Nitrogen Cycling Genes Research Articles

Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).

A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25g/L) and hydrogen sulfide (up to 1mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria. Based on the analysis of the morphological characteristics and sequence of individual genes (16S rRNA, rpoB and tilS), we could not attribute the Thiothrix from Lake Baikal to any of the known species of this genus. To determine metabolic capabilities and phylogenetic position of the Thiothrix sp. from Lake Baikal, we analyzed their whole genome. Like all members of this genus, the bacteria from Lake Baikal were capable of organo-heterotrophic, chemolithoheterotrophic, and chemolithoautotrophic growth and differed from its closest relatives in the spectrum of nitrogen and sulfur cycle genes as well as in the indices of average nucleotide identity (ANI < 75-94%), amino acid identity (AAI < 94%) and in silico DNA-DNA hybridization (dDDH < 17-57%), which were below the boundary of interspecies differences, allowing us to identify them as novel candidate species.

Contrasting potential impact patterns of unique and shared microbial species on nitrous oxide emissions in grassland soil on the Tibetan Plateau

Microbial nitrogen transformation processes in grasslands are important nitrous oxide (N2O) sources on the Tibetan Plateau. Different microorganisms carrying various functional nitrogen (N) cycling genes colonize different soil types and have varying impacts on N2O emissions. However, the role of specific microbial components such as unique and shared microbial species, in N2O flux in alpine grassland soils remains understudied. Thus, we combined gas chromatography-based static opaque chamber methods with metagenomic sequencing to investigate the role of unique and shared microbial species carrying N-cycling genes in N2O emissions from two alpine grassland types on the Tibetan Plateau. Our results showed that the N2O flux in the alpine meadows (9.48 × 10−9 g m−2 h−1) was higher than that in the alpine steppes (4.21 × 10−9 g m−2 h−1). Furthermore, our study revealed a significant negative correlation between the abundance of unique microbial species and the N2O flux in alpine steppes. In contrast, the abundance of shared microbial species was significantly and positively correlated with N2O flux. The unique microbial species in the phyla Chloroflexi and Actinobacteria carried the ureC, nasA and nirB genes, which could consume nitrogen substrates in forms other than producing N2O, which could explain the N2O reduction seen in the alpine steppes. In addition, the higher abundance of shared microbial species in the phyla Proteobacteria, Actinobacteria, Thaumarchaeota and Acidobacteria carried genes encoding denitrification pathways (nirK, narG, and norB) could interpret the higher N2O emissions in the alpine meadows. In addition, our study revealed that the soil substrate contents (e.g., soil organic carbon and total nitrogen) and soil environment factors (e.g., soil pH and soil moisture) were potentially important drivers of N2O emissions in soil via their regulation of the composition of unique and shared microbial communities carrying N-cycling genes. Collectively, our results suggested that identifying the unique and shared microbial species carrying different N-cycling genes could provide potential biological strategies for mitigating N2O emissions in alpine grasslands, such as blocking the growth of shared microbial species. Future management practices for mitigating N2O emissions in alpine grassland should also focus on adopting appropriate nutrient management strategies, such as balanced fertilization, to prevent excessive nutrient. Our findings provide insights for further elucidating the different potential regulatory effects of unique and shared microbial species on emissions under the control of the soil environment in different types of grasslands on the Tibetan Plateau.

Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.

Metagenomic Insight Reveals the Microbial Structure and Function of the Full-Scale Coking Wastewater Treatment System: Gene-Based Nitrogen Removal

Microbial communities play crucial roles in pollutant removal and system stability in biological systems for coking wastewater (CWW) treatment, but a comprehensive understanding of their structure and functions is still lacking. A five month survey of four sequential bioreactors, anoxic 1/oxic 1/anoxic 2/oxic 2 (A1/O1/A2/O2), was carried out in a full-scale CWW treatment system in China to elucidate operational performance and microbial ecology. The results showed that A1/O1/A2/O2 had excellent and stable performance for nitrogen removal. Both total nitrogen (TN; (17.38 ± 6.89) mg·L−1) and ammonium–nitrogen (NH4+-N; (2.10 ± 1.34) mg·L−1) in the final biological effluent satisfied the Chinese national standards for CWW. Integrated analysis of 16S ribosome RNA (rRNA) sequencing and metagenomic sequencing showed that the bacterial communities and metagenomic function profiles of A1 and O1 shared similar functional structures, while those of A2 significantly varied from those of other bioreactors (p < 0.05). The results indicated that microbial activity was strongly connected with activated sludge function. Nitrosospira, Nitrosomonas, and SM1A02 were responsible for nitrification during the primary anoxic–oxic (AO) stage and Azoarcus and Thauera acted as important denitrifiers in A2. Nitrogen cycling-related enzymes and genes work in the A1/O1/A2/O2 system. Moreover, the hao genes catalyzing hydroxylamine dehydrogenase (EC 1.7.2.6) and the napA and napB genes catalyzing nitrate reductase (EC 1.9.6.1) played important roles in the nitrification and denitrification processes in the primary and secondary AO stages, respectively. The mixed liquor suspended solids (MLSS)/total solids (TS), TN removal rate (RR), total organic carbon (TOC) (RR), and NH4+-N (RR) were the most important environmental factors for regulating the structure of core bacterial genera and nitrogen-cycling genes. Proteobacteria were the potential main participants in nitrogen metabolism in the A1/O1/A2/O2 system for CWW treatment. This study provides an original and comprehensive understanding of the microbial community and functions at the gene level, which is crucial for the efficient and stable operation of the full-scale biological process for CWW treatment.

Effects of C and N application on Azotobacter and nitrogen cycle in farmland soils of central Guizhou, China

Carbon sources and nitrogen sources are two important groups of substances in analyses of the effects of exogenous additives on soil microorganisms. Glucose (present in soil) and urea (extensively used in agricultural production) are substances often used to study the specific effects of carbon and nitrogen addition on microorganisms. Azotobacter, a non-symbiotic nitrogen-fixing bacterium, has been characterized in the laboratory and applied to soil in numerous studies. However, soil microorganisms display considerable diversity, and the effects of in exogenous substances stimulation on various microorganisms are uncertain. The potential effects of forced exogenous substance stimulation on Azotobacter are not well understood. Here, the effects of C and N application on Azotobacter growth and nitrogen cycle metabolism in farmland soil in central Guizhou, China, were studied through analysis of four treatment groups: control (CK), glucose treatment (C), urea treatment (N), and glucose + urea treatment (CN). The results showed that the relative abundances of the Azotobacter genus and relevant species were increased in group C, indicating promotion of Azotobacter growth (P < 0.001). The relative abundances of the Azotobacter genus and relevant species in group CN were significantly different from the abundances in group N and CK (P < 0.05). Furthermore, the relative abundances of nif genes (i.e., nifH, nifD, and nifK) and nirD were significantly increased in group C. However, the relative abundances of the aforementioned four nitrogen cycle-related genes did not significantly differ between group CN and groups CK and N. The main source species of the aforementioned four nitrogen cycle-related genes were Azotobacter species. The total nitrogen and alkali-hydrolyzed nitrogen contents in soil did not significantly differ in a comparison between group C and groups N and CN. Piecewise structural equation modeling analysis revealed that bacterial α-diversity, Azotobacter, and nitrogen cycle genes had significant direct effects on the alkali-hydrolyzed nitrogen content in soil and had negligible direct effects on the total nitrogen content in soil. These findings improve the broader understanding of Azotobacter and provide theoretical support for reduced Azotobacter utilization in soil.Graphical

Tree Species Influence Nitrate and Nitrous Oxide Production in Forested Riparian Soils

Abundance of soil microbial nitrogen (N) cycling genes responsible for nitrification, denitrification, and nitrous oxide reduction may vary with tree species and N inputs, and these variables may be used to predict or mediate nitrate (NO3−) and nitrous oxide (N2O) from soil. Nitrification and denitrification rates have also been linked to tree mycorrhizal associations, as soil beneath species associated with arbuscular mycorrhiza (AM) shows greater nitrification rates than species forming ectomycorrhizal (ECM) associations. In this study, we integrated N microbial functional gene abundance in the soil influenced by six tree species in two sub-catchments receiving either high or low N inputs. The soils beneath the two ECM-associated tree species and the four AM-associated tree species were analyzed for inorganic N content and potential N2O flux and microbial gene abundance (nirK and nosZ) was quantified using qPCR techniques. Other parameters measured include soil pH, moisture, and organic matter. We determined that tree species influence NO3− and N2O production in riparian soils, particularly under high N enrichment. The soil beneath black cherry had the lowest pH, NO3− concentration, potential N2O production, and OM, though this result did not occur in the low N catchment. The strongest predictors of soil NO3− and N2O across the study sites were N enrichment and pH, respectively. These results provide a framework for species selection in managed riparian zones to minimize NO3− and N2O production and improve riparian function.

Nitrogen-cycling genes in oyster reefs and surrounding sediments: Relationships with environmental factors and respective nitrogen rates

To investigate nitrogen (N) cycling in oyster reef habitats along the East coast of Australia, we assessed N-cycling gene abundances in oyster shell biofilms and surrounding sediments, and explored their correlation with environmental factors and respective N rates. We found higher abundances of the denitrification gene nosZII in oyster shell biofilms, while there were not significant differences in the denitrification genes nirS and nirK between oyster biofilms and sediments. Additionally, oyster shell biofilms had a lower (nirS + nirK)/nosZII ratio, indicating a greater capacity for N removal and limited nitrous oxide release compared to sediments. Abundance of nirS, nirK, and dissimilatory nitrate reduction to ammonium (nrfA) genes in sediments decreased with increasing content of organic material, suggesting the influence of large-scale environmental conditions. N-cycling gene abundances did not relate to N rates, emphasising the importance of investigating microbial genes to enhance our understanding of the N cycle in oyster reef habitats.

Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes.

Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor's nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor's performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (−18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Microbial denitrification characteristics of typical decentralized wastewater treatment processes based on 16S rRNA sequencing.

Despite the widespread application of decentralized wastewater treatment (WWT) facilities in China, relatively few research has used the multi-media biological filter (MMBF) facilities to investigate the microorganism characteristics. This study utilizes 16S rRNA high-throughput sequencing (HTS) technology to examine the microbial biodiversity of a representative wastewater treatment (WWT) system in an expressway service area. The pathways of nitrogen removal along the treatment route were analyzed in conjunction with water quality monitoring. The distribution and composition of microbial flora in the samples were examined, and the dominant flora were identified using LEfSe analysis. The FAPROTAX methodology was employed to investigate the relative abundance of genes associated with the nitrogen cycle and to discern the presence of functional genes involved in nitrogen metabolism. On average, the method has a high level of efficiency in removing COD, TN, NH3-N, and TP from the effluent. The analysis of the microbial community identified a total of 40 phyla, 111 classes, 143 orders, 263 families, and 419 genera. The phyla that were predominantly observed include Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Bacteroidetes. The results show that the system has achieved high performance in nitrogen removal, the abundance of nitrification genes is significantly higher than that of other nitrogen cycle genes such as denitrification, and there are six nitrogen metabolism pathways, primarily nitrification, among which Nitrospirae and Nitrospira are the core differentiated flora that can adapt to low temperature conditions and participate in nitrification, and are the dominant nitrogen removal flora in cold regions. This work aims to comprehensively investigate the diversity and functional properties of the bacterial community in decentralized WWT processes.

Biochar Enhances Soil Resource Availability and Suppresses Microbial Metabolism Genes in the Rhizosphere of Wheat.

Despite the well-documented role of biochar in promoting soil quality and crop productivity, the underlying biological mechanisms remain poorly understood. Here, we explored the effects of straw biochar on soil microbiome in the rhizosphere from wheat using metagenomic sequencing. Our results showed that straw return decreased the yields of wheat, while the straw biochar return increased the wheat yields. Further, both the richness and community composition confirmed different effects of the straw return and straw biochar return. The straw biochar return also resulted in greater rhizosphere effects from wheat, represented by resource availability, including soil organic carbon, soil total nitrogen, available phosphorus, and available potassium. The rhizosphere effects from wheat, represented by microbial metabolism genes involved in carbon, nitrogen, phosphorus, and potassium cycling, however, were decreased by straw biochar returning. In addition, the rhizosphere effects from nitrogen content and the nitrogen cycling genes showed negative relationships with wheat yields. Together, these results revealed that straw biochar enhanced soil resource availability but suppressed microbial metabolism genes in the rhizosphere from wheat, supporting the idea that straw biochar serves as a nutrient pool for crops.

Composition of soil bacterial communities associated with urban stormwater detention basins and their predicted functional roles in N cycle.

Stormwater detention basins serve as vital components in mitigating the adverse effects of urban runoff, and investigating the microbial dynamics within these systems is crucial for enhancing their performance and pollutant removal capabilities. The aim of this study was to examine and compare the soil bacterial communities in two stormwater detention basins located on the Edwards Aquifer in Bexar County, Texas, USA, and evaluate how soil physiochemical properties may affect them. Each basin soil was sampled in two different seasons at varying depths and the structure of microbial communities was examined using paired end Illumina sequencing using V3 and V4 region of 16S rRNA gene. PICRUSt2 was used to predict functional genes in the nitrogen cycle. In addition, soil physicochemical properties such as pH, carbon, nitrogen, and phosphorus and particle size were examined. A beta diversity analysis revealed that basins had distinctive microbial communities. Additionally, soil particle size, phosphorus and ammonia significantly correlated with some of the dominant phyla in the basins. Proteobacteria and Acidobacteria showed a positive correlation with the relative abundances of nitrogen-cycling genes, while Actinobacteria showed a negative correlation. This study evaluated the associations between soil physicochemical properties and microbial community dynamics in stormwater basins. The study also predicts the relative abundance of nitrogen cycling genes, suggesting shared functional traits within microbial communities. The findings have implications for understanding the potential role of microbial communities in nitrogen cycling processes and contribute to developing sustainable stormwater management strategies and protecting water quality in urban areas.

Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.

Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.

Decrease of nitrogen cycle gene abundance and promotion of soil microbial-N saturation restrain increases in N2O emissions in a temperate forest with long-term nitrogen addition

Increases in soil available nitrogen (N) influence N-cycle gene abundances and emission of nitrous oxide (N2O), which is primarily due to N-induced soil acidification in forest. Moreover, the extent of microbial-N saturation could control microbial activity and N2O emission. The contributions of N-induced alterations of microbial-N saturation and N-cycle gene abundances to N2O emission have rarely been quantified. Here, the mechanism underlying N2O emission under N additions (three chemical forms of N, i.e., NO3−-N, NH4+-N and NH4NO3–N, and each at two rates, 50 and 150 kg N ha−1 year−1, respectively) spanning 2011–2021 was investigated in a temperate forest in Beijing. Results showed N2O emissions increased at both low and high N rates of all the three forms compared with control during the whole experiment. However, N2O emissions were lower in high rate of NH4NO3–N and NH4+-N treatments than the corresponding low N rates in the recent three years. Effects of N on microbial-N saturation and abundances of N-cycle genes were dependent on the N rate and form as well as experimental time. Specifically, negative effects of N on N-cycle gene abundances and positive effects of N on microbial-N saturation were demonstrated in high N rate treatments, particularly with NH4+ addition during 2019–2021. Such effects were associated with soil acidification. A hump-backed trend between microbial-N saturation and N2O emissions was observed, suggesting N2O emissions decreased with increase of the microbial-N saturation. Furthermore, N-induced decreases in N-cycle gene abundances restrained N2O emissions. In particular, the nitrification process, dominated by ammonia-oxidize archaea, is critical to determination of N2O emissions in response to the N addition in the temperate forest. We confirmed N addition promoted soil microbial-N saturation and reduced N-cycle gene abundances, which restrained the continuous increase in N2O emissions. It is important for understanding the forest-N-microbe nexus under climate change.

Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil

Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.

The core microbiota as a predictor of soil functional traits promotes soil nutrient cycling and wheat production in dryland farming

Abstract Host plants and the microbiota living in the rhizosphere are interdependent, mutually reinforced and mutually beneficial but the assembly, functions and microbial interactions of the host‐associated microbiota are still unclear. Herein, winter wheat was selected as a test plant to explore the assembly process of total bacteria from bulk soil (BS) and rhizosphere soil (RS), and phoD‐harbouring bacteria in RS at a long‐term (14 years) trial site. We also identified core microbes that are potentially relevant to soil carbon (C), nitrogen (N) and phosphorus (P) cycling genes and soil biogeochemical properties, and investigated the relationships between soil variables, functional genes and wheat productivity. The results showed that the microhabitat of the plant, rather than P fertilizer input, was the main factor affecting the microbial diversity, composition and co‐occurrence networks. The BS bacterial community was driven by deterministic processes but the RS and phoD bacterial communities were dominated by stochastic processes. The influence of deterministic processes decreased with increasing soil nutrient content. A core microbial community consisted of 10 OTUs in different microhabitats and was significantly related to soil functional genes and properties. In the rhizosphere soil, significant correlations were found between soil variables, soil functional bacteria and genes, and crop productivity. Synthesis and applications. This study provides empirical evidence that the assembly process of the microbial community is governed by environmental factors in various soil environments and provides new perspectives on the sustainable improvement of crop productivity. Read the free Plain Language Summary for this article on the Journal blog.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Polyethylene microplastic and soil nitrogen dynamics: Unraveling the links between functional genes, microbial communities, and transformation processes

Microplastics (MPs) have emerged as pollutants of growing concern due to their potential threat to soil ecosystems. While some studies have investigated the effects of MPs on soil nitrogen content, the underlying physicochemical and microbial driving mechanisms still need to be explored. In this study, a six-month incubation experiment was conducted with varying polyethylene MP addition rates: CK (0%, mass ratio), MP0.5 (0.5%), MP1 (1%), MP2 (2%), MP4 (4%), and MP8 (8%). The experiment aimed to examine the effects of MPs on soil nitrogen content, physicochemical properties, nitrogen cycling-related genes, microorganisms, and gross nitrogen transformation rates. The results revealed no significant changes in soil total nitrogen and dissolved total nitrogen. However, dissolved organic nitrogen significantly decreased by 16.00–54.60% following MP addition, while ammonium (NH4+-N, 45.71–271.43%) and nitrate (NO3--N, 43.15–209.54%) nitrogen and microbial biomass nitrogen (46.02–123.70%) significantly increased. Soil pH, bulk density, and soil porosity decreased after MP addition, while soil carbon contents, water-stable macroaggregates, and redox potential increased. The soil microbial community structure changed significantly, and microbial diversity increased under MP treatment. MP addition significantly altered the abundance of soil nitrogen cycling functional genes. The relative abundance of nitrogen fixation and denitrification genes decreased with increasing MP addition rates, while organic degradation and synthesis genes increased. The soil nitrogen cycling functional microbial composition shifted dramatically with increased MP addition. Networks with high addition rates (MP2 +MP4 +MP8) exhibited more total nodes, total links, negative links, node degrees, and modules but shorter average path distances and lower modularity than those with low addition rates (CK +MP0.5 +MP1), reflecting increased network complexity induced by MPs. The gross ammonification rate, NH4+-N consumption and immobilization rates, and NO3--N immobilization rate increased, while the gross nitrification rate and net nitrification rate exhibited an initial increase followed by a decrease with increasing MP addition rates, peaking at MP2. Furthermore, redundancy analysis and structural equation modeling demonstrated that soil physicochemical properties significantly affected soil nitrogen cycling genes and microorganisms, ultimately altering nitrogen content. In conclusion, polyethylene MPs promoted soil nitrogen mineralization and transformation and changed the related functional microorganism community structure, exhibiting a noticeable dose-effect relationship. This study provides deeper insight into the effects of MPs on soil nitrogen cycling.

Bioaugmentation of woodchip bioreactors by Pseudomonas nicosulfuronedens D1-1 with functional species enrichment

A novel heterotrophic nitrification and aerobic denitrification (HN-AD) bacterium D1-1 was identified as Pseudomonas nicosulfuronedens D1-1. Strain D1-1 removed 97.24%, 97.25%, and 77.12% of 100 mg/L NH4+-N, NO3−-N, and NO2−-N, with corresponding maximum removal rates of 7.42, 8.69, and 7.15 mg·L−1·h−1, respectively. Strain D1-1 bioaugmentation enhanced woodchip bioreactor performance with an average NO3−-N removal efficiency of 93.8%. Bioaugmentation enriched N cyclers along with increased bacterial diversity and predicted genes for denitrification, DNRA (dissimilatory nitrate reduction to ammonium), and ammonium oxidation. It also reduced local selection and network modularity from 4.336 to 0.934, resulting in predicted nitrogen (N) cycling genes shared by more modules. These observations suggested that bioaugmentation could enhance the functional redundancy to stabilize the NO3−-N removal performance. This study provides insights into the potential applications of HN-AD bacteria in bioremediation or other environmental engineering fields, relying on their ability to shape bacterial communities.

Variations in litter-soil properties between planted and naturally restored forests drive microbial community structure and function

How forest restoration can affect soil microbial composition and functionality remains unclear, limiting our ability to evaluate restoration approaches. Here, we used metagenomes, 16S rRNA, and ITS gene sequencing to distinguish the composition and functional attributes of soil microbial communities between plantation forest of Pinus massoniana (PF) and naturally restored secondary forest (SF) in their organic horizon and mineral soil from a typical karst region in Southwest China. Our results showed that fungal communities differed more than bacterial communities between PF and SF, while the differences in archaeal communities were not significant. The most abundant fungal phylum in both mineral soil and organic horizon was Ascomycota at SF and Basidiomycota at PF, respectively. The PF soil had lower nitrogen (N) cycling gene abundance and lower inorganic N availability compared to SF soil probably because of the poor soil and lower litter quality. The SF soil had higher abundances of genes associated with labile carbon (C) (i.e., starch, hemicellulose, cellulose, pectin, and chitin) degradation compared with PF soil, but lower abundances of genes responsible for recalcitrant C (i.e., lignin and aromatics) degradation, which was strongly correlated with the litter properties. Simultaneous effects of soil and litter variables explained >50 % of the variation in microbial community structure and functional gene composition; soil nitrate-N had the strongest effect on the soil bacterial and fungal community structure. Our results highlight the superiority of naturally restored secondary forests for improving both soil fertility and soil microbial-mediated C and N cycling functions, which can support forest managers in selecting forest restoration approaches that optimize C and N storage in forest stands.