Do herbicides effect the soil microbiome that controls the root-knot nematode Meloidogyne paranaensis in coffee

Abstract

Brazil is the largest coffee producer in the world, having produced 2,993,780 tons on 1,836,741ha in 2021. Production has been fluctuating in recent years, due to various phytosanitary problems such as the root-knot nematode Meloidogyne paranaensis. The microbiome of a suppressive soil can act against root pathogen infections. The various herbicides that are used in coffee cultivation can impact the soil's native microbiota. Therefore, the objective of the dissertation was to evaluate the potential effect of five herbicides on the microbial functionality of a soil from an area with coffee in relation to the root-knot nematode Meloidogyne paranaensis. The soil was collected from a coffee agroforest with no history of herbicide application. The herbicides were Saflufenacil 100g/ha; Pyroxasulfone 400ml/ha; Glyphosate 3kg/ha; Flumioxazin 180ml/ha and Cletodim 0.9l/ha. The seedlings were inoculated with 4000 Meloidogyne paranaensis eggs and after 35 days the tomato plants were collected and the number of galls, g-1, and eggs, g-1, were counted. Another experiment to evaluate the chemotaxis of Meloidogyne paranaensis in response to exposure of the soil microbiome to herbicides was done. Furthermore, the isolation and quantification of total bacteria, endosporogenic bacteria and total fungi from the soil were carried out at different times of exposure to herbicides (0 days, 1 day, 5 days, 15 days and 35 days). Total soil DNA was extracted at the end of the in-vivo experiment and the bacterial community was evaluated. In the in-vivo experiment we found that Saflufenacil and Pyroxasulfone significantly increased the number of eggs and galls (P < 0.05) compared to the control. Glyphosate, Cletodim and Flumioxazin did not reduce soil suppressiveness, there was no statistical difference between these treatments and the inoculated control. In the chemotaxis experiment, the microbiome exposed to Glyphosate was repellent to the nematode, as was the control treatment. The microbiome exposed to Saflufenacil and Pyroxasulfone was highly attractive to J2 and differentiated from the control. Only Flumioxazin affected the fungal community 15 days after application. Saflufenacil reduced the total bacterial community 5 and 15 days after application, but at 35 days a significant increase was observed compared to the control. Clethodim, Pyroxasulfone, Saflufenacil, and Glyphosate began to inhibit endosporogenic bacteria 1 day after exposure. Microbiome analysis revealed the modulation of the microbiome when exposed to different herbicides. Using alpha diversity, it was possible to observe that bacterial diversity was lower in the control treatment and higher in soils exposed to herbicides. Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Gemmatimonadetes were the most predominant phyla in the soil. The importance of understanding the impact of herbicides on the microbiome that suppresses root diseases is highlighted.