Leaf-associated microbiomes of grafted tomato plants

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.

Fungal Endophytic Community Associated with Guarana (Paullinia cupana Var. Sorbilis): Diversity Driver by Genotypes in the Centre of Origin

“…The present results suggest that structuring of guarana fungal community (cultivable organisms) is directed both by the genetics of the host plant as well as by the geographic location, especially in leaves. These results are in line with previous studies of grapevines [ 99 ] and tomato [ 100 ] plants that have shown that different plant organs, genotypes of the same plant species and even sampling positions in the farmland can harbor partially different microbiomes. Guarana had high dominance of Colletotrichum and Fusarium , known as well established organisms, with different life style types [ 98 ].…”

Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

“…Another strategy for growing plants under drought conditions is the use of plant growth-promoting rhizobacteria (root), bacteria and fungi (PGPR, PGPB, and PGPF, respectively). A great variety of microbes are found to inhabit plant surfaces and different plant tissues and organs, including roots, rhizosphere, phyllosphere, stems, leaves, flowers, and seeds [ 7 , 8 , 9 ]. Root-associated microbes can improve host plant growth (such as N fixation [ 10 ], phosphate solubilization [ 11 ] and iron chelation), suppress pathogens, and mobilize some micronutrients, and they offer the potential to increase crop plant resilience to future drought [ 12 ].…”

Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

“…Our experiments represent an example of how cultivation-independent approaches can be efficiently deployed to investigate the plant microbiota under field conditions. Although this type of investigation is not novel per se in tomato (Toju et al, 2019), our results revealed fundamentally novel insights into plant’s adaptation to nitrogen fertilisers and the implication for crop yield. Similar to what has recently been postulated for tomato pathogen protection (Kwak et al, 2018), our results predicts that the use of field-derived, sequencing data will allow scientists to identify “signatures” of the plant microbiota that can be targeted to enhance plant performance.…”

“…Perhaps not surprisingly, tomato is gaining momentum as an experimental system to study host-microbiota interactions in crop plants. Recent investigations revealed novel insights into the assembly cues of the microbiota associated to this plant (Bergna et al, 2018; Toju et al, 2019) and the contribution of microbes thriving at the tomato root-soil interface to pathogen protection (Chialva et al, 2018; Kwak et al, 2018). However, the composition and functional potential of the tomato microbiota and their interdependency from nitrogen fertilisers remain to be elucidated.…”