Mycelial network-mediated rhizobial dispersal enhances legume nodulation

The ISME Journal volume 14, pages1015–1029(2020)Cite this article

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Abstract

The access of rhizobia to legume host is a prerequisite for nodulation. Rhizobia are poorly motile in soil, while filamentous fungi are known to grow extensively across soil pores. Since root exudates-driven bacterial chemotaxis cannot explain rhizobial long-distance dispersal, mycelia could constitute ideal dispersal networks to help rhizobial enrichment in the legume rhizosphere from bulk soil. Thus, we hypothesized that mycelia networks act as vectors that enable contact between rhizobia and legume and influence subsequent nodulation. By developing a soil microcosm system, we found that a facultatively biotrophic fungus, Phomopsis liquidambaris, helps rhizobial migration from bulk soil to the peanut (Arachis hypogaea) rhizosphere and, hence, triggers peanut–rhizobium nodulation but not seen in the absence of mycelia. Assays of dispersal modes suggested that cell proliferation and motility mediated rhizobial dispersal along mycelia, and fungal exudates might contribute to this process. Furthermore, transcriptomic analysis indicated that genes associated with the cell division, chemosensory system, flagellum biosynthesis, and motility were regulated by Ph. liquidambaris, thus accounting for the detected rhizobial dispersal along hyphae. Our results indicate that rhizobia use mycelia as dispersal networks that migrate to legume rhizosphere and trigger nodulation. This work highlights the importance of mycelial network-based bacterial dispersal in legume–rhizobium symbiosis.

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Fig. 1: Ph. liquidambaris transfers soil rhizobia to the rhizosphere of peanut.
Fig. 2: Ph. liquidambaris facilitates Bradyrhizobial dispersal in soil conditions.
Fig. 3: Ph. liquidambaris facilitates Bradyrhizobial dispersal, promotes Bradyrhizobial root infection, and triggers peanut–Bradyrhizobium interaction.
Fig. 4: Ph. liquidambaris networks help Bradyrhizobial dispersal.
Fig. 5: Analysis of Bradyrhizobial dispersal on mycelial networks of Ph. liquidambaris at 14 dai.
Fig. 6: Effects of Ph. liquidambaris exudates on Bradyrhizobial growth, biofilm formation, and chemotaxis.
Fig. 7: RNA-seq reveal the potential genetic mechanisms of rhizobial dispersal on Ph. liquidambaris networks.

References

  1. 1.

    Zipfel C, Oldroyd GED. Plant signalling in symbiosis and immunity. Nature. 2017;543:328–36.

    CAS  PubMed  Google Scholar 

  2. 2.

    Mus F, Crook MB, Garcia K, Costas AG, Geddes BA, Kouri ED, et al. Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol. 2016;82:3698–710.

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Burchill W, James EK, Li D, Lanigan GJ, Williams M, Iannetta PPM, et al. Comparisons of biological nitrogen fixation in association with white clover (Trifolium repens L.) under four fertilizer nitrogen inputs as measured using two 15N techniques. Plant Soil. 2014;385:287–302.

    CAS  Google Scholar 

  4. 4.

    López-García SL, Perticari A, Piccinetti C, Ventimiglia L, Arias N, De Battista JJ, et al. In-furrow inoculation and selection for higher motility enhances the efficacy of Bradyrhizobium japonicum nodulation. Agron J. 2009;101:357–63.

    Google Scholar 

  5. 5.

    Vicario JC, Dardanelli MS, Giordano W. Swimming and swarming motility properties of peanut-nodulating rhizobia. FEMS Microbiol Lett. 2015;362:1–6.

    CAS  PubMed  Google Scholar 

  6. 6.

    Bais HP, Park SW, Weir TL, Callaway RM, Vivanco JM. How plants communicate using the underground information superhighway. Trends Plant Sci. 2004;9:26–32.

    CAS  PubMed  Google Scholar 

  7. 7.

    Horiuchi J, Prithiviraj B, Bais HP, Kimball BA, Vivanco JM. Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria. Planta. 2005;222:848–57.

    CAS  PubMed  Google Scholar 

  8. 8.

    Zhang W, Wang HW, Wang XX, Xie XX, Siddikee MA, Xu RS, et al. Enhanced nodulation of peanut when co-inoculated with fungal endophyte Phomopsis liquidambari and bradyrhizobium. Plant Physiol Biochem. 2016;98:1–11.

    PubMed  Google Scholar 

  9. 9.

    Zhang W, Wang XX, Yang Z, Ashaduzzaman SM, Kong MJ, Lu LY, et al. Physiological mechanisms behind endophytic fungus Phomopsis liquidambari-mediated symbiosis enhancement of peanut in a monocropping system. Plant Soil. 2017;416:325–42.

    CAS  Google Scholar 

  10. 10.

    Xie XG, Fu WQ, Zhang FM, Shi XM, Zeng YT, Li H, et al. The endophytic fungus Phomopsis liquidambari increases nodulation and N2 fixation in Arachis hypogaea by enhancing hydrogen peroxide and nitric oxide signalling. Microb Ecol. 2017;74:427–40.

    CAS  PubMed  Google Scholar 

  11. 11.

    Zhang W, Sun K, Shi RH, Yuan J, Wang XJ, Dai CC. Auxin signalling of Arachis hypogaea activated by colonization of mutualistic fungus Phomopsis liquidambari enhances nodulation and N2-fixation. Plant Cell Environ. 2018;41:2093–108.

    CAS  PubMed  Google Scholar 

  12. 12.

    van Overbeek LS, Saikkonen. Impact of bacterial-fungal interactions on the colonization of the endosphere. Trends Plant Sci. 2016;21:230–42.

    PubMed  Google Scholar 

  13. 13.

    Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, et al. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev. 2018;42:335–52.

    CAS  PubMed  Google Scholar 

  14. 14.

    Ossler JN, Zielinski CA, Heath KD. Tripartite mutualism: facilitation or trade-offs between rhizobial and mycorrhizal symbionts of legume hosts. Am J Bot. 2015;102:1332–41.

    CAS  PubMed  Google Scholar 

  15. 15.

    Kohlmeier S, Smits THM, Ford RM, Keel C, Harms H, Wick LY. Taking the fungal highway: mobilization of pollutant-degrading bacteria fungi. Environ Sci Technol. 2005;39:4640–6.

    CAS  PubMed  Google Scholar 

  16. 16.

    Worrich A, König S, Miltner A, Banitz T, Centler F, Frank K, et al. Mycelium-like networks increase bacterial dispersal, growth, and biodegradation in a model ecosystem at various water potentials. Appl Environ Microbiol. 2016;82:2902–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Otto S, Bruni EP, Harms H, Wick LY. Catch me if you can: dispersal and foraging of Bdellovibrio bacteriovorus 109J along mycelia. ISME J. 2017;11:386–93.

    PubMed  Google Scholar 

  18. 18.

    Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. Microbiome. 2018;6:58.

    PubMed  PubMed Central  Google Scholar 

  19. 19.

    Porras-Alfaro A, Bayman P. Hidden fungi, emergent properties: endophytes and microbiomes. Annu Rev Phytopathol. 2011;49:291–315.

    CAS  PubMed  Google Scholar 

  20. 20.

    Zhou J, Li X, Huang PW, Dai CC. Endophytism or saprophytism: decoding the lifestyle transition of the generalist fungus Phomopsis liquidambari. Microbiol Res. 2018;206:99–112.

    CAS  PubMed  Google Scholar 

  21. 21.

    Wu JR, Xu FJ, Cao W, Zhang W, Guan YX, Dai CC. Fungal endophyte Phomopsis liquidambaris B3 enriches the diversity of nodular culturable endophytic bacteria associated with continuous cropping of peanut. Arch Agronom Soil Sci 2019;65:240–52.

    CAS  Google Scholar 

  22. 22.

    Xie XG, Zhang FM, Yang T, Chen Y, Li XG, Dai CC. Endophytic fungus drives nodulation and N2 fixation attributable to specific root exudates. mBi.o 2019;10:e00728–19.

    Google Scholar 

  23. 23.

    Guhr A, Borken W, Spohn M, Matzner E. Redistribution of soil water by a saprotrophic fungus enhances carbon mineralization. Proc Natl Acad Sci USA. 2015;112:14647–51.

    CAS  PubMed  Google Scholar 

  24. 24.

    Nazir R, Warmink JA, Boersma H, Van Elsas JD. Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats. FEMS Microbiol Ecol. 2009;71:169–85.

    PubMed  Google Scholar 

  25. 25.

    Worrich A, Stryhanyuk H, Musat N, König S, Banitz T, Centler F, et al. Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments. Nat Commun. 2017;8:15472.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Chen Y, Peng Y, Dai CC, Ju Q. Biodegradation of 4-hydroxybenzoic acid by Phomopsis liquidambari. Appl Soil Ecol. 2011;51:102–10.

    Google Scholar 

  27. 27.

    Chen Y, Wang HW, Li L, Dai CC. The potential application of the endophyte Phomopsis liquidambaris to the ecological remediation of long-term cropping soil. Appl Soil Ecol. 2013;67:20–26.

    Google Scholar 

  28. 28.

    Xie XG, Dai CC. Degradation of a model pollutant ferulic acid by the endophytic fungus Phomopsis liquidambari. Bioresour Technol. 2015;179:35–42.

    CAS  PubMed  Google Scholar 

  29. 29.

    Wang HW, Zhang W, Su CL, Zhu H, Dai CC. Biodegradation of the phytoestrogen luteolin by the endophytic fungus Phomopsis liquidambari. Biodegradation. 2015;26:197–210.

    CAS  PubMed  Google Scholar 

  30. 30.

    Sun K, Cao W, Hu LY, Fu WQ, Gong JH, Kang N, et al. Symbiotic fungal endophyte Phomopsis liquidambari-rice system promotes nitrogen transformation by influencing below-ground straw decomposition in paddy soil. J Appl Microbiol. 2019;126:191–203.

    CAS  PubMed  Google Scholar 

  31. 31.

    de Boer W, Folman LB, Summerbell RC, Boddy L. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 2005;29:795–811.

    PubMed  Google Scholar 

  32. 32.

    Haq IU, Dini-Andreote F, van Elsas JD. Transcriptional responses of the bacterium Burkholderia terrae BS001 to the fungal host Lyophyllum sp. strain Karsten under soil-mimicking conditions. Microb Ecol. 2017;73:236–52.

    CAS  PubMed  Google Scholar 

  33. 33.

    Zhang L, Xu M, Liu Y, Zhang F, Hodge A, Feng G. Carbon and phosphorus exchange may enable cooperation between an arbuscular mycorrhizal fungus and a phosphate-solubilizing bacterium. N. Phytol. 2016;210:1022–32.

    CAS  Google Scholar 

  34. 34.

    Jiang Y, Liu M, Zhang J, Chen Y, Chen L, Li H, et al. Nematode grazing promotes bacterial community dynamics in soil at the aggregate level. ISME J. 2017;11:2705–17.

    PubMed  PubMed Central  Google Scholar 

  35. 35.

    Sarita S, Sharma PK, Priefer UB, Prell J. Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol. 2005;54:1–11.

    CAS  PubMed  Google Scholar 

  36. 36.

    Stępkowski T, Moulin L, Krzyżańska A, Mclnnes A, Law IJ, Howieson J. European origin of Bradyrhizobium populations infecting lupins and serradella in soils of western Australia and South Africa. Appl Environ Microbiol. 2005;71:7041–52.

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Berendsen RL, Vismans G, Yu K, Song Y, Jonge R, Burgman WP, et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507.

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Zhang Y, Kastman EK, Guasto JS, Wolfe BE. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat Commun. 2018;9:336.

    PubMed  PubMed Central  Google Scholar 

  39. 39.

    Liu Y, Jiang X, Guan D, Zhou W, Ma M, Zhao B, et al. Transcriptional analysis of genes involved in competitive nodulation in Bradyrhizobium diazoefficiens at the presence of soybean root exudates. Sci Rep. 2017;7:10946.

    PubMed  PubMed Central  Google Scholar 

  40. 40.

    Schmittgen TD, Livak KJ. Analysing real-time PCR data by the comparative C (T) method. Nat Protoc. 2008;3:1101–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Riquelme M. Tip growth in filamentous fungi: a road trip to the apex. Annu Rev Microbiol. 2013;67:587–607.

    CAS  PubMed  Google Scholar 

  42. 42.

    Jost D, Winter J, Gallert C. Distribution of aerobic motile and non-motile bacteria within the capillary fringe of silica sand. Water Res. 2010;44:1279–87.

    CAS  PubMed  Google Scholar 

  43. 43.

    Mondo SJ, Lastovetsky OA, Gaspar ML, Schwardt NH, Barber CC, Riley R, et al. Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nat Commun. 2017;8:1843.

    PubMed  PubMed Central  Google Scholar 

  44. 44.

    Boogerd FC, van Rossum D. Nodulation of groundnut by Bradyrhizobium: a simple infection process by crack entry. FEMS Microbiol Rev. 1997;21:5–27.

    CAS  Google Scholar 

  45. 45.

    Ibáñez F, Wall L, Fabra A. Starting points in plant-bacteria nitrogen-fixing symbioses: intercellular invasion of the roots. J Exp Bot. 2017;68:1905–18.

    PubMed  Google Scholar 

  46. 46.

    Zhang L, Feng G, Declerck S. Signal beyond nutrient, fructose, exuded by an arbuscular mycorrhizal fungus triggers phytate mineralization by a phosphate solubilizing bacterium. ISME J. 2018;12:2339–51.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470.

    CAS  PubMed  Google Scholar 

  48. 48.

    Stopnisek N, Zühlke D, Carlier A, Barberán A, Fierer N, Becher D, et al. Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME J. 2016;10:253–64.

    CAS  PubMed  Google Scholar 

  49. 49.

    Deveau A, Barret M, Diedhiou AG, Leveau J, de Boer W, Martin F, et al. Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria. Micro Ecol. 2015;69:146–59.

    Google Scholar 

  50. 50.

    Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14:563–75.

    CAS  PubMed  Google Scholar 

  51. 51.

    Hansen SK, Rainey PB, Haagensen JA, Molin S. Evolution of species interactions in a biofilm community. Nature. 2007;445:533–6.

    CAS  PubMed  Google Scholar 

  52. 52.

    Sampedro I, Parales RE, Krell T, Hill JE. Pseudomonas chemotaxis. FEMS Microbiol Rev. 2014;39:17–46.

    PubMed  Google Scholar 

  53. 53.

    Springer WR, Koshland DE. Identification of a protein methyltransferase as the cheR gene product in the bacterial sensing system. Proc Natl Acad Sci USA. 1997;74:533–7.

    Google Scholar 

  54. 54.

    Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ, Li DF, et al. Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci USA. 2012;109:8629–34.

    CAS  PubMed  Google Scholar 

  55. 55.

    Poole P, Ramachandran V, Terpolilli J. Rhizobia: from saprophytes to endosymbionts. Nat Rev Microbiol. 2018;16:291.

    CAS  PubMed  Google Scholar 

  56. 56.

    Lowther WL, Patrick HN. Spread of Rhizobium and Bradyrhizobium in soil. Soil Biol Biochem. 1993;25:607–12.

    Google Scholar 

  57. 57.

    de la Peña TC, Pueyo JJ. Legume in the reclamation of marginal soils, from cultivar and inoculant selection to transgenic approaches. Agron Sustain Dev. 2012;32:65–91.

    Google Scholar 

  58. 58.

    Bordeleau LM, Prévost D. Nodulation and nitrogen fixation in extreme environments. Plant Soil. 1994;161:115–25.

    CAS  Google Scholar 

  59. 59.

    Denton MD, Phillips LA, Peoples MB, Pearce DJ, Swan AD, Mele PM, et al. Legume inoculant application methods: effects on nodulation patterns, nitrogen fixation, crop growth and yield in narrow-leaf lupin and faba bean. Plant Soil. 2017;419:25–39.

    CAS  Google Scholar 

  60. 60.

    Deaker R, Roughley RJ, Kennedy IR. Legume seed inoculation technology-a review. Soil Biol Biochem. 2004;36:1275–88.

    CAS  Google Scholar 

  61. 61.

    Schimel J, Balser TC, Wallenstein M. Microbial stress-response physiology and its implications for ecosystem function. Ecology. 2007;88:1386–94.

    PubMed  Google Scholar 

  62. 62.

    Smith GR, Finlay RD, Stenlid J, Vasaitis R, Menkis A. Growing evidence for facultative biotrophy in saprotrophic fungi: data from microcosm tests with 201 species of wood-decay basidiomycetes. N. Phytol. 2017;215:747–55.

    CAS  Google Scholar 

  63. 63.

    Baldrian P, Kohout P. Interactions of saprotrophic fungi with tree roots: can we observe the emergence of novel ectomycorrhizal fungi? N. Phytol. 2017;215:747–55.

    Google Scholar 

  64. 64.

    Man CX, Wang H, Chen WF, Sui XH, Wang ET, Chen WX. Diverse rhizobia associated with soybean grown in the subtropical and tropical regions of China. Plant Soil. 2008;310:77–87.

    CAS  Google Scholar 

  65. 65.

    Zhang YM, Li Y Jr, Chen WF, Wang ET, Tian CF, Li QQ, et al. Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol. 2011;77:6331–42.

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank Yin-Ping Zhang and Chao-Chao Hu of Analytical & Testing Center, Nanjing Normal University, for their help with the microscopic imaging. This work was financially supported by the National Natural Science Foundation of China (NSFC no. 31870478; 31370507); the Priority Academic Program Development of Jiangsu Higher Education Institutions; and Doctor Breeding Project of Nanjing Normal University (1812000006317).

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  1. These authors contributed equally: Wei Zhang, Xiao-Gang Li

Affiliations

  1. Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China

    Wei Zhang, Kai Sun, Meng-Jun Tang, Fang-Ji Xu & Chuan-Chao Dai

  2. Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China

    Xiao-Gang Li

  3. Department of Health Technology, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark

    Ming Zhang

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WZ, XGL, and CCD designed the experiments, analyzed the data, and wrote and revised the manuscript. WZ, KS, MJT, FJX, and MZ performed experiments. All of authors read and approved the final manuscript.

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Correspondence to Chuan-Chao Dai.

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Zhang, W., Li, XG., Sun, K. et al. Mycelial network-mediated rhizobial dispersal enhances legume nodulation. ISME J 14, 1015–1029 (2020). https://doi.org/10.1038/s41396-020-0587-5

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