The Laptev Sea is a major Marginal Sea in the Western Arctic Ocean. The Arctic amplification brought by global warming influences the hydrological properties of rivers passing through the permafrost zone, which would alter the biological community structure at continental margin. In this study, the structure, assembly, and gene expression of planktonic microbial communities in two estuaries (Protoka Ularovskaya River Estuary, PURE; Lena River Estuary, LRE) of Laptev Sea were examined to investigate the environmental effects of polar rivers. PURE and LRE exhibited distinct environmental characteristics: low temperature and high salinity for PURE, and high temperature and low salinity for LRE, influenced by runoff size. Salinity more closely influenced microbial communities in LRE, with freshwater species playing a significant role in community composition. The findings revealed differences between two estuaries in community composition and diversity. Prokaryotes and microeukaryotes had shown different assembly patterns in response to habitat changes caused by terrestrial freshwater input. Furthermore, compared with the PURE, the co-occurrence and inter-domain network of the LRE, which was more affected by terrestrial input, was more complex and stable. Functional gene prediction revealed a higher gene expression of methane metabolism in LRE than in PURE, particularly those related to methane oxidation, and this conclusion could help better explore the impact of global warming on the methane cycle in the Arctic Marginal Seas. This study explored the increased freshwater runoffs under the background of global warming dramatically affect Arctic microplankton communities from community structure, assembly and gene expression aspects.

Anaerobic co-digestion (AcoD) with kitchen waste (KW) is an alternative utilization strategy for algal bloom waste (AW). However, the kinetic characteristic and metabolic pathway during this process need to be explored further. This study conducted a comprehensive kinetic and metagenomic analysis for AcoD of AW and KW. A maximum co-digestion performance index (CPI) of 1.13 was achieved under the 12% AW addition. Co-digestion improved the total volatile fatty acids generation and the organic matter transformation efficiency. Kinetic analysis showed that the Superimposed model fit optimally (R2Adj = 0.9988-0.9995). The improvement of the kinetic process by co-digestion was mainly reflected in the increase of the methane production from slowly biodegradable components. Co-digestion enriched the cellulolytic bacterium Clostridium and the hydrogenotrophic methanogenic archaea Methanobacterium. Furthermore, for metagenome analysis, the abundance of key genes concerned in cellulose and lipid hydrolysis, pyruvate and methane metabolism were both increased in co-digestion process. This study provided a feasible process for the utilization of AW produced seasonally and a deeper understanding of the AcoD synergistic mechanism from kinetic and metagenomic perspectives.

The widely existed plastic additives plasticizers in organic wastes possibly pose negative influences on anaerobic digestion (AD) performance, the direct evidence about the effects of plasticizers on AD performance is still lacking. This study evaluated the influencing mechanism of two typical plasticizers bisphenol A (BPA) and dioctyl phthalate on the whole AD process. Results indicated that plasticizers addition inhibited methane production, and the inhibiting effects were reinforced with the increase of concentration. By contrast, 50 mg/L BPA exhibited the strongest inhibition on methane production. Physicochemical analysis showed plasticizers inhibited the metabolism efficiency of soluble polysaccharide and volatile fatty acids. Microbial communities analyses suggested that plasticizers inhibited the direct interspecies electron transfer participators of methanogenic archaea (especially Methanosarcina) and syntrophic bacteria. Furthermore, plasticizers inhibited the methane metabolisms, key coenzymes (CoB, CoM, CoF420 and methanofuran) biosynthesis and the metabolisms of major organic matters. This study shed light on the effects of plasticizers on AD performance and provided new insights for assessing the influences of plasticizers or plastic additives on the disposal of organic wastes.

Bioelectrochemical systems (BES) offer significant potential for treating refractory waste and recovering bioenergy. However, their ability to mitigate microplastic pollution in wastewater remains unexplored. This study showed that BES facilitated the treatment of polyethylene (PE), polyvinyl chloride (PVC), and Mix (PE+PVC) microplastic wastewater and the methane recovery (40.61%, 20.02%, 21.19%, respectively). The lactate dehydrogenase (LDH), adenosine triphosphate (ATP), cytochrome c, and nicotinamide adenine dinucleotide (NADH/NAD+) ratios were elevated with electrical stimulation. Moreover, the applied voltage improved the polysaccharides content of the extracellular polymeric substances (EPS) in the PE-BES but decreased in PVC-BES, while the proteins showed the opposite trend. Metatranscriptomic sequencing showed that the abundance of fermentation bacteria, acetogens, electrogens, and methanogens was greatly enhanced by applying voltage, especially at the anode. Methane metabolism was dominated by the acetoclastic methanogenic pathway, with the applied voltage promoting the enrichment of Methanothrix, resulting in the direct conversion of acetate to acetyl-CoA via acetate-CoA ligase (EC: 6.2.1.1), and increased metabolic activity in the anode. Moreover, applied voltage greatly boosted the function genes expression level related to energy metabolism, tricarboxylic acid (TCA) cycle, electron transport, and transporters on the anode biofilm. Overall, these results demonstrate that BES can mitigate microplastic pollution during wastewater treatment.

Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.

The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.

In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.

Periodic and significant water level fluctuations within the Three Gorges Reservoir (TGR) create a complex water level fluctuation zone (WLFZ) that can significantly influence greenhouse gas emissions. However, the scarcity of comprehensive studies investigating long-term monitoring and analysis of CH4 flux patterns and underlying mechanisms concerning water level variations, environmental characteristics, and microbial communities has limited our understanding. This study conducted a four-year monitoring campaign to examine in situ CH4 emissions from three representative sampling sites. Results indicated that the CH4 flux remained relatively stable at lower water levels, specifically at the control site (S1). However, water level fluctuations significantly influenced CH4 emissions at the sampling sites situated within the WLFZ. Notably, the highest CH4 flux of 0.252 ± 0.089 mg/(m2·h) was observed during the drying period (June to August), while the lowest CH4 flux of 0.048 ± 0.026 mg/(m2·h) was recorded during the flooding period. Moreover, CH4 emissions through the water-air interface surpassed those through the soil-air interface. The CH4 flux positively correlated with organic carbon, temperature, and soil moisture. The relative abundance of methane metabolism microorganisms peaked during the drying period and decreased during the impounding and flooding periods. The primary methanogenesis pathway was hydrogenotrophic, whereas methanotrophic processes were mainly aerobic, with Ca. Methylomirabilis governing the anaerobic methanotrophic process. Overall, the current findings serve as crucial theoretical references for understanding CH4 emissions and carbon metabolism processes within WLFZ environments.

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Most of methane (CH4) emissions contain low CH4 concentrations and typically occur at irregular intervals, which hinders the implementation and performance of methane abatement processes. This study aimed at understanding the metabolic mechanisms that allow methane oxidizing bacteria (MOB) to survive for long periods of time under methane starvation. To this aim, we used an omics-approach and studied the diversity and metabolism of MOB and non-MOB in bioreactors exposed to low CH4 concentrations under feast-famine cycles of 5 days and supplied with nutrient-rich broth. The 16S rRNA and the pmoA transcripts revealed that the most abundant and active MOB during feast and famine conditions belonged to the alphaproteobacterial genus Methylocystis (91-65%). The closest Methylocystis species were M. parvus and M. echinoides. Nitrifiers and denitrifiers were the most representative non-MOB communities, which likely acted as detoxifiers of the system. During starvation periods, the induced activity of CH4 oxidation was not lost, with the particulate methane monooxygenase of alphaproteobacterial MOB playing a key role in energy production. The polyhydroxyalkanoate and nitrification metabolisms of MOB had also an important role during feast-famine cycles, maintaining cell viability when CH4 concentrations were negligible. This research shows that there is an emergence and resilience of conventional alphaproteobacterial MOB, being the genus Methylocystis a centrepiece in environments exposed to dilute and intermittent methane emissions. This knowledge can be applied to the operation of bioreactors subjected to the treatment of dilute and discontinuous emissions via controlled bioaugmentation.