Rhizoctonia bare patch bacterial communities. soil metagenome

Rhizoctonia bare patch and root rot of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants, and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest USA. At a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside of patches, outside of patches, and recovered patches, were analyzed by pyrosequencing with primers designed to 16S rRNA. Taxa in the genera of Acidobacteria and Gemmatimonas were in higher frequency in the rhizosphere of healthy plants outside of patches, compared to diseased plants from inside of patches. Dyella and Acidobacteria Gp7 had higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia) and Chyseobacterium were higher in the rhizosphere of diseased plants from inside of patches. For selected taxa, trends were validated by real-time quantitative PCR, and shifts of frequency in the rhizosphere over time were duplicated with cycling experiments in the greenhouse, with successive plantings of wheat in Rhizoctonia-inoculated soil. Chryseobacterium soldanellicola was isolated from the rhizosphere inside of patches and exhibited significant antagonism against R. solani AG8 in vitro and in greenhouse tests. In conclusion, we identified novel bacterial taxa which respond to conditions affecting bare patch symptoms and may be involved in suppression of Rhizoctonia root rot and bare batch. This study was conducted at an 8-ha parcel on the Ron Jirava farm (47°8’34”N, 118°28’22”W) located near Ritzville, WA. The study site had four replicate blocks, each with 14 different rotation strips, 9 m wide by 152 m long. Mean annual precipitation at the site is 290 mm and the soil is a Ritzville silt loam (coarse-silty, mixed, superactive, mesic Calcidic Haploxerolls). The soil is > 180 cm deep and has no restrictive layers or rocks. Slope at the site is < 1%. Rhizoctonia bare patches appeared in the rotation strips three years after tillage was stopped. From 1999 to 2012, these 5 patches were mapped with a high resolution global positioning system (GPS) device to record the dynamics of patch formation and recovery. This study only focused on the continuous annual spring wheat strips to minimize the effects of crop rotation. Samples were collected in April or May 2008, 2009 and 2010. Both bulk and rhizosphere soil were collected from three locations: the center of an active Rhizoctonia patch (inside of patch); 1 m outside of the same patch (outside of patch); and an adjacent site that did not have a noticeable patch but which harbored a patch in the previous year (recovered 100 patch). Approximately 1 kg of soil from between the rows was taken for the bulk soil sample. For rhizosphere soil, 5-10 plants were taken with intact roots. Roots with attached rhizosphere soil from wheat plants were cut from the shoot, and placed in a 50-ml plastic tube containing 20 ml of sterile distilled water. The tubes were vortexed for 1 min, sonicated for 1 min and stored at -20oC for further use. The factorial experiment for pyrosequencing of the field samples consisted of three locations (inside, outside and recovered patches) for 2008, and two locations (inside and outside patches) for 2010 for each of two soil types (bulk and rhizosphere) in each of three replicates. The pyrosequencing of 2009 samples was not conducted.