Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem

Abstract

Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem. IMPORTANCE Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.

Keywords: community assembly processes; community diversity; desert ecosystem; microbial phenotypes; salinity.

FIG 1

Relationship between soil salinity and observed OTUs (A) and Faith’s phylogenetic diversity (B).

FIG 2

Relationship between Bray-Curtis dissimilarity and differences in soil salinity.

FIG 3

Balance tree estimated by genies analysis showing niche differentiation of soil microbial OTUs. (A) Heat map showing observed OTU proportions sorted by salinity from 46.2 μS/cm to 4,601 μS/cm. (B) Heat map showing predicted OTU proportions from ordinary least-squares linear regression on balances sorted by salinity. (C) Log ratio of proportions of OTUs with a low-salinity niche preference to proportions of OTUs with a high-salinity niche preference along a salinity gradient. y0_denominator represents low-salinity OTUs with salinity ranges from 46.2 μS/cm to 535 μS/cm, and y0_numerator represents high-salinity OTUs with salinity ranges from 535 μS/cm to 4,601 μS/cm. (D) Number of OTUs belonging to y0_denominator and y0_numerator sorted to the class level.

FIG 4

Relationship between soil salinity and relative abundances of nine potential phenotypes predicted by BugBase.

FIG 5

Relationship between soil salinity and within-community NTI (A) and between-community βNTI (B) of a microbial community.