Non-autotrophic methanogens dominate in anaerobic digesters

Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system

Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.

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.

Differential effects of petroleum-based and bio-based microplastics on anaerobic digestion: A review

The number of plastics is increasing owing to the rapid development of the plastics industry. Microplastics (MPs) are formed during the use of both petroleum-based plastics and newly developed bio-based plastics. These MPs are inevitably released into the environment and are enriched in wastewater treatment plant sludge. Anaerobic digestion is a popular sludge stabilization method for wastewater treatment plants. Understanding the potential impacts of different MPs on anaerobic digestion is critical. This paper provides a comprehensive review of the mechanisms of petroleum-based MPs and bio-based MPs in anaerobic digestion methane production and compares their potential effects on biochemical pathways, key enzyme activities, and microbial communities. Finally, it identifies problems that must be solved in the future, proposes the focus of future research, and predicts the future development direction of the plastics industry.

Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics

The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.

Oleate Impacts on Acetoclastic and Hydrogenotrophic Methanogenesis under Mesophilic and Thermophilic Conditions

This study investigated oleate inhibition concentration on mesophilic and thermophilic sludge by utilizing acetate and H2/CO2 (80:20, v/v) as substrate, respectively. In addition, another batch experiment was carried out to explore the influence of oleate loads (mM-oleate/g-VS) on methane production. Generally, the mesophilic anaerobic system was more stable than the thermophilic system, which embodied higher microbial abundance, higher methane yield, and higher oleate tolerance. Furthermore, this study provides a possible methanogenic pathway impacted by oleate under mesophilic and thermophilic conditions according to functional microbial composition. Lastly, this paper provides noticeable and avoidable oleate concentrations and loads under different experimental conditions as a guide for future anaerobic bioreactors of lipidic waste biodegradation.

A unified and simple medium for growing model methanogens

Apart from their archetypic use in anaerobic digestion (AD) methanogenic archaea are targeted for a wide range of applications. Using different methanogenic archaea for one specific application requires the optimization of culture media to enable the growth of different strains under identical environmental conditions, e.g., in microbial electrochemical technologies (MET) for (bio)electromethanation. Here we present a new culture medium (BFS01) adapted from the DSM-120 medium by omitting resazurin, yeast extract, casitone, and using a low salt concentration, that was optimized for Methanosarcina barkeri, Methanobacterium formicicum, and Methanothrix soehngenii. The aim was to provide a medium for follow-up co-culture studies using specific methanogens and Geobacter spp. dominated biofilm anodes. All three methanogens showed growth and activity in the BFS01 medium. This was demonstrated by estimating the specific growth rates ( μ ) and doubling times ( t d ) of each methanogen. The μ and t d based on methane accumulation in the headspace showed values consistent with literature values for M. barkeri and M. soehngenii. However, μ and t d based on methane accumulation in the headspace differed from literature data for M. formicicum but still allowed sufficient growth. The lowered salt concentration and the omission of chemically complex organic components in the medium may have led to the observed deviation from μ and t d for M. formicicum as well as the changed morphology. 16S rRNA gene-based amplicon sequencing and whole genome nanopore sequencing further confirmed purity and species identity.

Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters

Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types-namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO₂ and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood-Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology.

Enrichment of thermophilic methanogenic microflora from mesophilic waste activated sludge for anaerobic digestion of garbage slurry

This study investigated a startup strategy for thermophilic methanogenic enrichment. Conventional waste activated sludge (WAS) was used as the seed. The WAS seed was incubated at 55 °C in a continuous-flow stirred tank reactor, with garbage slurry fed continuously as a substrate. One of the two reactors (termed reactor-high, RH) was fed with a high concentration of substrate (30 g-COD/L), while the other (reactor-low, RL) received a lower concentration of feed (15 g-COD/L). The specific organic loading rate was 0.2 g-COD/L/day initially, which was gradually increased by shortening the hydraulic retention time. The final OLR was 3.2 g-COD/L/day, after more than 90% of the initial WAS got washed out from the reactor and thermophilic microorganisms became dominant in the reactors. Biogas production rate and methane conversion ratio depended on substrate concentration, although total chemical oxygen demand removal and methane content were almost the same in RH and RL. Biogas production rate in RH was 3.2 times higher than that in RL, while the conversion ratio of RH was 1.6 times higher than that of RL. Quantitative polymerase chain reaction analysis using specific primers for the mcrA gene and high-throughput sequencing analysis of 16S rRNA gene amplicons demonstrated post enrichment differences in the microbial community, relative to that in the WAS. There was no significant difference in the enriched microbial community composition between RH and RL. In conclusion, thermophilic methanogenic microflora can be enriched from mesophilic seeds. Methanothermobacter, Methanosarcina, and other thermophilic bacteria were enriched in the community over time, with these thermophiles collectively accounting for ∼80% of the stable thermophilic community.

Microbiome signature and diversity regulates the level of energy production under anaerobic condition

The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH₄%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH₄, respectively. The physicochemical analysis revealed that level of energy production (CH₄%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O₂ level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH₄ concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH₄ producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH₄ concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.

Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches

BACKGROUND

During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system.

RESULTS

Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities.

CONCLUSIONS

In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

Shewanella algae Relatives Capable of Generating Electricity from Acetate Contribute to Coastal-Sediment Microbial Fuel Cells Treating Complex Organic Matter

To identify exoelectrogens involved in the generation of electricity from complex organic matter in coastal sediment (CS) microbial fuel cells (MFCs), MFCs were inoculated with CS obtained from tidal flats and estuaries in the Tokyo bay and supplemented with starch, peptone, and fish extract as substrates. Power output was dependent on the CS used as inocula and ranged between 100 and 600 mW m^–2 (based on the projected area of the anode). Analyses of anode microbiomes using 16S rRNA gene amplicons revealed that the read abundance of some bacteria, including those related to Shewanella algae, positively correlated with power outputs from MFCs. Some fermentative bacteria were also detected as major populations in anode microbiomes. A bacterial strain related to S. algae was isolated from MFC using an electrode plate-culture device, and pure-culture experiments demonstrated that this strain exhibited the ability to generate electricity from organic acids, including acetate. These results suggest that acetate-oxidizing S. algae relatives generate electricity from fermentation products in CS-MFCs that decompose complex organic matter.

Performance of Anaerobic Digestion of Acidified Palm Oil Mill Effluent under Various Organic Loading Rates and Temperatures

This study compared the performance of thermophilic and mesophilic digesters of an anaerobic digestion system from palm oil mill effluent (POME), in which temperature is a key parameter that can greatly affect the performance of anaerobic digestion. The digesters were incubated at two distinct temperatures of 55 and 37 °C, and operated with varying organic loading rates (OLRs) of 2.4, 3.2, and 4.0 g COD/L.d by altering the chemical oxygen demand (COD) of acidified POME during feeding. The results indicated that the performance of anaerobic digestion increased as the OLR increased from 2.4 to 4.0 g COD/L.d. At the OLR of 4.0 g COD/L.d, the thermophilic condition showed the highest methane yield of 0.31 ± 0.01 L/g COD, accompanied by the highest COD removal and volatile solid reduction, which were found to be higher than the mesophilic condition. Microbial community analysis via denaturing gradient gel electrophoresis (DGGE) revealed that Methanothermobacter sp. emerges as the dominant microbe, which is known to utilize the carbon dioxide pathway with hydrogen acting as an electron donor for methane formation

Enhanced electricity generation in rice paddy-field microbial fuel cells supplemented with iron powders

Microbial fuel cells installed in rice paddy fields (RP-MFCs) are able to serve as on-site batteries for operating low-power environmental sensors. In order to increase the utility and reliability of RP-MFCs, however, further research is necessary for boosting the power output. Here we examined several powdered iron species, including zero valent iron (ZVI), goethite, and magnetite, for their application to increasing power outputs from RP-MFCs. Soil around anodes was supplemented with either of these iron species, and RP-MFCs were operated for several months during the transplanting and harvesting. It was found that power outputs from RP-MFCs supplemented with ZVI were more than double the outputs from control (not supplemented with iron species) and other RP-MFCs, even after iron corrosion was ceased, and the maximum power density reached 130 mW/m² (per projected area of the anode). Metabarcoding of 16S rRNA gene amplicons suggested that several taxa represented by fermentative and exoelectrogenic bacteria were substantially increased in MFCs supplemented with ZVI. Results suggest that ZVI lowers oxidation/reduction potential around anodes, activates anaerobic microbes involved in the conversion of organic matter into electricity and increases power output from RP-MFCs.

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

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

Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH

Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO₂ with H₂ to produce methane gas. It is the potential candidate in the biomethanation of CO₂ and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics

Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.

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

BACKGROUND

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

RESULTS

In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis.

CONCLUSIONS

An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

Isolation of an Obligate Mixotrophic Methanogen That Represents the Major Population in Thermophilic Fixed-Bed Anaerobic Digesters

Methanothermobacter Met2 is a metagenome-assembled genome (MAG) that encodes a putative mixotrophic methanogen constituting the major populations in thermophilic fixed-bed anaerobic digesters. In order to characterize its physiology, the present work isolated an archaeon (strain Met2-1) that represents Met2-type methanogens by using a combination of enrichments under a nitrogen atmosphere, colony formation on solid media and limiting dilution under high partial pressures of hydrogen. Strain Met2-1 utilizes hydrogen and carbon dioxide for methanogenesis, while the growth is observed only when culture media are additionally supplemented with acetate. It does not grow on acetate in the absence of hydrogen. The results demonstrate that Methanothermobacter sp. strain Met2-1 is a novel methanogen that exhibits obligate mixotrophy.

Biostimulation of sewage sludge solubilization and methanization by hyper-thermophilic pre-hydrolysis stage and the shifts of microbial structure profiles

This study evaluated the influence of hyper-thermophilic pre-hydrolysis stage (70 °C) on methane recovery of sewage sludge at 35 °C. In this configuration, the process performance in both temperatures were estimated and the microbial communities were characterized by full-length16S rRNA genes and/or microbial activities. In addition, the appropriate solubilization reaction time was assessed. The results revealed that the higher hydrolysis and acidogenesis activities were achieved with longer reaction time of pretreatment (5 days) and thus higher organic nitrogen conversion and alkalinity were attained. Under appropriate pretreatment reaction time, pretreated sludge was characterized by 65% higher organic matters solubilization and 1.4-fold higher volatile fatty acids (VFAs) concentration compared to raw sludge. The overall methane yield produced under this scenario was 179 L CH₄. KgVS_in, with 15% of the absolute yield was produced in hydrolysis reactor. 50% reduction in bacteria belong to Firmicurtes was observed at mesophilic reactor and meanwhile the relative abundance of Bacteroidetes and Cloacimonetes were enhanced. The predominant methanogens in both stages did not change implying adaptation of Methanothermobacter (>62%) to mesophilic condition. However, increasing acetoclastic methanogens up to 30% in mesophilic reactor indicating methane was produced from pretreated sludge mainly through H₂- mediated CO₂ reduction and partially from acetate cleavage. The results highlight the key role of hyper-thermophilic pre-hydrolysis stage for better stabilization of sewage sludge without further investments in current biogas plants.

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.

Metatranscriptomic Evidence for Magnetite Nanoparticle-Stimulated Acetoclastic Methanogenesis under Continuous Agitation

Conductive nanomaterials have been reported to accelerate methanogenesis by promoting direct interspecies electron transfer (DIET), while their effects seem to vary depending on operational conditions. The present study examined the effects of magnetite nanoparticles (MNPs) on methanogenesis from acetate by soil-derived anaerobic cultures under continuous agitation. We found that MNPs accelerated methanogenesis in agitated cultures, as has been observed previously for static cultures. Metabarcoding of 16S rRNA gene amplicons showed that Methanosarcina substantially increased in the presence of MNPs, while DIET-related Geobacter did not occur. Metagenomic and metatranscriptomic analyses confirmed the predominance of Methanosarcina in MNP-supplemented agitated cultures. In addition, genes coding for acetoclastic methanogenesis, but not those for hydrogenotrophic methanogenesis, were abundantly expressed in the dominant Methanosarcina in the presence of MNPs. These results suggest that MNPs stimulate acetoclastic methanogenesis under continuous agitation.IMPORTANCE Previous studies have shown that conductive nanoparticles, such as MNPs, accelerate methanogenesis and suggested that MNPs facilitate DIET between exoelectrogenic bacteria and methanogenic archaea. In these methanogens, electrons thus obtained are considered to be used for hydrogenotrophic methanogenesis. However, the present work provides evidence that shows that MNPs accelerate DIET-independent acetoclastic methanogenesis under continuous agitation. Since most of previous studies have examined effects of MNPs in static or weakly agitated methanogenic cultures, results obtained in the present work suggest that hydraulic conditions definitively determine how MNPs accelerate methanogenesis. In addition, the knowledge obtained in this study is useful for engineers operating stirred-tank anaerobic digesters, since we show that MNPs accelerate methanogenesis under continuous agitation.

Continuous n-valerate formation from propionate and methanol in an anaerobic chain elongation open-culture bioreactor

BACKGROUND

Chain elongation forms a new platform technology for the circular production of biobased chemicals from renewable carbon and energy sources. This study aimed to develop a continuous methanol-based chain elongation process for the open-culture production of a new-generation biofuel precursor and potential platform chemical: n-valerate. Propionate was used as a substrate for chain elongation to n-valerate in an anaerobic open-culture bioreactor. In addition, the co-production of n- and iso-butyrate in addition to n-valerate via, respectively, acetate and propionate elongation was investigated.

RESULTS

n-Valerate was produced during batch and continuous experiments with a pH in the range 5.5-5.8 and a hydraulic retention time of 95 h. Decreasing the pH from 5.8 to 5.5 caused an increase of the selectivity for n-valerate formation (from 58 up to 70 wt%) during methanol-based propionate elongation. n-Valerate and both n- and iso-butyrate were produced during simultaneous methanol-based elongation of propionate and acetate. Propionate was within the open-culture preferred over acetate as a substrate with 10-30% more consumption. Increasing the methanol concentration in the influent (from 250 to 400 mM) resulted in a higher productivity (from 45 to 58 mmol C/L/day), but a lower relative product selectivity (from 49 to 43 wt%) of n-valerate. The addition of acetate as a substrate did not change the average n-valerate productivities. Within the continuous bioreactor experiments, 6 to 17 wt% of formed products was methane. The microbial community during all steady-states in both methanol-based elongation bioreactors was dominated by species related to Clostridium luticellarii and Candidatus Methanogranum. C. luticellarii is the main candidate for n-valerate formation from methanol and propionate.

CONCLUSIONS

n-Valerate was for the first time proven to be produced from propionate and methanol by an open-culture bioreactor. Methanogenic activity can be inhibited by decreasing the pH, and the n-valerate productivity can be improved by increasing the methanol concentration. The developed process can be integrated with various biorefinery processes from thermochemical, (bio)electrochemical, photovoltaic and microbial technologies. The findings from this study form a useful tool to steer the process of biological production of chemicals from biomass and other carbon and energy sources.

Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure

Identification of the carbon (C) sources of methane (CH₄) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH₄ emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic ¹³C labelling was designed in this study. The objective was to investigate the main C sources for CH₄ emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of ¹³C was respectively distributed in CO₂, the plants, soil, and CH₄ at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH₄ ha⁻¹ vs. 2.00 kg·CH₄ ha⁻¹ for the no fertilizer treatment. Maximum CH₄ fluxes from organically fertilized (0.46 mg·m⁻²·h⁻¹) and non-fertilized (0.16 mg·m⁻²·h⁻¹) soils occurred on day 30 (tillering stage). The total percentage of CH₄ emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH₄ emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH₄ fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH₄ emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH₄ processes.

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LW showed similar values of LAS biological degradation (~47%) and removal (53-55%). Rarefaction analysis revealed that 1-2 million reads were sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative gene was ten times higher in UASB_SL and UASB_LW when compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.

Blended pulp mill, forest humus and mine residual material Technosols for mine reclamation: A growth-chamber study to explore the role of physiochemical properties of substrates and microbial inoculation on plant growth

A growth chamber trial was conducted to investigate the effects of blends of pulp and paper mill residuals and forest humus on soil properties, microbial communities and germination rate and biomass production of annual ryegrass (Lolium multiflorum) in both acid-producing and neutral to mildly alkaline mine tailings in a mine reclamation context. The organic residual amendments improved the nutritional status of the tailings substrates, and increased pH in acid-generating tailings, leading to higher germination rates and improved plant growth. A trace addition (<0.02% of sludge by dry weight) of natural forest floor material as a microbial inoculum to the sludge could increase plant biomass up to four-fold. The effects of sludge application on bioavailability of metals were variable, with the concentration of soluble copper (Cu) and nickel (Ni) increasing in some of the substrates following organic amendments. Addition of paper mill residuals to mine tailings modified the microbial communities observed in the oligotrophic tailings with the majority of DNA sequences in the sludge amended substrates being found to be closely related to heterotrophic bacterial species rather than the chemolithotrophic communities that dominate tailings environments.