Effect of Verticillium wilt on the cotton-associated soil microbiomes

Bruna Batista1, Juntao Wang1, Catriona Macdonald1, Simranjit Kaur1, Hongwei Liu1, Brajesh Singh1

1Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia


Cotton is a major global cash crop. Verticillium wilt caused by the soilborne pathogen Verticillium dahliae (VD), is a severe disease affecting cotton crops globally and in Australia, causing significant productivity loss. It is known that soil-borne diseases can influence below-ground plant-associated microbial communities, or the soil “microbiomes”. In turn, these microbiomes can help the plant to cope with the pathogen infection. Hence, understanding the dynamics of such microbiomes in the presence of the pathogen is key to develop strategies for the sustainable management of soilborne diseases.

We collected 560 bulk and rhizosphere soil samples from 35 cotton fields and 16 non-agricultural areas in four cotton-producing regions in NSW and QLD, Australia. Nineteen of the visited cotton fields were reported by the farmers to be infected by Verticillium wilt disease. We characterized bulk and rhizosphere bacterial and fungal communities of the collected samples using next-generation sequencing and analysed different physical, chemical, and biological soil parameters. We detected that the OTUs assigned to VD were 2 times more abundant in diseased plants from diseased farms when compared to healthy plants from diseased farms. The relative abundance (RA) of VD was positively correlated with mean average precipitation and soil water holding capacity. Moreover, the RA of VD was significantly and negatively correlated with the alpha-diversity of fungi in rhizosphere samples. Network analysis, exploring co-existing patterns of bacterial and fungal communities in the microbiome, revealed that samples collected from healthy fields and non-agricultural areas had a more complex network structure (i.e., present more connections among microbes) when compared to samples from diseased fields. Our results indicate that the microbial communities associated to cotton bulk soil and rhizosphere alter in the presence of VD. Managing cotton-microbiome interactions offers an opportunity for improving the efficiency and sustainability of agricultural production


Dr Bruna Batista is a research fellow within the Soil Biology & Genomics research theme at the Hawkesbury Institute for the Environment – Western Sydney University. Bruna has a BSc (2011) in Biotechnology from The Federal University of Alfenas (UNIFAL-MG), Brazil. She obtained her MSc (2013) and PhD (2017) in Sciences from the Department of Genetics and Plant Breeding, University of São Paulo (ESALQ/USP), Brazil. At USP, she was involved in a project that accessed, for the first time, the microbiome associated with a plant from the Brazilian Amazon. Bruna has experience working on microbial genetics, using culture-independent and -dependent methods to investigate the biotechnological potential to agriculture of plant and soil microbial communities. She also worked on screening biological products for agriculture at BASF-Agro, Brazil. In 2018, she received an Endeavour Research Fellowship from the Australian Government to work as a visiting postdoc in microbial ecology at The University of Queensland (UQ). Currently, Bruna is working on a project funded by CRDC (Cotton Research and Development Corporation) under the supervision of Prof. Brajesh Singh. The project aims to develop biological-based products and tools for improved cotton production.

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