Nitrogen Metabolism Research Articles

Soil pathogenic fungal groups and soil nutrient cycling under land use practices in Liupanshan Mountain in China

AbstractDifferent land‐use practices in temperate forests strongly affect soil quality and soil microbial communities, whereas the assembly and interactions of soil functional fungal communities provide positive feedback. Therefore, the effects of forest ecosystem degradation on the composition of functional soil fungal community and soil nutrient cycling are of particular importance. We studied forest ecosystems in the Liupanshan Mountains in the northwestern part of the Loess Plateau and analyzed the relationship of soil fungal community and soil nutrient cycling under different land use practices (natural forest [NF], plantation forest, and farmland [FL]). The results showed that soil pH and electrical conductivity were the highest in FL, whereas the soil carbon cycle index and nitrogen cycle index decreased. The soil total phosphorus content did not change significantly with an increase in available phosphorus content. The change from NF to FL significantly increased the number of operational taxonomic units, diversity, and richness of soil fungal communities. The composition of the soil fungal communities was also strongly influenced by carbon and nitrogen cycle indices. In addition, FL reclamation increased the complexity of the soil microorganism co‐occurrence network, and the interrelationships between soil functional fungal community were enhanced. Pathogenic fungal communities were enriched in FLs, and their relative abundance was significantly regulated by environmental factors such as pH and the ratio of nitrogen to phosphorus. The soil pathogenic fungal community affected carbon and nitrogen cycle indices to varying degrees.

Enhancing virus-induced gene silencing efficiency in tea plants (Camellia sinensis L.) and the functional analysis of CsPDS

Virus-induced gene silencing (VIGS) is an effective technology for gene functional analysis in tea plants, yet its efficiency needs enhancement, particularly in the Qiancha 1 (QC1) cultivar of Camellia sinensis. Employing pTRV1/pTRV2-CsPDS as a vector and leaf albinism rate as a silencing index, this study optimized the VIGS system by examining the effects of vacuum treatment duration, pressure, injection method, and cutting size on silencing efficiency. The results indicate that both injection and vacuum infiltration methods are viable in QC1, with the vacuum method exhibiting superior efficiency. The optimal vacuum infiltration conditions were determined to be 0.8 kPa for approximately 5 min. Phenotypic analysis showed that silencing the CsPDS gene resulted in leaves yellowing to varying degrees. Transcriptome analysis revealed disruptions in various pathways in these tea cuttings with differing levels of coloration, particularly in photosynthetic pigment biosynthesis and nitrogen metabolism. Interestingly, the content of theanine was higher in the cuttings with lower chlorophyll content. Analysis of differential gene expression profile and quantitative real-time PCR confirms that theanine accumulation is primarily due to increased synthesis and reduced degradation. These findings deepen our understanding of the metabolic and molecular mechanisms behind leaf coloration in tea plants.

Biotechnological Potential of the Soil Microbiome

Molecular biological techniques and bioinformatic analysis were used to investigate the phylogenetic and functional diversity of the prokaryotic complex of soil microcosms. The dominant organisms of the hydrolytic community were different in the samples from different climatic zones. In the soils subject to anthropogenic or abiogenic load, apart from decreased diversity and abundance of prokaryotes, the number of the genes marking the ability to degrade xenobiotics, as well as those encoding nitrogen conversion and metabolism of vitamins and cofactors, was found to increase. Under heavy oil contamination, the bacterial community was capable of nitrification; its role increased in the lower horizons of the soil profile. The patterns revealed in the work indicate high metabolic potential of the prokaryotic component of the studied soils.

Effect of the PotN Protein on Activities of the GlnR and PotA Proteins in the Cells of Lentilactobacillus hilgardii

Bacterial PII-like proteins are global regulators of nitrogen and energy metabolism, which respond to nutrient availability by binding their partner proteins, thus modulating their activity. The PotN protein from Lentilactobacillus hilgardii, a member of the new family of PII-like proteins, is capable of competitive binding of ATP and ADP, thus regulating metabolism in response to the cell energy status. Thus, under ADP excess, PotN binds this nucleotide and interacts mostly with the PotA subunit of the polyamine АВС transporter, suppressing its ATPase activity. PotN also dissociates from the transcription factor GlnR, restoring its ability to bind DNA and modulate expression of the genes of the GlnR regulon. On the contrary, in the ATP state PotN dissociates from PotA and binds to the GlnR factor.

Effects of iron-carbon on nitrogen metabolism of floc and aerobic granular sludge

The aerobic granular sludge (AGS) process had been extensively studied for its simultaneous nitrification and denitrification (SND) capabilities. Iron-carbon (IC) had enhanced AGS nitrogen removal efficiency, but the mechanism remained unclear. In this study, four reactors had been added with 50, 30, 10, and 0 g/L of IC. Total nitrogen removal efficiency increased with IC dosage under the same operation mode. IC enhanced sludge ammonia oxidation rate, denitrification rate, and specific oxygen uptake rate, allowing SND to complete 60 min earlier, potentially reducing wastewater treatment costs. Notably, IC eliminated nitrite accumulation in conventional AGS effluent. IC decreased the abundance of genes and enzyme activities related to NOR expression, while increasing those related to NOS, which may mitigate the potential for nitrous oxide formation by microorganisms. In this study, IC acted as an enzymatic reaction activator, affecting granules more than flocs, with the activity gap gradually decreasing with the IC dosage.

The poetry of nitrogen and carbon metabolic shifts: The role of C/N in pitaya phase change

Pitaya, a desert plant, has an underexplored flowering mechanism due to a lack of functional validation assays. This study reveals that the transition from vegetative to generative growth in pitaya is regulated by significant metabolic shift, underscoring the importance of understanding and address the challenging issue pitaya's phase change. Lateral buds from 6-years-old ‘Guanhuahong’ pitaya (Hylocereus monacanthus) plants were collected on April 8th, 18th, and 28th 2023, representing early, middle, and late stages of phase transition, respectively. Results showed diminished nitrogen levels concurrent with increased carbon levels and carbon-to-nitrogen (C/N) ratios during pitaya phase transition. Transcriptomic analysis identified batches of differentially expressed genes (DEGs) involved in downregulating nitrogen metabolism and upregulating carbon metabolism. These batches of genes play a central role in the metabolic shifts that predominantly regulate the transition to the generative phase in pitaya. This study unveils the intricate regulatory network involving 6 sugar synthesis and transport, 11 photoperiod (e.g., PHY, CRY, PIF) and 6 vernalization (e.g., VIN3) pathways, alongside 11 structural flowering genes (FCA, FLK, LFY, AGL) out of a vast array of potential candidates in pitaya phase change. These findings provide insights into the metabolic pathways involved in pitaya's phase transition, offering a theoretical framework for managing flowering, guiding breeding strategies to optimize flowering timing and improve crop yields under varied nitrogen conditions.

Effect of electrooxidation pretreatment on treatment efficiency, membrane fouling and microbial community of a membrane bioreactor treating sludge dewatering wastewater

This study investigated electrooxidation (EO) pretreatment for sludge dewatering wastewater and condensate generated during the process, aiming to enhance its treatment via a membrane bioreactor (MBR) and prevent membrane fouling. EO treatment could achieve a complete suspended solids (SS) removal along with 97.4 % EPS and 90.1 % colour removal under the optimum conditions. However, the NH4+-N and total organic carbon (TOC) concentration in wastewater increased (16 % and 72.8 %, respectively) due to break down of the complex organic substances present in the wastewater. MBR treating EO pretreated wastewater showed significant improvement against membrane fouling, as shown by reduction in transmembrane pressure (TMP) from 15 kPa in control to 0 kPa in the experimental reactor. The MBR operated with EO-treated wastewater and a 16-day HRT resulted in a low effluent NH4+-N concentrations of 469.3 mg/L (74.9 % removal) along with a very low TOC concentration of 24.3 mg/L (98.7 % removal). The microbial community analysis revealed that enrichment of selected organic carbon degraders (Defluviitoga, Pedobacter, and Flavobacteriaceae) and nitrogen cycle bacteria (Dechloromonas, Comamonas, Arenibacter, Brevundimonas, Thauera, and Aequorivita), including some aerobic denitrifiers (Aquamicrobium and Chryseobacterium) in the experimental reactor treating EO-pretreated wastewater is responsible for enhancing microbial degradation and its overall performance.

Quantifying the functional genes of C, N, P, and S cycling in a deep lake: Depth patterns and drivers

Microbial functional composition is important for biogeochemical cycles, and is usually constrained by taxonomic species pool and natural environmental gradients. However, the distribution of functional genes in deep lakes and the driving factors remains elusive. Here, we quantified the abundance of 71 functional genes relevant to carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus cycling, and sulfur cycling in 38 sediments along the water depth ranging from 0 to 90 m in Lugu Lake, China, using Quantitative Microbial Ecology Chip (QMEC) and then explored their water-depth diversity pattern and abiotic and biotic drivers. Functional gene diversity showed a hump-shaped pattern along the depth and peaked at around 50 m which is the low boundary of thermocline layer. There were specific environmental preferences among functional gene subgroups such as nitrogen and sulfur cycling genes preferring to deeper and shallow waters, respectively. The dissimilarity of total functional genes increased with water depth distance indicating a distance-decay relationship. There was a congruence between functional and taxonomic composition by showing the positive correlations between the compositions of functional genes and bacteria or archaea. This phenomenon is consistently observed for the six functional gene subgroups, and the congruence strength was highest for nitrogen cycling while lowest for sulfur cycling. Compared to abiotic factors, biotic factors were more relevant to the functional gene diversity and composition. Biotic factors explained 28.5 % of the variance of functional gene diversity, while water depth and other environmental factors such as water total phosphorus and sediment carbon explained 4.2 % and 3.8 %, respectively. For functional gene composition, biotic factors accounted for 25.2 % of the variance, whereas water depth and other environmental factors contributed to 0.7 % and 4.4 %, respectively. Among all explanatory variables for function genes, bacterial composition had the highest contribution, which was further supported by showing its direct effects of 1.45 and 0.86 on functional diversity and composition, respectively. This study for the first time quantified the microbial functional genes along water depth in deep lakes and provided a more comprehensive understanding of the functional dynamics in microbial communities within aquatic ecosystems.

The Effects of Mixed Robinia pseudoacacia and Quercus variabilis Plantation on Soil Bacterial Community Structure and Nitrogen-Cycling Gene Abundance in the Southern Taihang Mountain Foothills.

Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss.

Alterations in carbon and nitrogen cycling mediated by soil microbes due to the conversion of karst mountainous forests into urban parks

The conversion of mountainous karst forests into urban parks necessitates a critical analysis of its impact on existing ecosystems, particularly regarding soil microbial diversity and its role in carbon and nitrogen cycling. Our study targeted three established mountain parks in Guiyang, China, to discern the effects of habitat alteration and park age on the soil microbiota’s functional genes. The findings indicated pronounced differences in functional gene profiles between original remnant forests and created greenspaces. The artificial green spaces exhibited a heightened presence of genes related to aerobic methane oxidation, anaerobic carbon fixation, denitrification and nitrification, indicating that artificial green spaces may cultivate soil microbial communities with enhanced metabolic versatility. We revealed a positive correlation between soil nitrogen levels and the abundance of genes involved in various processes of the carbon and nitrogen cycles in these artificial green areas, highlighting the critical role of nitrogen in influencing the structure of microbial communities. Soil chemical properties (namely C, N, P, K content) and habitat type emerged as the most consequential for the gene composition related to the carbon and nitrogen cycles. The co-occurrence networks of functional genes constructed for these cycles suggest a tendency towards synergistic microbial interactions. To safeguard the interplay between human recreation and the conservation of native ecosystems, we recommend the integration of native flora preservation and meticulous soil condition management into the strategies for developing urban mountain parks.

Mitigating High-Temperature Stress in Peppers: The Role of Exogenous NO in Antioxidant Enzyme Activities and Nitrogen Metabolism

This study investigated the effects of exogenous nitric oxide (NO) on growth, antioxidant enzymes, and key nitrogen metabolism enzymes in pepper seedlings under high-temperature stress. In addition, targeted metabolomics was used to study the differential accumulation of amino acid metabolites, thereby providing theoretical support for the use of exogenous substances to mitigate high-temperature stress damage in plants. The results showed that high-temperature stress increased soluble sugar, soluble protein, amino acids, proline, malondialdehyde (MDA), and hydrogen peroxide (H2O2) content, electrolyte leakage, and superoxide anion (O2·-) production rate while altering the activities of antioxidant enzymes [superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX)] and key nitrogen metabolism enzymes [nitrate reductase (NR), glutamine synthetase (GS), glutamate dehydrogenase (GDH), and nitric oxide synthase (NOS)]. c-PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, an NO scavenger) exacerbates oxidative stress and further reduces NO content and enzyme activities. However, exogenous SNP (sodium nitroprusside, an NO donor) effectively alleviated these adverse effects by enhancing antioxidant defense mechanisms, increasing NO content, and normalizing amino acid metabolite levels (kynurenine, N-acetyl-L-tyrosine, L-methionine, urea, and creatine), thereby maintaining normal plant growth. These findings suggest that SNP can enhance stress tolerance in pepper seedlings by improving osmotic regulation, antioxidant capacity, and nitrogen metabolism, effectively mitigating the damage caused by high-temperature stress.

Manure-derived black soldier fly frass enhanced the growth of chilli plants (Capsicum annuum L.) and altered rhizosphere bacterial community

Sustainable manure management is crucial for minimising environmental impacts as the livestock industry expands to meet the increasing demand for protein. Black soldier fly (Hermetia illucens L.) larvae (BSFL) farming is an emerging waste management method that efficiently processes large volumes of organic waste, including manure, to produce valuable protein, oil and chitin products. Frass, a nutrient-rich by-product of black soldier fly farming, has potential as an organic fertiliser. However, research has primarily focused on frass derived from food waste, with little exploration of manure-derived BSFL frass. This study aimed to determine whether frass derived from manure could enhance the growth of chilli (Capsicum annuum L.) over 14 weeks under controlled glasshouse conditions. The impacts of manure-derived BSFL frass on soil properties and soil bacterial communities were characterised. The results indicated that a 0.6 % w/w application rate yielded the highest chilli plant biomass, with reduced growth observed at higher rates. The enhanced growth at optimal manure-derived BSFL frass application rates was due to increased nitrogen content, whereas reduced growth at higher rates was likely caused by phytotoxicity from not completely decomposed frass. Soil microbial biomass carbon and nitrogen also increased with manure-derived BSFL frass, implying microbial carbon and nitrogen immobilisation. Additionally, the changes in pH and nutrients due to manure-derived BSFL frass caused shifts in the bacterial community in the chilli plant rhizosphere, enriching the relative abundance of bacteria with potential growth-promoting properties. This study highlights the potential of integrating manure into black soldier fly waste management processes, demonstrating that manure-derived BSFL frass can be used as an organic fertiliser with circular economy benefits.

Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant

Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.

Analysis of bacterial community structure, functional variation, and assembly mechanisms in multi-media habitats of lakes during the frozen period

Ice, water, and sediment represent three interconnected habitats in lake ecosystems, and bacteria are crucial for maintaining ecosystem equilibrium and elemental cycling across these habitats. However, the differential characteristics and driving mechanisms of bacterial community structures in the ice, water, and sediments of seasonally frozen lakes remain unclear. In this study, high-throughput sequencing technology was used to analyze and compare the structure, function, network characteristics, and assembly mechanisms of bacterial communities in the ice, water, and sediment of Wuliangsuhai, a typical cold region in Inner Mongolia. The results showed that the bacterial communities in the ice and water phases had similar diversity and composition, with Proteobacteria, Bacteroidota, Actinobacteria, Campilobacterota, and Cyanobacteria as dominant phyla. The bacterial communities in sediments displayed significant differences from ice and water, with Chloroflexi, Proteobacteria, Firmicutes, Desulfobacterota, and Acidobacteriota being the dominant phyla. Notably, the bacterial communities in water exhibited higher spatial variability in their distribution than those in ice and sediment. This study also revealed that during the frozen period, the bacterial community species in the ice, water, and sediment media were dominated by cooperative relationships. Community assembly was primarily influenced by stochastic processes, with dispersal limitation and drift identified as the two most significant factors within this process. However, heterogeneous selection also played a significant role in the community composition. Furthermore, functions related to nitrogen, phosphorus, sulfur, carbon, and hydrogen cycling vary among bacterial communities in ice, water, and sediment. These findings elucidate the intrinsic mechanisms driving variability in bacterial community structure and changes in water quality across different media phases (ice, water, and sediment) in cold-zone lakes during the freezing period, offering new insights for water environmental protection and ecological restoration efforts in such environments.

Enhancing anaerobic ammonium oxidation via polymeric ferric sulfate (PFS)-Mediated dual-electron Acceptor: A solution to nitrite deficiency

In addressing the issue of the unstable supply of electron acceptors (nitrite) during Anammox, researchers have often overlooked that the electron transfer process in anammox bacteria (AnAOB) is not restricted to the intracellular, extracellular electron transfer can also serve as an alternative pathway. This study utilized Fe3+ as an adjunctive electron acceptor, coupling Anammox with ferric iron reduction (Feammox) by introducing polymeric ferric sulfate (PFS) in the Anammox system. This approach achieved effective nitrogen removal even when nitrite was deficient. At a NO2–-N to NH4+-N ratio of 0.5, the Feammox-Anammox combined system maintained stable nitrogen removal under the dual electron acceptor, with total nitrogen and NH4+-N removal efficiency of 85 % and 91 %, respectively. The contribution of Feammox and Anammox to NH4+-N removal was 45 % and 55 %, respectively. TEM-EDS confirmed the presence of iron elements across the periphery, periplasm, and cytoplasm of AnAOB, suggesting the involvement of PFS in the metabolic and electron transfer processes. Notably, the introduction of Fe3+ and the limitation of nitrite availability resulted in increased relative abundances of FeOB (Thermomonas) and FeRB (Ignavibacterium) to 30 % and 3.6 %, respectively, indicating that the electron transfer process with Fe3+ as the electron acceptor was continuously intensified, as well as a cycle of Fe3+ / Fe2+ was established. Due to unique nitrogen metabolism mode and high Fe3+ tolerance, the abundance of Candidatus_Brocadia was enriched up to 7.2 %, which alternately dominated the Anammox process with Candidatus_Kuenenia, providing favorable conditions for AnAOB to carry out the extracellular electron transfer process. These findings provide a novel strategy for improving the stability and efficiency of the Anammox process under deficient nitrite supply.

The effects of polypropylene microplastics on the removal of nitrogen and phosphorus from water by Acorus calamus, Iris tectorum and functional microorganisms

Polypropylene microplastics (PP-MPs), an emerging pollutant, adversely affect the ability of aquatic plants to restore water bodies, thereby compromising the functionality and integrity of wetland ecosystems. This study examines the effects of microplastic stress on the nitrogen and phosphorus removal capacities of Acorus calamus and Iris tectorum, as well as on functional microorganisms within the aquatic system. The findings indicate that under PP-MP stress, the nitrogen and phosphorus absorption capabilities of both plants were diminished. Additionally, there was a significant reduction in the metabolic enzyme activities related to nitrogen and phosphorus in the plants, alongside a notable decrease in leaf nitrogen content. PP-MPs hinder the nutrient uptake of plants, affecting their growth and indirectly reducing their ability to utilize nitrogen and phosphorus. Specifically, in the 10 mg L−1 treatment group, A. calamus and I. tectorum showed reductions in leaf nitrogen content by 23.1% and 31.0%, respectively, and by 14.8% and 27.7% in the 200 mg L−1 treatment group. Furthermore, I. tectorum had higher leaf nitrogen levels than A. calamus. Using fluorescent tagging, the distribution of PP-MPs was traced in the roots, stems, and leaves of the plants, revealing significant growth impairment in both species. This included a considerable decline in photosynthetic pigment synthesis, enhanced oxidative stress responses, and increased lipid peroxidation in cell membranes. PP-MP exposure also significantly reduced the abundance of functional microorganisms involved in denitrification and phosphorus removal at the genus level in aquatic systems. Ecological function predictions revealed a notable decrease in nitrogen cycling functions such as nitrogen respiration and nitrite denitrification among water microorganisms in both treatment groups, with a higher ecological risk potential in the A. calamus treatment group. This study provides new insights into the potential stress mechanisms of PP-MPs on aquatic plants involved in water body remediation and their impacts on wetland ecosystems.

Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria.

Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity. We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata. Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19 cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank. Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.

Species pool and local assembly processes drive β diversity of ammonia-oxidizing and denitrifying microbial communities in rivers along a latitudinal gradient.

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high-throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia-oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS-type denitrifying community co-varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia-oxidizing and nirK-type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia-oxidizing and nirK-type denitrifying communities. Additionally, biotic interactions drove ammonia-oxidizing and nirS-type denitrifying communities by influencing species co-occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N-cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale.

Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses

In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.

Nitrogen Deposition Reduces the Rate of Leaf Litter Decomposition: A Global Study

The litter decomposition of plant leaves is a vital process in carbon (C) and nitrogen (N) cycling in global terrestrial ecosystems. However, previous assessments of the key determinants of the N deposition effects of litter decomposition have been more controversial. In this meta-analysis, we compared the overall effects of N addition on the litter decomposition rates, litter nutrient content (C and N), and litter constituent (lignin and cellulose) residual rates using a log response ratio approach. Our results showed that exogenous N addition increased the N content and inhibited lignin degradation in litter. N deposition decreased the leaf litter decomposition rate by increasing the lignin and N residues and decreasing the litter C content and soil pH. The analysis also concluded that the initial litter C/N ratio, lignin content, and soil pH were main factors in mediating the effect of N deposition on litter decomposition rate. Overall, the results of this study indicate that N deposition can slow decomposition rates by inhibiting N release and lignin degradation of litter. Notably, these results emphasize that the effect of N deposition on litter decomposition mainly depends on the endogenous quality of the litter and soil pH in the decomposition environment.