N-cycling Genes Research Articles

The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere.

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

The effects of crude oil on microbial nitrogen cycling in coastal sediments

Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.

Impacts of directed evolution and soil management legacy on the maize rhizobiome

Domestication and agricultural intensification dramatically altered maize and its cultivation environment. Changes in maize genetics (G) and environmental (E) conditions increased productivity under high-synthetic-input conditions. However, novel selective pressures on the rhizobiome may have incurred undesirable tradeoffs in organic agroecosystems, where plants obtain nutrients via microbially mediated processes including mineralization of organic matter. Using twelve maize genotypes representing an evolutionary transect (teosintes, landraces, inbred parents of modern elite germplasm, and modern hybrids) and two agricultural soils with contrasting long-term management, we integrated analyses of rhizobiome community structure, potential microbe-microbe interactions, and N-cycling functional genes to better understand the impacts of maize evolution and soil management legacy on rhizobiome recruitment.We show complex shifts in rhizobiome communities during directed evolution of maize (defined as the transition from teosinte to modern hybrids), with a larger effect of domestication (teosinte to landraces) than modern breeding (inbreds to hybrids) on rhizobiome structure and greater impacts of modern breeding on potential microbe-microbe interactions. Rhizobiome structure was significantly correlated with plant nutrient composition. Furthermore, plant biomass and nutrient content were affected by G x E interactions in which teosinte and landrace genotypes had better relative performance in the organic legacy soil than inbred and modern genotypes. The abundance of six N-cycling genes of relevance for plant nutrition and N loss pathways did not significantly differ between teosinte and modern rhizospheres in either soil management legacy. These results provide insight into the potential for improving maize adaptation to organic systems and contribute to interdisciplinary efforts toward developing resource-efficient, biologically based agroecosystems.

Wastewater treatment plant upgrade induces the receiving river retaining bioavailable nitrogen sources

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Impact of Irrigation Strategies on Tomato Root Distribution and Rhizosphere Processes in an Organic System.

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root–soil–microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem

Riparian buffer systems (RBS) are considered a best management practice (BMP) in agricultural landscapes to intercept soil nitrogen (N) and phosphorus (P) leaching and surface runoff into aquatic ecosystems. However, these environmental benefits could be offset by increased greenhouse gas (GHG) emissions, including nitrous oxide (N2O). The main sources of N2O in soil are linked to processes which are mediated by soil microbial communities. These microorganisms play crucial roles in N-cycling and in the reduction of nitrate to N2, and N2O gases. This study was conducted to determine the abundance and diversity of microbial communities and functional genes associated with N-cycling and their influence on N2O emissions in different riparian land-use: undisturbed natural forest (UNF), rehabilitated site (RH), grass buffer (GRB), and an adjacent agricultural land (AGR). Soil was sampled concurrently with N2O emissions on July 13, 2017. DNA was extracted and used to target key N-cycling genes for N-fixation (nifH), nitrification: (amoA), and denitrification (nirS, nirK, and nosZ) via quantitative PCR, and for high throughput sequencing of total bacterial and fungal communities. Non-metric multidimensional scaling (NMDS) was used to examine microbial community composition and indicated significant differences in bacterial (p < 0.001) and fungal (p < 0.0085) communities between sites. Bacterial abundance differed significantly (p = 0.0005) between RBS and AGR sites with the highest populations occurring in the UNF (2.1 × 1010 copies g−1 dry soil), and lowest in AGR (5.3 × 109 copies g−1 dry soil). However, the AGR site had the highest ammonia-oxidizing bacteria (AOB) abundance, indicating that nitrification is highest at this site. The abundance of the nosZ gene was highest in RH and GRB demonstrating the capacity for complete denitrification at these sites, lowering measured N2O. These results suggest N-cycling microbial community dynamics differ among RBS and are influencing N2O emissions in the sites investigated.

Response of bacterial communities and plant-mediated soil processes to nitrogen deposition and precipitation in a desert steppe

Changes in nitrogen (N) and precipitation levels can substantially alter soil properties and plant growth, thereby altering soil microbial diversity and functionality. We used manipulated precipitation treatments (50% reduction, control, and plus 50%) and tested two N fertilization levels (control and plus 35 kg N ha−1 yr−1) from a 4-year field experiment to evaluate the effects on soil bacterial diversity, community composition, and N-cycle gene abundance. N additions significantly increased ammonia-oxidizing bacterial abundance (via AOB-amoA) but decreased denitrification genes (i.e., nirS and nosZ). Decreased precipitation significantly decreased the abundance of N-cycle genes (AOB-amoA, nirS, and nosZ), while increased precipitation conversely increased the abundance of these same genes. Decreased precipitation led to differences in the microbial community composition that favored drought resistance, indicating that plant-associated microbiomes may be able to modulate plant growth fitness in the context of extreme environmental conditions. N additions substantially altered soil bacterial communities, increasing the relative abundance of certain bacteria and of nitrification-related genes in a manner that depended on precipitation fluctuations. Differences in the bacterial community composition and N-cycle genes determined the functional response of a grassland ecosystem to decreased precipitation conditions, and therefore could affect the influence of N deposition on plant growth as well as the physical and chemical properties of the soil.

Release of plant nutrients and changes in N-Cycling genes in response to soil amendment with rice straw and waste from a food seasoning industry

Release of plant nutrients and changes in N-Cycling genes in response to soil amendment with rice straw and waste from a food seasoning industry

Release of plant nutrients and changes in the copies of N-cycling genes in response to soil amendment with rice straw and waste from a food seasoning industry

Release of plant nutrients and changes in the copies of N-cycling genes in response to soil amendment with rice straw and waste from a food seasoning industry

Short-term response of soil N-cycling genes and transcripts to fertilization with nitrification and urease inhibitors, and relationship with field-scale N2O emissions

In agroecosystems, efficient fertilizer use is key to optimizing productivity and reducing nutrient losses that can be detrimental for the environment, such as nitrous oxide (N2O) emissions. Because microbial communities regulate nitrogen (N) fate in soils, some agrochemicals inhibit specific transformations to reduce N losses. Our study aimed to describe short-term dynamics of N-cycling genes and transcripts and N2O emissions after fertilization with urea-ammonium nitrate (UAN) with or without the addition of nitrification plus urease inhibitors (NUI). The experiment consisted of 4-ha corn plots located in SE Ontario, Canada, where field-scale N2O emissions were monitored continuously using micro-meteorological techniques. Soil samples (0–10 cm) were taken 10 days before (baseline) and 2, 6, 9, 13 and 16 days after fertilization, and immediately flash-frozen. We co-extracted DNA and RNA and, using real-time PCR, quantified genes/transcripts targeting total bacteria (16S rRNA) and key N-cycling groups: ureolytic (ureC), ammonia-oxidizers (bacterial/archaeal amoA), nitrite-reducers (nirK/nirS) and N2O-reducers (clade I/II nosZ). The addition of NUI did not prevent an N2O flux event but reduced its duration and magnitude by more than 50%, and net cumulative N2O emissions for the sampling period by ~68%. NUI effects on N-cycling microorganisms were evident on day 9, as a transient reduction (40–56%) of ammonia-oxidizers and denitrifiers. Changes in transcripts were minor and only detectable on ureC (day 2), nirS and clade II nosZ (day 9). NUI did not interfere with temporal fluctuations in nirK and nirS, but it differentially affected nosZ response to a later rainfall event. Unexpectedly, N2O emissions were negatively associated with the ratio between nitrite-reducers and N2O-reducers. NUI effects on N-cycling microorganisms were minor and transient but resulted in a field-scale reduction in N2O emissions, possibly due to a combination of environmental factors and legacy effects from previous years of treatment.

Effects of urease and nitrification inhibitors on soil N, nitrifier abundance and activity in a sandy loam soil

Inhibitors of urease and ammonia monooxygenase can limit the rate of conversion of urea to ammonia and ammonia to nitrate, respectively, potentially improving N fertilizer use efficiency and reducing gaseous losses. Winter wheat grown on a sandy soil in the UK was treated with urea fertilizer with the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT), the nitrification inhibitor dicyandiamide (DCD) or a combination of both. The effects on soil microbial community diversity, the abundance of genes involved in nitrification and crop yields and net N recovery were compared. The only significant effect on N-cycle genes was a transient reduction in bacterial ammonia monooxygenase abundance following DCD application. However, overall crop yields and net N recovery were significantly lower in the urea treatments compared with an equivalent application of ammonium nitrate fertilizer, and significantly less for urea with DCD than the other urea treatments.

Ecoenzymatic stoichiometry reveals microbial phosphorus limitation decreases the nitrogen cycling potential of soils in semi-arid agricultural ecosystems

Variations in soil microbial metabolism currently represent one of the greatest areas of uncertainty with regard to soil nutrient cycles and the control of terrestrial carbon (C) and nitrogen (N) loss and are poorly understood in agricultural ecosystems with intensive farming practices. In this study, extracellular enzymatic stoichiometry models and quantitative PCR techniques were used to examine microbial metabolic limitation and its relationship with N-cycling gene expression in semi-arid agricultural ecosystems considering four N fertilization levels (N 0, N 100, N 250, and N 400 kg N ha−1) and two agronomic strategies (film mulching and no mulching). Film mulching increased microbial C limitation (reflecting microbial C metabolism size; 0.189 of the total effects), while very small effects on microbial phosphorus (P) limitation were observed (-0.007 of the total effects). N fertilization increased the microbial demand for P (microbial P limitation; 0.504 of the total effects). Increased microbial C metabolism was mainly attributed to increased soil moisture content after film mulching, which enhanced microbial decomposition of organic C (high C-acquiring enzyme activities). Changes in nutrient stoichiometry and the increase in N availability due to N fertilization were largely responsible for increased microbial P limitation. Furthermore, microbial P limitation negatively affected the abundance of AOA amoA, AOB amoA (involved in nitrification), nirK, nirS, nosZ (involved in denitrification) genes, strongly inhibiting nitrification and denitrification potential (-0.743 and -0.761 of the total effects, respectively). The present results suggest that agricultural ecosystems with film mulching are conducive to organic residue decomposition, while appropriate P limitation under N fertilization could reduce the loss of N due to nitrification and denitrification in soil. This study highlights the importance of elemental stoichiometry-driven microbial metabolic variation in understanding soil nutrient cycles and optimizing agricultural practices.

Access mats partially mitigate direct traffic impacts on soil microbial communities in temperate grasslands

Significant areas of the mixedgrass prairie (MGP) in Alberta have experienced heavy equipment traffic due to industrial infrastructure development, which may change edaphic conditions that influence soil microbial communities. Direct wheeled traffic effects may be alleviated by using access mats that spread traffic impacts over a larger area; however, no scientific assessments of access mat efficacy have been conducted on soil microbial responses. Our objectives were to assess soil properties and the diversity, community structure, and size of soil microbial communities, as impacted by wheeled traffic occurring with and without access mat use on grassland. Two representative sites with differing soil texture (sandy versus loamy) were selected from a set of MGP sites established at the University of Alberta Mattheis Research Ranch in SE Alberta, Canada. Treatments at each site included non-disturbed vegetation controls, areas affected by direct traffic, and grassland with access mats placed for 12 weeks with traffic applied. Soil was sampled in July 2015 (immediately after access mat/traffic treatments ended) and in 2016 (12 months after access mat/traffic treatments) from both sites. Soil DNA was extracted and used to target N-cycling genes via qPCR and for next-generation sequencing (Illumina Miseq) of bacterial, archaeal, and fungal communities. Direct wheeled traffic without access matting increased the size of the N2O-reducing community in the sandy soil and conversely deceased the size of this community in the loamy soil. Non-metric multidimensional scaling, perMANOVA, and indicator species analyses indicated a large effect of traffic without access mat use on fungal community structure, as well as distinct bacterial and fungal indicator OTUs associated with disturbed soils compared to control soils. Fungal community structure remained affected by traffic impacts 12 months later, highlighting the extended impacts of traffic on fungal communities. Access matting mitigated some of the impacts direct traffic had on fungal community structure, but in the loamy site increased soil N and decreased the size of the N2O-reducing bacterial community. The latter indicates that ecosystem functioning of these grasslands may not only be impacted by direct wheeled traffic but also by using matting as a mitigation technique.

The effect of biochar amendment on N-cycling genes in soils: A meta-analysis

Nitrogen (N) cycling by soil microbes can be estimated by quantifying the abundance of microbial functional genes (MFG) involved in N-transformation processes. In agro-ecosystems, biochars are regularly applied for increasing soil fertility and stability. In turn, it has been shown that biochar amendment can alter soil N cycling by altering MFG abundance and richness. However, the general patterns and mechanisms of how biochar amendment modifies N-cycling gene abundance have not been synthesized to date. Here, we addressed this knowledge gap by performing a meta-analysis of existing literatures up to 2019. We included five main marker genes involved in N cycling: nifH, amoA, nirK, nirS and nosZ. We found that biochar addition significantly increased the abundance of ammonia-oxidizing archaea (AOA), nirK, nirS and nosZ by an average of 25.3%, 32.0%, 14.6% and 17.0%, respectively. Particularly, biochar amendment increased the abundances of most N-cycling genes when soil pH changed from very acidic (pH < 5) to acidic (pH: 5.5–6.5). Experimental conditions, cover plants, biochar pyrolysis temperature and fertilizer application were also important factors regulating the response of most N-cycling genes to biochar amendment. Moreover, soil pH significantly correlated with ammonia-oxidizing bacteria (AOB) abundance, while we found that most genes involved in nitrification and denitrification were not significantly correlated with each other across studies. Our results contribute to developing quantitative models of microbially-mediated N-transforming processes in response to biochar addition, and stimulate research on how to use biochar amendment for reducing reactive N gas emissions and enhancing N bioavailability to crop plants in agro-ecosystems.

Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.

Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.

Defoliation management and grass growth habits modulated the soil microbial community of turfgrass systems.

Grass species selection and regular mowing are essential for maintaining aesthetic and environmentally sound turfgrass systems. However, their impacts on the soil microbial community, the driving force for soil N cycle and thus the environmental fate of N, are largely unknown. Here, the high throughput sequencing of 16S rRNA gene and internal transcribed spacer (ITS) region was used to evaluate how long-term defoliation management and grass growth habits (propagation types and photosynthetic pathways) modulated the soil microbial community. The investigation included three cool-season C3 grasses (creeping bentgrass, Kentucky bluegrass, and tall fescue) and three warm-season C4 grasses (bermudagrass, St. Augustinegrass, and zoysiagrass). Creeping bentgrass and bermudagrass were managed as putting greens with a lower mowing height; tall fescue spread in a tussock manner via tiller production whereas other grasses propagated in a creeping manner via rhizomes and/or stolons. Ordination analysis showed that both bacterial and fungal communities were primarily separated between putting green and non-putting green systems; and so were N-cycle gene relative abundances, with the putting greens being greater in N mineralization but lower in nitrification. Compared to warm-season grasses, cool-season grasses slightly and yet significantly enhanced the relative abundances of Chloroflexi, Verrucomicrobia, and Glomeromycota. Tall fescue yielded significantly greater bacterial and fungal richness than non-tussock grasses. As the main explanatory soil property, pH only contributed to < 18% of community compositional variations among turfgrass systems. Our results indicate that defoliation management was the main factor in shaping the soil microbial community and grass growth habits was secondary in modulating microbial taxon distribution.

Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil.

Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg−1 dry sediment day−1 during the period of 15–90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg−1 dry sediment day−1. The denitrification gene abundances of the N-cycling genes were 107-108 orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 105-106 orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Impacts of long term copper exposure on abundance of nitrogen cycling genes and denitrification activity in pasture soils

Soils are the main source of nitrous oxide (N2O) emissions, with 60–70% of global N2O production due to the enhanced denitrification activity with elevated nitrogen (N) availability associated with agricultural intensification. The amendment of agricultural soils with biosolids, the residual product of wastewater treatment, has been used for several decades as an inexpensive source of organic matter and N. Biosolids also contain elevated levels of trace elements such as copper (Cu), which influence the activity of the bacterial enzyme nitrous oxide reductase (N2OR). We extracted DNA from a pasture soil 20 years after application of biosolid and Cu salts and used an environmental genomics approach (GeoChip) to evaluate broad changes in the abundance and structure of families of N-cycling genes. We then focussed on abundances of individual bacterial genes involved in sequential N-reduction (nirS, nirK, and nosZ). There was no relationship between total soil Cu concentrations and the different N-cycling gene families (GeoChip; P > 0.1). However, increasing Zn was associated with decreased nitrification (amoA) and dissimilatory N-reduction (napA and nrfA) gene-family abundances (P < 0.1). When focused on individual bacterial denification pathway genes (qPCR), nosZ (nitrous oxide reductase) was found to be sensitive to Cu concentrations. Moreover, the activity of the Cu-dependent enzyme N2OR is potentially affected by historical Cu concentrations found in these pasture soils. The results highlight the sensitivity of a few key functional taxa (nosZ type denitrifying bacteria) to long-term Cu exposure in soil, and how these effects can translate into alteration of wider N-cycling processes such as those affecting net N2O emissions.

Urea fertilization decreases soil bacterial diversity, but improves microbial biomass, respiration, and N-cycling potential in a semiarid grassland

In this study, changes in plant diversity and aboveground biomass, soil chemical properties, microbial biomass and respiration, microbial composition, and microbial N-cycling potential (represented by the abundance of genes involved in N reaction) were studied after 3 years of urea fertilization (0, 25, 50, and 100 kg N ha−1 year−1) in a semiarid grassland in China. The microbial composition and N-cycling genes were determined using metagenome sequencing. Urea fertilization significantly decreased soil bacterial diversity, possibly through its negative effect on plant diversity, whereas it increased fungal diversity, and microbial biomass and respiration through enhancing aboveground biomass production with increases in the C input into the soil. However, above the threshold N rate of 50 kg N ha−1 year−1, microbial biomass and respiration decreased probably because of a strong N inhibitory effect on aboveground biomass. Further, urea fertilization increased the gene abundances of narH, nrfA, nirB, and napA, which are involved in dissimilatory nitrate reduction, and those of nifH and nifD, involved in N2 fixation, gdh, involved in organic N decomposition, and glnA, involved in glutamine synthesis and ureC. These findings suggested that urea addition has a positive effect on N-turnover potential. Burkholderiales and Rhizobiales play an important role in soil N cycling. Changes in plant community (diversity and biomass) were responsible for the shift in microbial diversity, biomass, and respiration, whereas alterations in inorganic N levels (exchangeable NH4+ and NO3−) potentially affected microbial N cycling. Our results show that N-mediated environmental stresses can play an important role in microbial diversity and functions, which appear to be mediated largely by plant–soil interactions.