Differentiated response of denitrifying communities to fertilization regime in paddy soil

The dynamic features and microbial mechanism of nitrogen transformation for hydrothermal aqueous phase as fertilizer in dryland soil

Hydrothermal aqueous phase (HAP) contains abundant organics and nutrients, which have potential to partially replace chemical fertilizers for enhancing plant growth and soil quality. However, the underlying reasons for low available nitrogen (N) and high N loss in dryland soil remain unclear. A cultivation experiment was conducted using HAP or urea to supply 160 mg N kg-1 in dryland soil. The dynamic changes of soil organic matters (SOMs), pH, N forms, and N cycling genes were investigated. Results showed that SOMs from HAP stimulated urease activity and ureC, which enhanced ammonification in turn. The high-molecular-weight SOMs relatively increased during 5-30 d and then biodegraded during 30-90 d, which SUV254 changed from 0.51 to 1.47 to 0.29 L-1 m-1. This affected ureC that changed from 5.58 to 5.34 to 5.75 lg copies g-1. Relative to urea, addition HAP enhanced ON mineralization by 8.40 times during 30-90 d due to higher ureC. It decreased NO3-N by 65.35%-77.32% but increased AOB and AOA by 0.25 and 0.90 lg copies g-1 at 5 d and 90 d, respectively. It little affected nirK and increased nosZ by 0.41 lg copies g-1 at 90 d. It increased N loss by 4.59 times. The soil pH for HAP was higher than that for urea after 11 d. The comprehensive effects of high SOMs and pH, including ammonification enhancement and nitrification activity inhibition, were the primary causes of high N loss. The core idea for developing high-efficiency HAP fertilizer is to moderately inhibit ammonification and promote nitrification.

Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics

Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.

Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland

Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

Legume-grass mixtures increase forage yield by improving soil quality in different ecological regions of the Qinghai-Tibet Plateau

Introduction

Information on the relationship between soil quality and forage yield of legume-grass mixtures in different ecological regions can guide decision-making to achieve eco-friendly and sustainable pasture production. This study's objective was to assess the effects of different cropping systems on soil physical properties, nitrogen fractions, enzyme activities, and forage yield and determine suitable legume-grass mixtures for different ecoregions.

Methods

Oats (Avena sativa L.), forage peas (Pisum sativum L.), common vetch (Vicia sativa L.), and fava beans (Vicia faba L.) were grown in monocultures and mixtures (YS: oats and forage peas; YJ: oats and common vetch; YC: oats and fava beans) in three ecological regions (HZ: Huangshui Valley; GN: Sanjiangyuan District; MY: Qilian Mountains Basin) in a split-plot design.

Results

The results showed that the forage yield decreased with increasing altitude, with an order of GN (3203 m a.s.l.; YH 8.89 t·ha-1) < HZ (2661 m; YH 9.38 t·ha-1) < MY (2513m; YH 9.78 t·ha-1). Meanwhile, the forage yield was higher for mixed crops than for single crops in all ecological regions. In the 0-10 cm soil layer, the contents of total nitrogen (TN), microbial biomass nitrogen (MBN), soil organic matter (SOM), soluble organic nitrogen (SON), urease (UE), nitrate reductase (NR), sucrase (SC), and bacterial community alpha diversity, as well as relative abundance of dominant bacteria, were higher for mixed crops than for oats unicast. In addition, soil physical properties, nitrogen fractions, and enzyme activities varied in a wider range in the 0-10 cm soil layer than in the 10-20 cm layer, with larger values in the surface layer than in the subsurface layer. MBN, SON, UE, SC and catalase (CAT) were significantly and positively correlated with forage yield (P < 0.05). Ammonium nitrogen (ANN), nitrate nitrogen (NN), SOM and cropping systems (R) were significantly and positively correlated with Shannon and bacterial community (P < 0.05). The highest yields in the three ecological regions were 13.00 t·ha-1 for YS in MY, 10.59 t·ha-1 for YC in GN, and 10.63 t·ha-1 for YS in HZ.

Discussion

We recommend planting oats and forage peas in the Qilian Mountains Basin, oats and fava beans in the Sanjiangyuan District, and oats and forage peas in Huangshui valley. Our results provide new insights into eco-friendly, sustainable, and cost-effective forage production in the Qinghai Alpine Region in China.

Bioremediation of phenanthrene in saline-alkali soil by biochar- immobilized moderately halophilic bacteria combined with Suaeda salsa L

Polycyclic aromatic hydrocarbon (PAH) contaminated saline-alkali soil is commonly salinized and hardened, which leads to low self-purification efficiency, making it difficult to reuse and remediate. In this study, pot experiments were conducted to investigate remediation of PAH contaminated saline-alkali soil using biochar-immobilized Martelella sp. AD-3, and Suaeda salsa L (S. salsa). Reduction in phenanthrene concentration, PAH degradation functional genes, and the microbial community in the soil were analyzed. The soil properties and plant growth parameters were also analyzed. After a 40-day remediation, the removal rate of phenanthrene by biochar-immobilized bacteria combined with S. salsa (MBP group) was 91.67 %. Additionally, soil pH and electrical conductivity (EC) reduced by 0.15 and 1.78 ds/m, respectively. The fresh weight and leaf pigment contents increased by 1.30 and 1.35 times, respectively, which effectively alleviated the growth pressure on S. salsa in PAH-contaminated saline-alkali soil. Furthermore, this remediation resulted in abundance of PAH degradation functional genes in the soil, with a value of 2.01 × 10³ copies/g. The abundance of other PAH degraders such as Halomonas, Marinobacter, and Methylophaga in soil also increased. Furthermore, the highest abundance of Martelella genus was observed after the MBP treatment, indicating that strain AD-3 has a higher survival ability in the rhizosphere of S. salsa under the protection of biochar. This study provides a green, low-cost technique for remediation of PAH-contaminated saline-alkali soils.

Mixed legume-grass seeding and nitrogen fertilizer input enhance forage yield and nutritional quality by improving the soil enzyme activities in Sichuan, China

Information regarding relationships between forage yield and soil enzymes of legume-grass mixtures under nitrogen (N) fertilization can guide the decision-making during sustainable forage production. The objective was to evaluate the responses of forage yield, nutritional quality, soil nutrients, and soil enzyme activities of different cropping systems under various N inputs. Alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), orchardgrass (Dactylis glomerata L.), and tall fescue (Festuca arundinacea Schreb.) were grown in monocultures and mixtures (A1: alfalfa, orchardgrass, and tall fescue; A2: alfalfa, white clover, orchardgrass, and tall fescue) under three N inputs (N1: 150 kg ha^-1; N2, 300 kg ha^-1; and N3: 450 kg ha^-1) in a split plot arrangement. The results highlight that A1 mixture under N2 input had a greater forage yield of 13.88 t ha^-1 year^-1 than the other N inputs, whereas A2 mixture under N3 input had a greater forage of 14.39 t ha^-1 year^-1 than N1 input, but it was not substantially greater than N2 input (13.80 t ha^-1 year^-1). The crude protein (CP) content of grass monocultures and mixtures significantly (P < 0.05) increased with an increase in the rate of N input, and A1 and A2 mixtures under N3 input had a greater CP content of 18.91% and 18.94% dry matter, respectively, than those of grass monocultures under various N inputs. The A1 mixture under N2 and N3 inputs had a substantially greater (P < 0.05) ammonium N content of 16.01 and 16.75 mg kg^-1, respectively, whereas A2 mixture under N3 had a greater nitrate N content of 4.20 mg kg^-1 than the other cropping systems under various N inputs. The A1 and A2 mixtures under N2 input had a substantial higher (P < 0.05) urease enzyme activity of 0.39 and 0.39 mg g^-1 24 h^-1 and hydroxylamine oxidoreductase enzyme activity of 0.45 and 0.46 mg g^-1 5 h^-1, respectively, than the other cropping systems under various N inputs. Taken together, growing legume-grass mixtures under N2 input is cost-effective, sustainable, and eco-friendly, which provide greater forage yield and improved nutritional quality by the better utilization of resources.

Organic carbon release, denitrification performance and microbial community of solid-phase denitrification reactors using the blends of agricultural wastes and artificial polymers for the treatment of mariculture wastewater

This paper explored the possibility of heterotrophic denitrification driven by composite solid carbon sources in low carbon/nitrogen ratio marine recirculating aquaculture wastewater. In this study, two agricultural wastes, reed straw (RS), corn cob (CC) and two artificial polymers, polycaprolactone (PCL), poly3-hydroxybutyrate-hydroxypropionate (PHBV) were mixed in a 1:1 ratio to compare the carbon release characteristics of the four composite carbon sources (RS+PCL, RS+PHBV, CC+PCL, and CC+PHBV) and their effects on improving the mariculture wastewater for denitrification. Dissolved organic carbon (DOC) after carbon source release (4.96-1.07 mg/g), total organic carbon/chemical oxygen demand (1.9-0.79) and short-chain fatty acids (SCFAs) (4.23-0.21 mg/g) showed that all the four composite solid carbon sources had excellent organic carbon release ability, and the CC+PCL group had the highest release of DOC and SCFAs. Energy-dispersive X-ray spectroscopy, scanning electron microscopy, and Fourier-transform infrared spectroscopy were used to observe the changes in the surface characteristics of the composite carbon source before and after application. And results showed that the stable internal structure enabled CC+PCL group to have continuous carbon release performance and achieved the maximum denitrification efficiency (93.32 %). The NRE results were supported by the abundance of the Proteobacteria microbial community at the phylum level and Marinobacter at the genus level. Quantitative real-time PCR (q-PCR) indicated CC-containing composite carbon source groups have good nitrate reduction ability, while PCL-containing composite carbon source groups have better nitrite reduction level. In conclusion, the carbon source for agricultural wastes and artificial polymers can be used as an economic and effective solid carbon source for denitrification and treatment of marine recirculating aquaculture wastewater.

Comparative investigation on heterotrophic denitrification driven by different biodegradable polymers for nitrate removal in mariculture wastewater: Organic carbon release, denitrification performance, and microbial community

Heterotrophic denitrification is widely studied to purify freshwater wastewater, but its application to seawater wastewater is rarely reported. In this study, two types of agricultural wastes and two types of synthetic polymers were selected as solid carbon sources in denitrification process to explore their effects on the purification capacity of low-C/N marine recirculating aquaculture wastewater (NO₃ ^--N 30 mg/L, salinity 32‰). The surface properties of reed straw (RS), corn cob (CC), polycaprolactone (PCL) and poly3-hydroxybutyrate-hydroxypropionate (PHBV) were evaluated by Brunauer-Emmett-Teller, Scanning electron microscope and Fourier-transform infrared spectroscopy. Short-chain fatty acids, dissolved organic carbon (DOC), and chemical oxygen demand (COD) equivalents were used to analyze the carbon release capacity. Results showed that agricultural waste had higher carbon release capacity than PCL and PHBV. The cumulative DOC and COD of agricultural waste were 0.56-12.65 and 1.15-18.75 mg/g, respectively, while those for synthetic polymers were 0.07-1.473 and 0.045-1.425 mg/g, respectively. The removal efficiency of nitrate nitrogen (NO₃ ^--N) was CC 70.80%, PCL 53.64%, RS 42.51%, and PHBV 41.35%. Microbial community analysis showed that Proteobacteria and Firmicutes were the most abundant phyla in agricultural wastes and biodegradable natural or synthetic polymers. Quantitative real-time PCR indicated the conversion from nitrate to nitrogen was achieved in all four carbon source systems, and all six genes had the highest copy number in CC. The contents of medium nitrate reductase, nitrite reductase and nitrous oxide reductase genes in agricultural wastes were higher than those in synthetic polymers. In summary, CC is an ideal carbon source for denitrification technology to purify low C/N recirculating mariculture wastewater.

The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies

Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO₃, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.

Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus

Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Response of N2O emission and denitrification genes to different inorganic and organic amendments

Denitrification is a key biochemical process in nitrogen cycling and nitrous oxide (N₂O) production. In this study, the impacts of different inorganic and organic amendments (OAs) on the abundance of denitrifying genes (nirS, nirK and nosZ) and the level of N₂O emission were examined with incubation experiments. Six treatments included the indicated applications: (i) no fertilization (CK); (ii) urea application alone (U); (iii) wheat straw plus urea (U + WS); (iv) pig manure plus urea (U + PM); (v) compost product plus urea (U + CP); and (vi) improved compost product plus urea (U + IC). The results indicated that all fertilization treatments increased accumulative N₂O emissions compared with the CK treatment. The U + WS, U + PM and U + CP treatments increased N₂O emissions by 2.12–141.3%, and the U + IC treatment decreased N₂O emissions by 23.24% relative to the U treatment. nirK was the dominant denitrification gene rather than nirS and nosZ found in soil. Additionally, the highest abundance of nirK gene was that with the U + PM treatment, and the lowest was that with the U + IC treatment. Additionally, changes in the nirK gene were highly correlated with levels of dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and nitrate nitrogen (NO₃^–N). Automatic linear modeling revealed that N₂O emission was closely related to the nirK gene, DOC and NO₃^–N. Overall, the use of urea and improved compost as co-amendments retarded N₂O emission to a considerable degree compared with other OA additions.

Effects of Plastic versus Straw Mulching Systems on Soil Microbial Community Structure and Enzymes in Strawberry Cultivation

This study aimed to evaluate changes in abundance, structure, and enzyme activity of the soil microbiome in response to 4 years of mulching using either black polyethylene plastic film (PM) or wheat straw (SM). Soil samples (depth 0–5 and 5–10 cm) were collected from conventional strawberry plots, in two samplings: 1 week prior (S1) and 7 weeks after straw application (S2). Selected soil properties were monitored in each system and the abundance and structure of microbial communities were characterized via phospholipid fatty acid (PLFA) analysis. The investigation of soil microbial functions included activities of the enzymes chitinase, leucine aminopeptidase, and acid phosphatase, as well as function genes involved in nitrogen transformation. Each mulch system resulted in distinct physicochemical properties. In particular, a pH value higher by one-unit under PM (7.6 ± 0.3) compared to SM (6.5 ± 0.3) was observed. Values for SOC, DOC, and total-N were 15%, 22%, and 16% higher in PM than in SM. The microbial biomass (total PLFAs) was 1.5-fold higher in SM compared to PM. The abundance of soil fungi (F) and bacteria (B) increased by 37% and 44% after straw incorporation compared to PM (S2). In particular, Gram-negative bacteria (gr–) increased by twofold in SM. Consequently, wider F:B and gr+:gr– ratios were observed in PM. According to the shifts in microbial abundance, the activity of the enzyme chitinase was lower by 27% in PM, while the activity of the acid phosphatase increased by 32%. Denitrification genes were not affected by the mulching systems. In conclusion, the abundance and structure of the investigated microbial groups and the enzyme activities were strongly influenced by the mulching system. In detail, effects on microbiota were primarily attributed to the altered soil pH and probably the input of degradable organic matter with straw mulching in SM. This resulted in higher abundance of soil microorganisms in SM, although measures within this cultivation system such as fungicide application may have exerted adverse effects on the microbiota.

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha^-1 year^-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha^-1 year^-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha^-1 year^-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha^-1 year^-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH₄⁺, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO₂^-/NH₄⁺ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.

Effects of increasing organic nitrogen inputs on CO2, CH4, and N2O fluxes in a temperate grassland

Understanding future climate change requires accurate estimates of the impacts of atmospheric nitrogen (N) deposition, composed of both inorganic and organic compounds, on greenhouse gas (GHG) fluxes in grassland ecosystems. However, previous studies have focused on inorganic compounds and have not considered the potential effects of organic N sources. Here, we conducted a grassland experiment that included organic, inorganic N, and a mix of them at a ratio of 4:6, with two input rates, to study N inputs induced CO₂, CH_4, and N₂O fluxes, as well as the potential abiotic and biotic mechanisms driving the fluxes. We found that N compositions significantly affected fluxes each of the three GHGs. Greater organic N decreased the impacts of N addition on CO₂ and N₂O emissions, caused primarily by low rates of increase in substrates (soil available N) for production of CO₂ and N₂O resulting from high ammonia volatilization rather than changes in microbial activity. Also, greater organic N slightly stimulated CH₄ uptake. Nitrogen composition effects on CO₂ emissions and CH₄ uptake were independent of N input rates and measurement dates, but N₂O emissions showed stronger responses to inorganic N under high N addition and in June. These results suggest that future studies should consider the source of N to improve our prediction of future climate impact of N deposition, and that management of N fertilization can help mitigate GHG emissions.

Effects of environmental factors on denitrifying bacteria and functional genes in sediments of Bohai Sea, China

The ability of denitrifying microorganisms to respond to different ecological pressures remains unknown, especially in marine sediments rich in various heavy metals. Here, gene abundance and transcriptional abundance of five functional denitrification genes (narG, nirK, nirS, norB, and nosZ) in Bohai Sea sediments were examined, and high-throughput Illumina sequencing was used to analyze the community structure of nirK and nirS denitrifying bacteria. The nirS- and nirK-type denitrifying bacteria were classified into different genera. The heavy metal content in sediments was negatively correlated with transcriptional abundance of denitrifying genes, and RNA: DNA ratio for each gene was highest in central Bohai Sea. These results indicated the distribution of nitrite reductase denitrifying bacterial communities was affected by depth, total nitrogen, total phosphorus and sediment grain size. Heavy metal contamination in sediment environment may negatively regulate the transcriptional abundance of denitrifying genes and cause geographical differences in the denitrifying bacterial community structure.

The responses of soil nitrogen transformation to nitrogen addition are mainly related to the changes in functional gene relative abundance in artificial Pinus tabulaeformis forests

The increase of soil nitrogen (N) availability may alter soil microbial community composition and the natural N cycle in forest ecosystems. However, the responses of soil microbial nitrogen functional genes (NFGs) to N addition and their consequent effect on the N-cycle processes are poorly understood. In this study, soil samples were collected from an artificial Pinus tabulaeformis forest located in Loess Plateau (China) to which N at four different concentrations was added (0 [N0], 3 [N3], 6 [N6], and 9 [N9] g N m^-2 y^-1) for 4 years. We quantified the relative abundance of NFGs using functional gene microarray GeoChip 5.0 and determined net N transformation and N₂O emission rates in a 14-day incubation experiment. The results showed that N3 and N6 treatments did not significantly affect the total relative abundance and diversity of NFGs assemblage but significantly increased the relative abundance of specific genes for the NH₃ cycle (ureC, nirA, and nrfA), and nitrification (amoA) and denitrification (norB). These positive effects were related to the increase in soil organic C, NO₃^--N, and microbial biomass C (MBC). N9 treatment significantly decreased the relative abundance of all NFGs, and this negative impact was correlated with reduced dissolved organic C and MBC. Moreover, N addition significantly changed net N nitrification, mineralization, and N₂O emission rates, and NFGs explained the higher variances in the N transformation processes than soil properties. Specifically, ammonia-oxidizing archaea (amoA-AOB) and MBC were the key factors related to net N nitrification; ureC, nirK, and MBC were the key factors related to net N mineralization; and narG and nirS were the key factors related to N₂O emission. Our results show that global N deposition may mainly influence N transformation processes by regulating the corresponding NFG relative abundance, thereby affecting the N cycle in forest soils.

Zeolite-supported nanoscale zero-valent iron for immobilization of cadmium, lead, and arsenic in farmland soils: Encapsulation mechanisms and indigenous microbial responses

Zeolite-supported nanoscale zero-valent iron (Z-NZVI) has great potential for metal(loid) removal, but its encapsulation mechanisms and ecological risks in real soil systems are not completely clear. We conducted long-term incubation experiments to gain new insights into the interactions between metal(loid)s (Cd, Pb, As) and Z-NZVI in naturally contaminated farmland soils, as well as the alteration of indigenous bacterial communities during soil remediation. With the pH-adjusting and adsorption capacities, 30 g kg^-1 Z-NZVI amendment significantly decreased the available metal(loid) concentrations by 10.2-96.8% and transformed them into strongly-bound fractions in acidic and alkaline soils after 180 d. An innovative magnetic separation of Z-NZVI from soils followed by XRD and XPS characterizations revealed that B-type ternary complexation, heterogeneous coprecipitation, and/or concurrent redox reactions of metal(loid)s, especially the formation of Cd₃(AsO₄)₂, PbFe₂(AsO₄)₂(OH)₂, and As⁰, occurred only under specific soil conditions. Sequencing of 16S rDNA using Illumina MiSeq platform indicated that temporary shifts in iron-resistant/sensitive, pH-sensitive, denitrifying, and metal-resistant bacteria after Z-NZVI addition were ultimately eliminated because soil characteristics drove the re-establishment of indigenous bacterial community. Meanwhile, Z-NZVI recovered the basic activities of bacterial DNA replication and denitrification functions in soils. These results confirm that Z-NZVI is promising for the long-term remediation of metal(loid)s contaminated farmland soil without significant ecotoxicity.

Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens)

Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N₂O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 10⁷ copies/g dry soils) and IM25 (5.42 × 10⁷ copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.

Quantification of denitrifier genes population size and its relationship with environmental factors

The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 10⁸, 2.25 × 10⁷, 2.9 × 10⁵, 4.0 × 10⁶ and 1.75 × 10⁷ copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N₂O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.

Dynamics and underlying mechanisms of N2O and NO emissions in response to a transient land-use conversion of Masson pine forest to tea field

Nowadays, there has been a rapid expansion of tea field converted from forestry for pursuing higher economic benefits. However, few researches focus on the effects of transient land-use conversion from Masson pine forest to artificial tea fields on soil N₂O and NO emissions and the underlying mechanisms. A parallel field experiment was conducted from Masson pine forest and a newly converted tea plantation from Masson pine forest from 2013 to 2017 in subtropical central China. Masson pine forest conversion to tea field dramatically increased soil N₂O and NO emissions (up to 4.00 ± 0.43 and 1.93 ± 0.45 kg N ha^-1 yr^-1, respectively) in the first year possibly due to enhanced soil organic N mineralization. With the extension of tea planting age, N₂O and NO emissions showed an upward trend (ranged from 1.19 to 5.28, and 0.15 to 1.78 kg N ha^-1 yr^-1, respectively) influenced by fertilization and soil organic matter accumulation. The direct emission factors for N₂O and NO in the newly converted tea fields were the largest in the first year (2.64 and 1.07%, respectively) after land-use conversion, and higher than the default value recommended by IPCC. The NO/N₂O ratio was mainly lower than 1 in the fertilized tea field, and soil N₂O and NO emission peaks mainly occurred in tea-growing season (wet season) with higher soil moisture and NH₄⁺-N concentrations, and dominated by amoA-containing bacteria (AOB), suggesting nitrifier-denitrification could be the dominant process involved in soil nitrogenous gases emissions in tea field. These results can be summarized as dramatically increased soil N₂O and NO emissions during the transient land-use conversion from Masson pine forest to tea field were possibly due to the substantial net soil organic N mineralization and the enhanced abundance of nitrification functional genes (AOB).

Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China

Background

The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years).

Methods

The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR).

Results

nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).

Effect of plant-based carbon source supplements on denitrification of synthetic wastewater: focus on the microbiology

The effects of plant-based carbon source addition on wastewater NO₃^--N removal and the involved microorganisms, especially denitrifying bacteria, were investigated. A synthetic wastewater (NO₃^--N, 15 mg/L) was treated through the batch experiment, which included three inoculation cycles (7 days/cycle), and was conducted at 25 °C. Four natural plant substrates, namely, rice straw (RS), wheat straw (WS), ryegrass (RG), and reed (RD), were used as carbon sources and supplemented at the rate of 1% (w/v). The results showed that both RS and WS performed well in promoting NO₃^--N removal (79.55-97.07%). While RG removed only 22.08% of NO₃^--N in the first cycle, the removal efficiency increased afterward (86.09-95.82%). Conversely, the NO₃^--N removal rate of RD decreased from 95.10 to 24.77% as a result of its low ability to supply carbon. With respect to the microorganisms, the RS treatment resulted in more bacteria and denitrifying genes such as narG, nirK, nirS, and norB than other treatments, while the highest number of nosZ gene copies was recorded in the WS treatment. Sequencing results revealed that Firmicutes (18.19-56.96%), Proteobacteria (38.82-74.80%), and Bacteroidetes (3.15-4.15%) were three dominant bacterial phyla for RS, WS, and RD treatments. Furthermore, the genera Enterobacter, Massilia, and Bacillus were the main denitrifying bacteria participating in the NO₃^--N removal. Furthermore, correlation analysis indicated that the denitrifying genus Sphingobacterium played an important role in enhancing nitrogen removal. This study suggested that RS is the superior plant-based carbon source for denitrifying bioreactors used in agricultural runoff treatment.

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

Remarkable N2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities

Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N₂O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N₂O concentrations in the soil and N₂O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N₂O concentrations in the soil and N₂O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N₂O net production and emissions after draining. Moreover, we observed that N₂O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH₄⁺-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N₂O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N₂O emissions as shorter distance of gas diffusion to the soil surface.

Restoration of Long-Term Monoculture Degraded Tea Orchard by Green and Goat Manures Applications System

Tea is an economic shrubby plant in tropical and subtropical regions of the world. To obtain high yield in tea cultivation, chemical fertilizer application rates have generally been used. However, a large quantity of chemical fertilizer application in a long-term continuously ratooned and monoculture tea orchard can inevitably lead to soil acidification and a decline in fertility. Therefore, the restoration of soil fertility and the sustainable development of tea planting by organic ways are critical for the tea industry. In this study, field trials were conducted in the tea orchard that was continuously ratooned and mono-cultured for 20 years. Nitrogen fertilizer (NF), Laredo soybeans green manure (LF), and goat manure (GM) treatments were applied to restore optimum acidity, soil fertility, microbial activity, and the community structure of a long-term continuously monoculture tea orchard. This paper investigated that the pH value was increased from 4.23 to 4.32 in GM and LF, respectively. Similarly, the content of exchangeable acidity (EA) was decreased by 1.21 and 1.46 cmol·kg−1 in GM and LF, respectively. Available nutrient results indicated that the content of NH4+-N was increased by 3.96, 4.38, NO3−-N by 1.07, 2.16, AP by 3.46, 6.86, AK by 0.26, 0.3 mg kg−1 in GM and LF treatments, respectively. Enzyme analysis revealed that the activity of urease and sucrase was promoted by 7.98 mg·g−1·24 h−1 and 6.77 mg·g−1·24 h−1, respectively, in LF treatment. Likewise, the activity of acid phosphatase and polyphenol oxidase was sharply increased by 2.3 mg·g−1 h−1 and 63.07 mg·g−1 h−1 in LF treatments. Additionally, the activity of urease, sucrase, acidic phosphatase, polyphenol oxidase, and peroxidase were also significantly increased by applying GM treatments. Meanwhile, LF and GM treatments significantly improved soil microbial biomass as well as low weight organic acid content in degraded tea rhizosphere. Furthermore, high throughput sequence results illustrated that the relative abundance of Rhizobiaceae and Bradyrhizobiaceae families increased in LF and GM treatments, respectively, which are mostly a kind of nitrogen fixer and plant growth promoting bacteria. Taken together, the physiological traits of the new sprouts and the biochemical components of new tea leaves were also significantly improved by GM and LF treatments. From this study, it is concluded that LF and GM are good agriculture management practices, which promote plant growth, yield, and nutrient availability by maintaining and improving pH, enhancing available nutrients status, improving the secretion of low molecular weight organic acids, and balancing the microbial community structure in the long-term mono-cultured tea orchard.

N2O emission contributions by different pathways and associated microbial community dynamics in a typical calcareous vegetable soil

Nitrous oxide, one of the powerful long-lived greenhouse gases, is emitted mainly through biological processes, especially from fertilized soil. It is critical to partition the contribution of different pathways to N₂O emissions and the relevant characteristics of microbial communities to identify the key N₂O processes. An microcosm was conducted to partition the N₂O emissions from different pathways, and the changes in soil mineral nitrogen and various nitrifiers (amoA bacteria and amoA archaea) and denitrifiers (nirS, nirK, and nosZ) were also determined using qPCR and high-throughput sequencing methods. Different gas inhibitor combinations (i.e., 0.06% acetylene, pure oxygen, 0.06% acetylene in pure oxygen, and pure helium) were used to partition the N₂O pathways. A 5% oxygen treatment, with and without acetylene, was also included so that the N₂O emissions could be measured under lower oxygen partial pressure. Results showed that ammonia-oxidation (AO) and successive nitrifier denitrification (NiD) were the main pathways contributing to N₂O emissions at the earlier period after ammonium sulfate application with the cumulative N₂O emissions accounting for 30.9% and 59.2% of the total N₂O emissions, respectively. The higher NiD N₂O contributions occurred when the soil nitrite concentration appeared higher, especially under the lower oxygen conditions. Higher N₂O emissions from AO and NiD were associated with the compositional proportion of some dominant AOB species. Denitrification contributed more N₂O (63.6%-69.3%) in the later period during incubation, coinciding with the following characteristics for denitrifiers: a) lower nosZ/(nirS + nirK) ratio, b) more diversity in nirS, and c) different proportions of some dominant species in nirK. Our results demonstrated that higher AO and successive NiD were the main N₂O emission pathways, suggesting that controlling the ammonium content and weakening the AO are critical in decreasing N₂O emissions.

The role of COD/N ratio on the start-up performance and microbial mechanism of an upflow microaerobic reactor treating piggery wastewater

This study investigated the role of COD/N ratio on the start-up and performance of an upflow microaerobic sludge reactor (UMSR) treating piggery wastewater at 0.5 mgO₂/L. At high COD/N ratio (6.24 and 4.52), results showed that the competition for oxygen between ammonia-oxidizing bacteria, nitrite-oxidizing bacteria and heterotrophic bacteria limited the removal of nitrogen. Nitrogen removal efficiency was below 40% in both scenarios. Decreasing the influent COD/N ratio to 0.88 allowed achieving high removal efficiencies for COD (∼75%) and nitrogen (∼85%) due to the lower oxygen consumption for COD mineralization. Molecular biology techniques showed that nitrogen conversion at a COD/N ratio 0.88 was dominated by the anammox pathway and that Candidatus Brocadia sp. was the most important anammox bacteria in the reactor with a relative abundance of 58.5% among the anammox bacteria. Molecular techniques also showed that Nitrosomonas spp. was the major ammonia-oxidiser bacteria (relative abundance of 86.3%) and that denitrification via NO₃^- and NO₂^- also contributed to remove nitrogen from the system.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics

Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies. This metatranscriptomic analysis provides novel insights into the diversity of RNT microbes present in paddy soils and the ecological function of Deltaproteobacteria predominating in these soils.

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors

Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.

Elevated N2O emission by the rice roots: based on the abundances of narG and bacterial amoA genes

Rice fields are an important source of nitrous oxide (N₂O), where rice plants could act as a key factor controlling N₂O fluxes during the flooding-drying process; however, the microbial driving mechanisms are unclear. In this study, specially designed equipment was used to grow rice plants and collect emitted N₂O from the root-growing zone (zone A), root-free zones (zones B, C, and D) independently, at tillering and booting stages under flooding and drying conditions. Soil samples from the four zones were also taken separately. Nitrifying and denitrifying community abundances were detected using quantitative polymerase chain reaction (qPCR). The N₂O emission increased significantly along with drying, but the N₂O emission capabilities varied among the four zones under drying, while zone B possessed the highest N₂O fluxes that were 2.7~4.5 times higher than those from zones C and D. However, zone A showed N₂O consumption potential. Notably, zone B also harbored the highest numbers of narG-containing denitrifiers and amoA-containing nitrifiers under drying at both tillering and booting stages. This study demonstrates that drying caused significant increase in N₂O emission from rhizosphere soil, in which the higher abundance of AOB would help to produce more nitrate and significantly higher narG-containing microbes would drive more N₂O production and emission.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils

The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.

Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices

The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.