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Title: Metagenomic analysis of microbial communities associated with Heterodera glycines in a suppressive soil

item HU, WEIMING - University Of Minnesota
item CHEN, SENYU - University Of Minnesota
item Samac, Deborah - Debby
item LIU, X - Chinese Academy Of Sciences

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/24/2015
Publication Date: 7/24/2015
Citation: Hu, W., Chen, S., Samac, D.A., Liu, X. 2015. Metagenomic analysis of microbial communities associated with Heterodera glycines in a suppressive soil[abstract]. 54th Annual Meeting of the Society of Nematologists. East Lansing, MI. July 19-24, 2015. p. 56-57.

Interpretive Summary:

Technical Abstract: Suppressive soil harbors potential biological agents for controlling plant diseases. However, given the rich and complex suppressive factors, the specific mechanisms of disease suppression have been difficult to identify. Also, the relationships between agricultural practices and suppressive factors are poorly understood. In order to investigate microbial factors involved in suppression of the soybean cyst nematode (SCN, Heterodera glycines) in various cropping systems, we conducted a metagenomic analysis of bacterial and fungal communities in bulk soil, rhizosphere soil, and SCN cysts in an SCN-suppressive field with conventional tillage (CT) and no-tillage (NT) as main treatments, and corn-soybean rotation, soybean monoculture, and soybean monoculture with formaldehyde treatment as sub-treatments. This field has a long history of soybean monoculture, and the main treatments and sub-treatments were maintained for four years before sampling. Bulk soil was sampled at planting and midseason, and cysts were extracted from bulk soil. In addition, rhizosphere soil was sampled at midseason. The Illumina Miseq platform was used to sequence the bacterial 16S rRNA V4 region and fungal rRNA ITS1. Using weighted UniFrac distance matrices, bacterial alpha diversity was enriched by CT compared to NT in all samples while beta diversity was not significantly changed by tillage. Formaldehyde reduced bacterial alpha diversity in cysts and rhizosphere soil and changed community composition in bulk soil and cysts dramatically. Specifically, formaldehyde enriched relative abundance of Proteobacteria in all three types of samples, beta-proteobacteria in bulk soil, and gamma-proteobacteria in cysts. In addition, rotation resulted in greater bacterial diversity than monoculture in rhizosphere soil. Among the three types of samples, bulk soil had the highest bacterial diversity while cysts had the lowest. The fungal community had a different response to tillage and rotation-formaldehyde treatments. Tillage did not affect fungal alpha diversity or richness. Rotation enriched a diversity but it was reduced in formaldehyde-treated bulk soil and rhizosphere soil. Non-metric multidimensional scaling using Bray-Curtis distance matrices showed that fungal community composition in all samples was affected by tillage, rotation, and formaldehyde. Some fungal taxa, which were frequently isolated from SCN cysts, or have shown potential for control of SCN such as Pochonia, Phoma, Cylindrocarpon, and Stagonosporopsis, were slightly reduced in cysts from formaldehyde-treated soil. Bacterial and fungal communities in formaldehyde-treated bulk soil and cysts from formaldehyde-treated soil clustered together using hierarchical clustering with Bray-Curtis distance matrices. This supports our conclusion that formaldehyde had a significant impact on the microbes of the suppressive soil. Tillage had minor effects on the soil microflora. Rotation resulted in the highest variation of bacterial and fungal communities in rhizosphere soil. These results support the role of specific microbial communities in suppression of SCN in suppressive soils developed through crop monoculture.