Evaluating the potential impact of proton carriers on syntrophic propionate oxidation

Electrical stress and acid orange 7 synergistically clear the blockage of electron flow in the methanogenesis of low-strength wastewater

Energy recovery from low-strength wastewater through anaerobic methanogenesis is constrained by limited substrate availability. The development of efficient methanogenic communities is critical but challenging. Here we develop a strategy to acclimate methanogenic communities using conductive carrier (CC), electrical stress (ES), and Acid Orange 7 (AO7) in a modified biofilter. The synergistic integration of CC, ES, and AO7 precipitated a remarkable 72-fold surge in methane production rate compared to the baseline. This increase was attributed to an altered methanogenic community function, independent of the continuous presence of AO7 and ES. AO7 acted as an external electron acceptor, accelerating acetogenesis from fermentation intermediates, restructuring the bacterial community, and enriching electroactive bacteria (EAB). Meanwhile, CC and ES orchestrated the assembly of the archaeal community and promoted electrotrophic methanogens, enhancing acetotrophic methanogenesis electron flow via a mechanism distinct from direct electrochemical interactions. The collective application of CC, ES, and AO7 effectively mitigated electron flow impediments in low-strength wastewater methanogenesis, achieving an additional 34% electron recovery from the substrate. This study proposes a new method of amending anaerobic digestion systems with conductive materials to advance wastewater treatment, sustainability, and energy self-sufficiency.

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.

Contribution analysis of different electron transfer pathways to methane production in anaerobic digestion coupled with bioelectrochemical system

The contribution analysis of different electron transfer pathways to CH₄ production was investigated in bioelectrochemical anaerobic digestion (BEAD). It demonstrates that the indirect interspecies electron transfer (IIET) pathway and the direct interspecies electron transfer (DIET) pathways contributed to 41.7 % and 58.3 % of the CH₄ production in the BEAD reactor, respectively. The DIET pathway was further divided into DIET via electrode (eDIET) and biological DIET (bDIET) in the bulk solution, and contributed 11.1 % and 47.2 % of CH₄ production, respectively. This indicates that the dominant electron transfer pathway for CH₄ production is from the bulk solution, rather than on the polarized electrode. The electroactive microorganisms were well enriched in the bulk solution by the electric field generated between anode and cathode. The enriched electroactive microorganisms significantly improved the CH₄ production in the bulk solution through the bDIET pathway.

Effect of magnetite particle size on propionate degradation in the propionate-based anaerobic system

The size effect of magnetite (Fe₃O₄) on the degradation of propionate (PA) in the PA-based anaerobic system was investigated. The sequential bench-scale experiments were conducted. Results showed that the effects of different sized magnetite particles on PA degradation varied, and reaction cycles also played a role in substrate removal/degradation. With the increase of reaction cycle, nano-magnetite promoted PA degradation and CH₄ production, which caused faster PA degradation rate (0.997 g/L·d) than the control group (CK) without magnetite (0.834 g/L·d), whereas the groups with micron- and millimeter-sized magnetite had slower PA degradation rates (0.746 and 0.636 g/L·d) than CK group. The particle size or surface characteristics of the magnetite may become the main factor determining the PA degradation rate. Furthermore, the analysis of PA conversion and volatile fatty acids (VFAs) distribution showed the C6-dismutation pathway, which converses PA to butyrate, enhanced by the introduction of magnetite. Microbial community analysis showed that PA was degraded mainly by methyl-malonyl-CoA (MMC) pathway. The relative abundance of Syntrophobacter that catalyze MMC pathway in the group with nano-magnetite were much higher after three reaction cycles at 39 %, as compared to micro-magnetite at 28 %, and millimeter-sized magnetite at 27 %, which contributed to faster degradation of PA. Functional enzyme-encoding genes for the four methanogenesis pathways were identified with reference to KEGG database entries. The methanogenesis pathway using acetate was the most abundant pathway in all groups. The observations have important implications for enhancing the PA removal in PA-inhibited anaerobic digester.

Microbial consortia adaptation to substrate changes in anaerobic digestion

Renewable natural gas (RNG) produced from anaerobic digestion (AD) of agricultural residues is emerging a serious biofuel alternative. Complex nature of lignocellulosic biomass residues coupled with complex biochemical transformations involving a large spectrum of microbial communities make anaerobic digestion of biomass difficult to understand and control. The present work aims at studying adaptation of microbial consortia in AD to substrates changes and correlating these to biogas generation. The double edged study deals with (a) using a common starting culture inoculum on different fractions of pretreated lignocellulosic biomass (LBM) fractions; and (b) using different starter inocula for gas generation from simple glucose substrate. Taxonomic analysis using 16S amplicon sequencing is shown to highlight changes in microbial community structure and predominance, majorly in hydrolytic bacterial populations. Observed variations in the rate of digestion with different starter inocula could be related to differences in microbial community structure and relative abundance. Results with different treated biomass fractions as substrates indicated that AD performance could be related to abundance of substrate-specific microbial communities. The work is a step to a deeper understanding of AD processes that may lead to better control and operation of AD for super-scale production of RNG from biomass feedstocks.

Bacterial Communities in Multiple Tissues Across the Body Surface of Three Coastal Shark Species

Bacteria are known to have explicit roles within the microbiomes of host tissues, therefore examining these communities may prove useful in assessing host health and responses to environmental change. The present study contributes to the emerging, yet understudied, field of microbiome research in elasmobranchs. We provide a screening of the culturable bacteria communities found on multiple tissue sites on the body surface of blacktip (Carcharhinus limbatus), bull (Carcharhinus leucas), and tiger (Galeocerdo cuvier) sharks near Miami, Florida. Tissue sites include mouth, gills, skin, and any visible wounds. The study adds to our understanding of the diversity of bacteria present on sharks in comparison to their natural environment. We also compare bacterial groups found within wounds in shark skin to healthy tissue sites on the same individual. Results indicate that wounds on an individual may allow for opportunistic bacteria to invade or overgrow where they would not normally be found, which may have potential health consequences for sharks that become wounded due to fishing practices. Identified bacteria belonged to the Actinobacteria, Firmicutes, and Proteobacteria phyla, known to be prominent bacterial groups associated with marine organisms. Results indicate shark species-specific differences in bacterial communities, including the presence of bacteria belonging to Planococcaceae exclusively on the skin of tiger sharks. To our knowledge, this is the first report of this family in any elasmobranch. While most tissue sites displayed commensal bacteria identified in similar studies, known pathogens belonging to Vibrionaceae and Staphylococcaceae were identified in the wounds of blacktip and bull sharks. Some bacteria may be normal residents, but the loss of protective dermal denticles due to a wound may allow colonization by pathogens. Continued research is needed to explore microbial communities associated with sharks and their influence on host health.

Effect of nano-magnetite on the propionic acid degradation in anaerobic digestion system with acclimated sludge

In this study, a batch of acid-tolerant inoculation sludge was domesticated as inoculum, and different concentrations of nano-magnetite were added to the propionic acid (PA) anaerobic digestion system to explore its effect on the PA degradation. It was found the PA degradation rates of nano-magnetite groups were 10.96-74.62% higher than the control group without magnetite in the 6th day, especially with the dosage of 100 mg/L. Microbial community analysis showed some potential DIET participants of Chloroflexi, Proteobacteria and Bacteroidetes had the highest abundance, while metabolite analysis showed that nano-magnetite promoted the transformation of malic acid to oxaloacetic acid and the PA disproportionation to butyric acid. It indicated that nano-magnetite could effectively promote the early degradation of PA in the sludge acclimation system by accelerating DIET or PA disproportionation, so as to prevent the PA accumulation, which could provide reference for the acid accumulation regulation of anaerobic digestion system.

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.

How Comparable are Microbial Electrochemical Systems around the Globe? An Electrochemical and Microbiological Cross-Laboratory Study

A cross-laboratory study on microbial fuel cells (MFC) which involved different institutions around the world is presented. The study aims to assess the development of autochthone microbial pools enriched from domestic wastewater, cultivated in identical single-chamber MFCs, operated in the same way, thereby approaching the idea of developing common standards for MFCs. The MFCs are inoculated with domestic wastewater in different geographic locations. The acclimation stage and, consequently, the startup time are longer or shorter depending on the inoculum, but all MFCs reach similar maximum power outputs (55±22 μW cm-2 ) and COD removal efficiencies (87±9 %), despite the diversity of the bacterial communities. It is inferred that the MFC performance starts when the syntrophic interaction of fermentative and electrogenic bacteria stabilizes under anaerobic conditions at the anode. The generated power is mostly limited by electrolytic conductivity, electrode overpotentials, and an unbalanced external resistance. The enriched microbial consortia, although composed of different bacterial groups, share similar functions both on the anode and the cathode of the different MFCs, resulting in similar electrochemical output.

Substrate availability drives mixed culture fermentation of glucose to lactate at steady state

Mixed-culture fermentation (MCF) enables carbon recycling from complex organic waste streams into valuable feedstock chemicals. Using complex microbial consortia, MCF systems can be tuned to produce a range of biochemicals to meet market demand. However, the metabolic mechanisms and community interactions which drive biochemical production changes under differing conditions are currently poorly understood. These mechanisms are critical to useful MCF production models. Furthermore, predictable product transitions are currently limited to pH-driven changes between butyrate and ethanol, and chain-elongation (fed by lactate, acetate, and ethanol) to butyrate, valerate, and hexanoate. Lactate, a high-value biopolymer feedstock chemical, has been observed in transition states, but sustained production has not been described. In this study, steady state lactate production was achieved by increasing the organic loading rate of a butyrate-producing system from limiting to nonlimiting conditions at pH 5.5. Crucially, butyrate production resumed upon return to substrate-limited conditions. 16S ribosomal DNA community profiling combined with metaproteomics demonstrated that the butyrate-producing lineage Megasphaera redirected carbon flow through the methylglyoxal bypass when substrate was nonlimiting, which altered the community structure and metabolic expression toward lactate production. This metabolic mechanism can be included in future MCF models to describe the changes in product generation in substrate nonlimiting conditions.

Establishment and differential performance of hyperthermophilic microbial community during anaerobic self-degradation of waste activated sludge

Hyperthermophilic anaerobic digestion, especially at 70 °C, has drawn wide attention. In order to acquire the inoculum and digestion characteristics, batch acclimation and continuous operation experiments were conducted under hyperthermophilic (70 °C), thermophilic (55 °C) and mesophilic (35 °C) conditions, respectively. Archaea at each temperature was successfully enriched from the sole-source waste activated sludge (WAS). Hyperthermophilic digestion achieved higher archaea diversity, close to the Shannon index 2.23 for the thermophilic digestion, but the population were not improved, at a 16S rRNA genes 5.99 × 10⁵ copies mL^-1. Hydrogenotrophic methanogens, Methanospirillum and Methanothermobacter, dominated in the hyperthermophilic digester, accounting for 27.15%, while the primary phylum Firmicutes was promoted to 36.31%, with the proteolytic genus Coprothermobacter in Firmicutes at 19.50%. Refractory organic fractions were converted more with a higher digestion temperature, which was demonstrated by the fact that the COD/VS increased to 5.8, 5.2 and 4.2 at 70 °C, 55 °C and 35 °C, respectively, at the end of batch acclimation. In addition, the most solubilization for the dominant fraction protein in the WAS occurred at 70 °C as well. Similar hydrolysis ratio, over 10%, and specific hydrolysis rate, around 0.025 g COD (g VSS·d)^-1, were achieved at 70 °C and 55 °C. The higher hydrolysis for hyperthermophilic digestion even resulted in a higher methane yield than that for the mesophilic digestion. Nevertheless, contrary to higher hydrolysis, methanogenesis limited hyperthermophilic digestion in WAS degradation, with an ultimate methane yield 71.2 mL g^-1 VS_added, despite an almost complete VFA conversion through the continuous operation.

Community profiling of the intestinal microbial community of juvenile Hammerhead Sharks (Sphyrna lewini) from the Rewa Delta, Fiji

Fourteen juvenile scalloped hammerhead sharks (Sphyrna lewini; SHS) were captured between November and December 2014 in the Rewa Delta in Fiji, and assessed for intestinal microflora characterisation using 16S rRNA amplicon sequencing by Illumina Miseq. The microbial population revealed a fluctuating dominance between the Enterobacteriaceae and Vibrionaceae families, namely Citrobacter and Photobacterium spp. Other related marine operational taxonomic units were closely related to Afipia felis, Chloroflexus aggregans, Psychrobacter oceani, Pontibacter actiniarum and Shigella sonnei. Two sharks had distinctive profiles that were dominated by known pathogens, namely Aeromonas salmonicida and Klebsiella pneumonia. The presence of a Methanosaeta species, and of Shigella and Psychrobacter, would suggest sewage contamination because of a spill that occurred on the 6^th of December 2014. This study successfully establishes a baseline for future research.

Recent advances in dissimilatory sulfate reduction: From metabolic study to application

Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.

Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques

For biogas-producing continuous stirred tank reactors, an increase in dilution rate increases the methane production rate as long as substrate input can be converted fully. However, higher dilution rates necessitate higher specific microbial growth rates, which are assumed to have a strong impact on the apparent microbial biomass yield due to cellular maintenance. To test this, we operated two reactors at 37°C in parallel at dilution rates of 0.18 and 0.07 days-1 (hydraulic retention times of 5.5 and 14 days, doubling times of 3.9 and 9.9 days in steady state) with identical inoculum and a mixture of volatile fatty acids as sole carbon sources. We evaluated the performance of the Anaerobic Digestion Model No. 1 (ADM1), a thermodynamic black box approach (TBA), and dynamic flux balance analysis (dFBA), to describe the experimental observations. All models overestimated the impact of dilution rate on the apparent microbial biomass yield when using default parameter values. Based on our analysis, a maintenance coefficient value below 0.2 kJ per carbon mole of microbial biomass per hour should be used for the TBA, corresponding to 0.12 mmol ATP per gram dry weight per hour for dFBA, which strongly deviates from the value of 9.8 kJ Cmol h-1 that has been suggested to apply to all anaerobic microorganisms at 37°C. We hypothesized that a decrease in dilution rate might select taxa with minimized maintenance expenditure. However, no major differences in the dominating taxa between the reactors were observed based on amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism analysis of mcrA genes. Surprisingly, Methanosaeta dominated over Methanosarcina even at a dilution rate of 0.18 days-1, which contradicts previous model expectations. Furthermore, only 23-49% of the bacterial reads could be assigned to known syntrophic fatty acid oxidizers, indicating that unknown members of this functional group remain to be discovered. In conclusion, microbial maintenance was found to be much lower for acetogenesis and methanogenesis than previously assumed, likely due to the exceptionally low growth rates in anaerobic digestion. This finding might also be relevant for other microbial systems operating at similarly low growth rates.

Enhancing methane production from food waste fermentate using biochar: the added value of electrochemical testing in pre-selecting the most effective type of biochar

BACKGROUND

Recent studies have suggested that addition of electrically conductive biochar particles is an effective strategy to improve the methanogenic conversion of waste organic substrates, by promoting syntrophic associations between acetogenic and methanogenic organisms based on interspecies electron transfer processes. However, the underlying fundamentals of the process are still largely speculative and, therefore, a priori identification, screening, and even design of suitable biochar materials for a given biotechnological process are not yet possible.

RESULTS

Here, three charcoal-like products (i.e., biochars) obtained from the pyrolysis of different lignocellulosic materials, (i.e., wheat bran pellets, coppiced woodlands, and orchard pruning) were tested for their capacity to enhance methane production from a food waste fermentate. In all biochar-supplemented (25 g/L) batch experiments, the complete methanogenic conversion of fermentate volatile fatty acids proceeded at a rate that was up to 5 times higher than that observed in the unamended (or sand-supplemented) controls. Fluorescent in situ hybridization analysis coupled with confocal laser scanning microscopy revealed an intimate association between archaea and bacteria around the biochar particles and provided a clear indication that biochar also shaped the composition of the microbial consortium. Based on the application of a suite of physico-chemical and electrochemical characterization techniques, we demonstrated that the positive effect of biochar is directly related to the electron-donating capacity (EDC) of the material, but is independent of its bulk electrical conductivity and specific surface area. The latter properties were all previously hypothesized to play a major role in the biochar-mediated interspecies electron transfer process in methanogenic consortia.

CONCLUSIONS

Collectively, these results of this study suggest that for biochar addition in anaerobic digester operation, the screening and identification of the most suitable biochar material should be based on EDC determination, via simple electrochemical tests.

Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors

The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i.e. 2 g/L-reactor and 3 g/L-reactor). The metagenomic analysis showed that only the microbes associated with LCFA degradation could encode proteins related to "chemotaxis" and "flagellar assembly", which promoted the ability to move towards the LCFA sources so as to degrade them. Moreover, the syntrophic interactions found between Syntrophomonas sp. together with Methanosarcina sp. were possibly assigned to the menaquinone-electron transfer. Finally, it was proven that a previously exposed to LCFA inoculum is more efficient in the degradation process of LCFA due to the specialization of the microbial consortium.