Methanogenic potential of formate in thermophilic anaerobic digestion

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.

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

BACKGROUND

Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO₂) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO₂ fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes.

RESULTS

The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange.

CONCLUSIONS

Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges. Video Abstract.

Insights into Ammonia Adaptation and Methanogenic Precursor Oxidation by Genome-Centric Analysis

Ammonia released from the degradation of protein and/or urea usually leads to suboptimal anaerobic digestion (AD) when N-rich organic waste is used. However, the insights behind the differential ammonia tolerance of anaerobic microbiomes remain an enigma. In this study, the cultivation in synthetic medium with different carbon sources (acetate, methanol, formate, and H2/CO2) shaped a common initial inoculum into four unique ammonia-tolerant syntrophic populations. Specifically, various levels of ammonia tolerance were observed: consortia fed with methanol and H2/CO2 could grow at ammonia levels up to 7.25 g NH+-N/L, whereas the other two groups (formate and acetate) only thrived at 5.25 and 4.25 g NH+-N/L, respectively. Metabolic reconstruction highlighted that this divergent microbiome might be achieved by complementary metabolisms to maximize biomethane recovery from carbon sources, thus indicating the importance of the syntrophic community in the AD of N-rich substrates. Besides, sodium/proton antiporter operon, osmoprotectant/K+ regulator, and osmoprotectant synthesis operon may function as the main drivers of adaptation to the ammonia stress. Moreover, energy from the substrate-level phosphorylation and multiple energy-converting hydrogenases (e.g., Ech and Eha) could aid methanogens to balance the energy request for anabolic activities and contribute to thriving when exposed to high ammonia levels.

Anaerobic digestion of food waste with aerobic post-treatment: Effect of fruit and vegetable content

A mesophilic anaerobic digester, followed by a psychrophilic aerobic post-treatment, was used to treat food waste (FW) with different proportions of fruit and vegetable waste (FVW). Two types of FW were used: low fruit and vegetable mix (LFV, with 56.5% of FVW) and high fruit and vegetable mix (HFV, with 78.3% of FVW). The anaerobic digester fed with LFV failed at an organic loading rate of 1.6 g VS.L^-1.d^-1 (volatile fatty acid (VFA) = 6000 mg.L^-1) due to high ammonia (reaching 3000 mg.L^-1). It was shown that, in an unstable anaerobic environment, ammonia is highly correlated ( r² = 0.77) with VFA and is negatively correlated with volatile solids, total solids, and chemical oxygen demand (COD) removal rates ( r² = 0.88, r² = 0.71, and r² = 0.91, respectively). In contrast, the anaerobic digester fed with HFV exhibited a stable performance (VFA = 1243 mg.L^-1), with limited ammonia accumulation (940 mg.L^-1). Methane generation was affected by the FVW content and reached 531 ml CH₄.g VS^-1 (CH₄ = 52%) with LFV feed and 478 ml CH₄.g VS^-1 (CH₄ = 57.4%) with HFV. The overall TS, VS and COD removal rates (all ranging between 94% and 97%), were closely similar for LFV and HFV. Accordingly, the aerobic post-treatment seems to compensate for the reduced performance of the disturbed anaerobic system fed with LFV.

Application of quadratic regression orthogonal design to develop a composite inoculum for promoting lignocellulose degradation during green waste composting

The aims of this study are to determine the feasibility of applying QROD (quadratic regression orthogonal design) to optimize a combination of microorganisms and to develop a composite inoculum for promoting lignocellulose degradation during GWC (green waste composting). This feasibility was studied in a laboratory scale experiment, using three lignocellulolytic microorganisms, isolated from the mature phase of GWC by the dilution plating method. After the feasibility was confirmed, a composite inoculum was developed through the results of the optimization, whose effect was evaluated by comparing it with Phanerochaete chrysosporium and EM (Effective Microorganisms) in a pilot scale experiment of GWC. The use of QROD to finish this optimization was proven feasible, because the p value of the regression equation was less than 0.05 (0.0108), meaning that the quadratic regression model is suitable for describing the relationship between the combination of the three microorganisms and their ability to degrade lignocellulose. Additional proof of this feasibility is that the composite inoculum in the quadratic regression orthogonal experiment demonstrated lignocellulose degradation ability similar to the GWC experiment. Although the lignin degradation ability of the composite inoculum did not surpass Phanerochaete chrysosporium, it was stronger than EM. Meanwhile, cellulose degradation ability and humus synthesis ability of the composite inoculum were stronger than for Phanerochaete chrysosporium and were close to EM. It is hard to tell which inoculum is the best since each inoculum had advantages in different aspects, while the composite inoculum still showed a considerable effect of lignocellulose degradation during GWC.

Application of a Portable Multi-Analyte Biosensor for Organic Acid Determination in Silage

Multi-analyte biosensors may offer the opportunity to perform cost-effective and rapid analysis with reduced sample volume, as compared to electrochemical biosensing of each analyte individually. This work describes the development of an enzyme-based biosensor system for multi-parametric determination of four different organic acids. The biosensor array comprises five working electrodes for simultaneous sensing of ethanol, formate, d-lactate, and l-lactate, and an integrated counter electrode. Storage stability of the biosensor was evaluated under different conditions (stored at +4 °C in buffer solution and dry at −21 °C, +4 °C, and room temperature) over a period of 140 days. After repeated and regular application, the individual sensing electrodes exhibited the best stability when stored at −21 °C. Furthermore, measurements in silage samples (maize and sugarcane silage) were conducted with the portable biosensor system. Comparison with a conventional photometric technique demonstrated successful employment for rapid monitoring of complex media.

Sample preparation, preservation, and storage for volatile fatty acid quantification in biogas plants

Volatile fatty acids (VFA) represent short-chain fatty acids consisting of six or fewer carbon atoms that can be distilled at atmospheric pressure. In anaerobic digestion processes VFAs are of central importance for maintaining stable reactor performance and biogas production, are used as indicators for arising problems and are important process monitoring parameters. In the present study, sludge derived form a full-scale anaerobic digester of a wastewater treatment plant was spiked with formate, acetate, propionate, and butyrate in order to evaluate various commonly used techniques for VFA extraction, preservation, and storage. It was shown that VFA extraction after centrifugation warranted the highest recovery rates for spiked VFAs. Moreover, experiments clearly indicated the importance of a fast sample handling, including the necessity of immediate cooling of the samples. Chemical sample preservation within a narrow time frame or deep freezing emerged as an alternative to instant VFA extraction. Short-time storage of extracted VFA samples at + 4°C is an option for up to 7 days, for longer periods storage at -20°C was found to be applicable.

Impact of several antibiotics and 2-bromoethanesulfonate on the volatile fatty acid degradation, methanogenesis and community structure during thermophilic anaerobic digestion

The main aim of the present study was to gain insight into the stability of an anaerobic digestion process suffering from exposure to antibiotics and the methanogenic inhibitor 2-bromoethanesulfonate (BES). For this purpose, eleven antibiotics and BES were investigated with regard to the degradation of volatile fatty acids (VFAs), methanogenesis, and impact on the microbial community structure. Only neomycin, gentamicin, rifampicin, and BES showed complete inhibitions of VFA degradations. This points to distinct interferences with important trophic degradation cascades. Based upon DGGE and sequencing approaches, Methanosarcina spp. were severely influenced by the treatments while hydrogenotrophic methanogens were less affected. Interestingly, BES and neomycin inhibited the degradation of acetate while only BES inhibited methanogenesis completely. It seems that Methanosarcina spp. were mandatory for the degradation of acetate at high rates. The present results highly emphasize the detrimental effects of antimicrobial compounds with the potential to significantly inhibit the anaerobic digestion.

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR

Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log₁₀ the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture

Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle.

Biohydrogen, biomethane and bioelectricity as crucial components of biorefinery of organic wastes: a review

Biohydrogen is a sustainable form of energy as it can be produced from organic waste through fermentation processes involving dark fermentation and photofermentation. Very often biohydrogen is included as a part of biorefinery approaches, which reclaim organic wastes that are abundant sources of renewable and low cost substrate that can be efficiently fermented by microorganisms. The aim of this work was to critically assess selected bioenergy alternatives from organic solid waste, such as biohydrogen and bioelectricity, to evaluate their relative advantages and disadvantages in the context of biorefineries, and finally to indicate the trends for future research and development. Biorefining is the sustainable processing of biomass into a spectrum of marketable products, which means: energy, materials, chemicals, food and feed. Dark fermentation of organic wastes could be the beach-head of complete biorefineries that generate biohydrogen as a first step and could significantly influence the future of solid waste management. Series systems show a better efficiency than one-stage process regarding substrate conversion to hydrogen and bioenergy. The dark fermentation also produces fermented by-products (fatty acids and solvents), so there is an opportunity for further combining with other processes that yield more bioenergy. Photoheterotrophic fermentation is one of them: photosynthetic heterotrophs, such as non-sulfur purple bacteria, can thrive on the simple organic substances produced in dark fermentation and light, to give more H2. Effluents from photoheterotrophic fermentation and digestates can be processed in microbial fuel cells for bioelectricity production and methanogenic digestion for methane generation, thus integrating a diverse block of bioenergies. Several digestates from bioenergies could be used for bioproducts generation, such as cellulolytic enzymes and saccharification processes, leading to ethanol fermentation (another bioenergy), thus completing the inverse cascade. Finally, biohydrogen, biomethane and bioelectricity could contribute to significant improvements for solid organic waste management in agricultural regions, as well as in urban areas.

Methanosarcina spp., the key to relieve the start-up of a thermophilic anaerobic digestion suffering from high acetic acid loads

This paper investigates if it is possible to produce inocula to counteract high acetic acid (CH3COO(-)) concentrations during thermophilic anaerobic digestion. To this end, fermenter sludge was exposed for different durations to either gradually increasing CH3COO(-) concentrations or directly exposed to a high concentration (150 mM). Altogether, these enrichments led to inocula with a distinct decrease of representatives of Methanobacteriales, while those of Methanoculleus spp. were hardly affected by any treatment. After the inoculation, good agreements of the abundance of Methanosarcinales and Methanoculleus spp. with total DNA content and methane production rate were apparent. In addition, a gradual adaptation of the inoculum for at least 4 weeks led to a significant increase of Methanosarcina spp. during the subsequent fermentation. These results demonstrate the potential of bioaugmentation to relieve the start-up of an anaerobic digestion suffering from high CH3COO(-) loads, especially pointing to the robust acetoclastic genus Methanosarcina.