Decreased diversity and connectivity of endophytic fungal assemblages within cultivated European olive trees compared to their native African counterpart
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Abdelfattah, 2015, Metabarcoding analysis of fungal diversity in the phyllosphere and carposphere of olive (Olea europaea), PLoS One, 10, 1, 10.1371/journal.pone.0131069
Adams, 2006, Cytospora species (Ascomycota, diaporthales, valsaceae): introduced and native pathogens of trees in South Africa. Australas, Plant Pathol., 35, 521
Agricultural Research Council, 2010, 1
Amabeoku, 2010, Evaluation of the effects of Olea europaea L. subsp. africana (Mill.) P.S. Green (Oleaceae) leaf methanol extract against castor oil-induced diarrhoea in mice, J. Pharm. Pharmacol., 62, 368, 10.1211/jpp.62.03.0012
Anderson, 2008, 1
Anderson, 2001, A new method for non-parametric multivariate analysis of variance, Austral Ecol., 26, 32
Anderson, 2006, Distance-based tests for homogeneity of multivariate dispersions, Biometrics, 62, 245, 10.1111/j.1541-0420.2005.00440.x
Arnold, 2003, Fungal endophytes limit pathogen damage in a tropical tree, Proc. Natl. Acad. Sci. U. S. A, 100, 15649, 10.1073/pnas.2533483100
Assenov, 2008, Computing topological parameters of biological networks, Bioinformatics, 24, 282, 10.1093/bioinformatics/btm554
Aumeeruddy-Thomas, 2017, Ongoing domestication and diversification in grafted olive – oleaster agroecosystems in Northern Morocco, Reg. Environ. Change, 17, 1315, 10.1007/s10113-017-1143-3
Bates, 2007, Lme4: linear mixed-effects models using S4 classes, vols. 1–29
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc. B, 57, 289
Besnard, 2007, On the origin of the invasive olives (Olea europaea L., Oleaceae), Heredity, 99, 608, 10.1038/sj.hdy.6801037
Besnard, 2002, Olea europaea (Oleaceae) phylogeography based on chloroplast DNA polymorphism, Theor. Appl. Genet., 104, 1353, 10.1007/s00122-001-0832-x
Bickford, 2018, Root endophytes and invasiveness: no difference between native and non-native Phragmites in the Great Lakes Region, Ecosphere, 9, 1, 10.1002/ecs2.2526
Bray, 1957, An ordination of the upland forest communities of southern Wisconsin, Ecol. Monogr., 27, 325, 10.2307/1942268
Bufford, 2016, Taxonomic similarity, more than contact opportunity, explains novel plant–pathogen associations between native and alien taxa, New Phytol., 212, 657, 10.1111/nph.14077
Burnham, 1978, Estimation of the size of a closed population when capture probabilities vary among animals, Biometrika, 65, 625, 10.1093/biomet/65.3.625
Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 415, 10.1038/nmeth.f.303
Castañeda, 2018, Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests, PeerJ, 6, 10.7717/peerj.5715
Chao, 1992, Estimating the number of classes via sample coverage, J. Am. Stat. Assoc., 87, 210, 10.1080/01621459.1992.10475194
Chliyeh, 2014, Bibliographic inventory of the olive tree (Olea europaea L.) fungal diseases in the world, Int. J. Pure App. Biosci., 2, 46
Christian, 2016, Plant host and geographic location drive endophyte community composition in the face of perturbation, Microb. Ecol., 72, 621, 10.1007/s00248-016-0804-y
Cline, 2007, Integration of biological networks and gene expression data using Cytoscape, Nat. Protoc., 2, 2366, 10.1038/nprot.2007.324
Colautti, 2004, Is invasion success explained by the enemy release hypothesis?, Ecol. Lett., 7, 721, 10.1111/j.1461-0248.2004.00616.x
Coleman-Derr, 2016, Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species, New Phytol., 209, 798, 10.1111/nph.13697
Collado, 1999, Geographical and seasonal influences on the distribution of fungal endophytes in Quercus ilex, New Phytol., 144, 525, 10.1046/j.1469-8137.1999.00533.x
Costa, 1998, 1
Costa, 2018, Advances and opportunities in olive production: why research and technology development is required for success?, Met. Ind. News, 48
Costa, 2021, Illuminating Olea europaea L. endophyte fungal community, Microbiol. Res., 245, 1, 10.1016/j.micres.2020.126693
Crous, 2017, Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees, AoB Plants, 9, 1
Crous, 2009, Unravelling Mycosphaerella: do you believe in genera?, Persoonia, 23, 99, 10.3767/003158509X479487
De Oliveira, 2022, Exploring the diversity and potential interactions of bacterial and fungal endophytes associated with different cultivars of olive (Olea europaea) in Brazil, Microbiol. Res., 263, 1, 10.1016/j.micres.2022.127128
de Wet, 2008, Phylogeny of the Botryosphaeriaceae reveals patterns of host association, Mol. Phylogenet. Evol., 46, 116, 10.1016/j.ympev.2007.08.016
Doyle, 1990, A rapid total DNA preparation procedure for fresh plant tissue, Focus, 12, 13
Dzoyem, 2017, Cytotoxicity, antioxidant and antibacterial activity of four compounds produced by an endophytic fungus Epicoccum nigrum associated with Entada abyssinica, Brazilian J. Pharmacogn., 27, 251, 10.1016/j.bjp.2016.08.011
Faiza, 2011, Antibacterial and antifungal activities of olive (Olea europaea L.) from Algeria, J. Microbiol. Biotechnol. Res., 1, 69
Fernández-González, 2020, Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive, Microbiome, 8, 1, 10.1186/s40168-020-0787-2
Fernández-González, 2020, Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management, PLoS One, 15, 1, 10.1371/journal.pone.0236796
Ferreira, 2012, ImageJ user guide, ImageJ/Fiji, 1, 155
Freeman, 1977, A set of measures of centrality based on betweenness, Sociometry, 40, 35, 10.2307/3033543
Gardes, 1993, ITS primers with enhanced specificity for basidiomycetes, application to the identification of mycorrhizae and rusts, Mol. Ecol., 2, 113, 10.1111/j.1365-294X.1993.tb00005.x
Gauch, 1973, A quantitative evaluation of the Bray-Curtis ordination, Ecology, 54, 829, 10.2307/1935677
Glen, 2007, Puccinia psidii: a threat to the Australian environment and economy - a review, Australas. Plant Pathol., 36, 1, 10.1071/AP06088
Gomes, 2018, Endophytic and epiphytic phyllosphere fungal communities are shaped by different environmental factors in a Mediterranean ecosystem, Microb. Ecol., 76, 668, 10.1007/s00248-018-1161-9
Gomes, 2019, Bacterial disease induced changes in fungal communities of olive tree twigs depend on host genotype, Sci. Rep., 9, 1, 10.1038/s41598-019-42391-8
Gore, 2007, Geographical and seasonal influences on the distribution of fungal endophytes in Laurus nobilis, For. Pathol., 37, 281, 10.1111/j.1439-0329.2007.00509.x
Gorter, 1956, Anthracnose fungi of olives, Nature, 178, 1129, 10.1038/1781129a0
Gorter, 1962, The identity of the fungus causing anthracnose of olives in South Africa, Bothalia, 7, 769, 10.4102/abc.v7i4.1680
Green, 2002, A revision of Olea L. (Oleaceae), Kew Bull., 57, 91, 10.2307/4110824
Hajishengallis, 2012, The keystone-pathogen hypothesis, Nat. Rev. Microbiol., 10, 717, 10.1038/nrmicro2873
Harrell, 2014, vols. 1–389
Hayward, 2015, A single ectomycorrhizal fungal species can enable a Pinus invasion, Ecology, 96, 1438, 10.1890/14-1100.1
Helander, 2007, Fragmented environment affects birch leaf endophytes, New Phytol., 175, 547, 10.1111/j.1469-8137.2007.02110.x
Hernández- Rodríguez, 2022, Diversity of Botryosphaeriaceae species causing stem canker and fruit rot in olive trees in Uruguay, J. Phytopathol., 170, 264, 10.1111/jph.13078
Hothorn, 2008, Simultaneous inference in general parametric models, Biom. J., 50, 346, 10.1002/bimj.200810425
Hyde, 2008, [Commentary] the fungal endophyte dilemma, Fungal Divers., 33, 163
Khan, 2016, Cytotoxic and antibacterial naphthoquinones from an endophytic fungus, Cladosporium sp. Toxicol. Reports, 3, 861, 10.1016/j.toxrep.2016.10.005
Kõljalg, 2013, Towards a unified paradigm for sequence-based identification of Fungi, Mol. Ecol., 22, 5271, 10.1111/mec.12481
Kosawang, 2018, Fungal communities associated with species of Fraxinus tolerant to ash dieback, and their potential for biological control, Fungal Biol, 122, 110, 10.1016/j.funbio.2017.11.002
Kosawang, 2019, Defining the twig fungal communities of Fraxinus species and Fraxinus excelsior genotypes with differences in susceptibility to ash dieback, Fungal Ecol, 42, 10.1016/j.funeco.2019.08.003
Lee, 2004, Diversity of saprobic hyphomycetes on proteaceae and Restionaceae from South Africa, Fungal Divers., 17, 91
Li, 2012, Ultrafast clustering algorithms for metagenomic sequence analysis, Briefings Bioinf., 13, 656, 10.1093/bib/bbs035
Lumibao, 2018, Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill, Sci. Total Environ., 642, 904, 10.1016/j.scitotenv.2018.06.077
Magurran, 2004, An index of diversity, 100
Manning, 2012, 1
Martín-García, 2012, ITS-based comparison of endophytic mycota in twigs of native Populus nigra and cultivated P. x euramericana (cv. I-214) stands in Northern Spain, Ann. For. Sci., 69, 49, 10.1007/s13595-011-0129-4
Martins, 2016, Fungal endophyte communities in above- and belowground olive tree organs and the effect of season and geographic location on their structures, Fungal Ecol, 20, 193, 10.1016/j.funeco.2016.01.005
Martins, 2021, Endophytic fungal community succession in reproductive organs of two olive tree cultivars with contrasting anthracnose susceptibilities, Fungal Ecol, 49, 1, 10.1016/j.funeco.2020.101003
McMurdie, 2013, Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, 1, 10.1371/journal.pone.0061217
Moral, 2010, Characterization and pathogenicity of Botryosphaeriaceae species collected from olive and other hosts in Spain and California, Ecol. Epidemiol., 100, 1340
Moyo, 2019, Diatrypaceae species overlap between vineyards and natural ecosystems in South Africa, Fungal Ecol, 39, 142, 10.1016/j.funeco.2018.11.015
Mucina, 2006
Newman, 2003, Mixing patterns in networks, Phys. Rev., 67, 1
Ngubane, 2022
Oksanen, 2008, The vegan package. Community ecology package, R Package, 1–191
Palmer, 1991, Estimating species richness: the Second-order Jackknife reconsidered, Ecology, 72, 1512, 10.2307/1941127
Perez, 2012, Species of Mycosphaerellaceae and Teratosphaeriaceae on native Myrtaceae in Uruguay: evidence of fungal host jumps, Fungal Biol, 117, 94, 10.1016/j.funbio.2012.12.002
Power, 2017, European Fraxinus species introduced into New Zealand retain many of their native endophytic fungi, Balt. For., 23, 74
R Development Core Team, 2015
Rebelo, 2006, Fynbos Biome, 53
Rodriguez, 2009, Fungal endophytes: diversity and functional roles, New Phytol., 182, 314, 10.1111/j.1469-8137.2009.02773.x
Rybakova, 2017, The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens, Microbiome, 5, 1, 10.1186/s40168-017-0310-6
Saikkonen, 2000, Endophytic fungi in wild and cultivated grasses in Finland, Ecography, 23, 360, 10.1111/j.1600-0587.2000.tb00292.x
Saikkonen, 1998, Fungal endophytes: a continuum of interactions with host plants, Annu. Rev. Ecol. Systemat., 29, 319, 10.1146/annurev.ecolsys.29.1.319
Santolini, 2018, Predicting perturbation patterns from the topology of biological networks, Proc. Natl. Acad. Sci. USA, 115, E6375, 10.1073/pnas.1720589115
Schulz, 2006, Microbial root endophytes, Soil Biol., 9, 1, 10.1007/3-540-33526-9_1
Slabbert, 2010, Microbial diversity and community structure in Fynbos soil, Mol. Ecol., 19, 1031, 10.1111/j.1365-294X.2009.04517.x
Slippers, 2005, Emerging pathogens: fungal host jumps following anthropogenic introduction, Trends Ecol. Evol., 20, 420, 10.1016/j.tree.2005.05.002
Slippers, 2007, Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact, Fungal Biol. Rev., 21, 90, 10.1016/j.fbr.2007.06.002
Spearman, 1904, Proof and measurement of association between two things, Am. J. Psychol., 15, 72, 10.2307/1412159
Spies, 2020, Dieback and decline pathogens of olive trees in South Africa, Persoonia Mol. Phylogeny Evol. Fungi, 45, 196, 10.3767/persoonia.2020.45.08
Stackebrandt, 1994, Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology, Int. J. Syst. Bacteriol., 168, 846, 10.1099/00207713-44-4-846
Therios, 2009, History of olive growing, 1
Torbati, 2014, Effect of fungal species involved in the olive fruit rot on the qualitative properties of olive oil, Arch. Phytopathol. Plant Protect., 47, 292, 10.1080/03235408.2013.809183
Úrbez-Torres, 2013, Olive twig and branch dieback: etiology, incidence, and distribution in California, Plant Dis., 97, 231, 10.1094/PDIS-04-12-0390-RE
Van Dyk, 2021, Pathogenicity testing of fungal isolates associated with olive trunk diseases in South Africa, Plant Dis., 105, 4060, 10.1094/PDIS-08-20-1837-RE
Van Dyk, 2021, Survey of trunk pathogens in South African olive nurseries, Plant Dis., 105, 1, 10.1094/PDIS-04-20-0798-RE
Van Niekerk, 2004, DNA phylogeny, morphology and pathogenicity of Botryosphaeria species on grapevines, Mycologia, 96, 781, 10.1080/15572536.2005.11832926
Varanda, 2019, Fungal communities associated with peacock and cercospora leaf spots in olive, Plants, 8, 1, 10.3390/plants8060169
Vossen, 2007, Olive oil: history, production, and characteristics of the world's classic oils, Hortscience, 42, 1093, 10.21273/HORTSCI.42.5.1093
Weiss, 2017, Normalization and microbial differential abundance strategies depend upon data characteristics, Microbiome, 5, 1, 10.1186/s40168-017-0237-y
White, 1996, Analysis of frequency count data using the negative binomial distribution, Ecology, 77, 2549, 10.2307/2265753
White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315
Zhou, 2014, Diversity and plant growth-promoting ability of endophytic fungi from the five flower plant species collected from Yunnan, Southwest China, J. Plant Interact., 9, 585, 10.1080/17429145.2013.873959