A Worldwide List of Endophytic Fungi with Notes on Ecology and Diversity

Mycosphere 10(1): 798–1079 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/19 A worldwide list of endophytic fungi with notes on ecology and diversity Rashmi M, Kushveer JS and Sarma VV* Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, Puducherry, India Rashmi M, Kushveer JS, Sarma VV 2019 – A worldwide list of endophytic fungi with notes on ecology and diversity. Mycosphere 10(1), 798–1079, Doi 10.5943/mycosphere/10/1/19 Abstract Endophytic fungi are symptomless internal inhabits of plant tissues. They are implicated in the production of antibiotic and other compounds of therapeutic importance. Ecologically they provide several benefits to plants, including protection from plant pathogens. There have been numerous studies on the biodiversity and ecology of endophytic fungi. Some taxa dominate and occur frequently when compared to others due to adaptations or capabilities to produce different primary and secondary metabolites. It is therefore of interest to examine different fungal species and major taxonomic groups to which these fungi belong for bioactive compound production. In the present paper a list of endophytes based on the available literature is reported. More than 800 genera have been reported worldwide. Dominant genera are Alternaria, Aspergillus, Colletotrichum, Fusarium, Penicillium, and Phoma. Most endophyte studies have been on angiosperms followed by gymnosperms. Among the different substrates, leaf endophytes have been studied and analyzed in more detail when compared to other parts. Most investigations are from Asian countries such as China, India, European countries such as Germany, Spain and the UK in addition to major contributions from Brazil and the USA. Key Words – Checklist – Continents – Diversity – Foliar endophytes – Geographical distribution – Host distribution – Substrate preference Introduction Definition The term ‘endophyte’ was introduced by Bary in 1866 (De Bary 1886), as any organism inhabiting a living tissue. There are many definitions that have been provided for endophytic fungi and one of the most widely accepted has been that of Petrini (1991), who also coined the term “endophytes”, as “All organisms inhabiting plant organs at some time in their life that can colonize internal plant tissues without causing apparent harm to the host.” Bacon & White (2000), define endophytes as “microbes that indwell living, internal tissues of host plants without causing any immediate, overt negative effects.” Hyde & Soytong (2008) reviewed various definitions of endophytes proposed by several researchers. Ecology of endophytes Recovery of endophytes from hosts of divergent ecological habitats such as xeric to arctic, Submitted 22 March 2019, Accepted 1 November 2019, Published 30 November 2019 Corresponding Author: V. Venkateswara Sarma – e–mail – [email protected] 798 temperate to tropical forests, grasslands to croplands and savannahs, have been discussed. A range of different hosts has been examined for endophytic fungi starting from mosses to ferns, non– vascular to vascular plants, seedless to flowering plants (Arnold 2008, Rodriguez et al. 2009). The universal presence of endophytes in flora of diverse ecosystems is a well–established fact. For example, algae (Hawksworth 1988), mosses (Schulz et al. 1993), pteridophytes (equisetopsids, ferns, lycophytes) (Fisher 1996), conifers (Bernstein & Carroll 1977, Legault et al. 1989) and angiosperms (monocots and dicots), including palms (Rodrigues 1996, Fröhlich & Hyde 1999), grasses (Clay 1989), and various dicotyledonous shrubs (Petrini et al. 1982) and trees (Faeth & Hammon 1997). The tropical host plants have also been investigated for endophytic fungal communities but the temperate host plants remain the most explored ones (Verma et al. 2017). Importance of endophytic fungi The role of endophytes has been much debated with grass–inhabiting category (Clavicipitales), which have been better understood than non–grass endophytes. Some of the roles of non–grass endophytes that have been attributed to them as mutualists include decreased herbivory, increased drought resistance, increased disease resistance and enhancement of plant growth (Hyde & Soytong 2008). Many endophytes in leaves and woody tissues are considered as host, host genus or host family-specific (Arnold 2007) and such a specificity seems to depend on factors such as initial endophyte colonization and/or substances within leaves and wood (Paulus et al. 2006, Arnold 2007, Hyde 2007, Hyde & Soytong 2008). The fate of endophytes has been shown to turn into either saprophytes or latent pathogens, and this depends largely upon different environmental factors (e.g. Promputtha et al 2007, Jeewon et al 2017, 2018). Screening of endophytes for novel compounds led to the discovery of thousands of metabolites with different kinds of biological activities. The trigger for a large–scale interest to screen endophytic fungi came from the fact that they could mimic the structure and function of host compounds (Strobel 2002). The reason for a higher number of bioactive compounds found in endophytes is that the diversity of endophytes is high and endophytes are relatively fast growing on artificial media (Strobel 2002, Gouda et al. 2016, Nair & Padmavathy 2014). By producing these compounds endophytic fungi ensure plants a better growth and sustainability within the hosts and protect them from herbivory and harsh environmental conditions, thus exhibiting mutualistic relationships (Dudeja et al. 2012, Das & Varma 2009, Gouda et al. 2016, Nair & Padmavathy 2014). Methods employed to study endophytic fungi Due to their cryptic presence within the healthy host tissues, it is difficult to visualize their symptoms or reproductive structures. Their hyphae can rarely be observed inside, and lack any identifying characteristics (Arnold 2008). The methods to study and isolate endophytes, particularly surface sterilization, influence the diversity of endophytic fungi. Thick leaves require more exposure to surface sterilizing agents and thin leaves less exposure. Any flaw in surface sterilization allows propping of an unduly large number of species belonging to Aspergillus, Cladosporium, Penicillium (Hyde & Soytong 2008). Sample size and/or sampling effort can also greatly influence species richness because small sample sizes may underestimate the differences in endophytic mycocommunities among different sites (Connolly 2005, Mazaris et al. 2008, Walther & Moore 2005). Sampling a particular host species but from different geographical sites resulted a higher endophytic fungal diversity when compared to within the site and the rich diversity observed had correlation with temperature and rainfall as important environmental parameters (Zimmerman & Vitousek 2012). The diversity of endophytic fungal communities among different host species varies with distinct geographic locations and hosts. Similarly, diversity also varies within different types of tissues and organs of a particular host e.g. leaves, inflorescence, stem and roots (Collado et al. 1999, Kumar & Hyde 2004, Saikkonen 2007, Abubacker & Devi 2014, Nalini et al. 2014). Other factors that influence the species diversity and richness are canopy levels and leaf age (Arnold & Herre 2003) and use of DNA sequence data to properly identify species(Guo et al. 799 2003, Arnold et al. 2007, Lumbsch et al. 2008, Rodriguez et al. 2009, Sun & Guo 2012, U’ren et al. 2012). Numbers and diversity of endophytic fungi The number of fungal endophytes has been estimated to be above a million according to Strobel & Daisy (2003) and Sun & Guo (2012). There is a universal presence of endophytes in every plant species. A single tropical leaf may harbour approximately 90 endophytic species, and 50 distinct genera in grassland species (Bayman 2006, Porras–Alfaro et al. 2008). Similarly, variation in the colonization rate is also from less than 1% to 44% in arctic and boreal ecosystems to more than 90% in tropical ones (Higgins et al. 2007). Arnold (2007) states that endophytes mostly belong to ascomycetes and their anamorphs and are ecologically an exceptionally diverse group. The hyperdiverse nature of endophytic fungi comes from the fact that they are ubiquitous and inhabit approximately 300,000 plant species on earth, indicating their number to be roughly about one million taxa based on 1:4 or 1:5 fungi per host. Most of the endophytic fungi have been found to be non–sporulating. However, in recent years, these non–sporulating fungi have been sequenced with the help of molecular tools that enabled many of the endophytic fungal taxa to be identified up to species level (e.g. Lacap et al. 2003, Promputtha et al. 2005, Jeewon et al. 2013, Doilom et al. 2017). The diversity of endophytes isolated from orchid tissues has been found to be more in the leaves when compared to the other tissue parts. Similarly, the locality of the orchids also decides the nature and diversity of the endophytes isolated (Chen et al. 2013). The complexity of the tissues and the nature of ecological habitats experienced by the endophytes also shape the endophytic associations within the roots, leaves or other parts of orchids (Chen et al. 2013, Liu et al. 2012). The endophytic fungal association of grasses has received much attention in various studies. Tanaka et al. (2005) have summarized our understanding of the systemic colonization of clavicipitaceous fungi, particularly Epichloë spp. (Ascomycota:

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