The seed microbiome: Origins, interactions, and impacts

  title={The seed microbiome: Origins, interactions, and impacts},
  author={Eric B. Nelson},
  journal={Plant and Soil},
  • E. Nelson
  • Published 2017
  • Environmental Science
  • Plant and Soil
BackgroundThe development and dispersal of seeds as well as their transition to seedlings represent perhaps the most critical stages of a plant’s life cycle. The endophytic and epiphytic microbial interactions that take place in, on, and around seeds during these stages of the plant’s life cycle may have profound impacts on plant ecology, health, and productivity. While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now… 
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Inheritance of seed and rhizosphere microbial communities through plant-soil feedback and soil memory.
This minireview suggests a new function of microbial inheritance from the seed to root and from the first generation of plants to the next, called microbiota-induced soil inheritance (MISI).
The Ecology of Seed Microbiota
  • P. Hardoim
  • Environmental Science, Biology
    Seed Endophytes
  • 2019
This study summarizes the results from the literature regarding the diversity of seed-inhabiting microbes, how environmental and host factors might affect seed microbial assembly and structure, and the putative mutualistic functions of microbes might have during seedling establishment.
Seed Endophytes and Their Potential Applications
Seed-inhabiting endophytes can facilitate the improvement of seed quality and plant growth of agriculturally important crops via different biotechnological applications; they have prospects in endophyte-mediated phytoremediation applications.
Bacterial Endophyte Colonization and Distribution within Plants
This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.
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The resulting seed biologicals can be harnessed for sustainable agricultural approaches by improving stress tolerance and resilience of modern crops and based on the rich diversity of seeds of wild ancestors or other native plants.
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This study reports a protocol for extracting metagenomic DNA from an individual seed with minimal disruption of host tissue, and applies this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health.


The plant microbiome explored: implications for experimental botany.
Analysis of plant microbiome data has brought about a paradigm shift in understanding of the diverse structure and functioning of the plant microbiome with respect to the high interplay of bacteria, archaea, fungi, and protists; the high specificity even at cultivar level; the vertical transmission of core microbiomes; the extraordinary function of endophytes; and several unexpected functions and metabolic interactions.
Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages
Assessment of the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations, showed that soil type is a major effector of the bacterial endophytes.
The root microbiota—a fingerprint in the soil?
Only by following a plant from its origin inside the flower to senescence, can the authors fully understand how the associated microbial community was assembled and what determined its composition.
Seed bacterial endophytes: Common genera, seed-to-seed variability and their possible role in plants
It is demonstrated that individual seeds of maize (Zea mays L.) taken from the same cob and bean seeds (Phaseolus vulgaris L.) from different pods and within individual pods differ in their bacterial content and population diversity, and suggested that this bacterial variability within seed population of individual plants may contribute to the species adaptation to diverse environments and be harnessed in the production of crop plants.
Bacterial seed endophytes: genera, vertical transmission and interaction with plants
The role of seed-associated microorganisms, and especially seed endophytic bacteria, still is underestimated, but these associations could be beneficial for germination and seedling establishment as seed endophical bacteria are already present in these very early plant growth stages.
Microbial dynamics and interactions in the spermosphere.
  • E. Nelson
  • Biology
    Annual review of phytopathology
  • 2004
This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the sper atmosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.
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It is proposed that seed transmission of bacterial endophytes requires adaptation of both plant and microbes, plays a role in germination and has evolutionary significance and implications for future plant breeding approaches, in Miscanthus and more widely.
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This work analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment of gyrB.
Plant microbiota affects seed transmission of phytopathogenic microorganisms.
The survey of seed‐associated microbial assemblages presented in this Opinion piece should provide novel options for the selection of biocontrol agents.
The importance of the microbiome of the plant holobiont.
It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment and to better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.