Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples

U’Ren, Jana M.; Dalling, James W.; Gallery, Rachel E.; Maddison, David R.; Davis, Emily; Gibson, Cara M.; Arnold, A. Elizabeth

doi:10.1016/j.mycres.2008.11.015

Cited by 125 publications

(97 citation statements)

References 57 publications

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“…Empirical estimates of percent sequence divergence between sister species for four endophyte-containing ascomycetous genera (Botryosphaeria, Colletotrichum, Mycosphaerella, and Xylaria) indicated that groups based on 95% ITS rDNA sequence similarity conservatively estimate species (65). We used Sequencher v. 4.5 (Gene Codes Corp., Ann Arbor, MI; default settings except for the requirement of a 20-character minimum overlap; see Arnold et al [3]) to estimate fungal operational taxonomic units (OTU) at 95% ITS rDNA sequence similarity and bacterial OTU at 97% 16S sequence similarity (61).…”

Section: Methodsmentioning

confidence: 99%

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes

Hoffman

Arnold

2010

Appl Environ Microbiol

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Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the Proteobacteria, but a small number of Bacillaceae also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur.Traits related to the establishment and outcome of plantfungus symbioses can reflect not only abiotic conditions and the unique interactions of particular fungal and plant genotypes (49,50,56,59,62,67) but also additional microbes that interact intimately with fungal mycelia (4, 12, 42). For example, mycorrhizosphere-associated actinomycetes release volatile compounds that influence spore germination in the arbuscular mycorrhizal (AM) fungus Gigaspora margarita (Glomeromycota) (14). Levy et al. (34) describe Burkholderia spp. that colonize spores and hyphae of the AM fungus Gigaspora decipiens and are associated with decreased spore germination. Diverse "helper" bacteria have been implicated in promoting hyphal growth and the establishment of ectomycorrhizal symbioses (23,26,57,70). Minerdi et al. (43) found that a consortium of ectosymbiotic bacteria limited the ability of the pathogen Fusarium oxysporum to infect and cause vascular wilts in lettuce, with virulence restored to the pathogen when ectosymbionts were removed.In addition to interacting with environmental and ectosymbiotic bacteria, some plant-associated fungi harbor bacteria within their hyphae (first ...

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Section: Methodsmentioning

confidence: 99%

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes

Hoffman

Arnold

2010

Appl Environ Microbiol

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229

224

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“…Leaf pieces were washed with deionized water, patted dry, cut into small fragments (ca. 2-mm 2 ), surface sterilized as above but using 0.525% NaClO, allowed to dry under sterile conditions, and plated on 2% MEA prepared without antibiotics (U'Ren et al, 2009;Del Olmo-Ruiz and Arnold, 2014;Del Olmo-Ruiz and Arnold, in revision;Arnold, unpublished data).…”

Section: Fungi Examinedmentioning

confidence: 99%

“…These vouchers were used in the present study. A diversity of fungi was obtained in culture (Gallery et al, 2007a,b;U'Ren et al, 2009;Del Olmo-Ruiz and Arnold, 2014;Del Olmo-Ruiz and Arnold, in revision;Sarmiento et al, 2015;Zalamea et al, 2015), but two genera were particularly common among isolates from seeds and leaves (putative Fusarium, Hypocreales; putative Xylaria, Xylariales). We therefore focused our work on these taxa, first using phylogenetic methods (below) to confirm the taxonomic placement and ecological diversity of isolates in each group.…”

Section: Fungi Examinedmentioning

confidence: 99%

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves

et al. 2016

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Interactions between fungi and tropical trees help shape some of the most biodiverse communities on earth. These interactions occur in the presence of additional microbes that can modify fungal phenotypes, such as endohyphal bacteria (EHB). Here we examine the occurrence, diversity, and taxonomic composition of EHB in fungi that colonize seeds and leaves of plants in tropical forests. We use PCR and fluorescence microscopy to detect EHB in fungi, and a phylogenetic approach to explore evolutionary relationships among seed-and leaf-inhabiting fungi and their bacterial partners. Analyses focusing on two prevalent orders of fungi (Hypocreales and Xylariales) revealed that seed-and leaf-inhabiting fungi have a shared evolutionary history, yet differ in the prevalence, richness, and composition of their endohyphal symbionts. Phylogenetic analyses detected that the endohyphal habit is widespread, here encompassing members of seven phyla of bacteria (including three classes of Proteobacteria). Occurring in seed-vs. leaf-associated fungi has not resulted in detectable structure in the evolution of EHB, and no congruence was observed in the phylogenetic relationships of these apparently facultative, horizontally transmitted symbionts, and their fungal hosts. Our results are consistent with multiple origins of fungus-bacterium associations and argue for evaluating focal pairs to determine how particular EHB affect the establishment or maintenance of fungal symbioses in seeds and leaves.

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“…Further molecular identification based on 18 S rDNA resulted that SH1 similar (99%) to Accession FJ524323 of GeneBank refer to Unculture endophytic fungus clone R3-63, obtained from wild rice root in China (Yuan et al 2010) (Table 2). SH2 was similar to Accession No FJ612897 of GeneBank, Fungal sp ARIZ B031, endophytic fungus of tree Cecropia insignis (U'Ren et al 2009). The rank of species from the most abundant to the least was Nigrospora, SH2, SH1, Coniothyrium sp.…”

Section: Resultsmentioning

confidence: 61%

Leaf endophytic fungi of chili (Capsicum annuum) and their role in the protection against Aphis gossypii (Homoptera: Aphididae)

2011

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Hernawati H, Wiyono S, Santoso S (2011) Leaf endophytic fungi of chili (Capsicum annuum) and their role in the protection againstAphis gossypii (Homoptera: Aphididae). . The objectives of the research were to study the diversity of leaf endophytic fungi of chili, and investigate its potency in protecting host plants against Aphis gossypii Glov. Endophytic fungi were isolated from chili leaves with two categories: aphid infested plants and aphid-free plants, collected from farmer's field in Bogor, West Java. Abundance of each fungal species from leave samples was determined by calculating frequency of isolation. The isolated fungi were tested on population growth of A. gossypii. The fungal isolates showed suppressing effect in population growth test, was further tested on biology attributes i.e. life cycle, fecundity and body length. Five species of leaf endophytic fungi of chili were found i.e. Aspergillus flavus, Nigrospora sp., Coniothyrium sp., and SH1 (sterile hypha 1), SH2 (sterile hypha 2). Even though the number of endophytic fungi species in aphid-free and aphid-infested plant was same, the abundance of each species was different. Nigrospora sp., sterile hyphae 1 and sterile hyphae 2 was more abundant in aphid-free plants, but there was no difference in dominance of Aspergillus flavus and Coniothyrium sp. Nigrospora sp., SH1 and SH2 treatment reduced significantly fecundity of A. gossypii. Only SH2 treatment significantly prolonged life cycle and suppress body length, therefore the fungus had the strongest suppressing effect on population growth among fungi tested. The abundance and dominance of endophytic fungal species has relation with the infestation of A. gossypii in the field.

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Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples

Cited by 125 publications

References 57 publications

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves

Leaf endophytic fungi of chili (Capsicum annuum) and their role in the protection against Aphis gossypii (Homoptera: Aphididae)

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