BACKGROUND: Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant-microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model. RESULTS: Although the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry. CONCLUSIONS: There are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere-rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant-microbial interactions in natural ecosystems and the microbiome features of plants.

Associated Research Unit of Plant Microorganism Interaction USAL CSIC 37008 Salamanca Spain

Departamento de Microbiología y Genética Universidad de Salamanca 37007 Salamanca Spain

Institute for Agribiotechnology Research Villamayor 37185 Salamanca Spain

Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague Czech Republic

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Perreault R, Laforest-Lapointe I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene. ISME J. 2022;16(2):339–345. doi: 10.1038/s41396-021-01109-3. PubMed DOI PMC

Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative genomics of the genus pseudomonas reveals host-and environment-specific evolution. Microbiol Spectrum. 2022; 10237022. PubMed PMC

Tri Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18(11):607–621. doi: 10.1038/s41579-020-0412-1. PubMed DOI

Wippel K, Tao K, Niu Y, Zgadzaj R, Kiel N, Guan R, et al. Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nat Microbiol. 2021;6(9):1150–1162. doi: 10.1038/s41564-021-00941-9. PubMed DOI PMC

Cobian GM, Egan CP, Amend AS. Plant–microbe specificity varies as a function of elevation. ISME J. 2019;13(11):2778–2788. doi: 10.1038/s41396-019-0470-4. PubMed DOI PMC

Dastogeer KM, Tumpa FH, Sultana A, Akter MA, Chakraborty A. Plant microbiome–an account of the factors that shape community composition and diversity. Curr Plant Biol. 2020;23:100161. doi: 10.1016/j.cpb.2020.100161. DOI

Wicaksono WA, Cernava T, Berg C, Berg G. Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria. Microbiome. 2021;9(1):1–16. doi: 10.1186/s40168-021-01117-7. PubMed DOI PMC

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 USA. 2018;115(6):E1157–E1165. doi: 10.1073/pnas.1717617115. PubMed DOI PMC

Dini-Andreote F, Raaijmakers JM. Embracing community ecology in plant microbiome research. Trends Plant Sci. 2018;23(6):467–469. doi: 10.1016/j.tplants.2018.03.013. PubMed DOI

Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CM, et al. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun. 2021;12(1):1–13. PubMed PMC

Downie JA. The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol Rev. 2010;34(2):150–170. doi: 10.1111/j.1574-6976.2009.00205.x. PubMed DOI

García-Fraile P, Seaman JC, Karunakaran R, Edwards A, Poole PS, Downie JA. Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant Soil. 2015;390(1):251–264. doi: 10.1007/s11104-015-2389-5. PubMed DOI PMC

Dong W, Zhu Y, Chang H, Wang C, Yang J, Shi J, et al. An SHR–SCR module specifies legume cortical cell fate to enable nodulation. Nature. 2021;589(7843):586–590. doi: 10.1038/s41586-020-3016-z. PubMed DOI

Genre A, Lanfranco L, Perotto S, Bonfante P. Unique and common traits in mycorrhizal symbioses. Nat Rev Microbiol. 2020;18(11):649–660. doi: 10.1038/s41579-020-0402-3. PubMed DOI

Roth R, Chiapello M, Montero H. A Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane in rice. Nat Commun. 2020;9:4677. doi: 10.1038/s41467-018-06865-z. PubMed DOI PMC

Levy A, Conway JM, Dangl JL, Woyke T. Elucidating bacterial gene functions in the plant microbiome. Cell Host Microbe. 2018;24(4):475–485. doi: 10.1016/j.chom.2018.09.005. PubMed DOI

Harrison JG, Griffin EA. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol. 2020;22:2107–2123. doi: 10.1111/1462-2920.14968. PubMed DOI PMC

Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 2016;209(2):798–811. doi: 10.1111/nph.13697. PubMed DOI PMC

Whitaker BK, Reynolds HL, Clay K. Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass) Ecology. 2018;99(12):2703–2711. doi: 10.1002/ecy.2543. PubMed DOI PMC

Garazhian M, Gharaghani A, Eshghi S. Genetic diversity and inter-relationships of fruit bio-chemicals and antioxidant activity in Iranian wild blackberry species. Sci Rep. 2020;10(1):1–13. doi: 10.1038/s41598-020-75849-1. PubMed DOI PMC

Ochmian I, Błaszak M, Lachowicz S, Piwowarczyk R. The impact of cultivation systems on the nutritional and phytochemical content, and microbiological contamination of highbush blueberry. Sci Rep. 2020;10(1):1–14. doi: 10.1038/s41598-020-73947-8. PubMed DOI PMC

Tsai HH, Schmidt W. The enigma of environmental pH sensing in plants. Nat Plants. 2021;7(2):106–115. doi: 10.1038/s41477-020-00831-8. PubMed DOI

Yurgel SN, Douglas GM, Comeau AM, Mammoliti M, Dusault A, Percival D, et al. Variation in bacterial and eukaryotic communities associated with natural and managed wild blueberry habitats. Phytobiomes. 2017;1(2):102–113. doi: 10.1094/PBIOMES-03-17-0012-R. DOI

Yurgel SN, Douglas GM, Dusault A, Percival D, Langille MG. Dissecting community structure in wild blueberry root and soil microbiome. Front Microbiol. 2018;9:1187. doi: 10.3389/fmicb.2018.01187. PubMed DOI PMC

Li J, Mavrodi OV, Hou J, Blackmon C, Babiker EM, Mavrodi DV. Comparative analysis of rhizosphere microbiomes of southern highbush blueberry (Vaccinium corymbosum L.), Darrow’s blueberry (V. darrowii Camp), and rabbiteye blueberry (V. virgatum Aiton) Front Microbiol. 2020;11:370. doi: 10.3389/fmicb.2020.00370. PubMed DOI PMC

Morvan S, Meglouli H, Lounès-Hadj Sahraoui A, Hijri M. Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota. Environ Microbiol. 2020;22(9):3803–3822. doi: 10.1111/1462-2920.15151. PubMed DOI

Zhang Y, Wang W, Shen Z, Wang J, Chen Y, Wang D, et al. Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties. BMC Microbiol. 2021;21(1):1–13. doi: 10.1186/s12866-021-02092-7. PubMed DOI PMC

White TJ, Bruns TD, Lee SB, Taylor JW. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. Academic Press: New York; 1990. pp. 315–322.

Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5(10):1571–1579. doi: 10.1038/ismej.2011.41. PubMed DOI PMC

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi: 10.1038/s41587-019-0209-9. PubMed DOI PMC

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J Am Stat Assoc. 1952;47(260):583–621. doi: 10.1080/01621459.1952.10483441. DOI

Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26(1):32–46.

Spearman C. The proof and measurement of association between two things. Am J Psychol. 1904;15(1):72–101. doi: 10.2307/1412159. PubMed DOI

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’hara RB, et al. Community ecology package. R package version, 2. 2013; pp 321–326

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41(D1):D590–D596. doi: 10.1093/nar/gks1219. PubMed DOI PMC

Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11(1):1–11. doi: 10.1038/s41467-020-17041-7. PubMed DOI PMC

Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag. 2016. New York. ISBN 978-3-319-24277-4.

Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017;33(18):2938–2940. doi: 10.1093/bioinformatics/btx364. PubMed DOI PMC

Põlme S, Abarenkov K, Henrik Nilsson R, Lindahl BD, Clemmensen KE, Kauserud H, et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 2020;105:1–16. doi: 10.1007/s13225-020-00466-2. DOI

Guo J, Ling N, Li Y, Li K, Ning H, Shen Q, et al. Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes. New Phytol. 2021;230(5):2047–2060. doi: 10.1111/nph.17297. PubMed DOI

Fulthorpe RR, Roesch LF, Riva A, Triplett EW. Distantly sampled soils carry few species in common. ISME J. 2008;2(9):901–910. doi: 10.1038/ismej.2008.55. PubMed DOI

Weon HY, Kim BY, Son JA, Song MH, Kwon SW, Go SJ, et al. Nevskia soli sp. Nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol. 2008;58(3):578–580. doi: 10.1099/ijs.0.64994-0. PubMed DOI

Kim SJ, Weon HY, Kim YS, Park IC, Son JA, Kwon SW. Nevskia terrae sp. Nov., isolated from soil. Int J Syst Evol Microbiol. 2011;61(5):1226–1229. doi: 10.1099/ijs.0.021238-0. PubMed DOI

Cupples AM, Thelusmond JR. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms. J Microbiol Methods. 2022;193:106401. doi: 10.1016/j.mimet.2021.106401. PubMed DOI

Rudolph RE, DeVetter LW, Zasada IA, Hesse C. Effects of annual and perennial alleyway cover crops on physical, chemical, and biological properties of soil quality in pacific northwest red raspberry. HortScience. 2020;55(3):344–352. doi: 10.21273/HORTSCI14511-19. DOI

Ramirez KS, Snoek LB, Koorem K, Geisen S, Bloem LJ, Ten Hooven F, et al. Range-expansion effects on the belowground plant microbiome. Nat Ecol Evol. 2019;3(4):604–611. doi: 10.1038/s41559-019-0828-z. PubMed DOI PMC

Yang H, Wu Y, Zhang C, Wu W, Lyu L, Li W. Growth and physiological characteristics of four blueberry cultivars under different high soil pH treatments. Environ Exp Boty. 2022;197:104842. doi: 10.1016/j.envexpbot.2022.104842. DOI

Walker JF, Aldrich-Wolfe L, Riffel A, Barbare H, Simpson NB, Trowbridge J, et al. Diverse Helotiales associated with the roots of three species of Arctic Ericaceae provide no evidence for host specificity. New Phytol. 2011;191(2):515–527. doi: 10.1111/j.1469-8137.2011.03703.x. PubMed DOI

Vohnik M, Sadowsky JJ, Kohout P, Lhotakova Z, Nestby R, Kolařík M. Novel root-fungus symbiosis in Ericaceae: sheathed ericoid mycorrhiza formed by a hitherto undescribed basidiomycete with affinities to Trechisporales. PLoS ONE. 2012;7(6):e39524. doi: 10.1371/journal.pone.0039524. PubMed DOI PMC

Lukešová T, Kohout P, Větrovský T, Vohník M. The potential of dark septate endophytes to form root symbioses with ectomycorrhizal and ericoid mycorrhizal middle European forest plants. PLoS ONE. 2015;10(4):e0124752. doi: 10.1371/journal.pone.0124752. PubMed DOI PMC

Urbina H, Breed MF, Zhao W, Gurrala KL, Andersson SG, Ågren J, et al. Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere. Fungal Biol. 2018;122(4):231–240. doi: 10.1016/j.funbio.2017.12.013. PubMed DOI

Martinović T, Mašínová T, López-Mondéjar R, Jansa J, Štursová M, Starke R, et al. Microbial utilization of simple and complex carbon compounds in a temperate forest soil. Soil Biol and Biochem. 2022;173:108786. doi: 10.1016/j.soilbio.2022.108786. DOI

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