Plant host habitat and root exudates shape soil bacterial community structure

Abstract

The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under 13 CO 2 (99% of atom 13 C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of 13 C-DNA and root DNA, whereas those assimilating SOM were identified from 12 C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots

“…DNA concentrations were fluorometrically quantified using PicoGreen staining kit. For each gradient, one fraction representative of 13 C-labelled ('heavy') DNA and one fraction representative of unlabelled ('light') DNA were chosen according to a standardized method based on previous studies in the laboratory (Haichar et al, 2007(Haichar et al, , 2008 following buoyant density and DNA content of each fraction in comparison with control gradient containing unlabelled soil DNA and 13 C labelled DNA from Escherichia coli. The heavy fraction was considered to contain DNA representative of populations involved directly or not, in root exudates assimilation and the light one, to contain DNA from populations degrading soil organic matter or inactive (Figure 1) (Rangel-Castro et al, 2005;Haichar et al, 2008).…”

“…It results from the introduction of the CYP79A1 gene from sorghum which led to the production of high levels of the tyrosine-derived glucosinolate p-hydroxybenzylglucosinolate not known to accumulate in wild-type A. thaliana ecotype Columbia (Bak et al, 1999). Transgenic CYP79A1 plant seeds were provided by Halkier BA (Royal Veterinary and Agricultural University, Copenhagen, Denmark) and together with wild-type Col, were grown in triplicate in soil under 13 CO 2 following the protocol described by Haichar et al (2008), to compare their rhizospheric microbial communities. Briefly, after seed sterilization, plants were grown in pots for 18 days before being continuously labelled for 25 days by injection of pure (499% atom 13 C) 13 CO 2 (Purchased from Cortec Net, Paris, France) monitored to maintain an isotope excess at 480% atom 13 C (Figure 1).…”

“…Root exudates are critical in determining the nature of plant-microorganisms interaction in the rhizosphere and shape microbial community structure present in the vicinity of the roots (Butler et al, 2003;Bais et al, 2006;Costa et al, 2006;Paterson et al, 2007;Broeckling et al, 2008;Haichar et al, 2008). Some studies have focused on the implication of a specific plant defense-signaling pathway as a driving force in structuring native soil microbial communities.…”

“…This culture-independent approach allows discriminating root exudate-assimilating microbial populations in plant rhizosphere from those dormant or degrading soil organic matter (Rangel-Castro et al, 2005;Haichar et al, 2008) and to link the identity of microorganisms to their function in soil (Radajewski et al, 2000;Lu et al, 2006).…”

Positive effects of plant diversity on soil microbial biomass and activity are associated with more root biomass production

“…Moreover, plants mainly provide carbon resources and other nutrients for soil microbial community in the form of plant litter and root exudates (Rodríguez-Loinaz et al 2008). Especially, root exudates are readily available sources of carbon and energy for microbes (Paterson et al 2007;Haichar et al 2008). Moreover, microbial growth (Oger et al 2004;Blagodatskaya et al 2009) and activity (Nannipieri et al 2012) can be stimulated by labile compounds (including enzymes) released by living roots.…”