Abundance Of Nitrogen Functional Genes Research Articles

Nitrogen removal performance and mechanisms of three aquatic plants for farmland tail water purification

Constructed wetlands (CWs) are commonly used to control excessive nitrogen from farmlands; however, the interactions between vegetation and microorganisms, nitrogen removal performance, and the mechanisms involved remain unclear in subtropical areas. This study aimed to investigate the nitrogen removal performance and mechanism of CWs containing Canna indica, Acorus calamus, and Thalia dealbata. The results show that CWs with plants had significantly higher nitrogen removal efficiencies than those without, with those planted with T. dealbata having the highest efficiency. T. dealbata performed better than the other two plants due to its high biomass and excellent nitrogen uptake capacity; more importantly, CWs with it had the highest abundance of nitrogen functional genes. Microbial nitrification-denitrification, the primary process of nitrogen removal in CWs, contributed to 88 %, 91 %, and 84 % of the TN removal in the CWs with C. indica, A. calamus, and T. dealbata, respectively, 29 %–158 % higher than that in CWs without plants. Microorganisms played a crucial role in nitrogen removal in the CWs, while plants significantly stimulated microbial activity by enhancing microbial abundance and creating a suitable environment for growth and metabolism. These results can help in understanding the contribution of plants in cleaning farmland tailwater and further optimization of plant configuration and management strategies in wetland ecosystems to improve nitrogen removal efficiency.

Response of rare and abundant rhizosphere microbial communities to inoculated rhizobium in cadmium-contaminated soil phytoremediation

Soil microorganisms play an important role in maintaining ecosystem balance and exerting ecological functions. The taxonomic and functional changes in rare and abundant communities during in bioremediation of cadmium-contaminated soils and their contributions to the remediation of ecosystem functions remain elusive despite the significance of rare and abundant microbial taxa in maintaining soil ecological function. Mesorhizobiumloti HZ76-inoculated seedlings of the Robinia pseudoacacia were used to create a symbiotic system. The effects of rhizobium inoculation on rare and abundant rhizosphere microbial populations were investigated in pot experiments. Despite having minimal effects on the α-diversity of rare and abundant microbial communities, inoculation altered microbial community composition and functional gene abundance. For example, abundant phyla such as Proteobacteria were enriched following inoculation, whereas rare phyla such as Ascomycota were depleted. After inoculation, the abundance of nifH gene increased, while the abundance of amoA, amoB, nirS, nirK and nosZ gene decreased. Rare bacterial populations were more susceptible to the inoculated rhizobium's environmental alterations. In rare communities compared to abundance communities, the α-diversity was higher. Stochastic processes predominated in the communities of uncommon and abundant microorganisms. Furthermore, keystone taxa, particularly rare bacterial taxa (Gemmatimonadaceae and Saprospiraceae) and rare fungal taxa (Ascomycota), more mediates nitrogen cycle processes and is directly associated to the abundance of nitrogen functional genes. Together, our findings demonstrate the different ways that rare and abundant microbial species react to rhizobia inoculation and their connections to the nitrogen cycle.

Soil N2O emissions and functional genes in response to grazing grassland with livestock: A meta-analysis

Livestock grazing affects nitrous oxide (N2O) emissions from grassland ecosystems by altering soil physical, chemical and biological properties. However, how soil N2O emissions related to nitrogen process rates and functional genes are unexplored. We compiled 83 published studies of soil N2O emissions, potential nitrification and denitrification rates, and the abundance of nitrogen functional genes to uncover their associations with varying intensities of livestock grazing. Compared to ungrazed condition, heavy and moderate grazing reduced N2O emissions by 22–25%, nitrification rate by 23–37%, and denitrification rate by 44–48%, respectively, while light grazing had no effect. Furthermore, moderate to heavy grazing intensities decreased the abundances of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) by 40–47%. Heavy grazing also simultaneously decreased ammonia-oxidizing archaea (AOA amoA) by 43%. Additionally, grazing significantly decreased the abundance of nitrate reductase (narG) and nitrite reductase (nirS) and by 28% and 35%, respectively, but did not affect the abundance of nitrous oxide reductase (nosZ). Overall, potential nitrification rate was positively correlated with AOB amoA and AOA amoA abundances. This global-scale assessment demonstrates that moderate to heavy livestock grazing can reduce grassland N2O emissions, and such reductions were linked to decreased abundances of amoA genes with decreasing soil moisture and inorganic N (NO3– and NH4+) availabilities. Considering that heavy grazing may increase the risk of grassland degradation, we recommend that livestock grazing at an appropriately moderate intensity is important for sustaining livestock production while contributing to greenhouse gas mitigation.

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.

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.

Comparative Microbial Nitrogen Functional Gene Abundances in the Topsoil vs. Subsoil of Three Grassland Habitats in Northern China.

The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers play vital roles in driving the nitrogen cycle in grassland ecosystems. However, the understanding of the abundance and distribution of these functional microorganisms as well as their driving factors were limited mainly to topsoil. In this study, the abundances of nitrogen functional genes (NFGs) involved in nitrogen fixation (nifH), ammonia oxidation (amoA), and denitrification (nirK, nirS, and nosZ) were investigated in both topsoil (0–10 cm, soil layer with concentrated root) and subsoil (30–40 cm, soil layer with spare root) of three grassland habitats in northern China. The abundance of NFGs decreased with soil depth except for the archaeal amoA gene and the distribution of nifH, archaeal amoA, nirK, and nirS gene was significantly impacted by grassland habitats. Moreover, the distribution of NFGs was more responsive to the vertical difference than horizontal spatial heterogeneity. Redundancy analysis revealed that the distribution pattern of overall NFGs was regulated by grassland habitats, and these regulations were more obvious in the subsoil than in the topsoil. Variance partitioning analysis further indicated that soil resource supply (e.g., organic matter) may control the vertical distribution of NFGs. Taken together, the findings in this study could fundamentally improve our understanding of the distribution of N cycling-associated microorganisms across a vertical scale, which would be useful for predicting the soil N availability and guiding the soil N management in grassland ecosystems.

Deciphering response effect and underlying mechanism of anammox-based nitrogen removal process under exposures to different antibiotics via big data analysis

Recently, little research has been devoted to the systematic investigation regarding the effect of different antibiotics on anammox-based system and its underlying mechanism. In this study, a critical inhibition concentration to the anammox-based system was obtained: 2, 0.5 and 5 mg/L for OTC, TC and SM, respectively. However, SPM had no significant inhibition. Furthermore, Exp model and Monod model were capable to describe the inhibition period, while Gauss model was suitable for the recovery period. A universal machine learning model could accurately predict the NRR (R2 over 0.9), especially when biomass information data was introduced. As a qualitative analysis, the inhibition effect of TC and OTC was strongest. The abundance of nitrogen functional genes was negatively correlated with antibiotics, while antibiotic resistance genes showed the opposite trend. Overall, the inhibition ratios of OTC, TC, SPM and SM on anammox process were calculated to be 91%, 82%, 50% and 30%, respectively.

Deciphering and predicting anammox-based nitrogen removal process under oxytetracycline stress via kinetic modeling and machine learning based on big data analysis

Anaerobic ammonium oxidation (anammox) is an advanced nitrogen removal process that is widely used in the nitrogen removal of various antibiotic containing wastewaters due to its high efficiency and energy saving characteristics. However, as a widely used antibiotic, the inhibitory effect of oxytetracycline (OTC) on anammox is unclear. In this study, the effect of OTC on the anammox-based nitrogen removal process was revealed by kinetic model and machine learning models. Statistical analysis showed that anammox started to be inhibited when the OTC concentration reached 2 mg/L. The inhibition and recovery periods were simulated under OTC stress. During the inhibition period, the R2 fitted by Exp model was higher, and the simulated maximum nitrogen removal rate (NRR) was between 0.47 and 17.05 kg/(m3·d). During the recovery period, both Boltzmann and Gauss models fit well. In addition, the machine learning model of the artificial neural network predicted the NRR more accurately, indicating that the importance of environmental factors was lower than the effluent parameters. Spearman correlation analysis showed that the NRR was negatively correlated with OTC under both short-term and long-term OTC stress. Furthermore, the hydraulic retention time and water quality parameters played an important role in the short-term and long-term experiment, respectively. Finally, redundancy analysis demonstrated that the abundance of nitrogen functional genes, such as hydrazine dehydrogenase, nitrite/nitric oxide oxidoreductase and hydrazine synthase, was negatively correlated with the amount of OTC, while antibiotic resistance genes showed the opposite trend.

Pathways and mechanisms of nitrogen transformation during co-composting of pig manure and diatomite

The aim of this study was to investigate the pathways and mechanisms of nitrogen transformation during the composting process, by adding diatomite (0%, 2.5%, 5%, 10%, 15% and 20%) into initial mixtures of pig manure and sawdust. The results revealed that diatomite facilitated the conversion from NH4+-N to amino acid nitrogen and hydrolysis undefined nitrogen, then reduced NH3 and N2O emission by 8.63–35.29% and 14.34–73.21%, respectively. Moreover, the structure and abundance of nitrogen functional genes provided evidence for nitrogen loss. Furthermore, compared with the control (0.03), the treatment blended with 10% diatomite (T3) had the highest value in composting score (-1.27). Additionally, the ratio of carbon and nitrogen (57.30%) was vital for reducing nitrogen loss among all physio-chemical parameters in this study. In conclusion, adding diatomite was a practical way to enhance nitrogen conservation and increase quality of end products, and the optimum added dosage was at 10%.

Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River

The increased anthropogenic activities in the Tibetan Plateau may threaten the river environmental safety. However, limited information is available on the Lhasa River in the Tibetan Plateau, which is known as the remaining pure land on Earth. Here, we firstly investigated the distribution patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge along the reaches of the Lhasa River. The total organic carbon, total Nitrogen (N), nitrate and ammonium contents and the relative abundance of bacteria and archaea significantly increased in reservoir sites in comparison with sites below dam, and they also gradually increased from upstream to downstream in sewage discharge sites. By contrast, the diversity of sediment bacteria and archaea in reservoir sites were significantly less than that in sites below dam and sewage discharge sites at Operational Taxonomic Units (OTUs) level. The dominant species were water-bloom cyanobacteria in the reservoir area of Zhikong Dam and Proteobacteria in the sewage discharge sites, which were significantly correlated with the nutrient concentration. The abundance of nitrogen functional genes significantly also increased in reservoir sites and the downstream of sewage discharge areas. These results suggested that dam construction and sewage discharge caused the increase of sediment bacterial communities and nutrient levels and potentially induced eutrophication in the Lhasa River.

Distinct pattern of nitrogen functional gene abundances in top- and subsoils along a 120,000-year ecosystem development gradient

Soil microorganisms are key players of the nitrogen cycle and relevant for soil development. While the community structure of nitrogen-cycling microorganisms during initial soil development is already well investigated, knowledge about the patterns during long-term ecosystem development is limited. In this study, nitrogen functional genes of ammonia-oxidizers (amoA), nitrate-reducers (narG), and chitin-degraders (chiA) were determined via quantitative PCR and the functional community composition of archaeal ammonia-oxidizers was analyzed via clone libraries and DNA sequencing (amoA) in soil depth profiles along the 120,000-year Franz Josef chronosequence (New Zealand). The results show that absolute nitrogen functional gene abundances change significantly during long-term soil development. In organic layers, narG and chiA gene abundances were highest in young to intermediate-aged soils and then decreased following progressive and retrogressive development of the vegetation. While relative archaeal amoA gene abundance (proportional to total cell counts) decreased in the oldest phosphorus-limited topsoils, relative narG and chiA gene abundances remained constant. In subsoils, archaeal amoA and narG gene abundances also decreased with ecosystem retrogression that coincided with the increasing content of iron and aluminum oxides as well as other clay-sized minerals. In contrast, subsoil chiA gene abundances were hardly affected by soil age. The analysis of the archaeal amoA community revealed a compositional shift during long-term ecosystem development. Our study provides evidence that the community structure of nitrogen-cycling microorganisms in top- and subsoils is significantly affected by long-term ecosystem development and suggests an important role of the mineral phase in subsoils.

Nitrogen removal and nitrogen functional gene abundances in three subsurface wastewater infiltration systems under different modes of aeration and influent C/N ratios

Matrix DO, nitrogen removal and nitrogen functional gene abundances in non-aerated (NA), continuously aerated (CA) and intermittently aerated (IA) subsurface wastewater infiltration systems (SWISs) under different influent C/N ratios were studied. Aeration created aerobic condition in 50cm depth and did not change anoxic or anaerobic condition in 80 and 110cm depths, which enhanced NH4+-N and TN removal and the enrichment of nitrogen removal functional genes (amoA, nxrA, narG, napA, nirK, nirS, qnorB and nosZ) compared to NA SWIS, especially under high influent C/N ratio. High TN removal rate (89.6%) was obtained in IA SWIS under the influent C/N ratio of 12, which was higher than that in CA SWIS (87.1%). The results suggested that intermittent aeration was a reliable option to achieve high TN removal in SWISs, especially under high influent C/N ratio.

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants.

This study aimed to investigate the variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems without prechlorination and associated effects on the transformation of nitrogen pollutants by using a designed model pipe system. The results showed the transformation of nitrogen pollutants was obvious during the biofilm formation. The richness and diversity of the microbial communities changed significantly. The higher abundance of Nitrospirae in biofilm samples significantly contributed to biological nitrification. In particular, the stable content of Bacteroidetes in the biofilm and soluble microbial products released by the biomass might have enhanced the increase in dissolved organic nitrogen. In addition, the variation tendency of nitrogen functional gene abundances and their strong effects on NH4+-N, NO2--N, and NO3--N transformation were clearly observed. These findings provide new insights into the evolution of microbial communities and functional genes during the initial operation period of real-world raw water distribution pipes and highlight management and possible safety issues in the subsequent water treatment process.

Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands.

Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ15N), and inorganic N pools. Soil pH and δ15N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4+ concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and denitrification and favor N retention. Mixed plantations could also allow an increase in soil C and N stocks without losing the source of income that teak trees represent for local communities.

Assessing nitrogen transformation processes in a trickling filter under hydraulic loading rate constraints using nitrogen functional gene abundances

A study was conducted of treatment performance and nitrogen transformation processes in a trickling filter (TF) used to treat micro-polluted source water under variable hydraulic loading rates (HLRs), ranging from 1.0 to 3.0m3/m2d. The TF achieved high and stable COD (97.7–99.3%) and NH4+-N (67.3–92.7%) removal efficiencies. Nitrification and anaerobic ammonium oxidation were the dominant nitrogen removal processes in the TF. Path analysis indicated that amoA/anammox and amoA/(narG+napA) were the two key functional gene groups driving the major processes for NH4+-N and NO2−-N, respectively. The analysis also revealed that anammox/amoA and nxrA/(nirK+nirS) were the two key functional gene groups affecting processes associated with the NO3−-N transformation rate. The direct and indirect effect of functional gene groups further confirmed that nitrogen transformation processes are coupled at the molecular level, resulting in a mutual contribution to nitrogen removal in the TF.

Parent material and vegetation influence bacterial community structure and nitrogen functional genes along deep tropical soil profiles at the Luquillo Critical Zone Observatory

Microbial communities mediate every step of the soil nitrogen cycle, yet the structure and associated nitrogen cycle functions of soil microbial communities remain poorly studied in tropical forests. Moreover, tropical forest soils are often many meters deep, but most studies of microbial nitrogen cycling have focused exclusively on surface soils. The objective of our study was to evaluate changes in bacterial community structure and nitrogen functional genes with depth in soils developed on two contrasting geological parent materials and two forest types that occur at different elevations at the Luquillo Critical Zone Observatory in northeast Puerto Rico. We excavated three soil pits to 140 cm at four different sites representing the four soil × forest combinations (n = 12), and collected samples at ten-centimeter increments from the surface to 140 cm. We used bacterial 16S rRNA gene-DGGE (denaturant gradient gel electrophoresis) to fingerprint microbial community structures, and quantitative PCR to measure the abundance of five functional genes involved in various soil nitrogen transformations: nifH (nitrogen fixation), chiA (organic nitrogen decomposition), amoA (ammonia oxidation), nirS (nitrite reduction) and nosZ (nitrous oxide reduction). Multivariate analyses of DGGE fingerprinting patterns revealed differences in bacterial community structure across the four soil × forest types that were strongly correlated with soil pH (r = 0.69, P < 0.01) and nutrient stoichiometry (r2 ≥ 0.36, P < 0.05). Across all soil and forest types, nitrogen functional genes declined significantly with soil depth (P < 0.001). Denitrification genes (nirS and nosZ) accounted for the largest proportion of measured nitrogen functional genes. Measured nitrogen functional genes were positively correlated with soil carbon, nitrogen and phosphorus concentrations (P < 0.001) and all genes except amoA were significantly more abundant in the Inceptisol soil type compared with the Oxisol soil type (P < 0.03). Greater abundances and a stronger vertical zonation of nitrogen functional genes in Inceptisols suggest more dynamic nitrogen transformation processes in this soil type. As the first study to examine bacterial nitrogen functional gene abundances below the surface 20 cm in tropical forest soils, our work provides insight into how pedogenically-driven vertical gradients control the nitrogen-cycling capacity of soil microbial communities. While previous studies have shown evidence for redox-driven hotspots in tropical nitrogen cycling on a watershed scale, our study corroborates this finding on a molecular scale.

Assessing Nitrogen Transformations in a Flooded Agroecosystem Using the Isotope Pairing Technique and Nitrogen Functional Gene Abundances

Predicting N losses in flooded agricultural systems is complex because of the large number of potential N transformation pathways. Although coupled nitrification/denitrification at the flooded sediment near-surface oxic/anoxic interface is a recognized pathway of fertilizer N loss, the role of the newly discovered anaerobic ammonium oxidation (anammox) pathway in agricultural systems is poorly understood. A survey study was implemented to characterize sediment denitrification rates, anammox activity, and fluxes of ammonium and nitrate, and the vertical distribution of N functional genes were measured in Hawaiian taro (Colocasia esculenta) fields under three fertilizer management regimens (conventional, organic, and hybrid) as a model for flooded agroecosystems. Potential denitrification rates and anammox activity were measured using a slurry-based isotope pairing technique, and fluxes were determined by porewater modeling. Although significant numbers of anammox 16S rRNA genes were detected, only negligible anammox activity was found, illustrating the need to quantify not only the presence but also the activity of these bacteria. Quantitative polymerase chain reaction was performed for bacterial amoA, nirS, nosZ, and the 16S rRNA gene at 1-cm soil depth increments. Slurry isotope pairing technique-based potential denitrification rates (4.3-12.3 mmol N 2 m -2 day -1 ) were on the high end of previous anaerobic incubation studies. Flux-derived denitrification rates were up to three orders of magnitude lower than slurry isotope pairing technique rates, suggesting strong nitrification regulation. Organically managed fields exhibited significantly lower slurry and flux-based denitrification rates than conventional and hybrid systems. This study supports the use of alternative fertilizer management techniques in flooded agroecosystems by the mitigation of N losses through denitrification and decreased overall N flux rates.