Denitrifier Community Composition Research Articles

Nitrogen loss by nirS-type denitrifying bacterial communities in eutrophic coastal sediments

Denitrification plays a dominant role in the removal of reactive inorganic nitrogen species in different ecosystems. In this study, we investigated the activity, abundance, and community composition of nirS-encoding denitrifying bacteria from sediments of Jiaozhou Bay (JZB). The rates of denitrification, measured by 15N amendment and incubation experiments, varied from 0.18 to 9.97 nmol N g−1 h−1 and contributed to 81.45–99.93% of the total N2 production, while the estimated flux of nitrogen removal was about 5.66 × 104 t N y−1 in surface sediments. Additionally, the abundance of nirS gene ranged from 5.20 × 105 to 3.01 × 108 copies per gram. High-throughput sequencing technique was used to target the nirS gene, which revealed 19 dominant OTUs at 93% similarity that were assigned to 7 clusters. Cluster 2 was mainly affiliated to Thiothrix, while Cluster 4 was mainly affiliated to Woeseia and the other clusters were similar to uncultured denitrifiers obtained from sediments of several coastal estuaries and bays. NH4+ and NO3− contents were identified as the two main factors affecting community composition and distribution of denitrifiers among the surface sediments of JZB. Overall, our results showed that the community of nirS-type denitrifying bacteria had a diverse composition and could highly contribute to nitrogen loss in eutrophic systems.

Nitrous oxide emission and the related denitrifier community: A short-term response to organic manure substituting chemical fertilizer.

Partially substituting chemical fertilizer with organic manure can aid in the disposal of agricultural wastes via recycling into agricultural land, reduce chemical fertilizer application, and influence nitrogen (N) transformation. However, relatively few studies have investigated the association between soil physicochemical properties, denitrifier communities and N2O emission after short-term substitution of organic manure in vegetable fields. We conducted a short-term vegetable field experiment which included one control treatment (CT, no fertilizer) and three fertilization treatments containing equal amount of total N, phosphorus and potassium (CF, chemical fertilizer only; CMR, chemical fertilizer plus mushroom residue; COM, chemical fertilizer plus cattle manure). The results showed that partial substitution of chemical fertilizer with organic manure greatly increased cumulative N2O emissions, N2O emission factors and yield-scaled N2O emissions by 122-203%, 238-600% and 128-181%, respectively. Compared with the CF treatment, short-term substitution with organic manure reduced the abundance of nirS- and nosZ-type denitrifiers, and increased that of nirK-type denitrifiers. Modeling indicated that nirS abundance, together with soil available N, NIR activity, nirK abundance, SOC, NH4+, and NO3- were the primary factors associated with cumulative N2O emissions. The denitrifier community composition of the CF- treated soil was separated from that of soils treated with CMR and COM, and was primarily influenced by soil NH4+ concentration. NIR activity showed a significant correlation with denitrifier community composition. Overall, short-term substitution of chemical fertilizer with cattle manure (lower C/N ratio) reduced the abundance of nirS- and nosZ-type denitrifiers, but stimulated N2O emission.

Denitrifier abundance and community composition linked to denitrification activity in an agricultural and wetland soil

We examined denitrifier community abundance and composition in an agricultural and a wetland soil. Both soils were subjected to manipulations of pH and moisture content in a microcosm experiment, to understand if similar environmental and biotic factors governed denitrification rates in the two ecosystems, and how these factors were linked to denitrification rates. Bacterial communities containing nirK, nirS, and nosZ-I all had distinct composition in the agricultural compared to the wetland soil, with nirK and nirS community composition being particularly distinct compared to that of nosZ-I. Lowering soil pH decreased gene abundance and altered the composition of nirK and nirS in both soils and increased the N2O: (N2+ N2O) ratio in agricultural soil. Re-wetting soil for the experimental manipulations led to increased denitrification rate in the agricultural soil but had no effect on the denitrification rate measured in the wetland soil. We found that the combination of abiotic variables, gene abundance, and diversity measures predicted denitrification better than any of these factors alone, showing the importance of including microbial measures for predicting denitrification. The manipulations of these soils provided evidence for niche differences between the homologous nirK and nirS genes. Notably, nirS abundance was more highly correlated to activity in higher pH soils, while nirK abundance was more correlated to activity in low pH soils. We show that nirK and nirS do not behave and contribute equally to denitrification under these varying conditions.

Chronic effects of different fertilization regimes on nirS-type denitrifier communities across the black soil region of Northeast China

Denitrification is one of the major processes causing nitrogen loss from arable soils. This study aimed to investigate the responses of nirS-type denitrifier communities to different chronic fertilization regimes across the black soil region of Northeast China. Soil samples were collected from sites located in the north (NB), middle (MB), and south (SB) of the black soil region of Northeast China, each with four chronic fertilization regimes: no fertilizer (NoF), chemical fertilizer (CF), manure (M), and chemical fertilizer plus manure (CFM). Methods of quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing were applied to assess the abundance and composition of denitrifier communities by targeting the nirS gene. The results showed that the M and CFM regimes significantly increased the abundances of nirS-type denitrifiers compared with NoF at the three locations. The majority of nirS sequences were grouped as unclassified denitrifiers, and the different fertilizers induced little variation in the relative abundance of known nirS-type denitrifier taxa. Over 90% of the sequences were shared among the four fertilization regimes at each location, but none of the abundant operational taxonomic units (OTUs) were shared among the three locations. Principal coordinate analysis (PCoA) revealed that the communities of nirS-type denitrifier were separated into three groups that corresponded with their locations. Although similar fertilization regimes did not induce consistent changes in the nirS-type denitrifier communities, soil pH and NO−3-N content simultaneously and significantly influenced the structure of nirS-type denitrifier communities at the three locations. Our results highlight that geographical separation rather than chronic fertilization was the dominant factor determining the nirS-type denitrifier community structures, and similar chronic fertilization regimes did not induce consistent shifts of nirS-type denitrifier communities in the black soils.

Effects of organic carbon consumption on denitrifier community composition and diversity along dissolved oxygen vertical profiles in lake sediment surface

At present, the understanding of the dynamics of denitrifiers at different dissolved oxygen (DO) layers under organic carbon consumption within the surface sediments remains inadequate. In this study, high-throughput sequencing and quantitative PCR targeting nirS gene were used to analyze the denitrifier abundance dynamics, community composition, and structure for aerobic (DO 0.5–6.9 mg/L), hypoxic-anoxic (DO 0–0.5 mg/L), and anoxic (DO 0 mg/L) layers in surface sediments under organic carbon consumption. Based on the analysis of nirS gene abundance, the values of denitrifying bacteria decreased with organic carbon consumption at different DO layers. When the bacterial species abundance at the genus level were compared between the high-carbon and low-carbon sediments, there was significant increase in 6 out of 36, 7 out of 36 and 6 out of 36 genera respectively for the aerobic, hypoxic-anoxic and anoxic layers. On the other hand, 14 out of 36, 9 out of 36 and 15 out of 36 genera showed significant decrease in bacterial species abundance respectively for the aerobic, hypoxic-anoxic and anoxic layers. Additionally, 14 out of 36, 20 out of 36, and 15 out of 36 genera had no change in bacterial species abundance respectively for the aerobic, hypoxic-anoxic, and anoxic layers. This indicates that the carbon utilization ability of different denitrifiers on each DO layers was generally different from each other. Diversity of denitrifying bacteria also presented significant differences in different DO layers between the high- and low-carbon content sediment layers. Moreover, under the high-carbon and low-carbon content, the abundance of nirS gene showed a high peak within the hypoxic-anoxic regions, suggesting that this region might be the main distribution area for the denitrifying bacteria within the surface sediments. Furthermore, community of unique denitrifiers occurred in different DO layers and the adaptive changes of the denitrifier community followed the organic carbon consumption.

Shifts in the Composition and Activities of Denitrifiers Dominate CO2 Stimulation of N2O Emissions.

Elevated atmospheric CO2 (eCO2) often increases soil N2O emissions, but the underlying mechanisms remain largely unknown. One hypothesis suggests that high N2O emissions may stem from increased denitrification induced by CO2 enhancement of plant carbon (C) allocation belowground. However, direct evidence illustrating linkages among N2O emissions, plant C allocation, and denitrifying microbes under eCO2 is still lacking. We examined the impact of eCO2 on plant C allocation to roots and their associated arbuscular mycorrhizal fungi and its subsequent effects on N2O emissions and denitrifying microbes in the presence of two distinct N sources, ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N). Our results showed that the form of the N inputs dominated the effects of eCO2 on N2O emissions: eCO2 significantly increased N2O emissions with NO3--N inputs but had no effect with NH4+-N inputs. eCO2 increased plant biomass N more with NH4+-N than with NO3--N inputs, likely reducing microbial access to available N under NH4+-N inputs and/or contributing to higher N2O emissions under NO3--N inputs. eCO2 enhanced root and mycorrhizal N uptake and also increased N2O emissions under NO3--N inputs. Further, eCO2 enhancement of N2O emissions under NO3--N inputs concurred with a shift in the soil denitrifier community composition in favor of N2O-producing (nirK- and nirS-type) over N2O-consuming (nosZ-type) denitrifiers. Together, these results indicate that eCO2 stimulated N2O emissions mainly through altering plant N preference in favor of NH4+ over NO3- and thus stimulating soil denitrifiers and their activities. These findings suggest that effective management of N sources may mitigate N2O emissions by negating the eCO2 stimulation of soil denitrifying microbes and their activities.

Denitrifying microbial communities along a boreal stream with varying land-use

Streams have an important role in regulating nitrogen (N) transportation from terrestrial ecosystems to downstream waters. Here, we examined how catchment land-use affects potential denitrification rates and the function and composition of denitrifier communities in boreal stream sediments, using stable isotope incubations and qPCR and 454-pyrosequencing targeted on nirS, nirK and nosZ genes. Although land-use influenced the water chemistry as higher nitrite + nitrate (NOx−) concentration at the agriculture-affected sampling point, sediment organic matter content was found to be the key factor in regulating potential denitrification rates. However, the abundance as well as the diversity and community composition of denitrifying microbes, and genetic N2O production potential (the ratio between nirS + nirK and nosZ gene abundances) were connected to both NOx− and sediment quality. Overall, our results suggest that catchment land-use-driven changes in N and carbon availability affect the denitrification rates, and possibly N2:N2O production ratio, in boreal streams, through altering denitrifier abundance and community composition.

Denitrification and anammox: Understanding nitrogen loss from Yangtze Estuary to the east China sea (ECS)

The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.

Variation of community structure and function of rhizospheric denitrifiers at tillering and booting stages of rice

We investigated the variation of denitrifying communities in rice rhizosphere at tillering and booting stages in comparison with bulk soils with a pot experiment. The techniques of quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to measure the abundance and community composition of denitrifiers (narG and nosZ), respectively. The results showed that the potential denitrification activity in the rhizosphere at tillering stage was significantly lower than bulk soils. No significant difference was detected between the rhizosphere and bulk soils at booting stage. The abundance of both narG- and nosZ-containing denitrifying bacteria was significantly higher in rhizosphere than in bulk soils at both tillering and booting stages. In comparison with narG-containing community, community composition and diversity of nosZ-containing bacteria were more sensitive to rice growth. In conclusion, the exudates of rice could induce significantly more denitrifying bacteria in rhizosphere, whose denitrifying activities were related to growth stage of rice. At the period with strong growth, the secretion of roots showed clear restriction to the functions of rhizospheric denitrifiers compared to booting stage.

Effects of Rhizosphere and Long-Term Fertilization Practices on the Activity and Community Structure of Denitrifiers Under Double-Cropping Rice Field

ABSTRACTThe soil physicochemical properties, soil denitrification rates (PDR), denitrifiers via nitrite reductases (nirK and nirS) and nitrous oxide reductase (nosZ), abundance and community composition of denitrifiers in both the rhizosphere and bulk soil from a long-term (32 year) fertilizer field experiment conducted during late rice season were investigated by using the MiSeq sequencing, quantitative PCR, terminal restriction fragment polymorphism (T-RFLP). The experiment including four treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), and organic manure and chemical fertilizer (OM). The results showed that the application of rice straw residue and organic manure increased soil organic carbon (C), total nitrogen (N), and NH4+-N contents. The nirK, nirS, and nosZ copy numbers with OM and RF treatments were significant higher than that of the MF and CK treatments in the rhizosphere and bulk soil (p < 0.05). The principal coordinate analysis (PCoA) analysis showed that the different parts of root zone are the most important factors for the variation of denitrifying bacteria community, and the different fertilization treatments is the second important factors for the variation of denitrifying bacteria community. The MiSeq sequencing result showed that nirK, nirS and nosZ-type denitrifiers communities within bulk soil had lower species diversity compared with rhizosphere soil, and were dominated by Rhizobiales, Rhodobacterales, Burkholderiales, and Pseudomonadales. As a result, the application of fertilization practices had significant effects on soil N and PDR levels, and affected the abundance and community composition of N-functional microbes.

Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients.

This study coupled a landscape-scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor, appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non-point source nitrogen pollution.

Linking soil N2O emissions with soil microbial community abundance and structure related to nitrogen cycle in two acid forest soils

Tree species and seasonal change influence N2O flux and microbial communities, but the mechanisms are unclear. We studied N2O flux in soils planted with slash pine and oil-seed camellia trees. We sampled on typical days of the four seasons. We tested whether N-cycling communities respond more to tree species or seasonal change. We assessed how tree species affect N2O flux. We used qPCR and RFLP to determine abundance and community composition of amoA-containing bacteria (AOB) and archaea (AOA), and denitrifiers that contain the narG, nirK, nirS, and nosZ genes. N2O flux rate and soil characteristics varied significantly between forest soils and sampling seasons. Abundance of all detected genes, but not of the nirS gene, was significantly affected by tree species. Differences in gene abundance between days in different seasons were found only for narG, nirK, and nosZ. Functional microbial community composition in the soil varied between the tree species for most of the genes studied, but varied, not significantly, slightly among sampling days. Differences in the abundance and community composition of nitrifiers and denitrifiers between tree species depended on soil concentration of NH4+, NO3−, and dissolved organic carbon (DOC). N2O flux rate was affected by community composition, but not abundance of nitrifiers and denitrifiers. Temperature, NO3−, and DOC concentrations significantly affected N2O flux. Tree species influenced N2O flux more than seasonal change, by altering community composition and environmental factors rather than nitrifier/denitrifier abundance.

Saltwater Intrusion Modifies Microbial Community Structure and Decreases Denitrification in Tidal Freshwater Marshes

Environmental changes can alter the interactions between biotic and abiotic ecosystem components in tidal wetlands and therefore impact important ecosystem functions. The objective of this study was to determine how saltwater intrusion affects wetland nutrient biogeochemistry, with a specific focus on the soil microbial communities and physicochemical parameters that control nitrate removal. Our work took place in a tidal freshwater marsh in South Carolina, USA, where a 3.5-year saltwater intrusion experiment increased porewater salinities from freshwater to oligohaline levels. We measured rates of denitrification, soil oxygen demand, and dissimilatory nitrate reduction to ammonium (DNRA) and used molecular genetic techniques to assess the abundance and community structure of soil microbes. In soils exposed to elevated salinities, rates of denitrification were reduced by about 70% due to changes in the soil physicochemical environment (higher salinity, higher carbon:nitrogen ratio) and shifts in the community composition of denitrifiers. Saltwater intrusion also affected the microbial community responsible for DNRA, increasing the abundance of genes associated with this process and shifting microbial community composition. Though rates of DNRA were below detection, the microbial community response may be a precursor to increased rates of DNRA with continued saltwater intrusion. Overall, saltwater intrusion reduces the ability of tidal freshwater marshes to convert reactive nitrogen to dinitrogen gas and therefore negatively affects their water quality functions. Continued study of the interrelationships between biotic communities, the abiotic environment, and biogeochemical transformations will lead to a better understanding of how the progressive replacement of tidal freshwater marshes with brackish analogues will affect the overall functioning of the coastal landscape.

Effects of biochar application on the abundance and community composition of denitrifying bacteria in a reclaimed soil from coal mining subsidence area

As a new soil amendment, biochar has become an environmentally friendly material. The application of biochar is one of the most promising management practice to improve soil quality. Using a reclaimed soil from a coal mine subsidence area, the plat soil cultivation experiment in this study investigated the effects of biochar application at varying rates on soil properties, the abundance and composition of soil denitrifier communities. Biochar application significantly increased the crop yield which might be associated with the increased level of cation exchange capacity (CEC), total nitrogen (N), ammonium-N, available phosphorus (P) and potassium (K) in soil. In combination with N fertilizer, the abundance of both nirK and nirS genes significantly increased only at biochar application rate of 4% compared with the nil-biochar treatment. Biochar application significantly increased the community diversity of nirK gene, while not for nirS gene. Redundancy analysis showed that the level of nitrate-N (NO3−-N), available P, and pH in soil significantly affected community structure of nirK gene, while the nirS community composition was only affected by soil NO3−-N level. Our results indicate that biochar application to the reclaimed soil in coal mine subsidence area could influence the abundance and diversity of soil denitrifiers and improve soil nutrients thus crop yield.

不同放牧强度下土壤氨氧化和反硝化微生物的变化特征

Soil nitrifiers and denitrifiers play key roles in determining soil nitrogen (N) availability, nitrate leaching, and N2O emission, and thus they could be indicative to the effects of grazing intensity on grassland ecosystems as well as grassland degradation. In this study, soil samples were collected from a long-term field experiment with different grazing intensities (low-level, middle-level, and high-level grazing) in arid and semi-arid grasslands in Inner Mongolia. We analyzed the responses of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifiers, in terms of abundance, community composition, and diversity, at different grazing intensities using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP) approaches. The results showed that soil pH and ammonium content ranged from 7.90-8.18 and 6.37-35.92 mg/kg, respectively. Middle-level grazing significantly increased soil pH (P = 0.03), whereas soil ammonium content was recorded as the highest in the high-level grazing treatment (P =0.02). Soil heterotrophic respiration was markedly lower owing to the effects of grazing intensity than that in the non-grazing treatment (P = 0.02). AOA-amoA and AOB-amoA gene abundances rang ed from (4.94-7.60) × 109 and (0.68-3.75) × 106 copies/g dry soil, respectively. AOA-amoA gene abundance showed no significant change in any of the treatments, whereas middle-level grazing strongly decreased AOB-amoA gene abundance (P =0.04). The abundance of nosZ gene (coding for nitrous oxide reductase) was significantly decreased in the low-level grazing treatment (P = 0. 03). The abundances of AOA and AOB were significantly influenced by ammonium content, whereas nosZ gene abundance was influenced by substrate content and soil aeration. Redundancy analysis showed that the variation in N availability induced by grazing was the major factor influencing the community composition of ammonia oxidizers and denitrifiers.

Water Quality and Diversity of Denitrifier Community Structure of Typical Scenic Water Bodies in Xi'an

Six micro-polluted landscape water bodies were selected to explore the relationship between water quality and the nirS-Type denitrifier community structure and diversity with an Illumina high-throughput sequencing technique. The results of a physico-chemical analysis of the water bodies showed that the Fengqing Park (FQ) and Laodong Park (LD) water bodies were classified as inferior Ⅴ water quality, the Qujiang Park (QJ), Mutasi Park (MTS), and Xinjiyuan Park (XJY) water bodies were classified as Ⅴ water quality, and the Yongyang Park (YY) water quality was classified as Ⅳ. The TN values varied from 1.21 mg·L-1 to 6.50 mg·L-1, with the lowest value found in YY and the highest in FQ (P<0.05). TP was significantly higher in LD (0.10 mg·L-1) and significantly lower in QJ[0.02 mg·L-1 (P<0.05)]. The NH4+-N in LD was 4.44 times higher than that in QJ and FQ (P<0.01). Illumina high-throughput sequencing revealed that the denitrifier community composition was significantly different among the six water bodies, and Paracoccus sp., Pseudomonas sp., and Rubrivivax sp. were the dominant genus species. A principle component analysis (PCA) indicated that the nirS-Type denitrifier communities of XJY and MTS were mainly regulated by NH4+-N and the permanganate index, LD and FQ were significantly influenced by NO3--N, NO2--N, TN, TP, and DO, and YY was significantly influenced by pH value. Our results showed that nirS-Type denitrifier communities were regulated by different water quality indicators.

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition.

Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems.

Overall bacterial community composition and abundance of nitrifiers and denitrifiers in a typical macrotidal estuary

Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay.

Multi-scale factors affecting composition, diversity, and abundance of sediment denitrifying microorganisms in Yangtze lakes.

Sediment denitrification is the dominant nitrogen removal pathway in many aquatic habitats and can be regulated by local-, landscape-, and regional-scale factors. However, the mechanisms for how these multiple scale factors and their interactions affect the sediment denitrifying communities remain poorly understood. In this study, we investigated the community composition, diversity, and abundance of nitrite reductase genes (nirK and nirS)-encoding denitrifiers in 74 sediment samples from 22 Yangtze lakes using clone library and quantitative PCR techniques. Information of location, climate, catchment land use, water quality, sediment properties, and plant communities at each sampling site was analyzed to elucidate the effects of regional, landscape, and local factors on the characteristics of sediment denitrifying communities. Results of canonical correspondence analysis indicated that local factors were the key determinants of denitrifying community composition, accounting for over 20% of the total variation. Additionally, certain regional and landscape factors, including elevation and catchment built-up land, were also significantly related to the composition of denitrifying communities. Variance partitioning analyses revealed that diversity and abundance in the nirK denitrifier community were largely influenced by local factors, while those in the nirS community were controlled by both local and regional factors. Our findings highlight the importance of using different scale factors to explain adequately the composition and structure of denitrifying communities in aquatic environments.

Hydrologic pulsing affects denitrification rates and denitrifier communities in a revegetated riparian ecotone

Hydrologic pulsing and revegetation strongly affect both denitrification rate and denitrifier communities in riparian zones, yet how they drive the shifts in the denitrifying bacterial community and consequently alter denitrification remains unclear. In this study, we investigated denitrification rate and denitrifier community structure and their abundance in different hydrological pulsing phases and vegetation types (tree, shrub, and herb) in the water-level-fluctuate-zone of the Three Gorges Reservoir, China. Results revealed that hydrologic pulsing greatly affected denitrification rate possibly by regulating the soil NO3−-N concentration, with higher denitrification rate in the reflooding phase in tree soils than that in the saturated and drying phases. Hydrologic pulsing also significantly regulated the abundance and structure of denitrifier communities in herb soils by altering soil temperature, moisture, and NH4+-N. As expected, vegetation types affected the denitrifier communities by altering soil texture, pH, temperature, moisture, soil organic C, and C:N ratio, with higher abundance of nirS genes and higher diversity of nirS and nirK genes in herb soils. However, there was no significant relationship between denitrification rate and denitrifier communities, indicating that hydrologic pulsing regulated denitrification rate primarily by changing soil environmental factors rather than community composition or abundance of denitrifiers. Our results suggest that tree and herb plantations would potentially improve water quality in the riparian zone and adjacent rivers by increasing denitrification rate and abundance of denitrifiers, respectively.