Ecological patterns of seed microbiome diversity, transmission, and assembly

Shade, Ashley; Martin, Jacques; Barret, Matthieu

doi:10.1016/j.mib.2017.03.010

Cited by 331 publications

(305 citation statements)

References 93 publications

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“…‘Battito’ and ‘Cuore di Bue’ are resistant and susceptible, respectively, to FOL races 1 and 2, as stated by the producer and verified in a previous study (Poli et al ., ). To remove the seed microbiota (Shade et al ., ), in all experiments seeds were disinfected as detailed in Chialva et al . (), at least removing the seed ectosphere.…”

Section: Methodsmentioning

confidence: 99%

Native soils with their microbiotas elicit a state of alert in tomato plants

et al. 2018

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Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The 'state of alert' detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.

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Section: Methodsmentioning

confidence: 99%

Native soils with their microbiotas elicit a state of alert in tomato plants

et al. 2018

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“…Thus, over the past several decades, a variety of phytosanitary measures have been developed for seed sterilization (Miché and Balandreau, 2001;Godefroid et al, 2016;Lindsey et al, 2017). However, recent developments in multi-omics-based analytical techniques suggest that seeds contain plant genotype-specific microorganisms that can be transferred vertically from one generation to the next (Adam et al, 2018;Johnston-Monje et al, 2016;Nelson, 2017;Shade et al, 2017). Microorganisms, mostly fungi and bacteria, enter the seeds through the outer seed coat or pollen granules, or naturally through infiltration of nectarthodes in flowers (Underwood et al, 2007;Frank et al, 2017).…”

Section: Genesis Of 'Microbiota-induced Soil Inheritance' (Misi)mentioning

confidence: 99%

Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory

Kong

Song

Ryu

2019

Environ Microbiol Rep

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Summary Since the discovery of the role of microbes in the phytobiome, microbial communities (microbiota) have been identified and characterized based on host species, development, distribution, and condition. The microbiota in the plant rhizosphere is believed to have been established prior to seed germination and innate immune development. However, the microbiota in seeds has received little attention. Although our knowledge of the distribution of microbiota in plant seeds and rhizosphere is currently limited, the impact of these microbiota is likely to be greater than expected. This minireview suggests a new function of microbial inheritance from the seed to root and from the first generation of plants to the next. Surprisingly, recruitment and accumulation of microbiota by biotic and abiotic stresses affect plant immunity in the next generation through plant–soil feedback and soil memory. To illustrate this process, we propose a new term called ‘microbiota‐induced soil inheritance (MISI).’ A comprehensive understanding of MISI will provide novel insights into plant–microbe interactions and plant immunity inheritance.

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“…However, seed-associated microbial communities are ecologically interesting because they both represent an endpoint and a starting point for community assembly of the plant microbiota (Shade et al 2017). Moreover seedassociated micro-organisms contribute to seed preservation (Chee-Sanford et al 2006) and the release of seeds from dormancy (Goggin et al 2015); they also have been associated with decreased germination rates (Nelson 2004;Munkvold 2009) and enhancement of ear emergence (Mitter et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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Background and aims Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Results Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. Conclusions These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

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Ecological patterns of seed microbiome diversity, transmission, and assembly

Cited by 331 publications

References 93 publications

Native soils with their microbiotas elicit a state of alert in tomato plants

Native soils with their microbiotas elicit a state of alert in tomato plants

Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory

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

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