Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China

Abstract

Karst rocky desertification (KRD) is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal) is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK), were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae), were active in nutrient limiting degraded soils. This study demonstrates the relationship of soil properties with bacterial community in KRD areas. Our results fill the gap of knowledge on change in soil bacterial community during KRD progression.

Keywords: Illumina HiSeq sequencing; driving factors; karst rocky desertification (KRD); soil bacteria; soil bacterial community; soil properties.

Figure 1

Change in soil properties along with karst rocky desertification gradient (A,B). No KRD (NKRD) is in red color, latent KRD (LKRD) is in green color, moderate KRD (MKRD) is in yellow color, and severe KRD (SKRD) is in purple color. Soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK).

Figure 2

The distance-based redundancy analysis (db-RDA) diagram shows distribution of soil bacterial communities in karst rocky desertification areas. Study sites are labeled in black No KRD (NKRD), latent KRD (LKRD), moderate KRD (MKRD), and severe KRD (SKRD). Soil properties are labeled in blue. Soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK). Phylum is labeled in red.

Figure 3

The Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis identifies phylum (A) and genus (B) that respond significantly to karst rocky desertification progression. Relative abundance is significant when P < 0.05, logarithmic LDA score ≥2.0. No KRD (NKRD).

Figure 4

The multivariate regression tree (MRT) is used to reveal the relationship of relative abundance of core phyla with change in soil properties caused by KRD progression.