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

Abstract

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.

Keywords: Alkaline stresses; Bacterial community diversity; Chloride stress; High-throughput sequencing; Potential nitrification rate; Sulfate stress.

Fig. 1

Effects of different types of salt and alkali stresses on soil properties and nitrification in a calcareous desert soil. a Soil water content (%), b salinity (dS m⁻¹), c pH, d NH₄-N (mg kg⁻¹), e NO₃-N (mg kg⁻¹), and f potential nitrification rate (μg NO₂-N g⁻¹ h⁻¹). Columns and error bars represent the mean ± standard error (n = 3), respectively. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 2

Effects of different types of salt and alkali stresses on gene copy numbers (no. g^− 1 dry soil (× 10⁶ or 10⁷)) of different soil bacterial communities involved in nitrification and denitrification in a calcareous desert soil. a amoA-AOA, b amoA-AOB, c amoA-AOA/amoA-AOB ratio, d nirK, e nirS, and f nosZ.. Columns and error bars represent the mean ± standard error (n = 3), respectively. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 3

Regressions of the relations between potential nitrification rate (μg NO₂-N g^− 1 h^− 1) and gene copy numbers (log no. g^− 1 dry soil) of a amoA-AOA communities and b amoA-AOB communities in a calcareous desert soil

Fig. 4

Venn diagrams based on operational taxonomic units of different communities under different salt and alkali stresses in a calcareous desert soil. The communities were a amoA-AOA, b amoA-AOB, c nirK, d nirS, and e nosZ. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 5

Non-metric multidimensional scaling (NMDS) analysis of different soil microbial communities involved in nitrification and denitrification under different salt and alkali stresses in a calcareous desert soil. The communities were a amoA-AOA, b amoA-AOB, c nirK, d nirS, e and nosZ. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 6

Genus-level composition (a, c) and linear discriminant analysis (LDA) effect size analysis (b, d) of bacterial communities based on nitrification functional genes under different types of salt and alkali stresses in a calcareous desert soil. a Relative abundance (%) of genera in amoA-AOA communities, b LDA scores of dominant genera in amoA-AOA communities, c relative abundance (%) of genera in amoA-AOB communities, and d LDA scores of dominant taxa in amoA-AOB communities. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 7

Genus-level composition (a, c, e) and linear discriminant analysis (LDA) effect size analysis (b, d, f) of bacterial communities based on denitrification functional genes under different types of salt and alkali stresses in a calcareous desert soil. Relative abundance (%) of genera in a nirK, c nirS, and e nosZ communities. LDA scores of dominant taxa in b nirK, d nirS, and f nosZ communities. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 8

Redundancy analyses (RDA) of the correlations between the genera of a amoA-AOA and b amoA-AOB communities and soil variables in a calcareous desert soil. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment

Fig. 9

Redundancy analyses of the correlations between the genera of the denitrifier a nirK, b nirS, and c nosZ communities and soil variables in a calcareous desert soil. CK, control treatment without salt or alkali stress; CS, NaCl stress treatment; SS, Na₂SO₄ stress treatment; AS, Na₂CO₃ + NaHCO₃ stress treatment