THE SEED MICROBIOME Written by Joel Williams In the last article we introduced the various habitats that exist on and within plant tissues where a range of microbes coexist with plants and provide many benefits to growth and development. Despite the majority of microbiota living around plant root systems, there are also a range of microbes that also uniquely associate with plant shoots, leaves, flowers or seeds; and we are only just beginning to understand their importance. In this article we will take a closer look specifically at the seed microbiome and explore some of the factors that shape this biome and how this can be of benefit toward a more sustainable agriculture.
Like many other examples in agriculture where we have tended to focus on the negative, the prevalence of pathogens on seeds has been extensively studied and has dominated much of the thinking regarding seed microbiota. However, the occurrence and role of other beneficial microorganisms – which constitute a majority of the seed associated organisms – are relatively unknown. Seeds generally present similar proportions of bacterial and fungal diversity, which contrasts with other aboveground plant compartments that are for the most part, highly dominated by bacterial diversity. Microbial communities associated with the seed coat are usually more diverse than those associated within the seed – only a smaller number of specialist microbial species have the ability to pass through the external barriers of plant tissues and colonise tissues within; most others can only associate with the external surfaces. In the same way that there are unique and distinct microbes that associate with different plant parts, there are also specific microbes that associate exclusively to distinct micro-habitats of the seed itself. There are three seed compartments where microbes associate – the embryo, the endosperm and the seed coat. Seed-associated microorganisms can be acquired either ‘horizontally’ from various and local environments (e.g. air, water, insects, seed processing) or ‘vertically’ passed down from the mother plant, and hence, transmitted across multiple generations. Overall, microbes associated with the embryo and endosperm (internally) are more likely to be transmitted vertically than those associated with the seed coat, these being mostly transmitted horizontally. Three main transmission pathways have been documented: 1. The internal pathway – whereby microorganisms colonise developing 8 DIRECT DRILLER MAGAZINE
seeds via the xylem or nonvascular tissue of the mother plant. 2. The floral pathway – whereby microorganisms colonise developing seeds via the xylem or nonvascular tissue of the mother plant. 3. The external pathway – that represents microbial colonisation of developing seeds through the stigma. Of course, the development and application of the majority of seed treatment technologies have focussed primarily on the external pathway. Some of these inoculants are designed to remain on the outside and colonise the roots as they develop while some are destined to become endophytes and enter the plant tissues (such as rhizobia or some mycorrhiza for example). The exact mechanisms which determine the final structure and composition of the seed microbiome are still being elucidated but factors that influence this include a range of environmental conditions, soil type and perhaps most importantly, the host plant itself plays a major role in shaping its seed microbiome. It is now understood that each and every plant species recruits and structures a microbiome unique to that species (referred to as its core
microbiome), and even going beyond this, different varieties also shape their own ‘varietal specific’ microbiomes. These kinds of insights are opening some fascinating doors to understanding the species specific nature of plant-microbe interactions, which in the future will no doubt help design efficient production systems whereby plant varieties and microbial strains are highly aligned and optimised for various outcomes (plant health, pest resistance, nutrient use efficiencies etc). Although I fully support the use of highly diverse, broad spectrum and DIY inoculants like compost extracts, there are many examples whereby successful suppression of a pathogen (for example) is dependent on a specific antagonistic mechanism from one particular microbial species (or even strain); so illuminating some of these highly specific crop-microbe interactions at the molecular level will be a fruitful endeavour in years to come. In the meantime, it is clear that the seed microbiome is of utmost importance to plant development – affecting growth, drought resistance, disease resistance and even flowering times. We know the seed microbiome becomes active immediately after sowing as the germination process begins. These microbes associated with the seed are the early risers so to speak and
The seed microbiome plays an important role in the formation of early root and shoot microbial communities.
ISSUE 16 | JANUARY 2022
