Qu Q, Zhang Z, Peijnenburg WJ, Liu W, Lu T, Hu B, Chen J, Chen J, Lin Z, Qian H. Rhizosphere microbiome assembly and its impact on plant growth. J Agric Food Chem. 2020;68(18):5024–38. https://doi.org/10.1021/acs.jafc.0c00073.
Article
CAS
PubMed
Google Scholar
Mendes R, Kruijt M, De Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science. 2011;332(6033):1097–100. https://doi.org/10.1126/science.1203980.
Article
CAS
PubMed
Google Scholar
Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013;11(11):789–99. https://doi.org/10.1038/nrmicro3109.
Article
CAS
PubMed
Google Scholar
Bulgarelli D, Schlaeppi K, Spaepen S, Van Themaat EV, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38. https://doi.org/10.1146/annurev-arplant-050312-120106.
Article
CAS
PubMed
Google Scholar
Lei S, Xu X, Cheng Z, Xiong J, Ma R, Zhang L, Yang X, Zhu Y, Zhang B, Tian B. Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa. MicrobiologyOpen. 2019;8(6): e00762. https://doi.org/10.1002/mbo3.762.
Article
PubMed
Google Scholar
Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 2013;14(6):1–10. https://doi.org/10.1186/gb-2013-14-6-209.
Article
CAS
Google Scholar
Wang J, Zhao T, Yang B, Zhang S. Sucrose metabolism and regulation in sugarcane. J Plant Physiol Pathol. 2017;5:2. https://doi.org/10.4172/2329-955X.1000167.
Article
Google Scholar
McCormick AJ, Watt DA, Cramer MD. Supply and demand: sink regulation of sugar accumulation in sugarcane. J Exp Bot. 2009;60(2):357–64. https://doi.org/10.1093/jxb/ern310.
Article
CAS
PubMed
Google Scholar
Papini-Terzi FS, Rocha FR, Vêncio RZ, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LE, Lembke CG, Costa MD, Nishiyama MY, Vicentini R. Sugarcane genes associated with sucrose content. BMC Genom. 2009;10(1):1–21. https://doi.org/10.1186/1471-2164-10-120.
Article
CAS
Google Scholar
Corneo PE, Suenaga H, Kertesz MA, Dijkstra FA. Effect of twenty four wheat genotypes on soil biochemical and microbial properties. Plant Soil. 2016;404(1):141–55. https://doi.org/10.1007/s11104-016-2833-1.
Article
CAS
Google Scholar
White PJ, Brown PH. Plant nutrition for sustainable development and global health. Ann Bot. 2010;105(7):1073–80. https://doi.org/10.1093/aob/mcq085.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mueller LO, Borstein SR, Tague ED, Dearth SP, Castro HF, Campagna SR, Bailey JK, Schweitzer JA. Populations of Populus angustifolia have evolved distinct metabolic profiles that influence their surrounding soil. Plant Soil. 2020;8:1–3. https://doi.org/10.1007/s11104-019-04405-2.
Article
CAS
Google Scholar
Lagomarsino A, Moscatelli MC, Di Tizio A, Mancinelli R, Grego S, Marinari S. Soil biochemical indicators as a tool to assess the short-term impact of agricultural management on changes in organic C in a Mediterranean environment. Ecol Indic. 2009;9(3):518–27. https://doi.org/10.1016/j.ecolind.2008.07.003.
Article
CAS
Google Scholar
Schmidt R, Ulanova D, Wick LY, Bode HB, Garbeva P. Microbe-driven chemical ecology:past, present and future. ISME J. 2019;13(11):2656–63. https://doi.org/10.1038/s41396-019-0469-x.
Article
PubMed
PubMed Central
Google Scholar
Massalha H, Korenblum E, Malitsky S, Shapiro OH, Aharoni A. Live imaging of root–bacteria interactions in a microfluidics setup. Proc Natl Acad Sci. 2017;114(17):4549–54. https://doi.org/10.1073/pnas.1618584114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin H, Yang X, Liu R, Yan Z, Li X, Li X, Su A, Zhao Y, Qin B. Bacterial community structure associated with the rhizosphere soils and roots of Stellera chamaejasme L. along a Tibetan elevation gradient. Ann Microbiol. 2018;68(5):273–86. https://doi.org/10.1007/s13213-018-1336-0.
Article
Google Scholar
Lima AB, Cannavan FS, Navarrete AA, Teixeira WG, Kuramae EE, Tsai SM. Amazonian dark earth and plant species from the Amazon region contribute to shaping rhizosphere bacterial communities. Microb Ecol. 2015;69(4):855–66. https://doi.org/10.1007/s00248-014-0472-8.
Article
CAS
Google Scholar
Cotton TA, Pétriacq P, Cameron DD, Al Meselmani M, Schwarzenbacher R, Rolfe SA, Ton J. Metabolic regulation of the maize rhizobiome by benzoxazinoids. ISME J. 2019;13(7):1647–58. https://doi.org/10.1038/s41396-019-0375-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schlemper TR, Leite MF, Lucheta AR, Shimels M, Bouwmeester HJ, van Veen JA, Kuramae EE. Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils. FEMS Microbiol Ecol. 2017;93:(8). https://doi.org/10.1093/femsec/fix096.
Zhang J, Zhang N, Liu YX, Zhang X, Hu B, Qin Y, Xu H, Wang H, Guo X, Qian J, Wang W. Root microbiota shift in rice correlates with resident time in the field and developmental stage. Sci China Life Sci. 2018;61(6):613–21. https://doi.org/10.1007/s11427-018-9284-4.
Article
PubMed
Google Scholar
Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, Burmølle M, Herschend J, Bakker PA, Pieterse CM. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12(6):146–507. https://doi.org/10.1038/s41396-018-0093-1.
Article
CAS
Google Scholar
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MT. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci. 2018;115(6):1157–65. https://doi.org/10.1073/pnas.1717617115.
Article
CAS
Google Scholar
Stringlis IA, Yu K, Feussner K, De Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PA, Feussner I, Pieterse CM. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci. 2018;115(22):5213–22. https://doi.org/10.1073/pnas.1722335115.
Article
CAS
Google Scholar
Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci. 2013;110(16):6458–553. https://doi.org/10.1073/pnas.1302837110.
Article
Google Scholar
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. Structure, variation and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci. 2015;112(8):911–20. https://doi.org/10.1073/pnas.1414592112.
Article
CAS
Google Scholar
Inceoglu O, Al-Soud WA, Salles JF, Semenov AV, van Elsas JD. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS ONE. 2011;6(8):8:e23321. https://doi.org/10.1371/journal.pone.0023321.
Mendes LW, Kuramae EE, Navarrete AA, Van Veen JA, Tsai SM. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 2014;8(8):1577–87. https://doi.org/10.1038/ismej.2014.17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bulgarelli D, Rott M, Schlaeppi K, van Themaat EV, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488(7409):91–5. https://doi.org/10.1038/nature11336.
Article
CAS
PubMed
Google Scholar
Dombrowski N, Schlaeppi K, Agler MT, Hacquard S, Kemen E, Garrido-Oter R, Wunder J, Coupland G, Schulze-Lefert P. Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. ISME J. 2017;11(1):43–55. https://doi.org/10.1038/ismej.2016.109.
Article
CAS
PubMed
Google Scholar
Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C. Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on the nutrient acquisition process. A review. Biol Fertil Soils. 2015;51(4):403–15. https://doi.org/10.1007/s00374-015-0996-1.
Article
CAS
Google Scholar
Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J. 2010;4(8):989–1001. https://doi.org/10.1002/9781118297674.ch105.
Article
PubMed
Google Scholar
Yang Y, Wang N, Guo X, Zhang Y, Ye B. Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing. PLoS ONE. 2017;12(5): e0178425. https://doi.org/10.1371/journal.pone.0178425.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tian BY, Cao Y, Zhang KQ. Metagenomic insights into communities, functions of endophytes and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots. Sci Rep. 2015;5(1):1–5. https://doi.org/10.1038/srep17087.
Article
CAS
Google Scholar
Jiang F, Wu X, Xiang W, Fang X, Zeng Y, Ouyang S, Lei P, Deng X, Peng C. Spatial variations in soil organic carbon, nitrogen and phosphorus concentrations related to stand characteristics in subtropical areas. Plant Soil. 2017;413(1–2):289–301. https://doi.org/10.1007/s11104-016-3101-0.
Article
CAS
Google Scholar
Sommers LE, Nelson DW. Determination of total phosphorus in soils: a rapid perchloric acid digestion procedure. Soil Sci Soc Am J. 1972;36(6):902–4. https://doi.org/10.2136/sssaj1972.03615995003600060020x.
Article
CAS
Google Scholar
Basta NT, Tabatabai MA. Determination of total potassium, sodium, calcium and magnesium in plant materials by ion chromatography. Soil Sci Soc Am J. 1985;49(1):76–81. https://doi.org/10.2136/sssaj1985.03615995004900010015x.
Article
CAS
Google Scholar
Bremner JM, Tabatabai MA. Use of an ammonia electrode for determination of ammonium in Kjeldahl analysis of soils. Commun Soil Sci Plant Anal. 1972;3(2):159–65. https://doi.org/10.1080/00103627209366361.
Article
CAS
Google Scholar
Seybold H, Demetrowitsch TJ, Hassani MA, Szymczak S, Reim E, Haueisen J, Lübbers L, Rühlemann M, Franke A, Schwarz K, Stukenbrock EH. A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition. Nat Commun. 2020;11(1):1–2. https://doi.org/10.1038/s41467-020-15633-x.
Article
CAS
Google Scholar
Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957–63. https://doi.org/10.1093/bioinformatics/btr507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1. https://doi.org/10.1093/bioinformatics/btq461.
Article
CAS
PubMed
Google Scholar
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42(D1):D643–8. https://doi.org/10.1093/nar/gkt1209.
Article
CAS
PubMed
Google Scholar
Ullah A, Akbar A, Luo Q, Khan AH, Manghwar H, Shaban M, Yang X. Microbiome diversity in cotton rhizosphere under normal and drought conditions. Microb Ecol. 2019;77(2):429–39. https://doi.org/10.1007/s00248-018-1260-7.
Article
CAS
PubMed
Google Scholar
Rich SM, Watt M. Soil conditions and cereal root system architecture: review and considerations for linking Darwin and Weaver. J Exp Bot. 2013;64(5):1193–208. https://doi.org/10.1093/jxb/ert043.
Article
CAS
PubMed
Google Scholar
Dong M, Yang Z, Cheng G, Peng L, Xu Q, Xu J. Diversity of the bacterial microbiome in the roots of four saccharum species: S. spontaneum, S. robustum, S. barberi and S. officinarum. Front Microbiol. 2018;9:267. https://doi.org/10.3389/fmicb.2018.00267.
Article
PubMed
PubMed Central
Google Scholar
Hennion N, Durand M, Vriet C, Doidy J, Maurousset L, Lemoine R, Pourtau N. Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere. Physiol Plant. 2019;165(1):44–57. https://doi.org/10.1111/ppl.12751.
Article
CAS
PubMed
Google Scholar
Miotto-Vilanova L, Jacquard C, Courteaux B, Wortham L, Michel J, Clement C, Barka EA, Sanchez L. Burkholderia phytofirmans PsJN confers grapevine resistance against Botrytis cinerea via a direct antimicrobial effect combined with better resource mobilization. Front Plant Sci. 2016;7:1236. https://doi.org/10.1371/journal.pone.0029382.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwachtje J, Karojet S, Thormahlen I, Bernholz C, Kunz S, Brouwer S, Schwochow M, Kohl K, van Dongen JT. A naturally associated rhizobacterium of Arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth. PLoS ONE. 2011;6(12): e29382. https://doi.org/10.1371/journal.pone.0029382.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao X, Jiang Y, Liu Q, Yang H, Wang Z, Zhang M. Effects of drought-tolerant Ea-DREB2B transgenic sugarcane on bacterial communities in soil. Front Microbiol. 2020;11:704. https://doi.org/10.3389/fmicb.2020.00704.
Article
PubMed
PubMed Central
Google Scholar
Bowles TM, Acosta-Martinez V, Calderon F, Jackson LE. Soil enzyme activities, microbial communities and carbon and nitrogen availability in organic agroecosystems across an intensively managed agricultural landscape. Soil Biol Biochem. 2014;68:252–62. https://doi.org/10.1016/j.soilbio.2013.10.004.
Article
CAS
Google Scholar
Bruto M, Prigent-Combaret C, Muller D, Moenne-Loccoz Y. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci Rep. 2014;4(1):1. https://doi.org/10.1038/srep06261.
Article
CAS
Google Scholar
Vurukonda SS, Vardharajula S, Shrivastava M, SkZ A. Enhancement of drought stress tolerance in crops by plant growth-promoting rhizobacteria. Microbiol Res. 2016;184:13–24. https://doi.org/10.1016/j.micres.2015.12.003.
Article
PubMed
Google Scholar
Da Costa DP, Dias AC, Cotta SR, Vilela D, De Andrade PA, Pellizari VH, Andreote FD. Changes of bacterial communities in the rhizosphere of sugarcane under the elevated concentration of atmospheric CO2. Glob Change Biol Bioenergy. 2018;10(2):137–45. https://doi.org/10.1111/gcbb.12476.
Article
CAS
Google Scholar
Lambais MR, Lucheta AR, Crowley DE. Bacterial community assemblages associated with the phyllosphere, dermosphere, and rhizosphere of tree species of the Atlantic forest are host taxon dependent. Microb Ecol. 2014;68(3):567–74. https://doi.org/10.1007/s00248-014-0433-2.
Article
PubMed
Google Scholar
Perez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol. 2016;90(6):635–44. https://doi.org/10.1007/s11103-015-0337-7.
Article
CAS
PubMed
Google Scholar