COMMENTARY COMMENTARY Root surface as a frontier for plant microbiome research

Marcel G. A. van der Heijdena,b,c and Klaus Schlaeppia,1 aPlant-Soil Interactions, Institute for Sustainability Sciences, Agroscope, 8046 Zürich, Switzerland; bPlant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands; and cInstitute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland

Plants associate—analogous to animals or us root microbiota acquisition based on a high humans—with a multitude of microorgan- spatial resolution of root habitats in time isms, which collectively function as a micro- series experiments. The authors trans- biome. A major discovery of the last decade planted sterile germinated seedlings into soil

is that numerous organisms of a microbiome and sampled the root-associated habitats Fig. 1. Acquisition of the plant root endosphere micro- (aka microbiota) are not unpretentious back- from time points between 1 and 13 d after biota from soil. Gradual shifts in microbiota composition ground actors. Instead, some microbiota transplantation. The microbiota comparison occur in the root-associated habitats including a zone of members influence host processes including in space and time revealed that the habitat- soil surrounding the roots (rhizosphere, gray shading) behavior, appetite, and health in animals (1) to which root exudates are secreted, the root surface specific community structures were largely (rhizoplane), and the inner host tissue (root endosphere). and contribute to nutrition and health of established after 1 d. Although the compo- Bars illustrate compositional changes in each microbial plants (2–4). Recently, the compositions of sition of the root endosphere was organized habitat due to enrichment (black arrows) and exclusion the plant root-associated microbiota from within 1 d, the steady-state size of the bac- (black T-symbol) processes. Bars are scaled using the numerous plant species, including major number of DNA sequences that change in abundance terial population was reached in 13 d. This (enrichment/exclusion) in the rhizosphere (152/17), the rhi- crops, were revealed using high-throughput work permitted refinement of a two-step zoplane (422/730), and the root endosphere (394/1,961) DNA sequencing. Factors such as soil type model of root microbiota assembly (2) to compared with soil (see ref. 5). or host genotype influence the root-associ- a model with at least three selective steps, ated microbiota. However, the processes that with the rhizoplane as a key component that it appears, paradoxically, that plants permit determine the acquisition of the root micro- serves a critical gating role for controlling endosphere colonization, whereas host cells biota, its resistance to stress, and its ecological microbial entry into the host tissue (Fig. 1). function remain poorly understood. Edwards initiate defense responses on the detection et al. (5) present the third publication in a re- Model of molecular epitopes, which are conserved cent series of PNAS articles about the bacte- The root endosphere microbiota results from throughout the bacterial kingdom (8). Hence, rial microbiota associated with plant roots of gradual community shifts including enrich- we speculate that the host immune system maize (6), related Brassicaceae (7), and now ment and, mainly, depletion processes from influences microbiota selection in general Oryza sativa (rice). It comprises a compre- the surrounding soil microbiota presenting and that it has a strong impact at the second hensive characterization of three microbial the start inoculum (Fig. 1). The enrichment step of exclusion from the rhizoplane to the habitats that are in the proximity of, on, processbeginstoactatadistanceinthe root endosphere microbiota (Fig. 1). and inside plant roots, which are named rhizosphere, continues at the rhizoplane, and Host genotype-dependent variation in rhizosphere, rhizoplane, and root endo- is likely to be largely driven by root exuda- microbiota composition may occur where sphere (Fig. 1). tion. Unlike enrichment, the exclusion pro- host physiological processes (e.g., root exu- A major advance of Edwards et al. is the cess appears to operate more intimately: dates or immune system) are involved. The description of the acquisition process of the first on the rhizoplane and then more pro- different rice cultivars varied noticeably in root endosphere microbiota (5). In contrast nounced in the root endosphere. One ex- their rhizosphere communities, whereas the to the gut microbiota, which is partly in- planation for the first step of exclusion is rhizoplane or root endosphere microbiota herited from the mother, the root endosphere that the rhizoplane selects for bacteria which was little affected by the host genotype (5). microbiota is largely reestablished every time are able to form biofilms and successfully Also, maize inbred lines exhibited quantita- a plant germinates. Until now, the acquisition compete in the presence of elevated nutrient tive differences in rhizosphere microbiota of the endosphere microbiota was proposed levels. Presumably, the second step of ex- composition (6). This contrasts observations to occur in two steps: root exudates, present- clusion results from the selection of the in Arabidopsis where endosphere and not ing a complex mixtures of organic compounds rhizoplane bacteria which possess traits en- rhizosphere communities were affected by that are secreted by plant roots, trigger a abling the colonization of the root endo- first general enrichment in the rhizosphere, sphere. Such microbial traits may allow the Author contributions: M.G.A.v.d.H. and K.S. wrote the paper. followed by a host genotype-dependent dif- bacteria e.g., to evade recognition or to The authors declare no conflict of interest. “ ferentiation of the microbiota thriving on manipulate host defense reactions. We as- See companion article on page E911. ” the rhizoplane and within plant roots (2). sume the involvement of microbial traits 1To whom correspondence should be addressed. Email: klaus. Edwards et al. (5) reveal the early steps of that subvert host immune processes because [email protected].

www.pnas.org/cgi/doi/10.1073/pnas.1500709112 PNAS | February 24, 2015 | vol. 112 | no. 8 | 2299–2300 Downloaded by guest on September 25, 2021 the host genotype (9, 10). It appears that host microbial communities in soil, including Tools genetic differences in microbiota composition major members of the plant root microbiota, One approach for new insights in the plant can occur in all root-associated habitats, but has a positive impact on a range of plant microbiome relies on the systematic isolation that the habitat where the host genotype- species and on the functionality of an eco- of root microbiota members (16). Reference dependent variation emerges depends on the system, exemplifies the benefits from com- stocks of pure isolates together with the in- plant species. Note that the host genotype- plex diverse microbial communities (13). formation on community composition allow dependent effects discussed here affect com- The advances in basic microbiome science the reconstruction of at least the cultivable munity composition at best at the level of in the human and animal fields have triggered fraction of the root microbiota. Inoculation microbial species because the 16S profiling experiments should make it possible to ex- technique(usedinrefs.5,6,9,and10)does Edwards et al. reveal amine the interaction of such synthetic com- not resolve subspecies variation between the early steps of root munities with the host plant to unravel the microbiota members, and this is the level of functions of whole communities and their variation that determines the outcomes microbiota acquisition individual members. Here, genome and tran- of most plant–microbe interactions (8). based on a high spatial script sequencing is expected to reveal the microbial traits which are expressed and rel- Frontiers resolution of root hab- evant in the interaction with the plant. Com- Numerous key questions emerge for further itats in time series plementary to such cultivation approaches, the plant microbiome research including the direct sequencing of complex mixtures of following. What is the ecological function of experiments. DNA from various organisms of a habitat the plant microbiome? What are the roles of efforts for using the microbiome to improve (metagenomics) reveals the metabolic capacity core microbiota members that are shared human health (1). Likewise, can we exploit of a microbiome. In rice, numerous microbial between many plant species? How do plants the microbiome to enhance plant produc- traits such as nitrogen fixation, the flagellum, interact with the microbiota and what is the tivity in agricultural settings (14)? The con- protein secretion systems, or quorum sensing, molecular cross-talk between host and asso- trol of pathogen burden or the increase of and their habitat specificity were predicted ciated microbes? Can we localize the micro- using metagenomics (17, 18). biota in the endosphere by, for example, nutrient use efficiency would permit the using in situ hybridization methods? Finally, reduction of agrochemical inputs, thereby Conclusion can we capitalize on the plant microbiome to promoting a more sustainable agriculture. The study by Edwards et al. (5) unifies in- enhance yield and sustainability in agricul- We may be able to manipulate the host side novative basic science, insights into applied ture? Below we detail three frontiers. of the interaction, as done during breeding aspects, and stimulating elements such as the The majority of microbiota studies includ- for disease-resistant cultivars, by selecting exploration of coabundance networks. As in ing Edwards et al. (5) focus on a single group lines with enhanced responsiveness to ben- this study, the use of state-of-the-art meth- of microbes, e.g., prokaryotes. However, eficial services of the root microbiota (15). odology in well-designed experiments and many plant species including major crops Complementarily, we might try to improve testing clearly formulated hypotheses with a such as rice, maize, and cereals are colonized plant performance through the active ma- high degree of scientific rigor advance the by a wide range of fungi, including mutual- nipulation of the root microbiome of crops field of plant–microbiota interactions and istic arbuscular mycorrhizae (4, 11). Clearly, (e.g., by coating seeds or preinoculating contribute to a more holistic understanding the simultaneous examination of bacteria and seedlings with particular microbes). of the plant microbiome. fungi in plant roots deserves further atten- tion. The study of multitrophic interactions between bacteria, archaea, and fungal mem- 1 Blaser M, Bork P, Fraser C, Knight R, Wang J (2013) The 10 Lundberg DS, et al. (2012) Defining the core Arabidopsis thaliana microbiome explored: Recent insights and future challenges. Nat Rev root microbiome. Nature 488(7409):86–90. bers of the root microbiota is currently in Microbiol 11(3):213–217. 11 Porras-Alfaro A, Bayman P (2011) Hidden fungi, emergent its infancy and is likely to reveal additional 2 Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, properties: Endophytes and microbiomes. Annu Rev Phytopathol insights in microbiota functionalities. Schulze-Lefert P (2013) Structure and functions of the bacterial 49:291–315. microbiota of plants. Annu Rev Plant Biol 64:807–838. 12 Lugtenberg B, Kamilova F (2009) Plant-growth-promoting Beyond the examination of community 3 Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere rhizobacteria. Annu Rev Microbiol 63:541–556. composition, a major frontier is to investigate microbiome and plant health. Trends Plant Sci 17(8):478–486. 13 Wagg C, Bender SF, Widmer F, van der Heijden MGA (2014) thefunctionsoftheplantmicrobiota.Indi- 4 Van der Heijden MGA, Martin F, Selosse MA, Sanders IR (2015) Soil biodiversity and soil community composition determine Mycorrhizal ecology and evolution: The past, the present and the ecosystem multifunctionality. Proc Natl Acad Sci USA 111(14): viduals of the plant microbiota can provide future. New Phytol 205:1406–1423. 5266–5270. a number of beneficial services to the host 5 Edwards J, et al. (2015) Structure, variation, and assembly of the 14 Schlaeppi K, Bulgarelli D (2014) The plant microbiome at work root-associated microbiomes of rice. Proc Natl Acad Sci USA [published online ahead of print December 16, 2014]. Mol Plant plant including delivery of nutrients, pro- 112:E911–E920. Microbe Interact, 10.1094/MPMI-10-14-0334-FI. tection against disease and tolerance to 6 Peiffer JA, et al. (2013) Diversity and heritability of the maize 15 Dangl JL, Horvath DM, Staskawicz BJ (2013) Pivoting the plant abiotic stress (2, 4, 11, 12). However, our rhizosphere microbiome under field conditions. Proc Natl Acad Sci immune system from dissection to deployment. Science 341(6147): USA 110(16):6548–6553. 746–751. knowledge of such plant growth-promoting 7 Schlaeppi K, Dombrowski N, Oter RG, Ver Loren van Themaat E, 16 Guttman DS, McHardy AC, Schulze-Lefert P (2014) Microbial microbesislargelybiasedtostudiescon- Schulze-Lefert P (2014) Quantitative divergence of the bacterial root genome-enabled insights into plant-microorganism interactions. Nat ducted on individual isolates under lab- microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA Rev Genet 15(12):797–813. 111(2):585–592. 17 Knief C, et al. (2012) Metaproteogenomic analysis of microbial oratory conditions, and we have a limited 8 Jones JDG, Dangl JL (2006) The plant immune system. Nature communities in the phyllosphere and rhizosphere of rice. ISME J 6(7): understanding of how entire microbial com- 444(7117):323–329. 1378–1390. 9 Bulgarelli D, et al. (2012) Revealing structure and assembly cues for 18 Sessitsch A, et al. (2012) Functional characteristics of an munities contribute to plant growth. Re- Arabidopsis root-inhabiting bacterial microbiota. Nature 488(7409): endophyte community colonizing rice roots as revealed by cent observations that a high diversity of 91–95. metagenomic analysis. Mol Plant Microbe Interact 25(1):28–36.

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