Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems

Magnetic porous microspheres altering interfacial thermodynamics of sewage sludge to drive metabolic cooperation for efficient methanogenesis

Controllable and recyclable magnetic porous microspheres (MPMs) have been proposed as a means for enhancing the anaerobic digestion (AD) of sludge, as they do not require continuous replenishment and can serve as carriers for anaerobes. However, the effects of MPMs on the interfacial thermodynamics of sludge and the biological responses triggered by abiotic effects in AD systems remain to be clarified. Herein, the underlying mechanisms by which MPMs alter the solid-liquid interface of sludge to drive methanogenesis were investigated. A significant increase in the contents of 13C and 2H (D) in methane molecules was observed in the presence of MPMs, suggesting that MPMs might enhance the CO2-reduction methanogenesis and participation of water in methane generation. Experimental results demonstrated that the addition of MPMs did not promote the anaerobic bioconversion of soluble organics for methanogenesis, suggesting that the enhanced methanogenesis and water participation were not achieved through promotion of the bioconversion of original liquid-state organics in sludge. Analyses of the capillary force, surface adhesion force, and interfacial proton-coupled electron transfer (PCET) of MPMs revealed that MPMs can enhance mass transfer, effective contact, and electron-proton transfer with sludge. These outcomes were confirmed by the statistical analyses of variations in the interfacial thermodynamics and PCET of sludge with and without MPMs during AD. It was thus proposed that the MPMs enhanced the PCET of sludge and PCET-driven release of protons from water by promoting the interfacial Lewis acid-base interactions of sludge, thereby resulting in the enrichment of free and attached methanogenic consortia and the high energy-conserving metabolic cooperation. This proposition was further confirmed by identifying the predominant syntrophic partners, suggesting that PCET-based efficient methanogenesis was attributable to the enrichment of genomes harbouring CO2-reducing pathway and genes encoding water-mediated proton transfer. These findings offer new insights into how substrate properties can be altered by exogenous materials to enable highly efficient methanogenesis.

Enhancement of anaerobic digestion from food waste via inert substances based on metagenomic analysis: Oxidative phosphorylation and metabolism

The application of anaerobic digestion (AD) in the treatment of food waste (FW) has become widespread. However, the presence of inert substances, such as bones, ceramics, and shells, within FW introduces a degree of uncertainty into the AD process. To clarify this intricate issue, this study conducted an in-depth investigation into the influence of inert substances on AD. The results revealed that when inert substances were present at a concentration of 0.08 g/g VSS, methane productivity in the AD process was significantly augmented by 86%. Subsequent investigations suggested that this positive effect was primarily evident in various biochemical processes, including solubilization, hydrolysis acidification, methanogenesis, and the accumulation of extracellular polymeric substances. Metagenomic analysis showed that inert substances enhance the relative abundance of hydrolytic bacteria and have a pronounced impact on the relative abundance of hydrogenotrophic methanogens (Methanosarcina) and acetotrophic methanogens (Methanobacterium). Additionally, inert substances significantly increased the relative abundance of functional genes in oxidative phosphorylation, a pivotal pathway for ATP synthesis. Furthermore, inert substances had a substantial effect on the functional genes related to the metabolic pathways associated with methanogenesis (both hydrogenotrophic and acetotrophic). This comprehensive study shed light on the substantial impact of inert substances on the AD of food waste, contributing to an enhanced understanding of the underlying mechanisms of anaerobic fermentation.

Stochastic processes drive the diversity and composition of methanogenic community in a natural mangrove ecosystem

Methanogens are considered to be crucial components of mangrove ecosystems with ecological significance. However, understanding the assembly processes of methanogenic communities in mangrove ecosystems is relatively insufficient. In the current study, a natural mangrove in a protection zone was employed to investigate the diversity and assembly processes of methanogenic community by using amplicon high-throughput sequencing, a null model as well as a neutral community model. The results showed that methanogenic community in mangrove sediments were highly diverse, with the predominance of methylotrophic Methanolobus, and hydrogenotrophic Methanogenium, Methanospirillum. The diversity, composition, and gene abundance varied obviously across the mangrove sampling sites, whereas the measured environmental variables exhibited a negligible effect. Null model showed that the values of beta nearest-taxon index were mostly between -2 and 2, indicating that stochastic processes contributed more than deterministic processes driving the methanogenic community assembly in mangrove sediments. Neutral community model revealed a high estimated migration rate of methanogenic community, further substantiating the significance of stochastic processes. Among the keystone species identified in network analysis, methanogens affiliated to hydrogenotrophic Methanospirillum may have a crucial role in maintaining the structure and function of methanogenic community. Notably, these keystone species were almost unaffected by measured environmental factors, indicating that the methanogenic community in mangrove sediments is more likely to be affected by stochastic processes. This study deepens the understanding of the diversity and assembly of methanogenic community in mangrove sediments, and provides clues to maintain mangrove ecosystem functioning.

Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types

As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

Methane emissions offset atmospheric carbon dioxide uptake in coastal macroalgae, mixed vegetation and sediment ecosystems

Coastal ecosystems can efficiently remove carbon dioxide (CO₂) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH₄) emissions from these ecosystems may counterbalance atmospheric CO₂ uptake. Still, knowledge of mechanisms sustaining such CH₄ emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH₄ in the range of 0.1 - 2.9 mg CH₄ m^-2 d^-1 to the atmosphere, revealing in situ CH₄ emissions from macroalgae that were sustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO₂-equivalent CH₄ emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO₂ uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO₂ release of unvegetated sediments by 57%. Accounting for CH₄ alongside CO₂ sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies.

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.

Revealing the methanogenic pathways for anaerobic digestion of key components in food waste: Performance, microbial community, and implications

Anaerobic digestion (AD) process is widely considered the most sustainable technology for food waste (FW) disposal due to its advantage of biomethane recovery and beneficial environmental consequences. However, the effects of key components in FW (i.e. starchy food, vegetables, fruits, and meats) on AD process and their methanogenic pathways remain unclear. In this study, the biochemical methane potential (BMP) of cooked rice, cabbage, banana peel, pork and local FW was 288, 283, 254, 630, and 476 NmL CH₄/g VS_added, with t₈₀ (time required for 80% methane produced) of 3, 9, 3, 11 and 11 days, respectively. Kinetic analysis suggested diverse hydrolysis rates (0.104-0.679 d^-1) and specific methane yields (39-119 NmL CH₄/g VS_added/d). The relative abundances of key methanogens in the reactors were diverse, leading to the variation in acetoclastic and hydrogenotrophic methanogenic pathways. This study provides fundamental information for the operation of AD systems with different FW compositions.