Metagenomics reveals the response of desert steppe microbial communities and carbon-nitrogen cycling functional genes to nitrogen deposition.

Introduction: Nitrogen (N) deposition seriously affects the function of carbon (C) and N cycling in terrestrial ecosystems by altering soil microbial communities, especially in desert steppe ecosystems. However, there is a need for a comprehensive understanding of how microorganisms involved in each C and N cycle process respond to N deposition. Methods: In this study, shotgun metagenome sequencing was used to investigate variations in soil C and N cycling-related genes in the desert steppe in northern China after 6 years of the following N deposition: N0 (control); N30 (N addition 30 kg ha-1 year-1): N50 (N addition 50 kg ha-1 year-1). Results: N deposition significantly increased the relative abundance of Actinobacteria (P < 0.05) while significantly decreased the relative abundances of Proteobacteria and Acidobacteria (P < 0.05). This significantly impacted the microbial community composition in desert steppe soils. The annual addition or deposition of 50 kg ha-1 year-1 for up to 6 years did not affect the C cycle gene abundance but changed the C cycle-related microorganism community structure. The process of the N cycle in the desert steppe was affected by N deposition (50 kg ha-1 year-1), which increased the abundance of the pmoA-amoA gene related to nitrification and the nirB gene associated with assimilation nitrite reductase. There may be a niche overlap between microorganisms involved in the same C and N cycling processes. Discussion: This study provides new insights into the effects of N deposition on soil microbial communities and functions in desert steppe and a better understanding of the ecological consequences of anthropogenic N addition.

Effects of micro-nano plastics on the environmental biogeochemical cycle of nitrogen: a comprehensive review.

Micro-nano plastics (MNPs; size < 5 mm), ubiquitous and emerging pollutants, accumulated in the natural environment through various sources, and are likely to interact with nutrients, thereby influencing their biogeochemical cycle. Increasing scientific evidences reveal that MNPs can affect nitrogen (N) cycle processes by affecting biotopes and organisms in the environmental matrix and MNPs biofilms, thus plays a crucial role in nitrous oxide (N2O) and ammonia (NH3) emission. Yet, the mechanism and key processes behind this have not been systematically reviewed in natural environments. In this review, we systematically summarize the effects of MNPs on N transformation in terrestrial, aquatic, and atmospheric ecosystems. The effects of MNPs properties on N content, composition, and function of the microbial community, enzyme activity, gene abundance and plant N uptake in different environmental conditions has been briefly discussed. The review highlights the significant potential of MNPs to alter the properties of the environmental matrix, microbes and plant or animal physiology, resulting in changes in N uptake and metabolic efficiency in plants, thereby inhibiting organic nitrogen (ON) formation and reducing N bioavailability, or altering NH3 emissions from animal sources. The faster the decomposition of plastics, the more intense the perturbation of MNPs to organisms in the natural ecosystem. Findings of this provide a more comprehensive analysis and research directions to the environmentalists, policy makers, water resources planners & managers, biologists, and biotechnologists to do integrate approaches to reach the practical engineering solutions which will further diminish the long-term ecological and climatic risks.

Agricultural fertilization near marshes impacts the potential for greenhouse gas emissions from wetland ecosystems by modifying microbial communities.

Ensuring agricultural security and preserving the health of wetland ecosystems are crucial concerns facing northeast China. However, the adverse effects of environmental pollution, especially nitrogen (N), caused by prolonged agricultural development on the health of marsh wetlands cannot be systematically recognized. To address this issue, an 18-year trial with four different levels of N application was carried out in a typical area of the Northeast region: 0, 6, 12, and 24 gN·m-2·a-1 (referred to as CK, N6, N12, and N24, respectively) to investigate changes in wetland ecological functioning. The results showed that long-term N input significantly enhanced soil N availability. High-level of N addition (N24) significantly reduced soil bacterial richness in October, while fungal diversity was significantly higher in June than in October for both control and N6 treatments. The main environmental factors affecting microorganisms in June were TN, NH4+, and EC, while bacterial and fungal communities were influenced by TN and Leaf Area Index (LAI), respectively, in October. It was found that the AN16S gene was significantly higher in June than in October, indicating that summer is the critical time for N removal in the wetland. N addition significantly reduced the abundance of the NIFH gene and decreased the N fixation potential of the wetland. In June, low and medium levels of N inputs promoted denitrification processes in the wetland and elevated the wetland N2O emission potential. The abundance of NARG, NIRK, and NOSZ genes decreased significantly in October compared to June, indicating a decrease in the wetland N2O emission potential. Additionally, it was observed that soil methanotrophs were positively affected by NH4+ and TN in October, thereby reducing the wetland CH4 emission potential. Our research provides a systematic understanding of the impact of agricultural N pollution on marsh wetlands, which can inform strategies to protect wetland health.

Nitrogen Forms Regulate the Response of Microcystis aeruginosa to Nanoplastics at Environmentally Relevant Nitrogen Concentrations.

As essential primary producers, cyanobacteria play a major role in global carbon and nitrogen cycles. Though the influence of nanoplastics on the carbon metabolism of cyanobacteria is well-studied, little is known about how nanoplastics affect their nitrogen metabolism, especially under environmentally relevant nitrogen concentrations. Here, we show that nitrogen forms regulated growth inhibition, nitrogen consumption, and the synthesis and release of microcystin (MC) in Microcystis aeruginosa exposed to 10 µg/mL amino-modified polystyrene nanoplastics (PS-NH2) with a particle size of 50 nm under environmentally relevant nitrogen concentrations of nitrate, ammonium, and urea. We demonstrate that PS-NH2 inhibit M. aeruginosa differently in nitrate, urea, and ammonium, with inhibition rates of 51.87, 39.70, and 36.69%, respectively. It is caused through the differences in impairing cell membrane integrity, disrupting redox homeostasis, and varying nitrogen transport pathways under different nitrogen forms. M. aeruginosa respond to exposure of PS-NH2 by utilizing additional nitrogen to boost the production of amino acids, thereby enhancing the synthesis of MC, extracellular polymeric substances, and membrane phospholipids. Our results found that the threat of nanoplastics on primary producers can be regulated by the nitrogen forms in freshwater ecosystems, contributing to a better understanding of nanoplastic risks under environmentally relevant conditions.

Controlled Synthesis of Unconventional Phase Alloy Nanobranches for Highly Selective Electrocatalytic Nitrite Reduction to Ammonia.

The controlled synthesis of metal nanomaterials with unconventional phases is of significant importance to develop high-performance catalysts for various applications. However, it remains challenging to modulate the atomic arrangements of metal nanomaterials, especially the alloy nanostructures that involve different metals with distinct redox potentials. Here we report the general one-pot synthesis of IrNi, IrRhNi and IrFeNi alloy nanobranches with unconventional hexagonal close-packed (hcp) phase. Notably, the as-synthesized hcp IrNi nanobranches demonstrate excellent catalytic performance towards electrochemical nitrite reduction (NO2RR), with superior NH3 Faradaic efficiency and yield rate of 98.2% and 34.6 mg h-1 mgcat-1 (75.5 mg h-1 mgIr-1) at 0 and -0.1 V (vs reversible hydrogen electrode), respectively. Ex/in-situ characterizations and theoretical calculations reveal that the Ir-Ni interactions within hcp IrNi alloy improve electron transfer to benefit both nitrite activation and active hydrogen generation, leading to a stronger reaction trend of NO2RR by greatly reducing energy barriers of rate-determining step.

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Effects of different nitrogen applications and straw return depth on straw microbial and carbon and nitrogen cycles in paddy fields in the cool zone.

Straw is an important source of organic fertilizer for soil enrichment, however, the effects of different nitrogen(N) application rates and depths on straw decomposition microorganisms and carbon and nitrogen cycling under full straw return conditions in cool regions of Northeast China are not clear at this stage. In this paper, we applied macro-genome sequencing technology to investigate the effects of different N application rates (110 kg hm-2, 120 kg hm-2, 130 kg hm-2, 140 kg hm-2, 150 kg hm-2) and depths (0-15 cm, 15-30 cm) on straw decomposing microorganisms and N cycling in paddy fields in the cool zone of Northeast China. The results showed that (1) about 150 functional genes are involved in the carbon cycle process of degradation during the degradation of returned straw, of which the largest number of functional genes are involved in the methane production pathway, about 42, the highest abundance of functional genes involved in the citric acid cycle pathway. There are 22 kinds of functional genes involved in the nitrogen cycle degradation process, among which there are more kinds involved in nitrogen fixation, with 4 kinds. (2) High nitrogen application (150 kg hm-2) inhibited the carbon and nitrogen conversion processes, and the abundance of straw-degrading microorganisms and nitrogen-cycling functional genes was relatively high at a nitrogen application rate of 130 kg hm-2. (3) Depth-dependent heterogeneity of the microbial community was reduced throughout the vertical space. At 71 days of straw return, the nitrogen cycling function decreased and some carbon functional genes showed an increasing trend with the increase of straw return depth. The nitrogen cycle function decreased with the increase of straw returning depth. The microbial community structure was best and the abundance of functional genes involved in the nitrogen cycling process was higher under the conditions of 0-15 cm of returning depth and 130 kg hm-2 of nitrogen application.

Inoculation with Stutzerimonas stutzeri strains decreases N2O emissions from vegetable soil by altering microbial community composition and diversity.

Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N2O) emissions from agricultural soils simultaneously. However, limited PGPR strains can mitigate N2O emissions from agricultural soils, and the microbial ecological mechanisms underlying N2O mitigation after inoculation are poorly understood. In greenhouse pot experiments, the effects of inoculation with Stutzerimonas stutzeri NRCB010 and NRCB025 on tomato growth and N2O emissions were investigated in two vegetable agricultural soils with contrasting textures. Inoculation with NRCB010 and NRCB025 significantly promoted tomato growth in both soils. Moreover, inoculation with NRCB010 decreased the N2O emissions from the fine- and coarse-textured soils by 38.7% and 52.2%, respectively, and inoculation with NRCB025 decreased the N2O emissions from the coarse-textured soil by 76.6%. Inoculation with NRCB010 and NRCB025 decreased N2O emissions mainly by altering soil microbial community composition and the abundance of nitrogen-cycle functional genes. The N2O-mitigating effect might be partially explained by a decrease in the (amoA + amoB)/(nosZI + nosZII) and (nirS + nirK)/(nosZI + nosZII) ratios, respectively. Soil pH and organic matter were key variables that explain the variation in abundance of N-cycle functional genes and subsequent N2O emission. Moreover, the N2O-mitigating effect varied depending on soil textures and individual strain after inoculation. This study provides insights into developing biofertilizers with plant growth-promoting and N2O-mitigating effects. IMPORTANCE: Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N2O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N2O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N2O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N2O-mitigating effect after inoculation. Inoculation with Stutzerimonas stutzeri strains decreased N2O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N2O emissions from vegetable agricultural soils.

Long-term saline water irrigation affected soil carbon and nitrogen cycling functional profiles in the cotton field.

Saline water irrigation (SWI) plays an important role in alleviating water resource shortages. At the same time, the salt input of irrigation water affects soil microorganisms which participate in various ecological processes of terrestrial ecosystems. However, the responses of soil microbial functional potential to long-term SWI remains unclear. Therefore, Metagenomics method was utilized in cotton fields under long-term SWI to reveal the microbial functional profiles associated with soil carbon and nitrogen cycles. Results indicated that SWI impacted the microbial functional profiles of soil carbon and nitrogen cycles in the cotton fields significantly. Especially, irrigation water salinity inhibited the relative abundances of sacC and vanB, which are soil carbon degradation genes. SWI also affected the functional gene abundance of nitrogen degradation, dissimilatory nitrate reduction, and nitrification. Moreover, SWI significantly increased the abundance of Candidatus_Cloacimonetes in both carbon and nitrogen cycles. In the discussion, we used person analysis found that soil salinity, pH, and ammonium nitrogen were important factors affecting the abundance of functional genes and microbial taxa. Overall, this study indicated that long-term SWI significantly influenced specific microbial functional genes and taxa abundance, which may lead to predictable outcomes for soil carbon and nitrogen cycling, and is of great importance in exploring the impact of SWI on soil environments.

Deep insights into the biofilm formation mechanism and nitrogen-transformation network in a nitrate-dependent anaerobic methane oxidation biofilm.

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) process offers a promising solution for simultaneously achieving methane emissions reduction and efficient nitrogen removal in wastewater treatment. Although nitrogen removal at a practical rate has been achieved by n-DAMO biofilm process, the mechanisms of biofilm formation and nitrogen transformation remain to be elucidated. In this study, n-DAMO biofilms were successfully developed in the membrane aerated moving bed biofilm reactor (MAMBBR) and removed nitrate at a rate of 159 mg NO3--N L-1 d-1. The obvious increase in the content of extracellular polymeric substances (EPS) indicated that EPS production was important for biofilm development. n-DAMO microorganisms dominated the microbial community, and n-DAMO bacteria were the most abundant microorganisms. However, the expression of biosynthesis genes for proteins and polysaccharides encoded by n-DAMO archaea was significantly more active compared to other microorganisms, suggesting the central role of n-DAMO archaea in EPS production and biofilm formation. In addition to nitrate reduction, n-DAMO archaea were revealed to actively express dissimilatory nitrate reduction to ammonium and nitrogen fixation. The produced ammonium was putatively converted to dinitrogen gas through the joint function of n-DAMO archaea and n-DAMO bacteria. This study revealed the biofilm formation mechanism and nitrogen-transformation network in n-DAMO biofilm systems, shedding new light on promoting the application of n-DAMO process.

The dosage- and size-dependent effects of micro- and nanoplastics in lettuce roots and leaves at the growth, photosynthetic, and metabolomics levels.

The occurrence of microplastics (MPs) and nanoplastics (NPs) in soils potentially induce morphological, physiological, and biochemical alterations in plants. The present study investigated the effects of MPs/NPs on lettuce (Lactuca sativa L. var. capitata) plants by focusing on (i) four different particle sizes of polyethylene micro- and nanoplastics, at (ii) four concentrations. Photosynthetic activity, morphological changes in plants, and metabolomic shifts in roots and leaves were investigated. Our findings revealed that particle size plays a pivotal role in influencing various growth traits of lettuce (biomass, color segmentation, greening index, leaf area, and photosynthetic activity), physiological parameters (including maximum quantum yield - Fv/Fmmax, or quantum yield in the steady-state Fv/FmLss, NPQLss, RfdLss, FtLss, FqLss), and metabolomic signatures. Smaller plastic sizes demonstrated a dose-dependent impact on aboveground plant structures, resulting in an overall elicitation of biosynthetic processes. Conversely, larger plastic size had a major impact on root metabolomics, leading to a negative modulation of biosynthetic processes. Specifically, the biosynthesis of secondary metabolites, phytohormone crosstalk, and the metabolism of lipids and fatty acids were among the most affected processes. In addition, nitrogen-containing compounds accumulated following plastic treatments. Our results highlighted a tight correlation between the qPCR analysis of genes associated with the soil nitrogen cycle (such as NifH, NirK, and NosZ), available nitrogen pools in soil (including NO3- and NH4), N-containing metabolites and morpho-physiological parameters of lettuce plants subjected to MPs/NPs. These findings underscore the intricate relationship between specific plastic contaminations, nitrogen dynamics, and plant performance.

Nitrification Control by Plants and Preference for Ammonium versus Nitrate: Positive Feedbacks Increase Productivity but Undermine Resilience.

AbstractSome plants, via their action on microorganisms, control soil nitrification (i.e., the transformation of ammonium into nitrate). We model how the covariation between plant control of nitrification and preference for ammonium versus nitrate impacts ecosystem properties such as productivity, nitrogen (N) losses, and overall resilience. We show that the control of nitrification can maximize productivity by minimizing total inorganic N losses. We initially predicted that plants with an ammonium preference should achieve the highest biomass when inhibiting nitrification, and conversely that plants preferring nitrate should achieve the highest biomass by stimulating nitrification. With a parametrization derived from the Lamto savanna (Ivory Coast), we find that productivity is maximal for plants that slightly prefer ammonium and inhibit nitrification. Such situations, however, lead to strong positive feedbacks that can cause abrupt shifts from a highly to a lowly productive ecosystem. The comparison with other parameter sets (Pawnee short-grass prairie [United States], intensively cultivated field, and a hypothetical parameter set in which ammonium is highly volatilized and nitrate inputs are high) shows that strategies yielding the highest biomass may be counterintuitive (i.e., preferring nitrate but inhibiting nitrification). We argue that the level of control yielding the highest productivity depends on ecosystem properties (quantity of N deposition, leaching rates, and baseline nitrification rates), not only preference. Finally, while contrasting N preferences offer, as expected, the possibility of coexistence through niche partitioning, we stress how control of nitrification can be framed as a niche construction process that adds an additional dimension to coexistence conditions.

Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China.

Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg-1 as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.

Astrobiological implications of the organic and inorganic cyanide utilization by a novel Antarctic hyperthermophilic Pyrococcus strain.

Organic and inorganic cyanides are widely distributed in nature, yet not much is known about the ability of microorganisms to use these compounds as a source of nitrogen and/or carbon at high temperatures (>80 °C). Here we studied the capacity of organic and inorganic cyanides to support growth of an hyperthermophilic Pyrococcus strain isolated from Deception Island, Antarctica. This microorganism was capable of growing with aromatic nitriles, aliphatic nitriles, heterocyclic nitriles, amino aromatic nitriles and inorganic cyanides as nitrogen and/or carbon source. This is the first report of an hyperthermophilic microorganism able to incorporate these compounds in its nitrogen and carbon metabolism. Based on enzymatic activity and genomic information, it is possibly that cells of this Pyrococcus strain growing with nitriles or cyanide, might use the carboxylic acid and/or the ammonia generated through the nitrilase enzymatic activity, as a carbon and/or nitrogen source respectively. This work expands the temperature range at which microorganisms can use organic and inorganic cyanides to growth, having important implications to understand microbial metabolisms that can support life on Earth and the possibility to support life elsewhere.

Lower soil nitrogen-oxide emissions associated with enhanced denitrification under replacing mineral fertilizer with manure in orchard soils.

Emerging evidence suggests that replacing mineral fertilizers with organic livestock manure can effectively suppress reactive gaseous nitrogen (N) emissions from soils. However, the extent of this mitigation potential and the underlying microbial mechanisms in orchards remain unclear. To address this knowledge gap, we measured nitrous and nitric oxide (N2O and NO) emissions, microbial N cycling gene abundance, and N2O isotopomer ratios in pear and citrus orchards under three different fertilization regimes: no fertilization, mineral fertilizer, and manure plus mineral fertilizer. The results showed that although manure application caused large transient peaks of N2O, it reduced cumulative emissions of N2O and NO by an average of 20 % and 17 %, respectively, compared to the mineral fertilizer treatment. Partial replacement of mineral fertilizers with manure enhanced the contribution of AOA to nitrification and reduced the contribution of AOB, thus reducing N2O emissions from nitrification. Isotope analysis suggested that the pathway for N2O production in the soils of both orchards was dominated by bacterial denitrification and nitrifier denitrification. The manure treatment reduced the ratio of denitrification products. Additionally, the dual isotope mixing model results indicated that partially replacing mineral fertilizers with manure could promote soil denitrification, resulting in more N2O being reduced. N-oxide emissions were on average 67 % higher in the pear orchard than in the citrus orchard, probably due to the differences in soil physicochemical properties and growth habits between the two orchards. These findings underscore the potential of partially replacing mineral fertilizers with organic manure in orchards to reduce gaseous N emissions, contributing to the transition towards environmentally sustainable and climate-smart agricultural practices.

Effects of Antibiotics on the DAMO Process and Microbes in Cattle Manure.

Denitrifying anaerobic methane oxidation (DAMO) can mitigate methane emissions; however, this process has not been studied in cattle manure, an important source of methane emissions in animal agriculture. The objective of this study was to investigate the occurrence of DAMO microbes in cattle manure and examine the impacts of veterinary antibiotics on the DAMO process in cattle manure. Results show that DAMO archaea and bacteria consistently occur at high concentrations in beef cattle manure. During the long-term operation of a sequencing batch reactor seeded with beef cattle manure, the DAMO activities intensified, and DAMO microbial biomass increased. Exposure to chlortetracycline at initial concentrations up to 5000 µg L-1 did not inhibit DAMO activities or affect the concentrations of the 16S rRNA gene and functional genes of DAMO microbes. In contrast, exposure to tylosin at initial concentrations of 50 and 500 µg L-1 increased the activities of the DAMO microbes. An initial concentration of 5000 µg L-1 TYL almost entirely halted DAMO activities and reduced the concentrations of DAMO microbes. These results show the occurrence of DAMO microbes in cattle manure and reveal that elevated concentrations of dissolved antibiotics could inhibit the DAMO process, potentially affecting net methane emissions from cattle manure.

Towards an integrated view on microbial CH4, N2O and N2 cycles in brackish coastal marsh soils: A comparative analysis of two sites.

Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.

A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant.

In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.

Elevated atmospheric CO2 drives decreases in stable soil organic carbon in arid ecosystems: Evidence from a physical fractionation and organic compound analysis.

The increasing concentration of CO2 in the atmosphere is perturbing the global carbon (C) cycle, altering stocks of organic C, including soil organic matter (SOM). The effect of this disturbance on soils in arid ecosystems may differ from other ecosystems due to water limitation. In this study, we conducted a density fractionation on soils previously harvested from the Nevada Desert FACE Facility (NDFF) to understand how elevated atmospheric CO2 (eCO2 ) affects SOM stability. Soils from beneath the perennial shrub, Larrea tridentata, and from unvegetated interspace were subjected to a sodium polytungstate density fractionation to separate light, particulate organic matter (POM, <1.85 g/cm3 ) from heavier, mineral associated organic matter (MAOM, >1.85 g/cm3 ). These fractions were analyzed for organic C, total N, δ13 C and δ15 N, to understand the mechanisms behind changes. The heavy fraction was further analyzed by pyrolysis GC/MS to assess changes in organic compound composition. Elevated CO2 decreased POM-C and MAOM-C in soils beneath L. tridentata while interspace soils exhibited only a small increase in MAOM-N. Analysis of δ13 C revealed incorporation of new C into both POM and MAOM pools indicating eCO2 stimulated rapid turnover of both POM and MAOM. The largest losses of POM-C and MAOM-C observed under eCO2 occurred in soils 20-40 cm in depth, highlighting that belowground C inputs may be a significant driver of SOM decomposition in this ecosystem. Pyrolysis GC/MS analysis revealed a decrease in organic compound diversity in the MAOM fraction of L. tridentata soils, becoming more similar to interspace soils under eCO2 . These results provide further evidence that MAOM stability may be compromised under disturbance and that SOC stocks in arid ecosystems are vulnerable under continued climate change.