Nitrification Genes Research Articles

Silver Sulfide Nanoparticles Reduce Nitrous Oxide Emissions by Inhibiting Denitrification in the Earthworm Gut.

The accumulation of Ag2S in agricultural soil via application of Ag-containing sludge potentially affects the functioning of soil microorganisms and earthworms (EWs) due to the strong antimicrobial properties of Ag. This study examined the effects of Ag2S nanoparticles (Ag2S-NPs) on the EW-mediated (Eisenia fetida and Pontoscolex corethrurus) soil N cycle. We used 16S rRNA gene-based sequencing and quantitative polymerase chain reaction to examine the bacterial community and nitrification/denitrification-related gene abundance. The presence of either EWs or Ag significantly increased denitrification and N2O emissions. However, the addition of Ag2S to EW-inhabited soil reduced N2O emissions by 14-33%. Furthermore, Ag2S caused a low-dose stimulation but a high-dose inhibition to N2O flux from the EW gut itself. Accordingly, an increase in Ag in the EW gut caused a decrease in the relative abundance of denitrifiers in both the soil and the gut, especially for the dominant genus Bacillus. Ag2S also decreased the copy numbers of nitrification gene (nxrB) and denitrification genes (napA, nirS, and nosZ) in EW gut, leading to the observed decrease in N2O emissions. Collectively, applying Ag2S-containing sludge disturbs the denitrification function of the EW gut microbiota and the cycling of N in soil-based systems.

Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru

Abstract. Oxygen-deficient zones (ODZs) are major sites of net natural nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ in the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N tracer experiments in combination with quantitative PCR (qPCR) and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with a mean of 8.7 nmol L−1 d−1 but up to 118±27.8 nmol L−1 d−1 just below the oxic–anoxic interface. The highest N2O production from ammonium oxidation (AO) of 0.16±0.003 nmol L−1 d−1 occurred in the upper oxycline at O2 concentrations of 10–30 µmol L−1 which coincided with the highest archaeal amoA transcripts/genes. Hybrid N2O formation (i.e., N2O with one N atom from NH4+ and the other from other substrates such as NO2-) was the dominant species, comprising 70 %–85 % of total produced N2O from NH4+, regardless of the ammonium oxidation rate or O2 concentrations. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L−1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold, suggesting increased N2O production during times of high particulate organic matter export. High N2O yields of 2.1 % from AO were measured, but the overall contribution by AO to N2O production was still an order of magnitude lower than that of denitrification. Hence, these findings show that denitrification is the most important N2O production process in low-oxygen conditions fueled by organic carbon supply, which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation.

Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China.

Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO3--N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation.IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.

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.

The Structure and Diversity of Nitrogen Functional Groups from Different Cropping Systems in Yellow River Delta.

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn–wheat rotation system (Wheat–Corn), soybean–corn rotation system (Soybean–Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer–, denitrifier– and nitrogen (N)–fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N–cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat–Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean–Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N–cycling microbial.

Nitrogen removal in recirculating aquaculture water with high dissolved oxygen conditions using the simultaneous partial nitrification, anammox and denitrification system

The efficient removal of nitrogen pollutants in the aquaculture systems is still a challenge due to the low concentration of organic carbon and high concentration of dissolved oxygen (DO) in the wastewater. The simultaneous partial nitrification, anammox and denitrification (SNAD) bioreactor was firstly used for the treatment of aquaculture wastewater in recirculating aquaculture system. The bioreactor operated for 180 days without adding extra organic carbon. After 60-day operation, the bioreactor reached the stable stage with the average concentration of ammonia/nitrate/nitrite/COD in the effluent with 0.26/0.75/0.47/0.27 mg/L. The Pseudoxanthomonas was the dominant genus in the biofilm samples. The typical nitrogen functional bacteria and genes for nitrification, anammox and denitrification were detected with different abundance in different procedures along the bioreactor. Network analysis revealed the significant correlations between nitrogen functional bacteria and genes. The SNAD bioreactor achieved the effective removal for nitrogen and COD under high DO conditions in recirculating aquaculture system.

Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome.

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-defined as the number of unique within-gene phylotypes-across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

Effect of nitrogen fertilisers on nitrous oxide emission, nitrifier and denitrifier abundance and bacterial diversity in closed ecological systems

In a 3-year microcosm study the nitrous oxide (N2O) emission from an agricultural soil amended with urea, ammonium sulphate or potassium nitrate were examined. Soil samples were taken every year to determine the soil physicochemical properties, the total abundance of bacteria, archaea, nitrifier and denitrifier communities and the changes in the structure and composition of the bacterial community. Gene abundance and biodiversity were estimated using quantitative PCR and pyrosequencing, respectively. The soils were watered weekly to reach 80% water filled pore space and varied from 80 to 62% during that time. N-fertilisation increased the abundance of bacteria and decreased that of archaea. Soils treated with ammonium or urea emitted more N2O than that amended with potassium nitrate and produced yearly increases in the abundance of nitrification genes. Also, the abundance of the denitrification genes gradually increased during the experimental period. N2O emission decreased on a yearly basis and so did the ratio of the genes involved in N2O production and reduction. A non-metric multidimensional scaling plot showed that N2O emission was positively related with the norB gene and negatively with the nosZ. The Shannon and Simpson diversity indices indicated that N-fertilisation reduced the number of operational taxonomic units (OTUs) and that the bacterial community became dominated by a small group of OTUs, respectively. N-fertilisation reduced the number of OTUs whose relative abundance was lower than 1%. We conclude that potassium nitrate reduces N2O emissions and increases the abundance of the N2O reducers. This work also shows that N-fertilisation decreases soil biodiversity and that its response depends on the type of the N-fertiliser.

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere

In water-scarce regions, alternate-furrow irrigation (AFI)—alternately wetting half of the plant roots—has proven to be an effective water-saving approach without compromising yield. However, the extent to which AFI with wastewater affects N cycling genes remains poorly studied. We aimed to investigate changes in main N transformation processes, bacterial and fungal community composition, as well as relative abundance of N cycle-associated genes in soil receiving AFI with swine wastewater. The experimental plan included three irrigation rates, irrigating pepper plants with 50%, 65%, and 80% of the amount of water required under conventional furrow irrigation to prevent the crop suffering water stress. Each treatment had a groundwater irrigation control. We measured edaphic factors, microbial community composition, and relative abundance of genes in rhizosphere and bulk soils. Altering water use in AFI did not exert a significant effect on bacterial and fungal communities. By increasing the irrigation rate of wastewater, relative abundances of nifH, bacterial and archaeal amoA and nosZ genes decreased, whereas those of nirK and nirS genes increased in the rhizosphere soil; nitrification rate did not decrease and the denitrification rate remained unchanged in both rhizosphere and bulk soil, implying that appropriate increase of wastewater use by AFI can improve N use efficiency.

The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes of damaged glutathione in Arabidopsis.

The tripeptide glutathione (GSH) is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1-10 mM range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has high and specific amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons in Arabidopsis Nit1 were used and confocal microscopy of Nit1-GFP fusions in plant cells confirmed both cytoplasmic and plastidial localization. Furthermore, we show that Arabidopsis enzymes present in leaf extracts convert GSH to dGSH at a rate of 2.8 pmol min-1 mg-1 in the presence of glyoxalate as an amino acceptor. Our data demonstrate that plants have a dGSH repair system that is directed to at least two cellular compartments via the use of alternative translation start sites.

Easily mineralizable carbon in manure‐based biochar added to a soil influences N2O emissions and microbial‐N cycling genes

AbstractManure‐based biochar is an effective amendment to increase both carbon sequestration and the fertility of degraded soils, whereas the responses of N2O emissions and microbial‐N cycling genes to its application and the underlying mechanisms are poorly understood. Here, four biochars were produced under two pyrolysis temperatures (300 and 700°C) and with two organic C extraction procedures (water and acetone extraction). The resulting biochars were either with relative enrichment or depletion in easily mineralizable carbon (EMC) compared with recalcitrant C. We added biochars, with urea and sodium nitrate, to a degraded red soil and incubated the amended soils at moisture levels of 60% and 130% field capacity. All the biochars decreased nitrification gene abundance, that is, amoA. Biochars with EMC had greater stimulatory effects on the abundance of denitrification genes (nirK, nirS, and nosZ) and N2O emission, regardless of moisture level and N form, compared with biochar without EMC. Biochar‐induced microbial activity, biochar aliphatics, and alkyl groups correlated positively with N2O emission and denitrification gene abundance. The water dissolved organic C of biochar facilitated the conversion of N2O to N2, whereas the acetone extractable C fraction postponed the completion of denitrification. In conclusion, the N2O emission and denitrification gene abundance increased with decreasing biochar aromaticity and increasing EMC content. Our study emphasizes that the EMC supply in manure‐based biochars also importantly mediates soil N2O emission and microbial N cycling genes, adding to current understanding of influencing factors such as biochar pH, porosity, N availability, and redox property.

Effects of ofloxacin on nitrogen removal and microbial community structure in constructed wetland

Constructed wetlands (CWs) have emerged as a promising technology for the purification of micro-polluted water. However, their nitrogen removal performance can be significantly degraded by design, operational, and environmental factors. The present study investigates the effects of ofloxacin (OFL: 0.1, 10, and 1000 μg L−1) and plants (Cyperus alternifolius L. and Typha angustifolia L.) on nitrogen removal in a micro-polluted CW system over a duration of 12 weeks. The effects were evaluated by investigating NH4-N and NO3-N removal efficiency, nitrification genes (amoA-AOA and amoA-AOB), denitrification genes (nirK and nirS), fungal 18S rRNA gene and microorganism community structure. The results showed that in unplanted CWs, OFL increased the NH4-N removal efficiency (from 72.6% to 80.7–82.1%), the abundances of amoA-AOA, nirS, nirK and fungal 18S rRNA gene, and the bacterial diversity but decreased the abundance of both amoA-AOB and bacterial richness. In contrast, both the nitrogen removal efficiency (83.4–89.5% for NH4-N and 33.8–38.5% for NO3-N) and bacterial diversity/richness were not significantly affected by OFL in planted CWs. In planted systems, OFL increased the relative abundance of Arthrobacter, Pseudomonas, and Enterococcus, which are proven antibiotic-resistant bacteria. This study showed that CWs are able to remove nitrogen from antibiotic-contaminated micro-polluted water, which might primarily be attributed to the presence of plants that protect the microorganism community.

Changes in the nitrogen biogeochemical cycle in sediments of an urban river under different dissolved oxygen levels

Abstract Urban rivers are considered as a hot spot of microbial nitrogen cycling due to extensive N loading. However, microbial nitrogen transformation dynamics in urban rivers with different dissolved oxygen (DO) conditions are still unclear. This study investigated the effects of DO concentration changes (anaerobic to aerobic) in overlying water on nitrogen-cycling gene abundance in incubation conditions using sediment from a typical urban river in the Yangtze River Delta. Quantitative polymerase chain reaction (qPCR) results revealed that the abundances of the nitrification gene amoA, denitrification gene nirS/K, norB, nosZ, and anammox gene hzo increased by one to two orders of magnitude from anaerobic to aerobic conditions. Ammonia-oxidizing archaea (AOA) predominated the ammonium oxidation microbial populations, about tenfold more than the ammonia-oxidizing bacteria (AOB) populations. Significant correlations were found among the abundances of AOA-amoA, AOB-amoA, nirS, nirK, and hzo genes, implying a close coupling of aerobic ammonium oxidation (AAO), denitrification, and anammox processes at the molecular level. Moreover, the nitrogen transformation rates were calculated using a box model linking the measured dissolved inorganic nitrogen species. The contribution of anammox to N2 production was 85% under saturated treatment, and the AAO rate was significantly positive correlated to the anammox rate. Our results suggested that coupled AAO and anammox might be the dominant pathway for reactive nitrogen removal in urban rivers with elevated DO levels.

Nitrogen-cycling genes and rhizosphere microbial community with reduced nitrogen application in maize/soybean strip intercropping

Soil microbes are essential links between above- and below-ground ecosystems and play an important role in regulating ecological functions in the soil. Dynamic interactions within the soil-microbial community in a cereal-legume intercropping ecosystem influence the composition and structure of N-cycling microbial groups (e.g. nitrogen-fixing bacteria). However, these effects have not been extensively studied in some intercropping patterns or in response to varying nitrogen fertilization levels. In the present study, we evaluated the effects of reduced and conventional nitrogen application in a sweet maize (Zea may L.)/soybean (Glycine max L.) strip intercropping system under three cropping patterns over a 3-year time period. High-throughput sequencing and quantitative PCR techniques were used to investigate changes to both the microbial community structure and the expression of key nitrogen-cycling genes in the rhizosphere. Our results indicate that reduced nitrogen application affected the microbial community structure in the rhizosphere, but microbial diversity in the sweet maize rhizosphere was relatively stable. Both the abundance and activity of functional marker genes for microbial nitrogen fixation (nifH), nitrification (amoA), denitrification (nirS, nirK, nosZ), and decomposition (chiA) increased significantly from 2013 to 2016. Taken together, these data demonstrate that the quantified shifts in the soil microbial community and the observed increases in the expression of key functional genes involved in N-cycling were the result of reduced nitrogen application in this strip intercropping system. This study, therefore, provides essential insight into the potential relationships between functional nitrogen-cycling genes and mitigation of nitrogen-loss and N2O emissions in a cereal-legume strip intercropping system.

Removal of nitrogen from low pollution water by long-term operation of an integrated vertical-flow constructed wetland: Performance and mechanism

The efficiency of nitrogen removal and its mechanism, aquatic organism distribution characteristics and regeneration capability of zeolite from an integrated vertical-flow constructed wetland (IVFCW) for low pollution water treatment were evaluated after steady and continuous operation for eight years. After running for eight years, better than average COD and NH4+-N removal were observed in the IVFCW. The NH4+-N removal rate in this system was controlled by ammoxidation and adsorption and ion exchange of zeolite. The low total nitrogen (TN) removal efficiency was due to NO3−-N accumulation and zeolite desorption. In addition, this phenomenon indicated that because of poor organic carbon sources, nitrification was stronger than denitrification, consistent with the distribution of the functional genes for nitrification and denitrification. The biological activity in this system was abundant, especially that of spirogyra and navicula. The saturated adsorption capacity of zeolite was as high as 1.35 mg g−1 with a desorption rate of <20%. There were no obvious differences among the effects of aeration, water cleaning, drained reoxygenation and steam stripping for zeolite regeneration (adsorption capacity of >50%). However, the drained reoxygenation performance of was better due to zero energy consumption and regeneration in situ.

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

Much of the diversity of prokaryotic viruses has yet to be described. In particular, there are no viral isolates that infect abundant, globally significant marine archaea including the phylum Thaumarchaeota. This phylum oxidizes ammonia, fixes inorganic carbon, and thus contributes to globally significant nitrogen and carbon cycles in the oceans. Metagenomics provides an alternative to culture-dependent means for identifying and characterizing viral diversity. Some viruses carry auxiliary metabolic genes (AMGs) that are acquired via horizontal gene transfer from their host(s), allowing inference of what host a virus infects. Here we present the discovery of 15 new genomically and ecologically distinct Thaumarchaeota virus populations, identified as contigs that encode viral capsid and thaumarchaeal ammonia monooxygenase genes (amoC). These viruses exhibit depth and latitude partitioning and are distributed globally in various marine habitats including pelagic waters, estuarine habitats, and hydrothermal plume water and sediments. We found evidence of viral amoC expression and that viral amoC AMGs sometimes comprise up to half of total amoC DNA copies in cellular fraction metagenomes, highlighting the potential impact of these viruses on N cycling in the oceans. Phylogenetics suggest they are potentially tailed viruses and share a common ancestor with related marine Euryarchaeota viruses. This work significantly expands our view of viruses of globally important marine Thaumarchaeota.

Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages.

We investigated the impact of native freshwater mussel assemblages (order Unionoida) on the abundance and composition of nitrogen‐cycling genes in sediment of an upper Mississippi river habitat. We hypothesized that the genomic potential for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages, presumably due to mussel biodeposition products, namely ammonia and organic carbon. Regardless of the presence of mussels, upper Mississippi river sediment microbial communities had the largest genomic potential for nitrogen fixation followed by urea catabolism, nitrate metabolism, and nitrate assimilation, as evidenced by analysis of nitrogen cycling pathway abundances. However, genes encoding nitrate and nitrite redox reactions, narGHI and nxrAB, were the most abundant functional genes of the nitrogen cycling gene families. Using linear discriminant analysis (LDA), we found nitrification genes were the most important biomarkers for nitrogen cycling genomic potential when mussels were present, and this presented an opposing effect on the abundance of genes encoding nitric oxide reduction. The genes involved in nitrification that increased the most were amoA associated with comammox Nitrospira and nxr homologs associated with Nitrospira. On the other hand, the most distinctive biomarkers of microbial communities without mussels were norB and nrfA, as part of denitrification and dissimilatory nitrate reduction to ammonium pathways, respectively. Ultimately, this research demonstrates the impact of native mollusks on microbial nitrogen cycling in an aquatic agroecosystem.

Profiling of the Microbiome Associated With Nitrogen Removal During Vermifiltration of Wastewater From a Commercial Dairy.

Vermifiltration is a biological treatment process during which earthworms (e.g., Eisenia fetida) and microorganisms reduce the organic load of wastewater. To infer microbial pathways responsible for nutrient conversion, past studies characterized the microbiota in vermifilters and suggested that nitrifying and denitrifying bacteria play a significant role during this wastewater treatment process. In contrast to previous studies, which were limited by low-resolution sequencing methods, the work presented here utilized next generation sequencing to survey in greater detail the microbiota of wastewater from a commercial dairy during various stages of vermifiltration. To complement sequence analysis, nitrogenous compounds in and gaseous emissions from the wastewater were measured. Analysis of 16S rRNA gene profiles from untreated wastewater, vermifilter influent, and vermifilter effluent suggested that members of Comamonadaceae, a family of the Betaproteobacteria involved in denitrification, increased in abundance during the vermifiltration process. Subsequent functional gene analysis indicated an increased abundance of nitrification genes in the effluent and suggested that the nitrogen removal during vermifiltration is due to the microbial conversion of ammonia, a finding that was also supported by the water chemistry and emission data. This study demonstrates that microbial communities are the main drivers behind reducing the nitrogen load of dairy wastewater during vermifiltration, providing a valuable knowledge framework for more sustainable and economical wastewater management strategies for commercial dairies.

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils.

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.

A missing link in the estuarine nitrogen cycle?: Coupled nitrification-denitrification mediated by suspended particulate matter

In estuarine and coastal ecosystems, the majority of previous studies have considered coupled nitrification-denitrification (CND) processes to be exclusively sediment based, with little focus on suspended particulate matter (SPM) in the water column. Here, we present evidence of CND processes in the water column of Hangzhou Bay, one of the largest macrotidal embayments in the world. Spearman’s correlation analysis showed that SPM was negatively correlated with nitrate (rho = −0.372, P = 0.018) and marker genes for nitrification and denitrification in the water column were detected by quantitative PCR analysis. The results showed that amoA and nir gene abundances strongly correlated with SPM (all P < 0.01) and the ratio of amoA/nir strongly correlated with nitrate (rho = −0.454, P = 0.003). Furthermore, aggregates consisting of nitrifiers and denitrifiers on SPM were also detected by fluorescence in situ hybridization. Illumina MiSeq sequencing further showed that ammonia oxidizers mainly belonged to the genus Nitrosomonas, while the potential denitrifying genera Bradyrhizobium, Comamonas, Thauera, Stenotrophomonas, Acinetobacter, Anaeromyxobacter, Sulfurimonas, Paenibacillus and Sphingobacterium showed significant correlations with SPM (all P < 0.01). This study suggests that SPM may provide a niche for CND processes to occur, which has largely been missing from our understanding of nitrogen cycling in estuarine waters.