Chinese Journal of Plant Ecology >
Impacts and action pathways of domestication on diversity and community structure of crop microbiome: a review
* Contributed equally to this work
Received date: 2021-02-22
Accepted date: 2021-08-02
Online published: 2021-08-27
Supported by
National Natural Science Foundation of China(31772397);National Natural Science Foundation of China(31400365);Guangdong “Yangfan” Innovative and Entepreneurial Research Team Project(2015YT02H032)
Interactions between plants and coexisting microorganisms have significant impacts on plant growth, development, and health. Human domestication has resulted in significant differences between modern crops and their wild ancestors in physiological and genetic characteristics and growth environment, which will inevitably affect the interaction between crops and their microbiomes. Understanding the impact of domestication on the diversity and community structure of microbiome and the mechanisms involved is an important theoretical basis for application of microbiome during crop improvement and breeding. In this review, we summarize the research progress of the effects of domestication on the community composition and diversity of root and shoot microbiome (bacteria and fungi) in crops. We also analyze the involved action pathways in shaping crop microbiomes by domestication, considering the domestication effect on crop morphology, root configuration, exudates and other physiological characteristics, and the change in growth environment. The research directions that need to be focused on in this field were proposed.
Key words： domestication; microbiome; crop; diversity; community structure; bacteria; fungi
XIE Yu-Hang, JIA Pu, ZHENG Xiu-Tan, LI Jin-Tian, SHU Wen-Sheng, WANG Yu-Tao . Impacts and action pathways of domestication on diversity and community structure of crop microbiome: a review[J]. Chinese Journal of Plant Ecology, 2022 , 46(3) : 249 -266 . DOI: 10.17521/cjpe.2021.0059
| [1] | Abbo S, Gopher A (2017). Near eastern plant domestication: a history of thought. Trends in Plant Science, 22, 491-511. |
| [2] | Abbo S, Pinhasi van-Oss R, Gopher A, Saranga Y, Ofner I, Peleg Z (2014). Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends in Plant Science, 19, 351-360. |
| [3] | Abboud MAA (2014). Bioimpact of application of pesticides with plant growth hormone (gibberellic acid) on target and non-target microorganisms. Journal of Saudi Chemical Society, 18, 1005-1010. |
| [4] | Alegria Terrazas R, Balbirnie-Cumming K, Morris J, Hedley PE, Russell J, Paterson E, Baggs EM, Fridman E, Bulgarelli D (2020). A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota. Scientific Reports, 10, 12916. DOI: 10.1038/s41598-020-69672-x. |
| [5] | Armalytė J, Skerniškytė J, Bakienė E, Krasauskas R, Šiugždinienė R, Kareivienė V, Kerzienė S, Klimienė I, Sužiedėlienė E, Ružauskas M (2019). Microbial diversity and antimicrobial resistance profile in microbiota from soils of conventional and organic farming systems. Frontiers in Microbiology, 10, 892. DOI: 10.3389/fmicb.2019.00892. |
| [6] | Badri DV, Vivanco JM (2009). Regulation and function of root exudates. Plant, Cell & Environment, 32, 666-681. |
| [7] | Banik A, Kumar U, Mukhopadhyay SK, Dangar TK (2017). Dynamics of endophytic and epiphytic bacterial communities of Indian cultivated and wild rice (Oryza spp.) genotypes. Ecological Genetics and Genomics, 3-5, 7-17. |
| [8] | Berendsen RL, Pieterse CMJ, Bakker PAHM (2012). The rhizosphere microbiome and plant health. Trends in Plant Science, 17, 478-486. |
| [9] | Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K (2017). Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiology Ecology, 93, fix050. DOI: 10.1093/femsec/fix050. |
| [10] | Berg G, Raaijmakers JM (2018). Saving seed microbiomes. The ISME Journal, 12, 1167-1170. |
| [11] | Berg G, Rybakova D, Grube M, Köberl M (2016). The plant microbiome explored: implications for experimental botany. Journal of Experimental Botany, 67, 995-1002. |
| [12] | Bodenhausen N, Bortfeld-Miller M, Ackermann M, Vorholt JA (2014). A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLOS Genetics, 10, e1004283. DOI: 10.1371/journal.pgen.1004283. |
| [13] | Bourion V, Heulin-Gotty K, Aubert V, Tisseyre P, Chabert-Martinello M, Pervent M, Delaitre C, Vile D, Siol M, Duc G, Brunel B, Burstin J, Lepetit M (2018). Co-inoculation of a pea core-collection with diverse rhizobial strains shows competitiveness for nodulation and efficiency of nitrogen fixation are distinct traits in the interaction. Frontiers in Plant Science, 8, 2249. DOI: 10.3389/fpls.2017.02249. |
| [14] | Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014). Metabolic potential of endophytic bacteria. Current Opinion in Biotechnology, 27, 30-37. |
| [15] | Brisson VL, Schmidt JE, Northen TR, Vogel JP, Gaudin ACM (2019). Impacts of maize domestication and breeding on rhizosphere microbial community recruitment from a nutrient depleted agricultural soil. Scientific Reports, 9, 15611. DOI: 10.1038/s41598-019-52148-y. |
| [16] | Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL (2017). Research priorities for harnessing plant microbiomes in sustainable agriculture. PLOS Biology, 15, e2001793. DOI: 10.1371/journal.pbio.2001793. |
| [17] | Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, et al. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366, 606-612. |
| [18] | Cassman NA, Leite MF, Pan Y, de Hollander M, van Veen JA, Kuramae EE (2016). Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Scientific Reports, 6, 23680. DOI: 10.1038/srep23680. |
| [19] | Chaluvadi S, Bennetzen JL (2018). Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria. Frontiers in Plant Science, 9, 1183. DOI: 10.3389/fpls.2018.01183. |
| [20] | Chang CL, Chen W, Luo SS, Ma LN, Li XJ, Tian CJ (2019). Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions. Archives of Agronomy and Soil Science, 65, 74-87. |
| [21] | Chang CL, Zhang JX, Liu TT, Song KJ, Xie JH, Luo SS, Qu TB, Zhang JJ, Tian CJ, Zhang JF (2020). Rhizosphere fungal communities of wild and cultivated soybeans grown in three different soil suspensions. Applied Soil Ecology, 153, 103586. DOI: 10.1016/j.apsoil.2020.103586. |
| [22] | Chen L, Brookes PC, Xu JM, Zhang JB, Zhang CZ, Zhou XY, Luo Y (2016). Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass. Soil Biology & Biochemistry, 98, 1-10. |
| [23] | Chen LX, Méndez-García C, Dombrowski N, Servín-Garcidueñas LE, Eloe-Fadrosh EA, Fang BZ, Luo ZH, Tan S, Zhi XY, Hua ZS, Martinez-Romero E, Woyke T, Huang LN, Sánchez J, Peláez AI, et al. (2018a). Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. The ISME Journal, 12, 756-775. |
| [24] | Chen YH, Bernal CC (2011). Arthropod diversity and community composition on wild and cultivated rice. Agricultural and Forest Entomology, 13, 181-189. |
| [25] | Chen YH, Gols R, Benrey B (2015). Crop domestication and its impact on naturally selected trophic interactions. Annual Review of Entomology, 60, 35-58. |
| [26] | Chen YH, Ruiz-Arocho J, von Wettberg EJ (2018b). Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems. Current Opinion in Insect Science, 29, 56-63. |
| [27] | Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG (2016). Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytologist, 209, 798-811. |
| [28] | Compant S, Samad A, Faist H, Sessitsch A (2019). A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. Journal of Advanced Research, 19, 29-37. |
| [29] | Cordovez V, Dini-Andreote F, Carrión VJ, Raaijmakers JM (2019). Ecology and evolution of plant microbiomes. Annual Review of Microbiology, 73, 69-88. |
| [30] | Corneo PE, Suenaga H, Kertesz MA, Dijkstra FA (2016). Effect of twenty four wheat genotypes on soil biochemical and microbial properties. Plant and Soil, 404, 141-155. |
| [31] | da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, et al. (2015). The origin and evolution of maize in the Southwestern United States. Nature Plants, 1, 14003. DOI: 10.1038/nplants.2014.3. |
| [32] | da Silva K, da Silva EE, Farias ENC, Chaves JS, Albuquerque CNB, Cardoso C (2018). Agronomic efficiency of Bradyrhizobium pre-inoculation in association with chemical treatment of soybean seeds. African Journal of Agricultural Research, 13, 726-732. |
| [33] | de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A (2020). Harnessing rhizosphere microbiomes for drought- resilient crop production. Science, 368, 270-274. |
| [34] | Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015). Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America, 112, E911-E920. |
| [35] | Emmett BD, Buckley DH, Smith ME, Drinkwater LE (2018). Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition. Plant and Soil, 431, 53-69. |
| [36] | Fan K, Delgado-Baquerizo M, Guo X, Wang D, Wu Y, Zhu M, Yu W, Yao H, Zhu YG, Chu H (2019). Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome, 7, 143. DOI: 10.1186/s40168-019-0757-8. |
| [37] | Faris JD, Zhang Q, Chao S, Zhang Z, Xu SS (2014). Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map. Theoretical and Applied Genetics, 127, 2333-2348. |
| [38] | Firrincieli A, Khorasani M, Frank AC, Doty SL (2020). Influences of climate on phyllosphere endophytic bacterial communities of wild poplar. Frontiers in Plant Science, 11, 203. DOI: 10.3389/fpls.2020.00203. |
| [39] | Francioli D, Schulz E, Lentendu G, Wubet T, Buscot F, Reitz T (2016). Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Frontiers in Microbiology, 7, 1446. DOI: 10.3389/fmicb.2016.01446. |
| [40] | Haas M, Schreiber M, Mascher M (2019). Domestication and crop evolution of wheat and barley: genes, genomics, and future directions. Journal of Integrative Plant Biology, 61, 204-225. |
| [41] | Hassan S, Mathesius U (2012). The role of flavonoids in root-rhizosphere signalling: opportunities and challenges for improving plant-microbe interactions. Journal of Experimental Botany, 63, 3429-3444. |
| [42] | Hassani MA, Özkurt E, Franzenburg S, Stukenbrock EH (2020). Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species. Phytobiomes Journal, 4, 217-224. |
| [43] | Hassani MA, Özkurt E, Seybold H, Dagan T, Stukenbrock EH (2019). Interactions and coadaptation in plant metaorganisms. Annual Review of Phytopathology, 57, 483-503. |
| [44] | Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J (2014). Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nature Communications, 5, 5320. DOI: 10.1038/ncomms6320. |
| [45] | Hu M, Lv SW, Wu WG, Fu YC, Liu FX, Wang BB, Li WG, Gu P, Cai HW, Sun CQ, Zhu ZF (2018). The domestication of plant architecture in African rice. The Plant Journal, 94, 661-669. |
| [46] | Huang LN, Kuang JL, Shu WS (2016). Microbial ecology and evolution in the acid mine drainage model system. Trends in Microbiology, 24, 581-593. |
| [47] | Hunter PJ, Pink DAC, Bending GD (2015). Cultivar-level genotype differences influence diversity and composition of lettuce (Lactuca sp.) phyllosphere fungal communities. Fungal Ecology, 17, 183-186. |
| [48] | Iannucci A, Fragasso M, Beleggia R, Nigro F, Papa R (2017). Evolution of the crop rhizosphere: impact of domestication on root exudates in tetraploid wheat (Triticum turgidum L.). Frontiers in Plant Science, 8, 2124. DOI: 10.3389/fpls.2017.02124. |
| [49] | Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ (2018). How can we define “optimal microbiota?”: a comparative review of structure and functions of microbiota of animals, fish, and plants in agriculture. Frontiers in Nutrition, 5, 90. DOI: 10.3389/fnut.2018.00090. |
| [50] | Ji L, Shi SH, Tian L, Tian CJ (2019). A discussion on issues related to the recruit of rhizosphere microbes caused by crop domestication. Soils and Crops, 8, 368-372. |
| [50] | [吉丽, 石少华, 田磊, 田春杰 (2019). 作物驯化对根际微生物组的选择. 土壤与作物, 8, 368-372.] |
| [51] | Jiang Y, Luan L, Hu K, Liu M, Chen Z, Geisen S, Chen X, Li H, Xu Q, Bonkowski M, Sun B (2020). Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences. Microbiome, 8, 142. DOI: 10.1186/s40168-020-00918-6. |
| [52] | Johnston-Monje D, Mousa WK, Lazarovits G, Raizada MN (2014). Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize. BMC Plant Biology, 14, 233. DOI: 10.1186/s12870-014-0233-3. |
| [53] | Johnston-Monje D, Raizada MN (2011). Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. PLOS ONE, 6, e20396. DOI: 10.1371/journal.pone.0020396. |
| [54] | Kim DH, Kaashyap M, Rathore A, Das RR, Parupalli S, Upadhyaya HD, Gopalakrishnan S, Gaur PM, Singh S, Kaur J, Yasin M, Varshney RK (2014). Phylogenetic diversity of Mesorhizobium in chickpea. Journal of Biosciences, 39, 513-517. |
| [55] | Kim H, Lee KK, Jeon J, Harris WA, Lee YH (2020). Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed. Microbiome, 8, 20. DOI: 10.1186/s40168-020-00805-0. |
| [56] | Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA (2012). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. The ISME Journal, 6, 1378-1390. |
| [57] | Kobae Y (2019). Dynamic phosphate uptake in arbuscular mycorrhizal roots under field conditions. Frontiers in Environmental Science, 6, 159. DOI: 10.3389/fenvs.2018.00159. |
| [58] | Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee PA, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, et al. (2018). Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nature Biotechnology, 36, 1100-1109. |
| [59] | Lajoie G, Maglione R, Kembel SW (2020). Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. Microbiome, 8, 70. DOI: 10.1186/s40168-020-00844-7. |
| [60] | Leff JW, Lynch RC, Kane NC, Fierer N (2017). Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus. New phytologist, 214, 412-423. |
| [61] | Liang JL, Liu J, Jia P, Yang TT, Zeng QW, Zhang SC, Liao B, Shu WS, Li JT (2020). Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining. The ISME Journal, 14, 1600-1613. |
| [62] | Liu A, Ku YS, Contador CA, Lam HM (2020a). The impacts of domestication and agricultural practices on legume nutrient acquisition through symbiosis with rhizobia and arbuscular mycorrhizal fungi. Frontiers in Genetics, 11, 583954. DOI: 10.3389/fgene.2020.583954. |
| [63] | Liu F, Hewezi T, Lebeis SL, Pantalone V, Grewal PS, Staton ME (2019). Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly. BMC Microbiology, 19, 201. DOI: 10.1186/s12866-019-1572-x. |
| [64] | Liu H, Brettell LE, Qiu Z, Singh BK (2020b). Microbiome- mediated stress resistance in plants. Trends in Plant Science, 25, 733-743. |
| [65] | Liu HY, Li QP, Xing YZ (2018a). Genes contributing to domestication of rice seed traits and its global expansion. Genes, 9, 489. DOI: 10.3390/genes9100489. |
| [66] | Liu J, Abdelfattah A, Norelli J, Burchard E, Schena L, Droby S, Wisniewski M (2018b). Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. Microbiome, 6, 18. DOI: 10.1186/s40168-018-0403-x. |
| [67] | Liu J, Fernie AR, Yan J (2020c). The past, present, and future of maize improvement: domestication, genomics, and functional genomic routes toward crop enhancement. Plant Communications, 1, 100010. DOI: 10.1016/j.xplc.2019.100010. |
| [68] | Llorens E, Sharon O, Camañes G, García-Agustín P, Sharon A (2019). Endophytes from wild cereals protect wheat plants from drought by alteration of physiological responses of the plants to water stress. Environmental Microbiology, 21, 3299-3312. |
| [69] | Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488, 86-90. |
| [70] | Lynch JP, Brown KM (2012). New roots for agriculture: exploiting the root phenome. Philosophical Transactions of the Royal Society B, 367, 1598-1604. |
| [71] | Maignien L, DeForce EA, Chafee ME, Eren AM, Simmons SL (2014). Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. mBio, 5, e00682-13. DOI: 10.1128/mBio.00682-13. |
| [72] | Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D (2020). Plant microbiota modified by plant domestication. Systematic and Applied Microbiology, 43, 126106. DOI: 10.1016/j.syapm.2020.126106. |
| [73] | Martín-Robles N, Lehmann A, Seco E, Aroca R, Rillig MC, Milla R (2018). Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species. New Phytologist, 218, 322-334. |
| [74] | Massart S, Martinez-Medina M, Jijakli MH (2015). Biological control in the microbiome era: challenges and opportunities. Biological Control, 89, 98-108. |
| [75] | Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM (2018). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. The ISME Journal, 12, 212-224. |
| [76] | Meyer RS, DuVal AE, Jensen HR (2012). Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytologist, 196, 29-48. |
| [77] | Meyer RS, Purugganan MD (2013). Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics, 14, 840-852. |
| [78] | Mezzasalma V, Sandionigi A, Guzzetti L, Galimberti A, Grando MS, Tardaguila J, Labra M (2018). Geographical and cultivar features differentiate grape microbiota in northern Italy and Spain vineyards. Frontiers in Microbiology, 9, 946. DOI: 10.3389/fmicb.2018.00946. |
| [79] | Milla R, Matesanz S (2017). Growing larger with domestication: a matter of physiology, morphology or allocation? Plant Biology, 19, 475-483. |
| [80] | Mina D, Pereira JA, Lino-Neto T, Baptista P (2020). Epiphytic and endophytic bacteria on olive tree phyllosphere: exploring tissue and cultivar effect. Microbial Ecology, 80, 145-157. |
| [81] | Oburger E, Jones DL (2018). Sampling root exudates—Mission impossible? Rhizosphere, 6, 116-133. |
| [82] | Ofek-Lalzar M, Gur Y, Ben-Moshe S, Sharon O, Kosman E, Mochli E, Sharon A (2016). Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis. FEMS Microbiology Ecology, 92, fiw152. DOI: 10.1093/femsec/fiw152. |
| [83] | Özkurt E, Hassani MA, Sesiz U, Künzel S, Dagan T, Özkan H, Stukenbrock EH (2020). Seed-derived microbial colonization of wild emmer and domesticated bread wheat (Triticum dicoccoides and T. aestivum) seedlings shows pronounced differences in overall diversity and composition. mBio, 11, e02637-20. DOI: 10.1128/mBio.02637-20. |
| [84] | Pang ZQ, Xu P, Yu DQ (2020). Environmental adaptation of the root microbiome in two rice ecotypes. Microbiological Research, 241, 126588. DOI: 10.1016/j.micres.2020.126588. |
| [85] | Pascale A, Proietti S, Pantelides IS, Stringlis IA (2020). Modulation of the root microbiome by plant molecules: the basis for targeted disease suppression and plant growth promotion. Frontiers in Plant Science, 10, 1741. DOI: 10.3389/fpls.2019.01741. |
| [86] | Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, de Hollander M, Garcia AAF, Ramírez CA, Mendes R, Raaijmakers JM (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. The ISME Journal, 11, 2244-2257. |
| [87] | Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM (2018). The wild side of plant microbiomes. Microbiome, 6, 143. DOI: 10.1186/s40168-018-0519-z. |
| [88] | Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ (2019). Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome, 7, 114. DOI: 10.1186/s40168-019-0727-1. |
| [89] | Pérez-Jaramillo JE, Mendes R, Raaijmakers JM (2016). Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology, 90, 635-644. |
| [90] | Popowska M, Rzeczycka M, Miernik A, Krawczyk-Balska A, Walsh F, Duffy B (2012). Influence of soil use on prevalence of tetracycline, streptomycin, and erythromycin resistance and associated resistance genes. Antimicrobial Agents and Chemotherapy, 56, 1434-1443. |
| [91] | Porter SS, Sachs JL (2020). Agriculture and the disruption of plant-microbial symbiosis. Trends in Ecology & Evolution, 35, 426-439. |
| [92] | Preece C, Peñuelas J (2020). A return to the wild: root exudates and food security. Trends in Plant Science, 25, 14-21. |
| [93] | Putra IP, Rahayu G, Hidayat I (2015). Impact of domestication on the endophytic fungal diversity associated with wild Zingiberaceae at Mount Halimun Salak National Park. HAYATI Journal of Biosciences, 22, 157-162. |
| [94] | Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015). Roots shaping their microbiome: global hotspots for microbial activity. Annual Review of Phytopathology, 53, 403-424. |
| [95] | Rho H, Hsieh M, Kandel SL, Cantillo J, Doty SL, Kim SH (2018). Do endophytes promote growth of host plants under stress? A meta-analysis on plant stress mitigation by endophytes. Microbial Ecology, 75, 407-418. |
| [96] | Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux JP, LʼHaridon F (2016). The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytologist, 210, 1033-1043. |
| [97] | Robertson-Albertyn S, Alegria Terrazas R, Balbirnie K, Blank M, Janiak A, Szarejko I, Chmielewska B, Karcz J, Morris J, Hedley PE, George TS, Bulgarelli D (2017). Root hair mutations displace the barley rhizosphere microbiota. Frontiers in Plant Science, 8, 1094. DOI: 10.3389/fpls.2017.01094. |
| [98] | Roman-Reyna V, Pinili D, Borja FN, Quibod IL, Groen SC, Alexandrov N, Mauleon R, Oliva R (2020). Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project. Rice, 13, 72. DOI: 10.1186/s12284-020-00432-1. |
| [99] | Rosenblueth M, Ormeño-Orrillo E, López-López A, Rogel MA, Reyes-Hernández BJ, Martínez-Romero JC, Reddy PM, Martínez-Romero E (2018). Nitrogen fixation in cereals. Frontiers in Microbiology, 9, 1794. DOI: 10.3389/fmicb.2018.01794. |
| [100] | Rosier A, Bishnoi U, Lakshmanan V, Sherrier DJ, Bais HP (2016). A perspective on inter-kingdom signaling in plant- beneficial microbe interactions. Plant Molecular Biology, 90, 537-548. |
| [101] | Roucou A, Violle C, Fort F, Roumet P, Ecarnot M, Vile D (2018). Shifts in plant functional strategies over the course of wheat domestication. Journal of Applied Ecology, 55, 25-37. |
| [102] | Ruan YL (2014). Sucrose metabolism: gateway to diverse carbon use and sugar signaling. Annual Review of Plant Biology, 65, 33-67. |
| [103] | Saleem M, Law AD, Sahib MR, Pervaiz ZH, Zhang Q (2018). Impact of root system architecture on rhizosphere and root microbiome. Rhizosphere, 6, 47-51. |
| [104] | Sangabriel-Conde W, Maldonado-Mendoza IE, Mancera-López ME, Cordero-Ramírez JD, Trejo-Aguilar D, Negrete-Yankelevich S (2015). Glomeromycota associated with Mexican native maize landraces in Los Tuxtlas, Mexico. Applied Soil Ecology, 87, 63-71. |
| [105] | Sapkota R, Knorr K, Jørgensen LN, OʼHanlon KA, Nicolaisen M (2015). Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytologist, 207, 1134-1144. |
| [106] | Schardl CL, Leuchtmann A, Spiering MJ (2004). Symbioses of grasses with seedborne fungal endophytes. Annual Review of Plant Biology, 55, 315-340. |
| [107] | Schmidt JE, Bowles TM, Gaudin ACM (2016). Using ancient traits to convert soil health into crop yield: impact of selection on maize root and rhizosphere function. Frontiers in Plant Science, 7, 373. DOI: 10.3389/fpls.2016.00373. |
| [108] | Schmidt JE, Kent AD, Brisson VL, Gaudin ACM (2019). Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome, 7, 146. DOI: 10.1186/s40168-019-0756-9. |
| [109] | Schmidt JE, Mazza Rodrigues JL, Brisson VL, Kent A, Gaudin ACM (2020). Impacts of directed evolution and soil management legacy on the maize rhizobiome. Soil Biology & Biochemistry, 145, 107794. DOI: 10.1016/j.soilbio.2020.107794. |
| [110] | Schreiter S, Sandmann M, Smalla K, Grosch R (2014). Soil type dependent rhizosphere competence and biocontrol of two bacterial inoculant strains and their effects on the rhizosphere microbial community of field-grown lettuce. PLOS ONE, 9, e103726. DOI: 10.1371/journal.pone.0103726. |
| [111] | Shade A, Jacques MA, Barret M (2017). Ecological patterns of seed microbiome diversity, transmission, and assembly. Current Opinion in Microbiology, 37, 15-22. |
| [112] | Shaposhnikov AI, Morgounov AI, Akin B, Makarova NM, Belimov AA, Tikhonovich IA (2016). Comparative characteristics of root systems and root exudation of synthetic, landrace and modern wheat varieties. Agricultural Biology, 51, 68-78. |
| [113] | Shenton M, Iwamoto C, Kurata N, Ikeo K (2016). Effect of wild and cultivated rice genotypes on rhizosphere bacterial community composition. Rice, 9, 42. DOI: 10.1186/s12284-016-0111-8. |
| [114] | Shi S, Chang J, Tian L, Nasir F, Ji L, Li X, Tian C (2019a). Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean. Archives of Microbiology, 201, 879-888. |
| [115] | Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M (2015). Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio, 6, e00746. DOI: 10.1128/mBio.00746-15. |
| [116] | Shi S, Richardson AE, O’Callaghan M, DeAngelis KM, Jones EE, Stewart A, Firestone MK, Condron LM (2011). Effects of selected root exudate components on soil bacterial communities. FEMS Microbiology Ecology, 77, 600-610. |
| [117] | Shi S, Tian L, Nasir F, Li X, Li W, Tran LP, Tian C (2018). Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae. Plant Physiology and Biochemistry, 132, 156-165. |
| [118] | Shi S, Tian L, Xu S, Ji L, Nasir F, Li X, Song Z, Tian C (2019b). The rhizomicrobiomes of wild and cultivated crops react differently to fungicides. Archives of Microbiology, 201, 477-486. |
| [119] | Singh P, Santoni S, This P, Péros JP (2018). Genotype-environment interaction shapes the microbial assemblage in grapevine’s phyllosphere and carposphere: an NGS approach. Microorganisms, 6, 96. DOI: 10.3390/microorganisms6040096. |
| [120] | Singh P, Santoni S, Weber A, This P, Péros JP (2019). Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures. Scientific Reports, 9, 14294. DOI: 10.1038/s41598-019-50839-0. |
| [121] | Spor A, Roucou A, Mounier A, Bru D, Breuil MC, Fort F, Vile D, Roumet P, Philippot L, Violle C (2020). Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat. Scientific Reports, 10, 12234. DOI: 10.1038/s41598-020-69175-9. |
| [122] | Stenberg JA, Heil M, Åhman I, Björkman C (2015). Optimizing crops for biocontrol of pests and disease. Trends in Plant Science, 20, 698-712. |
| [123] | Stitzer MC, Ross-Ibarra J (2018). Maize domestication and gene interaction. New Phytologist, 220, 395-408. |
| [124] | Stringlis IA, Yu K, Feussner K, de Jonge R, van Bentum S, van Verk MC, Berendsen RL, Bakker PAHM, Feussner I, Pieterse CMJ (2018). MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proceedings of the National Academy of Sciences of the United States of America, 115, E5213-E5222. |
| [125] | Szczepaniec A, Widney SE, Bernal JS, Eubanks MD (2013). Higher expression of induced defenses in teosintes (Zea spp.) is correlated with greater resistance to fall armyworm, Spodoptera frugiperda. Entomologia Experimentalis et Applicata, 146, 242-251. |
| [126] | Szoboszlay M, Lambers J, Chappell J, Kupper JV, Moe LA, McNear Jr DH (2015). Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars. Soil Biology & Biochemistry, 80, 34-44. |
| [127] | Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS (2019). Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. The ISME Journal, 13, 2044-2057. |
| [128] | Tian L, Lin X, Tian J, Ji L, Chen Y, Tran LP, Tian C (2020a). Research advances of beneficial microbiota associated with crop plants. International Journal of Molecular Sciences, 21, 1792. DOI: 10.3390/ijms21051792. |
| [129] | Tian L, Shi S, Ma L, Tran LSP, Tian C (2020b). Community structures of the rhizomicrobiomes of cultivated and wild soybeans in their continuous cropping. Microbiological Research, 232, 126390. DOI: 10.1016/j.micres.2019.126390. |
| [130] | Tkacz A, Pini F, Turner TR, Bestion E, Simmonds J, Howell P, Greenland A, Cheema J, Emms DM, Uauy C, Poole PS (2020). Agricultural selection of wheat has been shaped by plant-microbe interactions. Frontiers in Microbiology, 11, 132. DOI: 10.3389/fmicb.2020.00132. |
| [131] | Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015). Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environmental Microbiology Reports, 7, 40-50. |
| [132] | Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE (2016). The phyllosphere: microbial jungle at the plant- climate interface. Annual Review of Ecology, Evolution and Systematics, 47, 1-24. |
| [133] | van der Heijden MGA, Schlaeppi K (2015). Root surface as a frontier for plant microbiome research. Proceedings of the National Academy of Sciences of the United States of America, 112, 2299-2300. |
| [134] | van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, et al. (2018). Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology, 16, e2006352. DOI: 10.1371/journal.pbio.2006352. |
| [135] | Vandenkoornhuyse P, Quaiser A, Duhamel M, van AL, Dufresne A (2015). The importance of the microbiome of the plant holobiont. New phytologist, 206, 1196-1206. |
| [136] | Wagner MR, Busby PE, Balint-Kurti P (2020a). Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-pectrum disease resistance. New Phytologist, 225, 2152-2165. |
| [137] | Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T (2016). Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications, 7, 12151. DOI: 10.1038/ncomms12151. |
| [138] | Wagner MR, Roberts JH, Balint-Kurti P, Holland JB (2020b). Heterosis of leaf and rhizosphere microbiomes in field-grown maize. New Phytologist, 228, 1055-1069. |
| [139] | Wallace JG, Kremling KA, Kovar LL, Buckler ES (2018). Quantitative genetics of the maize leaf microbiome. Phytobiomes Journal, 2, 208-224. |
| [140] | Wang YT, Li T, Li Y, Björn LO, Rosendahl S, Olsson PA, Li SS, Fu XL (2015). Community dynamics of arbuscular mycorrhizal fungi in high-input and intensively irrigated rice cultivation systems. Applied and Environmental Microbiology, 81, 2958-2965. |
| [141] | Wang YT, Li YW, Bao XZ, Björn LO, Li SS, Olsson PA (2016). Response differences of arbuscular mycorrhizal fungi communities in the roots of an aquatic and a semiaquatic species to various flooding regimes. Plant and Soil, 403, 361-373. |
| [142] | Wang YT, Li YW, Li SS, Rosendahl S (2021). Ignored diversity of arbuscular mycorrhizal fungi in co-occurring mycotrophic and non-mycotrophic plants. Mycorrhiza, 31, 93-102. |
| [143] | Wei N, Ashman TL (2018). The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ. Scientific Reports, 8, 5195. DOI: 10.1038/s41598-018-23518-9. |
| [144] | White JF, Kingsley KL, Zhang Q, Verma R, Obi N, Dvinskikh S, Elmore MT, Verma SK, Gond SK, Kowalski KP (2019). Review: Endophytic microbes and their potential applications in crop management. Pest Management Science, 75, 2558-2565. |
| [145] | Whitehead SR, Turcotte MM, Poveda K (2017). Domestication impacts on plant-herbivore interactions: a meta-analysis. Philosophical Transactions of the Royal Society B, 372, 20160034. DOI: 10.1098/rstb.2016.0034. |
| [146] | Xing X, Koch AMP, Jones AM, Ragone D, Murch S, Hart MM (2012). Mutualism breakdown in breadfruit domestication. Proceedings of the Royal Society B, 279, 1122-1130. |
| [147] | Xiong C, Zhu YG, Wang JT, Singh B, Han LL, Shen JP, Li PP, Wang GB, Wu CF, Ge AH, Zhang LM, He JZ (2021). Host selection shapes crop microbiome assembly and network complexity. New Phytologist, 229, 1091-1104. |
| [148] | Yoneyama K (2019). How do strigolactones ameliorate nutrient deficiencies in plants? Cold Spring Harbor Perspectives in Biology, 11, a034686. DOI: 10.1101/cshperspect.a034686. |
| [149] | Yu K, Pieterse CMJ, Bakker PAHM, Berendsen RL (2019). Beneficial microbes going underground of root immunity. Plant, Cell & Environment, 42, 2860-2870. |
| [150] | Zachow C, Müller H, Tilcher R, Berg G (2014). Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets. Frontiers in Microbiology, 5, 415. DOI: 10.3389/fmicb.2014.00415. |
| [151] | Zhang J, Liu YX, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y (2021). High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols, 16, 988-1012. |
| [152] | Zhang SW, Wang Y, Chen X, Cui BJ, Bai ZH, Zhuang GQ (2020). Variety features differentiate microbiota in the grape leaves. Canadian Journal of Microbiology, 66, 653-663. |
| [153] | Zheng YF, Liang J, Zhao DL, Meng C, Xu ZC, Xie ZH, Zhang CS (2020). The root nodule microbiome of cultivated and wild halophytic legumes showed similar diversity but distinct community structure in Yellow River Delta saline soils. Microorganisms, 8, 207. DOI: 10.3390/ microorganisms8020207. |
| [154] | Zhou WH, Wang YT, Lian ZH, Yang TT, Zeng QW, Feng SW, Fang Z, Shu WS, Huang LN, Ye ZH, Liao B, Li JT (2020). Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond. Science of the Total Environment, 744, 140793. DOI: 10.1016/j.scitotenv.2020.140793. |
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