Methodological Approaches Frame Insights into Endophyte Richness and Community Composition

Oita, Shuzo; Carey, Jamison; Kline, Ian; Ibáñez, Alicia; Yang, Nathaniel W.; Hom, Erik F. Y.; Carbone, Ignazio; U’Ren, Jana M.; Arnold, A. Elizabeth

doi:10.1007/s00248-020-01654-y

Cited by 18 publications

(16 citation statements)

References 91 publications

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“…Endophytes were isolated from living, apparently healthy photosynthetic tissues of plants and lichens (Table 1) as described by Hoffman and Arnold (2008), U'Ren et al (2012), and Oita et al (2021. Briefly, fresh tissues were rinsed in running tap water for 30 s and then cut into 2 mm pieces.…”

Section: Methodsmentioning

confidence: 99%

“…We sequenced cleaned products with the original primers (5 μM) on an Applied Biosystems Table 1. Taxon sampling, including proposed taxonomic placement, isolate codes, host taxa, regions of origin, isolation medium, storage period (the number of days between host tissue collection and fungal isolation, as described in Oita et al 2021), and references for original isolation of each strain. Species names are based on the present study (see Fig.…”

Section: Multilocus Sequencingmentioning

confidence: 99%

“…Temperate and boreal plants and lichens frequently harbor endophytes in the genus Coniochaeta (Coniochaetaceae; Coniochaetales; Sordariomycetes, Ascomycota). Diverse strains can be isolated readily from healthy, surface-sterilized tissues on standard media such as malt extract agar (MEA) (e.g., Arnold & Hoffman 2008;U'Ren et al 2012;del Olmo Ruiz 2012;Huang et al 2016;Chen 2017;Harrington et al 2019;U'Ren et al 2019;Oita et al 2021). As described in Harrington et al (2019), Coniochaeta is a diverse genus with species that inhabit a wide range of substrates, including butter, dung, wood, soil, uranium mine wastewater, lichens, and healthy, diseased, or senescent tissues of mosses, ferns, conifers, and angiosperms (see also Weber 2002;García et al 2006;del Olmo Ruiz 2012;Rafa et al 2012;Vázquez-Campos et al 2014;Xie et al 2015;Chen 2017;U'Ren et al 2019).…”

Section: Introductionmentioning

confidence: 99%

“…As an extension of that study we sought to classify additional isolates that were obtained as endophytes from diverse plants and lichens (Table 1) and accessioned as part of the living collection of endophytes at the Robert L. Gilbertson Mycological Herbarium of the University of Arizona (ARIZ) (Hoffman & Arnold 2008;U'Ren et al 2012;U'Ren et al 2019;Oita et al 2021). Sequencing of the barcode locus for these isolates suggested that they are members of the C. prunicola / C. endophytica clade, but their relationships and species identities could not be inferred from ITS rDNA data alone.…”

Section: Introductionmentioning

confidence: 99%

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Two new endophytic species enrich the Coniochaeta endophytica / C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov.

Arnold¹,

Harrington²,

U’Ren³

et al. 2021

Pl. Fung. Systt.

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Coniochaeta (Coniochaetaceae, Ascomycota) is a diverse genus that includes a striking richness of undescribed species with endophytic lifestyles, especially in temperate and boreal plants and lichens. These endophytes frequently represent undescribed species that can clarify evolutionary relationships and trait evolution within clades of previously classified fungi. Here we extend the geographic, taxonomic, and host sampling presented in a previous analysis of the clade containing Coniochaeta endophytica, a recently described species occurring as an endophyte from North America; and C. prunicola, associated with necroses of stonefruit trees in South Africa. Our multi-locus analysis and examination of metadata for endophyte strains housed in the Robert L. Gilbertson Mycological Herbarium at the University of Arizona (ARIZ) (1) expands the geographic range of C. endophytica across a wider range of the USA than recognized previously; (2) shows that the ex-type of C. prunicola (CBS 120875) forms a well-supported clade with endophytes of native hosts in North Carolina and Michigan, USA; (3) reveals that the ex-paratype for C. prunicola (CBS 121445) forms a distinct clade with endophytes from North Carolina and Russia, is distinct morphologically from the other taxa considered here, and is described herein as Coniochaeta lutea; and (4) describes a new species, Coniochaeta palaoa, here identified as an endophyte of multiple plant lineages in the highlands and piedmont of North Carolina. Separation of CBS 120875 and CBS 121445 into C. prunicola sensu stricto and C. lutea is consistent with previously described genomic differences between these isolates, and morphological and functional differences among the four species (C. endophytica, C. prunicola, C. palaoa, and C. lutea) underscore the phylogenetic relationships described here. The resolving power of particular loci and the emerging perspective on the host- and geographic range of Coniochaeta and the C. endophytica / C. prunicola clade are discussed.

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Section: Methodsmentioning

confidence: 99%

Section: Multilocus Sequencingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Two new endophytic species enrich the Coniochaeta endophytica / C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov.

Arnold¹,

Harrington²,

U’Ren³

et al. 2021

Pl. Fung. Systt.

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“…Saxena et al provide a review of the ecological and potential industrial and agronomic use of members of the genus Muscodor [33]. Oita et al report that endophyte diversity is likely best assessed by combining culture and high-throughput sequencing [34]. Bao et al describe host-dependent response to endophyte colonization towards grass parasitism [35].…”

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confidence: 99%

Fungal Ecology Special Issue: Editorial

Carbonero

Strobel

2021

Microb Ecol

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Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques

et al. 2022

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Premise Several ferns and lycophytes produce subterranean gametophytes, including the Ophioglossaceae, Psilotaceae, and some members of the Schizaeaceae, Gleicheniaceae, and Lycopodiaceae. Despite the surge in plant‐microbiome research, which has been particularly boosted by high‐throughput sequencing techniques, the microbiomes of these inconspicuous fern gametophytes have rarely been examined. The subterranean gametophytes are peculiar due to their achlorophyllous nature, which makes them rely on fungi to obtain nutrients. Furthermore, the factors that shape the fungal communities (mycobiomes) of fern gametophytes have not been examined in depth. Methods and Results We present a workflow to study the mycobiome of the achlorophyllous gametophytes of Ophioderma pendulum using a high‐throughput metabarcoding approach. Simultaneously, each gametophyte was investigated microscopically to detect fungal structures. Two primer sets of the nuclear ITS sequence targeting general fungi were applied, in addition to a primer set that specifically targets the nuclear small subunit ribosomal rDNA region of arbuscular mycorrhizal fungi. Both the microscopic and metabarcoding approaches revealed many diverse fungi inhabiting a single gametophyte of O . pendulum . Discussion This study provides methodological details and discusses precautions for the mycobiome investigation of achlorophyllous gametophytes. This research is also the first to uncover the mycobiome assembly of an achlorophyllous gametophyte of an epiphytic fern.

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Methodological Approaches Frame Insights into Endophyte Richness and Community Composition

Cited by 18 publications

References 91 publications

Two new endophytic species enrich the Coniochaeta endophytica / C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov.

Two new endophytic species enrich the Coniochaeta endophytica / C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov.

Fungal Ecology Special Issue: Editorial

Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques

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