Extracellular quinones affecting methane production and methanogenic community in paddy soil

Role of interspecies electron transfer stimulation in enhancing anaerobic digestion under ammonia stress: Mechanisms, advances, and perspectives

Ammonia stress is a commonly encountered issue in anaerobic digestion (AD) process when treating proteinaceous substrates. The enhanced relationship between syntrophic bacteria and methanogens triggered by interspecies electron transfer (IET) stimulation is one of the potential mechanisms for an improved methane yield from the AD plant under ammonia-stressed condition. There is, however, lack of synthesized information on the mechanistic understanding of IET facilitation in the ammonia-stressed AD processes. This review critically discusses recovery of AD system from ammonia-stressed condition, focusing on H₂ transfer, redox compound-mediated IET, and conductive material-induced direct IET. The effects and the associated mechanisms of IET stimulation on mitigating ammonia stress and promoting methanogenesis were elucidated. Finally, prospects and challenges of IET stimulation were critically discussed. This review highlights, for the first time, the critical role of IET stimulation in enhancing AD process under ammonia-stressed condition.

Control the greenhouse gas emission via mediating the dissimilatory iron reduction: Fulvic acid inhibit secondary mineralization of ferrihydrite

Reducing methane emission is of great importance to control the global greenhouse effect. Dissimilatory iron reduction (DIR) coupling of organic matter decomposition may suppress methane production via reducing primary electron donors available for methanogenesis. However, during DIR, the amorphous iron oxides (e.g., ferrihydrite) are easy to transform into more stable crystalline iron minerals, which slowdowns the rate of DIR. Humic substance (HS) with redox activity has been extensively reported to facilitate DIR via "electron shuttles" mechanism, yet little known about the effect of HS on mediating the mineralization of iron oxides and the subsequent influences on DIR and methanogenesis. To clarify this, ferrihydrite and fulvic acid (FA) (as the model substance of HS) were supplied to anaerobic methanogenesis systems. Results showed that FA could significantly decrease the formation of crystalline iron oxides, enhance DIR rate by 13.72% and suppress methanogenesis by 25.13% compared to ferrihydrite supplemented only. By X-ray absorption spectra analysis, it was found that FA could complex with ferrihydrite via forming a Fe-C/O structure on the second shell of Fe atom. Quantum chemical calculation further confirmed that FA reduced the adsorption energy between Fe(II) and ferrihydrite. Our study suggested that rational use of HS to mediate mineralization pathway of iron oxides could efficiently improve the availability of iron oxides to drive DIR and control the conversion of organics into CH₄ in natural or engineered systems.

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.

Syntrophic butyrate-oxidizing methanogenesis promoted by anthraquinone-2-sulfonate and cysteine: Distinct tendencies towards the enrichment of methanogens and syntrophic fatty-acid oxidizing bacteria

Interspecies electron transfer (IET) between syntrophic fatty-acid oxidizing bacteria (SFOBs) and methanogens decided the performance of anaerobic digestion. Electron shuttles, as potential IET accelerators, were controversial concerning their influences on methanogenesis. In this study, concentration-dependent effects of anthraquinone-2-sulfonate (AQS) and cysteine on glucose digestion were firstly demonstrated: low dosage of AQS and cysteine (50 and 100 µM, respectively) had highest methane yield (133.5% and 148.6%, respectively). Using butyrate as substrate, distinct tendencies towards the enrichment of methanogenic community were further revealed. Cysteine just acted as a reductant which lowered ORP quickly and enriched most methanogens. It benefited methanogenesis right until methanogenic substrates accumulated. AQS, however, showed characteristic features of electron shuttles: it was firstly oxidized by SFOBs and then reduced by hydrogenotrophic methanogens, which accelerated methanogenic butyrate degradation. This study showed wide spectrum of SFOBs and methanogens benefited from the addition of electron shuttles, which laid foundation for future application.

The process of methanogenesis in paddy fields under different elevated CO2 concentrations

Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH₄ production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO₂ concentrations (e[CO₂]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH₄ flux in paddy fields under various (e[CO₂]). CH₄ flux and CH₄ production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO₂ concentration), C₁ (C + 160 ppm CO₂), and C₂ (C + 200 ppm CO₂) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C₂ treatment significantly increased CH₄ flux and MPP at the tillering stage. E[CO₂] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO₂] did not significantly change the overall community structure and diversity of methanogens, C₂ treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH₄ flux under e[CO₂]. Overall, our results demonstrated that CH₄ flux in paddy fields under e[CO₂] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of Fe^III reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory Fe^III-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

The role of humic substances in mitigating greenhouse gases emissions: Current knowledge and research gaps

Humic substances (HS) constitute a highly transformed fraction of natural organic matter (NOM) with a heterogeneous structure, which is rich in electron-transferring functional moieties. Because of this feature, HS display a versatile reactivity with a diversity of environmentally relevant organic and inorganic compounds either by abiotic or microbial processes. Consequently, extensive research has been conducted related to the potential of HS to drive relevant processes in bio-engineered systems, as well as in the biogeochemical cycling of key elements in natural environments. Nevertheless, the increase in the number of reports examining the relationship between HS and the microorganisms related to the production and consumption of greenhouse gases (GHG), the main drivers of global warming, has just emerged in the last years. In this paper, we discuss the importance of HS, and their analogous redox-active organic molecules (RAOM), on controlling the emission of three of the most relevant GHG due to their tight relationship with microbial activity, their abundance on the Earth's atmosphere, and their important global warming potentials: carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). The current knowledge gaps concerning the microbial component, on-site occurrence, and environmental constraints affecting these HS-mediated processes are provided. Furthermore, strategies involving the metabolic traits that GHG-consuming/HS-reducing and -oxidizing microbes display for the development of environmental engineered processes are also discussed.

Thermodynamic analysis of direct interspecies electron transfer in syntrophic methanogenesis based on the optimized energy distribution

The aim of this study was to investigate the syntrophic methanogenesis from the perspective of energy transfer and competition. Effects of redox materials and redox potential on direct interspecies electron transfer (DIET) were examined through thermodynamic analysis based on the energy distribution principle. Types of redox materials could affect the efficiency of DIET via changing the total energy supply of the syntrophic methanogenesis. Decreasing system redox potential could facilitate DIET through increasing the total available energy. The competition between hydrogenotrophic methanogens and DIET methanogens might be the reason for the low proportion of the DIET pathway in the syntrophic methanogenesis. A facilitation mechanism of DIET was proposed based on the energy distribution. Providing sufficient electrons, inhibiting hydrogenotrophic methanogens and adding more competitive redox couples to avoid hydrogen generation might be beneficial for the facilitation of DIET.

Biochar Modulates Methanogenesis through Electron Syntrophy of Microorganisms with Ethanol as a Substrate

Biochar has the potential to influence methanogenesis which is a key component of global carbon cycling. However, the mechanisms governing biochar's influence on methanogenesis is not well understood, especially its effects on interspecies relationships between methanogens and anaerobic bacteria (e.g., Geobacteraceae). To understand how different types of biochar influence methanogenesis, biochars derived from rice straw (RB), wood chips (WB), and manure (MB) were added to the methanogenic enrichment culture system of a paddy soil. Compared to the nonbiochar control, RB and MB additions accelerated methanogenesis remarkably, showing 10.7 and 12.3-folds higher methane production rate, respectively; while WB had little effect on methanogenesis. Using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electrochemical methods, RB and MB also had higher redox-active properties or charging and discharging capacities than WB, and the functional groups, mainly quinones, on the biochar surface played an important role in facilitating methanogenesis. Quantitative polymerase chain reaction results demonstrated that electronic syntrophy did exist between methanogens and Geobacteraceae. RB and MB stimulate methanogenesis by facilitating direct interspecies electron transfer between methanogens and Geobacteraceae. Our findings contribute to a better understanding of the effects of biochars from different feedstocks on methanogenesis and provide new evidence to the mechanisms of stimulating methanogenesis via biochar.

Cysteine-Accelerated Methanogenic Propionate Degradation in Paddy Soil Enrichment

Propionate degradation is a critical step during the conversion of complex organic matter under methanogenic conditions, and it requires a syntrophic cooperation between propionate-oxidizing bacteria and methanogenic archaea. Increasing evidences suggest that interspecies electron transfer for syntrophic metabolism is not limited to the reducing equivalents of hydrogen and formate. This study tested the ability of an electron shuttle to mediate interspecies electron transfer in syntrophic methanogenesis. We found that cysteine supplementation (100, 400, and 800 μM) accelerated CH₄ production from propionate in paddy soil enrichments. Of the concentrations tested, 100 μM cysteine was the most effective at enhancing propionate degradation to CH₄, and the rates of CH₄ production and propionate degradation were increased by 109 and 79%, respectively, compared with the cysteine-free control incubations. We eliminated the possibility that the stimulatory effect of cysteine on methanogenesis was attributable to the function of cysteine as a methanogenic substrate in the presence of propionate. The potential catalytic effect involved cysteine serving as an electron carrier to mediate interspecies electron transfer in syntrophic propionate oxidization. The redox potential of cystine/cysteine, which is dependent on the concentration, might be more suitable to facilitate interspecies electron transfer between syntrophic partners at a concentration of 100 μM. Pelotomaculum, obligately syntrophic, propionate-oxidizing bacteria, and hydrogenotrophic methanogens of the family Methanobacteriaceae are predominant in cysteine-mediated methanogenic propionate degradation. The stimulatory effect of cysteine on syntrophic methanogenesis offers remarkable potential for improving the performance of anaerobic digestion and conceptually broaden strategies for interspecies electron transfer in syntrophic metabolism.

Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats

This study was performed to investigate the initial colonization of metabolically active methanogens and subsequent changes in four fractions: the rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) from 1 to 60 d after birth, and manipulate methanogen community by early weaning on 40 d and supplementing rhubarb from 40 to 60 d in black goats. The RNA-based real-time quantitative PCR and 16S rRNA amplicon sequencing were employed to indicate the metabolically active methanogens. Results showed that active methanogens colonized in RL and RE on 1 d after birth. RP and RE contained the highest and lowest density of methanogens, respectively. Methanobrevibacter, Candidatus Methanomethylophilus, and Methanosphaera were the top three genera. The methanogen communities before weaning differed from those post weaning and the structure of the methanogen community in RE was distinct from those in the other three fractions. The discrepancies in the distribution of methanogens across four fractions, and various fluctuations in abundances among four fractions according to age were observed. The addition of rhubarb significantly (P < 0.05) reduced the abundances of Methanimicrococcus spp. in four fractions on 50 d, but did not change the methanogen community composition on 60 d.

Dual roles of AQDS as electron shuttles for microbes and dissolved organic matter involved in arsenic and iron mobilization in the arsenic-rich sediment

Microbially-mediated arsenic (As) metabolism and iron (Fe) bioreduction from sediments play crucial roles in global As/Fe cycle, and their mobilization is associated with the various effects within the alliance of "mediator-bacteria-DOM (Dissolved Organic Matter)". The gradient levels (0.05, 0.10 and 1.00mM) of sodium anthraquinone-2,6-disulphonate (AQDS) as a mediator were investigated for their impact on reductive dissolution of As(V) and Fe(III) from arsenic-rich sediment. For the overall performance of AQDS-mediated reductive dissolution on As(V) and Fe(III), a more positive effect resulting from 0.05mM AQDS was observed compared to 0.10mM, whereas an inhibitory effect was observed with 1.00mM. Compared to the biotic supplementation with acetate as electron donors, approximately 13- and 6-fold increased levels of As(III) were released with 0.05 and 0.10mM, respectively, compared to 1.00mM AQDS (107.51μg/L), and approximately 4- and 3-fold increased Fe(II) levels (40.72mg/L) were observed during the same conditions. Multiple-dynamic effects of "bacteria-AQDS-DOM", which result from AQDS, shifted the microbial community and synchronously derived terrestrial DOM, which potentially changes the DOM substrate and complex formation of As(III)-Fe(II)-humic DOM. High-throughput sequencing results indicated an increase in the abundance of metal-reducing bacteria (e.g., Bacillus (>16%), Lactococcus (>13%), Pseudomonas (>4%) and Geobacter (>3%)) when supplemented with 0.05 and 0.10mM of AQDS. However, a boost increasing the abundance of metal oxidizing bacteria was observed with Alicyclobacillus (>16%), Burkholderia (>7%), and Bradyrhizobium (>5%) upon supplementation with 1.00mM AQDS. These novel insights have profound environmental implications and significance in terms of engineering, not only for understanding the cycle of As/Fe in sediment biochemical processes but for considering future alternative bioremediation treatments.

A novel AQDS–rGO composite to enhance the bioreduction of As(v)/Fe(iii) from the flooded arsenic-rich soil

Anthraquinone-2,6-disulphonate (AQDS) and reduced Graphene Oxide (rGO) were selected to prepare the AQDS–rGO composites for investigating the bioreduction performance of As(v)/Fe(iii) from the flooded arsenic-rich soil.

Nano-graphene induced positive effects on methanogenesis in anaerobic digestion

The effects of nano-graphene on methanogenesis in anaerobic digestion was investigated. Short-term results showed that graphene (30 and 120mg/L) had significantly positive effects on methane production rate, which increased by 17.0% and 51.4%. Further investigation indicated that acetate-consuming methanogenesis was enhanced. The failure of quinones to replicate graphene stimulation effects on methanogenesis suggested that graphene did not function as electron shuttles. After 55 day's operation at room temperature (from 20 to 10°C, the methane production rate with 30mg/L graphene was 14.3% higher than that of the control, while 120mg/L graphene showed a slight inhibition on methane yield. Illumina sequencing data showed that the archaeal community structure remained fairly constant as the incubated sludge with graphene at low temperature, in which Methanoregula, Methanosaeta and Methanospirillum were the dominant species. Besides, Geobacter enrichment was observed with graphene, suggesting that the direct interspecies electron transfer might be promoted.

Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens

The reductive dechlorination of pentachlorophenol (PCP) by Geobacter sulfurreducens in the presence of different biochars was investigated to understand how biochars affect the bioreduction of environmental contaminants. The results indicated that biochars significantly accelerate electron transfer from cells to PCP, thus enhancing reductive dechlorination. The promotion effects of biochar (as high as 24-fold) in this process depend on its electron exchange capacity (EEC) and electrical conductivity (EC). A kinetic model revealed that the surface redox-active moieties (RAMs) and EC of biochar (900 °C) contributed to 56% and 41% of the biodegradation rate, respectively. This work demonstrates that biochars are efficient electron mediators for the dechlorination of PCP and that both the EC and RAMs of biochars play important roles in the electron transfer process.

Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation

Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.

Link between capacity for current production and syntrophic growth in Geobacter species

Electrodes are unnatural electron acceptors, and it is yet unknown how some Geobacter species evolved to use electrodes as terminal electron acceptors. Analysis of different Geobacter species revealed that they varied in their capacity for current production. Geobacter metallireducens and G. hydrogenophilus generated high current densities (ca. 0.2 mA/cm(2)), comparable to G. sulfurreducens. G. bremensis, G. chapellei, G. humireducens, and G. uraniireducens, produced much lower currents (ca. 0.05 mA/cm(2)) and G. bemidjiensis was previously found to not produce current. There was no correspondence between the effectiveness of current generation and Fe(III) oxide reduction rates. Some high-current-density strains (G. metallireducens and G. hydrogenophilus) reduced Fe(III)-oxides as fast as some low-current-density strains (G. bremensis, G. humireducens, and G. uraniireducens) whereas other low-current-density strains (G. bemidjiensis and G. chapellei) reduced Fe(III) oxide as slowly as G. sulfurreducens, a high-current-density strain. However, there was a correspondence between the ability to produce higher currents and the ability to grow syntrophically. G. hydrogenophilus was found to grow in co-culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET), but not with Methanospirillum hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC) stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron exchange via DIET. These findings, coupled with the previous finding that G. metallireducens and G. sulfurreducens are also capable of DIET, suggest that evolution to optimize DIET has fortuitously conferred the capability for high-density current production to some Geobacter species.

Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours

The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0-20 mins after birth), day 1 (24 ± 1 h after birth), day 2 (48 ± 1 h after birth), and day 3 (72 ± 1 h after birth). Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose.

Methanogenesis affected by the co-occurrence of iron(III) oxides and humic substances

Iron oxides and humic substances (humics) have substantial effects on biochemical processes, such as methanogenesis, due to their redox reactivity and ubiquitous presence. This study aimed to investigate how methanogenesis is affected by the common occurrence of these compounds, which has not been considered to date. The experiment was conducted with anoxic paddy soil microcosms receiving a humics surrogate compound (anthraquinone-2,6-disulfonate, AQDS) and three iron(III) oxides (ferrihydrite, hematite, and magnetite) differing in crystallinity and conductivity. Ferrihydrite suppressed methanogenesis, whereas AQDS, hematite, and magnetite facilitated methanogenesis. CH4 production in co-occurring ferrihydrite + AQDS, hematite + AQDS, and magnetite + AQDS cultures was 4.1, 1.3, and 0.9 times greater than the corresponding cultures without AQDS, respectively. Syntrophic cooperation between Geobacter and Methanosarcina occurred in the methanogenesis-facilitated cultures. Experimental results suggested that the conductive characteristics of iron(III) oxides was an important factor determining the methanogenic response to the co-occurrence of iron(III) oxides and humics in anaerobic paddy soil. This work indicated that the type of iron(III) oxides may significantly affect carbon cycling under anoxic conditions in natural wetlands.