Microbial communities in the cysts of soybean cyst nematode affected by tillage and biocide in a suppressive soil

•Formaldehyde increased soybean cyst nematode (SCN) population density consistently.•Formaldehyde changed the bacterial and fungal communities in the cysts of SCN.•Streptomyces were more dominant at planting than at midseason.•Some bacteria colonize cysts of SCN were reduced by formaldehyde.•Potential fungal biological control agents were reduced by formaldehyde.

Suppressive soil harbors biological agents with potential for managing plant diseases. However, given the rich and complex composition of suppressive factors, the microbes involved in disease suppression have been difficult to identify. We conducted amplicon-based metagenomic analysis of microbial communities in the cysts of soybean cyst nematode (SCN, Heterodera glycines) from an SCN-suppressive field to study bacteria and fungi involved in SCN suppression. The experiment was a split-plot design with conventional tillage and no-till as main treatments, and formaldehyde as a biocide and no-formaldehyde (control) as sub-treatments. All plots were planted with SCN-susceptible soybean from 2009 to 2013. Tillage had little effect on SCN, while formaldehyde increased SCN population density, suggesting biological factors are involved in SCN suppression. SCN cysts were collected at planting and midseason in 2013 for bacterial 16S rRNA and fungal ITS1 sequencing. Tillage did not affect bacterial and fungal diversity, composition, or relative abundance of taxa. However, formaldehyde lowered bacterial community diversity, and changed the bacterial and fungal community composition when compared to the control. Formaldehyde reduced the bacterial genera Lysobacter and Actinocorallia, which are frequently isolated from cysts, but increased the relative abundance of Pseudomonas in the cysts. Streptomyces were found to be more dominant at planting than at midseason. The fungi important in regulating SCN population such as Pochonia, Exophiala, and Clonostachys had lower relative abundance, whereas Trichoderma and Phoma had higher relative abundance under formaldehyde treatment than control. Our study suggests that both bacteria and fungi played important roles in suppression of the SCN.