Table 1.
The microbiomes of various plants.
| Plant | Location | Comment | Reference |
|---|---|---|---|
| Artemisia herba-alba | Rhizosphere | Highest number of bacterial species compared to the microbiota of 13 other plant species of the Algerian desert. | [25] |
| Brassica napus (canola) | Rhizosphere | Examined field grown plants at 3 separate sites. Found stable bacterial core microbiome. | [26] |
| Brassica napus | Rhizosphere | Different microbiome complexity at different stages of plant growth. | [27] |
| Oryza sativa (rice) | Root surface, root endosphere, shoot surface, shoot endosphere | Compared microbiome of rice seedlings to microbiome of rice seed. Greatest abundance and diversity found in roots. | [28] |
| Oryza sativa | Rhizosphere, endosphere, rhizoplane | The three root-associated compartments that were studied, each had distinct microbiota. | [29] |
| Oryza sativa | Rhizosphere | Elevated levels of CO2 suppresses methane oxidation thereby promoting methanogenesis in rice roots. | [30] |
| Oryza sativa | Rhizosphere soil, plant stems/leaves, plant roots | Transgenic rice expressing a Bt protoxin gene did not significantly change the plant bacterial strains compared to the parental strain. | [31] |
| Oryza sativa | Rhizosphere | Indica and japonica varieties recruit distinct root microbiota. NRT1.1B, a rice nitrate transporter, is involved in recruitment of the indica-enriched bacteria. | [32] |
| Oryza sativa | Endosphere | In three different varieties, the endophytic microbiome varied significantly between young and mature plants. | [24] |
| Vitis vinifera (grape) | Rhizosphere | Compared rhizosphere to bulk soil in a conventionally managed vineyard. | [33] |
| Vitis vinifera | Rhizosphere | Microbiomes of the same cultivar were different when they were grafted onto 2 different rootstocks. | [34] |
| Vitis vinifera | Rhizosphere | Compared rhizosphere to bulk soil in an integrated pest management vineyard. | [35] |
| Rubus chamaemorus, Andromeda polifolia, Empetrum vaginatum, Sphagnum sp., Carex rotundata, E. angustifolium | Phyllosphere and rhizosphere | All plants were from arctic peatlands. Microbiomes were compared to peat. Methanogen abundance was strongly influenced by the individual plant. | [36] |
| Zea mays (corn) | Rhizosphere | Samples were from corn farms. | [37] |
| Zea mays | Rhizosphere | Isolated and sequenced the genomes of several rhizosphere bacteria. | [38] |
| Zea mays | Endosphere | Strong relationship between endosphere community and corn productivity. | [39] |
| Zea mays | Rhizosphere | The rhizosphere community following crop rotation was more abundant than following monocropping. | [40] |
| Zea mays | Bulk soil, rhizosphere, endosphere | Different cultivars had different biomass, root exudates and different microbiota in bulk soil, rhizosphere and endosphere. Also, different soils contributed to microbiome variation. | [41] |
| Zea mays and Glycine max (soybean) | Rhizosphere | Found no significant difference between plants treated with glyphosate and those not treated with this herbicide. | [42] |
| Glycine max | Rhizosphere | Determined the effect of nodulation phenotypes on soybean microbiomes. | [43] |
| Brassica napus, Buglossoides arvensis (corn gromwell) and Glycine max | Rhizosphere | Inoculation with Pseudomonas strain promoted seed oil accumulation, increased abundance of 29 taxa and decreased abundance of 30 taxa. | [44] |
| Gossypium hirsutum (cotton) | Rhizosphere | Characterized the microbiome associated with Verticillium wilt. | [45] |
| Gossypium hirsutum | Rhizosphere, bulk soil | Biota diversity increased in soil with cotton plants. Drought stress increased the abundance of some bacteria which help sustain the plants. | [46] |
| Triticum aestivum (wheat) | Rhizosphere | Compared eight wheat cultivars grown under field conditions for root diameter and root length and microbiome. | [47] |
| Triticum aestivum | Rhizosphere | Irrigation adversely affected the bacteria that produce the antibiotic phenazine-1-carboxylic acid. | [48] |
| Triticum aestivum | Rhizosphere | Examined effect of long term nitrogen fertilization. Acidobacteria increased and Actinobacteria decreased. | [49] |
| Fragaria x ananassa (strawberry) | Rhizosphere | Examined 16 strawberry cultivars in two field studies. Plants had a genotype-dependent microbiome. | [50] |
| Curcurbita pepo (pumpkin) | Rhizosphere, seed and soil | Seed microbiome diversity is lower than rhizosphere or soil. | [51] |
| Solanum tuberosum (potato) | Tuber microbiome | Examined four potato varieties and five soil types. In all cases, bacterial community shifted from harvest to dormancy break. | [52] |
| Ipomoea batatas (sweet potato) | Rhizosphere | Adding low level of urea to soil increased abundance of P- and K-solubilizing bacteria, and N-fixing bacteria. | [53] |
| Populus cathayana (poplar) | Phyllosphere | Both female and male plants had unique bacterial microbiota. | [54] |
| Picea spp. (spruce) | Rhizosphere, phyllosphere | Correlations between microbiota and plant phenotypes suggest that plant genotype determines microbiota. | [16] |
| Populus trichocarpa (black cottonwood) | Phyllosphere endosphere | Observed a core microbiome. Nevertheless, variation existed between trees growing at different sites. | [55] |
| Fagus grandifolia (beech), Liriodendron tulipifera (yellow poplar) | Soil surrounding tree, rhizosphere | Soil microbial communities are unique to each tree species, however, urbanization decreased these differences. | [56] |
| Solanum lycopersicum, S. pimpinellifolium (tomato) | Rhizosphere and root endosphere | Examined eight tomato varieties and found that both endosphere and rhizosphere were affected by plant genotype. | [57] |
| Solanum lycopersicum | Rhizosphere | In tomato plants, the rhizosphere microbiota in neighboring plants is affected by volatile organic compounds. | [58] |
| Thalassia hemprichii, Enhalus acoroides (tropical seagrass) | Rhizosphere | This data suggests that the main determinant in selecting the rhizosphere microbiome is the plant habitat and not the plant species. | [59] |
| Persea americana (avocado) | Rhizosphere | Phytophthora root rot modified the bacterial composition and increases the amount of opportunistic fungal pathogens. | [60] |
| Pisum sativum (pea) | Seeds | Compared microbiota of seeds from 3 different countries. All peas shared a common core microbiota but also showed differences according to origin. | [61] |
| Sorghum bicolor (sorghum) | Rhizosphere | Microbiota of 5 different lines of sorghum were correlated with total flavonoid and luteolinidin concentrations. | [62] |
| Sorghum bicolor | Rhizosphere | Drought significantly delays the development of the root microbiome. | [63] |
| Panicum virgatum (switchgrass) | Shoots, roots and root-influenced soil | Different plant parts have different microbiomes (which are also influenced by climate, season and host genotype). | [64] |
| Panicum virgatum | Rhizosphere | Each of 12 cultivars that were tested selected a different microbiome. | [65] |
| Legumes | Nodules | Highly diverse population of bacteria within nodules that do not elicit nodulation or nitrogen fixation. | [66] |
| Saccharum arundinaceum (sugarcane) | Rhizosphere, rhizoplane, bulk soil | Bacterial communities of the transgenic plants were altered in comparison to the wild-type plant communities. | [67] |
| Arabidopsis thaliana | Rhizosphere | Coumarin biosynthesis dictates root biota composition. | [68] |
| Arabidopsis thaliana | Rhizosphere | Three different root triterpenes dictate root biota composition. | [69] |
| Arabidopsis thaliana | Rhizosphere | The defense hormone salicylic acid modulates root colonization by specific bacteria. | [70] |
| Arabidopsis thaliana | Rhizosphere | Used synthetic microbiome. Found Variovorax spp. responsible for optimizing root growth. | [71] |
| Arabidopsis thaliana | Phyllosphere | Isolated and sequenced 275 microbiomes. Found only weak associations with site of origin and plant genotype. | [72] |
| Oxyria digyna, Saxifraga oppositifolia | Endosphere | The plants shared a core microbiome. In addition, geographic region was a major determinant of biota composition. | [73] |
| Citrus | Rhizosphere | Characterized rhizospheres and bulk soil from 23 locations worldwide including 7 soil types and 6 climate types and 12 plant varieties and found a core microbiome. | [74] |
| Apples | Fruit | Different tissues, including stem, peel, fruit pulp, seeds and calyx, had distinct bacterial microbiomes. | [75] |
| Echinacea purpurea (purple coneflower), E. angustifolia | Rhizosphere, stem, leaf | Bacterial microbiomes were significantly different in these two plants and within different tissues. | [14] |
| Phoenix dactylifera (date palm) | Root endosphere | Bacterial and fungal community structures were not significantly affected in the presence of high salt. | [76] |
| Phoenix dactylifera | Root and leaf endosphere | Leaf and root tissues respond differently to salt stress. | [77] |
| Medicago truncatula (caliph medic) | Root endosphere | The abundance of ~70% of the biota characterized was altered in the presence of high salt. | [78] |
| Cucumis sativus (cucumber) | Rhizosphere | A Bacillus amyloliquefaciens strain addition significantly altered the bacterial rhizosphere community. | [79] |
| Hordeum vulgare (barley) | Rhizosphere | Comparing wild-type and root hair mutant barley, root hairs are critical in determining rhizosphere community. | [18] |