Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System

Abstract

The biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. The Populus root microbiome is a diverse community that has high abundance of β- and γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand the contribution of individual microbiome members in a community, we studied the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Both strains increased lateral root formation and root hair production in Arabidopsis plate assays and are predicted to encode for different functions related to growth and plant growth promotion in Populus hosts. Inoculation individually, with either bacterial isolate, increased root growth relative to uninoculated controls, and while root area was increased in mixed inoculation, the interaction term was insignificant indicating additive effects of root phenotype. Complementary data including photosynthetic efficiency, whole-transcriptome gene expression and GC-MS metabolite expression data in individual and mixed inoculated treatments indicate that the effects of these bacterial strains are unique and additive. These results suggest that the function of a microbiome community may be predicted from the additive functions of the individual members.

Root bacterial endophytes alter plant phenotype, but not physiology

“…(BT03), hereafter termed Pseudomonas GM30, Pseudomonas GM41, and Burkholderia BT03 were isolated from Populus deltoides endospheres from east Tennessee and western North Carolina, USA (originally described in Brown et al, 2012). For full isolate descriptions, see Brown et al (2012), Weston et al (2012), Utturkar et al (2014), Timm et al (2015) and Timm et al (2016). We selected these three strains because previous work ( Pseudomonas GM30–Weston et al, 2012; Labbé et al, 2014; Pseudomonas GM41–Labbé et al, 2014; Timm et al, 2016; Burkholderia Bt03–Timm et al, 2016) had given us indication that strains were able to influence traits in Arabidopsis thaliana (Weston et al, 2012), were able to manipulate plant gene expression and hormonal signaling in P. deltoides (Timm et al, 2015; Timm et al, 2016), and were able to influence host interactions with mycorrhizal symbionts (Labbé et al, 2014).…”

“…For full isolate descriptions, see Brown et al (2012), Weston et al (2012), Utturkar et al (2014), Timm et al (2015) and Timm et al (2016). We selected these three strains because previous work ( Pseudomonas GM30–Weston et al, 2012; Labbé et al, 2014; Pseudomonas GM41–Labbé et al, 2014; Timm et al, 2016; Burkholderia Bt03–Timm et al, 2016) had given us indication that strains were able to influence traits in Arabidopsis thaliana (Weston et al, 2012), were able to manipulate plant gene expression and hormonal signaling in P. deltoides (Timm et al, 2015; Timm et al, 2016), and were able to influence host interactions with mycorrhizal symbionts (Labbé et al, 2014). Although strains were isolated from P. deltoides , strains from Pseudomonas and Burkholderia readily colonize natural P. trichocarpa tissues (Moore et al, 2006; Xin et al, 2009; Knoth et al, 2014; Khan et al, 2014; Doty et al, 2016).…”

“…For example, inoculation with common root-colonizing bacterial strains influenced root and leaf architectural traits, such as specific leaf area and specific root length, as well as plant physiological traits such as carbon fixation and chlorophyll content (Harris, Pacovsky & Paul, 1985; Ma et al, 2003; Friesen, 2013). Further, inoculation by different members of the plant microbiome may differentially alter plant phenotype (Zamioudis et al, 2013; Timm et al, 2016). The presence of unique bacterial strains in legume genotypes explained more variation in shoot biomass, root biomass, and plant height than plant genotype did (Tan & Tan, 1986).…”

“…Inoculation of common endophytes can also inhibit primary root elongation and promote lateral root formation and root hair production (Zamioudis et al, 2013; Weston et al, 2012). Recent breakthroughs in the multitude of the −omics fields have allowed for unprecedented mechanistic investigations of microbe-induced changes in host function (Verhagen et al, 2004; Walker et al, 2011; Weston et al, 2012; Vandenkoornhuyse et al, 2015; Timm et al, 2015; Timm et al, 2016) and have been the subject of multiple recent reviews (Friesen et al, 2011; Friesen, 2013; Vandenkoornhuyse et al, 2015; Hacquard & Schadt, 2015; Lebeis, 2015; and many others). This work demonstrated that plant growth promoting bacteria elicit numerous changes in host gene expression through multiple and simultaneous hormonal and immune response pathways (Verhagen et al, 2004; Walker et al, 2011; Weston et al, 2012; Drogue et al, 2014; Timm et al, 2016).…”

“…Pseudomonas fluorescens accounted for approximately 34% of the sequences found in the Populus endosphere, but only 2–3% of the sequences in the rhizosphere and soil samples originating from the same roots (Gottel et al, 2011). Pseudomonas strains can alter plant host function by modifying plant growth (Kloepper et al, 1980; Lugtenberg & Kamilova, 2009; Timm et al, 2015), nutrient allocation (Bisht et al, 2009), hormone signaling (Stearns et al, 2012), up-regulating/down-regulating of gene expression pathways (Timm et al, 2016), and immune function (Verhagen et al, 2004; Weston et al, 2012). Additionally, the Pseudomonas fluorescens clade has a large amount of functional diversity (Jun et al, 2016), thus selecting two Pseudomonas strains allows us to explore how plant traits and overall phenotype respond to closely related bacterial strain genomes.…”