Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks

Abstract

The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in April, 2018 in the same soil environment and harvested in May, 2019 were evaluated to determine the role of genotype on the composition of both the bacterial and fungal communities. Results demonstrated a clear impact of genotype and root size on microbial composition and diversity. The fungal community was more affected by plant genotype whereas the bacterial community was shaped by root size. Fungal and bacterial abundance was equal between different-sized roots however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. This study provides information that can be used to develop a comprehensive and readily applicable understanding of the impact of genotype and environmental factors on the establishment of plant microbiome, as well as its potential function and impact on host physiology.

References

[1] Charrier G, Delzon S, Domec JC et al. Drought will not leave your glass empty: low risk of hydraulic failure revealed by long-term drought observations in world’s top wine regions. Sci Adv. 2018; 4: eaao6969.

[2] Kviklys D, Samuolienė G . Relationships among the rootstock, crop load, and sugar hormone signaling of apple tree, and their effects on biennial bearing. Front Plant Sci. 2020; 11: 1213.

[3] Foster TM, Ledger SE, Janssen BJ et al. Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees. J Exp Bot. 2018; 69: 2379-90.

[4] Singh J, Fabrizio J, Desnoues E et al. Root system traits impact early fire blight susceptibility in apple (Malus × domestica) . BMC Plant Biol. 2019; 19: 579.

[5] Thompson AA, Williams MA, Pecka GM . Compost and Geneva^® series rootstocks increase young ‘Gala’ apple tree growth and change root-zone microbial communities . Sci Hortic. 2019; 256: 108573.

[6] Wei Z, Gu Y, Friman VP et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv. 2019; 5: eaaw0759.

[7] Leff JW, Lynch RC, Kane NC et al. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower Helianthus annuus . New Phytol. 2017; 214: 412-23.

[8] Fierer NS, Wood A, de Mesquita CPB . How microbes can, and cannot, be used to assess soil health. Soil Biol Biochem. 2021; 153: 108111.

[9] Mercado-Blanco J, Abrantes I, Caracciolo AB et al. Below-ground microbiota and the health of tree crops. Front Microbiol. 2018; 9: 1006.

[10] Rho H, Van Epps V, Kim SH et al. Endophytes increased fruit quality with higher soluble sugar production in Honeycrisp apple (Malus pumila) . Microorganisms. 2020; 8: 699.

[11] Van Horn C, Somera TS, Mazzola M . Comparative analysis of the rhizosphere and endophytic microbiomes across apple rootstock genotypes in replant orchard soils. Phytobiomes J. 2021; 5: 231-43. https://doi.org/10.1094/PBIOMES-08-20-0058-R in press.

[12] Cordovez V, Dini-Andreote F, Carrion VJ et al. Ecology and evolution of plant microbiomes. Annu Rev Microbiol. 2019; 73: 69-88.

[13] Abdelfattah A, Wisniewski M, Droby S et al. Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase. Hortic Res. 2016; 3: 16047.

[14] Chiniquy D, Barnes EM, Zhou J et al. Microbial community field surveys reveal abundant Pseudomonas population in sorghum rhizosphere composed of many closely related phylotypes. Front Microbiol. 2021; 12: 598180.

[15] Liu J, Abdelfattah A, Norelli J et al. Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. Microbiome. 2018; 6: 18.

[16] Levy A, Gonzalez IS, Mittelviefhaus M et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2017; 50: 138- 50.

[17] Bai Y, Müller DB, Srinivas G et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature. 2015; 528: 364-9.

[18] Bais HP, Weir TL, Perry LG et al. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol. 2006; 57: 233-66.

[19] Bakker PAHM, Berendsen RL, Doornbos RF et al. The rhizosphere revisited: root microbiomics. Front Plant Sci. 2013; 4: 165.

[20] Leisso R, Rudell D, Mazzola M . Metabolic composition of apple rootstock rhizodeposits differs in a genotype-specific manner and affects growth of subsequent plantings. Soil Biol Biochem. 2017; 113: 201-14.

[21] Wagner MR, Lundberg DS, Del Rio TG et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun. 2016; 7: 12151.

[22] Philippot L, Raaijmakers JM, Lemanceau P et al. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013; 11: 789-99.

[23] Gaiero JR, McCall CA, Thompson KA et al. Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am J Bot. 2013; 100: 1738-50.

[24] Trivedi P, Leach JE, Tringe SG et al. Plant-microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607-21.

[25] Arrigoni E, Antonielli L, Pindo M et al. Tissue age and plant genotype affect the microbiota of apple and pear bark. Microbiol Res. 2018; 211: 57-68.

[26] Laurent AS, Merwin IA, Fazio G et al. Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil. Plant Soil. 2010; 337: 259-72.

[27] Reig G, Lordan J, Sazo MM et al. Long-term performance of ‘Gala’, ‘Fuji’ and ‘Honeycrisp’ apple trees grafted on Geneva(R) rootstocks and trained to four production systems under New York state climatic conditions. Sci Hortic. 2019; 244: 277-93.

[28] Poudel R, Jumpponen A, Kennelly MM et al. Rootstocks shape the rhizobiome: rhizosphere and endosphere bacterial communities in the grafted tomato system. Appl Environ Microbiol. 2019; 85: e01765-18.

[29] Kim MJ, Do H, Cho G et al. Comparison of microbial community of rhizosphere and endosphere in kiwifruit. Plant Pathol J. 2019; 35: 705-11.

[30] Wang L, Mazzola M . Interaction of Brassicaceae seed meal soil amendment and apple rootstock genotype on microbiome structure and replant disease suppression. Phytopathology. 2019; 109: 607-14.

[31] Manici LM, Caputo F, Nicoletti F et al. Impact of cover crop in pre-plant of apple orchards: relationship between crop health, root inhabiting fungi and rhizospheric bacteria. Can J Plant Sci. 2015; 95: 947-58.

[32] Wang L, Somera TS, Hargarten H et al. Comparative analysis of apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: implications for plant health. Microorganisms. 2021; 9: 763.

[33] Marasco R, Rolli E, Fusi M et al. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Microbiome. 2018; 6: 3.

[34] Emmett B, Nelson EB, Kessler A et al. Fine-root system development and susceptibility to pathogen colonization. Planta. 2014; 239: 325-40.

[35] Fazio G, Lordan J, Grusak MA et al. Mineral nutrient profiles and relationships of ‘Honeycrisp’ grown on a genetically diverse set of rootstocks under Western New York climatic conditions. Sci Hortic. 2020; 266: 108477.

[36] Chai X, Xie L, Wang X et al. Apple rootstocks with different phosphorus efficiency exhibit alterations in rhizosphere bacterial structure. J Appl Microbiol. 2020; 128: 1460-71.

[37] Deakin G, Fernández-Fernández F, Bennett J et al. The effect of rotating apple rootstock genotypes on apple replant disease and rhizosphere microbiome. Phytobiomes J. 2019; 3: 273-85.

[38] Vink SN, Dini-Andreote F, Höfle R et al. Interactive effects of scion and rootstock genotypes on the root microbiome of grapevines (Vitis spp. L.) . Appl Sci. 2021; 11: 1615.

[39] Pérez-Izquierdo L, Zabal-Aguirre M, Flores-Rentería D et al. Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests. Environ Microbiol. 2017; 19: 1639-52.

[40] Yu C, Hu X, Deng W et al. Soil fungal community comparison of different mulberry genotypes and the relationship with mulberry fruit sclerotiniosis. Sci Rep. 2016; 6: 28365.

[41] Bálint M, Tiffin P, Hallström B et al. Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera) . PLoS One. 2013; 8: e53987.

[42] Berlanas C, Berbegal M, Elena G et al. The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. Front Microbiol. 2019; 10: 1142.

[43] Adams S, Lordan J, Fazio G et al. Effect of scion and graft type on transpiration, hydraulic resistance and xylem hormone profile of apples grafted on Geneva(R) 41 and M.9-NIC(TM) 29 rootstocks. Sci Hortic. 2018; 227: 213-22.

[44] Backer R, Rokem JS, Ilangumaran G et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front Plant Sci. 2018; 9: 1473.

[45] Getahun A, Muleta D, Assefa D et al. Plant growth-promoting rhizobacteria isolated from degraded habitat enhance drought tolerance of acacia (Acacia abyssinica Hochst. Ex Benth.) seedlings . Int J Microbiol. 2020; 2020: 8897998.

[46] Hashem A, Tabassum B, Abd Allah EF . Bacillus subtilis: a plant-growth promoting rhizobacterium that also impacts biotic stress . Saudi J Biol Sci. 2019; 26: 1291-7.

[47] Konappa N, Krishnamurthy S, Arakere UC et al. Efficacy of indigenous plant growth promoting rhizobacteria and Trichoderma strains in eliciting resistance against bacterial wilt in a tomato. Egypt J Biol Pest Control. 2020; 30: 106.

[48] Abdelfattah A, Whitehead SR, Macarisin D et al. Effect of washing, waxing and low-temperature storage on the postharvest microbiome of apple. Microorganisms. 2020; 8: 944.

[49] Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019; 37: 852-7.

[50] Köberl M, Müller H, Ramadan EM et al. Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One. 2011; 6: e24452.

[51] White TJ, Bruns T, Lee S et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR Protocols: A Guide to Methods and Applications, Vol. 64. Academic Press: San Diego, 1990, 315-22.

[52] Callahan BJ, McMurdie PJ, Rosen MJ et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016; 13: 581-3.

[53] Abarenkov K, Nilsson RH, Larsson KH et al. The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol. 2010; 186: 281-5.

[54] DeSantis TZ, Hugenholtz P, Larsen N et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb. 2006; 72: 5069- 72.

[55] Paulson JN, Stine OC, Bravo HC et al. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013; 10: 1200-2.

[56] Bray JR, Curtis JT . An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957; 27: 326-49.

[57] Arbizu M. Pairwise multilevel comparison using Adonis. R Package v.0.4. https://github.com/pmartinezarbizu/pairwiseAdonis 2019.

[58] Bates D, Maechler M, Bolker B et al. Lme4: linear mixed-effects models using ‘Eigen’ and S4 (version 1.1-27). https://cran.r-project.org/web/packages/lme4/index.html 2021.

[59] Hothorn T, Bretz F, Westfall P . Simultaneous inference in general parametric models. Biom J. 2008; 50: 346-63. https://doi.org/10.1002/bimj.200810425. PMID: 18481363.

[60] McMurdie PJ, Holmes S . Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013; 8: e61217.

[61] Oksanen J, Kindt R, Legendre P et al. The VEGAN package. Community ecology package. 2007; 10: 631-37.

[62] Kruskal WH, Wallis WA . Use of ranks in one-criterion variance analysis. J Am Stat Assoc. 1952; 47: 583-621.

[63] Oliveros J. Venny C . An interactive tool for comparing lists with Venn’s diagram. https://bioinfogp.cnb.csic.es/tools/venny/index.html 2007.

[64] Faust K, Raes J . CoNet app: inference of biological association networks using Cytoscape. F1000Research. 2016; 5: 1519.

[65] Agg B, Császár A, Szalay-Bekő M et al. The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks. Bioinformatics. 2019; 35: 4490-2.