Table 1.

Annotated list of selected important plants and the endophytes they harbor. Note: * = see article, ** = see table in article, N/A; not applicable.

Endophyte	Host Plant	Infection Location	Research Topic	Notable Findings	Reference
Numerous **	Azadirachta indica	Numerous **	Discusses the antimicrobial, antioxidant and pathogenicity target compounds produced by the endophytic fungi.	N/A	[44]
Numerous **	Dendrobium moniliforme	Roots	Identifying the endophytic fungi and their role in plant growth and development.	Nine fungi isolated; unidentified Fusarium sp. was dominant. The presence of phenolic compounds suggests their contribution to antimicrobial and antioxidant properties for their host plant. Colletotrichum alatae showed highest concentration of IAA and as a fungal elicitor it resulted in the highest total chlorophyll content.	[234]
Numerous *	Dendrobium loddigesii	Roots and seeds	The diversity of endophytic fungi was explored and cultures were tested for antimicrobial activity.	Forty-eight isolates identified to 18 genera including Fusarium and Acremonium. Antimicrobial activity was tested on 17 isolates belonging to 9 genera and again Fusarium was dominant.	[235]
Many Fusarium spp. **	Orchid spp. **		Fusarium-orchid interactions and the challenges when dealing with the pathogen.	There is evidence that Fusarium can induce host resistance against many pathogens in crops such as banana, tomato, as well as orchid.	[236]
Trichoderma spp.	Numerous **		Overview of Trichoderma spp. as symbionts.	Many Trichoderma spp., including T. virens, T. atroviride and T. harzianum can induce localized and systemic host plant resistance to a variety of plant pathogens. Induced resistance increases the expression of defence-related genes in the plant, similar to systematic acquired resistance. Generally, this is short term, except for in one case (T. asperellum and cucumber) where a longer response was shown, and elements were similar to rhizobacteria-induced systemic resistance.	[237]
Clavicipitaceae and others **	Grasses **		Overview of endophytic fungi in grasses.	Protection against plant pathogens is a possible benefit as seen in endophyte infected tall fescue being resistant to seedling blight (a disease caused by Rhizoctonia). Infected plants are also more resistant to oat crown rust (Puccinia coronata) compared to uninfected plants. Tall fescue was more resistant to barley yellow dwarf virus, with uninfected plants showing twice the frequency of disease. This shows deterrence of aphid vectors of the virus. Panicum agrostoides (a wetland grass) had less leaf blight (Alternaria triticina) infection when infected with Balansia henningsiana. Epichlöe- infected timothy grass was resistant to purple eyespot disease (Cladosporium phlei)	[238]
Trichoderma reesei, T. atroviride and T. virens.	N/A	N/A	Identifying gene clusters associated with secondary metabolism in Trichoderma spp.	One new NRPS and six new PKS clusters were found in the Trichoderma reesei genome. T. atroviride had four NRPS and eight PKS clusters while T. virens had four NRPS and 8 PKS clusters.	[239]
Trichoderma spp. *	N/A	N/A	Discussing the bioactivity, regulation and biological roles of secondary metabolites produced by Trichoderma spp.		[240]
Trichoderma atroviride, T. reesei and T. virens	N/A	N/A	Looking at the mechanisms of mycoparasitism by comparing the transcriptional responses of Trichoderma spp. with different lifestyles against Rhizoctonia solani.	Trichoderma atroviride and T. virens expressed different genes for antagonism when confronted with R. solani. T. virens up-regulated genes for gliotoxin biosynthesis, poisoning R. solani, while T. atroviride followed a strategy involving antibiosis and hydrolytic enzymes. T. reesei appeared to mainly express genes for nutrient acquisition suggesting an attempt at competition instead of mycoparasitism.	[241]
Trichoderma atroviride, T. reesei and T. virens	N/A	N/A	Comparing genomes of different Trichoderma spp.	Genome analysis and comparison of Trichoderma atroviride, T. virens and T. reesei. Phylogenetic analysis showed that T. reesei and T. virens derived from T. atroviride, suggesting mycoparasitism-specific genes arose in a common Trichoderma ancestor but were lost in T. reesei.	[242]
Fusarium equiseti, Pochonia chlamydosporia	Barley	Roots	Evaluating the root population dynamics of fungi under non-axenic conditions. Fungi were examined for their presence, effect on plant growth and response to Gaeumannomyces graminis var. tritici (causal agent of take-all disease).	Both fungi can protect host plants from G. graminis var. tritici in laboratory conditions. Clear suppressive effect on the pathogen could not be detected but F. equiseti isolates reduced the mean root lesion length. Root colonization by P. chlamydosporia promoted plant growth.	[128]
Many including Cryptosporiopsis cf. quercina, Colletotrichum spp.	N/A	N/A	Brief review of biological activities and applications of endophytes.	Suggest that the nutritional status and fitness of the host plant (which are enhanced by the endophytes) as well as their ability to tolerate abiotic stress are key factors in the plants ability to resist disease. Cryptosporiopsis cf. quercina and Colletotrichum spp. have been shown to be effective against plant pathogens including Rhizoctonia cerealis, Phytophthora capsici, Pyricularia oryzae and Gaeumannomyces graminis. Endophytes demonstrate potential for phytoremediation.	[51]
97 isolates **	12 genera of orchids	Leaves, stems, flowers	Analysing the antifungal, antioxidant, chemical composition and antimutagenicity properties of compounds produced by fungal endophytes.	Thirteen endophyte isolates showed antifungal activity against Fusarium sp., Colletotrichum sp. and Curvularia sp. Fusarium oxysporum strain showed the highest antifungal activity and was selected for further study including characterizing secondary metabolites.	[243]
Numerous **	Stanhopea tigrine	Leaf, pseudobulb, root and flower	Examining the microbiome of Stanhopea tigrine.	Used morphological and molecular characteristics for identification and found 63 genera, with Trichoderma, Penicillium, Fusarium and Aspergillus as the dominant genera. 21 fungal isolates produced gibberellins.	[244]
Numerous **	Cephalanthera longibracteata	Roots	The goal was to determine if the fungal communities were preferentially correlated with the sites.	Thirty species of fungi were identified, endophytic community composition was affected by site.	[245]
Numerous **	Dendrobium nobile, Dendrobium chrysanthum	Mature roots and protocorms	Analyzing diversity of fungal symbionts of threatened plant species to improve conservation and commercial production.	A total of 127 fungi were isolated: Xylaria, Fusarium, Trichoderma, Colletotrichum, Pestalotiopsis, and Diaporthe were dominant.	[246]
Numerous **	Cyrtochilum myanthum, Scaphyglottis punctulata, Stelis superbiens	Roots	Analyzing the diversity of fungal root associates for conservation purposes.	A total of 115 fungal isolates were identified corresponding to 49 OTUs. Ascomycetes were dominant, with Trichoderma sp. as the most frequent taxon.	[247]
Numerous **	Pomatocalpa decipiens	Leaf segments and root	Obtaining potential phosphate solubilising strains from endophytic mycoflora.	A total of 928 endophytic phosphate solubilising fungal isolates were obtained from the leaf segments. Twenty endophytic phosphate solubilising fungi were isolated from the root samples.	[248]
Numerous including saprotrophic basidiomycetes *	Mycoheterotrophy orchids		Investigating how Mycoheterotrophic orchids receive their carbon in regions where ectomycorrhizal fungi, are not present.	Different fungi were found and identified. Research suggests that temperature and moisture in rainforests may favour sufficient saprotrophic activity to support development of mycoheterotrophy.	[249]
Numerous	N/A	N/A	What makes a fungus parasitic or endophytic and how plants avoid exploitation by parasites but benefit from mutualistic endophytes.	If the symbiosis is not equal, disease symptoms appear on the host plant and/or the fungus is expelled by host defence reactions and no longer receives benefits.	[48]
Numerous *	Heisteria concinna, Ouratea lucens	Leaves	Endophyte colonization patterns, richness, host preference and spatial variation were examined.	A total of 347 taxa were collected. Host preference and spatial heterogeneity were suggested by the data.	[46]
Numerous *	Sasa borealis, Potentilla fragarioides, Viola mandshurica	Leaves	Looking at the effects of foliar endophytic fungi and AMF on community structure in experimental microcosms.	Endophytic fungi were isolated and identified to species level. Results of this study show that AMF affect plant productivity and plant community structure.	[250]
Numerous *	Camptotheca cuminata, Gastrodia elata, Pinellia ternate	Leaves, twigs, root tissues, flower tissues	Looking at potential sources for biomedical compounds.	A total of 193 endophytes were isolated and 42 taxa were identified and tested for different bioactive compounds. Analagous bioactive compounds were produced in host endophyte cultures: three taxa isolated from C. cuminata produced high yields of camptothecin, Colletotrichum gloeosporioides from C. cuminata produced 10-hydroxycamptothecin, three taxa isolated from G. elata produced gastrodin, three taxa from P. ternata produced low amounts of ephedrine hydrochloride.	[251]
Neotyphodium coenophialum	Festuca arundinacea	Root	Greenhouse experiment conducted to identify effects of endophyte strains on copper acquisition by tall fescue varieties.	Extracellular root exudates of infected plants had a higher copper binding activity.	[252]
Numerous *	Gymnadenia conopsea	Root	Looking at the different factors that determine the spatial structure and presence of fungi associated with orchid roots.	The investigation revealed a large diversity and taxonomical range of fungi. This diversity is likely responsible for the orchids ability to live in such diverse habitats.	[253]
Numerous *	Laelia autumnalis, L. speciosa, Euchile citrina, P. squalida	Root	Looking at the community composition and diversity of fungi associated with orchids.	A total of 71 isolates were obtained, representing 20 genera. Euchile citrina showed the lowest endophytic diversity implying that the plant is specific when choosing endophytes. L. speciosa and P. squalida were generalists.	[254]
Numerous including Epulorhiza spp. and Tulasnella spp. *	Paphiopedilum, Cymbidium, Dendrobium.	Root	Looking at the diversity of fungi in orchids in understudied sites.	Twenty-seven fungal isolates were identified including Epulorhiza repens (the most common fungi found in roots from all three genera) and Epulorhiza calendulina (only found in Paphiopedilum species). Four new Tulasnella spp. were isolated and described.	[255]
Numerous *	Dendrobium sinense	Roots	Analyzing whether the endophytes were preferentially correlated with the host tree species.	A total of 56 fungal species were identified and results show that species richness and diversity were influenced by host tree species. D. sinense roots had the highest diversity.	[256]
Numerous **	Aerides odorata, Arundina graminifolia, Cymbidium aloifolium, Cymbidium munronianum, Dendrobium fimbriatum, Dendrobium moschatum, Eria flava, Paphiopedilum fairrieanum, Pholidota imbricata, Rhynchostylis retusa, Vanilla planifolia	Leaf and root tissues	Analyzing endophyte assemblages.	Xylaria spp. were found in both the leaves and the roots. The diversity of endophytes was higher in the leaves and tissue specificity was shown.	[41]
Pestalotiopsis versicolor and P. neglecta	Taxus cuspidata	Healthy leaves and bark	Investigating alternative sources of taxol.	The fungi screened produced taxol and showed a strong cytotoxic activity in the in vitro culture of tested human cancer cells.	[257]