One or millions: how much does a microbiologically-buffered soil withstand chemical and biological pesticides?

Abstract

Disease suppressive soil is defined as a type of soil where the pathogen cannot establish or persist, or causes only minimal damage to crops, due to the presence of specific microorganisms and their activity in the soil, despite the persistence of pathogens in the soil. Disease suppressive soils substantially contribute to plant protection against various soil-borne plant pathogens such as bacteria, fungi, oomycetes, and nematodes. The foundation of specific disease suppression in most soils affiliates commonly to soil microbial communities. Therefore, the soil microbiota of suppressive soils is considered one of the radical factors contributing to disease suppressiveness against soil-borne diseases. To date, a multitude of microbial taxa and genes have been documented as central players in participating disease suppressiveness of soils. Still, the dominant genera, their sensitivity to alien biocontrol advocacy, agrochemicals and the complexity of microbiome interactions and their underlying mechanisms remain elusive for most disease suppressive soils. The main objective of the current research is to manipulate the existing suppressive soil microbiome through the introduction of various biological control agents and agrochemicals to explore the microbiome functionality towards soil-born (root-knot) nematodes disease. Suppressive soil assay revealed that suppressive soil significantly reduced galls-1 (14.25%) and egg masses (74.85%) in relation to sterilized soil. Intriguingly suppressive soil microbiome manipulation by biological control agent Bacillus velezensis strain BMH intervened in the microbial functions and reduced its suppressiveness. BMH inoculated suppressive soil significantly increased the galls-1 and eggs-1 32% and 47.96% respectively as compared to un-inoculated suppressive soil. Interestingly, suppressive soil slurry blending with antibiotics (Streptomycin 100 ppm) and fungicide (Cyproconazole 100 ppm) significantly modulated the soil microbiome functionality. Soil slurry mixed with antibiotics (and fungicide significantly increased the number of galls-1 174.23% and 87.79% respectively as compared to the untreated slurry. Following the same pattern, antibiotics and fungicide inoculation significantly increased the number of egg masses by 276.24% and 38.17% respectively as compared to the untreated slurry. Biocontrol based on bacteria such as Quatrzo (Bacillus subtilis; Bacillus licheniformis), Biobac (Bacillus subtilis), Onix (Bacillus methylotrophicus) and Rizos(Bacillus subtilis) turbulent the soil microbiome performance and insignificantly increased the galls and eggs mass index in relation to suppressive soil. To understand and explore the intrinsic fundamental candidates of the disease suppressive soil, the research promoted to the next level and recovered the responsible candidates from the reported suppressive soil and deciphered their potential role against root-knot nematode (RKN) Meloidogyne incognita in the tomato plant. A total of 42 bacterial strains were isolated from the suppressive soil and 18 of them were identified with high potential to control M. incognita. The isolates were sequenced based on 16S rRNA and identified 6 different genera namely Bacillus, Pseudomonas, Leclercia, Paenarthrobacter, Pantoea, and Exiguobacterium. Eighteen bacteria of six different genera were selected based on preliminary screening. The plant was inoculated with strains Bacillus sp. P10, Bacillus sp. P16, Bacillus sp. P19, and Bacillus sp. P21 significantly reduced the root galling 47% and the significant average reduction of egg mass was recorded 75.5% in relation to control. Three Pseudomonas sp. P17, Pseudomonas sp. X11, and Pseudomonas sp. X18 exhibited high biocontrol efficacy and significantly reduced the galls and egg masses 54% and 75% in both trials as compared to the control. The isolates such as Leclercia sp. P12, Leclercia sp. P18 and Leclercia sp. P20 exhibited high potential and consistency in controlling gall and egg biomass index in both trials the significant reduction was observed in root galling 47% and egg biomass index 70% as compared to the untreated plants. The bacterial strain, Paenarthrobacter sp. X12 showed consistency and maintained the biocontrol capability and significantly reduced the number of galls and egg biomass 57% and 89% respectively in rlation to uninoculated plant. Additionally, all six genera' volatile organic compounds (VOCs) and metabolites in cell-free supernatants had significant effects against the plant pathogens M. incognita, Fusarium oxysporum, and Rhizoctonia solani, but only five strains Pseudomonas sp. P7, Pseudomonas sp. X11, Bacillus sp. P10, Bacillus sp. P21, and Leclercia sp. P12 significantly inhibited the growth of Ralstonia solanacearum. Moreover, all bacterial isolates inherit nematicidal activities and dramatically reduced the egg hatching. These findings recommend that exogenous biological control agents, biostimulants and agrochemicals massively perturb the microbiome structure, composition, ecological and biological activities and detract or infertile the endogenous microbiota functionality. The study aimed to evaluate the biocontrol efficacy of biocontrol products against soybean cyst-nematode (SCN) employing two seed or furrow treatments under field conditions. The commercially-available biological products based on Pochonia chlamydosporua (CEPA PC-10) (Rizotec), Bacillus methylotrophicus UFPEDA 20 (Onix) and Trichoderma koningiopsis GF362 (not commercially available) were applied as seed treatment or in-furrow upon planting. The total number of females in root, cysts, eggs, J2 population (%) eggs/cyst and J2 population (%) mortality rate at 30 and 60 days after sowing as well as plant yield were assessed in two consecutive years, but no significant differences were observed between control and bioproducts applied treatments. Additionally, we evaluated the diversity and community composition of bacteria, fungi and eukaryotes in the rhizosphere soil of bioproducts treated plants and the dominant phyla in bacterial, fungal and eukaryotic community were Proteobacteria, Acidobacteria Actinobacteria, Ascomycota, Basidiomycota, Mortierellomycota, and Ascomycota, Cercozoa respectively in both consecutive years. Overall, no significant difference was observed in bacterial, fungal, and eukaryotic community's diversity in both years of data. The co-occurrence network unearthed that bacterial, fungal and eukaryotic species formed a network structure of high complexity in all bioproducts applied treatments. Our findings suggest that the introduction of exogenous beneficial microbes into field conditions is unable to modulate overall the microbial structure but the selective recruitment of key microbial taxa, some of which is also implicated in the nematode suppressiveness. The aim of this study was to analyze the effects of the biological control agent based bioproducts and chemical nematicides at different combination on root-knot nematodes and the microbial community profiling of the coffee plant rhizomicrobiome in a field trial. All the biological control products and chemical nematicide had not shown significant impact on root-knot nematodes control between control and treatments. The total number of number of galls-1 and eggs-1 and plant yield were assessed in two consecutive years, but no significant differences were observed between control and bioproducts applied treatments. Additionally, we evaluated the diversity and community composition of bacteria, fungi and eukaryotes in the rhizosphere soil of bioproducts treated plants and the dominant phyla in bacterial, fungal and community were, Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota, Mortierellomycota, and Ascomycota, Cercozoa respectively in both consecutive years. Overall, no significant difference was observed in bacterial, fungal, and eukaryotic community's diversity in both years of data. The co-occurrence network unearthed that bacterial, fungal and eukaryotic species formed a complicated network structure in all bioproducts applied treatments. Our findings assist in comprehending the introduction of exogenous beneficial microbes into field conditions that exerted selective recruitment implicated in nematode parasitism.