Community structure of fern-affiliated endophytes in three neotropical forests

Environmental and host plant effects on taxonomic and phylogenetic diversity of root fungal endophytes

Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here, we investigated environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three to four dominant plant species from each of three sites of varying salinity. We assessed taxonomic diversity and composition as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD). When we analyzed plant hosts present across the entire gradient, we found that the effect of the environment on phylogenetic diversity (as measured by MPD) was host dependent and suggested phylogenetic clustering in some circumstances. We found that both environment and host plant affected taxonomic composition of fungal endophytes, but only host plant affected phylogenetic composition, suggesting different host plants selected for fungal taxa drawn from distinct phylogenetic clades, whereas environmental assemblages were drawn from similar clades. Our study demonstrates that including phylogenetic, as well as taxonomic, community metrics can provide a deeper understanding of community assembly in endophytes.

Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum

PREMISE

Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs.

METHODS

Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA.

RESULTS

Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves.

CONCLUSIONS

Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.

Foliar phenols and flavonoids level in pteridophytes: an insight to culturable fungal endophyte colonisation

There are many available reports of secondary metabolites as bioactive molecules from culturable endophytes, nevertheless, there are scarce research pertaining to the levels of metabolites in plants with respect to the incidence and colonisation of fungal endophytes in the same foliar tissues. Therefore, the study was focussed to examine whether fungal endophyte colonisation and the accumulation of secondary metabolites, such as flavonoids and phenols, in the plants are related in any way. For this reason, the study aims to analyse phenols and flavonoids from the fronds of eleven pteridophytes along with the culture-dependent isolation of fungal endophytes from the host plants subsequently assigning them to morphological category and their quantitative analysis and further resolving its identities through molecular affiliation. The results revealed that nine morpho-categories of fungal endophytes were allotted based on culture attributes, hyphal patterns and reproductive structural characters. Highest numbers of species were isolated from Adiantum capillus-veneris and least was recorded from Pteris vittata and Dicranopteris linearis. Maximum phenol content was analysed from the fronds of P. vittata and lowest was recorded in A. capillus-veneris. Highest flavonoid content was measured in D. linearis and lowest was detected in Christella dentata. Significant negative correlation was observed between phenol content of ferns and species richness of fungi. Moreover, significant positive correlation was observed with the relative abundance of Chaetomium globosum and flavonoid content of ferns and negative significant relation was found between relative abundance of Pseudopestalotiopsis chinensis and phenol content of pteridophytes. The occurrence and the quantitative aspects of endophytes in ferns and their secondary metabolites are discussed.

Molecular and morphological characterization of Xylaria karsticola (Ascomycota) isolated from the fruiting body of Macrolepiota procera (Basidiomycota) from Bulgaria

The present study is the first to report Xylaria karsticola isolated from the basidiocarp of Macrolepiota procera (Basidiomycota), from Stara Planina Mountain, Bulgaria and second report for such species found in Europe. The fungal isolate was in vitro cultivated and the morphology was observed. It was primarily determined as a xylariaceous morphotype at the intragenus level, based on the evaluation of colony growth rate, color, and stromatic structure formation and was confirmed by unique conidiophores and conidia. The molecular identification of the isolate was performed by amplification of ITS1-5.8S-ITS2 region and the strain was identified as Xylaria karsticola with 97.57% of confidence. The obtained sequence was deposited in the GenBank database under the accession number MW996752 and in the National Bank of Industrial Microorganisms and Cell Cultures of Bulgaria under accession number NBIMCC 9097. The phylogenetic analysis of the isolate was also conducted by including 26 sequences obtained from different Xylaria isolates. Considering the phylogenetic data, X. karsticola NBIMCC 9097 was grouped along with other X. karsticola isolates, although the DNA sequence of the novel X. karsticola was rather distantly related to the other X. karsticola sequence data. The results were supported by the bootstrap analysis (100%) and indicated the different origin of the examined X. karsticola NBIMCC 9097.

Taxonomic Advances from Fungal Flora Associated with Ferns and Fern-like Hosts in Northern Thailand

Ferns are one of the most significant plant groupings that comprise a substantial proportion of the plant flora due to the fact of their great diversity, especially in tropical areas. The biodiversity of fungi associated with ferns and fern-like hosts has also received little attention in studies. Plant samples were collected from diseased and dead plants of ten fern or fern-like species from Chiang Rai in northern Thailand. Forty-one isolates were selected from the obtained isolates for molecular and morphological analysis, with a focus on pathogenic fungal genera and consideration of the diversity in host and geographical location. Twenty-six species belonging to seven genera (Colletotrichum, Curvularia, Diaporthe, Fusarium, Lasiodiplodia, Neopestalotiopsis, and Pestalotiopsis) in six families were identified. Thirty new hosts, eight new geographical hosts, and one new species, Colletotrichum polypodialium, are described. Nepestalotiopsis phangngaensis, N. pandancola, Diaporthe tectonendophytica, D. chiangraiensis, and D. delonicis were isolated for the first time from leaf spots. Additionally, new reservoirs and geographical locations for species previously isolated from leaf spots or whose pathogenicity was established were found. However, more studies are necessary to prove the pathogenicity of the fungi isolated from the leaf spots and to identify the fungi associated with other species of ferns.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Deep sequencing across multiple host species tests pine-endophyte specificity

PREMISE

Foliar fungal endophytes vary in their distributions across landscapes or plant host taxa, indicative of specialized ecologies and host specific adaptations. Accounts of specialization, however, depend on the taxonomic breadth and geographic range of the host plants included in each study. A broad region-scale study or deep sampling of diverse potential host species still remains relatively rare but is becoming increasingly possible with high-throughput sequencing.

METHODS

Amplicon sequencing was used to rapidly identify the fungal endophytic community among six pine (Pinus, Pinaceae) species co-occurring across northeastern United States and to test for site and host specialization. We focused on the endophytic genus Lophodermium (Rhytismataceae), whose species members are thought to specialize on different pine species, to test if amplicon sequencing could rapidly verify previously implied or discover new patterns of host specificity.

RESULTS

While amplicon sequencing could analyze more samples at greater depths and recover greater numbers of unique Lophodermium taxa than when endophyte communities were surveyed with traditional culturing methods, patterns of specialization were not better supported. This may be because amplicon sequencing can indiscriminately capture non-host specific organisms found incidentally from plant tissues or because we have overestimated host-specificity in the past with biased culturing techniques.

CONCLUSIONS

Amplicon sequencing can quickly identify patterns of host specificity by allowing large-scale surveys but has limitations in quantifying the level of intimacy of these relationships.

Habitat-scale heterogeneity maintains fungal endophyte diversity in two native prairie legumes

The assembly of fungal endophyte communities within plants depends on the complex interactions of fungal taxa, their host plants, and the abiotic environment. Prairie plant communities provide a unique avenue to explore the interplay of biotic and abiotic factors affecting endophyte communities, since the historical distribution of prairies spans a broad range of temperature and precipitation, while the distances between small fragments of contemporary prairie communities may challenge the dispersal capabilities of these otherwise ubiquitous fungi. We sampled foliar fungal endophytes from two native prairie legumes, purple and white prairie clovers (Dalea purpurea and D. candida), in 17 remnant prairie sites across Minnesota in order to evaluate the relative contributions of abiotic factors, host species, and dispersal limitation to the diversity and structure of these communities. We found that similarity of communities was significantly associated with their location along a temperature and precipitation gradient, and we showed a distance-decay relationship that suggests dispersal limitations only over very large spatial scales. Although the effect of host species was small relative to these other factors, the two Dalea species maintained distinct communities within sites where they co-occur. Our results illustrate the capacity of many of these endophyte taxa to disperse over large distances and across heterogeneous biotic and abiotic environments and suggest that the interplay of biotic and abiotic factors maintains high diversity observed in endophyte communities.

Double lives: transfer of fungal endophytes from leaves to woody substrates

Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree (Nectandra lineatifolia) directly onto sterile wood fragments and incubating them for 6 weeks. Fungi from the wood were subsequently isolated in culture and identified to the genus level by ITS sequences or morphology. Four-hundred and seventy-seven fungal isolates comprising 24 taxa were cultured from the wood. Of these, 70.8% of taxa (82.3% of isolates) belong to saprotrophic genera according to the FUNGuild database. Furthermore, 27% of OTUs (6% of isolates) were basidiomycetes, an unusually high proportion compared to typical endophyte communities. Xylaria flabelliformis, although absent in our original isolations, formed anamorphic fruiting structures on the woody substrates. We introduce the term viaphyte (literally, "by way of plant") to refer to fungi that undergo an interim stage as leaf endophytes and, after leaf senescence, colonize other woody substrates via hyphal growth. Our results support the FA hypothesis and suggest that viaphytism may play a significant role in fungal dispersal.

Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistry

PREMISE

Interactions between fungal endophytes and their host plants present useful systems for identifying important factors affecting assembly of host-associated microbiomes. Here we investigated the role of secondary chemistry in mediating host affinity of asymptomatic foliar endophytic fungi using Psychotria spp. and Theobroma cacao (cacao) as hosts.

METHODS

First, we surveyed endophytic communities in Psychotria species in a natural common garden using culture-based methods. Then we compared differences in endophytic community composition with differences in foliar secondary chemistry in the same host species, determined by liquid chromatography-tandem mass spectrometry. Finally, we tested how inoculation with live and heat-killed endophytes affected the cacao chemical profile.

RESULTS

Despite sharing a common environment and source pool for endophyte spores, different Psychotria host species harbored strikingly different endophytic communities that reflected intrinsic differences in their leaf chemical profiles. In T. cacao, inoculation with live and heat-killed endophytes produced distinct cacao chemical profiles not found in uninoculated plants or pure fungal cultures, suggesting that endophytes, like pathogens, induce changes in secondary chemical profiles of their host plant.

CONCLUSIONS

Collectively our results suggest at least two potential processes: (1) Plant secondary chemistry influences assembly and composition of fungal endophytic communities, and (2) host colonization by endophytes subsequently induces changes in the host chemical landscape. We propose a series of testable predictions based on the possibility that reciprocal chemical interactions are a general property of plant-endophyte interactions.

Multilocus phylogeny of Acrospermaceae: New epibiotic species and placement of Gonatophragmium, Pseudovirgaria, and Phaeodactylium anamorphs

Acrospermum is a poorly known genus of epibiotic and saprophytic species with a subcosmopolitan distribution. Here, we investigate the intriguing relationship between Acrospermum and its host plants in the fern family Polypodiaceae, where it occurs upon approximately 45 neotropical species. We conducted phylogenetic analyses using an eight-marker comprehensive ascomycete data set comprising 719 species representing all major lineages along with 23 new Acrospermum specimens sampled from ferns. We ask whether fern-dwelling Acrospermum are monophyletic, whether epibiotic Acrospermum have evolved independently from saprophytic ancestors, and identify anamorphic phases by incorporating sequences for all suspected taxa. Our results corroborate the placement of Acrospermales within the Dothideomycetes with strong support. However, the order remains incertae sedis due to weak support along the branches subtending the clade that includes the Acrospermales plus Dyfrolomycetales. Our results show a strong phylogenetic pattern in lifestyles but do not clearly identify an ancestral life history state. The first divergence in Acrospermaceae splits fungicolous taxa from taxa that inhabit plants; saprophytes and anamorphic phases found on angiosperms occur in both clades. Fungicolous species are monophyletic, whereas species with an epibiotic or necrotic life history upon plants are nonmonophyletic due to the position of the saprophyte A. longisporium. Previously, all Acrospermum collected from ferns were identified as A. maxonii. Our results indicate that this is not monophyletic due to the inclusion of Gonatophragmium triuniae. Two species are described herein as A. gorditum, sp. nov., and A. leucocephalum, sp. nov. We find no instances of co-cladogenesis; however, our ability to detect this is limited by the lack of resolution in the A. maxonii clade. Rather, we see that that the distribution of epibiotic Acrospermum is explained by the overlap between the ecological niche of the Acrospermum species and its host.

Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera

Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.

Diversity and bioactive potential of culturable fungal endophytes of Dysosma versipellis; a rare medicinal plant endemic to China

The plant Dysosma versipellis is known for its antimicrobial and anticancer properties but is a rare and vulnerable perennial herb that is endemic to China. In this study, 224 isolates were isolated from various tissues of D. versipellis, and were classified into 53 different morphotypes according to culture characteristics and were identified by sequence analyses of the internal transcribed spacer (ITS) region of the rRNA gene. Although nine strains were not assignable at the phylum level, 44 belonged to at least 29 genera of 15 orders of Ascomycota (93%), Basidiomycota (6%), and Zygomycota (1%). Subsequent assays revealed antimicrobial activities of 19% of endophytic extracts against at least one pathogenic bacterium or fungus. Antimicrobial activity was also determined using the agar diffusion method and was most prominent in extracts from four isolates. Moreover, high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry analyses (UPLC-QTOF MS) showed the presence of podophyllotoxin in two Fusarium strains, with the highest yield of 277 μg/g in Fusarium sp. (WB5121). Taken together, the present data suggest that various endophytic fungi of D. versipellis could be exploited as sources of novel natural antimicrobial or anticancer agents.