Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest.

Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 107 copies g-1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 105 and 104 copies g-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106 cells g-1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.

Cumulative dietary risk assessment for French consumers exposed to succinate dehydrogenase inhibitor pesticides.

Consumers are exposed to succinate dehydrogenase inhibitor (SDHI) pesticides through their diet. A cumulative dietary risk assessment for the French population has been performed with French monitoring data (2017-2021) and consumption data from INCA3. The calculation followed a two-tiered approach, using deterministic then probabilistic methods. It was carried out, using European health based guidance values (HBGV) derived for each active substance to characterise their toxicity. In Tier I, the calculated hazard index of 0.12 was below the threshold of 1 and in Tier II, the total margin of exposure at percentile 99.9 remains above the trigger value of 100 (1798 [1631-2311]). In Tier II, the three main risk drivers identified at the upper tail of the distribution were strawberries-fluopyram (19.1%), peaches-fluopyram (14.1%) and table grapes-boscalid (10.5%). Finally, the impact of the major sources of uncertainties was qualitatively evaluated. All together, they were considered of low impact on the outcomes. This work demonstrates the absence of unacceptable chronic risk related to the cumulative exposure of SDHI for French consumers during the 2017-2021 period.

The interplay of soil physicochemical properties, methanogenic diversity, and abundance governs methane production potential in paddy soil subjected to multi-decadal straw incorporation.

Straw incorporation holds significant promise for enhancing soil fertility and mitigating air pollution stemming from straw burning. However, this practice concurrently elevates the production and emission of methane (CH4) from paddy ecosystems. Despite its environmental impact, the precise mechanisms behind the heightened CH4 production resulting from long-term straw incorporation remain elusive. In a 32-year field experiment featuring three fertilization treatments (CFS-chemical fertilizer with wheat straw, CF-chemical fertilizer, and CK-unamended), we investigated the impact of abiotic (soil physicochemical properties) and biotic (methanogenic abundance, diversity, and community composition) factors on CH4 production in paddy fields. Results revealed a significantly higher CH4 production potential under CFS treatment compared to CF and CK treatments. The partial least squares path model revealed that soil physicochemical properties (path coefficient = 0.61), methanogenic diversity (path coefficient = -0.43), and methanogenic abundance (path coefficient = 0.29) collectively determined CH4 production potential, explaining 77% of the variance. Enhanced soil organic carbon content and water content, resulting from straw incorporation, emerged as pivotal factors positively correlated with CH4 production potential. Under CFS treatment, lower Shannon index of methanogens, compared to CF and CK treatments, was attributed to increased Methanosarcina. Notably, the Shannon index and relative abundance of Methanosarcina exhibited negative and positive correlations with CH4 production potential, respectively. Methanogenic abundance, bolstered by straw incorporation, significantly amplified overall potential. This comprehensive analysis underscores the joint influence of abiotic and biotic factors in regulating CH4 production potential during multi-decadal straw incorporation.

Selective trace elements significantly enhanced methane production in coal bed methane systems by stimulating microbial activity.

Trace elements are associated with the microbial degradation of organic matter and methanogenesis, as enzymes in metabolic pathways often employ trace elements as essential cofactors. However, only a few studies investigated the effects of trace elements on the metabolic activity of microbial communities associated with biogenic coalbed methane production. We aimed to determine the effects of strategically selected trace elements on structure and function of active bacterial and methanogenic communities to stimulate methane production in subsurface coalbeds. Microcosms were established with produced water and coal from coalbed methane wells located in the Powder River Basin, Wyoming, USA. In initial pilot experiments with eight different trace elements, individual amendments of Co, Cu, and Mo lead to significantly higher methane production. Transcript levels of mcrA, the key marker gene for methanogenesis, positively correlated with increased methane production. Phylogenetic analysis of the mcrA cDNA library demonstrated compositional shifts of the active methanogenic community and increase of their diversity, particularly of hydrogenotrophic methanogens. High-throughput sequencing of cDNA obtained from 16S rRNA demonstrated active and abundant bacterial groups in response to trace element amendments. Active Acetobacterium members increased in response to Co, Cu, and Mo additions. The findings of this study yield new insights into the importance of essential trace elements on the metabolic activity of microbial communities involved in subsurface coalbed methane and provide a better understanding of how microbial community composition is shaped by trace elements.IMPORTANCEMicrobial life in the deep subsurface of coal beds is limited by nutrient replenishment. While coal bed microbial communities are surrounded by carbon sources, we hypothesized that other nutrients such as trace elements needed as cofactors for enzymes are missing. Amendment of selected trace elements resulted in compositional shifts of the active methanogenic and bacterial communities and correlated with higher transcript levels of mcrA. The findings of this study yield new insights to not only identify possible limitations of microbes by replenishment of trace elements within their specific hydrological placement but also into the importance of essential trace elements for the metabolic activity of microbial communities involved in subsurface coalbed methane production and provides a better understanding of how microbial community composition is shaped by trace elements. Furthermore, this finding might help to revive already spent coal bed methane well systems with the ultimate goal to stimulate methane production.

Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system.

Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.

Cumulative risk assessment with pesticides in the framework of MRL setting.

This abstract presents a report on the proposed work programme, focus on cumulative risk assessment (CRA) for chemical risks, specifically pesticide residues in food. While not a scientific publication, this technical report aims to provide insights without including the fellow's data to avoid publication restrictions. This report focuses on addressing the question concerning the trigger value to perform a prospective CRA in case of a new maximum residue level (MRL) setting. The 1,000 margin of exposure (MOE) threshold value was tested and compared to preliminary ANSES results. Alternative thresholds were calculated and explored. The EU-FORA fellow selected two cumulative assessment groups (CAGs) related to acute craniofacial alterations and chronic thyroid effects. The fellow performed exposure assessments, integrating effects data, French monitoring data, processing factors, agricultural uses, MRLs and extrapolations into Monte Carlo risk assessment (MCRA). Retrospective cumulative exposures using MCRA were conducted for children, adults and a vulnerable group of childbearing women based on the French survey INCA3, identifying background levels at P99.9. The fellow also performed prospective assessments with MCRA, analysing results at P99.9 to evaluate the adequacy of the 1,000 MOE threshold. Alternative thresholds are discussed and proposed.

A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California.

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.

Candidate composite biomarker to inform drug treatments for diabetic kidney disease.

Introduction: Current guidelines recommend renin angiotensin system inhibitors (RASi) as key components of treatment of diabetic kidney disease (DKD). Additional options include sodium-glucose cotransporter-2 inhibitors (SGLT2i), glucagon-like peptide 1 receptor agonists (GLP1a), and mineralocorticoid receptor antagonists (MCRa). The identification of the optimum drug combination for an individual is difficult because of the inter-, and longitudinal intra-individual heterogeneity of response to therapy. Results: Using data from a large observational study (PROVALID), we identified a set of parameters that can be combined into a meaningful composite biomarker that appears to be able to identify which of the various treatment options is clinically beneficial for an individual. It uses machine-earning techniques to estimate under what conditions a treatment of RASi plus an additional treatment is different from the treatment with RASi alone. The measure of difference is the annual percent change (ΔeGFR) in the estimated glomerular filtration rate (ΔeGFR). The 1eGFR is estimated for both the RASi-alone treatment and the add-on treatment. Discussion: Higher estimated increase of eGFR for add-on patients compared with RASi-alone patients indicates that prognosis may be improved with the add-on treatment. The personalized biomarker value thus identifies which patients may benefit from the additional treatment.

Antibiotics inhibit methanogenesis during municipal solid waste decomposition.

Municipal solid waste (MSW) landfills are significant sources of antibiotics. However, the effects of antibiotics on MSW decomposition process and methanogenesis during solid waste decomposition remain insufficiently characterized. This study investigated the effects of environmentally relevant concentrations (ERCs) of antibiotics (200 µg/kg for each antibiotic) on MSW decomposition and methanogenesis in bioreactors treated with and without eight antibiotics (three tetracyclines, three sulfonamides, and two macrolides). The key phases of MSW decomposition, namely the aerobic, anaerobic acid, and methanogenic phases, were determined by analyzing the key physiochemical parameters of the leachate, including pH, chemical oxygen demand, and biochemical oxygen demand. We assessed the bacterial and archaeal compositions, along with the abundance of the gene encoding the alpha subunit of methyl-coenzyme M reductase (mcrA), during MSW decomposition using high throughput 16S ribosomal RNA (rRNA) gene sequencing and quantitative polymerase chain reactions, respectively. Our results revealed that antibiotics significantly altered the compositions of bacteria and methanogens, leading to decreased mcrA abundance and methanogenesis. Specifically, antibiotics inhibited cellulose-degrading bacteria (Firmicutes) and archaea (E2) in the anaerobic acid phase and hydrolytic bacteria (Proteobacteria) in the methanogenic phase, resulting in lower degradation of biodegradable matter than that of the biodegradation without antibiotics treatment. However, the typical MSW decomposition process indicated by the key decomposition phases was successfully separated in both bioreactors, suggesting that antibiotics did not affect overall MSW decomposition process development or the associated individual decomposition phases establishment. These findings suggest that antibiotics at ERCs may inhibit methanogenesis during MSW decomposition, thereby providing fundamental information for methane management and climate change studies.

Microbial diversity and authigenic siderite mediation in sediments surrounding the Kedr-1 mud volcano, Lake Baikal.

The gas hydrate-bearing structure-mud volcano Kedr-1 (Lake Baikal, southern basin)-is located near the coal-bearing sediments of the Tankhoy formation of Oligocene-Miocene age and can be an ideal source of gas-saturated fluid. A significant amount of siderite minerals (FeCO3 ) were collected from sediments at depths ranging from 0.5 to 327 cm below the lake floor (cmblf). An important feature of these carbonate minerals is the extremely strong enrichment in the heavy 13 C isotope, reaching values of +33.3‰ VPDB. The δ13 C of the siderite minerals, as well as their morphology and elemental composition, and the δ13 CDIC of the co-existing pore water, differed across layers of the core, which implies at least two generations of siderite formation. Here, we leverage mineralogical and geochemical data with 16S rRNA data from the microbial communities in sediments surrounding layers containing siderite minerals. Statistical data reveal the formation of three clusters of microbial communities based on taxonomical composition, key taxa among bacteria and archaea, and environmental parameters. Diversity and richness estimators decrease with sediment depth, with several similar prevailing clades located at the bottom of the core. Most of the taxa in the deep sediments could be associated with putative metabolisms involving organotrophic fermentation (Bathyarchaeia, Caldatribacteriota, and Chloroflexota). Various groups of methanogens (Methanoregulaceae, Methanosaetaceae, and Methanomassiliicoccales) and methanotrophic (Methanoperedenaceae) archaea are present in the sediment at variable relative abundances throughout the sampled depth. Based on the physicochemical characteristics of the sediment, carbon isotope analysis of carbonate minerals and DIC, and phylogenetic analysis of individual taxa and their metabolic potential, we present several models for subsurface siderite precipitation in Lake Baikal sediments.

Variations of methane fluxes and methane microbial community composition with soil depth in the riparian buffer zone of a sponge city park.

Riparian buffers benefit both natural and man-made ecosystems by preventing soil erosion, retaining soil nutrients, and filtering pollutants. Nevertheless, the relationship between vertical methane fluxes, soil carbon, and methane microbial communities in riparian buffers remains unclear. This study examined vertical methane fluxes, soil carbon, and methane microbial communities in three different soil depths (0-5 cm, 5-10 cm, and 10-15 cm) within a riparian buffer of a Sponge City Park for one year. Structural equation model (SEM) results demonstrated that vertical methane fluxes varied with soil depths (λ = -0.37) and were primarily regulated by methanogenic community structure (λ = 0.78). Notably, mathematical regression results proposed that mcrA/pmoA ratio (R2 = 0.8) and methanogenic alpha diversity/methanotrophic alpha diversity ratio (R2 = 0.8) could serve as valid predictors of vertical variation in methane fluxes in the riparian buffer of urban river. These findings suggest that vertical variation of methane fluxes in riparian buffer soils is mainly influenced by carbon inputs and methane microbial abundance and community diversity. The study's results quantitatively the relationship between methane fluxes in riparian buffer soils and abiotic and biotic factors in the vertical direction, therefore contributing to the further development of mathematical models of soil methane emissions.

Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench.

The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.

Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens.

Rewetted peatlands are reestablished hot spots for CH4 emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH4 fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH4 fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH4 fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH4 fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH4 turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.

Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples.

Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples-or in this case, chicken droppings.

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.

Exploring the mechanism associated with methane emissions during composting: Inoculation with lignocellulose-degrading microorganisms.

Inoculation with microorganisms is an effective strategy for improving traditional composting processes. This study explored the effects of inoculation with lignocellulose-degrading microorganisms (LDM) on the degradation of organic matter (OM), methane (CH4) emissions, and the microbial community (bacteria and methanogens) during composting. The results showed that LDM accelerated the degradation of OM (including the lignocellulose fraction) and increased the CH4 releases in the later thermophilic and cooling stages during composting. At the ending of composting, LDM increased the CH4 emissions by 38.6% compared with the control. Moreover, LDM significantly increased the abundances of members of the bacterial and methanogenic community during the later thermophilic period (P < 0.05). In addition, LDM promoted the growth and activity of major bacterial genera (e.g., Ureibacillus) with the ability to degrade macromolecular OM, as well as affecting key methanogens (e.g., Methanocorpusculum) in the composting system. Network analysis and variance partitioning analysis indicated that OM and temperature were the main factors that affected the bacterial and methanogen community structures. Structural equation modeling demonstrated that the higher CH4 emissions under LDM were related to the growth of methanogens, which was facilitated by the anaerobic environment produced by large amounts of CO2. Thus, aerobic conditions should be improved during the end of the thermophilic and cooling composting period when inoculating with lignocellulose-degrading microorganisms in order to reduce CH4 emissions.

Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.

Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 106 ~ 4.62 × 106 copies g-1 dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.

COVID-19 diagnosis via chest X-ray image classification based on multiscale class residual attention.

Aiming at detecting COVID-19 effectively, a multiscale class residual attention (MCRA) network is proposed via chest X-ray (CXR) image classification. First, to overcome the data shortage and improve the robustness of our network, a pixel-level image mixing of local regions was introduced to achieve data augmentation and reduce noise. Secondly, multi-scale fusion strategy was adopted to extract global contextual information at different scales and enhance semantic representation. Last but not least, class residual attention was employed to generate spatial attention for each class, which can avoid inter-class interference and enhance related features to further improve the COVID-19 detection. Experimental results show that our network achieves superior diagnostic performance on COVIDx dataset, and its accuracy, PPV, sensitivity, specificity and F1-score are 97.71%, 96.76%, 96.56%, 98.96% and 96.64%, respectively; moreover, the heat maps can endow our deep model with somewhat interpretability.

Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin.

Small regulatory RNAs (sRNAs) are present in almost all investigated microbes, regarded as modulators and regulators of gene expression and also known to play their regulatory role in the environmentally significant process. It has been estimated that less than 1% of the microbes in nature are culturable in the laboratory, hindering our understanding of their physiology, and living strategies. However, recent big advancing of DNA sequencing and omics-related data analysis makes the understanding of the genetics, metabolic potentials, even ecological roles of uncultivated microbes possible. In this study, we used a metagenome and metatranscriptome-based integrated approach to identify small RNAs in the microbiome of Guaymas Basin sediments. Hundreds of environmental sRNAs comprising 228 groups were identified based on their homology, 82% of which displayed high similarity with previously known small RNAs in Rfam database, whereas, "18%" are putative novel sRNA motifs. A putative cis-acting sRNA potentially binding to methyl coenzyme M reductase, a key enzyme in methanogenesis or anaerobic oxidation of methane (AOM), was discovered in the genome of ANaerobic MEthane oxidizing archaea group 1 (ANME-1), which were the dominate microbe in the sample. These sRNAs were actively expressed in local Guaymas Basin hydrothermal environment, suggesting important roles of sRNAs in regulating microbial activity in natural environments.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils.

Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an ana-lysis of microbial communities using 16S rRNA gene sequencing and the mole-cular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. "Candidatus Bathyarchaeia", archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.