Soil bacterial community response to continuous cropping of cotton

Abstract

Introduction: Long-term continuous cropping may result in the outbreak and proliferation of soil-borne diseases, as well as reduction in annual crop production. Overcoming the obstacles of continuous cropping is critical for the long-term growth of modern agriculture. Soil microbes are essential for plant health, but the consequences of continuous cropping on soil microbiome are still poorly understood.

Methods: This study analyzed changes in soil bacterial community composition of Aksu (AKS) and Shihezi (SHZ) in Xinjiang Province during 1-20 years of continuous cropping by 16S amplicon sequencing. The results showed that the incidence of cotton Verticillium wilt rose with the number of cropping years. The bacterial alpha diversity in the AKS soil grew as the number of continuous cropping years increased, however it declined in the SHZ soil.

Results: The results of beta diversity analysis showed that there were significant differences in soil bacterial communities between different continuous cropping years and between different soils. The results of community composition changes at the level of main phyla and genus showed that the relative abundance of Actinobacteria, Bacteroidetes and Streptomyces decreased with the increase of continuous cropping years in the AKS and the SHZ soils. In addition, Actinobacteria, Propionibacteriales, and Nocardioidaceae were significantly enriched during the early stages of continuous cropping. Network analysis showed that long-term (≥8 years) continuous cropping interfered with the complexity of soil bacterial co-occurrence networks and reduced collaboration between OTUs.

Discussion: These findings suggested that continuous cropping and soil origin jointly affected the diversity and structural of bacterial communities, and the loss of Nocardioidaceae and Streptomyces in Actinobacteria might be one of the reasons of continuous cropping obstacles.

Keywords: Verticillium wilt; amplicon sequencing; continuous cropping obstacle; cotton; soil microbe.

Figure 1

Chao1 index (A,C) and Shannon index (B,D) of cotton field soil samples bacterial community with different continuous cropping years in AKS and SHZ soils. AKS1, AKS3, AKS5, AKS8, AKS10, AKS15, and AKS20: AKS soils of continuous cropping 1, 3, 5, 8, 10, 15, and 20 years; SHZ1, SHZ3, SHZ5, SHZ8, SHZ10, SHZ15, and SHZ20: SHZ soils of continuous cropping 1, 3, 5, 8, 10, 15, and 20  years. The letters ‘a’, ‘b,’ and ‘c’ represent statistically significant differences between different treatments (p < 0.05, Tukey test).

Figure 2

Principal coordinate analysis (PCoA) based on Bray-Curtis distance for the bacterial community structure of cotton field soil samples with different continuous cropping years in AKS and SHZ soils.

Figure 3

The relative abundance of the top 10 bacterial phyla in cotton field soil samples with different continuous cropping years in AKS (A) and SHZ (B) soils.

Figure 4

Composition of high-abundance bacterial genera (relative abundance >0.5%) in cotton field soil samples with different continuous cropping years in AKS (A) and SHZ (B) soils.

Figure 5

Cladograms of cotton field soil samples bacterial taxa with different continuous cropping years in AKS (A) and SHZ (B) soils based on linear discriminant analysis effect size (LEfSe).

Figure 6

Co-occurrence networks of bacterial communities in cotton field soil samples under short-term continuous cropping (ST) and long-term continuous cropping (LT) in AKS and SHZ soils. ST is the sample summary of 1, 3, 5, and 8 years of continuous cropping. LT is the sample summary of 8, 10, 15, and 20 years of continuous cropping.