoside hydrolase (GH) represents a crucial category of enzymes for carbohydrate utilization in most organisms. A series of glycoside hydrolase families (GHFs) have been classified, with relevant information deposited in the CAZy database. Statistical analysis indicated that most GHFs (134 out of 154) were prone to exist in bacteria rather than archaea, in terms of both occurrence frequencies and average gene numbers. Co-occurrence analysis suggested the existence of strong or moderate-strong correlations among 63 GHFs. A combination of network analysis by Gephi and functional classification among these GHFs demonstrated the presence of 12 functional categories (from group A to L), with which the corresponding microbial collections were subsequently labeled, respectively. Interestingly, a progressive enrichment of particular GHFs was found among several types of microbes, and type-L as well as type-E microbes were deemed as functional intensified species which formed during the microbial evolution process toward efficient decomposition of lignocellulose as well as pectin, respectively. Overall, integrating network analysis and enzymatic functional classification, we were able to provide a new angle of view for GHs from known prokaryotic genomes, and thus this study is likely to guide the selection of GHs and microbes for efficient biomass utilization.

A microbial gene catalog of anaerobic digestion from full-scale biogas plants

BACKGROUND

Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood.

FINDINGS

In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination.

CONCLUSIONS

This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

Effects of bamboo leaf extract on the production performance, rumen fermentation parameters, and rumen bacterial communities of heat-stressed dairy cows

Objective

An experiment was conducted to evaluate the effects of bamboo leaf extract (BLE) on the production performance, rumen fermentation parameters, and rumen bacterial communities of heat-stressed dairy cows.

Methods

The experiment comprised a 14-day adaptation period and a 21-day experimental period and was conducted in a high-temperature and humidity environment (daily mean ambient temperature = 33.5°C±1.3°C; daily mean relative humidity = 64.9%±0.8%, daily mean temperature-humidity index = 86.2±0.4). Twelve Holstein dairy cows were randomly allocated into two groups. A total mixed ration supplemented with BLE at 0 (CON) and 1.3 g/kg dry matter (DM) were fed, respectively. Feed intake and milk yield were recorded daily. Milk samples were collected on 1, 11, and 21 d of the experimental period to analyze milk performance. Rumen fluid samples were collected on 21 d of the experimental period to analyze rumen fermentation parameters and rumen bacterial communities.

Results

Compared with the control group, supplementation of BLE increased milk yield (p<0.01), milk fat yield (p = 0.04), 4% fat-corrected milk (p<0.01) and milk fat content (p<0.01); reduced somatic cell count (p<0.01). No differences in DM intake and milk protein or lactose content were observed between two groups. Supplementation of BLE also increased the rumen total volatile fatty acid (p<0.01), acetate (p<0.01), butyrate (p<0.01), and valerate (p = 0.05) concentrations. However, no significant effects were observed on rumen pH, ammonia nitrogen, propionate, acetate/propionate ratio, isobutyrate, or isovalerate. Furthermore, BLE increased the rumen bacterial abundance and the diversity of the rumen bacterial community. The BLE reduced the Firmicutes/Bacteroidetes abundance ratio and increased the abundances of Butyrivibrio_2 (p<0.01) and Ruminococcus_2 (p<0.01).

Conclusion

The BLE supplementation at 1.3 g/kg DM could improve production performance and rumen fermentation in dairy cows during heat stress.

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases

Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.

A Need for Improved Cellulase Identification from Metagenomic Sequence Data

Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.

Decolorization and detoxification of azo dye by halo-alkaliphilic bacterial consortium: Systematic investigations of performance, pathway and metagenome

The high pH and salinity of textile wastewater is a major hindrance to azo dye decolorization. In this study, a mixed bacterial consortium ZW1 was enriched under saline (10% salinity) and alkaline (pH 10.0) conditions to decolorize Methanil Yellow G (MY-G). Consortium ZW1 was mainly composed of Halomonas (49.8%), Marinobacter (30.7%) and Clostridiisalibacter (19.2%). The effects of physicochemical factors were systematically investigated, along with the degradation pathway and metagenome analysis. The co-carbon source was found to be necessary, and the addition of yeast extract led to 93.3% decolorization of 100 mg/L MY-G within 16 h (compared with 1.12% for control). The optimum pH, salinity, temperature and initial dye concentration were 8.0, 5-10%, 40 °C and 100 mg/L, respectively. The typical dye-related degradation enzymes were most effective at 10% salinity. Consortium ZW1 was also able to differentially decolorize five other direct and acidic dyes in a short period. Phototoxicity tests revealed the detoxification of MY-G degradation products. Combining UV-vis, FTIR and GC-MS detection, the MY-G degradation pathway by consortium ZW1 was proposed. Furthermore, metagenomic approach was used to elucidate the functional potential of genes in MY-G biodegradation. These results signify the broad potential application of halo-alkaliphilic consortia in the bioremediation of dyeing wastewater.

Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Digitalization in microbiology - Paving the path to sustainable circular bioeconomy

The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.

MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.

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 HBCDs biodegradation using a Pseudomonas strain and its application in soil phytoremediation

Hexabromocyclododecanes (HBCDs) are the second-most widely used brominated flame retardants. They cause inappropriate antidiuretic hormone syndrome and can induce cancer. However, little information is available about bacterial degradation of HBCDs. In this study, HBCDs (α-, β- and γ-HBCD) degrading strain Pseudomonas aeruginosa HS9 was isolated, identified, and characterized. The strain HS9 could remove 69% (± 0.05%) of 1.7 mg/L HBCDs in 14 days. Based on identification of metabolites, this bacterium could oxidize HBCDs by two pathways. In the first, HBCDs are sequentially debromized to tetrabromocyclododecene, dibromocyclododecadiene, and then debromized once more to cis, trans, trans-1, 5, 9-cyclododecatriene (CDT). After that, CDT is then oxidized to 1,2-epoxy-5,9-cyclododecadiene. The second identified pathway is a simultaneous debrominating and hydroxylating process based on the detection of 2,5,6,9,10-pentabromocyclododecanols, which were newly identified. The strain's effects on plant-maize growth were tested and bioremediation evaluation trials were performed. The addition of strain HS9 could decrease HBCDs of 4.08 mg/g (87.6% removed) and 0.1 mg/g (25% removed) in soil and plants, respectively. Microbial diversity analysis shows that the addition of strain HS9 can promote the abundance of plant-beneficial bacteria, such as Methylobacillus, Nitrosomonas, Plancoccus, Bacillus, and Rhodococcus. The results provide insights for the bioremediation of HBCDs-contaminated soils.

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters

Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome

The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.

Effects of thermal hydrolytic pre-treatment on biogas process efficiency and microbial community structure in industrial- and laboratory-scale digesters

This study examined the impact of thermal hydrolysis process (THP) pre-treatment on anaerobic co-digestion of wastewater sludge and household waste and assessed whether THP was vital to achieve higher process capacity. Performance data were collected for both industrial- and laboratory-scale digesters and response in microbial community structure was evaluated by Illumina sequencing. Implementation of THP at the industrial-scale plant increased methane yield by 15% and enhanced substrate degradability. Possibility to extend the sludge retention time due to a higher solid content of the substrate, sanitisation of the digestate and improved fertiliser quality of the digestate were other industrial-scale benefits of THP installation. Continuously-fed laboratory-scale digesters were fed THP-treated or untreated substrate at an organic loading rate (OLR) of 5 g volatile solid (VS)/L/day, a feeding rate necessary at the corresponding industrial-scale plant to meet the estimated population increase within the municipality. The results indicated that the plant could have increased the capacity with unimpaired stability independently of THP installation, even though the retention time was significantly shortened during operation with untreated substrate. Microbial community analyses revealed increased contribution of the Clostridia class after THP installation in industrial-scale digesters and positive correlation between Firmicutes:Bacteriodetes and methane yield in all digesters. Differentiated profiles in laboratory-scale digesters indicated that a temperature increase from 37 to 42 °C in association with THP installation and altered substrate composition were strong determining factors shaping the microbial community. Overall, these findings can assist industrial-scale plants in choosing management strategies aimed at improving the efficiency of anaerobic digestion processes.

Preservation of rumen fluid for the pretreatment of waste paper to improve methane production

It is necessary to preserve rumen fluid for transport from slaughterhouses to the pretreatment facilities for use in treating lignocellulosic biomass. In this study, we investigated how the preservation of rumen fluid at various temperatures affects its use in hydrolysis of waste paper. Rumen fluid was preserved anaerobically at 4, 20, and 35 °C for 7 days. The number of protozoa and fibrolytic enzyme activity after preservation at 4 °C were significantly higher than that after preservation at either 20 or 35 °C. Waste paper was subsequently treated with preserved rumen fluid at 37 °C for 48 h. Preservation at 20 °C remarkedly decreased the hydrolysis of waste paper. Xylanase activity in rumen fluid preserved at 35 °C increased during the treatment, which enhanced the solubilization of waste paper as comparable to the control and preservation at 4 °C. Pretreatment of waste paper with rumen fluid preserved at 4 °C showed that the fluid retained high fibrolytic activity, and reduced the loss of organic carbon as substrate for methanogens. Our results suggest that preservation of rumen fluid at 4 °C is most suitable for efficient pretreatment and methane fermentation of waste paper.

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis

Ammonia caused disturbance of biogas production is one of the most frequent incidents in regular operation of biogas reactors. This study provides a detailed insight into the microbial community of a mesophilic, full-scale biogas reactor (477 kWh h-1 ) fed with maize silage, dried poultry manure and cow manure undergoing initial process disturbance by increased ammonia concentration. Over a time period of 587 days, the microbial community of the reactor was regularly monitored on a monthly basis by high-throughput amplicon sequencing of the archaeal and bacterial 16S rRNA genes. During this sampling period, the total ammonia concentrations varied between 2.7 and 5.8 g l-1 [NH4 + -N]. To gain further inside into the active metabolic pathways, for selected time points metatranscriptomic shotgun analysis was performed allowing the quantification of marker genes for methanogenesis, hydrolysis and syntrophic interactions. The results obtained demonstrated a microbial community typical for a mesophilic biogas plant. However in response to the observed changing process conditions (e.g. increasing NH4 + levels, changing feedstock composition), the microbial community reacted highly flexible by changing and adapting the community composition. The Methanosarcina-dominated archaeal community was shifted to a Methanomicrobiales-dominated archaeal community in the presence of increased ammonia conditions. A similar trend as in the phylogenetic composition was observed in the transcription activity of genes coding for enzymes involved in acetoclastic methanogenesis and syntrophic acetate oxidations (Codh/Acs and Fthfs). In accordance, Clostridia simultaneously increased under elevated ammonia concentrations in abundance and were identified as the primary syntrophic interaction partner with the now Methanomicrobiales-dominated archaeal community. In conclusion, overall stable process performance was maintained during increased ammonia concentration in the studied reactor based on the microbial communities' ability to flexibly respond by reorganizing the community composition while remaining functionally stable.

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

BACKGROUND

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

RESULTS

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

CONCLUSIONS

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.