Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Sulfate reduction behavior in response to landfill dynamic pressure changes

During the long-term stabilization process of landfills, the pressure field undergoes constant changes. This study constructed dynamic pressure changes scenarios of high-pressure differentials (0.6 MPa) and low-pressure differentials (0.2 MPa) in the landfill pressure field at 25 °C and 50 °C, and investigated the sulfate reduction behavior in response to landfill dynamic pressure changes. The results showed that the pressurization or depressurization of high-pressure differentials caused more significant differences in sulfate reduction behavior than that of low-pressure differentials. The lowest hydrogen sulfide (H2S) release peak concentration under pressurization was only 29.67% of that under initial pressure condition; under depressurization, the highest peak concentration of H2S was up to 21,828 mg m-3, posing a serious risk of H2S pollution. Microbial community and correlation analysis showed that pressure had a negative impact on the sulfate-reducing bacteria (SRB) community, and the SRB community adjusted its structure to adapt to pressure changes. Specific SRBs were further enriched with pressure changes. Differential H2S release behavior under pressure changes in the 25 °C pressure environments were mediated by Desulfofarcimen (ASV343) and Desulfosporosinus (ASV1336), while Candidatus Desulforudis (ASV24) and Desulfohalotomaculum (ASV94) played a key role at 50 °C. This study is helpful in the formulation of control strategies for the source of odor pollution in landfills.

Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities

Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.

Strain-resolved metagenomics approaches applied to biogas upgrading

Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count-two for both hydrogenotrophic archaea-and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process.

Biomethane is produced by acetate cleavage, not direct interspecies electron transfer: genome-centric view and carbon isotope

Understanding the source of methane (CH4) is of great significance for improving the anaerobic fermentation efficiency in bioengineering, and for mitigating the emission potential of natural ecosystems. Microbes involved in the process named direct interspecies electron transfer coupling with CO2 reduction, i.e., electrons released from electroactive bacteria to reduce CO2 into CH4, have attracted considerable attention for wastewater treatment in the past decade. However, how the synergistic effect of microbiota contributes to this anaerobic carbon metabolism accompanied by CH4 production still remains poorly understood, especial for wastewater with antibiotic exposure. Results show that enhancing lower-abundant acetoclastic methanogens and acetogenic bacteria, rather than electroactive bacteria, contributed to CH4 production, based on a metagenome-assembled genomes network analysis. Natural and artificial isotope tracing of CH4 further confirmed that CH4 mainly originated from acetoclastic methanogenesis. These findings reveal the contribution of direct acetate cleavage (acetoclastic methanogenesis) and provide insightsfor further regulation of methanogenic strategies.

Ex-situ biomethanation for CO2 valorization: State of the art, recent advances, challenges, and future prospective

Ex-situ biomethanation is an emerging technology that facilitates the use of surplus renewable electricity and valorizes carbon dioxide (CO2) for biomethane production by hydrogenotrophic methanogens. This review offers an up-to-date overview of the current state of ex-situ biomethanation and thoroughly analyzes key operational parameters affecting hydrogen (H2) gas-liquid mass transfer and biomethanation performance, along with an in-depth discussion of the technical challenges. To the best of our knowledge, this is the first review article to discuss microbial community structure in liquid and biofilm phases and their responses after exposure to H2 starvation during ex-situ biomethanation. In addition, future research in areas such as reactor configuration and optimization of operational parameters for improving the H2 mass transfer rate, inhibiting opportunistic homoacetogens, integration of membrane technology, and use of conductive packing material is recommended to overcome challenges and improve the efficiency of ex-situ biomethanation. Furthermore, this review presents a techno-economic analysis for the future development and facilitation of industrial implementation. The insights presented in this review will offer useful information to identify state-of-the-art research trends and realize the full potential of this emerging technology for CO2 utilization and biomethane production.

Ecological distribution of anaerobic granular sludge towards efficient anaerobic reactor

Anaerobic reactors often underperform compared to expectations. To identify the key factors, an ecological anaerobic reactor (EAR) with vertical partitions was developed and compared to a physical anaerobic reactor (PAR) as the control. It was observed that EAR achieved a much higher organic loading rate (OLR) compared to PAR (>100 vs 45 kg/m3·d). The different vertical distribution characteristics of anaerobic granular sludge could be ascribed to two vertical distribution patterns dominated in EAR and PAR, i.e., ecological and physical distributions. It was revealed that ecological distribution was formed by the habitat selection, resulting in promoted substrate availability and higher OLR. While physical distribution was mainly affected by hydraulic selection via granule settleability, causing declined substrate availability and lower OLR. Consequently, the promoted ecological distribution and weakened hydraulic selection in EAR contributed to its good performance. Overall, these findings could offer novel concepts for the development of reactors towards high performance.

Modelling of microbial interactions in anaerobic digestion: from black to glass box

Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.

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

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

An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil

The free radicals released from the advanced oxidation processes can enhance microplastics degradation, however, the existence of microbes acting synergistically in this process is still uncertain. In this study, magnetic biochar was used to initiate the advanced oxidation process in flooded soil. paddy soil was contaminated with polyethylene and polyvinyl chloride microplastics in a long-term incubation experiment, and subsequently subjected to bioremediation with biochar or magnetic biochar. After incubation, the total organic matter present in the samples containing polyvinyl chloride or polyethylene, and treated with magnetic biochar, significantly increased compared to the control. In the same samples there was an accumulation of "UVA humic" and "protein/phenol-like" substances. The integrated metagenomic investigation revealed that the relative abundance of some key genes involved in fatty acids degradation and in dehalogenation changed in different treatments. Results from genome-centric investigation suggest that a Nocardioides species can cooperate with magnetic biochar in the degradation of microplastics. In addition, a species assigned to the Rhizobium taxon was identified as a candidate in the dehalogenation and in the benzoate metabolism. Overall, our results suggest that cooperation between magnetic biochar and some microbial species involved in microplastic degradation is relevant in determining the fate of microplastics in soil.

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.

Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production

Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25 °C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H₂ production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.

Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm

BACKGROUND

Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond.

RESULTS

We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system.

CONCLUSIONS

Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.

Substance bioconversion, hydrolases activity, and metagenomic analysis to unravel the enhanced biomethanation of corn stover with urea-hydrothermal pretreatment

Corn stover (CS) is a promising feedstock for producing biomethane, that can replace diminishing fossil fuels. However, the recalcitrant structure of CS resulted in low degradability in anaerobic digestion (AD). Numerous studies investigated the pretreatment of CS before AD, but the insight mechanism of biomethanation enhancement is not fully revealed. Therefore, this study advanced low-temperature urea-hydrothermal pretreatment of CS, and the biomethane production, substance bioconversion, hydrolase activity, and metagenomic analysis were conducted to unravel the intrinsic mechanisms of pretreatment for the enhanced biomethanation. The results showed that the pretreatment improved 11.5% of the specific surface area of CS, providing 111.5% higher total volatile fatty acids and 19.9% higher reducing sugars than the control, potentially enriching more anaerobic microorganisms. As a result, the pretreated CS achieved 19.1% higher biomethane yield, 9.1% higher volatile solid removal rate, and 3 days shorter digestion time. The mass balance and microbial community succession analysis indicated that the pretreatment reinforced the biomethane conversion from carbohydrate, which was attributed to the rapid enrichment of hydrolytic acidification bacteria (g__unclassified_o__Bacteroidales) (33.2%) and mixotrophic archaea (Methanosarcina) (72.3%). Meanwhile, the activity of cellulase and xylanase was enhanced up to 23.7% and 66.7%. Metagenomic analysis revealed that the combined pretreatment of CS promoted methanogenesis by enhancing various CAZymes secretion (such as oligosaccharide-degrading enzymes), and functional genes expression of hydrolytic, acidification and acetate-methane pathways at days 1-5. The study indicated that the combined pretreatment could influence microbial composition and function by changing the physicochemical properties of the CS, thereby improving methanogenic performance.

Impacts of organic loading rate and hydraulic retention time on organics degradation, interspecies interactions and functional traits in thermophilic anaerobic co-digestion of food waste and sewage sludge

This study provided novel insights into the effects of organic loading rate (OLR) and hydraulic retention time (HRT) on thermophilic anaerobic co-digestion of food waste and sewage sludge. The obtained maximum methane (CH₄) yield of 328 ± 4 mL CH₄/g COD_fed at HRT of 15 days (OLR = 5.8 g VS/L/d) was partly attributable to the enhanced acidogenesis, acetogenesis, and methanogenesis phases. The increased key enzyme activities, particularly acetate kinase (improved by 5.2-fold), providing substantial methanogenic substrates for efficient CH₄ production. The functional syntrophs that were related to syntrophic decarboxylation, novel acetate oxidation & reductive acetyl-CoA, and β-oxidation pathways could drive trophic interactions with methanogens. This markedly stimulated hydrogenotrophic Methanoculleus thermophilus metabolism and concomitantly enriched mixotrophic Methanosarcina thermophila. The distinctive cross-feeding interspecies interactions significantly affected the assembly and dynamics of thermophilic consortia. These findings shed light on the physicochemical and microbial mechanisms of HRT- and OLR-dependent enhancement of methanogenesis.

Effect of pressure on biomethanation process and spatial stratification of microbial communities in trickle bed reactors under decreasing gas retention time

The current study investigated the effect of elevating gas pressure on biomethanation in trickle-bed reactors (TBRs). The increased pressure led to successful biomethanation (CH₄ > 90 %) at a gas retention time (GRT) of 21 min, due to the improved transfer rates of H₂ and CO₂. On the contrary, the non-pressurized TBR performance was reduced at GRTs shorter than 40 min. Metagenomic analysis revealed that the microbial populations collected from the lower and middle parts of the reactor under the same GRT were more homogeneous compared with those developed in the upper layer. Comparison with previous experiments suggest that microbial stratification is mainly driven by the nutrient provision strategy. Methanobacterium species was the most dominant methanogen and it was mainly associated with the bottom and middle parts of TBRs. Overall, the increased pressure did not affect markedly the microbial composition, while the GRT was the most important parameter shaping the microbiomes.