Stimulation of Smithella-dominating propionate oxidation in a sediment enrichment by magnetite and carbon nanotubes

Effect of carbon nanomaterials on functional diversity and structure of soil microbial community under single and repeated exposures

The extensive application of carbon nanomaterials (CNMs) has attracted increasing studies concerned about its environmental impact. These studies focus on single exposure to CNMs, but repeated exposures with relatively low concentration are more likely to occur under actual exposure scenario. In this study, we studied the metabolic functional and structure of soil microorganism community under single and repeated exposures to multiwalled carbon nanotubes (MW), graphene (GR), and fullerene (C60) by Biolog EcoPlates and high-throughput sequencing. Our findings revealed that repeated exposures to CNMs significantly increase the metabolic activity and diversity of the soil microbial community as compared with single exposure. Principal component and similarity analysis not only indicated that GR exerted a stronger effect on soil microbial diversity among three exposures compared to C60 and MW, but also revealed that the metabolic activity of the soil microbial community was more affected by the exposure scenarios of CNMs than the type of CNMs. These findings elucidated the effect of CNMs under different exposure scenarios on soil microorganism community, providing a new perspective on the risk assessment of nanomaterials.

Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil

BACKGROUND

Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic investigation into the mechanism of straw decomposition in a paddy soil.

RESULTS

The chemical analysis of 16-day soil microcosm incubation revealed that straw decomposition could be divided into two stages based on the dynamics of methane, short chain fatty acids, dissolved organic carbon and monosaccharides. Metagenomic analysis revealed that the relative abundance of glucoside hydrolase (GH) encoding genes for cellulose decomposition increased rapidly during the initial stage (3-7 days), while genes involved in hemicellulose decomposition increased in the later stage (7-16 days). The increase of cellulose GH genes in initial stage was derived mainly from Firmicutes while Bacteroidota contributed mostly to the later stage increase of hemicellulose GH genes. Flagella assembly genes were prevalent in Firmicutes but scarce in Bacteroidota. Wood-Ljungdahl pathway (WLP) was present in Firmicutes but not detected in Bacteroidota. Overall, Bacteroidota contained the largest proportion of total GHs and the highest number of carbohydrate active enzymes gene clusters in our paddy soil metagenomes. The strong capacity of the Bacteroidota phylum to degrade straw polymers was specifically attributed to Bacteroidales and Chitinophagales orders, the latter has not been previously recognized.

CONCLUSIONS

This study revealed a collaborating sequential contribution of microbial taxa and functional genes in the decomposition of straw residues in a paddy soil. Firmicutes with the property of mobility, WLP and cellulose decomposition could be mostly involved in the initial breakdown of straw polymers, while Bacteroidota became abundant and possibly responsible for the decomposition of hemicellulosic polymers during the later stage.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Effects of ferroferric oxide on propionate methanogenesis in sequencing batch reactors: Microbial community structure and metagenomic analysis

This study investigated the effects of ferroferric oxide (Fe₃O₄) on propionate methanogenesis in anaerobic sequencing batch reactor (ASBR). Compared to ASBR_C (without Fe₃O₄ addition), the addition of 10 g/L Fe₃O₄ (ASBR_Fe) decreased the maximum methane production rate by 69.6 % when propionate was used as the sole substrate. The addition of Fe₃O₄ reduced the contents of humic substances, riboflavin and nicotinamide adenine dinucleotide in extracellular polymeric substances. Therefore, Fe₃O₄ inhibited interspecies electron transfer of microorganisms through electronic mediators. Microbial community analysis revealed that Fe₃O₄ addition increased the relative abundance of acetate oxidizing bacterium (Mesotoga), but decreased the abundance of hydrogenotrophic methanogen (Methanobacterium). Further metagenomics analysis indicated that Fe₃O₄ increased the abundance of acetate oxidation genes and decreased that of hydrogenotrophic methanogenesis, quorum sensing and V/A-type ATPase genes. Thus, Fe₃O₄ reduced propionate methanogenesis during anaerobic digestion. The overall results indicate that Fe₃O₄ addition inhibits methanogenesis for treatment of propionate-contaminated wastewater in ASBR.

Quantitative and Qualitative Changes in the Genetic Diversity of Bacterial Communities in Anaerobic Bioreactors with the Diatomaceous Earth/Peat Cell Carrier

This paper analyses the impact of the diatomaceous earth/peat (DEP; 3:1) microbial carrier on changes in the bacterial microbiome and the development of biofilm in the anaerobic digestion (AD) of confectionery waste, combined with digested sewage sludge as inoculum. The physicochemical properties of the carrier material are presented, with particular focus on its morphological and dispersion characteristics, as well as adsorption and thermal properties. In this respect, the DEP system was found to be a suitable carrier for both mesophilic and thermophilic AD. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, carried out using next-generation sequencing (NGS), showed that the material has a modifying effect on the bacterial microbiome. While Actinobacteria was the most abundant cluster in the WF-control sample (WF—waste wafers), Firmicutes was the dominant cluster in the digested samples without the carrier (WF-dig.; dig.—digested) and with the carrier (WF + DEP). The same was true for the count of Proteobacteria, which decreased twofold during biodegradation in favor of Synergistetes. The Syntrophomonas cluster was identified as the most abundant genus in the two samples, particularly in WF + DEP. This information was supplemented by observations of morphological features of microorganisms carried out using fluorescence microscopy. The biodegradation process itself had a significant impact on changes in the microbiome of samples taken from anaerobic bioreactors, reducing its biodiversity. As demonstrated by the results of this innovative method, namely the BioFlux microfluidic flow system, the decrease in the number of taxa in the digested samples and the addition of DEP contributed to the microbial adhesion in the microfluidic system and the formation of a stable biofilm.

Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge

Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H₂ ), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H₂ and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.

Potential treatment of aged cow manure using spare capacity in anaerobic digesters treating a mixture of food waste and pig manure

With the increasing production of cow manure (CM) and the continuing decrease in the demand for manure compost, CM management has become an urgent and challenging task in Korea. In most cattle farms in Korea, CM mixed with bedding materials is left in pens exposed to the open air for several months before treatment, which makes CM an unsuitable feedstock for anaerobic digestion. This study examined the co-digestion of aged CM with a mixture of food waste and pig manure as the base substrate to assess the possibility of treating and valorizing CM using spare capacity in existing anaerobic digesters dealing with other wastes. The duplicate digesters initially fed with the base substrate were subjected to the addition of increasing amounts of CM (3-10% in the feed, w/v) over nine months. Co-feeding CM up to 5% in the feed (w/v) did not compromise the methanogenic degradation of the substrates, but adding more CM led to a significant performance deterioration likely related to the buildup of inhibitory free ammonia and H₂S. Adding CM substantially influenced the digester microbial communities, especially methanogenic communities, and induced a dominance shift from aceticlastic Methanothrix to hydrogenotrophic methanogens as the CM fraction increased. The overall results suggest that the CM fraction should not exceed 5% in the feed (w/v) for its stable treatment with the base substrate in the experimental digesters. Although further studies are needed, anaerobic treatment using spare capacity in existing digesters can be a useful strategy for the management of aged CM.

Multiple pathways for the anaerobic biodegradation of microcystin-LR in the enriched microbial communities from Lake Taihu

Anaerobic biodegradation is a non-negligible elimination approach for microcystin (MC) pollution and exhibits important bioremediation potential for environmental problems. However, the specific anaerobic MC-degrading mechanism remains unclear and few functional bacteria have been found. In this study, three microbial communities of sludges from different locations in Lake Taihu were collected and further enriched by microcystin-LR (MC-LR) under anaerobic conditions. MC-LR (1 mg/L) could be completely degraded by these enriched microbial communities under anaerobic conditions, but their degradation rates were significantly different. In addition, two different ring-opening sites of MC-LR in Ala-Leu and Arg-Adda were observed, and three new anaerobic degradation products were first identified, including two hexapeptides (MeAsp-Arg-Adda-Glu-Mdha-Ala and Adda-Glu-Mdha-Ala-Leu-MeAsp) and one end-product pentapeptide (Glu-Mdha-Ala-Leu-MeAsp). Based on the chemical structures and temporal trends of all detected degradation products, two novel anaerobic biodegradation pathways of MC-LR were proposed. Moreover, the MC-degrading genes mlrABC were not detected among all microbial communities, which suggested that some new MC-degrading mechanisms might exist under anaerobic conditions. Finally, through the comparison of microbial community structure, Gemmatimonas and Smithella were deduced as possible anaerobic MC-degrading bacteria. These findings strongly indicate that anaerobic biodegradation is an important method of self-repair in the natural environment and provides a potential removal strategy for MC pollution.

New insights into the r/K selection theory achieved in methanogenic systems through continuous-flow and sequencing batch operational modes

Anaerobic digestion is achieved through cooperation among various types of microorganisms, and the regulation of microbial communities is key to achieving stable system operation. In this study, the r/K selection theory was adopted to examine the system performance and microbial characteristics in anaerobic reactors with different operating modes (continuous-flow reactors, CFRs; sequencing batch reactors, SBRs) and sludge retention times (25 and 10 days). Four lab-scale reactors (CFR_25d, CFR_10d, SBR_25d, and SBR_10d) were operated. In the cycle reaction, CFR_25d achieved the highest methane yield (678.0 mL/L) and methane production rate (140.8 mL/(L·h)); while those in CFR_10d were the lowest, which could have been due to an accumulation of volatile fatty acids. CFR could wash out r-strategists efficiently, such as Methanosarcina. CFR_25d and CFR_10d significantly enriched the K-strategist Geobacter, with the relative abundances of 34.0% and 72.6%, respectively. In addition, the hydrogenotrophic methanogens of Methanolinea and Methanospirillum (K-strategists) dominated in CFR_25d and CFR_10d. Methanobacterium adapted to the diverse operational conditions, but the slow grower Methanosaeta only accounted for 0.9% in CFR_10d. Failure to enrich propionate oxidizers resulted in a functional absence of propionate degradation in the CFRs.

Core-shell structured polyaniline/polypyrrole composites promoted methane production from anaerobic sludge

The core-shell structured polypyrrole/polyaniline (PPy@PANI) were synthesized by in-situ polymerization method and were used as the conductive medium to enhance methane production from the anaerobic wastewater treatment. It was found that the PPy@PANI has a good performance on methane production from the anaerobic wastewater treatment, and it composites can improve the methane production rate and yield by 70.2% and 28.3% in the initial 4 h compared with the control group. A high methane production rate was achieved when the dosage of PPy@PANI was 0.6 g/L, which suggested that 0.6 g/L was the optimal dosage. Finally, the mechanisms involved in the improved methane production rate by the PPy@PANI were disclosed. The PPy@PANI can enrich the functional microorganisms to enhance both the degradation of organics and the electron transfer, which contributed to the improved methane production rate from the anaerobic wastewater treatment.

Anaerobic bacterial responses to carbonaceous materials and implications for contaminant transformation: Cellular, metabolic, and community level findings

Carbonaceous materials (CM) enhance the abundance and activity of bacteria capable of persistent organic (micro)pollutant (POP) degradation. This review synthesizes anaerobic bacterial responses to minimally modified CM in non-fuel cell bioremediation applications at three stages: attachment, metabolism, and biofilm genetic composition. Established relationships between biological behavior and CM surface properties are identified, but temporal relationships are not well understood, making it difficult to connect substratum properties and "pioneer" bacteria with mature microorganism-CM systems. Stark differences in laboratory methodology at each temporal stage results in observational, but not causative, linkages as system complexity increases. This review is the first to critically examine relationships between material and cellular properties with respect to time. The work highlights critical knowledge gaps that must be addressed to accurately predict microorganism-CM behavior and to tailor CM properties for optimized microbial activity, critical frontiers in establishing this approach as an effective bioremediation strategy.

Response of Methanogen Communities to the Elevation of Cathode Potentials in Bioelectrochemical Reactors Amended with Magnetite

Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO₂ to CH₄. Setting low cathode potentials is essential for this process. In this study, we tested if magnetite, an iron oxide mineral widespread in the environment, can facilitate the adaptation of methanogen communities to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from paddy field soil. We elevated cathode potentials stepwise from the initial -0.6 V versus the standard hydrogen electrode (SHE) to -0.5 V and then to -0.4 V over the 130 days of acclimation. Only weak current consumption and CH₄ production were observed in the bioreactors without magnetite. However, significant current consumption and CH₄ production were recorded in the magnetite bioreactors. The robustness of electroactivity of the magnetite bioreactors was not affected by the elevation of cathode potentials from -0.6 V to -0.4 V. However, the current consumption and CH₄ production were halted in the bioreactors without magnetite when the cathode potentials were elevated to -0.4 V. Methanogens related to Methanospirillum were enriched on the cathode surfaces of magnetite bioreactors at -0.4 V, while Methanosarcina relatively dominated in the bioreactors without magnetite. Methanobacterium also increased in the magnetite bioreactors but stayed off electrodes at -0.4 V. Apparently, the magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite, Methanospirillum spp. can adapt to the high cathode potentials, performing efficient electromethanogenesis. IMPORTANCE Converting CO₂ to CH₄ through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. In this study, we tested if magnetite, a conductive iron mineral, can facilitate the adaptation of methanogens to the elevation of cathode potentials. In two-chamber reactors constructed by using inoculants obtained from paddy field soil, biocathodes developed robustly in the presence of magnetite, whereas only weak activities in CH₄ production and current consumption were observed in the bioreactors without magnetite. The elevation of cathode potentials did not affect the robustness of electroactivity of the magnetite bioreactors over the 130 days of acclimation. Methanospirillum strains were identified as the key methanogens associated with the cathode surfaces during the operation at high potentials. The findings reported in this study shed new light on the adaptation of methanogen communities to the elevated cathode potentials in the presence of magnetite.

Thermodynamics shapes the biogeography of propionate-oxidizing syntrophs in paddy field soils

Soil biogeochemical processes are not only gauged by the dominant taxa in the microbiome but also depend on the critical functions of its 'rare biosphere' members. Here, we evaluated the biogeographical pattern of 'rare biosphere' propionate-oxidizing syntrophs in 113 paddy soil samples collected across China. The relative abundance, activity and growth potential of propionate-oxidizing syntrophs were analysed to provide a panoramic view of syntroph biogeographical distribution at the continental scale. The relative abundances of four syntroph genera, Syntrophobacter, Pelotomaculum, Smithella and Syntrophomonas were significantly greater at the warm low latitudes than at the cool high latitudes. Correspondingly, propionate degradation was faster in the low latitude soils compared with the high latitude soils. The low rate of propionate degradation in the high latitude soils resulted in a greater increase of the total syntroph relative abundance, probably due to their initial low relative abundances and the longer incubation time for propionate consumption. The mean annual temperature (MAT) is the most important factor shaping the biogeographical pattern of propionate-oxidizing syntrophs, with the next factor being the soil's total sulfur content (TS). We suggest that the effect of MAT is related to the thermodynamic conditions, in which the endergonic constraint of propionate oxidation is leveraged with the increase of MAT. The TS effect is likely due to the ability of some propionate syntrophs to facultatively perform sulfate respiration.

Enhancing anaerobic digestion process with addition of conductive materials

Anaerobic digestion is widely used for the treatment of wastewater for its low costs and bioenergy production, but the performances of anaerobic digestion often need improving in practical applications. The addition of conductive materials could lead to direct interspecies electron transfer (DIET) among the anaerobic microorganisms, and consequently enhance the efficiencies of anaerobic digestion. In this paper, the effects of DIET via conductive materials on chemical organic demand (COD) removal, volatile fatty acid (VFA) consumption and methane production were reviewed. The reports on the increase of conductive microorganisms due to the addition of conductive materials were discussed. Results regarding activities of microorganisms and morphology and properties of sludge were described and commented, and future research needs were also proposed which included better understanding of the roles of DIET in each step of anaerobic digestion, mechanisms of metabolism of pollutants in DIET-established systems and inhibition of excessive dosage of conductive materials.

Direct interspecies electron transfer mechanism in enhanced methanogenesis: A mini-review

The role of direct interspecies electron transfer (DIET) on enhancement of methanogenesis has been studied. This mini-review updated the current researches on the potential role of DIET on enhanced performance for anaerobic digestion of organic substrates with effective strategies implemented. Since most experimental observations correlated with the DIET mechanism are yet to be consolidated, this article categorized and discussed the current experimental observations supporting DIET mechanism for methanogenesis, mainly based on those with supplement of carbon materials, from which the prospects and challenges for further studies to confirm the role of DIET in anaerobic digestion processes were highlighted.

Variation of Metagenome From Feedstock to Digestate in Full-Scale Biogas Plants

Anaerobic digestion (AD) has been widely used to resolve the problem of organic wastes worldwide. Previous studies showed that the types of feedstock have a great influence on the AD microbiome, and a huge number of AD populations are migrated from upstream feedstocks. However, the changes of microbial compositions from feedstock to AD digestate are still less understood. We collected feedstock samples from 56 full-scale biogas plants, generated 1,716 Gb feedstock metagenomic data in total, and constructed the first comprehensive microbial gene catalog of feedstock containing 25.2 million genes. Our result indicated that the predominant phyla in feedstock are Firmicutes, Bacteroidetes, and Proteobacteria, which is similar to that in AD digestate, and the microbial diversity of feedstock samples is higher than that of AD digestate samples. In addition, the relative abundance of most genes involved in methanogenesis increase from feedstock to AD digestate. Besides, the amount of antibiotic resistance genes (ARGs) and pathogenic bacteria in AD are effectively reduced compared to feedstocks. This study provides a comprehensive microbial gene catalog of feedstock, and deepens the understanding of variation of microbial communities from feedstock to AD digestate of full-scale AD. The results also suggest the potential of AD to reduce the level of ARGs and pathogens in animal manure.

Putative Extracellular Electron Transfer in Methanogenic Archaea

It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H₂ or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.

Link between characteristics of Fe(III) oxides and critical role in enhancing anaerobic methanogenic degradation of complex organic compounds

Fe(III) oxides have been investigated to accelerate anaerobic methanogenic degradation of complex organic compounds. However, the critical role linked to the characteristics of different types of Fe(III) oxides is still unclear. Study presented here performed a side-by-side comparison of four types of Fe(III) oxides including Fe(III)-citrate, ferrihydrite, hematite and magnetite to evaluate their effectiveness in methanogenic degradation of phenol. Results showed that, amorphous Fe(III)-citrate group showed the fastest phenol degradation and Fe²⁺ release among all the groups, followed by poorly crystalline ferrihydrite. Although Fe(III)-citrate group also showed the fastest methane production rate, the efficiency of electron recovery in methane production was only 58-78%, which was evidently lower than that in both crystalline hematite (86-89%) and magnetite (93-97%) groups. Methane production rate with non-conductive ferrihydrite was nearly same as that with conductive magnetite, both of which were significantly higher than that with semi-conductive hematite. X-ray Diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis showed that sludge collected from hematite and magnetite group still respectively presented a relatively intact characteristic spectra involved in hematite and magnetite. Differently, the characteristic spectra involved in ferrihydrite was not evident in sludge collected from ferrihydrite group, whereas the characteristic spectra involved in magnetite was detected. Microbial community analysis showed that, both Fe(III)-citrate and ferrihydrite specially enriched Fe(III)-reducing bacteria capable of degrading phenol into fatty acids (Trichococcus and Caloramator) via dissimilatory Fe(III) reduction. Fe(III)-citrate also stimulated the growth of Syntrophus capable of degrading phenol/benzoate into acetate and proceeding direct interspecies electron transfer (DIET). In magnetite and hematite group, the abundance of Enterococcus species evidently increased, and they might proceed DIET with Methanothrix species in syntrophic conversion of fatty acids into methane.

Electron transfer and mechanism of energy production among syntrophic bacteria during acidogenic fermentation: A review

Volatile fatty acids (VFAs) production plays an important role in the process of anaerobic digestion (AD), which is often the critical factor determining the metabolic pathways and energy recovery efficiency. Fermenting bacteria and acetogenic bacteria are in syntrophic relations during AD. Thus, clear elucidation of the interspecies electron transfer and energetic mechanisms among syntrophic bacteria is essential for optimization of acidogenic. This review aims to discuss the electron transfer and energetic mechanism in syntrophic processes between fermenting bacteria and acetogenic bacteria during VFAs production. Homoacetogenesis also plays a role in the syntrophic system by converting H₂ and CO₂ to acetate. Potential applications of these syntrophic activities in bioelectrochemical system and value-added product recovery from AD of organic wastes are also discussed. The study of acidogenic syntrophic relations is in its early stages, and additional investigation is required to better understand the mechanism of syntrophic relations.

Impacts of conductive materials on microbial community during syntrophic propionate oxidization for biomethane recovery

Propionate is one of the most important intermediates in anaerobic digestion, and its degradation requires a syntrophic partnership between propionate-oxidizing bacteria and hydrogenotrophic methanogens. Anaerobic digestion efficiency can be improved by direct interspecies electron transfer (DIET) through conductive materials. This study aimed to investigate the effects of DIET on syntrophic propionate oxidization under room temperature (20°C) and reveal the syntrophic partners. Firstly, conventional anaerobic consortium and conductive material-enriched consortium were tested for DIET under high H₂ partial pressure. The latter supplemented with granular activated carbon (GAC) can mitigate H₂ inhibition through DIET. Secondly, a DIET consortium was enriched for testing GAC and magnetite, both showed DIET facilitation. Microbial communities in GAC- and magnetite-supplemented reactors were similar. Syntrophic propionate-oxidizing bacteria, for example, Smithella (3.9%-9.9%) and a genus from the family Syntrophaceae (1.9%-3.6%) and methanogens Methanobacterium (30.3%-75.2%), Methanolinea (8.5%-25.2%), Methanosaeta (11.4%-36.7%), and Candidatus Methanofastidiosum (3.6%-6.6%), were predominant. Functional genes for cell mobility and membrane transport (3.3% and 9.5% in control reactor) increased with GAC (3.7% and 11.1%, respectively) and magnetite (3.7% and 10.9%, respectively) addition. Syntrophic propionate-oxidizing bacteria and methanogenesis partners were revealed by co-occurrence network, for example, Methanobacterium with Smithella, Syntrophobacter, Dechloromonas, and Trichococcus, signifying the importance of the syntrophic partnership in DIET environment. PRACTITIONER POINTS: DIET improved syntrophic propionate oxidization under room temperature condition (20°C). Microbial communities were similar for GAC- and magnetite-supplemented reactors, different with control reactor. Syntrophic propionate-oxidizing bacteria and methanogenesis partners were revealed by co-occurrence network. Methanobacterium and Smithella, Syntrophobacter, Dechloromonas, and Trichococcus were correlated.

Sparking Anaerobic Digestion: Promoting Direct Interspecies Electron Transfer to Enhance Methane Production

Anaerobic digestion was one of the first bioenergy strategies developed, yet the interactions of the microbial community that is responsible for the production of methane are still poorly understood. For example, it has only recently been recognized that the bacteria that oxidize organic waste components can forge electrical connections with methane-producing microbes through biologically produced, protein-based, conductive circuits. This direct interspecies electron transfer (DIET) is faster than interspecies electron exchange via diffusive electron carriers, such as H2. DIET is also more resilient to perturbations such as increases in organic load inputs or toxic compounds. However, with current digester practices DIET rarely predominates. Improvements in anaerobic digestion associated with the addition of electrically conductive materials have been attributed to increased DIET, but experimental verification has been lacking. This deficiency may soon be overcome with improved understanding of the diversity of microbes capable of DIET, which is leading to molecular tools for determining the extent of DIET. Here we review the microbiology of DIET, suggest molecular strategies for monitoring DIET in anaerobic digesters, and propose approaches for re-engineering digester design and practices to encourage DIET.

Inhibition mitigation of methanogenesis processes by conductive materials: A critical review

Methanogenesis can be promoted by the addition of conductive materials. Although stimulating effects of conductive materials on methane (CH₄) production has been extensively reported, the crucial roles on recovering methanogenic activities under inhibitory conditions have not been systematically discussed. This critical review presents the current findings on the effects of conductive materials in methanogenic systems under volatile fatty acids (VFAs), ammonia, sulfate, and nano-cytotoxicity stressed conditions. Conductive materials induce fast VFAs degradation, avoiding VFAs accumulation during anaerobic digestion. Under high ammonia concentrations, conductive materials may ensure sufficient energy conservation for methanogens to maintain intracellular pH and proton balance. When encountering the competition of sulfate-reducing bacteria, conductive materials can benefit electron competitive capability of methanogens, recovering CH₄ production activity. Conductive nanomaterials stimulate the excretion of extracellular polymeric substances, which can prevent cells from nano-cytotoxicity. Future perspectives about unraveling mitigation mechanisms induced by conductive materials in methanogenesis processes are further discussed.

Coupled effects of ferroferric oxide supplement and ethanol co-metabolism on the methanogenic oxidation of propionate

Direct interspecies electron transfer (DIET) is a new electron-transfer strategy for enhanced propionate degradation. Ethanol can enrich the DIET species of Geobacter and conductive ferroferric oxide (Fe₃O₄) can promote DIET. Therefore, coupled effects of ethanol and Fe₃O₄ on propionate degradation were investigated. The maximum CH₄ production rate was increased by 81.4% by adding Fe₃O₄ when simultaneously fed with ethanol and propionate, while the improvement could not be observed without ethanol. The sludge conductivity and the electron transfer system activity by adding Fe₃O₄ were increased by 2.66 and 2.73 times, respectively. Besides, the relative abundance of functional microbes such as Geobacter, Syntrophobacter, Smithella, and Methanosaeta, and their functional genes were increased by the supplement of Fe₃O₄. The improvement of propionate degradation by adding Fe₃O₄ was largely attributed to the co-existence of ethanol degradation. The DIET between Geobacter and Methanosaeta might provide more energies or rapidly consume the oxidation products to promote the propionate degradation.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

Anaerobic co-digestion of Pennisetum hybrid and pig manure: A comparative study of performance and microbial community at different mixture ratio and organic loading rate

To investigate how the changes in performance and the microbial community of the co-digestion system of Pennisetum hybrid and pig manure, two co-digestion systems in a semi-continuous mode were established at different grass:manure mixture ratios (50:50 and 75:25), and at variable organic loading rates (OLRs). The two reactors were in a steady-state at the OLRs of 2.0-5.0 g VS/(L·d), with the specific and volumetric biogas yields of 383.86 ± 65.13 to 574.28 ± 72.04 mL/g VS and 0.87 ± 0.07 to 2.36 ± 0.13 m³/(m³·d), respectively. The co-digestion system with a mixture ratio of 75:25 failed at an OLR of 5.5 g VS/(L⋅d). This failure could be attributed to the accumulation of volatile fatty acids (VFAs) owing to the imbalance between acid-production and -oxidation bacteria. By contrast, the co-digestion system with mixture ratio of 50:50 failed at an OLR of 7.0 g VS/(L⋅d), which was likely due to mechanical issues or improper reactor configuration. The genus Proteiniphilum contributed to the increase in total ammonia nitrogen. These findings provide useful guidance for optimizing co-digestion system, enhancing reactor performance and improving the wastes treatment.

Potential interactions between syntrophic bacteria and methanogens via type IV pili and quorum-sensing systems

Interspecies electron transfer plays an important role in syntrophic methanogenesis. Direct interspecies electron transfer (DIET) between syntrophic oxidizers and methanogens via conductive pili has been only confirmed in some specific co-cultures. This study examined potential syntrophic cooperation via type IV pili and quorum sensing between widespread syntrophic bacteria and methanogens through a metagenomic analysis of 12 anaerobic sludge samples. We found that Methanosaeta and Methanosarcina, which are reported to have DIET ability, were dominant in most methanogenic samples. Putative conductive pili genes were found in some typical syntrophic bacteria, which has rarely been reported previously. The existence of diverse quorum-sensing genes suggested that various quorum-sensing systems might participate in the communication of anaerobic microorganisms. Specifically, the diffusible signal factor and 3'-5' cyclic diguanosine monophosphate related genes were mainly assigned to syntrophic bacteria. These results suggest that the combined regulation of these signals might be responsible for the biosynthesis of type IV pili and affect syntrophic interaction during methanogenesis. These novel results provide fresh evidence to support the widespread existence of DIET in anaerobic methanogenic systems; therefore, regulating the quorum-sensing system may promote syntrophic interaction.

TiO2 nanoparticles accelerate methanogenesis in mangrove wetlands sediment

In this study, the response of methane (CH₄) production to the addition of titanium dioxide nanoparticles (TiO₂ NPs) with three types of short-chain fatty acids (sodium acetate, sodium propionate and sodium butyrate) as carbon sources in mangrove sediment was investigated. The results showed that the maximum CH₄ formation rate increased by 45.2%, 32.7% and 48.6% and the maximum cumulative CH₄ production increased by 25.2%, 7.7% and 6.3% with the addition of TiO₂ NPs in the sodium acetate, sodium propionate and sodium butyrate systems, respectively. The microbial community analysis revealed that the electrogenic bacteria Proteiniclasticum and Pseudomonas, butyrate oxidizing bacteria Syntrophomonas and methanogens Methanobacterium and Methanosarcina were significantly enriched in the presence of TiO₂ NPs, indicating that TiO₂ NPs can enhance CH₄ production by stimulating the growth of different species of methanogens and butyrate oxidizing bacteria. The enlarged distance between microbes, the enhanced conductivity of the sediment and the typical microorganisms for direct interspecies electron transfer (DIET) with the addition of TiO₂ NPs suggest that the promoted DIET between distinct microorganisms could be another possible explanation for the improvement in CH₄ production. It can be speculated that a weaker effect on methanogenesis increases under the natural concentration of TiO₂ NPs compared with the experimental conditions; however, the amounts of TiO₂ NPs are increasing enriched in wetland environments. Therefore, the findings of this study increase current knowledge about the effect of nanomaterials on global CH₄ emissions and suggest that the discharge of wastewater containing TiO₂ NPs from the synthesis and incorporation of TiO₂ NPs in customer products needs to be monitored.

Redox cycling of Fe(II) and Fe(III) in magnetite accelerates aceticlastic methanogenesis by Methanosarcina mazei

It has been recently shown that magnetite nanoparticles (nanoFe₃ O₄ ) can facilitate methanogenic syntrophy but the effect of magnetite on methanogenesis alone remains elusive. Here we show that aceticlastic methanogenesis by Methanosarcina mazei is accelerated by magnetite and is correlated with the redox cycling of structural Fe(II) and Fe(III) in the mineral. An enrichment and its closest pure culture relative, Ms. mazei zm-15, both obtained from a natural wetland of the Tibetan plateau were tested in this experiment. The Fe(II) to Fe(III) ratios in magnetite, as measured by multiple approaches, show an initial increase in both the methanogenic cultures and the blank preparations containing no microbes. The Fe(II)/Fe(III) ratio then displays a distinct decline followed by an increase towards the end of incubation only in the enrichment and pure culture cultivations. This redox cycling of magnetite is in accordance with the stimulation of aceticlastic methanogenesis. Microscopic observation reveals the precipitation of nanoFe₃ O₄ on methanogen cell surface. The genomic analysis predicts that in addition to electron transfer components essential for aceticlastic methanogenesis, Ms. mazei zm-15 contains an outer-surface multiheme c-type cytochrome (MHC) and a few function-unknown surface proteins that harbour monoheme motif. We hypothesize that the redox cycling of nanoFe₃ O₄ delivers a positive influence via the MHC to the membrane electron transfer chain and hence promote the aceticlastic methanogenesis.

Inhibition mitigation and ecological mechanism of mesophilic methanogenesis triggered by supplement of ferroferric oxide in sulfate-containing systems

Methanogenesis can be inhibited by volatile fatty acids (VFAs) accumulation and sulfate during anaerobic wastewater treatment. In this study, effects of ferroferric oxide (Fe₃O₄) on VFAs degradation and methanogenesis in sulfate-containing environment were investigated. Methanogenesis in reactors with or without sulfate were both favored through the addition of Fe₃O₄. In reactors without sulfate, the dosage of Fe₃O₄ increased the maximum methane production rate by 21.7% accompanied with faster acetate and propionate degradation. Metagenomic analysis showed that Fe₃O₄ mainly promoted electron exchange between Mesotoga, Syntrophobacter, Smithella and Methanosaeta without altering the syntrophic patterns. However, in the sulfate-containing reactor with low methanogenic efficiency, syntrophic ethanol users and Methanosaeta were replaced by sulfate-reducing bacteria and Methanosarcina, respectively. The supplement of Fe₃O₄ re-enriched the syntrophic partners inhibited by sulfate and rebuilt a new syntrophic interaction with high efficiency similar to that in sulfate-free environment, leading to better methanogenic performance in sulfate-containing environment.