Root-Associated Bacterial and Fungal Community Profiles ofArabidopsis thalianaAre Robust Across Contrasting Soil P Levels

Abstract

Plant survival depends on the ability of roots to sense and acquire nutrients in soils, which harbor a rich diversity of microbes. A subset of this microcosm interacts with plant roots and collectively forms root-associated microbial communities, termed the root microbiota. Under phosphorus-limiting conditions, some plants can engage in mutualistic interactions, for example with arbuscular mycorrhizal fungi. Here, we describe how Arabidopsis thaliana, which lacks the genetic capacity for establishing the aforementioned symbiosis, interacts with soil-resident bacteria and fungi in soil from a long-term phosphorus fertilization trial. Long-term, contrasting fertilization regimes resulted in an ∼6-fold and ∼2.4-fold disparity in bioavailable and total phosphorous, respectively, which may explain differences in biomass of A. thaliana plants. Sequencing of marker genes enabled us to characterize bacterial and fungal communities present in the bulk soil, rhizosphere, and root compartments. Phosphorus had little effect on alpha- or beta-diversity indices, but more strongly influences bacterial and fungal community shifts in plant-associated compartments compared with bulk soil. The significant impact of soil P abundance could only be resolved at operational taxonomic unit level, and these subtle differences are more pronounced in the root compartment. We conclude that despite decades of different fertilization, both bacterial and fungal soil communities remained unexpectedly stable in soils tested, suggesting that the soil biota is resilient over time to nutrient supplementation. Conversely, low-abundance, root-associated microbes, which collectively represent 2 to 3% of the relative abundance of bacteria and fungi in the roots, exhibited a subtle, yet significant shift between the two soils. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana

“…Although the composition of the root microbiota has been shown to be strongly dependent on the soil in which the plant grows (Peiffer et al ., ; Schlaeppi et al ., ), the mechanistic basis underlying the control of root‐associated microbial communities by soil nutrient availability is largely unknown. Recent reports on A. thaliana root microbiota revealed a higher impact of long‐term soil fertilization with P on fungal communities compared with bacteria (Robbins et al ., ). In this article, we significantly expanded this knowledge by studying how P availability in natural nonsterile soil and the plant's response to soil P (controlled by the PSR) jointly shape the root‐associated fungal microbiota of the AM nonhost species A. thaliana in the short term.…”

“…; Tables S6, S7). This contrasts with long‐term fertilization studies, which have reported shifts in fungal soil communities on long‐term amendment of the soil with P fertilizer (Leff et al ., ; Robbins et al ., ), and suggests that P fertilization exerts rapid effects specifically on root‐associated microbes. It is also possible that short‐term effects of P concern primarily the activity of soil fungi, rather than their presence or abundance; therefore, RNA‐ rather than DNA‐based fungal community studies are needed to account for these effects.…”

“…All available studies have shown that the structure of the rootassociated fungal microbiome is strongly dependent on the soil in which the plant grows (Shakya et al, 2013;Coleman-Derr et al, 2016;Almario et al, 2017). This 'soil effect' usually accounts for the overlapping effects of different soil characteristics associated with the soil's geographical origin and with edaphic factors, such as mineral nutrient content and, more specifically, soil P content (Almario et al, 2017;Robbins et al, 2018;Yu et al, 2018). Although such studies provide evidence that plants growing in soils which have been subjected to contrasting long-term P fertilization regimes assemble different fungal microbiomes, the assembly rules and plant-mediated effects of P remain enigmatic.…”

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

“…Root-specific enrichment for widespread OTUs, compared to soil and RS samples was tested with a generalized linear model, as described in ref. 22 (FDR, p < 0.05). To compare generalist OTUs from this study with OTUs found in roots of Lotus japonicus 26 bacterial OTUs were directly compared using the representative sequences (Blastn, 98% sequence identity).…”

“…However, the relative importance of different abiotic and biotic factors for the evolution and maintenance of local adaptation is poorly known 17, 18 . Particularly, soil edaphic factors and soil microbes are known to influence flowering phenology and modulate host fitness in natural soils 19, 20, 21, 22, 23 , even at the scale of a few meters 24 . Yet, information about the extent to which differences in soil properties contribute to divergent selection and the maintenance of adaptive differentiation among plant populations is still limited beyond classical examples of adaptation to extreme soil conditions 25 .…”