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Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity’ methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane. Atmospheric methane may be consumed by microorganisms in soil, but the mechanisms behind high-affinity methane oxidization remain poorly understood. Here, Jia et al . show that known methanotrophic bacteria are responsible for atmospheric methane uptake in periodically drained wetland ecosystems.

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined 13 C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol c exchangeable Na + kg −1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus , which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of “ Candidatus Nitrosococcus sp. Sol14”, a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na + extrusion/H + import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na + content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO 3 − -N g −1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13 C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13 CO 2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13 C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13 C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter . A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.

Upland soil clusters alpha and gamma (USCα and USCɤ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A 189f/A682r successfully amplified pmoA genes (mainly RA 14 of USCα) in only three forest soils. A189f/mb661 could amplify USCa (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH₄⁺-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA 14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1’s preferences for temperature and elevation were opposite to RA 14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.

This study examines how intensive agricultural management influences ammonia-oxidizing microbial communities (AOB and AOA) in banana monoculture systems, with implications for nitrogen cycling and soil acidification dynamics. While previous research has documented the impact of synthetic fertilizers and pathogens on microbial populations in agroecosystems, the responses of active AOB/AOA taxa under combined nitrogen and disease stressors remain largely uncharacterized. We employed soil microcosms established from a native forest (Y0), a two-year-old (Y2), and a twelve-year-old (Y12) banana plantation. Treatments included urea amendment, Fusarium oxysporum f. sp. cubense ( Foc) inoculation, and their combination. AOB/AOA activity was quantified via ¹³CO₂ DNA stable isotope probing, while community composition was analyzed through high-throughput 16 S rRNA gene sequencing. Our results revealed distinct microbial community patterns across land-use types and treatments. AOB dominated in banana plantation soils, with their abundance significantly increasing ( p  < 0.05) in the Y12 system compared to Y0. Conversely, AOA were predominant in the forest soil. Urea amendment and Foc co-application synergistically enhanced AOB activity in banana soils, withariant community shifts observed across all microcosms. Specifically, urea addition in Y0 soil promoted Nitrosotaleales 1.1 -AOA (20.16%) and Nitrosospira cluster 2AOB (88.23%), whereas co-treatment induced a dominance shift to Nitrosospira cluster 3a (72.12%). In Y2 soils, urea alone supported Nitrosospira cluster 2-AOB (84.53%) and Nitrososphaerales Group 1.1b-AOA (72.4%), while combined amendments further increased Nitrosospira cluster 3a-AOB abundance compared to urea-only treatment. These findings establish that AOB play a critical functional role in nitrogen transformation under intensive cropping systems, with their activity patterns strongly influenced by both fertilization and pathogen stressors.

Methane (CH 4 ) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH 4 emissions from high-latitude regions. Using sediments from an active CH 4 seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH 4 . Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from 13 CH 4 -SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH 4 oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H 4 MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH 4 profiles in the persistent CH 4 seep site, suggested that oxidation of CH 4 , or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH 4 oxidation in the Arctic, especially under lakes that experience extended O 2 limitations during ice cover.

Land use changes soil microbial and chemical properties, but the mechanism of biological nitrogen fixation under different land use patterns is rarely reported, so we used four types of soil: Natural forest soil (NS), healthy banana soil (HS), diseased banana soil (DS) and paddy soil (PS). Treatments included the control (CK), addition of glucose (G), addition of glucose and ammonium nitrate (GN), addition of banana straw (BS), addition of banana straw and ammonium nitrate (BSN), addition of banana root (BR), and addition of banana root and ammonium nitrate (BRN). The study found that the change of soil utilization types, glucose addition increased carbon dioxide emissions (Compared with the control, increased by 963.11%, 508.39%, 794.77% and 511.34%, respectively) and enhanced the ability of soil microbial nitrogen fixation. Importantly, natural forest soil microorganisms have a higher biological nitrogen fixation capacity compared to other types of soils. Glucose addition caused the accumulation of ammonium nitrogen (Compared with the control, increased by 426.08%, 934.21%, 420% and 1065.95%, respectively), indicating that microorganisms had higher utilization efficiency of soluble carbon and enhanced the biological nitrogen fixation capacity, and nitrogen addition caused the accumulation of ammonium nitrogen, thereby weakening the biological nitrogen fixation capacity. At the same time, glucose significantly increased the Fimicutes phylum (83.73%, 66.38%, 67.18% and 70.36%) and lowered the level of other bacterial phylums, thereby reducing the bacterial network structure, and the stability of the soil environment has decreased. Forest analysis showed that CO 2 was an important factor in predicting the bacterial community structure of different soil types, an increase in CO 2 content can predict drastic changes in the bacterial community. Bacteria at the Fimicutes phylum level preferred glucose, which may also have a negative effect on bacteria at the level of other phylums.

Non-alcoholic steatohepatitis (NASH) is the severe form of non-alcoholic fatty liver disease, and is characterized by liver inflammation and fat accumulation. Dietary interventions, such as fibre, have been shown to alleviate this metabolic disorder in mice via the gut microbiota. Here, we investigated the mechanistic role of the gut microbiota in ameliorating NASH via dietary fibre in mice. Soluble fibre inulin was found to be more effective than insoluble fibre cellulose to suppress NASH progression in mice, as shown by reduced hepatic steatosis, necro-inflammation, ballooning and fibrosis. We employed stable isotope probing to trace the incorporation of 13 C-inulin into gut bacterial genomes and metabolites during NASH progression. Shotgun metagenome sequencing revealed that the commensal Parabacteroides distasonis was enriched by 13 C-inulin. Integration of 13 C-inulin metagenomes and metabolomes suggested that P. distasonis used inulin to produce pentadecanoic acid, an odd-chain fatty acid, which was confirmed in vitro and in germ-free mice. P. distasonis or pentadecanoic acid was protective against NASH in mice. Mechanistically, inulin, P. distasonis or pentadecanoic acid restored gut barrier function in NASH models, which reduced serum lipopolysaccharide and liver pro-inflammatory cytokine expression. Overall this shows that gut microbiota members can use dietary fibre to generate beneficial metabolites to suppress metabolic disease. The gut commensal Parabacteroides distasonis uses inulin to produce the odd-chain fatty acid pentadecanoic acid, which alleviates non-alcoholic steatohepatitis via improved barrier function in mice.

Most studies about the effects of N addition on soil microbial biomass evaluate soil microbial and physicochemical characteristics using single-test methods, and these studies have not been integrated and analyzed to comprehensively assess the impact of N fertilization on soil microbial biomass. Here, we conduct a meta-analysis to analyze the results of 86 studies characterizing how soil microbial biomass C (MBC), N (MBN), and P (MBP) pools respond to exogenous N addition across multiple land use types. We found that low N addition (5–50 kg/hm2) rates significantly affect soil microbial biomass, mainly by increasing MBC but also by decreasing MBP and significantly increasing MBC/MBP. N addition affects soil physicochemical properties, significantly reducing pH and significantly increasing the soil dissolved organic N and inorganic N content. Our analysis also revealed that the effects of N application vary across ecosystems. N addition significantly decreases MBP and total P in planted forests but does not significantly affect soil microbial biomass in grasslands. In farmland soil, N addition significantly increases total P, NH4+, NO3−, MBN, and MBP but significantly decreases pH. Although N addition can strongly influence soil microbial biomass, its effects are modulated by ecosystem type. The addition of N can negatively affect MBC, MBN, and MBP in natural forest ecosystems, thereby altering global ecosystem balance.

The phyllosphere, the aerial parts of terrestrial plants, represents the largest biological interface on Earth. This habitat is colonized by diverse microorganisms that affect plant health and growth. However, the community structure of these phyllosphere microorganisms and their responses to environmental changes, such as rising atmospheric CO₂, are poorly understood. Using a massive parallel pyrosequencing technique, we investigated the feedback of a phyllosphere bacterial community in rice to elevated CO₂ (eCO₂) at the tillering, filling, and maturity stages under nitrogen fertilization with low (LN) and high application rates (HN). The results revealed 9,406 distinct operational taxonomic units that could be classified into 8 phyla, 13 classes, 26 orders, 59 families, and 120 genera. The family Enterobacteriaceae within Gammaproteobacteria was the most dominant phylotype during the rice growing season, accounting for 61.0–97.2 % of the total microbial communities. A statistical analysis indicated that the shift in structure and composition of phyllosphere bacterial communities was largely dependent on the rice growing stage. eCO₂ showed a distinct effect on the structure of bacterial communities at different growth stages, and the most evident response of the community structure to eCO₂ was observed at the filling stage. eCO₂ significantly increased the relative abundance of the most dominant phylotype (Enterobacteriaceae) from 88.6 % at aCO₂ (ambient CO₂) to 97.2 % at eCO₂ under LN fertilization at the filling stage, while it significantly decreased the total relative abundance of other phylotypes from 7.48 to 1.35 %. Similarly, higher value for the relative abundance of the most dominant family (Enterobacteriaceae) and lower value for the total relative abundance of other families were observed under eCO₂ condition at other growth stages and under different N fertilizations, but the difference was not statistically significant. No consistent response pattern was observed along growth stages that could be attributed to N treatments. These results provide useful insights into our understanding of the response of a phyllosphere bacterial community to eCO₂ with regards to the diversity, composition, and structure during rice growing seasons.