**5. Conclusions**

In summary, we report that soybean infected by *S. sclerotiorum* (Lib.) de Bary had a higher populations of actinobacteria and enhanced root colonization of antagonistic populations. In addition, eight known compounds and one new compound that exerted significant antifungal activity against *S. sclerotiorum* were obtained. These findings suggest that diseased plant samples could be a potential source for screening novel agroactive compounds, which contribute to a better understanding of plant–microbe interactions and provide new strategies for the development of agricultural antibiotics.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2076-2607/7/8/243/s1.

**Author Contributions:** C.L., X.Z., Z.W. and X.G. performed the experiments. Z.Y. and Y.W. analyzed the data. C.L. wrote the paper. W.X. and S.H. designed the experiments and reviewed the manuscript. All authors read and approved the final manuscript.

**Funding:** This research was supported by the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province (UNPYSCT-2016153), the Academic Backbone Project of Northeast Agricultural University (17XG17), and the National Natural Science Foundation of China (No. 31872037).

**Conflicts of Interest:** The authors declare that they have no conflicts of interest.
