The need to study the holobiome for gainful uses of endophytes

Agler, 2016, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS Biol., 14, 10.1371/journal.pbio.1002352 Arendt, 2016, Isolation of endohyphal bacteria from foliar Ascomycota and in vitro establishment of their symbiotic associations, Appl. Environ. Microbiol., 82, 2943, 10.1128/AEM.00452-16 Banerjee, 2018, Keystone taxa as drivers of microbiome structure and functioning, Nat. Rev. Microbiol., 16, 567, 10.1038/s41579-018-0024-1 Bilal, 2018, Endophytic microbial consortia of phytohormones-producing fungus Paecilomyces formosus LHL10 and bacteria Sphingomonas sp. LK11 to Glycine max L. regulates physio-hormonal changes to attenuate aluminum and zinc stresses, Front. Plant Sci., 9, 1273, 10.3389/fpls.2018.01273 Brader, 2017, Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes, Annu. Rev. Phytopathol., 55, 61, 10.1146/annurev-phyto-080516-035641 Busby, 2016, Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity, New Phytol., 209, 1681, 10.1111/nph.13742 Compant, 2019, A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application, J. Adv. Res., 19, 29, 10.1016/j.jare.2019.03.004 Cord-Landwehr, 2016, A chitin deacetylase from the endophytic fungus Pestalotiopsis sp. efficiently inactivates the elicitor activity of chitin oligomers in rice cells, Sci. Rep., 6, 38018, 10.1038/srep38018 da Costa Stuart, 2018, Effect of agrochemicals on endophytic fungi community associated with crops of organic and conventional soybean (Glycine max L. Merril), Agric. Nat. Resour., 52, 388 Delmas, 2019, Analysing ecological networks of species interactions, Biol. Rev., 94, 16, 10.1111/brv.12433 Devarajan, 2006, Evidence for the role of phytophagous insects in dispersal of non-grass fungal endophytes, Fungal Divers., 23, 111 Duhamel, 2018, Keystone mutualists can facilitate transition between alternative ecosystem states in the soil, bioRxiv Furtado, 2019, Bacterial and fungal endophytic microbiomes of Salicornia europaea, Appl. Environ. Microbiol., 85, 10.1128/AEM.00305-19 Gilbert, 2007, Phylogenetic signal in plant pathogen-host range, Proc. Natl. Acad. Sci. U.S.A., 104, 4979, 10.1073/pnas.0607968104 Girivasan, 2004, Intact leaves as substrate for fungi: distribution of endophytes and phylloplane fungi in rattan palms, Czech Mycol., 56, 33, 10.33585/cmy.56103 Gond, 2015, Endophytic Bacillus spp. produce antifungal lipopeptides and induce host defence gene expression in maize, Microbiol. Res., 172, 79, 10.1016/j.micres.2014.11.004 Govinda Rajulu, 2014, Several fungi from fire-prone forests of southern India can utilize furaldehydes, Mycol. Prog., 13, 1049 Griffin, 2019, Tree diversity reduces fungal endophyte richness and diversity in a large-scale temperate forest experiment, Diversity, 11, 234, 10.3390/d11120234 Griffin, 2019, Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: Is disturbance an alternative explanation?, J. Ecol., 107, 1876, 10.1111/1365-2745.13145 Harrison, 2019, A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression, bioRxiv Hartley, 2015, Infection by a foliar endophyte elicits novel arabidopside-based plant defence reactions in its host, Cirsium arvense, New Phytol., 205, 816, 10.1111/nph.13067 Hashizume, 2010, Effects of summer temperature on fungal endophyte assemblages in Japanese beech (Fagus crenata) leaves in pure beech stands, Botany, 88, 266, 10.1139/B09-114 Hassani, 2018, Microbial interactions within the plant holobiont, Microbiome, 6, 58, 10.1186/s40168-018-0445-0 Herren, 2018, Keystone taxa predict compositional change in microbial communities, Environ. Microbiol., 20, 2207, 10.1111/1462-2920.14257 Hoffman, 2010, Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes, Appl. Environ. Microbiol., 76, 4063, 10.1128/AEM.02928-09 Huang, 2018, Endophytic fungi specifically introduce novel metabolites into grape flesh cells in vitro, PLoS One, 13 Huang, 2020, The construction of CRISPR-Cas9 system for endophytic Phomopsis liquidambaris and its PmkkA-deficient mutant revealing the effect on rice, Fungal Genet. Biol., 136, 103301, 10.1016/j.fgb.2019.103301 Jones, 2019, Plant host-associated mechanisms for microbial selection, Front. Plant Sci., 10, 862, 10.3389/fpls.2019.00862 Khan, 2017, Culturable endophytic fungal diversity in the cadmium hyperaccumulator Solanum nigrum L. and their role in enhancing phytoremediation, Environ. Exp. Bot., 135, 126, 10.1016/j.envexpbot.2016.03.005 Khare, 2018, Multifaceted interactions between endophytes and plant: developments and prospects, Front. Microbiol., 9, 2732, 10.3389/fmicb.2018.02732 Kim, 2020, Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed, Microbiome, 8, 20, 10.1186/s40168-020-00805-0 Krings, 2009, A Late Pennsylvanian fungal leaf endophyte from Grand-Croix, France, Rev. Palaeobot. Palynol., 156, 449, 10.1016/j.revpalbo.2009.04.010 Kryuchkova, 2014, Isolation and characterization of a glyphosate-degrading rhizosphere strain, Enterobacter cloacae K7, Microbiol. Res., 169, 99, 10.1016/j.micres.2013.03.002 Kumaresan, 2002, Ecology of mangrove endophytes, 145 Lee, 2019, Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats, Ecology, 100, e02790, 10.1002/ecy.2790 Li, 2012, Diversity and cold adaptation of endophytic fungi from five dominant plant species collected from the Baima Snow Mountain, southwest China, Fungal Divers., 54, 79, 10.1007/s13225-012-0153-1 Li, 2019, Effects of dark septate endophytes on the performance of Hedysarum scoparium under water deficit stress, Front. Plant Sci., 10, 903, 10.3389/fpls.2019.00903 Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237 Lv, 2019, Strengthening insights in microbial ecological networks from theory to applications, mSystems, 4, 10.1128/mSystems.00124-19 Mejía, 2014, Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree, Front. Microbiol., 5, 479 Miller, 2017, Plant immunity: unravelling the complexity of plant responses to biotic stresses, Ann. Bot., 119, 681, 10.1093/aob/mcw284 Mohandoss, 2009, Effect of fungicide treatment on foliar fungal endophyte diversity in mango, Sydowia, 61, 11 Murphy, 2018, From concept to commerce: Developing a successful fungal endophyte inoculant for agricultural crops, J. Fungi (Basel), 4 Neal, 2012, Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere, PLoS One, 7, e35498, 10.1371/journal.pone.0035498 Niu, 2017, Simplified and representative bacterial community of maize roots, Proc. Natl. Acad. Sci. U.S.A., 114, E2450, 10.1073/pnas.1616148114 Oberholster, 2018, Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation, Sci. Total Environ., 624, 530, 10.1016/j.scitotenv.2017.12.170 Pakvaz, 2016, Endohyphal bacteria from fungal endophytes of the Mediterranean cypress (Cupressus sempervirens) exhibit in vitro bioactivity, For. Pathol., 46, 569, 10.1111/efp.12274 Photita, 2004, Are some endophytes of Musa acuminata latent pathogens?, Fungal Divers., 16, 131 Qin, 2018, Effects of an endophytic fungus Umbelopsis dimorpha on the secondary metabolites of host–plant Kadsura angustifolia, Front. Microbiol., 9, 2845, 10.3389/fmicb.2018.02845 Raman, 2017, Fungus–plant interaction influences plant-feeding insects, Fungal Ecol., 29, 123, 10.1016/j.funeco.2017.06.004 Ray, 2019, Endophytic consortium with diverse gene-regulating capabilities of benzylisoquinoline alkaloids biosynthetic pathway can enhance endogenous morphine biosynthesis in Papaver somniferum, Front. Microbiol., 10, 925, 10.3389/fmicb.2019.00925 Rho, 2018, Do endophytes promote growth of host plants under stress? A meta-analysis on plant stress mitigation by endophytes, Microb. Ecol., 75, 407, 10.1007/s00248-017-1054-3 Rodriguez, 2008, More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis, J. Exp. Bot., 59, 1109, 10.1093/jxb/erm342 Rodriguez, 2009, Fungal endophytes: diversity and functional roles, New Phytol., 182, 314, 10.1111/j.1469-8137.2009.02773.x Rodriguez, 2019, Systems biology of plant microbiome interactions, Mol. Plant, 12, 804, 10.1016/j.molp.2019.05.006 Rúa, 2014, Climate drivers, host identity and fungal endophyte infection determine virus prevalence in a grassland ecosystem, J. Ecol., 102, 690, 10.1111/1365-2745.12238 Sanchez-Azofeifa, 2012, Relationships between endophyte diversity and leaf optical properties, Trees, 26, 291, 10.1007/s00468-011-0591-5 Schroeder, 2019, Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens, J. Ecol., 107, 1557, 10.1111/1365-2745.13166 Schulz, 2015, Fungal endophytes are involved in multiple balanced antagonisms, Curr. Sci., 109, 39 Seghers, 2004, Impact of agricultural practices on the Zea mays L. endophytic community, Appl. Environ. Microbiol., 70, 1475, 10.1128/AEM.70.3.1475-1482.2004 Shaffer, 2017, An endohyphal bacterium (Chitinophaga, Bacteroidetes) alters carbon source use by Fusarium keratoplasticum (F. solani species complex, Nectriaceae), Front. Microbiol., 8, 350, 10.3389/fmicb.2017.00350 Shefferson, 2019, Does evolutionary history determine specificity in broad ecological interactions?, J. Ecol., 107, 1582, 10.1111/1365-2745.13170 Shen, 2017, The early response during the interaction of fungal phytopathogen and host plant, Open Biol., 7, 170057, 10.1098/rsob.170057 Soliman, 2013, A fungal endophyte induces transcription of genes encoding a redundant fungicide pathway in its host plant, BMC Plant Biol., 13, 93, 10.1186/1471-2229-13-93 Stuart, 2010, Culturable endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane and its non-transgenic isolines, Arch. Microbiol., 192, 307, 10.1007/s00203-010-0557-9 Suryanarayanan, 2013, Endophyte research: going beyond isolation and metabolite documentation, Fungal Ecol., 6, 561, 10.1016/j.funeco.2013.09.007 Suryanarayanan, 2004, Temporal variation in endophyte assemblages of Plumeria rubra leaves, Fungal Divers., 15, 197 Suryanarayanan, 2006, Incidence of Leptosphaerulina crassiasca in symptomless leaves of peanut in southern India, J. Basic Microbiol., 46, 305, 10.1002/jobm.200510126 Suryanarayanan, 2011, Endophytic fungal communities in woody perennials of three tropical forest types of the Western Ghats, southern India, Biodivers. Conserv., 20, 913, 10.1007/s10531-011-0004-5 Suryanarayanan, 2011, A comparison of endophyte assemblages in transgenic and non-transgenic cotton plant tissues, Curr. Sci., 101, 1472 Suryanarayanan, 2011, Agni's fungi: heat-resistant spores from the Western Ghats, southern India, Fungal Biol., 115, 833, 10.1016/j.funbio.2011.06.011 Suryanarayanan, 2018, The host range of multi-host endophytic fungi, Curr. Sci., 115, 1963, 10.18520/cs/v115/i10/1963-1969 Suryanarayanan, 2018, Biological control through fungal endophytes: gaps in knowledge hindering success, Curr. Biotechnol., 7, 185, 10.2174/2211550105666160504130322 Thirumalai, 2013, Mycotoxins of endophytic Fusarium mangiferae and F. pallidoroseum from betel leaves (Piper betle L.) Tian, 2014, The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit, Phytochemistry, 108, 95, 10.1016/j.phytochem.2014.09.021 Toju, 2014, Assembly of complex plant–fungus networks, Nat. Commun., 5, 5273, 10.1038/ncomms6273 Trivedi, 2017, Keystone microbial taxa regulate the invasion of a fungal pathogen in agroecosystems, Soil Biol. Biochem., 111, 10, 10.1016/j.soilbio.2017.03.013 Vandenkoornhuyse, 2015, The importance of the microbiome of the plant holobiont, New Phytol., 206, 1196, 10.1111/nph.13312 Vega, 2018, The use of fungal entomopathogens as endophytes in biological control: a review, Mycologia, 110, 4, 10.1080/00275514.2017.1418578 Voges, 2019, Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome, Proc. Natl. Acad. Sci. U.S.A., 116, 12558, 10.1073/pnas.1820691116 Webb, 2008, Phylocom: software for the analysis of phylogenetic community structure and trait evolution, Bioinformatics, 24, 2098, 10.1093/bioinformatics/btn358 Wheeler, 2019, From pathogen to endophyte: an endophytic population of Verticillium dahliae evolved from a sympatric pathogenic population, New Phytol., 222, 497, 10.1111/nph.15567 Whitaker, 2018, Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass), Ecology, 99, 2703, 10.1002/ecy.2543 White, 2018, Rhizophagy cycle: An oxidative process in plants for nutrient extraction from symbiotic microbes, Microorganisms, 6, 95, 10.3390/microorganisms6030095 White, 2019, Review: Endophytic microbes and their potential applications in crop management, Pest Manag. Sci., 75, 2558, 10.1002/ps.5527 Woolhouse, 2001, Population biology of multihost pathogens, Science, 292, 1109, 10.1126/science.1059026 Yuan, 2019, Comparative transcriptomics and proteomics of Atractylodes lancea in response to endophytic fungus Gilmaniella sp. AL12 reveals regulation in plant metabolism, Front. Microbiol., 10, 1208, 10.3389/fmicb.2019.01208 Zimmerman, 2012, Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape, Proc. Natl. Acad. Sci. U.S.A., 109, 13022, 10.1073/pnas.1209872109 Zomorrodi, 2016, Synthetic ecology of microbes: Mathematical models and applications, J. Mol. Biol., 428, 837, 10.1016/j.jmb.2015.10.019