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Aims Phytophthora root and stem rot caused by the oomycete plant pathogen Phytophthora sojae (Kaufmann & Gerdemann), is a destructive disease of soybean [Glycine max (L.) Merr.]. There is no straightforward available method to control this disease. The present study aimed to isolate a biocontrol agent (BCA) to control Phytophthora rot and gain insights into the mechanisms of biocontrol activity. Methods Antagonistic bacteria screening, inoculation assays, histochemical and fluorometric staining and real-time polymerase chain reaction (RT-PCR) were used to achieve the goals of the present study.Results The results indicated that the isolated BCA strain JSCX-1 was characterized as Bacillus altitudinis. Further studies showed that JSCX-1 bacterial filtrate inhibited the mycelial growth and zoospore germination of P. sojae. Greenhouse experiments showed that biocontrol efficiency of JSCX-1 against P. sojae was 49.28 ± 3.42%. Our results revealed that JSCX-1 increased the reactive oxygen species (ROS) production and callose deposition of soybean leaves. Moreover, JSCX-1 upregulated the transcriptional level of the G. max PR1a gene but not that of the LOX and ERF genes. Conclusions B. altitudinis JSCX-1 can effectively reduce the infectivity of P. sojae via increasing the ROS production and callose deposition on soybean, and up-regulating the expression of salicylate-responsive gene GmPR1a.

Root knot nematodes (RKN, Meloidogyne spp.) are serious pathogens of numerous crops worldwide. Understanding the roles plant rhizosphere soil microbiome play during RKN infection is very important. The current study aims at investigating the impacts of soil microbiome on the activity of RKN. In this study, the 16S rRNA genes of the bacterial communities from nematode-infested and non-infested rhizosphere soils from four different plants were sequenced on the Illumina Hi-Seq platform. The soil microbiome effects on RKN infection were tested in a greenhouse assay. The non-infested soils had more microbial diversity than the infested soils from all plant rhizospheres, and both soil types had exclusive microbial communities. The inoculation of the microbiomes from eggplant and cucumber non-infested soils to tomato plants significantly alleviated the RKN infection, while the microbiome from infested soil showed increased the RKN infection. Furthermore, bacteria Pseudomonas sp. and Bacillus sp. were screened out from non-infested eggplant soil and exhibited biocontrol activity to RKN on tomato. Our findings suggest that microbes may regulate RKN infection in plants and are involved in biocontrol of RKN. Electronic supplementary material The online version of this article (10.1007/s00248-019-01319-5) contains supplementary material, which is available to authorized users.