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Majority rule consensus tree of 20,002 trees generated from alignment method 2 (MUSCLE, with manual adjustment) of Botryosphaeria spp. using Bayesian analysis of ITS rDNA data, with reconstruction of ancestral states estimating the origins of fungal guilds. Taxon names of endophytes and seed-associated fungi indicate ecological role-numerical identifierhost genus. The number of seed-associated isolates with identical genotypes at 95% similarity is indicated in parentheses. Support values are PPs generated in MrBayes using model GTR + I + G for three different alignment methods: (1) MUSCLE unedited (before slash; category 1 alignment) (2) MUSCLE with manual editing (after slash; category 2 alignment) and (3) manual alignment in MacClade (below branch; category 3 alignment). A dash (-) indicates the node was not present in the majority rule consensus for that alignment. Thickened lines represent neighbor-joining bootstrap support !70% generated from the category 2 alignment. Pie charts indicate two methods for ancestral state reconstruction: (1) the proportion of trees in which a given state was significantly more likely than alternative states, or in which a node was equivocal or absent (top); and (2) among the trees in which a node was present, the average probability of any given state (bottom). The * indicates this sequence was obtained from Ficus insipida instead of C. insignis.
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Fungi associated with seeds of tropical trees pervasively affect seed survival and germination, and thus are an important, but understudied, component of forest ecology. Here, we examine the diversity and evolutionary origins of fungi isolated from seeds of an important pioneer tree (Cecropia insignis, Cecropiaceae) following burial in soil for fiv...
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... topologies inferred using Bayesian methods were largely consistent both among alignments and with regard to different models of evolution, a representative alignment (category 2: MUSCLE, with manual adjustment) and a single model (GTR þ Iþ G) was selected for subsequent phylogenetic estimations (Figs 2-5). ...
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... found that within each genus, Bayesian analyses were relatively robust to the different alignments and models of evolution used here: different alignments and evolutionary models yielded different topologies for each genus, but differ- ences among those topologies were not supported by signifi- cant PPs (Figs 2-5). However, Bayesian analyses revealed that genera differed from one another in their sensitivity to align- ment methods (one-way ANOVA based on incongruency scores, F 3,8 ¼ 4.403; P ¼ 0.042). ...
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... most robust phylogenetic analysis methods (Bayesian analyses based on category 2 alignments implementing GTR þ I þ G) revealed several well-supported clades contain- ing both seed-associated fungi and endophytes for three of the four focal genera, including four clades in Botryosphaeria (Fig 2), one in Mycosphaerella (Fig 4), and three in Xylaria ( Fig 5). The Colletotrichum tree contained one clade with pathogens, seed-associated fungi, and endophytes, but this clade was not well supported and lacked resolution (Fig 3), and thus was not used in ancestral state reconstructions. ...
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... state reconstruction illustrated several prelimi- nary hypotheses for the evolutionary history of seed-associated fungi, as well as their relationships to pathogens, endophytes, and saprotrophs in Botryosphaeria, Mycosphaerella, and Xylaria. In general, more frequent evolutionary associations were seen among endophytes, pathogens, and seed-associated fungi than between any of those guilds and saprotrophs (Figs 2, 4, 5). However, the evolutionary interplay of these ecological modes differed among genera. ...
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... Botryosphaeria, ancestral state reconstructions suggested that several endophytes arose from putatively seed-associated ancestors (e.g. Fig 2: Endo-6755-Gustavia and Endo-6718-Gustavia), and highlighted several transi- tions from pathogenicity to seed-association (e.g. the line- age containing B. obtusa). Transitions from endophytism to seed-association were not observed. ...
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... contrast, genera did not differ in their sensitivity to different alignments when NJ analyses were performed. In general, BS values are generally in agreement with PPs for category 2 align- ments under both inference methods (Figs 2-5), which supports the validity of our subsequent analyses regarding the evolution of seed-associated fungi in these genera. ...
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In this study seven new species of the Botryosphaeriaceae are described from baobab (Adansonia gibbosa) and surrounding endemic tree species growing in the Kimberley region of northwestern Australia. Members of the Botryosphaeriaceae were predominantly endophytes isolated from apparently healthy sapwood and bark of endemic trees; others were isolat...
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... The members of Xylaria have a worldwide distribution, but they are highly diverse in the tropics and subtropics (Dennis 1956;Ju and Rogers 1999;Lodge et al. 2008;Fournier et al. 2011;Wangsawat et al. 2021). Species of Xylaria are saprobic, pathogenic, or endophytic and associated with a wide range of host (Rogers 1979a;Vannini et al. 1996;Whalley 1996;Crozier et al. 2006; Thomas et al. 2008;U'Ren et al. 2009;de Vega et al. 2010). According to the substrate in which these fungi grow, the taxa of the genus can be divided into four different ecological types, viz., wood-inhabiting type, termite nests inhabiting type, foliicolous type, and fructicolous/seminicolous type. ...
Morphological and phylogenetic analyses on samples of Xylaria species associated with fallen fruits from China were carried out, and two new species were described, namely X. aleuriticola and X. microcarpa. Xylaria aleuriticola is found on fallen fruits of Aleurites moluccana, and characterized by stromata dichotomously branched several times with long acute sterile apices, fertile parts roughened with perithecia and tomentose, and ellipsoid to fusiform ascospores. Xylaria microcarpa differs in its very small stromata with dark brown tomentum, light brown ascospores with an inconspicuous straight germ slit, and grows on leguminous pods. The differences between the new species and morphologically similar species are discussed. Phylogenetic analyses on ITS-RPB2-TUB sequences confirmed that the two species are clearly separated from other species of the genus Xylaria. Xylaria liquidambaris is reported as a new record from China. A key to the Xylaria species associated with fallen fruits and seeds reported from China is provided to facilitate future studies of the genus.
... Refs. [67][68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83][84][85][86] Funding: MXR-G was funded by the Secretaría Nacional de Educación Superior, Ciencia, Tecnología e Innovación (SENESCYT: www.educacionsuperior.gob.ec/) with a Prometeo Fellowship, and a María Zambrano distinguished researcher contract by both the Ministerio de Universidades (Gobierno de España) and the Next generation EU. ...
Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.
... This can include via wind as aerosols or, more commonly, direct colonisation from soil microbes when the seed is dormant in the soil seed bank (Gallery et al. 2007;Klaedtke et al. 2016;Dai et al. 2020). The relative proportion of species transmitted vertically to horizontally is largely unknown, although studies have indicated that most of the microbiome of crops is assembled horizontally from the surrounding environment and only a subset is vertically transmitted (U'ren et al. 2009;Sarmiento et al. 2017;Abdelfattah et al. 2023). In our comparisons of the fungi cultured from the five host species, we found that very few taxa were shared. ...
Context: Seeds harbour a diversity of microbes, which in some plants aid with germination and establishment. Seeds form a critical part in the lifecycle of plants and a role in many conservation and restoration activities. Aims: Because this is an emerging field in seed biology, we aim to highlight the key research gaps of interest to seed on the basis of restoration and ex situ conservation. Methods: We identify knowledge gaps associated with the seed endophytic microbiome of native Australian plants through undertaking a literature review. Additionally, culturing methods were used to identify the fungal seed endophytes of five native Australian species. Key results: We identified a diversity of taxa within the native seed and show three taxa that are common to all study hosts. Sampling seed from additional hosts at a site and additional sites of a host species showed new fungal diversity. Our literature review showed that little information is available on native seed microbiomes and we identified four key areas where research gaps exist, linking with seed-based restoration practices. Conclusions: We provide evidence that there is a complex and diverse seed microbiome within some Australian native plants and suggest ways that it could be integrated into restoration and conservation practices. Implications: We propose that by taking into consideration the presence of a seed microbiome and its potential impacts on plant health, seed microbiomes could be used as one method to restore microbial diversity into an ecosystem and to contribute to the seedling microbiome and plant health at restored sites. © 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing.
... Isolates are representative of culturable oak endophyte communities, which are typically comprised of phylogenetically diverse Ascomycota, including numerous species of Dothideomycetes (Capnodiales, Helotiales, Pleosporales), Sordariomycetes (Xylariales, Coniochaetales), and Pezizomycetes (Pezizales) (Faeth and Hammon, 1997;U'Ren et al., 2012;Voříšková and Baldrian, 2013;. As 5% ITS-LSU rDNA sequence divergence (i.e., 95% sequence similarity) was demonstrated to conservatively estimate sister species boundaries for four endophyte-rich genera in the Sordariomycetes and Dothideomycetes when compared against published phylogenies (U'Ren et al., 2009;Liggenstoffer et al., 2010), fungal species were defined by clustering ITS-partial LSU rDNA sequences at 95% sequence similarity (i.e., 95% operational taxonomic units (OTUs) as previously described by U' Ren et al. (2012)). Selected oak-associated endophyte species were isolated from three distinct geographic locations in North America (AZC: a Denotes species that were also grown on plates containing no glucose to examine their use of phenolic compounds as sole carbon sources (see Supplemental Madrean Sky Island Archipelago of southeastern Arizona; NCH: Appalachian Mountains of western North Carolina; and FLA: sub-tropical scrub forest in Florida). ...
... Given the economic importance of plants in forestry, agriculture, and horticulture, most of the research on seed mycobiota has focused on putative pathogens, such as species of Rhabdocline and Fusarium in Douglas-fir (Pseudotsuga menziesii) [14,15], Sydowia polyspora in Western white pine (Pinus monticola) [16], Monilinia vaccinii-corymbosi in blueberry (Vaccinium corymbosum) [17], and species of Fusarium in cheatgrass (Bromus tectorum) and maize (Zea mays) [18][19][20]. Moreover, most of the surveys of seed fungi have been culture-based [12,[21][22][23], which introduces a bias by favoring fungi that grow well on the selected medium. To minimize such bias, environmental sequencing has been used to identify fungi in seeds (e.g., [24][25][26][27]), providing higher resolution data about fungal community patterns. ...
... 3. While potato dextrose agar (PDA) has been used in many seed fungi surveys [12,21,22], multiple media types are conducive or specific for fungal growth. Commonly used media include malt extract agar (MEA) [22,23], malt yeast extract agar (MYE) [25], and yeast extract media (YM) [49]. Additionally, there are various antibiotics (e.g., chloramphenicol, streptomycin) that can be used to mitigate bacterial contamination. ...
Seed fungi are potentially important for their roles in seedling microbiome assembly and seedling health, but surveys of full seed fungal communities remain limited. While culture-dependent methods have been used to characterize some members of the seed mycobiota, recent culture-independent studies have improved the ease in identifying and characterizing full seed fungal communities. In this chapter, we describe how to survey seed fungi using both traditional culture-based methods and culture-free metabarcoding. We first describe protocols for the isolation and long-term preservation of fungal strains from individual seeds and for the extraction and amplification of DNA from such fungal isolates for identification with Sanger sequencing. We also detail how to extract, amplify, and sequence fungal DNA directly from individual seeds. Finally, we provide suggestions for troubleshooting media choices, PCR inhibition by isolates and plant tissue, and PCR limitation by low fungal DNA.
... We used the Tree-Based Alignment Selector (T-BAS) toolkit to determine phylogenetic placement of isolates within the Pezizomycotina (Ascomycota), to visualize relationships and metadata in a phylogenetic context (Miller et al., 2015;Carbone et al., 2017), and to designate operational taxonomic units (OTUs) on the basis of sequence similarity (95, 97, and 99% sequence similarity). Groups based on 95% sequence similarity approximate species boundaries in focal taxa of tropical endophytes and were used to define OTUs for statistical analyses (U'Ren et al., 2009;Oita et al., 2021a,b). Results for analyses with 97 and 99% similarity groups were comparable (data not shown) but had more singleton OTUs. ...
Leaf traits of plants worldwide are classified according to the Leaf Economics Spectrum (LES), which links leaf functional traits to evolutionary life history strategies. As a continuum ranging from thicker, tough leaves that are low in nitrogen (N) to thinner, softer, leaves that are high in N, the LES brings together physical, chemical, and ecological traits. Fungal endophytes are common foliar symbionts that occur in healthy, living leaves, especially in tropical forests. Their community composition often differs among co-occurring host species in ways that cannot be explained by environmental conditions or host phylogenetic relationships. Here, we tested the over-arching hypothesis that LES traits act as habitat filters that shape communities of endophytes both in terms of composition, and in terms of selecting for endophytes with particular suites of functional traits. We used culture-based and culture-free surveys to characterize foliar endophytes in mature leaves of 30 phylogenetically diverse plant species with divergent LES traits in lowland Panama, and then measured functional traits of dominant endophyte taxa in vitro . Endophytes were less abundant and less diverse in thick, tough, leaves compared to thin, softer, leaves in the same forest, even in closely related plants. Endophyte communities differed according to leaf traits, including leaf punch strength and carbon and nitrogen content. The most common endophyte taxa in leaves at different ends of the LES differ in their cellulase, protease, chitinase, and antipathogen activity. Our results extend the LES framework for the first time to diverse and ecologically important endophytes, opening new hypotheses regarding the degree to which foliar symbionts respond to, and extend, the functional traits of leaves they inhabit.
... The plant microbiota, defined here as the community of bacteria, fungi, archaea, viruses, and other microscopic organisms that live on (i.e., epiphytically) or in (i.e., endophytically) plant tissues (Hardoim et al., 2015), confer many services as well as disservices to their hosts, including disease development and defense (Busby et al., 2016), protection against herbivory (Shikano et al., 2017), tolerance of abiotic stress (Rodriguez et al., 2004), and aid in nutrient uptake (Christian et al., 2019). These microbial communities associate with all plant tissues (Hardoim et al., 2015), including seeds (Mundt and Hinkle, 1976;Ganley and Newcombe, 2006;U'Ren et al., 2009;Hodgson et al., 2014;Barret et al., 2015). Seeds play a major role in plant communities as agents of dispersal, genetic diversity, and regeneration (Fenner and Thompson, 2005), and they have significant economic and social value through agriculture (Nabhan, 2012). ...
... Previous work on seed microbiota has primarily taken a pattern-based approach to studying assembly processes (e.g., Rezki et al., 2018). Such an approach uses culturing (Ganley and Newcombe, 2006;U'Ren et al., 2009;Heitmann et al., 2021) and/or next-generation sequencing (e.g., Barret et al., 2015;Rezki et al., 2018;Prado et al., 2020;Bergmann and Busby, 2021;Fort et al., 2021) to compare, contrast, and correlate patterns in microbial community composition, diversity, and species co-occurrences. Typically, however, these community data provide limited (i.e., mostly indirect) insights into processes such as dispersal, microbe-plant interactions, and microbemicrobe interactions. ...
Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.
... Currently, species identification is built on the basis of a multiloci DNA barcode rather than a single locus. A useful tool for this is multilocus sequence typing (MLST) [74][75][76]. ...
Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat–fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.
... In addition to dead plant substrates, Xylaria is also known to perpetuate as endophytes in a wide range of live tissues (e.g. trees, palms, orchids, aroids, bromeliads and liverworts) (Bayman et al. 1998;Davis et al. 2003;U'ren et al. 2009;Linnakoski et al. 2012;Rajulu et al. 2013;Jin et al. 2017). To overcome uncertainty among several closely resembling species of Xylaria, phylogenetic studies have been undertaken using different sequences (ITS, α-actin, β-tubulin and rpb2) and resolved that Xylaria is a paraphyletic genus (Lee et al. 2000;Hsieh et al. 2010). ...
Xylaria is one of the common ascomycetous genera occurring in different niches of the scrub jungles of southwest India. Many species of Xylaria are known for their medicinal potential. Mature sporocarps of Xylaria escharoidea, X. hypoxylon, X. longipes and X. polymorpha occurring in different habitats in scrub jungles of southwest India were assessed for functional groups, elemental composition and antioxidant properties. The FTIR analysis revealed presence of amines, carboxylic acids (O-H) and other functional groups. Elemental analysis through EDS showed differences in their elemental composition. Xylaria escharoidea and X. polymorpha were consistent in total antioxidant activity (TAA), ferrous ion-chelation capacity (FCC) and DPPH radical-scavenging activity. Although X. hypoxylon showed high TAA, the rest of the activities like FCC and DPPH radical-scavenging were relatively low. Xylaria longipes showed relatively low antioxidant activities. One-way ANOVA revealed a significant difference between the four species (p<0.001) for three antioxidant activities. The functional groups, elemental composition and antioxidant potential of Xylaria spp. seem to be dependent on the specific species, substrate, habitat and geographic location. These Xylaria spp. are known for production of a variety of metabolites effective in inhibition of microbes (pathogenic bacteria and fungi), apoptotic, cytotoxic, antioxidants and photocatalytic features. Further studies on the metabolites, bioactive compounds and therapeutic significance of Xylaria occurring in the scrub jungles are warranted.
Keywords: Macrofungi, Ascomycetes, Medicinal mushrooms, Bioactive profile, Antioxidant potential
... Since the sieve tubes in the maternal tissues (seed coat and integument) and the offspring tissue (endosperm and embryo) of seed are not connected (Thorne, 1985), endophyte is generally not present in the latter tissue. Fungi from soil also infect fallen seeds and are retained and spread to the aerial tissues as endophytes (U'Ren et al., 2009). ...
Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.
