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Reduction potentials of the electron producing and electron consuming physiologies constrain the window of opportunity in direct interspecies electron transfer (DIET).Reduction potentials of the electron producing and electron consuming physiologies constrain the window of opportunity in direct interspecies electron transfer (DIET).

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name ‘ Candidatus Thermosyntrophopropionicum ammoniitolerans’ was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H 2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L −1 day −1 at hydrogen partial pressure 4–30 Pa and available energy was around −20 mol −1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism. Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.

Background Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13 C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition. Results While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13 C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility. Conclusions This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. 3uWhKDWFjqsFeP9DMWUatJ Video abstract

Anode potential can affect the degradation pathway of complex substrates in bioelectrochemical systems (BESs), thereby influencing current production and coulombic efficiency. However, the intricacies behind this interplay are poorly understood. This study used glucose as a model substrate to comprehensively investigate the effect of different anode potentials (− 150 mV, 0 mV and + 200 mV) on the relationship between current production, the electrogenic pathway and the abundance of the electrogenic microorganisms involved in batch mode fed BESs. Current production in glucose-acclimatized reactors was a function of the abundance of Geobacteraceae and of the availability of acetate and formate produced by glucose degradation. Current production was increased by high anode potentials during acclimation (0 mV and + 200 mV), likely due to more Geobacteraceae developing. However, this effect was much weaker than a stimulus from an artificial high acetate supply: acetate was the rate-limiting intermediate in these systems. The supply of acetate could not be influenced by anode potential; altering the flow regime, batch time and management of the upstream fermentation processes may be a greater engineering tool in BES. However, these findings suggest that if high current production is the focus, it will be extremely difficult to achieve success with complex waste streams such as domestic wastewater.

Two strategies exist for seeding low-temperature anaerobic reactors: the use of specialist psychrophilic biomass or mesophilic bioreactor sludge acclimated to low temperature. We sought to determine the low-temperature limitation of anaerobic sludge from a bioreactor acclimated to UK temperatures (<15 °C). Anaerobic incubation tests using low-strength real domestic wastewater (DWW) and various alternative soluble COD sources were conducted at 4, 8 and 15 °C; methanogenesis and acidogenesis were monitored separately. Production of methane and acetate was observed; decreasing temperature resulted in decreased yields and increased ‘start-up’ times. At 4 °C methanogenesis not hydrolysis/acidogenesis was rate-limiting. The final methane yields at 4 °C were less than 35% of the theoretical potential whilst at 8 and 15 °C more than 75 and 100% of the theoretical yield was achieved respectively. We propose that the lower temperature limit for DWW treatment with anaerobic bioreactor sludge lies between 8 and 4 °C and that 8 °C is the threshold for reliable operation.

Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)–resource acquisition (A)–stress tolerance (S) life‐history strategies (Y‐A‐S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial‐/plant‐derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid‐composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade‐offs and microbial−/plant‐derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y‐strategy and the accumulation of microbial‐derived DOM components, while a greater dominance of virulent phages favoured the A‐strategy and plant‐derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting. This study demonstrates that previously overlooked phages drive microbial life‐history trade‐offs, shape organic matter transformation, and provide implications for soil carbon stability in agricultural ecosystems.

Deep subsurface formations (for example, high-temperature oil reservoirs) are candidate sites for carbon capture and storage technology. However, very little is known about how the subsurface microbial community would respond to an increase in CO 2 pressure resulting from carbon capture and storage. Here we construct microcosms mimicking reservoir conditions (55 °C, 5 MPa) using high-temperature oil reservoir samples. Methanogenesis occurs under both high and low CO 2 conditions in the microcosms. However, the increase in CO 2 pressure accelerates the rate of methanogenesis to more than twice than that under low CO 2 conditions. Isotope tracer and molecular analyses show that high CO 2 conditions invoke acetoclastic methanogenesis in place of syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis that typically occurs in this environment (low CO 2 conditions). Our results present a possibility of carbon capture and storage for enhanced microbial energy production in deep subsurface environments that can mitigate global warming and energy depletion. Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO 2 partial pressure via carbon capture and storage more than doubles the rate of methanogenesis.

We revealed abiotic components (extracellular polymeric substances, EPSs) in the periphytic biofilms. Further, the effect of the microbial community on the EPS, and the geodistribution patterns and ecological functions of the EPS were studied.

Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleum reservoirs and anoxic environments contaminated with petroleum. There are several possible routes whereby hydrocarbons may be converted to methane: (i) complete oxidation of alkanes to H 2 and CO 2 , linked to methanogenesis from CO 2 reduction; (ii) oxidation of alkanes to acetate and H 2 , linked to acetoclastic methanogenesis and CO 2 reduction; (iii) oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction; (iv) oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis and (v) oxidation of alkanes to acetate alone, linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction. We have developed the concept of a ‘window of opportunity’ to evaluate the range of conditions under which each route is thermodynamically feasible. On this basis the largest window of opportunity is presented by the oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis. This contradicts field-based evidence that indicates that in petroleum rich environments acetoclastic methanogenesis is inhibited and that methanogenic CO 2 reduction is the predominant methanogenic process. Our analysis demonstrates that under those biological constraints oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction offers a greater window of opportunity than complete oxidation of alkanes to H 2 and CO 2 linked to methanogenic CO 2 reduction, and hence is the process most likely to occur.