References analysis of the Wikipedia article "Root microbiome" in the English version

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Mendes R, Garbeva P, Raaijmakers JM (September 2013). "The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms". FEMS Microbiology Reviews. 37 (5): 634–63. doi:10.1111/1574-6976.12028. PMID 23790204.

Gottel NR, Castro HF, Kerley M, et al. (September 2011). "Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types". Applied and Environmental Microbiology. 77 (17): 5934–44. Bibcode:2011ApEnM..77.5934G. doi:10.1128/AEM.05255-11. PMC 3165402. PMID 21764952.

Nguyen C (2009), "Rhizodeposition of Organic C by Plant: Mechanisms and Controls", Sustainable Agriculture, pp. 97–123, doi:10.1007/978-90-481-2666-8_9, ISBN 978-90-481-2665-1

Kogel KH, Franken P, Hückelhoven R (August 2006). "Endophyte or parasite—what decides?". Current Opinion in Plant Biology. 9 (4): 358–63. doi:10.1016/j.pbi.2006.05.001. PMID 16713330.

Kristin A, Miranda H (2013). "The root microbiota—a fingerprint in the soil?". Plant and Soil. 370 (1–2): 671–86. doi:10.1007/s11104-013-1647-7. S2CID 14961515.

Nemergut DR, Schmidt SK, Fukami T, O'Neill SP, Bilinski TM, Stanish LF, Knelman JE, Darcy JL, Lynch RC, Wickey P, Ferrenberg S (September 2013). "Patterns and processes of microbial community assembly". Microbiology and Molecular Biology Reviews. 77 (3): 342–56. doi:10.1128/MMBR.00051-12. PMC 3811611. PMID 24006468.

Buée M, De Boer W, Martin F, van Overbeek L, Jurkevitch E (2009). "The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors". Plant and Soil. 321 (1–2): 189–212. doi:10.1007/s11104-009-9991-3. S2CID 45768977.

Dean SL, Farrer EC, Taylor DL, Porras-Alfaro A, Suding KN, Sinsabaugh RL (March 2014). "Nitrogen deposition alters plant-fungal relationships: linking belowground dynamics to aboveground vegetation change". Molecular Ecology. 23 (6): 1364–78. doi:10.1111/mec.12541. PMID 24112704. S2CID 15540300.

Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2014). "Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors". Environmental Microbiology Reports. 7 (1): 102–110. doi:10.1111/1758-2229.12194. PMID 25870878.

Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD (July 2011). "Rice root-associated bacteria: insights into community structures across 10 cultivars". FEMS Microbiology Ecology. 77 (1): 154–64. doi:10.1111/j.1574-6941.2011.01092.x. PMC 4339037. PMID 21426364.

Egerton-Warburton, Louise M.; Johnson, Nancy Collins; Allen, Edith B. (November 2007). "Mycorrhizal Community Dynamics following Nitrogen Fertilization: A Cross-Site Test in Five Grasslands". Ecological Monographs. 77 (4): 527–44. doi:10.1890/06-1772.1. JSTOR 27646105.

Tedersoo L, Bahram M, Toots M, Diédhiou AG, Henkel TW, Kjøller R, Morris MH, Nara K, Nouhra E, Peay KG, Põlme S, Ryberg M, Smith ME, Kõljalg U (September 2012). "Towards global patterns in the diversity and community structure of ectomycorrhizal fungi". Molecular Ecology. 21 (17): 4160–70. doi:10.1111/j.1365-294X.2012.05602.x. hdl:11336/18182. PMID 22568722.

van der Heijden MG, Bardgett RD, van Straalen NM (March 2008). "The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems". Ecology Letters. 11 (3): 296–310. doi:10.1111/j.1461-0248.2007.01139.x. PMID 18047587.

Marschner P, Crowley D, Rengel Z (2011). "Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis – model and research methods". Soil Biology and Biochemistry. 43 (5): 883–94. doi:10.1016/j.soilbio.2011.01.005.

Green LE, Porras-Alfaro A, Sinsabaugh RL (September 2008). "Translocation of Nitrogen and Carbon Integrates Biotic Crust and Grass Production in Desert Grassland". Journal of Ecology. 96 (5): 1076–85. doi:10.1111/j.1365-2745.2008.01388.x. JSTOR 20143553.

Lugtenberg B, Kamilova F (2009). "Plant-growth-promoting rhizobacteria". Annual Review of Microbiology. 63: 541–56. doi:10.1146/annurev.micro.62.081307.162918. PMID 19575558.

Latch, Garrick C.M. (1993). "Physiological interactions of endophytic fungi and their hosts. Biotic stress tolerance imparted to grasses by endophytes". Agriculture, Ecosystems & Environment. 44 (1–4): 143–56. doi:10.1016/0167-8809(93)90043-O.

Rodriguez R, Redman R (2008). "More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis". Journal of Experimental Botany. 59 (5): 1109–14. doi:10.1093/jxb/erm342. PMID 18267941.

Lau JA, Lennon JT (October 2011). "Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits". The New Phytologist. 192 (1): 215–24. doi:10.1111/j.1469-8137.2011.03790.x. PMID 21658184.

Porras-Alfaro A, Bayman P (2011). "Hidden fungi, emergent properties: endophytes and microbiomes". Annual Review of Phytopathology. 49: 291–315. doi:10.1146/annurev-phyto-080508-081831. PMID 19400639. S2CID 12770904.

Doornbos RF, van Loon LC, Bakker PA (2011). "Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review" (PDF). Agronomy for Sustainable Development. 32 (1): 227–43. doi:10.1007/s13593-011-0028-y. S2CID 26283073.

Bakker AH, Doornbos RF, Zamioudis C, Berendsen RL, Pieterse CM (2013). "Induced Systemic Resistance and the Rhizosphere Microbiome". The Plant Pathology Journal. 29 (2): 136–43. doi:10.5423/PPJ.SI.07.2012.0111. PMC 4174772. PMID 25288940.

Packer A, Clay K (March 2000). "Soil pathogens and spatial patterns of seedling mortality in a temperate tree". Nature. 404 (6775): 278–81. Bibcode:2000Natur.404..278P. doi:10.1038/35005072. PMID 10749209. S2CID 23292138.

Zeilinger S, Gupta VK, Dahms TE, Silva RN, Singh HB, Upadhyay RS, Gomes EV, Tsui CK, Nayak SC (March 2016). "Friends or foes? Emerging insights from fungal interactions with plants". FEMS Microbiology Reviews. 40 (2): 182–207. doi:10.1093/femsre/fuv045. PMC 4778271. PMID 26591004.

Jumpponen A, Trappe JM (October 1998). "Dark Septate Endophytes: A Review of Facultative Biotrophic Root-Colonizing Fungi". New Phytologist. 140 (2): 295–310. doi:10.1046/j.1469-8137.1998.00265.x. JSTOR 2588371. PMID 33862835.

Downie JA (March 2010). "The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots". FEMS Microbiology Reviews. 34 (2): 150–70. doi:10.1111/j.1574-6976.2009.00205.x. PMID 20070373.

Wheatley RM, Poole PS (July 2018). "Mechanisms of bacterial attachment to roots". FEMS Microbiology Reviews. 42 (4): 448–461. doi:10.1093/femsre/fuy014. PMID 29672765.

Udvardi M, Poole PS (2013-04-29). "Transport and metabolism in legume-rhizobia symbioses". Annual Review of Plant Biology. 64 (1): 781–805. doi:10.1146/annurev-arplant-050312-120235. PMID 23451778.

Steenhoudt O, Vanderleyden J (October 2000). "Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects". FEMS Microbiology Reviews. 24 (4): 487–506. doi:10.1111/j.1574-6976.2000.tb00552.x. PMID 10978548.

Moissl-Eichinger, Christine; Pausan, Manuela; Taffner, Julian; Berg, Gabriele; Bang, Corinna; Schmitz, Ruth A. (2017-08-18). "Archaea Are Interactive Components of Complex Microbiomes". Trends in Microbiology. 26 (1): 70–85. doi:10.1016/j.tim.2017.07.004. ISSN 0966-842X. PMID 28826642.

Chelius, M.K.; Triplett, E.W. (2001-02-23). "The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L.". Microbial Ecology. 41 (3): 252–263. doi:10.1007/s002480000087. ISSN 0095-3628. PMID 11391463. S2CID 20069511.

Prudence, Samuel M.M.; Worsley, Sarah; Balis, Lucas; Murrell, J. Colin; Lehtovirta-Morley, Laura; Hutchings, Matthew L. (2019-03-01). "Root-associated archaea: investigating the niche occupied by ammonia oxidising archaea within the wheat root microbiome". Access Microbiology. 1 (1A). doi:10.1099/acmi.ac2019.po0112. ISSN 2516-8290.

Leininger, S.; Urich, T.; Schloter, M.; Schwark, L.; Qi, J.; Nicol, G. W.; Prosser, J. I.; Schuster, S. C.; Schleper, C. (2006-08-17). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–809. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. ISSN 0028-0836. PMID 16915287. S2CID 4380804.

Taffner, Julian; Erlacher, Armin; Bragina, Anastasia; Berg, Christian; Moissl-Eichinger, Christine; Berg, Gabriele (2018-05-09). "What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs". mSphere. 3 (3). doi:10.1128/msphere.00122-18. ISSN 2379-5042. PMC 5956146. PMID 29743201.

Pump, Judith; Pratscher, Jennifer; Conrad, Ralf (2015-01-27). "Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission". Environmental Microbiology. 17 (7): 2254–2260. doi:10.1111/1462-2920.12675. ISSN 1462-2912. PMID 25367104.

Wang, Haitao; Su, Jianqiang; Zheng, Tianling; Yang, Xiaoru (2015-02-04). "Insights into the role of plant on ammonia-oxidizing bacteria and archaea in the mangrove ecosystem". Journal of Soils and Sediments. 15 (5): 1212–1223. doi:10.1007/s11368-015-1074-x. ISSN 1439-0108. S2CID 84753901.

Herrmann, M.; Saunders, A. M.; Schramm, A. (2008-03-14). "Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora". Applied and Environmental Microbiology. 74 (10): 3279–3283. Bibcode:2008ApEnM..74.3279H. doi:10.1128/aem.02802-07. ISSN 0099-2240. PMC 2394948. PMID 18344332.

Liu, Yin; Li, Hong; Liu, Qun Fang; Li, Yan Hong (2015-03-05). "Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland". World Journal of Microbiology and Biotechnology. 31 (5): 823–832. doi:10.1007/s11274-015-1836-z. ISSN 0959-3993. PMID 25739566. S2CID 19039050.

Chen, Xue-Ping; Zhu, Yong-Guan; Xia, Yue; Shen, Ju-Pei; He, Ji-Zheng (2008-07-08). "Ammonia-oxidizing archaea: important players in paddy rhizosphere soil?". Environmental Microbiology. 10 (8): 1978–1987. doi:10.1111/j.1462-2920.2008.01613.x. ISSN 1462-2912. PMID 18430011.

Ke, Xiubin; Lu, Yahai; Conrad, Ralf (2013-08-28). "Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms". FEMS Microbiology Ecology. 87 (1): 18–29. doi:10.1111/1574-6941.12188. ISSN 0168-6496. PMID 23909555.

Song, Geun Cheol; Im, Hyunjoo; Jung, Jihye; Lee, Soohyun; Jung, Man-Young; Rhee, Sung-Keun; Ryu, Choong-Min (2019-01-21). "Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae". Environmental Microbiology. 21 (3): 940–948. doi:10.1111/1462-2920.14486. ISSN 1462-2912. PMID 30461142. S2CID 53944018.

Cheung, Man Kit; Wong, Chong Kim; Chu, Ka Hou; Kwan, Hoi Shan (2018-09-26). "Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments". Scientific Reports. 8 (1): 14397. Bibcode:2018NatSR...814397C. doi:10.1038/s41598-018-32529-5. ISSN 2045-2322. PMC 6158284. PMID 30258074.

Cadillo-Quiroz, Hinsby; Yavitt, Joseph B.; Zinder, Stephen H.; Thies, Janice E. (2009-12-22). "Diversity and Community Structure of Archaea Inhabiting the Rhizoplane of Two Contrasting Plants from an Acidic Bog". Microbial Ecology. 59 (4): 757–767. doi:10.1007/s00248-009-9628-3. ISSN 0095-3628. PMID 20024684. S2CID 22134029.

Marschner P, Yang CH, Lieberei R, Crowley DE (2001). "Soil and plant specific effects on bacterial community composition in the rhizosphere". Soil Biology and Biochemistry. 33 (11): 1437–45. doi:10.1016/S0038-0717(01)00052-9.

Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (February 2008). "Root exudates regulate soil fungal community composition and diversity". Applied and Environmental Microbiology. 74 (3): 738–44. Bibcode:2008ApEnM..74..738B. doi:10.1128/AEM.02188-07. PMC 2227741. PMID 18083870.

Bogar LM, Kennedy PG (March 2013). "New wrinkles in an old paradigm: neighborhood effects can modify the structure and specificity of Alnus-associated ectomycorrhizal fungal communities". FEMS Microbiology Ecology. 83 (3): 767–77. doi:10.1111/1574-6941.12032. PMID 23078526.

Meinhardt KA, Gehring CA (March 2012). "Disrupting mycorrhizal mutualisms: a potential mechanism by which exotic tamarisk outcompetes native cottonwoods". Ecological Applications. 22 (2): 532–49. doi:10.1890/11-1247.1. PMID 22611852.

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Kogel KH, Franken P, Hückelhoven R (August 2006). "Endophyte or parasite—what decides?". Current Opinion in Plant Biology. 9 (4): 358–63. doi:10.1016/j.pbi.2006.05.001. PMID 16713330.

Lugtenberg B, Kamilova F (2009). "Plant-growth-promoting rhizobacteria". Annual Review of Microbiology. 63: 541–56. doi:10.1146/annurev.micro.62.081307.162918. PMID 19575558.

Wheatley RM, Poole PS (July 2018). "Mechanisms of bacterial attachment to roots". FEMS Microbiology Reviews. 42 (4): 448–461. doi:10.1093/femsre/fuy014. PMID 29672765.

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Kristin A, Miranda H (2013). "The root microbiota—a fingerprint in the soil?". Plant and Soil. 370 (1–2): 671–86. doi:10.1007/s11104-013-1647-7. S2CID 14961515.

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Root microbiome (English Wikipedia)

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