Application of Natural Blends of Phytochemicals Derived from the Root Exudates of Arabidopsis to the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome

Abstract

Background: Roots can alter the rhizosphere microbial composition presumably by the secretion of root exudates. Results: Natural blends of phytochemicals present in the root exudates can modulate the soil microbiome in the absence of the plant. Conclusion: Different groups of compounds impact soil microbe composition at various levels. Significance: Identifying natural mixes of compounds that could positively influence plant-microbiome interactions can increase crop yield and sustainability.

Rhizosphere microbiome assemblage is affected by plant development

“…The soil is described in detail in Broeckling et al (2008); soil from the same site was used in previous studies (Broeckling et al, 2008;Badri et al, , 2013a. Arabidopsis thaliana seeds were surface-sterilized with Clorox for one minute and subsequently rinsed four times with sterile distilled water.…”

“…The bacterial hypervariable regions V1-V3 of the 16S rRNA gene were PCR-amplified using individually bar-coded forward primers 27F, 5 0 -AGAGTTTGATYMTGGCT CAG-3 0 and reverse primer 533R, 5 0 -TTACCGCGGCT GCTGGC -3 0 . PCR was performed using Taq DNA polymerase (Takara, Mountain View, CA, USA) as previously described (Badri et al, 2013a). Briefly, DNA samples were diluted to a concentration of 5 ng ml À 1 and one microliter was used per PCR reaction.…”

“…16S rRNA sequencing analysis Sequence reads were processed using Mothur v. 1.25.1 (Schloss et al, 2009) as previously described (Badri et al, 2013a). Sampling effort was equalized to the depth of the smallest sample (2769 reads) and operational taxonomic units (OTUs) were defined at X97% sequence identity, using the average neighbor algorithm.…”

“…Evidence demonstrating the close ties root exudates have on the microbial composition of the rhizosphere is mounting (Broeckling et al, 2008;Badri et al, , 2013aMicallef et al, 2009b;Chaparro et al, 2012Chaparro et al, , 2013, whereby many chemicals present in root exudates act as substrates, chemotactic or signaling molecules to orchestrate changes in microbial composition (Shaw, 1991;de Weert et al, 2002;Jain and Nainawatee, 2002;Horiuchi et al, 2005;Bais et al, 2006;Badri and Vivanco, 2009;Neal et al, 2012;Badri et al, 2013a). Recently, it was reported that the composition of Arabidopsis root exudates change following a plant developmental gradient (Chaparro et al, 2013).…”

“…In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. Accordingly, it was hypothesized that seedlings of roots release sugars as substrates for a wide diversity of microbes at early stages of development but as the plant ages it releases specific substrates and potentially antimicrobial compounds in an effort to select for particular microbial inhabitants of the rhizosphere (Badri et al, 2013a;Chaparro et al, 2013). This potential selection of microbes in the rhizosphere as the plant ages might be associated with the ability of beneficial microbes to suppress pathogenic ones (Mendes et al, 2011), trigger induced systemic tolerance to overcome abiotic stress (Selvakumar et al, 2012), increase the plant's innate immunity (Zamioudis and Pieterse, 2012), help in mineral nutrition (Bolan, 1991;van der Heijden et al, 2008) and in overall plant health (Berendsen et al, 2012;Chaparro et al, 2012).…”