Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Chaparro, Jacqueline M.; Badri, Dayakar V.; Bakker, Matthew G.; Sugiyama, Akifumi; Manter, Daniel K.; Vivanco, Jorge M.

doi:10.1371/journal.pone.0055731

Cited by 542 publications

(418 citation statements)

References 68 publications

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“…Recent studies have shown that root secretion of defense-related proteins is enhanced during flowering time (De-la-Pena et al, 2010), suggesting an involvement of plant roots in ARR. Similarly, Chaparro et al (2013) have shown that Arabidopsis roots release more phenolic-related compounds at later stages of life which might be correlated to defense strategies against pathogens as secondary metabolites are involved in plant immunity against bacterial and fungal pathogens (Rogers et al, 1996;Clay et al, 2009;Millet et al, 2010;An and Mou, 2011;Bednarek, 2012). Thus, there is a need to understand the influence of plant development on microbial associations that might occur naturally in the rhizosphere related to defense but also to other vital plant necessities such as nutrient acquisition.…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, it was reported that the composition of Arabidopsis root exudates change following a plant developmental gradient (Chaparro et al, 2013). Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through plant growth.…”

Section: Introductionmentioning

confidence: 99%

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Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Rhizosphere microbiome assemblage is affected by plant development

2013

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“…After 3 d, in vitro plants were washed (three times) in distilled water and transferred into distilled water for 3 d before collecting root exudates (10 plants per 50 mL in a Falcon tube; adapted from Chaparro et al, 2013). Root exudates were centrifuged (2500 g for 5 min) to remove cell debris and border cells, freeze-dried and weighed before use.…”

Section: Collection Of Root Exudatesmentioning

confidence: 99%

Root exudate ofSolanum tuberosumis enriched in galactose-containing molecules and impacts the growth ofPectobacterium atrosepticum

Koroney

Plasson

Pawlak

et al. 2016

Ann Bot

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Background and aims Potato (Solanum tuberosum) is an important food crop and is grown worldwide. It is, however, significantly sensitive to a number of soil-borne pathogens that affect roots and tubers, causing considerable economic losses. So far, most research on potato has been dedicated to tubers and hence little attention has been paid to root structure and function.Methods In the present study we characterized root border cells using histochemical staining, immunofluorescence labelling of cell wall polysaccharides epitopes and observation using laser confocal microscopy. The monosaccharide composition of the secreted exudates was determined by gas chromatography of trimethylsilyl methylglycoside derivatives. The effects of root exudates and secreted arabinogalactan proteins on bacterial growth were investigated using in vitro bioassays.Key Results Root exudate from S. tuberosum was highly enriched in galactose-containing molecules including arabinogalactan proteins as major components. Treatment of the root with an elicitor derived from Pectobacterium atrosepticum, a soil-borne pathogen of potato, altered the composition of the exudates and arabinogalactan proteins. We found that the growth of the bacterium in vitro was differentially affected by exudates from elicited and nonelicited roots (i.e. inhibition versus stimulation).Conclusions Taken together, these findings indicate that galactose-containing polymers of potato root exudates play a central role in root-microbe interactions.

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“…Also shifts in diversity and abundance of microorganisms (e.g. methane oxidizing bacteria) during rice growth have been observed (Eller and Frenzel, 2001;Dianou et al, 2012), which could be partially attributed to the shift in the quantity and quality of root exudates during the growth of rice (Badri and Vivanco, 2009;Chaparro et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil

Yang

Weng

et al. 2016

Soil Biology and Biochemistry

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a b s t r a c tAnaerobic oxidation of ammonium (anammox) plays an important role in nitrogen (N) loss from agricultural systems. Recently, the rice rhizosphere was demonstrated to be a hotspot for anammox, yet the dynamics of anammox activity and the distribution of anammox bacteria in rhizosphere soil at different phenological stages of rice growth are still unknown. In this study, the activity, diversity and abundance of anammox bacteria in both rhizosphere and bulk soils were investigated over the entire rice growth season. From tillering to ripening stage, significantly higher anammox bacterial abundance was detected in rhizosphere soils compared to bulk soils. The rhizosphere soils also had significantly higher anammox rates at tillering and booting stages (0.71 and 0.32 nmol N g À1 dry soil h À1 , respectively) compared to bulk soils. The anammox rate in rhizosphere soil was positively correlated to the concentrations of NO x À (total of nitrate and nitrite) and acetate. The abundance of anammox bacteria was significantly correlated with the concentration of succinate in rhizosphere soils. A total of five anammox genera of Brocadia, Kuenenia, Anammoxoglobus, Jettenia and Scalindua were detected, with Brocadia predominating in all examined samples. The distribution of anammox bacteria in rhizosphere and bulk soils varied with phenological stages. Statistical analysis indicated that C/N ratio, formate, citrate and ammonium were key factors influencing the composition of anammox bacteria. Variations in activity, abundance and distribution of anammox bacteria in rhizosphere were observed over the phenological progression, demonstrating that the root exudates might be influential for the anammox process. This study implies that future efforts in estimating the rate of anammox should consider the temporal variation during plant life cycles.

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Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Cited by 542 publications

References 68 publications

Rhizosphere microbiome assemblage is affected by plant development

Rhizosphere microbiome assemblage is affected by plant development

Root exudate ofSolanum tuberosumis enriched in galactose-containing molecules and impacts the growth ofPectobacterium atrosepticum

The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil

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