Missing microbes and the wild side of plants

Wild relatives of crop plants tend to be less vulnerable to diseases and pests. A possible explanation lies in the 'microbiome', the sum total of micro-organisms in and around the plant. An article published recently by a team of NIOO-researchers points at significant differences between the microbiomes of wild plants and those of their domesticated cousins.

Earlier research had already shown that in the case of the common bean (Phaseolus vulgaris), the root microbiome changed as a result of domestication, significantly altering its potential for symbiosis with certain bacteria. Similar studies exist for a small number of other crop plants. However, write Juan Pérez-Jaramillo and his fellow researchers, very little is known about the impact of domestication on the microbiomes of the vast majority of plant species.

That's why the researchers decided to perform a meta-analysis: they reprocessed raw data from a number of earlier studies, in order to cover as broad a range as possible. Their "computational walk on the wild side" comprised six experiments, with a total of nine different plants species.

Important bacteria

The researchers write that they found significant and consistent differences between the microbiomes of the wild plants and those of the domesticated plants, even taking into account possible inconsistencies between the original experiments in sampling strategies, sequencing techniques etc. One thing they found was that the microbe group Bacteroidetes was more abundant in/on the roots of wild plants.

Bacteroidetes are also important in the gut microbiota of humans. Comparative analyses have revelead a higher abundance of Bacteroidetes in the gut of hunter-gatherer populations of rural communities in non-industrialized regions than in the gut of Westernized populations, and there appears to be a link to obesity: slim people have a higher proportion of Bacteroidetes.

Whether a higher relative abundance of Bacteroidetes affects plant growth and health in the same way, write the researchers, "is not known to date". Representatives of this phylum, such as the genus Flavobacterium, have indeed been associated with plant growth promotion and disease protection, but for at least one species (Trifolium pratense) it actually impaired shoot growth.

Unclear relationship

Further research is also needed to establish the exact relationship between the domestication of plants and the shifts in the composition of their microbiome. Plant root exudates may be a factor, as these organic compounds can have a major impact on the structure and functioning of microbial communities in soil environments.

Bacteroidetes are recognized for their ability to degrade complex biopolymers, so their prevalence in the root compartments of wild plant species may be associated with the presence of complex biopolymers in their root exudates. But the researchers note that as yet, "very little is known about the qualitative and quantitative differences between root exudation profiles of crop plants and their wild relatives."

Another possible factor is root architecture: the prevalence of Bacteroidetes in the rhizosphere of wild bean correlated significantly with a higher specific root length and a lower root density compared to its domesticated relatives. This allows wild plant species to be more efficient in the search for and uptake of water and nutrients in low-fertile soils.

Missing microbes

Follow-up research is underway into the importance of these factors.

"Establishing a phenotypically and genomically diverse and well-characterized collection of Bacteroidetes species from multiple wild plant relatives", write the researchers, "followed by controlled bioassays to test the effects of individual species/strains and consortia on plant growth and health under diverse environmental conditions will shed more light on their functional importance for the growth and survival of wild plant species in their native, environmentally harsh habitats.

Their conclusion: "understanding the functional importance of these 'missing plant microbes' can be highly instrumental in plant breeding programs and for improving our future crop production systems in a changing environment."

• Article: 'The wild side of plant microbiomes', Juan E. Pérez-Jaramillo,Víctor J. Carrión, Mattias de Hollander en Jos M. Raaijmakers, in Microbiome 2018 6:143 (https://doi.org/10.1186/s40168-018-0519-z)