Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil

Background Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil. Results Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO3-N; increased pH, salinity, water content, and NH4-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities. Conclusion These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.

Saline and Alkaline Stresses Alter Soil Properties And Composition And Structure of Gene-Based Nitrifier And Denitrifier Communities In A Calcareous Desert Soil

Background: Saline and alkaline stresses damages the health of soil systems. Meanwhile, Little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil. Results: Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO3-N; increased pH, salinity, water content, and NH4-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments.The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities. Conclusion: These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.

Warming shapes nirS- and nosZ-type denitrifier communities and stimulates N2O emission in acidic paddy soil

Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms under warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35 °C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers, but not ammonia-oxidising archaea or ammonia-oxidising bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25 °C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. By contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35 °C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanbacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. Importance The interdependence between global warming and greenhouse gas N2O has always been the hotspot. However, information on factors contributing to N2O and temperature-dependent community structure changes are scarce. This study demonstrated high temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study’s findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Denitrifier community phenotypes often result in transient accumulation of denitrification (NO3−→NO2−→NO→N2O→N2) intermediates. Consequently, anoxic spells drive NO-, N2O- and possibly HONO-emissions to the atmosphere, affecting both climate and tropospheric chemistry. Soil pH is a key controller of intermediate levels, and while there is a clear negative correlation between pH and emission of N2O, NO2− concentrations instead increase with pH. These divergent trends are probably a combination of direct effects of pH on the expression/activity of denitrification enzymes, and an indirect effect via altered community composition. This was studied by analyzing metagenomics/transcriptomics and phenomics of two soil denitrifier communities, one of pH 3.8 (Soil3.8) and the other 6.8 (Soil6.8). Soil3.8 had severely delayed N2O reduction despite early transcription of nosZ, encoding N2O reductase, by diverse denitrifiers, and of several nosZ accessory genes. This lends support to a post-transcriptional, pH-dependent mechanism acting on the NosZ apo-protein or on enzymes involved in its maturation. Metagenome/metatranscriptome reads of nosZ were almost exclusively clade I in Soil3.8 while clade II dominated in Soil6.8. Reads of genes and transcripts for NO2−-reductase were dominated by nirK over nirS in both soils, while qPCR-based determinations showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK community. The -omics results suggested that low NO2− concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to enzymatic activity. The NO reductase gene qnor was strongly expressed in Soil3.8, suggesting an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2− accumulating soil, was estimated to be ten times higher from Soil3.8 than from Soil6.8. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

Intensive Rain Hampers the Effectiveness of Nitrification Inhibition in Controlling N2O Emissions from Dairy Slurry-Fertilized Soils

Nitrification inhibitors have been proposed as a tool to mitigate nitrous oxide (N2O) emissions from agriculture, which are caused mainly by fertilization. The nitrification inhibitor 3,4-Dimethylpyrazole phosphate (DMPP) was tested in a winter rapeseed field after dairy slurry application in Central Estonia. N2O emissions were monitored using the closed chamber method. Soil and leachate chemical parameters were also analyzed. N2O emissions increased from pre-slurry application values of 316 and 264 µg m−2 h−1 for the control and treatment plot, respectively, to maximum values of 3130.71 and 4834 µg m−2 h−1, with cumulative emissions during the study period of 12.30 kg ha−1 for the control plot and 17.70 kg ha−1 for the treatment plot. The intense precipitation period that began with the application of the slurry resulted in changes in soil moisture and water-filled pore space (WFPS), modifying the nitrification/denitrification balance. Positive significant correlations (p = 0.016 and p = 0.037, for the control and treatment plot, respectively) were found between N2O fluxes and WFPS. Future studies should consider the role of nitrifier and denitrifier communities in order to better assess in-field nitrification inhibitor effectiveness.