Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time

Abstract

Recent field and laboratory experiments with perennial Boechera stricta and annual Arabidopsis thaliana suggest that the root microbiota influences flowering time. Here we examined in long-term time-course experiments the bacterial root microbiota of the arctic-alpine perennial Arabis alpina in natural and controlled environments by 16S rRNA gene profiling. We identified soil type and residence time of plants in soil as major determinants explaining up to 15% of root microbiota variation, whereas environmental conditions and host genotype explain maximally 11% of variation. When grown in the same soil, the root microbiota composition of perennial A. alpina is largely similar to those of its annual relatives A. thaliana and Cardamine hirsuta. Non-flowering wild-type A. alpina and flowering pep1 mutant plants assemble an essentially indistinguishable root microbiota, thereby uncoupling flowering time from plant residence time-dependent microbiota changes. This reveals the robustness of the root microbiota against the onset and perpetual flowering of A. alpina. Together with previous studies, this implies a model in which parts of the root microbiota modulate flowering time, whereas, after microbiota acquisition during vegetative growth, the established root-associated bacterial assemblage is structurally robust to perturbations caused by flowering and drastic changes in plant stature.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

“…Recent studies have shown that upon microbiota acquisition, the root-associated bacterial assemblage remains robust against major changes in plant stature and source-sink relationships (9,11). This microbiota stability is also observed here, where a clear separation between the root and rhizosphere of WT and symbiosis-impaired Lotus plants is retained when plants are grown under different nitrate conditions (SI Appendix, Fig.…”

“…2B). This similarity is likely related to our stringent root fractionation protocol (10,11), depleting both epiphytes and epidermal endophytes. However, we cannot rule out differences between the communities of the tested mutants of a magnitude smaller than the effect caused by soil batch variation and technical noise present in the pyrosequencing data.…”

“…This root-associated bacterial assemblage is mostly derived from the highly diverse bacterial soil biome surrounding roots and is established rapidly within a few days after seed germination (6,8). Soil type is the main driver of diversification of the bacterial root microbiota at low taxonomic ranks (i.e., at genus and species level), with less variation detectable at the higher phylum rank (8)(9)(10)(11). However, root exudates are thought to play an important role as cues to initiate a substrate-driven competition between, and differential proliferation of, soil-resident microbes for root colonization (3,12).…”

Assembly of seed-associated microbial communities within and across successive plant generations

“…soil physiochemical properties) and to a lesser extend selection by the host (e.g. plant genotype) influence the variation of bacterial root microbiota profiles (Bulgarelli et al 2012;Lundberg et al 2012;Peiffer et al 2013;Edwards et al 2015;Dombrowski et al 2017). Selection by the environment and the host are also important drivers of leaf-associated microbiota composition Horton et al 2014;Wagner et al 2016).…”

“…The plant microbiota can influence multiple plant traits such as biomass accumulation (Sugiyama et al 2013), metabolite production , drought tolerance (Lau and Lennon 2012;Rolli et al 2015), flowering time (Wagner et al 2014;PankeBuisse et al 2015;Dombrowski et al 2017) and disease resistance (Busby et al 2016;Ritpitakphong et al 2016;Mendes et al 2011;Santhanam et al 2015).…”