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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 NO 3 -N; increased pH, salinity, water content, and NH 4 -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 .

bmc microbiology

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