A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds

Abstract

The microbial component of healthy seeds – the seed microbiome – appears to be inherited between plant generations and can dynamically influence germination, plant performance, and survival. As such, methods to optimize the seed microbiomes of major crops could have far-reaching implications for plant breeding and crop improvement to enhance agricultural food, feed, and fiber production. Here, we describe a new approach to modulate seed microbiomes of elite crop seed embryos and concomitantly design the traits to be mediated by seed microbiomes. Specifically, we discovered that by introducing the endophyte Paraburkholderia phytofirmans PsJN to the flowers of parent plants we could drive its inclusion in progeny seed microbiomes, thereby inducing vertical inheritance to the offspring generation. We demonstrated the introduction of PsJN to seeds of monocot and dicot plant species and the consequential modifications to seed microbiome composition and growth traits in wheat, illustrating the potential role of novel seed-based microbiomes in determining plant traits.

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

“…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). Recent diversity surveys of the seed microbiota revealed a high level of variation in microbial assemblages composition (LopezVelasco et al 2013;Links et al 2014;Barret et al 2015;Klaedtke et al 2016;Rezki et al 2016).…”

Elucidating the influence of resident seed and soil microbiota on the developing creeping bentgrass microbiome

“…Data presented covers both experimental runs, as the taxonomic breakdown was similar between both runs observed rhizosphere bacterial communities of maize grown on sterile sand and non-sterile soils all contained the same dominant operational taxonomical units (OTUs), indicating the seed as a common source of inoculum (Johnston-Monje, Lundberg, Lazarovits, Reis, & Raizada, 2016). While two taxa may not seem meaningful, Mitter et al (2017) observed that by introducing a single bacterial endophyte to the flowers of parent wheat plants, vertical transmission of the endophyte into the seed was successfully achieved. The vertical transmission of this single bacterial endophyte also translated into benefits in faster spike onset in the greenhouse and ears per square meter in the field compared with seeds without the endophyte present (Mitter et al, 2017).…”

“…While two taxa may not seem meaningful, Mitter et al (2017) observed that by introducing a single bacterial endophyte to the flowers of parent wheat plants, vertical transmission of the endophyte into the seed was successfully achieved. The vertical transmission of this single bacterial endophyte also translated into benefits in faster spike onset in the greenhouse and ears per square meter in the field compared with seeds without the endophyte present (Mitter et al, 2017). Even small contributions to the microbiome from seed bacterial communities can result in increased plant health.…”

Unravelling native plant resistomes – The Sphagnum microbiome harbours versatile and novel antimicrobial resistance genes

“…S. marcescens , a common plant-associated bacterium, also exhibits various antibiotic resistances and opportunistic traits 29 . Less is known to this end for the identified Paraburkholderia and Rouxiella species, especially for P. phytofirmans , which is a promising plant growth promoting agent 30 . Interestingly, plants in general and Sphagnum in particular constitute reservoirs for plant growth promoting bacteria with antifungal and antibacterial activity 31 , while simultaneously hosting species known as opportunistic human pathogens 16,32 .…”