Rhizosphere Competence and Biocontrol Effect of Pseudomonas sp. RU47 Independent from Plant Species and Soil Type at the Field Scale

Abstract

Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the indigenous microbial community in the rhizosphere. It is known that many factors, among them plant species and soil type shape the rhizosphere microbial community composition. However, microbial community composition in the rhizosphere can also be influenced by the presence of a pathogen. We hypothesized that plant species, soil type, and a pathogen affect the rhizosphere competence of a biocontrol strain and its biocontrol effect against a soil-borne pathogen. To test the hypothesis, we used an experimental plot system with three soil types (diluvial sand, alluvial loam, loess loam) kept under similar agricultural management at the same field site for 12 years. We investigate the rhizosphere competence of Pseudomonas sp. RU47 in two plant species (potato and lettuce) and its biocontrol effect against Rhizoctonia diseases. The colonization density of a rifampicin resistant mutant of RU47 in the rhizosphere of both crops was evaluated by plate counts. Bacterial community compositions were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA. The inoculant RU47 was able to colonize the rhizosphere of both model crops in a sufficient density and to reduce disease severity of black scurf on potato and bottom rot on lettuce in all three soils. DGGE indicated that RU47 affected the bacterial community composition stronger in the rhizosphere of lettuce than in the potato rhizosphere. In contrast, the effect of the pathogen Rhizoctonia solani on the bacterial community was much stronger in the rhizosphere of potato than in the lettuce rhizosphere. A significant effect of RU47 on the Pseudomonas-specific gacA fingerprints of the rhizosphere was only observed in lettuce in alluvial soil. The soil type and plant species independent biocontrol effects of RU47 and its minor influence on the indigenous bacterial community composition might be important criteria for the registration and use of RU47 as biocontrol strain.

What drives the assembly of plant-associated protist microbiomes?

“…The bacterial taxa in our networks have been identified as typical members of lettuce and potato ‘core microbiomes’ (Cardinale et al , 2015; Mitter et al , 2016; Schreiter et al , 2014a; Schreiter et al , 2018). The term ‘microbiome’ sensu stricto denotes the microbial genes encoding specific traits supplementing the plant genome by microbial functions such as nutrient provision or pathogen defense (Berg et al , 2014a; Sánchez-Cañizares et al , 2017; Vandenkoornhuyse et al , 2015).…”

“…Rhizosphere soil samples of lettuce were collected two weeks after planting, rhizosphere soil samples of potato were taken seven weeks after planting. More details on the experimental design can be found in (Schreiter et al , 2018).…”

“…The roots of two potato plants or three lettuce plants per plot were pooled to reduce intra-plot variability. Adhering soil was removed by a short root washing step and afterwards the roots were cut into pieces of 1 cm, mixed and 5 g of roots were treated three times by a Stomacher 400 Circulator (Seward Ltd., Worthing, United Kingdom) as described in Schreiter et al (2018). The portion of soil still sticking to the root was denoted as rhizosphere soil.…”

“…In order to verify the existence of plant-specific protist ‘microbiomes’ under natural conditions, we applied the cercozoan primers used by Sapp et al (2017) in a factorial field experiment with two plant species, lettuce and potato. These plants were grown in close proximity to one another in an experimental field plot system with three contrasting soils (see Schreiter et al , 2018) to obtain a robust measure of the factors influencing protist rhizosphere microbiomes. Variance partitioning allowed the quantification of the influence of the environmental filters (soil type and plant species) on community assembly of Cercozoa.…”

“…Variance partitioning allowed the quantification of the influence of the environmental filters (soil type and plant species) on community assembly of Cercozoa. We further performed network analyses of Cercozoa and their co-occurrence with their potential bacterial prey on lettuce and potato (Schreiter et al , 2018) to better characterize bacteria-protist relationships.…”