Abstract
Bacteria and fungi form complex communities (microbiomes) in above- and below-ground organs of plants, contributing to hosts’ growth and survival in various ways. Recent studies have suggested that host plant genotypes control, at least partly, plant-associated microbiome compositions. However, we still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes could determine the assembly of leaf endophytic microbes in field conditions. An Illumina sequencing analysis showed that both bacterial and fungal community structures did not significantly differ among tomato plants with different rootstock genotypes: rather, sampling positions in the farmland contributed to microbiome variation in a major way. Nonetheless, a further analysis targeting respective microbial taxa suggested that some bacteria and fungi could be preferentially associated with particular rootstock treatments. Specifically, a bacterium in the genus Deinococcus was found disproportionately from ungrafted tomato individuals. In addition, yeasts in the genus Hannaella occurred frequently on the tomato individuals whose rootstock genotype was “Ganbarune”. Overall, this study suggests to what extent leaf microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants.
Highlights
Bacteria and fungi form complex communities in above- and below-ground organs of plants, contributing to hosts’ growth and survival in various ways
All the prokaryote operational taxonomic units (OTUs) belonged to Bacteria: no archaeal OTUs were observed
Detailed analyses suggested the existence of leaf microbial taxa whose associations with host plants might be affected by below-ground plant genotypes (Figs 2 and 3; Tables 2–4)
Summary
Bacteria and fungi form complex communities (microbiomes) in above- and below-ground organs of plants, contributing to hosts’ growth and survival in various ways. We still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes could determine the assembly of leaf endophytic microbes in field conditions. This study suggests to what extent leaf microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants. In both natural and agricultural ecosystems, bacteria and fungi in diverse taxonomic groups are associated with plants, positively and/or negatively influencing the survival and growth of their hosts[1,2,3,4]. New lines of studies examining relationships between scion/rootstock genotypes and whole microbiome structures in roots/leaves have been awaited
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