Presence of diverse nitrate‐dependent anaerobic methane oxidizing archaea in sewage sludge

Evidence for the anaerobic oxidation of methane coupled to nitrous oxide reduction in landfill cover soils: Promotor and inhibitor

Anaerobic oxidation of methane coupled to nitrous oxide reduction (N2O-AOM) is an important microbial pathway for mitigating greenhouse gases. However, it remains largely unknown whether this process could occur in landfills, which are important anthropogenic sources of greenhouse gases emissions. Here, 13CH4 was supplied in microcosm incubations to track potential rates for the N2O-AOM process in landfill cover soils (LCS). The highest rates for the N2O-AOM process were observed in the bottom layers of LCS and it could be remarkably promoted by the addition of electron shuttles. In addition, 2-bromoethanesulfonic sodium inhibited the N2O-AOM process and reduced the expression of the mcrA gene, showing that ANME archaea/methanogens might be the methane oxidizers for the N2O-AOM process. Our results implied that the N2O-AOM process was an overlooked process for synchronous control of methane and nitrous oxide and may contribute to the future management of greenhouse gases emissions from landfills.

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.

First evidence for anaerobic oxidation of methane process in landfill cover soils: Activity and responsible microorganisms

Landfill cover soils (LCS) play important roles in mitigating methane emissions from landfills. Anaerobic oxidation of methane (AOM) has been demonstrated as a potential methane removal process in aquatic ecosystems. However, whether AOM could occur in LCS is largely unknown. Here, microcosm incubations with ¹³CH₄ were applied to track the potential activities of AOM and quantitative PCR was used to identify the responsible microorganisms. AOM was found to be active in the bottom and middle layers of LCS. In the bottom layer, sulfate-AOM was the most active process, mainly dominated by ANME archaea (without ANME-2d). Meanwhile, in the middle layer, nitrate and nitrite were the major electron acceptors involved in AOM with high abundances of ANME-2d archaea and NC10 bacteria. Our results implied a spatial segregation of methane oxidizing microbes in LCS and might be helpful for future control of methane emissions by the enhancement of AOM.

Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.

Microbial dynamics and activity of denitrifying anaerobic methane oxidizers in China's estuarine and coastal wetlands

Estuarine and coastal wetlands, which act as large sources of methane (CH₄) and undergo substantial loading of anthropogenic nitrogen (N), provide ideal conditions for denitrifying anaerobic methane oxidation (DAMO) to occur. Yet the microbial mechanisms governing DAMO and the main driving factors in estuarine and coastal ecosystems remain unclear. This study investigated the spatiotemporal distribution and associated activity of DAMO microorganisms along a wide swath of China's coastline (latitudinal range: 22-41°N) using molecular assays and isotope tracing techniques. We uncovered significant spatial and seasonal variation in DAMO bacterial community structure, whereas DAMO archaeal community structure exhibited no seasonal differences. The abundance of DAMO bacterial pmoA gene (2.2 × 10⁵-1.0 × 10⁷ copies g^-1) was almost one order of magnitude higher than that of DAMO archaeal mcrA gene (8.7 × 10⁴ -1.8 × 10⁶ copies g^-1). A significant positive correlation between pmoA and mcrA gene abundances (p < 0.01) was observed, indicating that DAMO bacteria and archaea may cooperate closely and thus complete nitrate elimination. Potential DAMO rates, in the range of 0.09-23.4 nmol ¹³CO₂ g^-1 day^-1 for nitrite-DAMO and 0.03-43.7 nmol ¹³CO₂ g^-1 day^-1 for nitrate-DAMO, tended to be greater in the relatively warmer low-latitudes. Potential DAMO rates were weakly positively correlated with gene abundances, suggesting that DAMO microbial activity could not be predicted directly by gene abundance alone. The heterogeneous variability of DAMO was shaped by interactions among key environmental characteristics (sediment texture, N availability, TOC, Fe³⁺, salinity of water, and temperature). On a broader continental scale, potential N removal rates of 0.1-11.2 g N m^-2 yr^-1 were estimated via nitrite-DAMO activity in China's coastal wetlands. Overall, our results highlight the widespread distribution of DAMO microbes and their potential role in eliminating excess N inputs and reducing CH₄ emissions in estuarine and coastal ecosystems, which could help mitigate global warming.

Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea

Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.

High-throughput characterization of the expressed antibiotic resistance genes in sewage sludge with transcriptional analysis

Antibiotic resistance genes (ARGs) are emerging micro-pollutants that pose potential threats to environments and humans. Sewage sludge from wastewater is an important source for ARGs and current studies mainly focus on their existence in microbial genomes. However, little is known about which ARGs are expressed even though ARGs expression remains a better proxy for functional activity. In this study, the expressed ARGs in sewage sludge were characterized by high-throughput quantitative PCR (296 primer sets) combined with transcriptional analysis. A total of 202 ARG transcripts were detected and their abundances ranged from 3.1 × 10⁹ to 1.2 × 10¹⁰ copies/g dry weight. The sum abundance of five most abundant ARG transcripts (qacEdelta1-02, sul2, qacEdelta1-01, aadA2-03, tetX) exhibited a linear correlation with the total abundance of ARG transcripts (R² = 0.88, p < 10^-4), suggesting that these genes could be regarded as indicators to quantitatively predict the total abundance of expressed ARGs. Dynamics of expressed ARGs were observed with lower abundances in summer and winter than those in other seasons (p < 0.05, Kruskal-Wallis test). Variation partitioning analysis indicated that the shift in bacterial community structures induced by changes in environmental attributes might be the main driver for the dynamics of expressed ARGs. Results of this study provided new insights into the ARGs in sewage sludge.