Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

Hui Xi,Dingyi Yang,Longfu Zhu,Xinhui Nie,Shiming Liu,Zheng Qu,Jili Shen

doi:10.1038/s41598-019-54771-1

Hui Xi, Dingyi Yang + Show 5 more

Open Access

https://doi.org/10.1038/s41598-019-54771-1

Copy DOI

Abstract

Verticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

Highlights

Continuous cropping regimes can cause crop yield reduction, soil-borne plant pathogen accumulation[1,2,3], and soil microbial community disruption[4,5,6]
15 V. dahliae isolates proceeding from the three cotton fields was determined via a specific PCR assay
Isolates from fields 7F and 8F belonged to the defoliating (D) pathotype (462 bp specific fragment), whereas those from field 5F belonged to the nondefoliating (ND) one (824 bp specific fragment) (Fig. 1A and S1)

Summary

Introduction

Continuous cropping regimes can cause crop yield reduction, soil-borne plant pathogen accumulation[1,2,3], and soil microbial community disruption[4,5,6]. We tested pathotype, growth rate, spore production and pathogenicity of 15 representative V. dahliae isolates, and analyzed fungal and bacterial community compositions of 15 bulk soils, from three cotton producing regions, using Ilumina MiSeq sequencing. The study aim was to (i) determine the diversity and pathogenic differentiation of V. dahliae from cotton in north Xinjiang; (ii) compare the structure and composition of fungal and bacterial communities in soils of three cotton fields; and (iii) to explore potential links between Verticillium wilt prevalence and soil properties or microbial communities

Methods

Results

Discussion

Conclusion