Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines

Bullington, Lorinda; Larkin, Beau

doi:10.1016/j.funeco.2015.07.005

Cited by 34 publications

(17 citation statements)

References 56 publications

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“…Tsuga chinensis and T. dumosa had approximately two times higher relative Chytridiomycota abundances than either T. canadensis or T. sieboldii. Few studies have found Chytridiomycota on conifers, but one study found a representative of this group on the needles of a single white pine (Bullington and Larkin 2015). Chytridiomycota are known to parasitize pollen grains of conifers that have fallen from the parent tree (Goldstein 1960).…”

Section: Discussionmentioning

confidence: 99%

Exploring variation in phyllosphere microbial communities across four hemlock species

et al. 2018

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The hemlock woolly adelgid (HWA) is an insect native to Asia and likely western North America. First reported in eastern North America in 1951, it has devastated eastern hemlock (Tsuga canadensis) populations. Loss of hemlock will greatly affect the structure and function of eastern forests. Susceptibility to adelgid infestation varies within eastern hemlocks and across other hemlock species. Our study was conducted to determine whether eastern hemlocks share a similar stem (phyllosphere) microbial community with other co‐occurring hemlocks and whether community‐level shifts are associated within trees of the same species based on HWA infestation. Surprisingly, we found no difference in microbial community composition or diversity between trees of the same species based on the level of HWA infestation. However, microbial communities varied significantly across the four hemlock trees sampled, native T. canadensis and three non‐natives: Tsuga chinensis, Tsuga dumosa, and Tsuga sieboldii. Within these tree hosts, microbial communities from T. dumosa and T. chinensis clustered together, and microbial communities from T. canadensis and T. sieboldii clustered separately from all other tree species. Additionally, specific indicator taxa were identified for all the tree species sampled. These results indicate that Asian hemlocks might not fill the same niche in eastern forests as the native eastern hemlock. Further work should be conducted to determine how differences in hemlock species and associated microbial communities might scale up to alter organismal interactions involving hemlocks.

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Section: Discussionmentioning

confidence: 99%

Exploring variation in phyllosphere microbial communities across four hemlock species

et al. 2018

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“…Rhizosphaera kalkhoffii often co-occurs with Lophodermium piceae on Picea abies and its conidiomata are abundant on fallen needles (Livsey and Barklund 1992), although Scattolin and Montecchio (2009) showed that the abundance of R. kalkhoffi was negatively correlated with the abundance of L. piceae . Rhizosphaera kalkhoffii is implicated in needle cast and blight in Abies and Picea and is also reported from asymptomatic foliage (Kobayashi 1967, Juzwik 1993, Butin 1995, Manter and Livingston 1996, Stone et al 2004, Talgoslash and Stensv 2012 Sydowia polyspora was isolated as a Picea endophyte in this study and reported as an endophyte in other conifers (Petrini et al 1989, Kowalski 1993, Linaldeddu et al 2003, Gil et al 2009, Martin et al 2012, Bullington and Larkin 2015. It is also known as a saprotroph on dead foliage, branches, stems, and cones of a wide variety of conifer hosts and is a common isolate from surface-sterilized Abies seeds (Smerlis 1970, Minter 1981, Talgø et al 2010a.…”

Section: Rhytismataceaesupporting

confidence: 56%

“…Basidiomycete wood endophytes are also isolated in lower abundance compared to ascomycetes; for example, Giordano et al (2009) and Robles et al (2015) reported that basidiomycetes represented 12% and 26% of the total number of endophytes isolated from Pinus sylvestris and Platanus acerifolia, respectively, despite including media selecting for basidiomycetes. Bullington and Larkin (2015) reported a negative correlation between basidiomycete and ascomycete endophytes in Pinus monticola seedlings. Basidiomycete endophytes detected in this study, such as Peniophora spp., Schizophyllum commune, and Trametes versicolor, are also reported as sapwood and root endophytes of conifers (Giordano et al 2009, Min et al 2014).…”

Section: )mentioning

confidence: 99%

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A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada

Tanney¹

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Research interest in endophytic fungi has increased substantially, yet is the current research paradigm capable of addressing fundamental taxonomic questions?More than half of the ca. 30,000 endophyte sequences accessioned into GenBank are unidentified to the family rank and this disparity grows every year. The problems with identifying endophytes are a lack of taxonomically informative morphological characters in vitro and a paucity of relevant DNA reference sequences. A study involving ca. 2,600Picea endophyte cultures from the Acadian Forest Region in Eastern Canada sought to address these taxonomic issues with a combined approach involving molecular methods, classical taxonomy, and field work. It was hypothesized that foliar endophytes have complex life histories involving saprotrophic reproductive stages associated with the host foliage, alternative host substrates, or alternate hosts. Based on inferences from phylogenetic data, new field collections or herbarium specimens were sought to connect unidentifiable endophytes with identifiable material. Approximately 40 endophytes were connected with identifiable material, which resulted in the description of four novel genera and 21 novel species and substantial progress in endophyte taxonomy. Endophytes were connected with saprotrophs and exhibited reproductive stages on non-foliar tissues or different hosts. These results provide support for the foraging ascomycete hypothesis, postulating that for some fungi endophytism is a secondary life history strategy that facilitates persistence and dispersal in the absence of a primary host. This thesis provides an alternate approach to identifying endophytes by considering the whole fungus interacting within its natural habitat.iii Acknowledgements I would first like to thank my supervisor Dr. Keith A. Seifert for providing me with the freedom and support to conduct the research presented in this thesis as well as many other side projects and curiosities. Keith generously provided many opportunities to travel to domestic and international conferences, which made me more aware of the directions of global mycological research and provided the opportunity to meet many of the great mycological heroes and their contemporaries. Our discussions over the last five years have contributed to my development as a more well-rounded and openminded researcher, professional, and person; his honesty and integrity are qualities that all professionals should aspire to have. I am indebted to Keith for the knowledge, experience, and personal growth I gained over the last five years in his lab. I thank Dr. J. David Miller for providing stimulating discourse, travel and collecting opportunities, and of course the unique opportunity to work on this project, which proved to be an exciting and captivating experience. I hope that we can continue collaborating on this and other projects in the near future. Myron Smith provided support and advice throughout this process. The Carleton University Graduate Administrators Darlene Moss and Lisa Chiarel...

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“…Identifying endophytes and investigating their diversity and the factors affecting the community composition of this group of fungi have been a subject of many studies (Unterseher, Siddique, Brachmann, & Persoh, 2016;Vaz et al, 2014;Yuan, Rao, Chen, Zhang, & Wu, 2011). The next-generation sequencing methods, which have been extensively used to study the diversity of plant-related fungal communities in almost all types of terrestrial ecosystems, enable researchers to gain a more comprehensive evaluation of fungal richness compared to the culture-based methods (Bullington & Larkin, 2015). Yet, culture-based methods are still very useful since they can provide researchers with the opportunity of having a valid functional and morphological description of species and with opportunities for further experiments on the described species (e.g.…”

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confidence: 99%

Culture‐based methods using low‐temperature incubation revealed cold‐adapted fungal endophytes from semiarid forests

et al. 2019

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Fungal endophytes are an important part of the plant microbiome and participate in maintaining the stability of ecosystems. Culture‐based methods are frequently considered in studying fungal communities because of their advantages in providing cultures for further experiments and their low cost. In comparison with next‐generation sequencing methods, their ability to assess fungal diversity is questionable. Here, we show how using two different incubation temperatures can improve the yield of fungal endophytes by culture‐based methods. Diversity, organ preference and spatiotemporal variability of endophytic fungal communities living within Quercus brantii L. were investigated using two different incubation temperatures. To test the effects of using low‐temperature incubation on diversity estimations, twigs and leaves of Quercus brantii were incubated under 25°C and 4°C conditions. Isolation rate and Hill's series of diversity were calculated for each sample. Model‐based analysis was used to evaluate the effects of (a) incubation temperature, (b) organ type and (c) spatiotemporal variations on fungal isolation rate, fungal diversity and community composition. Our results showed a strong organ specificity and temporal dynamics among endophytic fungal communities, but the location of the forest stand had only a limited effect on fungal community composition. Low‐temperature incubation enabled us to improve culture‐based methods by discovering the diversity of cold‐adapted fungal endophytes and a significantly different part of the endophytic communities that is usually missed by customary culturing temperature. The isolation of cold‐adapted endophytes from a semiarid environment opens a new window to further studies on this kind of fungi in such ecosystems.

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Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines

Cited by 34 publications

References 56 publications

Exploring variation in phyllosphere microbial communities across four hemlock species

Exploring variation in phyllosphere microbial communities across four hemlock species

A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada

Culture‐based methods using low‐temperature incubation revealed cold‐adapted fungal endophytes from semiarid forests

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