Nitrogen Functional Genes Research Articles

Nitrification and denitrification processes in a zero-water exchange aquaculture system: characteristics of the microbial community and potential rates

​The zero-water exchange aquaculture has been identified as a promising method of farming to decrease the environment pressure of aquaculture and to increase profits. However, the ecological functions (e.g., nitrogen removal) and microbial biodiversity of the zero-water exchange pond aquaculture system are relatively understudied. In the present study, the zero-water exchange pond aquaculture system were constructed to investigated the microbial communities, sediment potential nitrification and denitrification production rates. And five functional genes (AOA amoA, AOB amoA, nirS, nosZ, and hzsB) were used to quantify the abundance of nitrifying and denitrifying microorganisms. The results showed that the sediment of the system had excellent potential nitrification-denitrification performance, with potential nitrification and denitrification rate were 149.77-1024.44 ng N g−1 h−1 and 48.32-145.01 ng N g−1 h−1, respectively. The absolute copy numbers of nitrogen functional genes and total bacterial 16S rRNA were 1.59×105-1.39×109 and 1.55×1010-2.55×1010copies g−1, respectively, with the dominant phyla, i.e., Proteobacteria, Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes. The relative abundances of the genera related to nitrification and denitrification, varied from 0.01% to 0.79% and from 0.01% to 15.54%, respectively. The potential nitrification rate was positively related to the sediment TOC concentration; and the potential denitrification rate had a positive correlation with sediment nitrate concentration. The genera Bacillus positively correlated with sediment NO3‐-N concentration, whereas Flavobacterium and Shewanella positively correlated with sediment NH4+-N concentration, which could be the functional bacteria for nitrogen removal. These findings may shed light on quantitative molecular mechanisms for nitrogen removal in zero-water exchange ponds, providing a sustainable solution to nitrogen pollution problem in the freshwater aquaculture ecosystems.

Metabolism characteristics of nitrogen functional microorganisms in bioretention system under multiple dry-wet alternation

In this study, we used metagenomic sequencing to explore the metabolism characteristics of nitrogen-cycling microorganisms in a bioretention system under multiple dry-wet alternation conditions. The results revealed that different dry-wet alternation conditions affected the composition of nitrogen-cycling microbes in bioretention soil media (BSM). In addition, the metagenomic analyses showed a higher relative abundance of key denitrifiers (Proteobacteria and Actinobacteria) under constant periods than unordered period. Furthermore, there was increased expression of nitrification functional genes and decreased expression of denitrifying functional genes during the unordered period, leading to nitrate accumulation in BSM. Under the constant dry-wet conditions, a short dry period (5 d) was shown to be beneficial to the nitrate reduction process. However, there was a risk of nitrite accumulation, which could be improved by rewetting. Moreover, our data proved that the NADH production process was inhibited in unordered period, causing nitrate accumulating. In conclusion, this study revealed that the different dry-wet alternation conditions could drive the expression of nitrogen functional genes, thus affected the biological nitrogen metabolism in bioretention systems.

The layout measures of micro-sprinkler irrigation under plastic film regulate tomato soil bacterial community and root system.

The change in rhizosphere soil bacterial community and root system under new water-saving device is not clear. A completely randomized experimental design was used to explore the effects of different micropore group spacing (L1: 30 cm micropore group spacing, L2: 50 cm micropore group spacing) and capillary arrangement density (C1: one pipe for one row, C2: one pipe for two rows, C3: one pipe for three rows) on tomato rhizosphere soil bacteria community, roots and tomato yield under MSPF. The bacteria in tomato rhizosphere soil were sequenced by 16S rRNA gene amplicon metagenomic sequencing technology, the interaction of bacterial community, root system and yield in tomato rhizosphere soil was quantitatively described based on regression analysis. Results showed that L1 was not only beneficial to the development of tomato root morphology, but also promoted the ACE index of tomato soil bacterial community structure and the abundance of nitrogen and phosphorus metabolism functional genes. The yield and crop water use efficiency (WUE) of spring tomato and autumn tomato in L1 were about 14.15% and 11.27%, 12.64% and 10.35% higher than those in L2. With the decrease of capillary arrangement density, the diversity of bacterial community structure in tomato rhizosphere soil decreased, and the abundance of nitrogen and phosphorus metabolism functional genes of soil bacteria also decreased. The small abundance of soil bacterial functional genes limited the absorption of soil nutrients by tomato roots and roots morphological development. The yield and crop water use efficiency of spring and autumn tomato in C2 were significantly higher than those in C3 about 34.76% and 15.23%, 31.94% and 13.91%, respectively. The positive interaction between soil bacterial community and root morphological development of tomato was promoted by the capillary layout measures of MSPF. The L1C2 treatment had a stable bacterial community structure and good root morphological development, which positively promoted the increase of tomato yield. The interaction between soil microorganisms and roots of tomato was regulated by optimizing the layout measures of MSPF to provide data support for water-saving and yield-increasing of tomato in Northwest China.

Agricultural practice negatively affects soil bacterial diversity and nitrogen functional genes comparing to adjacent native forest soils

Soil bacterial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from forest, transition, to crop soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on the bacterial 16S rRNA gene was performed for bacterial diversity and community analyses. Nitrifying and denitrifying functional genes (amoA and nirK respectively) of bacteria were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences was significantly different between crop and forest soils (p < 0.01) as well as between crop and transition soils (p = 0.01), however, there was no significant difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial relative abundance, richness, and Shannon diversity. Soil pH and nitrate contents together contributed highest to the observed different bacterial communities (Correlations = 0.381). Two operational taxonomic units (OTUs) belonging to Acidobacteriales species (OTU5, OTU8) decreased in crop soils, however, agricultural practices significantly increased an OTU of Nitrobacteraceae (OTU4). The relative abundance of ammonia-oxidizing bacteria (AOB) amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed, and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Soil pH and organic contents together contributed highest to the observed different nirK communities (Correlations = 0.443). Anthropogenic effects through agricultural practices decreased bacterial richness and Shannon diversity, increased abundance of nitrifying bacteria, and decreased diversity of denitrifying bacteria, potentially affecting the N cycling processes for healthy soils, plant productivity, and water and air quality.

Significant changes in soil microbial community structure and metabolic function after Mikania micrantha invasion

Currently, Mikania micrantha (M. micrantha) has invaded Guangdong, Guangxi and other provinces in China, causing serious harm to the forests of southeastern China. Soil microorganisms play an important role in the establishment of M. micrantha invasion, affecting plant productivity, community dynamics, and ecosystem function. However, at present, how M. micrantha invasion affects soil carbon, nitrogen, and phosphorus phase functional genes and the environmental factors that cause gene expression changes remain unclear, especially in subtropical forest ecosystems. This study was conducted in Xiangtoushan National Forest Park in Guangdong Province to compare the changes in soil nutrients and microorganisms after M. micrantha invasion of a forest. The microbial community composition and metabolic function were explored by metagenome sequencing. Our results showed that after M. micrantha invasion, the soil was more suitable for the growth of gram-positive bacteria (Gemmatimonadetes). In addition, the soil microbial community structure and enzyme activity increased significantly after M. micrantha invasion. Correlation analysis and Mantel test results suggested that total phosphorus (TP), nitrate nitrogen (NO3–-N), and soil dissolved organic matter (DOM; DOC and DON), were the strong correlates of soil microbial nitrogen functional genes, while soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), and available phosphorus (Soil-AP) were strongly correlated with the expression of soil microbial phosphorus functional gene. Mikania micrantha invasion alters soil nutrients, microbial community composition and metabolic function in subtropical forests, creates a more favorable growth environment, and may form a positive feedback process conducive to M. micrantha invasion.

Continuous-cropping-tolerant soybean cultivars alleviate continuous cropping obstacles by improving structure and function of rhizosphere microorganisms.

Soybean continuous cropping will change soil microorganisms and cause continuous cropping obstacles, resulting in a significant yield decline. Different soybean cultivars have different tolerances to continuous cropping, but the relationship between continuous cropping tolerance and soil microorganisms is not clear. Two soybean cultivars with different tolerances to continuous cropping were used to study the effects of continuous cropping on soil physical and chemical properties, nitrogen and phosphorus cyclic enzyme activities, rhizosphere soil microbial community and function. The results showed that the yield reduction rate of a continuous-cropping-tolerant cultivar (L14) was lower than that of a continuous-cropping-sensitive cultivar (L10) under continuous cropping. At R1 and R6 growth stages, soil nutrient content (NH4 +-N, NO3 --N, AP, DOM, TK, and pH), nitrogen cycling enzyme (URE, NAG, LAP) activities, phosphorus cycling enzyme (ALP, NPA, ACP) activities, copy numbers of nitrogen functional genes (AOA, AOB, nirK, nirK) and phosphorus functional genes (phoA, phoB) in L14 were higher than those in L10. Soybean cultivar was an important factor affecting the structure and functional structure of bacterial community under continuous cropping. The relative abundances of Proteobacteria, Bacteroidota, Acidobacteriota and Verrucomicrobiota with L14 were significantly higher than those of L10. The complexity of the soil bacterial community co-occurrence network in L14 was higher than that in L10. The continuous-cropping-tolerant soybean cultivar recruited more beneficial bacteria, changed the structure and function of microbial community, improved soil nitrogen and phosphorus cycling, and reduced the impact of continuous cropping obstacles on grain yield.

氮磷添加对草甸草原土壤氮磷转化功能基因丰度的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 氮磷添加对草甸草原土壤氮磷转化功能基因丰度的影响 DOI: 10.5846/stxb202112093495 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（31772653，31861143001） Responses of soil nitrogen and phosphorus transformation functional genes abundances to nitrogen and/or phosphorus additions in a meadow steppe Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:氮添加是提高退化草地生产力的主要养分管理措施，而过量的氮输入会导致土壤酸化、增加硝酸盐淋溶损失和温室气体排放。旨在明确草原割草利用下土壤氮、磷转化功能基因丰度对氮磷添加的响应规律，为定向调控打草场土壤氮、磷转化过程，提高养分利用效率，减少温室气体N2O排放提供科学依据。2018-2020年在呼伦贝尔草甸草原打草场设置了5个施氮水平（0、1.55、4.65、13.95、27.9 g N m-2 a-1）和3个磷水平（0、5.24、10.48 g P m-2 a-1），裂区试验设计，在植物不同生长时期测定土壤氨氧化（amoA-AOA和amoA-AOB）、反硝化（narG、nirK、nirS和nosZ）和磷转化（phoD）基因丰度。结果表明，土壤氮转化基因丰度受到氮、磷添加的调控，而氮、磷添加对土壤磷转化功能基因丰度无显著影响（P>0.05）。氮添加可提高amoA-AOB基因丰度，增加氨氧化细菌调控土壤总硝化速率的相对重要性，因此能增加硝酸盐淋溶损失潜势。高氮处理下添加磷可降低amoA-AOB基因丰度，降低硝酸盐淋溶损失潜势。反硝化基因nirK和nosZ的丰度受植物生长季节的影响，氮添加仅对8月份nirK和nosZ基因丰度有显著的促进作用，增加气态氮损失潜势。土壤氮的过量输入可在一定程度促进土壤氨氧化和反硝化进程，增加硝酸盐淋溶和气态氮损失的风险。磷添加可能会在一定程度上降低土壤硝酸盐淋溶损失的风险，对提高氮的利用效率具有重要作用。 Abstract:Nitrogen (N) addition is a primary nutrient management practice to improve the productivity of degraded grasslands. Excessive N input leads to soil acidification, the increase of nitrate leaching loss and greenhouse gas emissions. This study aims to understand the response characteristics of the abundances of soil N and phosphorus (P) transformation functional genes to nitrogen and phosphorus additions, and provide reference for directionally regulating the transformation process of soil nitrogen and phosphorus, improving nutrient utilization efficiency, and reducing greenhouse gas N2O emissions in grassland which is used mostly for haymaking. We conducted a spit-plot experiment of nutrient additions that included five N levels (0, 1.55, 4.65, 13.95, 27.9 g N m-2 a-1) and three P levels (0, 5.24, 10.48 g P m-2 a-1) and their interactions in Hulunber meadow steppe for three years (2018-2020). The abundance of genes involved in soil ammonium oxidation (amoA-AOA and amoA-AOB), denitrification (narG, nirK, nirS and nosZ) and organophosphate transformation (phoD) processes at different growth stages of plants were determined. The abundances of soil N-cycle genes were regulated by N and P additions, while the abundances of soil organophosphate transformation gene maintained constant in response to N and P additions. N addition increased the abundance of amoA-AOB and increased the relative importance of ammonia oxidizing bacteria in regulating soil nitrification rate, resulting in increasing the potential of nitrate leaching loss. P addition reduced the abundance of amoA-AOB under high N treatments, thereby decreased the potential of nitrate leaching loss. The abundance of denitrification genes (nirK and nosZ) in response to N addition varied with plant growth seasons. N addition significantly promoted the abundance of nirK and nosZ in August, thereby increasing gaseous N loss potential. Excessive N input might promote the process of soil ammonia oxidation and denitrification, and increase the potential of nitrate leaching loss and gaseous N loss. P addition may reduce the potential of nitrate leaching loss and play a potential role in improving N utilization efficiency. 参考文献 相似文献 引证文献

Nitrogen loss, nitrogen functional genes, and humification as affected by hydrochar addition during chicken manure composting

This study investigated the effect of hydrochar addition on nitrogen (N) transformation, N functional genes, and humification during chicken manure composting. The addition of 10 % hydrochar reduced cumulative ammonia (NH3) and nitrous oxide emissions by 55.24 % and 45.30 %, respectively, and N losses by 32.07 %. Further, it increased the relative abundance of amoA while decreasing that of nirK, nirS, and nosZ in compost. Hydrochar reduces NH3 emissions during composting owing to its acid–carbon properties that lower the pH of the composting pile and promote ammonia oxidation. Moreover, hydrochar addition enhances the humification of the composting pile and significantly increases the content of humic substances. Moreover, after hydrochar addition, the germination index of the compost product reached >80 % 10 days earlier. The results demonstrate that hydrochar is a suitable composting additive for reducing N loss and shortening the composting time.

Community characteristics and functional gene response analysis of phosphorus-metabolizing bacteria in plateau saline lake sediments

Microbial phosphorus metabolism in sediments and the biogeochemical cycling of phosphorus have been central issues in lake ecosystems, but the analysis of microbial community characteristics and influential factors of phosphorus metabolic processes in sediments from highland saline lakes have not been well documented. In this study, metagenome sequencing technology was used to analyze the diversity of community characteristics and the relationship between nitrogen and phosphorus functional genes of microorganisms involved in phosphorus metabolic processes in Daihai sediments under high saline conditions, as well as the response of microorganisms involved in phosphorus metabolic processes to changes in environmental factors, including salinity, pH, and the N/P ratio. The results showed that 1) salinity had positive correlations with Bacteroidetes involved in the major metabolic pathways (ko00030, ko00562, and ko00190) and positively correlated with the specific dominant bacteria involved in the minor pathways (ko00564 and ko00440); 2) norB and nirS denitrification genes were involved in a major component of phosphorus metabolism, and these functional genes of nitrogen metabolism had significant (p &amp;lt; 0.05) effects on phytate hydrolysis, phosphate hydrolysis, and polyphosphate synthesis and decomposition; and 3) environmental factors influenced the diversity of the bacterial community characteristics in the order of salinity &amp;gt; N/P ratio &amp;gt; pH. This study provides new insights into the analysis of the causes of eutrophication and the current state of imbalance in the hydroecological structure of saline lakes on plateaus, as well as an indication of the interactions between the global lake nitrogen and phosphorus cycles.

Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition.

Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.

Nitrogen removal performance and microbiological characteristics for the landfill leachate treatment in a three-stage vertical flow constructed wetlands system

Landfill leachate (LL) has the characteristics of high NH 4 + -N and low C/N ratio, increasing the cost and difficulty of efficient treatment. Constructed wetlands system (CWs) has proven to be feasible for the treatment of LL. A constructed three-stage series of vertical flow CWs (termed CW1, CW2, and CW3) based on effluent recirculation (T-VF) was used to treat LL, and nitrogen removal effect and microbiological characteristics was investigated. The results show that the nitrogen removal efficiency showed a increased trend from CW1 to CW3. The average removal efficiencies of TN, NH 3 + -N, and NO 3 − -N in T-VF were 91.43%, 94.19%, and 98.11%, respectively, which showed good nitrogen removal performance. Furthermore, application of the combined CW1, CW2 and CW3 increased diversity of substrate bacterial communities and decreased the relative abundances of the dominant nitrifying(e.g. Nitrosomonas , Nitrobacter ) and heterotrophic denitrifying bacteria (e.g. Thauera ). The relative abundances of autotrophic denitrification (e.g. Thiobacillus ) increased. Pathway of nitrogen metabolism and functional genes analysis showed that the abundance of enzymes associated with the denitrification and dissimilatory nitrate reduction increased and that the abundance of enzymes associated with the nitrification decreased. Application of the combined CW1, CW2 and CW3 could be respectively formed corresponding nitrogen removal microbial community, influent quality and pathways of nitrogen to enhance the nitrogen removal effect of T-VF to treat LL. • The removal rate of nitrogen was over 90% in vertical flow constructed wetlands. • Nitrosomonas and Nitrobacter were the dominant nitrification bacteria. • Denitrifying bacteria Thauera , Thiobacillus , and Lautropia predominated.

Characteristics of carbon, nitrogen, phosphorus and sulfur cycling genes, microbial community metabolism and key influencing factors during composting process supplemented with biochar and biogas residue

Carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling functional genes and bacterial and fungal communities during composting with biochar and biogas residue amendments were studied. Correlations between microbial community structure, functional genes and physicochemical properties were investigated by network analysis and redundancy analysis. It was shown that the gene of acsA abundance accounted for about 50% of the C-related genes. Biogas residue significantly decreased the abundance of denitrification gene nirK. Biogas residues can better promote the diversity of bacteria and fungi during composting. Biochar significantly increased the abundance of Humicola. Redundancy analysis indicated that pile temperature, pH, EC were the main physicochemical factors affecting the microbial community. WSC and NO3−-N have significant correlation with C, N, P, S functional genes. The research provides a theoretical basis for clarifying the metabolic characteristics of microbial communities during composting and for the application of biochar and biogas residues in composting.

Mechanisms underlying the succession of plant rhizosphere microbial community structure and function in an alpine open-pit coal mining disturbance zone

Elucidating the responses and potential functions of soil microbial communities during succession is important for understanding biogeochemical processes and the sustainable development of plant communities after environmental disturbances. However, studies of such dynamics during post-mining ecological restoration in alpine areas remain poorly understood. Microbial diversity, nitrogen, and phosphorus cycle functional gene potential in the Heishan mining area of Northwest China was studied, including primitive succession, secondary succession, and artificial succession disturbed by mining. The results revealed that: (1) The dominant bacteria in both categories (non-remediated and ecologically restored) of mining area rhizosphere soil were Proteobacteria, adopting the r strategy, whereas in naturally occurring soil outside the mining area, the dominant bacteria were actinomycetes and Acidobacteria, adopting the k strategy. Notably, mining perturbation significantly reduced the relative abundance of archaea. (2) After restoration, more bacterial network node connections were observed in mining areas than were originally present, whereas the archaeal network showed the opposite trend. (3) The networks of microbial genes related to nitrogen and phosphorus cycle potential differed significantly, depending on the succession type. Namely, prior to restoration, there were more phosphorus related functional gene network connections; these were also more strongly correlated, and the network was more aggregated. (4) Soil factors such as pH and NO3–N affected both the mining area remediation soil and the soil outside the mining area, but did not affect the soil of the original vegetation in the mining area. The changes in the structure and function of plant rhizosphere microorganisms after mining disturbance can provide a theoretical basis for the natural restoration of mining areas.

Hydrochar amendments stimulate soil nitrous oxide emission by increasing production of hydroxyl radicals and shifting nitrogen functional genesin the short term: A culture experiment.

The application of waste biomass-derived hydrochar to soil may cause extremely intensive nitrous oxide (N2O) fluxes that can challenge our current mechanistic understanding of the global nitrogen cycle in the biosphere. In this study, two waste biomasses were used to prepare cyanobacterial biomas-derived hydrochar (CHC) and wheat straw-derived hydrochar (SHC) for short-term incubation experiments to identify their effects and mechanisms of waste biomass-derived hydrochar on soil N2O efflux, with time-series samples collected for N2O efflux and soil analysis. The results showed that CHC and SHC caused short-term bursts of N2O effluxes without nitrogen inputs. Moreover, the enrichment of exogenous organics and nutrients at the hydrochar-soil interface was identified as the key factor for enhancing N2O fluxes, which stimulated microbial nitrification (i.e., increased gene copy number of ammonia oxidizing bacteria) and denitrification (i.e., increased gene copy number of nitrate and N2O reducing bacteria) processes. The concentrations of Fe (II) and hydroxyl radicals (HO•) were 6.49 and 5.63 times higher, respectively, in the hydrochar layer of CHC than SHC amendment. Furthermore, structural equation models demonstrated that HO•, as well as soil microbiomes, played an important role in driving N2O fluxes. Together, our findings provide a deeper insight into the assessment and prognosis of the short-term environmental risk arising from agricultural waste management in integrated agriculture. Further studies under practical field application conditions are warranted to verify the findings.

Soil nitrogen functional transformation microbial genes response to biochar application in different irrigation paddy field in southern China.

Growing evidence points to the controlled irrigation (CI) and biochar application (BA) having agricultural economic value and ecological benefits, but their synergistic effect and microbial mechanism of nitrogen conversion remain unknown in paddy fields. The effects of different BA (0, 20, 40 t/hm2) on the soil nitrogen functional transformation microbial genes (nifH, AOA-amoA, AOB-amoA) in different irrigation (CI, flooding irrigation) were clarified. After one seasonal growth of paddy, the correlation between the abundance of functional genes OUT and soil nitrogen transformation environment factors during the typical growth period was analyzed. High-throughput sequencing results illustrated that the application of CC (40 t/hm2 biochar) increased the nifH genes bacterial community abundance; the abundance of dominant microorganism increased by 79.68~86.19%. Because biochar can potentially control the rates of N cycling in soil systems by adsorbing ammonia and increasing NH4+ storage, it increased soil NH4+-N and NO3--N content by 60.77% and 26.14%, improving microbial nitrogen fixation. Rare species Nitrosopumilus, Nitrosococcus, and Methylocystis appeared in biochar treatments group, which increased the diversity of microbial in paddy. The combined use of CI and BA affected soil inorganic nitrogen content, temperature (T), pH, Eh, etc., which affected urease, urea hydrolysis, and nitrogen functional transformation microorganism genes. Correlation analysis shows that soil NH4+-N, T, and Eh, respectively, are significant factors for the formation of nifH, AOA-amoA, and AOB-amoA soil bacterial communities, respectively. This study suggests that to maintain the biodiversity of soil and realize the sustainable development of rice cultivation, CI is of great importance in combination with BA.

Molecular analysis of microbial nitrogen transformation and removal potential in the plant rhizosphere of artificial tidal wetlands across salinity gradients

This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0–30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 103–9.12 × 108 (nitrogen functional genes) and 1.24 × 108–8.43 × 109 copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23–9.23, 400.03–755.91, 3.12–35.24 and 30.51–300.04 nmolN2·g−1·d−1, respectively. The denitrification process contributed to 73.59–88.65% of NOx− reduction, compared to 0.71–13.20% and 8.20–15.42% via DNRA and anammox, as 83.83–90.74% of N2 production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28–99.23% of NH4+ oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.

Nitrogen process in stormwater bioretention: effect of the antecedent dry days on the relative abundance of nitrogen functional genes.

In this study, we evaluated the relative abundance of nitrogen functional genes (amoA, nirK and nirS) involved in ammonia oxidation and denitrification bacteria in laboratory-scale bioretention columns in response to environmental factors (e.g., moisture content, pH, soil organic matter, soil nitrogen) under different antecedent dry days (ADDs). We observed a decrease tendency of the relative abundance of ammonia-oxidizing bacteria at first and then increased when increasing ADDs from 1 to 22 day, while the relative abundance of denitrifying bacteria showed a downward trend. The abundance of bacteria gene amoA was positively associated with soil ammonia nitrogen concentration (r2 = 0.389, p < 0.05) and soil organic matter concentration (r2 = 0.334, p < 0.05), while the abundance of bacteria gene nirS was positively correlated with soil ammonia nitrogen (r2 = 0.730, p < 0.01), soil organic matter (r2 = 0.901, p < 0.01) and soil total nitrogen (r2 = 0.779, p < 0.01). Furthermore, gene counts for bacteria gene nirS were correlated negatively with plant root length (r2 = 0.364, p < 0.05) and plant biomass (r2 = 0.381, p < 0.05). Taken together, these results suggest that both nitrification and denitrification can occur in bioretention systems, which can be affected by environmental factors.

Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale.

Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.

Effects of pyroxsulam on soil enzyme activity, nitrogen and carbon cycle-related gene expression, and bacterial community structure

Pyroxsulam is a new herbicide which is being widely used to prevent the growth of broad-leaved weeds in wheat fields because of its low quantity of application and high efficiency. However, its ecotoxic effects on soil microorganisms have yet to be clarified. In the present study, the effects of pyroxsulam on soil enzymes, nitrogen and carbon cycle functional genes, and bacterial community structure in the soil were investigated. The effect of pyroxsulam on urease and dehydrogenase activities was not obvious at the end of the experiment (56 d), but β-glucoside activity was consistently promoted. At the enzyme level, the effect of different concentrations of pyroxsulam on soil enzymes was within an acceptable range. Functional gene expression analysis indicated that the expression of the nitrogen-fixing gene (nifH), nitrifying gene (amoA), and carbon fixation gene (cbbL) was inhibited by three different doses of pyroxsulam, and the inhibition was most effective at 2.5 mg kg−1. Therefore, the 2.5 mg kg−1 pyroxsulam dose had adverse effects on functional genes, and application should be controlled. Combined with the results of soil bacterial community structure analysis, we concluded that pyroxsulam inhibited soil nitrogen fixation, nitrification, and carbon dioxide fixation and promoted soil denitrification. In addition, pyroxsulam increased the abundance of beneficial bacteria with the ability to inhibit the spread of soil diseases and degrade organic pollutants. According to the integrated biomarker response calculations, the green-like cbbL gene was the most sensitive indicator of pyroxsulam toxicity. A high concentration of pyroxsulam may have a negative impact on soil microorganisms in different aspects and dosage should therefore be carefully considered.

Long-term nitrogen and phosphorus removal, shifts of functional bacteria and fate of resistance genes in bioretention systems under sulfamethoxazole stress

To understand the long-term performance of bioretention systems under sulfamethoxazole (SMX) stress, an unplanted bioretention system (BRS) and two modified BRSs with coconut-shell activated carbon (CAC) and CAC/zero-valent-iron (Fe0) granules (CAC-BRS and Fe/CAC-BRS) were established. Both CAC-BRS and Fe/CAC-BRS significantly outperformed BRS in removing total nitrogen (TN) (CAC-BRS: 82.48%; Fe/CAC-BRS: 78.08%; BRS: 47.51%), total phosphorous (TP) (CAC-BRS: 79.36%; Fe/CAC-BRS: 98.26%; BRS: 41.99%), and SMX (CAC-BRS: 99.74%, Fe/CAC-BRS: 99.80%; BRS: 23.05%) under the long-term SMX exposure (0.8 mg/L, 205 days). High-throughput sequencing revealed that the microbial community structures of the three BRSs shifted greatly in upper zones after SMX exposure. Key functional genera, dominantly Nitrospira, Rhodoplanes, Desulfomicrobium, Geobacter, were identified by combining the functional prediction by the FAPROTAX database with the dominant genera. The higher abundance of nitrogen functional genes (nirK, nirS and nosZ) in CAC-BRS and Fe/CAC-BRS might explain the more efficient TN removal in these two systems. Furthermore, the relative abundance of antibiotic-resistant genes (ARGs) sulI and sulII increased in all BRSs along with SMX exposure, suggesting the selection of bacteria containing sul genes. Substrates tended to become reservoirs of sul genes. Also, co-occurrence network analysis revealed distinct potential host genera of ARGs between upper and lower zones. Notably, Fe/CAC-BRS succeeded to reduce the effluent sul genes by 1-2 orders of magnitude, followed by CAC-BRS after 205-day exposure. This study demonstrated that substrate modification was crucial to maintain highly efficient nutrients and SMX removals, and ultimately extend the service life of BRSs in treating SMX wastewater.