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

The effects of different pretreatment technologies on microbial community in anaerobic digestion process: A systematic review

Here we comprehensively review the available knowledge on effects of different pretreatment technologies on microbial population and microbial dynamics in anaerobic digestion (AD) fed with different substrates and different operational parameters. To identify peer-reviewed studies published in English-language journals, a comprehensive search was performed across multiple electronic databases. The eligible studies were analyzed to extract data and information pertaining to the configuration of anaerobic reactors, operational parameters, and various pretreatment processes such as chemical, biological, enzymatic, thermal, microaerobic, and ultrasonic. The findings derived from this current review demonstrated that different chemical, biological, and physical pretreatment technologies improve the biomethane potential (BMP) and potentially affect the dominant bacteria and archaea. Moreover, although hydrogenotrophic methanogenesis are more observed due to resistance to extreme conditions, methane production follows both aceticlastic and hydrogenotrophic pathways in AD assisted with different pretreatment process. Firmicutes and Bacteroidetes phyla of bacteria were the dominant hydrolytic bacteria due to synergetic effects of different pretreatment process on solubilization and bioavailability of recalcitrant substrates. In summary, a holistic understanding on bacteria and archaea communities, along with the mechanisms of the dominant microorganisms leads to enhanced stability and overall performance of anaerobic digestion (AD) processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40201-024-00917-x.

Enhancing biogas production from palm oil mill effluent through the synergistic application of surfactants and iron supplements

In this study, the effects of various surfactants on the soluble chemical oxygen demand (COD) fraction and biogas production from palm oil mill effluent (POME) were investigated. A cationic surfactant (cetyltrimethylammonium bromide, CTAB) and a nonionic surfactant (Tween 80; TW80) were found to adsorb onto the particulate matter from POME, markedly reducing the soluble COD, unlike an anionic surfactant (sodium dodecyl sulfate, SDS). The mechanism underlying this phenomenon might be the adsolubilization of oil on particulate matter induced by the adsorbed surfactants. In terms of biogas production, 0.1 % w/v SDS and CTAB dramatically reduced the biogas yield, while 0.1 % w/v TW80 did not have this negative effect. A synergistic effect was observed when TW80 (0.1 % w/v) was combined with FeSO4 (400 mg/L), resulting in a 17 % greater biogas yield than that achieved with treatments using TW80 or FeSO4 alone. Moreover, the combination of TW80 and FeSO4 increased the biogas production rate. Surprisingly, the water-soluble iron fraction remained consistent across all treatments, suggesting that the adsorption of TW80 on particulate matter may limit micelle formation. Importantly, the proportion of methane in the generated biogas remained stable in all the treatments. Microbial community analysis revealed that the introduction of TW80 and FeSO4 had no discernible impact on the microbial community of the system. Pretreatment with TW80 and an iron supplement significantly enhanced biogas production and reduced the retention time of the anaerobic digestion (AD) system while maintaining the biogas quality and microbial community stability.

Proteomic profiling of robust acetoclastic methanogen in chrysene-altered anaerobic digestion: Global dissection of enzymes

Methanogen is a pivotal player in pollution treatment and energy recovery, and emerging pollutants (EPs) frequently occur in methanogen-applied biotechnology such as anaerobic digestion (AD). However, the direct effect and underlying mechanism of EPs on crucial methanogen involved in its application still remain unclear. The positive effect of chrysene (CH) on semi-continuous AD of sludge and the robust methanogen was dissected in this study. The methane yield in the digester with CH (100 mg/kg dry sludge) was 62.1 mL/g VS substrate, much higher than that in the control (46.1 mL/g VS substrate). Both methane production from acetoclastic methanogenesis (AM) and the AM proportion in the methanogenic pathway were improved in CH-shaped AD. Acetoclastic consortia, especially Methanosarcina and functional profiles of AM were enriched by CH in favor of the corresponding methanogenesis. Further, based on pure cultivation exposed to CH, the methanogenic performance, biomass, survivability and activity of typical Methanosarcina (M. barkeri) were boosted. Notably, iTRAQ proteomics revealed that the manufacturing (transcription and translation), expression and biocatalytic activity of acetoclastic metalloenzymes, particularly tetrahydromethanopterin S-methyltransferase and methyl-coenzyme M reductase with cobalt/nickel-cofactor (F₄₃₀ and cobalamin), and acetyl-CoA decarbonylase/synthase with cobalt/nickel-active site, of M. barkeri were upregulated significantly with fold changes in the range of 1.21-3.20 due to the CH presence. This study shed light on EPs-affecting industrially crucial methanogen at the molecular biology level during AD and had implications in the technical relevance of methanogens.

Role of interspecies electron transfer stimulation in enhancing anaerobic digestion under ammonia stress: Mechanisms, advances, and perspectives

Ammonia stress is a commonly encountered issue in anaerobic digestion (AD) process when treating proteinaceous substrates. The enhanced relationship between syntrophic bacteria and methanogens triggered by interspecies electron transfer (IET) stimulation is one of the potential mechanisms for an improved methane yield from the AD plant under ammonia-stressed condition. There is, however, lack of synthesized information on the mechanistic understanding of IET facilitation in the ammonia-stressed AD processes. This review critically discusses recovery of AD system from ammonia-stressed condition, focusing on H₂ transfer, redox compound-mediated IET, and conductive material-induced direct IET. The effects and the associated mechanisms of IET stimulation on mitigating ammonia stress and promoting methanogenesis were elucidated. Finally, prospects and challenges of IET stimulation were critically discussed. This review highlights, for the first time, the critical role of IET stimulation in enhancing AD process under ammonia-stressed condition.

Anaerobic digester microbiome dynamics in response to moderate and failure-inducing shock loads of fats, oils and greases

Accidental organic overloading (shock loading) is common during the anaerobic co-digestion of fats, oils and greases (FOG) and may lead to decreased performance or reactor failure due to the effects on the microbiome. Here, adapted and non-adapted lab-scale anaerobic digesters were exposed to FOG shocks of varying organic strengths. The microbiome was sequenced during the recovery periods employed between each shock event. Non-failure-inducing shocks resulted in enrichment of fermentative bacteria, and acetoclastic and methylotrophic methanogens. However, sub-dominant bacterial populations were largely responsible for increased biogas production observed after adaptation. Following failure events, early recovery communities were dominated by Pseudomonas and Methanosaeta while late recovery communities shifted toward sub-dominant bacterial taxa and Methanosarcina. Generally, the recovered microbiome structure diverged from that of both the initial and optimized microbiomes. Thus, while non-failure-inducing FOG shocks can be beneficial, the adaptations gained are lost after a failure event and adaptation must begin again.

Perspectives on microbial community in anaerobic digestion with emphasis on environmental parameters: A systematic review

This paper review is aiming to comprehensively identify and appraise the current available knowledge on microbial composition and microbial dynamics in anaerobic digestion with focus on the interconnections between operational parameters and microbial community. We systematically searched Scopus, Web of Science, pubmed and Embase (up to August 2019) with relative keywords to identify English-language studies published in peer-reviewed journals. The data and information on anaerobic reactor configurations, operational parameters such as pretreatment methods, temperature, trace elements, ammonia, organic loading rate, and feedstock composition and their association with the microbial community and microbial dynamics were extracted from eligible articles. Of 306 potential articles, 112 studies met the present review objectives and inclusion criteria. The results indicated that both aceticlastic and hydrogenotrophic methanogenesis are dominant in anaerobic digesters and their relative composition is depending on environmental conditions. However, hydrogenotrophic methanogens are more often observed in extreme conditions due to their higher robustness compared to aceticlastic methangoens. Firmicutes and Bacteroidetes phyla are most common fermentative bacteria of the acidogenic phase. These bacteria secrete lytic enzymes to degrade organic matters and are able to survive in extreme conditions and environments due to their spores. In addition, among archaea Methanosaeta, Methanobacterium, and Methanosarcinaceae are found at high relative abundance in anaerobic digesters operated with different operational parameters. Overall, understanding the shifts in microbial composition and diversity as results of operational parameters variation in anaerobic digestion process would improve the stability and process performance.

Energetic Valorization of Cereal and Exhausted Coffee Wastes Through Anaerobic Co-digestion With Pig Slurry

In the past years, there has been steady growth in work relating to improve resource efficiency through waste minimization and bioenergy recovery to mitigate climate change. Agro-food industries produce large amounts of bio-waste, challenging innovative energetic valorization strategies in the framework of circular economy principles. Anaerobic digestion (AD) technology is an interesting route to stabilize organic matter and produce biogas as a renewable energy source. This study involves continuous co-digestion of pig slurry (PS), cereal and exhausted coffee wastes (CECW) performed in a continuously stirred tank reactor, with a hydraulic retention time (HRT) of 16 days under at mesophilic conditions (36.9 ± 0.3°C). The experimental trials, were designed to include different cereal and exhausted coffee liquor (CECL) shares in the feeding mixture, corresponding to different PS to CECL ratios (PS:CECL), respectively: 100:0 (T0), 90:10 (T1), 80:20 (T2), and 70:30 (T3), in terms of percentage of inlet feeding rate (v:v). The results obtained for the feeding rate (70:30) yield to the highest specific methane production (SMP = 341 ml.gVS−1) led to a 3.5-fold improvement in comparison with the reference scenario. The synergetic effect between the microbial consortia of PS and the high carbon to nitrogen ratio (C/N) of CECL explain the improvements achieved. The maximum soluble chemical oxygen demand (SCOD) reduction (84.0%) due to the high content and soluble chemical oxygen demand to total chemical oxygen demand ratio (SCOD/TCOD) corroborate the results achieved. The digester stability, evaluated by specific energetic loading rate, was below the limit (0.4 d−1). Results from ANOVA showed a significant effect of CECL on the resulting GPR and SMP values. Additionally, Tukey's “Honest Significant Difference” method, confirmed statistically significant differences between the trials T3-T0, T3-T1, T3-T2, and T2-T0. Thus, co-digestion of PS and of CECL seems to be a promising approach for bioenergy recovery and promoting biowastes circularity.

Ammonia-induced inhibition of manure-based continuous biomethanation process under different organic loading rates and associated microbial community dynamics

Three Continuously Stirred Tank Reactors (CTSRs) were operating at steady state conditions with Organic Loading Rates (OLR) of 2.09, 3.024 and 4.0 g VS L^-1 d^-1. Glucose was used as the sole factor for increasing the OLR, linking the increase of the OLR with the C/N ratio increase. The reactors were stressed by increasing the ammonia concentration to 5 g L^-1 from 1.862 g L^-1. The results showed elevating inhibition of the anaerobic process by increasing the C/N ratio just by increasing the OLR, under the high ammonia concentration. A different response of the bacterial and archaeal community under ammonia stressed conditions was also observed. Under the high ammonia concentration, hydrogen-depended methylotrophic was the dominant methanogenesis route at OLR of 2.09 g VS L^-1d^-1, while the hydrogenotrophic route was the dominant at the high OLR of 4 g VS L^-1d^-1, which coincided with high acetate and propionate concentrations.

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.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

The microbiome driving anaerobic digestion and microbial analysis

The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.

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.

Reduction in Hg phytoavailability in soil using Hg-volatilizing bacteria and biochar and the response of the native bacterial community

Biological approaches are considered promising and eco-friendly strategies to remediate Hg contamination in soil. This study investigated the potential of two 'green' additives, Hg-volatilizing bacteria (Pseudomonas sp. DC-B1 and Bacillus sp. DC-B2) and sawdust biochar, and their combination to reduce Hg(II) phytoavailability in soil and the effect of the additives on the soil bacterial community. The results showed that the Hg(II) contents in soils and lettuce shoots and roots were all reduced with these additives, achieving more declines of 12.3-27.4%, 24.8-57.8% and 2.0-48.6%, respectively, within 56 days of incubation compared to the control with no additive. The combination of DC-B2 and 4% biochar performed best in reducing Hg(II) contents in lettuce shoots, achieving a decrease of 57.8% compared with the control. Pyrosequencing analysis showed that the overall bacterial community compositions in the soil samples were similar under different treatments, despite the fact that the relative abundance of dominant genera altered with the additives, suggesting a relatively weak impact of the additives on the soil microbial ecosystem. The low relative abundances of Pseudomonas and Bacillus, close to the background levels, at the end of the experiment indicated a small biological disturbance of the local microbial niche by the exogenous bacteria.