[en] The rhizosphere is a dynamic interface where plant- and soil-derived factors jointly influence microbial community assembly. In chicory (
Cichorium intybus
L.), the respective roles of genotype, developmental stage, and root metabolites in structuring rhizosphere communities remain insufficiently understood. This study aimed to characterize patterns of microbial assembly and to assess their associations with root metabolite profiles. Rhizosphere and bulk soil from three chicory genotypes were sampled at two developmental stages and analyzed using bacterial and fungal metabarcoding. Diversity metrics, differential abundance analyses, and literature-based functional annotation were integrated with root metabolite profiling to explore associations between microbial taxa and metabolite profiles. Rhizosphere microbial communities associated with chicory differed from bulk soil and were structured by plant genotype and developmental stage. Lower α-diversity at early stages may reflect the selective enrichment of specific taxa, suggesting non-random assembly. Community variation was associated with root metabolite profiles, including primary metabolites and sesquiterpene lactones (STLs). Across development, the microbiome shifted from taxa linked to nutrient transformation and microbial interactions including
Nitratireductor
,
Sphingomonas
, and
Serratia
, toward communities dominated by saprotrophic and organic matter-degrading taxa such as
Streptomyces
,
Pseudarthrobacter
, and
Lecanicillium
. Genotype-dependent differences further suggested that plant genetic background contributed to rhizosphere assembly patterns. However, these relationships are correlative, and the underlying mechanisms require validation through targeted experimental approaches. The observed correlations led us to propose a hypothesis of temporally structured chemical-trophic filtering, meaning that plant metabolites and soil nutrient conditions jointly contribute to shaping microbial communities in a genotype-dependent manner.
Adhikari M. Kim S. Yadav D. Um Y. Kim H. Lee H., et al. et al. (2016). A new record of Pseudeurotium bakeri from crop field soil in Korea. Korean J. Mycol. 44 145–149. 10.4489/KJM.2016.44.3.145.
An D. S. Im W.-T. Yoon M.-H., (2008). Microlunatus panaciterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil in a ginseng field. Int. J. Syst. Evol. Microbiol. 58 2734–2738. 10.1099/ijs.0.65004-0 19060049.
Anderson M. J., (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26 32–46. 10.1111/j.1442-9993.2001.01070.pp.x.
BR4 BacDive (2025). BacDive – The Bacterial Diversity Metadatabase. The Leibniz Institute DSMZ. Available online at: https://bacdive.dsmz.de/strain/16920 (accessed June 30, 2025).
Badri D. V. Vivanco J. M., (2009). Regulation and function of root exudates. Plant Cell Environ. 32 666–681. 10.1111/j.1365-3040.2009.01926.x.
Bais H. P. Weir T. L. Perry L. G. Gilroy S. Vivanco J. M., (2006). The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol. 57 233–266. 10.1146/annurev.arplant.57.032905.105159 16669762.
Benjamini Y. Hochberg Y., (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57 289–300. 10.1111/j.2517-6161.1995.tb02031.x.
Bensch K. Braun U. Groenewald J. Z. Crous P. W., (2012). The genus Cladosporium. Stud. Mycol. 72 1–401. 10.3114/sim0003 22815589.
Bray J. R. Curtis J. T., (1957). An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27 325–349. 10.2307/1942268 34212107.
Brown C. T. Hug L. A. Thomas B. C. Sharon I. Castelle C. J. Singh A., et al. et al. (2015). Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523 208–211. 10.1038/nature14486 26083755.
Bulgarelli D. Schlaeppi K. Spaepen S. van Themaat E. V. L. Schulze-Lefert P., (2013). Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64 807–838. 10.1146/annurev-arplant-050312-120106 23373698.
Busse H.-J., (2016). Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int. J. Syst. Evol. Microbiol. 66 9–37. 10.1099/ijsem.0.000702 26486726.
Castelle C. J. Banfield J. F., (2018). Biosynthetic capacity and unusual biology in the CPR radiation. Nat. Rev. Microbiol. 16 629–645. 10.1038/s41579-018-0076-2 30181663.
Chadwick M. Trewin H. Gawthrop F. Wagstaff C., (2013). Sesquiterpenoids lactones: Benefits to plants and people. Int. J. Mol. Sci. 14 12780–12805. 10.3390/ijms140612780 23783276.
Chao A., (1984). Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11 265–270.
Chaparro J. M. Badri D. V. Vivanco J. M., (2014). Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8 790–803. 10.1038/ismej.2013.196 24196324.
Chaverri P. Salgado C. Hirooka Y. Rossman A. Y. Samuels G. J., (2011). Delimitation of neonectria and cylindrocarpon (Nectriaceae, hypocreales, ascomycota) and related genera with cylindrocarpon-like anamorphs. Stud. Mycol. 68 57–78. 10.3114/sim.2011.68.03 21523189.
Cotrufo M. F. Lavallee J. M. Zhang Y. Hansen P. M. Paustian K. H. Schipanski M., et al. et al. (2021). In-N-out: A hierarchical framework to understand and predict soil carbon storage and nitrogen recycling. Glob. Change Biol. 27 4465–4468. 10.1111/gcb.15782 34480393.
de Hoog G. S. Vicente V. A. Najafzadeh M. J. Harrak M. J. Badali H. Seyedmousavi S., (2011). Waterborne Exophiala species causing disease in cold-blooded animals. Persoonia 27 46–72. 10.3767/003158511X614258 22403476.
DeAngelis K. M. Brodie E. L. DeSantis T. Z. Andersen G. L. Lindow S. E. Firestone M. K., (2009). Selective progressive response of soil microbial community to wild oat roots. ISME J. 3 168–178. 10.1038/ismej.2008.103 19005498.
Dennis P. G. Miller A. J. Hirsch P. R., (2010). Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol. Ecol. 72 313–327. 10.1111/j.1574-6941.2010.00860.x 20370828.
FAO. (2021). Standard Operating Procedure for Soil pH Determination. Rome: Food and Agriculture Organization of the United Nations.
Fitzpatrick C. R. Copeland J. Wang P. W. Guttman D. S. Johnson M. T. J., (2018). Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl. Acad. Sci. U S A. 115 E1157–E1165. 10.1073/pnas.1717617115 29358405.
Fredrickson J. K. Balkwill D. L. Drake G. R. Romine M. F. Ringelberg D. B. White D. C., (1995). Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl. Environ. Microbiol. 61 1917–1922. 10.1128/aem.61.5.1917-1922.1995 7544095.
Fukasawa Y. Osono T. Takeda H., (2011). Wood decomposing abilities of diverse lignicolous fungi on nondecayed and decayed beech wood. Mycologia 103 474–482. 10.3852/10-246 21262989.
Gérard A. El-Hajjaji S. Burteau S. Fall P. Pirard B. Taminiau B., et al. et al. (2021). Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria ocytogenes. Food Microbiol. 100:103861. 10.1016/j.fm.2021.103861 34416961.
Gibson G. R. Hutkins R. Sanders M. E. Prescott S. L. Reimer R. A. Salminen S. J., et al. et al. (2017). The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat. Rev. Gastroenterol. Hepatol. 14 491–502. 10.1038/nrgastro.2017.75 28611480.
Gis Sol. (n.d.). Inventaire, gestion et conservation des sols (IGCS). Available online at: https://www.gissol.fr/le-gis/programmes/inventaire-gestion-et-conservation-des-sols-igcs-67 (accessed March 2026)
Haichar F. E. Z. Marol C. Berge O. Rangel-Castro J. I. Prosser J. I. Balesdent J., et al. et al. (2008). Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2 1221–1230. 10.1038/ismej.2008.80 18754043.
Häkkinen S. T. Sokoviæ M. Nohynek L. Æiriæ A. Ivanov M. Stojkoviæ D., et al. et al. (2021). Chicory extracts and sesquiterpene lactones show potent activity against bacterial and fungal pathogens. Pharmaceuticals 14:941. 10.3390/ph14090941 34577641.
Harman G. E. Howell C. R. Viterbo A. Chet I. Lorito M., (2004). Trichoderma species—Opportunistic, avirulent plant symbionts. Nat. Rev. Microbiol. 2 43–56. 10.1038/nrmicro797 15035008.
Hartman K. van der Heijden M. G. A. Roussely-Provent V. Walser J. C. Schlaeppi K., (2017). Deciphering composition and function of the root microbiome of a legume plant. Microbiome 5:2. 10.1186/s40168-016-0220-z 28095877.
Heiri O. Lotter A. F. Lemcke G., (2001). Loss on ignition as a method for estimating organic and carbonate content in sediments: Reproducibility and comparability of results. J. Paleolimnol. 25 101–110. 10.1023/A:1008119611481.
Hernández-Pacheco C. E. Orozco-Mosqueda M. D. C. Flores A. Valencia-Cantero E. Santoyo G., (2021). Tissue-specific diversity of bacterial endophytes in Mexican husk tomato plants (Physalis ixocarpa Brot. ex Horm.), and screening for their multiple plant growth-promoting activities. Curr. Res. Microb. Sci. 2: 100028. 10.1016/j.crmicr.2021.100028 34841319.
Hilbert J.-L. Rambaud C., (2023). “Industrial chicory and its specialized metabolites: Diversification of uses and varietal selection, ” in Natural Products in Beverages (Reference Series in Phytochemistry, eds Grumezescu A. M. Holban A. M., (Berlin: Springer International Publishing), 1–35. 10.1007/978-3-031-04195-2_134-1.
Hopwood D. A., (2007). Streptomyces in Nature and Medicine: The Antibiotic Makers. Oxford: Oxford University Press.
Hosoya T., (2021). Systematics, ecology, and application of Helotiales: Recent progress and future perspectives for research with special emphasis on activities within Japan. Mycoscience 62 1–9. 10.47371/mycosci.2020.05.002 37090017.
Inderjit Duke S. O., (2003). Ecophysiological aspects of allelopathy. Planta 217 529–539. 10.1007/s00425-003-1054-z 12811559.
IUSS WRB. (2022). World Reference Base For Soil Resources 2022: International Soil Classification System for Naming Soils and Creating Legends for Soil Maps, 4th Edn. Rome: International Union of Soil Sciences.
Jones D. L. Nguyen C. Finlay R. D., (2009). Carbon flow in the rhizosphere: Carbon trading at the soil–root interface. Plant Soil 321 5–33. 10.1007/s11104-009-9925-0.
Jumpponen A. Trappe J. M., (1998). Dark septate endophytes: A review of facultative biotrophic root-colonizing fungi. New Phytol. 140 295–310. 10.1046/j.1469-8137.1998.00265.x 33862835.
Kabata-Pendias A., (2011). Trace Elements in Soils and Plants, 4th Edn. Boca Raton, FL: CRC Press, 10.1201/b10158.
Kageyama A. Takahashi Y. Seki T. Tomoda H. Ōmura S., (2005). Oryzihumus leptocrescens gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 55 2555–2559. 10.1099/ijs.0.63799-0 16280526.
Kämpfer P. Rosselló-Mora R. Scholz H. C. Welinder-Olsson C. Falsen E. Busse H.-J., (2006). Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov. Int. Int. J. Syst. Evol. Microbiol. 56 1823–1829. 10.1099/ijs.0.64256-0 16902015.
Karimi E. Aliloo A. A. Mosavi S. B., (2024). Effect of Bacillus simplex as a growth-promoting bacterium on some growth characteristics of pepper (Capsicum annuum L.) seedlings under different water conditions. Water Soil Sci. 34 125–141. 10.22034/ws.2024.58833.2542.
Kielak A. M. Barreto C. C. Kowalchuk G. A. van Veen J. A. Kuramae E. E., (2016). The ecology of acidobacteria: Moving beyond genes and genomes. Front. Microbiol. 7:744. 10.3389/fmicb.2016.00744 27303369.
Kim J.-H. Kim W., (2016). Tumebacillus soli sp. nov., isolated from non-rhizosphere soil. Int. J. Syst. Evol. Microbiol. 66 2292–2296. 10.1099/ijsem.0.001009 26956136.
Kirkby C. A. Kirkegaard J. A. Richardson A. E. Wade L. J. Blanchard C. Batten G., (2011). Stable soil organic matter: A comparison of C:N:P:S ratios in Australian and other world soils. Geoderma 163 197–208. 10.1016/j.geoderma.2011.04.010.
Kulkova I. Dobrzyński J. Kowalczyk P. Bełżecki G. Kramkowski K., (2023). Plant growth promotion using Bacillus cereus. Int. J. Mol. Sci. 24:9759. 10.3390/ijms24119759 37298706.
Kwon K. K. Woo J.-H. Yang S.-H. Kang J.-H. Lee S.-T., (2007). Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus as Altererythrobacter luteolus comb. nov. Int. J. Syst. Evol. Microbiol. 57 2187–2191. 10.1099/ijs.0.64863-0 17911284.
Labeda D. P. Dunlap C. A. Rong X. Huang Y. Doroghazi J. R. Ju K.-S., et al. et al. (2017). Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 110 563–583. 10.1007/s10482-016-0824-0 28039547.
Lattanzio V. Lattanzio V. M. T. Cardinali A., (2006). “Role of phenolics in the resistance mechanisms of plants against fungal pathogens and insects, ” in Phytochemistry: Advances in Research, ed. Imperato F., Trivandrum, India: (Research Signpost), 23–67.
Leclercq L. Debarre S. Lloret E. Taminiau B. Daube G. Rambaud C., et al. et al. (2025). Unveiling the hidden allies of industrial chicory: A metagenomic exploration of rhizosphere microbiota and their impact on productivity and plant health. Front. Microbiol. 16:1509094. 10.3389/fmicb.2025.1509094 40415946.
Liu X. Z. Wang Q. M. Göker M. Groenewald M. Kachalkin A. V. Lumbsch H. T., et al. et al. (2015). Towards an integrated phylogenetic classification of the Tremellomycetes. Stud. Mycol. 81 85–147. 10.1016/j.simyco.2015.12.001 26955199.
Lombard L. van der Merwe N. A. Groenewald J. Z. Crous P. W., (2015). Generic concepts in nectriaceae. Stud. Mycol. 80 189–245. 10.1016/j.simyco.2014.12.002 26955195.
Loria R. Kers J. Joshi M., (2006). Evolution of plant pathogenicity in Streptomyces. Annu. Rev. Phytopathol. 44 469–487. 10.1146/annurev.phyto.44.032905.091147 16719719.
Love M. I. Huber W. Anders S., (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550. 10.1186/s13059-014-0550-8 25516281.
Lovley D. R., (1993). Dissimilatory metal reduction. Annu. Rev. Microbiolo. 47 263–290. 10.1146/annurev.mi.47.100193.001403 8257100.
Lovley D. R. Holmes D. E. Nevin K. P., (2004). Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49 219–286. 10.1016/S0065-2911(04)49005-5 15518832.
Ma Y. Li X. Wang F. Zhang L. Zhou S. Che X., et al. et al. (2023). Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax. PLoS Biol. 21:e3002189. 10.1371/journal.pbio.3002189 37459330.
Madden R. H., (1983). Isolation and characterization of Clostridium stercorarium sp. nov., cellulolytic thermophile. Int. J. Syst. Bacteriol. 33 837–840. 10.1099/00207713-33-4-837.
Marik D. Sharma P. Chauhan N. S. Jangir N. Shekhawat R. S. Verma D., et al. et al. (2024). Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana. J. Appl. Microbiol. 135:lxae066. 10.1093/jambio/lxae066 38486365.
McBride M. J., (2014). “The family flavobacteriaceae, ” in The Prokaryotes, 4th Edn, eds Rosenberg E. DeLong E. F. Lory S. Stackebrandt E. Thompson F., (Berlin: Springer), 643–676. 10.1007/978-3-642-38954-2_130.
Mendes R. Kruijt M. de Bruijn I. Dekkers E. van der Voort M. Schneider J. H. M., et al. et al. (2011). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332 1097–1100. 10.1126/science.1203980 21551032.
Mountfort D. O. Rainey F. A. Burghardt J. Kaspar H. F. Stackebrandt E., (1997). Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica. Arch. Microbiol. 167 54–60. 10.1007/s002030050416 9000342.
Nakamura L. K., (1998). Bacillus pseudomycoides sp. nov. Int. J. Syst. Bacteriol. 48 1031–1035. 10.1099/00207713-48-3-1031 9734060.
Oberwinkler F. Riess K. Bauer R. Garnica S. Weiß M., (2013). Enigmatic sebacinales. Mycol. Prog. 12 1–27. 10.1007/s11557-012-0880-4.
Ofek M. Hadar Y. Minz D., (2012). Ecology of root colonizing Massilia (Oxalobacteraceae). PLoS One 7:e0040117. 10.1371/journal.pone.0040117 22808103.
Ogaki M. B. Vieira R. Muniz M. C. Zani C. L. Alves T. M. A. Junior P. A. S., et al. et al. (2020). Diversity, ecology, and bioprospecting of culturable fungi in lakes impacted by anthropogenic activities in Maritime Antarctica. Extremophiles 24 637–655. 10.1007/s00792-020-01183-z 32533308.
Oksanen J. Simpson G. L. Blanchet G. Kindt R. Legendre P. Minchin P. R., et al. et al. (2022). vegan: Community Ecology Package (R package version x.x-x). Available online at: https://CRAN.R-project.org/package=vegan.
Ou D. Huang H. Bai R. Li Q. Wang Y. Yin Y., (2017). Nitratireductor aestuarii sp. nov., a marine alphaproteobacterium isolated from an estuary. Int. J. Syst. Evol. Microbiol. 67 1722–1727. 10.1099/ijsem.0.001771 28056221.
Ozimek E. Hanaka A., (2021). Mortierella species as the plant growth-promoting fungi present in the agricultural soils. Agriculture 11:7. 10.3390/agriculture11010007.
Pagnier I. Raoult D. La Scola B., (2011). Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure. Int. J. Syst. Evol. Microbiol. 61 2151–2154. 10.1099/ijs.0.025775-0 20889765.
Pascale A. Proietti S. Pantelides I. S. Stringlis I. A., (2020). Modulation of the root microbiome by plant molecules: The basis for targeted disease suppression and plant growth promotion. Front. Plant Sci. 10:1741. 10.3389/fpls.2019.01741 32038698.
Philippot L. Raaijmakers J. M. Lemanceau P. van der Putten W. H., (2013). Going back to the roots: The microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11 789–799. 10.1038/nrmicro3109 24056930.
Phillips K. E. Stevens D. C. Whitworth D. E., (2022). Concepts and conjectures concerning predatory performance of myxobacteria. Microbiology 168:1226. 10.1099/mic.0.001226 35960548.
Picman A. K., (1986). Biological activities of sesquiterpene lactones. Biochem. Syst. Ecol. 14, 255–281. 10.1016/0305-1978(86)90101-8.
Pielou E. C., (1966). The measurement of diversity in different types of biological collections. J. Theoretical Biol. 13 131–144. 10.1016/0022-5193(66)90013-0.
Poehlein A. Zverlov V. V. Daniel R. Schwarz W. H. Liebl W., (2013). Complete genome sequence of Clostridium stercorarium subsp. stercorarium strain DSM 8532, a thermophilic degrader of plant cell wall fibers. Genome Announcements 1:e00073-13. 10.1128/genomeA.00073-13 23516204.
Pouille C. L. Ouaza S. Roels E. Behra J. Tourret M. Molinié R., et al. et al. (2022). Chicory: Understanding the effects and effectors of this functional food. Nutrients 14: 957. 10.3390/nu14050957 35267932.
Powell M. J., (2017). “Chytridiomycota, ” in Handbook of the Protists, eds Archibald J. Simpson A. Slamovits C., (Berlin: Springer), 10.1007/978-3-319-28149-0_18.
Proença D. N. Schwab S. Vidal M. S. Baldani J. I. Xavier G. R. Morais P. V., (2019). The nematicide Serratia plymuthica M24T3 colonizes Arabidopsis thaliana, stimulates plant growth, and presents plant beneficial potential. Braz. J. Microbiol. 50 777–789. 10.1007/s42770-019-00098-y 31177380.
Puhlmann M.-L. de Vos W. M., (2021). Back to the roots: Revisiting the use of the fiber-rich Cichorium intybus L. taproots. Adv. Nutr. 12 878–889. 10.1093/advances/nmaa136 33130884.
Reichenbach H., (2001). Myxobacteria, producers of novel bioactive substances. J. Industrial Microbiol. Biotechnol. 27 149–156. 10.1038/sj.jim.7000025 11780785.
Roden E. E. Lovley D. R., (1993). Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans. Appl. Environ. Microbiol. 59 734–742. 10.1128/aem.59.3.734-742.1993 16348888.
Rognes T. Flouri T. Nichols B. Quince C. Mahé F., (2016). VSEARCH: A versatile open source tool for metagenomics. Peer J. 4:e2584. 10.7717/peerj.2584 27781170.
Rossman A. Y. Samuels G. J. Rogerson C. T. Lowen R., (1999). Genera of bionectriaceae, hypocreaceae and nectriaceae (hypocreales, ascomycetes). Stud. Mycol. 42 1–248.
Saini N. Gupta R. S., (2021). A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades. Antonie van Leeuwenhoek 114 957–982. 10.1007/s10482-021-01569-9 33881638.
Saman S. Saman S. Slattery P., (2010). Isolation of a potential new member of the Bacillus cereus group from snow covered soil. Life Sci. Med. Res..
Santos P. Pinhal I. Rainey F. Empadinhas N. Costa J. Fields B., et al. et al. (2003). Gamma-proteobacteria Aquicella lusitana gen. nov., sp. nov., and Aquicella siphonis sp. nov. infect protozoa and require activated charcoal for growth in laboratory media. Appl. Environ. Microbiol. 69 6533–6540. 10.1128/AEM.69.11.6533-6540.2003 14602611.
Sasse J. Martinoia E. Northen T., (2018). Feed your friends: Do plant exudates shape the root microbiome? Trends Plant Sci. 23 25–41. 10.1016/j.tplants.2017.09.003 29050989.
Schlaeppi K. Dombrowski N. Oter R. G. Ver Loren, van Themaat E. Schulze-Lefert P., (2014). Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc. Natl. Acad. Sci. U S A. 111 585–592. 10.1073/pnas.1321597111 24379374.
Schmidt T. J., (2006). “Structure–activity relationships of sesquiterpene lactones, ” in Studies in Natural Products Chemistry, Vol. 33 (Amsterdam: Elsevier), 309–392. 10.1016/S1572-5995(06)80030-X.
Shade A. Caporaso J. G. Handelsman J. Knight R. Fierer N., (2013). A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 7 1493–1506. 10.1038/ismej.2013.54 23575374.
Shannon C. E., (1948). A mathematical theory of communication. Bell Syst. Techn. J. 27 379–423. 10.1002/j.1538-7305.1948.tb01338.x.
Shi S. Nuccio E. E. Herman D. J. Rijkers R. Estera K. Li J., et al. et al. (2015). Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6:e00746-15. 10.1128/mBio.00746-15 26242625.
Stackebrandt E. Rainey F. A. Ward-Rainey N. L., (1997). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47 479–491. 10.1099/00207713-47-2-479.
Sun S.-L. Yang W.-L. Fang W.-W. Zhao Y.-X. Guo L. Dai Y.-J., (2018). The plant growth-promoting rhizobacterium Variovorax boronicumulans CGMCC 4969 regulates the level of indole-3-acetic acid synthesized from indole-3-acetonitrile. Appl. Environ. Microbiol. 84:e00298-18. 10.1128/AEM.00298-18 29884755.
Świątczak J. Kalwasińska A. Brzezińska M. S., (2024). Plant growth–promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions. Front. Plant Sci. 14:1233237. 10.3389/fpls.2023.1233237 38259930.
Takeuchi M. Hamana K. Hiraishi A., (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium gen. nov., Novosphingobium gen. nov. and Sphingopyxis gen. nov., on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51 1405–1417. 10.1099/00207713-51-4-1405 11491340.
Thomma B. P. H. J., (2003). Alternaria spp.: From general saprophyte to specific parasite. Mol. Plant Pathol. 4 225–236. 10.1046/j.1364-3703.2003.00173.x 20569383.
Tkacz A. Cheema J. Chandra G. Grant A. Poole P. S., (2015). Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 9 2349–2359. 10.1038/ismej.2015.41 25909975.
Trivedi P. Leach J. E. Tringe S. G. Sa T. Singh B. K., (2020). Plant–microbiome interactions: From community assembly to plant health. Nat. Rev. Microbiol. 18 607–621. 10.1038/s41579-020-0412-1 32788714.
Ueda K. Yamashita A. Ishikawa J. Shimada M. Watsuji T. O. Morimura K., et al. et al. (2004). Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res. 32 4937–4944. 10.1093/nar/gkh830 15383646.
Uroz S. Calvaruso C. Turpault M.-P. Frey-Klett P., (2009). Mineral weathering by bacteria: Ecology, actors and mechanisms. Trends Microbiol. 17 378–387. 10.1016/j.tim.2009.05.004 19660952.
Urzì C. Salamone P. Schumann P. Stackebrandt E., (2000). Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int. J. Syst. Evol. Microbiol. 50 529–536. 10.1099/00207713-50-2-529 10758857.
Wagner L. Stielow B. de Hoog S. Bensch K. Schwartze V. Voigt K., et al. et al. (2013). A comprehensive molecular phylogeny of the Mortierellales. Persoonia 30 77–93. 10.3767/003158513X666268 24027348.
Wang Y. Zhang Z. Ramanan N., (1997). The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J. Bacteriol. 179 3270–3276. 10.1128/jb.179.10.3270-3276.1997 9150223.
Wang Z. Kadouri D. E. Wu M., (2011). Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 12:453. 10.1186/1471-2164-12-453 21936919.
White D. C. Sutton S. D. Ringelberg D. B., (1996). The genus sphingomonas: Physiology and ecology. Curr. Opin. Biotechnol. 7 301–306. 10.1016/s0958-1669(96)80034-6 8785434.
Willems A. De Ley J. Gillis M. Kersters K., (1991). Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis, 1969). Int. J. Syst. Bacteriol. 41 445–450. 10.1099/00207713-41-3-445.
Yao L. Zhang J.-J. Yu L.-L. Chen Q. Zhu J.-C. He J., et al. et al. (2016). Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost. Int. J. Syst. Evol. Microbiol. 66 3317–3323. 10.1099/ijsem.0.001194 27255344.
Yoon J.-H. Kang S.-J. Lee S.-Y. Lee J.-S. Park S., (2011). Ohtaekwangia koreensis gen. nov., sp. nov. and Ohtaekwangia kribbensis sp. nov., isolated from marine sand, deep-branching members of the phylum Bacteroidetes. Int. J. Syst. Evol. Microbiol. 61 1066–1072. 10.1099/ijs.0.025874-0 20511453.
Yoon J.-H. Lee K.-C. Weiss N. Kho Y.-H. Kang K.-H. Park Y.-H., (2001). Sporosarcina aquimarina sp. nov., a bacterium isolated from seawater in Korea, and transfer of Bacillus globisporus (Larkin and Stokes 1967), Bacillus psychrophilus (Nakamura 1984) and Bacillus pasteurii (Chester 1898) to the genus Sporosarcina as Sporosarcina globispora comb. nov., Sporosarcina psychrophila comb. nov. and Sporosarcina pasteurii comb. nov., and emended description of the genus Sporosarcina. Int. J. Syst. Evol. Microbiol. 51 1079–1086. 10.1099/00207713-51-3-1079 11411676.
Yoon J.-H. Rhee S.-K. Lee J.-S. Park Y.-H. Lee S. T., (1997). Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int. J. Syst. Evol. Microbiol. 47 933–938. 10.1099/00207713-47-4-933 9336889.
Zare R. Gams W., (2001). A revision of verticillium section prostrata. IV. the genera lecanicillium and simplicillium gen. nov. Nova Hedwigia 73 1–50. 10.1127/nova.hedwigia/71/2001/1.
Zare R. Gams W. Starink M. Summerbell R. C., (2007). Gibellulopsis, a suitable genus for Verticillium nigrescens, and Musicillium, a new genus for V. theobromae. Nova Hedwigia 85 463–489. 10.1127/0029-5035/2007/0085-0463.
Zhalnina K. Louie K. B. Hao Z. Mansoori N. da Rocha U. N. Shi S., et al. et al. (2018). Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3 470–480. 10.1038/s41564-018-0129-3 29556109.
Zhou G.-C. Wang Y. Zhai S. Ge F. Liu Z.-H. Dai Y.-J., et al. et al. (2013). Biodegradation of the neonicotinoid insecticide thiamethoxam by the nitrogen-fixing and plant-growth-promoting rhizobacterium Ensifer adhaerens strain TMX-23. Appl. Microbiol. Biotechnol. 97 4065–4074. 10.1007/s00253-012-4638-3 23274958.
