Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota

[en] The epiphytic plant microbial communities living at the surface of fruit have been the source of most current biocontrol agents (BCAs) and can influence fruit quality during storage. Despite this interest, their taxonomical and functional composition has been poorly studied so far. This paper describes the use of high-throughput sequencing (HTS) technologies to characterise the microbial phytobiome residing on apple surface at the taxonomic and functional levels through shotgun metagenome sequencing. Apples from the Pinova cultivar bearing no symptom of disease development were sampled in an orchard at harvest, and their epiphytic microbiota was isolated. After DNA extraction, 14.1 Gbases of raw sequences were generated by HTS. These sequences were annotated following two pipelines in parallel: (i) they were individually analysed by the MG-RAST server, and (ii) they were de novo assembled into contigs and the contigs were annotated by the IMG server. Our results showed a very high fungal and bacterial diversity, with a higher proportion of fungal sequences (79.0%) than bacterial sequences (13.8%). Among fungi, the phylum Ascomycota prevailed, while Bacteroides were dominant in the bacterial population. Among them, 24 species corresponded to known apple pathogens like Aspergillus spp., Botrytis spp., Sclerotinia spp., and Penicillium spp. for fungi, and Erwinia spp. and Agrobacterium spp. for bacteria. Moreover, several contigs were assigned to species of known BCA strains belonging to the following genera: Filobasidiella spp., Talaromyces spp, Candida spp., Saccharomyces spp., Bacillus spp., and Enterobacter spp. The functional analysis showed similar patterns of abundance and function in all samples, identified genes potentially involved in biocontrol properties, but also underlined the complexity of datum interpretation and the incompleteness of current databases.

Disciplines :

Agriculture & agronomy

Author, co-author :

Angeli, Dario; Fondazione Edmund Mach > Department of Sustainable Agro-eEcosystems and Bioresources, Research and Innovation Centre

Sare, Abdoul Razack ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs

Jijakli, Haissam ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs

Pertot, Ilaria; Fondazione Edmund Mach > Department of Sustainable Agro-eEcosystems and Bioresources, Research and Innovation Centre

Massart, Sébastien ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs

Language :

English

Title :

Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota

Alternative titles :

[fr] Aperçus du microbiote épiphyte de la pomme fruit par séquençage métagénomique non ciblé

Publication date :

2019

Journal title :

Postharvest Biology and Technology

ISSN :

0925-5214

eISSN :

1873-2356

Publisher :

Elsevier, Netherlands

Volume :

153

Pages :

96 - 106

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

http://www.sciencedirect.com/science/article/pii/S0925521418311013

Available on ORBi :

since 08 April 2019

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Bibliography

Abdelfattah, A., Wisniewski, M., Droby, S., Schena, L., Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase. Hortic. Res., 3(August), 2016, 16047.
Andrews, J.H., Kenerley, C.M., Microbial populations associated with buds and young leaves of apple. Can. J. Bot. 58:April (8) (1980), 847–855.
Andrews, J., Kenerley, C., Direct observation and enumeration of microbes on plant surfaces by light microscopy. Blakeman, J.P., (eds.) Microbial Ecology of the Phylloplane, 1981, Academic Press, London, 3–14.
Blakeman, J., Microbial Ecology of the Phylloplane. 1981, Academic P. London.
Buchholz, F., Kostić, T., Sessitsch, A., Mitter, B., The potential of plant microbiota in reducing postharvest food loss. Microb. Biotechnol.(March), 2018.
Bulgarelli, D., et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:March (3) (2015), 392–403.
Cardinale, M., Grube, M., Erlacher, A., Quehenberger, J., Berg, G., Bacterial networks and co-occurrence relationships in the lettuce root microbiota. Environ. Microbiol. 17:1 (2015), 239–252.
Chand-Goyal, T., Spotts, R.A., Enumeration of bacterial and yeast colonists of apple fruits and identification of epiphytic yeasts on pear fruits in the Pacific Northwest United States. Microbiol. Res. 151:December (4) (1996), 427–432.
Chen, I.-M.A., et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 45:January (D1) (2017), D507–D516.
Daguerre, Y., Siegel, K., Edel-Hermann, V., Steinberg, C., Fungal proteins and genes associated with biocontrol mechanisms of soil-borne pathogens: a review. Fungal Biol. Rev. 28:December (4) (2014), 97–125.
Delmotte, N., et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. U. S. A. 106:September (38) (2009), 16428–16433.
Dini-Andreote, F., van Elsas, J.D., Back to the basics: the need for ecophysiological insights to enhance our understanding of microbial behaviour in the rhizosphere. Plant Soil 373:December (1–2) (2013), 1–15.
Gawad, C., Koh, W., Quake, S.R., Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17:March (3) (2016), 175–188.
Gladka, M.M., et al. Single-cell sequencing of the healthy and diseased heart reveals Ckap4 as a new modulator of fibroblasts activation. Circulation(January), 2018 p. CIRCULATIONAHA.117.030742.
Glenn, D.M., Bassett, C., Dowd, S.E., Effect of pest management system on ‘Empire’ apple leaf phyllosphere populations. Sci. Hortic. (Amsterdam) 183 (2015), 58–65.
Granado, J., et al. Culturable Fungi of stored ‘Golden delicious’ apple fruits: a one-season comparison study of organic and integrated production systems in Switzerland. Microb. Ecol. 56:November (4) (2008), 720–732.
Hirano, S.S., Upper, C.D., Ecology and epidemiology of foliar bacterial plant pathogens. Annu. Rev. Phytopathol. 21:September (1) (1983), 243–270.
Huntemann, M., et al. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand. Genomic Sci., 11(December (1)), 2016, 17.
Knief, C., et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6:July (7) (2012), 1378–1390.
Kröber, M.S., et al. Effect of the biocontrol strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing. Front. Microbiol., 5, 2014.
Lahlali, R., Massart, S., De Clercq, D., Serrhini, M.N., Jijakli, M.H., Assessment of Pichia anomala (strain K) efficacy against blue mould of apples when applied pre- or post-harvest under laboratory conditions and in orchard trials - Springer. Eur. J. Plant Pathol. 123 (2008), 37–45.
Leff, J.W., Fierer, N., Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 8:3 (2013), 1–9.
Lemanceau, P., Blouin, M., Muller, D., Moënne-Loccoz, Y., Let the core microbiota be functional. Trends Plant Sci. 22:July (7) (2017), 583–595.
Lindow, S.E., Brandl, M.T., Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69:4 (2003), 1875–1883.
Louca, S., et al. High taxonomic variability despite stable functional structure across microbial communities. Nat. Ecol. Evol. 1:December (2016), 1–12.
Massart, S., Martinez-Medina, M., Jijakli, M.H., Biological control in the microbiome era: challenges and opportunities. Biol. Control 89:June (2015), 98–108.
Mendes, L.W., Kuramae, E.E., Navarrete, A.A., van Veen, J.A., Tsai, S.M., Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 8:August(8) (2014), 1577–1587.
Pelliccia, C., Antonielli, L., Corte, L., Bagnetti, A., Fatichenti, F., Cardinali, G., Preliminary prospection of the yeast biodiversity on apple and pear surfaces from Northern Italy orchards. Ann. Microbiol. 61:December (4) (2011), 965–972.
Pennycook, S.R., Newhook, F.J., Seasonal changes in the apple phylloplane microflora. New Zeal. J. Bot. 19:July (3) (1981), 273–283.
Ravanbakhsh, M., Sasidharan, R., Voesenek, L.A.C.J., Kowalchuk, G.A., Jousset, A., Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences. Microbiome, 6(December (1)), 2018, 52.
Saminathan, T., et al. Metagenomic and metatranscriptomic analyses of diverse watermelon cultivars reveal the role of fruit associated microbiome in carbohydrate metabolism and ripening of mature fruits. Front. Plant Sci., 9(January), 2018, 4.
Sessitsch, A., et al. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant Microbe Interact. 25:January (1) (2012), 28–36.
Shade, A., McManus, P.S., Handelsman, J., Unexpected diversity during community succession in the apple flower microbiome. MBio, 4(February (2)), 2013 pp. e00602-12-e00602-12.
Shen, Y., et al. Differentiated surface fungal communities at point of harvest on apple fruits from rural and peri-urban orchards. Sci. Rep., 8(December (1)), 2018, 2165.
Sylla, J., Alsanius, B.W., Krüger, E., Reineke, A., Strohmeier, S., Wohanka, W., Leaf microbiota of strawberries as affected by biological control agents. Phytopathology 103:10 (2013), 1001–1011.
Teixidó, N., Usall, J., Gutierrez, O., Viñas, I., Effect of the antagonist Candida sake on apple surface microflora during cold and ambient (shelf life) storage. Eur. J. Plant Pathol. 104:4 (1998), 387–398.
Teixidó, N., Usall, J., Viñas, I., Efficacy of preharvest and postharvest Candida sake biocontrol treatments to prevent blue mould on apples during cold storage. Int. J. Food Microbiol. 50:September (3) (1999), 203–210.
van den Bos, H., Bakker, B., Spierings, D.C.J., Lansdorp, P.M., Foijer, F., Single-cell sequencing to quantify genomic integrity in cancer. Int. J. Biochem. Cell Biol. 94:January (2018), 146–150.
Vepštaitė-Monstavičė, I., et al. Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic. Microbiol. Res. 206 (2018), 1–8.
Violle, C., et al. Let the concept of trait be functional!. Oikos 116:May (5) (2007), 882–892.
Vorholt, J.A., Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10:12 (2012), 828–840.
Yashiro, E., McManus, P.S., Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere. PLoS One, 7(January (5)), 2012, e37131.
Yashiro, E., Spear, R.N., Mcmanus, P.S., Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere. J. Appl. Microbiol. 110:5 (2011), 1284–1296.
Zarraonaindia, I., et al. The soil microbiome influences grapevine-associated microbiota. MBio, 6(March (2)), 2015 pp. e02527-14.