Arendt KR, Hockett KL, Araldi-Brondolo SJ, Baltrus DA, Arnold AE. 2016. Isolation of endohyphal bacteria from foliar Ascomycota and in vitro establishment of their symbiotic associations. Applied and Environmental Microbiology. 82: 2943-2949. https://doi.org/10.1128/AEM.00452-16
Arora P, Riyaz-Ul-Hassan S. 2019. Endohyphal bacteria: the prokaryotic modulators of host fungal biology. Fungal Biology Reviews. 33: 72-81. https://doi.org/10.1016/j.fbr.2018.07.001
Baedke J. 2024. The plant individuality problem in historical perspective. History and Philosophy of the Life Sciences. 46: 1-18. https://doi.org/10.1007/s40656-023-00598-0
Barbieri E, Potenza L, Rossi I, Sisti D, Giomaro G, … et al. 2000. Phylogenetic characterization and in situ detection of a Cytophaga–Flexibacter–Bacteroides phylogroup bacterium in Tuber borchii Vittad. ectomycorrhizal mycelium. Applied and Environmental Microbiology. 66: 5035-5042. https://doi.org/10.1128/AEM.66.11.5035-5042.2000
Barbieri E, Riccioni G, Pisano A, Sisti D, Zeppa S, … et al. 2002. Competitive PCR for quantitation of a Cytophaga–Flexibacter–Bacteroides phylum bacterium associated with the Tuber borchii Vittad. mycelium. Applied and Environmental Microbiology. 68: 6421-6424. https://doi.org/10.1128/AEM.68.12.6421-6424.2002
Bertaux J, Schmid M, Hutzler P, Hartmann A, Garbaye J, … et al. 2005. Occurrence and localization of bacterial microflora in the mycelium of the ectomycorrhizal fungus Hebeloma cylindrosporum. Microbiological Research. 160: 1-9. https://doi.org/10.1016/j.micres.2004.06.005
Bianciotto V, Schüßler A, Bauer R, Bonfante P. 1996. Presence of an arbuscular mycorrhizal fungus in the cytoplasm of a plant-parasitic fungus. Nature. 381: 297-299. https://doi.org/10.1038/381297a0
Bianciotto V, Lumini E, Lanfranco L, Minerdi D, Bonfante P, … et al. 2003. Detection and identification of bacterial endosymbionts in arbuscular mycorrhizal fungi belonging to the family Gigasporaceae. Applied and Environmental Microbiology. 69: 4597-4606. https://doi.org/10.1128/AEM.69.8.4597-4606.2003
Bianciotto V, Giovannetti M, Lumini E, Becard G, Bescher J, et al. 2004. Presymbiotic growth and spore germination of an arbuscular mycorrhizal fungus are promoted by a bacterium isolated from its spores. Applied and Environmental Microbiology. 70: 3149-3155. https://doi.org/10.1128/AEM.70.5.3149-3155.2004
Bonfante P, Desirò A. 2017. Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota. The ISME Journal. 11: 1727-1735. https://doi.org/10.1038/ismej.2017.21
Booth A. 2014. Symbiosis, selection, and individuality. Biology & Philosophy. 29: 657-673. https://doi.org/10.1007/s10539-014-9454-y
Bordenstein SR, Theis KR. 2015. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biology. 13: e1002226. https://doi.org/10.1371/journal.pbio.1002226
Boynton PJ, Peterson CN, Pringle A. 2019. A novel method for the establishment of stable fungal-bacterial endosymbioses. mBio. 10: e02467-19. https://doi.org/10.1128/mBio.02467-19
Bright M, Bulgheresi S. 2010. A complex journey: transmission of microbial symbionts. Nature Reviews Microbiology. 8: 218-230. https://doi.org/10.1038/nrmicro2262
Bryner SF, Rigling D, Brunner PC. 2012. Invasion history and demographic pattern of Cryphonectria hypovirus 1 across European populations of the chestnut blight fungus. Ecology and Evolution. 2: 3227-3241. https://doi.org/10.1002/ece3.421
Chiba S, Salaipeth L, Lin YH, Sasaki A, Kanematsu S, … et al. 2009. A novel bipartite dsRNA mycovirus from the white root rot fungus Rosellinia necatrix: molecular and biological characterization, taxonomic considerations, and potential for biological control. Journal of Virology. 83: 12801-12812. https://doi.org/10.1128/JVI.01429-09
Chiba S, Castón JR, Ghabrial SA, Suzuki N. 2018. ICTV Virus Taxonomy Profile: Quadriviridae. Journal of General Virology. 99: 1480-1481. https://doi.org/10.1099/jgv.0.001139
Chiu L, Eberl G. 2016. Microorganisms as scaffolds of biological individuality: an eco-immunity account of the holobiont. Biology & Philosophy. 31: 819-837. https://doi.org/10.1007/s10539-016-9541-3
Chiu L, Gilbert SF. 2020. Niche construction and the transition to herbivory: phenotype switching and the organization of new nutritional modes. In: Levine H, Jolly MK, Kulkarni P, Nanjundiah V, editors. Phenotypic Switching: Implications in Biology and Medicine. Academic Press, UK, pp. 459-482. https://doi.org/10.1016/B978-0-12-817996-3.00019-9
Clarke E. 2012. Plant individuality: a solution to the demographer’s dilemma. Biology & Philosophy. 27: 321-361. https://doi.org/10.1007/s10539-012-9308-4
Clavé C, Dyrka W, Turcotte EA, Granger-Farbos A, Ibarzola L, … et al. 2022. Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proceedings of the National Academy of Sciences of the United States of America. 119: e2109418119. https://doi.org/10.1073/pnas.2109418119
Cooper A, Ton J. 2022. Immune priming in plants: from the onset to transgenerational maintenance. Essays in Biochemistry. 66: 635-646. https://doi.org/10.1042/EBC20210077
Daskalov A. 2023. Emergence of the fungal immune system. iScience. 26: 106793. https://doi.org/10.1016/j.isci.2023.106793
Daskalov A. 2026. Regulated cell death in fungi from a comparative immunology perspective. Cell Death & Differentiation. 33: 244-258. https://doi.org/10.1038/s41418-025-01570-z
Daskalov A, Dyrka W, Saupe SJ. 2020. NLR function in fungi as revealed by the study of self/non-self recognition systems. In: Benz JP, Schipper K, editors. Genetics and Biotechnology. Springer, Switzerland, pp. 123-141. https://doi.org/10.1007/978-3-030-49924-2_6
Daskalov A, Habenstein B, Sabaté R, Berbon M, Martinez D, et al. 2016. Identification of a novel cell death-inducing domain reveals that fungal amyloid-controlled programmed cell death is related to necroptosis. Proceedings of the National Academy of Sciences of the United States of America. 113: 2720-2725. https://doi.org/10.1073/pnas.1522361113
Daskalov A, Heller J, Herzog S, Fleißner A, Glass NL. 2017. Molecular mechanisms regulating cell fusion and heterokaryon formation in filamentous fungi. In: Heitman J, Howlett BJ, Crous PW, Stukenbrock EH, James TY, Gow NAR, editors. The Fungal Kingdom. ASM Press, pp. 215-229.
Debets F, Yang X, Griffiths AJ. 1994. Vegetative incompatibility in Neurospora: its effect on horizontal transfer of mitochondrial plasmids and senescence in natural populations. Current Genetics. 26: 113-119.
Desirò A, Salvioli A, Ngonkeu EL, … et al. 2014. Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi. The ISME Journal. 8: 257-270. https://doi.org/10.1038/ismej.2013.151
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, et al.. 2018. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews. 42: 335-352. https://doi.org/10.1093/femsre/fuy008.
Diepeningen AD, Debets AJM, Hoekstra RF. 1997. Heterokaryon incompatibility blocks virus transfer among vegetatively incompatible strains of Aspergillus niger. Mycological Research. 101: 1451-1455. https://doi.org/10.1017/S0953756297004305.
Douglas AE, Werren JH. 2016. Holes in the hologenome: why host-microbe symbioses are not holobionts. mBio. 7: e02099-15. https://doi.org/10.1128/mBio.02099-15.
Dyrka W, Lamacchia M, Durrens P, Kobe B, Daskalov A, … et al. 2014. Diversity and variability of NOD-like receptors in fungi. Genome Biology and Evolution. 6: 3137-3158. https://doi.org/10.1093/gbe/evu247
Espino-Vázquez AN, Bermúdez-Barrientos JR, Cabrera-Rangel JF, Córdova-López G, Cardoso-Martínez F, … et al. 2020. Narnaviruses: novel players in fungal-bacterial symbioses. The ISME Journal. 14: 1743-1754. https://doi.org/10.1038/s41396-020-0636-0.
Filippou C, Garrido-Jurado I, Meyling NV, Quesada-Moraga E, Coutts RHA, … et al. 2018. Mycoviral population dynamics in Spanish isolates of the entomopathogenic fungus Beauveria bassiana. Viruses. 10: 665. https://doi.org/10.3390/v10120665
Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, … et al. 2011. Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiology and Molecular Biology Reviews. 75: 583-609. https://doi.org/10.1128/MMBR.00020-11
Funkhouser LJ, Bordenstein SR. 2013. Mom knows best: the universality of maternal microbial transmission. PLoS Biology. 11: e1001631. https://doi.org/10.1371/journal.pbio.1001631
Ghabrial SA, Suzuki N. 2009. Viruses of plant pathogenic fungi. Annual Review of Phytopathology. 47: 353-384. https://doi.org/10.1146/annurev-phyto-080508-081932
Ghabrial SA, Castón JR, Jiang D, Nibert ML, Suzuki N. 2015. 50-plus years of fungal viruses. Virology. 479-480: 356-368. https://doi.org/10.1016/j.virol.2015.03.007
Gilbert SF, Epel D. 2015. Ecological Developmental Biology: The Environmental Regulation of Development, Health, and Evolution. Sinauer Associates, USA.
Gilbert SF, Sapp J, Tauber AI. 2012. A symbiotic view of life: we have never been individuals. The Quarterly Review of Biology. 87: 325-341. https://doi.org/10.1086/668166
Glass NL, Rasmussen C, Roca MG, Read ND. 2004. Hyphal homing, fusion and mycelial interconnectedness. Trends in Microbiology. 12: 135-141.
Golpayegani S, Pakdel A, Soltani J. 2026. Mycovirome: biology, diversity, structures, advantages, and applications in plant protection. Mycologia Iranica. 13: 1-23. https://doi.org/10.22092/mi.2026.371143.1331
Greslehner GP. 2020. Not by structures alone: can the immune system recognize microbial functions? Studies in History and Philosophy of Biological and Biomedical Sciences. 84: 101336.
Heller J, Clavé C, Gladieux P, Saupe SJ, Daskalov A. 2018. NLR surveillance of essential SEC-9 SNARE proteins induces programmed cell death upon allorecognition in Neurospora crassa. Proceedings of the National Academy of Sciences of the United States of America. 115: E2292-E2301. https://doi.org/10.1073/pnas.1718842115
Hillman BI, Suzuki N. 2004. Viruses of the chestnut blight fungus, Cryphonectria parasitica. Advances in Virus Research. 63: 423-472.
Hoffman MT, Arnold AE. 2010. Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes. Applied and Environmental Microbiology. 76: 4063-4075. https://doi.org/10.1128/AEM.02928-09
Hoffman MT, Gunatilaka M, Wijeratne EMK, Gunatilaka AAL, Arnold AE. 2013. Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte. PLoS ONE. 8: e73132. https://doi.org/10.1371/journal.pone.0073132
Hollings M. 1962. Viruses associated with a die-back disease of cultivated mushroom. Nature. 196: 962-965. https://doi.org/10.1038/196962a0
Hyder R, Pennanen T, Hamberg L, Vainio EJ, Piri T, … et al. 2013. Two viruses of Heterobasidion confer beneficial, cryptic or detrimental effects to their hosts in different situations. Fungal Ecology. 6: 387-396. https://doi.org/10.1016/j.funeco.2013.04.003
Jones JD, Dangl JL. 2006. The plant immune system. Nature. 444: 323-329. https://doi.org/10.1038/nature05286
Kanematsu S, Shimizu T, Salaipeth L, Yaegashi H, Sasaki A, Ito T, Suzuki N. 2014. Genome rearrangement of a mycovirus Rosellinia necatrix megabirnavirus 1 affecting its ability to attenuate virulence of the host fungus. Virology. 450-451: 308-315. https://doi.org/10.1016/j.virol.2013.12.002
Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, … et al. 2023. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. Microbiome. 11: 192. https://doi.org/10.1186/s40168-023-01623-4
Kobayashi DY, Crouch JA. 2009. Bacterial/fungal interactions: from pathogens to mutualistic endosymbionts. Annual Review of Phytopathology. 47: 63-82. https://doi.org/10.1146/annurev-phyto-080508-081729
Kondo H, Chiba S, Toyoda K, et al. 2013. Evidence for negative-strand RNA virus infection in fungi. Virology. 435: 201-209. https://doi.org/10.1016/j.virol.2012.09.008
Kondo H, Botella L, Suzuki N. 2022. Mycovirus diversity and evolution. Annual Review of Phytopathology. 60: 307-330. https://doi.org/10.1146/annurev-phyto-021021-095744
Kotta-Loizou I, Coutts RHA. 2017. Studies on the virome of the entomopathogenic fungus Beauveria bassiana reveal novel dsRNA elements and mild hypervirulence. PLoS Pathogens. 13: e1006183. https://doi.org/10.1371/journal.ppat.1006183
Krupovic M, Dolja VV, Koonin EV. 2015. Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Biology Direct. 10: 12. https://doi.org/10.1186/s13062-015-0050-0
Kuo C. 2015. Common trends in two facultative endosymbionts of fungal hosts: genome reduction and horizontal gene transfer. PeerJ. 3: e778. https://doi.org/10.7717/peerj.778
Lackner G, Scherlach K, Korfist C, Schmidt T, Hertweck C. 2009. Nonpathogenic bacteria living in a fungal host: genome reduction, host dependence, and horizontal gene transfer. mBio. 1: e00005-10. https://doi.org/10.1128/mBio.00005-10
Lackner G, Moebius N, Hertweck C. 2011. Endofungal bacterium controls its host by an Hrp type III secretion system. The ISME Journal. 5: 252-261. https://doi.org/10.1038/ismej.2010.126
Lackner G, Hertweck C. 2011. Impact of endofungal bacteria on infection biology, food safety, and drug development. PLoS Pathogens. 7: e1002096. https://doi.org/10.1371/journal.ppat.1002096
Liu L, Xie J, Cheng J, Fu Y, Li G, Yi X, Jiang D. 2014. Fungal negative-stranded RNA virus that is related to Bornaviruses and Nyaviruses. Proceedings of the National Academy of Sciences of the United States of America. 111: 12205-12210. https://doi.org/10.1073/pnas.1401786111
Luna E, Bruce TJA, Roberts MR, Flors V, Ton J. 2012. Next-generation systemic acquired resistance. Plant Physiology. 158: 844-853. https://doi.org/10.1104/pp.111.187468
Lupini S, Peña-Bahamonde J, Bonito G, Rodrigues DF. 2022. Effect of endosymbiotic bacteria on fungal resistance toward heavy metals. Frontiers in Microbiology. 13: 822541.
Margulis L, Fester R, (eds.). 1991. Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis. MIT Press, USA.
Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ. 2007. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science. 315: 513-515. https://doi.org/10.1126/science.1136377
Mondo SJ, Lastovetsky OA, Gaspar ML, Schwardt NH, Barber CC, Riley R, Sun H, Grigoriev IV, Pawlowska TE. 2017. Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nature Communications. 8: 1843. https://doi.org/10.1038/s41467-017-02052-8
Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evolution of heritable bacterial symbionts. Annual Review of Genetics. 42: 165-190. https://doi.org/10.1146/annurev.genet.41.110306.130119
Moran NA, Sloan DB. 2015. The hologenome concept: helpful or hollow? PLoS Biology. 13: e1002311. https://doi.org/10.1371/journal.pbio.1002311
Mosse B. 1970. Honey-coloured, sessile Endogone spores: II. Changes in fine structure during spore development. Archiv für Mikrobiologie. 74: 129-145. https://doi.org/10.1007/BF00446901
Myers JM, Gillespie AF, Kuo HC, Patterson WI, Fountain JC, … et al. 2020. A global survey of mycoviruses in fungi. Nature Communications. 11: 1-11. https://doi.org/10.1038/s41467-020-16355-w
Naito M, Morton JB, Pawlowska TE. 2015. Minimal genomes of obligate fungal endobacteria reveal evolutionary adaptation to an intracellular lifestyle. Genome Biology and Evolution. 7: 2403-2417. https://doi.org/10.1093/gbe/evv151
Naito M, Desirò A, González JB, Tao G, Morton JB, Bonfante P, Pawlowska TE. 2017. ‘Candidatus Moeniiplasma glomeromycotorum’, an endobacterium of arbuscular mycorrhizal fungi. International Journal of Systematic and Evolutionary Microbiology. 67: 1177-1184. https://doi.org/10.1099/ijsem.0.001785
Naumann M, Schüßler A, Bonfante P. 2010. The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. The ISME Journal. 4: 862-871.
Ninomiya A, Urayama S, Suo R, … et al. 2020. Mycovirus-induced tenuazonic acid production in a rice blast fungus Magnaporthe oryzae. Frontiers in Microbiology. 11: 1641. https://doi.org/10.3389/fmicb.2020.01641
Nuss DL. 2005. Hypovirulence: mycoviruses at the fungal–plant interface. Nature Reviews Microbiology. 3: 632-642. https://doi.org/10.1038/nrmicro1207
O’Malley MA. 2015. Endosymbiosis and its implications for evolutionary theory. Proceedings of the National Academy of Sciences of the United States of America. 112: 10270-10277. https://doi.org/10.1073/pnas.1421378112
Özkan S, Mohorianu I, Xu P, et al. 2017. Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses. BMC Genomics. 18: 416. https://doi.org/10.1186/s12864-017-3773-6
Pakvaz S, Soltani J. 2016. Endohyphal bacteria from fungal endophytes of the Mediterranean cypress (Cupressus sempervirens) exhibit in vitro bioactivity. Forest Pathology. 46: 569-581. https://doi.org/10.1111/efp.12274
Paoletti M, Saupe SJ. 2009. Fungal incompatibility: evolutionary origin in pathogen defense? BioEssays. 31: 1201-1210. https://doi.org/10.1002/bies.200900073
Partida-Martinez LP. 2024. Fungal holobionts as blueprints for synthetic endosymbiotic systems. PLoS Biology. 22: e3002587. https://doi.org/10.1371/journal.pbio.3002587
Partida-Martinez LP, Hertweck C. 2005. Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature. 437: 884-888. https://doi.org/10.1038/nature03997
Partida-Martinez LP, Hertweck C. 2007. A gene cluster encoding rhizoxin biosynthesis in ‘Burkholderia rhizoxina’, the bacterial endosymbiont of the fungus Rhizopus microsporus. ChemBioChem. 8: 41-45. https://doi.org/10.1002/cbic.200600393
Partida-Martinez LP, Monajembashi S, Greulich KO, Hertweck C. 2007. Endosymbiont-dependent host reproduction maintains bacterial–fungal mutualism. Current Biology. 17: 773-777. https://doi.org/10.1016/j.cub.2007.03.051
Pawlowska TE, Gaspar ML, Lastovetsky OA, Mondo SJ, Real-Ramirez I, … et al. 2018. Biology of fungi and their bacterial endosymbionts. Annual Review of Phytopathology. 56: 289-309. https://doi.org/10.1146/annurev-phyto-080417-050030
Pearson MN, Beever RE, Boine B, Arthur K. 2009. Mycoviruses of filamentous fungi and their relevance to plant pathology. Molecular Plant Pathology. 10: 115-128. https://doi.org/10.1111/j.1364-3703.2008.00500.x
Plessner H. 1928. Die Stufen des Organischen und der Mensch. De Gruyter.
Pradeu T. 2010. What is an organism? An immunological answer. History and Philosophy of the Life Sciences. 32: 247-268.
Pradeu T. 2012. The Limits of the Self: Immunology and Biological Identity. Oxford University Press, UK.
Pradeu T. 2016. The many faces of biological individuality. Biology & Philosophy. 31: 761-773.
Pradeu T. 2019. Philosophy of biology: immunology and individuality. eLife. 8: e47384. https://doi.org/10.7554/eLife.47384
Pradeu T, Carosella ED. 2006. The self model and the conception of biological identity in immunology. Biology & Philosophy. 21: 235-252. https://doi.org/10.1007/s10539-005-0436-y
Rayner ADM. 1995. Fungal holomorphs and the concept of the individual. Mycological Research. 99: 1131-1140. https://doi.org/10.1016/S0953-7562(09)80781-3
Rigling D, Prospero S. 2018. Cryphonectria parasitica and chestnut blight: a global perspective. Annual Review of Phytopathology. 56: 451-472. https://doi.org/10.1146/annurev-phyto-080417-050053
Roossinck MJ. 2011. The good viruses: viral mutualistic symbioses. Nature Reviews Microbiology. 9: 99-108. https://doi.org/10.1038/nrmicro2501
Salvioli A, Ghignone S, Novero M, Navazio L, Bagnaresi P, et al. 2016. Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential. The ISME Journal. 10: 130-144. https://doi.org/10.1038/ismej.2015.91
Sánchez-Cañizares C, Jorrin B, Poole PS, Tkacs A. 2017. Understanding the holobiont: the interdependence of plants and their microbiome. Current Opinion in Microbiology. 38: 188-196. https://doi.org/10.1016/j.mib.2017.05.004
Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, et al. 2018. Whole genome analyses suggest that Burkholderia sensu lato contains two additional novel genera (Mycetohabitans gen. nov. and Trinickia gen. nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae. Genes. 9: 389. https://doi.org/10.3390/genes9080389
Scherlach K, Busch B, Lackner G, Paszkowski U, Hertweck C. 2012. Symbiotic cooperation in the biosynthesis of a phytotoxin. Angewandte Chemie International Edition. 51: 9615-9618. https://doi.org/10.1002/anie.201204338
Schmitt MJ, Breinig F. 2002. The viral killer system in yeast: from molecular biology to application. FEMS Microbiology Reviews. 26: 257-276. https://doi.org/10.1111/j.1574-6976.2002.tb00614.x
Schmitt MJ, Breinig F. 2006. Yeast viral killer toxins: lethality and self-protection. Nature Reviews Microbiology. 4: 212-221. https://doi.org/10.1038/nrmicro1347
Schneider T. 2021. The holobiont self: understanding immunity in context. History and Philosophy of the Life Sciences. 43: 99. https://doi.org/10.1007/s40656-021-00451-1
Shaffer JP, Sarmiento C, Zalamea P-C, Gallery RE, Davis AS, Baltrus DA, Arnold AE. 2016. Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves. Frontiers in Ecology and Evolution. 4: 116. https://doi.org/10.3389/fevo.2016.00116
Shaffer JP, U’Ren JM, Gallery RE, Baltrus DA, Arnold AE. 2017. An endohyphal bacterium (Chitinophaga, Bacteroidetes) alters carbon source use by Fusarium keratoplasticum (F. solani species complex, Nectriaceae). Frontiers in Microbiology. 8: 350. https://doi.org/10.3389/fmicb.2017.00350
Sharmin D, Guo Y, Nishizawa T, Ohshima S, Sato Y, … et al. 2018. Comparative genomic insights into endofungal lifestyles of two bacterial endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica. Microbes and Environments. 33: 66-76. https://doi.org/10.1264/jsme2.ME17153
Sharma M, Schmid M, Rothballer M, Hause G, Zuccaro A, … et al. 2008. Detection and identification of bacteria intimately associated with fungi of the order Sebacinales. Cellular Microbiology. 10: 2235-2246.
Skillings D. 2016. Holobionts and the ecology of organisms: multi-species communities or integrated individuals? Biology & Philosophy. 31: 875-892. https://doi.org/10.1007/s10539-016-9547-x
Soltani J. 2017. Endophytism in Cupressoideae (Coniferae): a model in endophyte biology and biotechnology. In: Maheshwari D, editor. Endophytes: Biology and Biotechnology. Sustainable Development and Biodiversity, vol. 15. Springer, Cham, pp. 127-143.
Stencel A, Proszewska AM. 2018. How research on microbiomes is changing biology: a discussion on the concept of the organism. Foundations of Science. 23: 603-620. https://doi.org/10.1007/s10699-017-9543-x
Suárez J. 2020. The stability of traits conception of the hologenome: an evolutionary account of holobiont individuality. History and Philosophy of the Life Sciences. 42: 11. https://doi.org/10.1007/s40656-020-00305-2
Suárez J, Stencel A. 2020. A part-dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously. Biological Reviews. 95: 1308-1324. https://doi.org/10.1111/brv.12612
Toepfer G. 2011. Individuum. In: Historisches Wörterbuch der Biologie. J.B. Metzler, Germany, pp. 159–180.
Torres-Cortés G, Ghignone S, Bonfante P, Schüßler A. 2015. Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: transkingdom gene transfer in an ancient mycoplasma–fungus association. Proceedings of the National Academy of Sciences of the United States of America. 112: 7785-7790. https://doi.org/10.1073/pnas.1501540112
Triviño V, Suárez J. 2020. Holobionts: ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systems. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. 84: 101323. https://doi.org/10.1016/j.shpsc.2020.101323
Uehling J, Deveau A, Paoletti M. 2017. Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems. PLoS Pathogens. 13: e1006578. https://doi.org/10.1371/journal.ppat.1006578
Vainio EJ, Chiba S, Ghabrial SA, et al. 2018a. ICTV Virus Taxonomy Profile: Partitiviridae. Journal of General Virology. 99: 17-18. https://doi.org/10.1099/jgv.0.000985
Vainio EJ, Jurvansuu J, Hyder R, Kashif M, Piri T, et al. 2018b. Heterobasidion partitivirus 13 mediates severe growth debilitation and major alterations in the gene expression of a fungal forest pathogen. Journal of Virology. 92: e01744-17. https://doi.org/10.1128/JVI.01744-17
Valadez-Cano C, Olivares-Hernández R, Espino-Vázquez AN, Partida-Martínez LP. 2024. Genome-scale model of Rhizopus microsporus: metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts. Environmental Microbiology. 26: e16551. https://doi.org/10.1111/1462-2920.16551
Vandenkoornhuyse P, Quince C, Young JPW, Poole PS. 2015. The importance of the microbiome of the plant holobiont. New Phytologist. 206: 1196-1206. https://doi.org/10.1111/nph.13312
Veigl SJ. 2022a. Adaptive immunity or evolutionary adaptation? Transgenerational immune systems at the crossroads. Biology & Philosophy. 37: 41. https://doi.org/10.1007/s10539-022-09869-8
Veigl SJ. 2022b. Do heritable immune responses extend physiological individuality? History and Philosophy of the Life Sciences. 44: 67. https://doi.org/10.1007/s40656-022-00549-0
Wojciechowski JW, Tekoglu E, Gasior-Glogowska M, Coustou V, Szulc N, … et al. 2022. Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. PLoS Computational Biology. 18: e1010787. https://doi.org/10.1371/journal.pcbi.1010787
Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, … et al. 2010. A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proceedings of the National Academy of Sciences of the United States of America. 107: 8387-8392. https://doi.org/10.1073/pnas.0914503107
Yu A, Lepère G, Jay F, Wang J, Bapaume L, … et al. 2013. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proceedings of the National Academy of Sciences of the United States of America. 110: 2389-2394. https://doi.org/10.1073/pnas.1215404110
Zhang H, Xie J, Fu Y, Cheng J, Qu Z, et al. 2020. A 2-kb mycovirus converts a pathogenic fungus into a beneficial endophyte for Brassica protection and yield enhancement. Molecular Plant. 13: 1420-1433. https://doi.org/10.1016/j.molp.2020.07.022
Zoll J, Verweij PE, Melchers WJG. 2018. Discovery and characterization of novel Aspergillus fumigatus mycoviruses. PLoS ONE. 13: e0200511. https://doi.org/10.1371/journal.pone.0200511