Abstract
Proper quantification of the relative influence of soil and plant host on the root-associated microbiome can only be achieved by studying its distribution along an environmental gradient. Here, we used an undisturbed salt marsh chronosequence to study the bacterial communities associated with the soil, rhizosphere and the root endopshere of Limonium vulgare using 454-pyrosequencing. We hypothesize that the selective force exerted by plants rather than soil would regulate the dynamics of the root-associated bacterial assembly along the chronosequence. Our results showed that the soil and rhizosphere bacterial communities were phylogenetically more diverse than those in the endosphere. Moreover, the diversity of the rhizosphere microbiome followed the increased complexity of the abiotic and biotic factors during succession while remaining constant in the other microbiomes. Multivariate analyses showed that the rhizosphere and soil-associated communities clustered by successional stages, whereas the endosphere communities were dispersed. Interestingly, the endosphere microbiome showed higher turnover, while the bulk and rhizosphere soil microbiomes became more similar at the end of the succession. Overall, we showed that soil characteristics exerted an overriding influence on the rhizosphere microbiome, although plant effect led to a clear diversity pattern along the succession. Conversely, the endosphere microbiome was barely affected by any of the environmental measurements and very distinct from other communities.
Highlights
Assessments of microbial diversity have revealed soils—the habitats where plants and microbes live together and build highly diverse interactions—as being among the most biologically diverse on Earth (Curtis et al, 2002; Gans et al, 2005; Philippot et al, 2013; Saleem and Moe, 2014)
Compared to other successional stages, the 5-year stage showed the lowest level of nutrients (TN, SOC, NO−3, NH4+, P2O5, Ca, Mg, K), salinity, and soil water content (SWC)
In this study we directly examined the relative contribution of soil and plant effect on the diversity and structure of bacterial communities varying in their degree of association with plants, by making use of a gradient of soil development in a salt marsh primary succession
Summary
Assessments of microbial diversity have revealed soils—the habitats where plants and microbes live together and build highly diverse interactions—as being among the most biologically diverse on Earth (Curtis et al, 2002; Gans et al, 2005; Philippot et al, 2013; Saleem and Moe, 2014). The rhizosphere community represents the source of endophytic bacteria, which cross the root barrier and colonize the plant tissues, the endosphere (Sessitsch et al, 2002; Compant et al, 2005; Hardoim et al, 2008). Opportunistic and competent endophytes, show particular root colonization characteristics (e.g., chemotaxis response), in addition, competent endophytes could be well adapted to the plant environment and lead to the beneficial maintenance of the plant-microbe association (Hardoim et al, 2008). From the bulk soil and rhizosphere microbiome, plant roots recruit a very rare fraction of microbiota as endophytes, whereas their distribution across root morphological gradient may vary depending on plant and soil types (Saleem et al, 2015)
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