Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites

In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.

Nitrogen deposition stimulated winter nitrous oxide emissions from bare sand more than biological soil crusts in cold desert ecosystem

Dryland ecosystems are often nitrogen-limited, and small nitrogen inputs may produce large responses to dryland ecological processes, such as gaseous nitrogen emission. The effect of increased anthropogenic nitrogen deposition on N₂O and NO emissions in desert ecosystems is unclear, especially in non-growing seasons when the surface is covered with snow. In this study, nitrogen applications were performed on biological soil crusts (lichen crust and moss crust, bare sand for control) in the Gurbantunggut Desert, Northwest China. We measured the fluxes of N₂O and NO and related nitrogen cycle functional gene abundances in winter for three-years period. Nitrogen addition significantly affected N₂O emissions and increased the abundances of key functional gene for nitrogen cycle, while it only slightly influenced NO emissions. These effects of nitrogen addition depended on composition of biological soil crusts. For bare sand and lichen crust, nitrogen addition significantly increased N₂O emissions, whereas for moss crust, only a negligible effect was observed. Meanwhile, significant differences in nitrogen cycle functional gene abundances were found among different composition of biological soil crusts. Abundance of amoA, narG, and nosZ genes were highly related to N₂O and NO emissions. Thus, our results indicate that gaseous nitrogen emissions were generally increased by nitrogen addition through their effects on related functional microbial groups. The effects were regulated by composition of biological soil crusts which can buffer the effects of increasing nitrogen addition during winter.

Effects of reclaimed wastewater irrigation on soil-crop systems in China: A review

Reclaimed wastewater (RW) use represents a substantial opportunity to alleviate the growing scarcity of water for irrigation of agricultural crops in China. However, insufficient understanding of the effects and fates of possible contaminants in RW promotes concerns over crop safety and prevents the extensive incorporation of RW in agriculture. We reviewed the characteristics of contaminants in RW, the fate of contaminants in soil-crop systems, and the effects of RW irrigation on soil quality and crop growth in China. We found that concentrations of heavy metals in RW were higher than the permissible limits in some areas. The total concentrations and main categories of emerging contaminants and pathogens in RW varied markedly among municipal wastewater treatment plants, and the greatest risks of contamination were posed by ofloxacin, sulfamethoxazole, and erythromycin, the most frequently observed compounds with risk quotients >1. The negative effects of salts and nutrients in RW on soil quality and crop growth were minor and manageable. The accumulation of heavy metals and emerging contaminants in soils irrigated with RW did not pose an immediate risk to soils and crops. Changes in soil microbial populations, diversity, and activity caused by RW irrigation increased crop yields and protected crops against contaminants. However, attention is necessary to the risks of bioaccumulation in soils and crops of heavy metals, emerging contaminants, intermediate metabolites, and pathogens, and their effects on human health with long-term RW irrigation. We recommend irrigation practices, crop screening, soil treatments, prioritizing the risks of contaminants, and comprehensive management to increase safety in RW used for agricultural irrigation.

Spatial and temporal variations of Cu and Cd mobility and their controlling factors in pore water of contaminated paddy soil under acid mine drainage: A laboratory column study

Acid mine drainage (AMD) poses a potential threat to human health worldwide, due to its high content of inorganic contaminants including heavy metals. Nevertheless, AMD is commonly used for irrigation of paddy soils. To determine the extent to which AMD affects contaminant levels in such practices, the effect of continuous AMD flooding on pH, redox potential Eh and the migration of Cu and Cd in contaminated paddy soil was studied in column experiments. By means of simulated AMD, dynamic changes of Cu and Cd concentrations in pore water were measured and the controlling factors pH, Eh and presence of Fe, dissolved organic carbon and sulfate were determined over a period of 60 days. Minerals in the soil were assessed by means of an Eh-pH diagram and solid-phase mineral detection. During continuous flooding with AMD-simulated water the soil pH increased, while Eh decreased over time. After 60 days the soil pH stabilized. Cu and Cd concentrations in the pore water negatively correlated with pH and with sulfate concentrations. Five-step sequential extraction illustrated that the fraction of exchangeable Cu increased significantly during AMD flooding. The overall content of Cu increased from initially 0.29 mg/g to 0.41 mg/g, while the content of Cd decreased from 9.2 mg/g to approximately 7.2 mg/g. Mobility factors were calculated and these conformed that Cd mobility significantly increased in contaminated soils during continuous AMD flooding. Our findings indicate that the release of Cu and Cd under AMD flooding can increase potential environmental risks, even though they lead to formation of metal sulfide deposits under anaerobic conditions. The presented data improves our understanding of the impact of overlying water conditions on the mobility of toxic metals in contaminated paddy soils.

A modified slow sand filtration system of epikarst spring water in karst mountainous areas, China

Epikarst springs are commonly used for drinking water in karst mountainous areas, but they tend to bring health risks to residents because of their vulnerability. In this work, a modified slow sand filtration system (M-SSF) was established as a case study to purify and conserve the epikarst spring water. The outcomes indicate that the purification of M-SSF relies mainly on the adsorption and ion exchange of the filter medium (mixtures of heat-treated red clay and crushed limestone, MHRCCL) during the schmutzdecke juvenility, and on the schmutzdecke-formed food chain of pollutants → bacteria → protozoa after the schmutzdecke maturity. The closed water cellar lined with ceramic tiles could reduce the deterioration of epikarst spring water during storage. Via 16S rRNA sequencing, it was found that the high abundance of TM6_Dependentiae in purified epikarst spring water (PESW) suggested that the M-SSF system relies on the formation of a closed food chain to achieve effective water purification. The decrease of Pseudarcicella abundance in PESW indicated that M-SSF could effectively prevent the water quality from external influences represented by leeches. Besides, the 16S function prediction was used to qualitatively characterize microbial nitrogen metabolism, as well as organic matter degradation in water purification.

Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil

Nitrous oxide (N₂O) is a strong greenhouse gas, and it is of great significance for N₂O reduction to study the effects of biochar on its production pathway. In this research, the contributions and mechanisms of biochar on autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and denitrification (DF) to N₂O emissions were studied by using ¹⁵N stable isotopes and high-throughput sequencing after laboratory incubation. The results showed that biochar addition at 2% (B2) significantly reduced the N₂O emissions from the ANF by an average of 20.6%, while adding 5% biochar (B5) had no significant effect on the ANF. Both B2 and B5 significantly reduced the N₂O emissions from the HNF by 15.7% and 13.2%, respectively, and reduced the N₂O emissions from the DF by 40.9% and 11.7%, respectively. B2 enhanced the relative contribution rate of the ANF to N₂O emissions by 6.3%, while B5 had little effect on it. Biochar addition significantly changed the copy numbers of the AOA and AOB, as well as the nirK, nirS, and nosZ genes, but it had no significant effect on the community composition of the AOA and had minimal effect on the AOB community. B2 significantly increased the abundance of the genus Rhodococcus of nirK type denitrifiers and had a significant effect on the relative abundance of Cupriavidus and Pseudomonas of the nosZ type denitrifiers. These results revealed that the inhibitory effects of biochar on N₂O emissions from nitrification might be attributed to the direct immobilization and adsorption of inorganic N by biochar and to its promotion of the genus Rhodococcus of nirK-type denitrifiers and the genera Cupriavidus and Pseudomonas of the nosZ-type denitrifiers. The soil exchangeable NH₄⁺-N and NO₃^--N concentrations were the primary factors affecting the N₂O emission rates. These results help to elucidate the effects and mechanisms of biochar on N₂O production pathways in agricultural soil.

Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil

Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community's resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Calcium Superphosphate-Mediated Reshaping of Denitrifying Bacteria Community Contributed to N2O Mitigation in Pig Manure Windrow Composting

Composting is recognized as an effective strategy for the sustainable use of organic wastes, but also as an important emission source of nitrous oxide (N2O) contributing to global warming. The effects of calcium superphosphate (CaSSP) on N2O production during composting are reported to be controversial, and the intrinsic microbial mechanism remains unclear. Here, a pig manure windrow composting experiment lasting for ~60 days was performed to evaluate the effects of CaSSP amendment (5%, w/w) on N2O fluxes in situ, and to determine the denitrifiers' response, and their driving factors. Results indicated that CaSSP amendment significantly reduced N2O emissions as compared to the control pile (maximum N2O emission rate reduced by 64.5% and total emission decreased by 49.8%). CaSSP amendment reduced the abundance of nirK gene encoding for nitrite reductase, while the abundance of nosZ gene (N2O reductase) was enriched. Finally, we built a schematic model and indicated that the abundance of nirK gene was likely to play a key role in mediating N2O production, which were correlated with NH4+-N and NO3--N changing responsive to CaSSP. Our finding implicates that CaSSP application could be a potential strategy for N2O mitigation in manure windrow composting, and the revealed microbial mechanism is helpful for deepening the understanding of the interaction among N-cycle functional genes, physicochemical factors, and greenhouse gases (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.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Differences in distribution of functional microorganism at DNA and cDNA levels in cow manure composting

Denitrification and nitrification processes are the two prominent pathways of nitrogen (N) transformation in composting matrix. This study explored the dynamics of denitrifying and nitrifying bacteria at different composting stages of cow manure and corn straw using functional gene sequencing at DNA and cDNA levels. Corresponding agreement among OTUs, NMDS, mental test and network analyses revealed that functional bacteria community compositions and responses to physicochemical factors were different at DNA and cDNA levels. Specifically, some OTUs were detected at the DNA level but were not observed at cDNA level, differences were also found in the distribution patterns of nitrifying and denitrifying bacteria communities at both levels. Furthermore, co-occurrence network analysis indicated that Pseudomonas, Paracoccus and Nitrosomonas were identified as the keystone OTUs at the DNA level, while Paracoccus, Agrobacterium and Nitrosospira were keystone OTUs at the cDNA level. Mantel test revealed that TN, C/N and moisture content significantly influenced both the denitrifying bacteria and ammonia-oxidizing bacteria (AOB) communities at the DNA level. NO₃^--N, NH₄⁺-N, TN, C/N, and moisture content only registered significant correlation with the nosZ-type denitrifiers and ammonia-oxidizing bacteria (AOB) communities at the cDNA level. Structural equation model (SEM) showed that TN, NH₄⁺-N, and pH were direct and significantly influenced the gene abundance of denitrifying bacteria. Howbeit, TN, NH₄⁺-N, and NO₃^--N had significant direct effects on amoA gene abundance.

Manure application increased denitrifying gene abundance in a drip-irrigated cotton field

Application of inorganic nitrogen (N) fertilizer and manure can increase nitrous oxide (N₂O) emissions. We tested the hypothesis that increased N₂O flux from soils amended with manure reflects a change in bacterial community structure and, specifically, an increase in the number of denitrifiers. To test this hypothesis, a field experiment was conducted in a drip-irrigated cotton field in an arid region of northwestern China. Treatments included plots that were not amended (Control), and plots amended with urea (Urea), animal manure (Manure) and a 50/50 mix of urea and manure (U+M). Manure was broadcast-incorporated into the soil before seeding while urea was split-applied with drip irrigation (fertigation) over the growing season. The addition treatments did not, as assessed by nextgen sequencing of PCR-amplicons generated from rRNA genes in soil, affect the alpha diversity of bacterial communities but did change the beta diversity. Compared to the Control, the addition of manure (U+M and Manure) significantly increased the abundance of genes associated with nitrate reduction (narG) and denitrfication (nirK and nosZ). Manure addition (U+M and Manure) did not affect the nitrifying enzyme activity (NEA) of soil but resulted in 39–59 times greater denitrifying enzyme activity (DEA). In contrast, urea application had no impact on the abundances of nitrifier and denitrifier genes, DEA and NEA; likely due to a limitation of C availability. DEA was highly correlated (r = 0.70–0.84, P < 0.01) with the abundance of genes narG, nirK and nosZ. An increase in the abundance of these functional genes was further correlated with soil NO₃⁻, dissolved organic carbon, total C, and total N concentrations, and soil C:N ratio. These results demonstrated a positive relationship between the abundances of denitrifying functional genes (narG, nirK and nosZ) and denitrification potential, suggesting that manure application increased N₂O emission by increasing denitrification and the population of bacteria that mediated that process.

Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil

This study intended to evaluate the combined effects of both biochar and organic fertilizer on nitrous oxide (N₂O) fluxes and composition of nitrifier and denitrifier of saline-alkali soil. Therefore, four different treatments such as CK (only chemical fertilizer), B (only biochar), M (only organic fertilizer), BM (B:M = 1:1) were used in this experiment. The results showed that N₂O emissions were decreased in B and BM treatments compare to the control. In contrast, N₂O emissions were highest before day 12 but lowest after day 19 in M treatment compare to the control. Application of biochar, organic fertilizer and biochar plus organic fertilizer decreased the nirS and nirK genes copies and enhanced the nosZ gene copies which resulting in the lower N₂O fluxes. The ammonia-oxidizing bacteria (AOB) amoA and nirK genes copies were significantly increased by organic fertilizer before day 12, leading to high N₂O emissions. The genera Nitrosospira (AOB) and Nitrososphaera (ammonia-oxidizing archaea, AOA) assumed absolute superiority. Additionally, Nitrosospira (AOB) was also appeared in nirK-type denitrifiers, illustrating denitrification was carried out by nitrifiers. The genera Azospirillum (nirS), Burkholderia (nosZ) and Polymorphum (nosZ) were dominant in CK. There was only one dominant genus, Mesorhizobium (nosZ) in the B treatment. The genera Mesorhizobium (nirK), Azoarcus (nirS), Kocuria (nirS) and Pseudomonas (nosZ) occupied the main status in the M treatment. The relative abundance of Rhodanobacter (nirS) and Azospirillum (nosZ) were higher in the BM treatment compared with other treatments. Soil water content (SWC), pH, NH₄⁺-N and NO₃^--N were the main factors affecting AOB and denitrifiers, which influencing N₂O emissions. Overall, combined application of biochar and organic fertilizer can reduce the N₂O emission where AOB and nirK-type denitrifier were the main contributors to the N₂O emission.

Shifts of the nirS and nirK denitrifiers in different land use types and seasons in the Sanjiang Plain, China

Denitrification is a key nitrogen removal process that involves many denitrifying bacteria. In this study, the denitrification performance was estimated for soil samples from different land use types including farmland soil, restored wetland soil, and wetland soil. The quantitative real-time polymerase chain reaction results showed that the average abundance of nirS and nirK genes was notably affected by seasonal changes, increasing from 2.34 × 10 ⁶ and 2.81 × 10 ⁶ to 1.97 × 10 ⁶ and 4.55 × 10 ⁶ gene copies/g of dry soil, respectively, from autumn to spring. This suggests that the abundance of nirS and nirK denitrifiers in spring is higher than those in autumn. Furthermore, the abundance of nirS and nirK genes was higher in the farmland soil than in restored wetland soil and wetland soil in both seasons. According to the analyses of MiSeq sequencing of nirS and nirK genes, Halobacteriaceae could be used as a special strain to distinguish wetland soil from farmland soil and restored wetland soil. Furthermore, redundancy analysis indicated that the soil environmental variables of total carbon, total nitrogen, moisture content, and organic matter were the main factors affecting the community structures of nirS and nirK denitrifiers existing in wetland soil. These findings could contribute to understanding the differences in nirS and nirK denitrifiers between different land use types during seasonal changes.

Analysis of microbial community in a continuous flow process at gene and transcription level to enhance biological nutrients removal from municipal wastewater

In biological municipal wastewater treatment, gene level analysis of community structure could not determine functional genes that actually played a role and expression of viable microorganism. In this study, reverse transcriptional PCR (RT-PCR), cDNA high throughput sequencing and transcriptional activity analysis were conducted to investigate active microbial community with nitrogen and phosphorus removal from municipal wastewater. RT-PCR and correlation heatmap analysis suggested that transcriptional activities of bacteria had strong correlation with performance of nitrogen and phosphorus removal, they might be therefore regarded as an indicator for wastewater treatment monitoring. When DO concentration were raised from 0.6 mg/L to 2 mg/L and C/N ratio from 3-4 to 5, the increase of population abundance and transcriptional activities of denitrifying genes improved the removal efficiencies of COD and TN. The species with relatively high abundance at gene level were not really active species at transcription level, and vice versa.

Population characteristics and influential factors of nitrogen cycling functional genes in heavy metal contaminated soil remediated by biochar and compost

Sixteen treatments of soil contaminated by Cu, Pb, and Zn by the addition of a different percentage of biochar and compost were incubated for 120 days. The abundance of denitrifying genes such as narG, nirK, nirS and nosZ and the ammonia-oxidizing amoA genes of ammonia-oxidizing archaea/bacteria (AOA/AOB), soil nitrite reductase activity (S-NiR) and their shaping factors were also determined. The relationships between functional genes, S-NiR, and physico-chemical parameters were analyzed using the Pearson correlation method. The study found that the changes in physico-chemical parameters, including water-soluble organic carbon (WSC), nitrate (NO₃^-) and ammonium (NH₄⁺), were predominant in different treatments. The abundance of nirK and narG genes is most sensitive to the changes in the properties of the soil sample. Bacterial 16S rDNA gene abundance was significantly affected by NO₃^- and S-NiR (P < 0.05). Nitrifying genes were mainly correlated to WSC and S-NiR, while denitrifying genes were associated with pH, electrical conductivity, NO₃^- and S-NiR. The systematic study for the relationship between the genes and the environmental parameters will help us to deep understand the biological mechanisms of nitrogen cycle in heavy metal contaminated soils remediated by biochar and compost.

Diversity and abundance of denitrifiers during cow manure composting

Diversity and abundance of the denitrifying genes nirK, nirS and nosZ were investigated in cow manure compost using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time quantitative PCR (qPCR), respectively. These three genes were detected in all the stages of the composting process. Phylogenetic analysis showed that the nirK gene was closely related to Rhizobiales, Burkholderiales, the nirS gene was closely related to Pseudomonadales and Burkholderiales, and the nosZ gene was closely related to Rhodospirillales, Rhizobiales, Pseudomonadales, and Alteromonadales. qPCR results showed that the abundance of these three genes (nirK, nirS and nosZ) reached the peak value in the late thermophilic stage of composting and abundance of the nirK gene was higher than that of the nosZ gene and the nirS gene. Redundancy analysis (RDA) showed that the diversity of the nirK and nirS genes was significantly correlated with ammonium (p<0.05), the diversity of the nosZ gene was significantly correlated with pH (p<0.05) and the abundance of the nirK nirS and nosZ genes was significantly correlated with temperature (p<0.05).

The Abundance of Fungi, Bacteria and Denitrification Genes during Insect Outbreaks in Scots Pine Forests

Outbreaks of defoliating insects may affect microbial populations in forests and thereby mass balances and ecosystem functioning. Here, we investigated the microbial dynamics in Scots pine (Pinus sylvestris L.) forests during outbreaks of the nun moth (Lymantria monacha L.) and the pine-tree lappet (Dendrolimus pini L.). We used real-time PCR (polymerase chain reaction) to quantify genes that characterize bacterial and fungal abundance and the denitrification processes (nirK, nirS, nosZ clades I and II) in different forest compartments and we analyzed the C and N content of pine needles, insect feces, larvae, vegetation layers, organic layers, and mineral soil horizons. The infestation of the nun moth increased the bacterial abundance on pine needles, in the vegetation layer, and in the upper organic layer, while fungal populations were increased in the vegetation layer and upper organic layer during both outbreaks. In soil, the abundance of nirK increased after insect defoliation, while the C/N ratios decreased. nosZ clades I and II showed variable responses in different soil layers and to different defoliating insects. Our results illustrate changes in the microbial populations in pine forests that were infested by defoliating insects and changes in the chemical soil properties that foster these populations, indicating a genetic potential for increased soil N2O emissions during the defoliation peak of insect outbreak events.

Assessment of heavy metal pollution and human health risks in urban soils around an electronics manufacturing facility

Heavy metal pollution has pervaded many parts of the world, especially in developing countries. The purpose of this study was to determine the concentrations and health risks of heavy metals in urban soils around an electronics manufacturing site in the Hubei Province of China. Soils samples were collected from commercial, roadside, farmland, and residential areas around the electronics manufacturing facility. A total of 136 topsoil samples were collected, and these samples were analyzed for Cr, Cu, Zn, As, Cd, Ni, and Pb. The geoaccumulation index (Igeo), pollution index (PI), and potential ecological risk index (PER) were calculated to assess the soil pollution levels. The hazard index (HI) was used to assess the human health risks posed by the presence of heavy metals. The total concentrations of the seven congeners (∑metals) ranged from 3738.86 to 5173.25mgkg^-1, and the concentrations were highest in the commercial area followed (in decreasing order) by the roadside, farmland, and residential areas. The HI for children and adults descended in the order of Cr>As>Pb>Cd>Cu>Ni>Zn. The carcinogenic risks of two metals, namely, Cr and As, for children and adults were higher than 10^-4, and children faced greater health risks.

Benzyldimethyldodecyl ammonium chloride shifts the proliferation of functional genes and microbial community in natural water from eutrophic lake

Benzylalkyldimethylethyl ammonium compounds are pervasive in natural environments and toxic at high concentrations. The changes in functional genes and microbial diversity in eutrophic lake samples exposed to benzyldimethyldodecyl ammonium chloride (BAC) were assessed. BAC exerted negative effects on bacteria abundance, particularly at concentrations of 100 μg L^-1 and higher. A significant increase in the number of the quaternary ammonium compound-resistant gene qacA/B was recorded within the 10 μg L^-1 treatment after the first day of exposure. Not all antibiotic resistance genes increased in abundance as the concentrations of BAC increased; rather, gene abundances were dependent on the gene type, concentrations of BAC, and contact time. The nitrogen fixation-related gene nifH and ammonia monooxygenase gene amoA were inhibited by high concentrations of BAC after the first day, whereas an increase of the nitrite reductase gene nirK was stimulated by exposure. Microbial communities within higher treatment levels (1000 and 10 000 μg L^-1) exhibited significantly different community composition compared to other treatment levels and the control. Selective enrichment of Rheinheimera, Pseudomonas, and Vogesella were found in the higher treatment levels, suggesting that these bacteria have some resistance or degradation capacity to BAC. Genes related with RNA processing and modification, transcription, lipid transport and metabolism, amino acid transport and metabolism, and cell motility of microbial community function were involved in the process exposed to the BAC stress.

A comparison of denitrifying bacterial community structures and abundance in acidic soils between natural forest and re-vegetated forest of Nanling Nature Reserve in southern China

Denitrification plays a key role in converting reactive nitrogen species to dinitrogen gas back into the atmosphere to maintain the equilibrium of nitrogen cycling in ecosystems. In this study, functional genes of nirK and nosZ were used to detect the community structure and abundance of denitrifying microorganisms in acidic forest soils in southern China. Three sets of factors were considered for a comparison among 5 forests, including forest types (natural vs. re-vegetated), depths (surface layer vs. lower layer) and seasons (winter vs. summer). The community of nirK gene detected from these acidic forest soils was closely related to Proteobacteria especially α-Proteobacteria and uncultured soil sequences, while that of nosZ gene was affiliated with the α-, β- and γ-Proteobacteria. Higher diversity of denitrifiers was observed in re-vegetated forest soils than natural ones. Not only the community but also the abundance showed significant differences between forest types as well as depths. The abundance of denitrifiers ranged from 10⁵ to 10⁷ gene copies g^-1 dry soil in this study. For nirK gene, the abundance was much higher in the lower layer than surface layer in both forest types, and the differences between winter and summer in natural forest soils were higher than those in re-vegetated forest soils. The abundance of nosZ and nirK genes showed a similar trend in natural forest, but the former was higher in matured forest than re-vegetated forest. This study provided a direct comparison on community composition and abundance of denitrifying bacteria in natural and re-vegetated acidic forest soils to allow further assessment of the nitrogen cycling.

Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System

Manure composting is a significant source of atmospheric methane (CH₄) and nitrous oxide (N₂O) that are two potent greenhouse gases. The CH₄ and N₂O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH₄ and N₂O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH₄ and N₂O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH₄-related functional genes (mcrA and pmoA genes) and N₂O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH₄ and N₂O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH₄⁺ together as the best predictors for CH₄ fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N₂O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH₄ and N₂O fluxes to elevated atmospheric CO₂ concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.

Quantitative impact of influent characteristics on nitrogen removal via anammox and denitrification in a landfill bioreactor case

In this paper, Quantitative Polymerase Chain Reaction (qPCR), Illumina MiSeq sequencing and ¹⁵N stable isotopic tracing methods were applied to study the effects of influent organic loading, BOD₅/TN and NO₂-N/NH₄-N ratios on the combined nitrogen removal through denitrification and anammox. The results show that, the total nitrogen removal was above 90% at the optimum reaction condition: organic loading 0.04kg/m³·day, BOD₅/TN 0.2, and NO₂-N/NH₄-N 1.0. Approximately 9.43% of the nitrogen removal occurred through anammox process when BOD₅/TN was 0.1, and increased to 21.46% when BOD₅/TN was 0.2. The anammox accounted for 10% when NO₂-N/NH₄-N was 0.5, and that increased to 20.72% when NO₂-N/NH₄-N was 1.0-1.5. hzsA was directly proportional to the influent BOD₅/TN. A positive correlation between BOD₅/TN and anammox microorganisms existed. Similarly, there was a positive correlation between NO₂-N/NH₄-N and denitrification microorganisms. Therefore, it is feasible to regulate the influent to improve nitrogen removal efficiency.

Effects of polybrominated diphenyl ethers and plant species on nitrification, denitrification and anammox in mangrove soils

Little is known about polybrominated diphenyl ethers (PBDEs) and planting affect biogeochemical processes, and their impact on microbial nitrogen (N) transformation in soil. A 12-month microcosm experiment was conducted to understand the effects of a mixture of PBDEs at two contamination levels, 2 and 20 mg kg(-1)dry weight representing low and high soil contamination, respectively, using two mangrove plant species, namely Kandelia obovata (Ko) and Bruguiera gymnorrhiza (Bg), on nitrification, denitrification and anammox in mangrove soils. No significant changes in these N transformation processes were found at month 3 and at a low level of PBDEs in both plant species, suggesting that short-term exposure to 2 mg kg(-1) contamination did not affect microbial N transformation. At month 12, a high level of PBDE contamination significantly decreased the nitrification potential activity and the copy numbers of archaeal amoA and bacterial amoA gene in Ko soil, but such inhibitory effect was not significant in Bg soil. On the contrary, the denitrification-related parameters, including the activities of nitrate reductase and nitrite reductase, potential denitrification activity and copy numbers of nirK, nirS and nosZ gene, were stimulated by a high level of PBDE contamination in both Ko and Bg soils, and the stimulation was higher in the more anaerobic Bg soil. Different from denitrification, a high level of PBDE contamination decreased the copy numbers of anammox bacterial 16S rRNA gene in Bg soil but not in Ko soil; this was possibly related to the lower nitrate concentration in Bg soil that might inhibit the growth of anammox bacteria. These results indicated that the effects of PBDEs on microbial N transformation were plant species-specific, with the nitrifying microorganisms in Ko soil more susceptible to PBDE contamination, while denitrification and anammox in Bg soil were more sensitive.

Non-target effects of repeated chlorothalonil application on soil nitrogen cycling: The key functional gene study

The widespread and increasing application of chlorothalonil (CTN) raises concerns about its non-target impacts, but little information is available on the effect of CTN on the key functional genes related to soil nitrogen (N) cycling, especially in the case of repeated applications. In the present study, a microcosm incubation was conducted to determine CTN residues and the impacts on the abundances of key functional genes related to N cycling after repeated CTN applications. The results demonstrated that repeated CTN applications at the recommended application rate and five times the recommended rate led to the accumulation of CTN residue in soil at concentrations of 5.59 and 78.79 mg kg(-1), respectively, by the end of incubation. Real time PCR (RT-PCR) revealed that repeated CTN applications had negative effects on the chiA and aprA gene abundances. There were significantly negative correlations between CTN residues and abundances of AOA and AOB genes. In addition, the abundances of key functional genes involved in soil denitrification were declined by repeated CTN applications with the sole exception of the nosZ gene. This study suggests that repeated CTN applications could lead to the accumulation of CTN residue and generate somewhat inconsistent and erratic effects on the abundances of key functional genes related to soil N cycling.

Nitrogen removal characteristics of enhanced in situ indigenous aerobic denitrification bacteria for micro-polluted reservoir source water

Indigenous oligotrophic aerobic denitrifiers nitrogen removal characteristics, community metabolic activity and functional genes were analyzed in a micro-polluted reservoir. The results showed that the nitrate in the enhanced system decreased from 1.71±0.01 to 0.80±0.06mg/L, while the control system did little to remove and there was no nitrite accumulation. The total nitrogen (TN) removal rate of the enhanced system reached 38.33±1.50% and the TN removal rate of surface sediment in the enhanced system reached 23.85±2.52%. TN removal in the control system experienced an 85.48±2.37% increase. The densities of aerobic denitrifiers in the enhanced system ranged from 2.24×10(5) to 8.13×10(7)cfu/mL. The abundance of nirS and nirK genes in the enhanced system were higher than those of in the control system. These results suggest that the enhanced in situ indigenous aerobic denitrifiers have potential applications for the bioremediation of micro-polluted reservoir system.

Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N₂O). The potential changes with metal pollution in soil microbial community for N₂O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N₂O production rate were both reduced under heavy metal pollution of the two sites, the N₂O reduction rate showed no significant change. These findings suggest that N₂O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N₂O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N₂O emission from paddy soils.

Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China

Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and PO4 (3-) (p < 0.001). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and PO4 (3-) together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with PO4 (3-), tend to affect the abundance of denitrifiers.

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem.

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils

Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India

Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal "group 1.1b (Nitrososphaera clusters)." We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils.

Nitrite reductase genes as functional markers to investigate diversity of denitrifying bacteria during agricultural waste composting

The purpose of this study was to investigate the diversity of denitrifier community during agricultural waste composting. The diversity and dynamics of the denitrifying genes (nirK and nirS) were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Relationships between physico-chemical parameters and denitrifying genes structures were simultaneously evaluated by redundancy analysis (RDA). Phylogenetic analysis indicated that nirK clones grouped into six clusters and nirS clones into two major clusters, respectively. The results showed a very high diversity of nir gene sequences within composting samples. RDA showed that the nirK and nirS gene structures were significantly related to pH and pile temperature (P < 0.05). Significant amounts of the variation (49.2 and 38.3 % for nirK and nirS genes, respectively) were explained by pH and pile temperature, suggesting that those two parameters were the most likely ones to influence, or be influenced by the denitrifiers harboring nirK and nirS genes.

The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ

Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.

Gaseous nitrogen and bacterial responses to raw and digested dairy manure applications in incubated soil

A study was conducted under laboratory conditions to compare rates of nitrous oxide (N(2)O) and ammonia (NH(3)) emissions when soil was amended with anaerobically digested dairy manure slurry containing <30% food byproducts, raw dairy manure slurry, or urea. Slurries were applied via surface and subsurface methods. A second objective was to correlate genes regulating nitrification and denitrification with rates of N(2)O production, slurry treatment, and application method. Ammonia volatilization from incubated soil ranged from 140 g kg(-1) of total N applied in digested slurry to 230 g kg(-1) in urea. Subsurface application of raw dairy manure slurry decreased ammonia volatilization compared with surface application. Anaerobic digestion increased N(2)O production. Cumulative N(2)O loss averaged 27 g kg(-1) of total N applied for digested slurry, compared with 5 g kg(-1) for raw dairy slurry. Genes of interest included a 16S rRNA gene selective for β-subgroup proteobacterial ammonia-oxidizers, amoA, narG, and nosZ quantified with quantitative polymerase chain reaction (qPCR) and real-time polymerase chain reaction (RT-PCR). Application of anaerobically digested slurry increased nitrifier and denitrifier gene copies that correlated with N(2)O production. Expression of all genes measured via mRNA levels was affected by N applications to soil. This study provides new information linking genetic markers in denitrifier and nitrifier populations to N(2)O production.