Root-associated Fungal Endophytes Research Articles

Temporal Variation in Community Composition of Root Associated Endophytic Fungi and Carbon and Nitrogen Stable Isotope Abundance in Two Bletilla Species (Orchidaceae).

Mycorrhizae are an important energy source for orchids that may replace or supplement photosynthesis. Most mature orchids rely on mycorrhizae throughout their life cycles. However, little is known about temporal variation in root endophytic fungal diversity and their trophic functions throughout whole growth periods of the orchids. In this study, the community composition of root endophytic fungi and trophic relationships between root endophytic fungi and orchids were investigated in Bletilla striata and B. ochracea at different phenological stages using stable isotope natural abundance analysis combined with molecular identification analysis. We identified 467 OTUs assigned to root-associated fungal endophytes, which belonged to 25 orders in 10 phyla. Most of these OTUs were assigned to saprotroph (143 OTUs), pathotroph-saprotroph (63 OTUs) and pathotroph-saprotroph-symbiotroph (18 OTUs) using FunGuild database. Among these OTUs, about 54 OTUs could be considered as putative species of orchid mycorrhizal fungi (OMF). For both Bletilla species, significant temporal variation was observed in the diversity of root endophytic fungi. The florescence and emergence periods had higher fungal community richness of total species and endemic species than did other periods. Both Bletilla species were dominated by Agaricomycetes and Basidiomycota fungi throughout the whole year; however, their abundances varied between two Bletilla species and among phenological stages. Meanwhile, the ranges of 13C and 15N natural abundance were also highly dynamic across all growth stages of Bletilla species. Compared with the surrounding autotrophic plants, significant 13C enrichments (ε13C) were found across all phenological stages, while significant 15N enrichment in the florescence period and strong 15N depletion during the fruiting period were found for both Bletilla species. We can deduce that both Bletilla species obtained carbon from root endophytic fungi during the whole year. Additionally, the temporal varying tendency of root endophytic fungal diversity was consistent with 13C enrichments, which was also accord with the nutritional requirement of plant.

Untangling factors that drive community composition of root associated fungal endophytes of Neotropical epiphytic orchids

Abstract In orchids, most of the root-associated fungal endophytes remain undescribed as well as the drivers that affect their interactions with the plants. We characterized root-associated fungal endophytes of co-existing orchids across sites in two areas of montane rainforest in the southern Ecuadorian Andes. We amplified the nrDNA ITS2 region of 130 orchid individuals with Illumina MiSeq technology and tested whether changes in the structure of fungal communities are associated with hosts' phylogeny or the sites where the orchids grow. We identified 3492 OTUs corresponding to the Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Zygomycota phyla. Fungal communities associated with orchids at the lower geographic areas (between 2050 and 2800 m a.s.l.) showed that host evolution and sites are drivers that could shape distinct fungal communities, while at the highest geographic areas (between 3000 and 3500 m a.s.l.), no distinct fungal communities were found neither between co-existing orchid species nor between sites. These results suggested that among orchid species, abiotic and biotic factors do not influence the composition of fungal communities in the same way.

Soil Influences Colonization of Root-Associated Fungal Endophyte Communities of Maize, Wheat, and Their Progenitors

Root-associated fungal endophytes are vital component of root microbiome as some mitigate their host’s abiotic and biotic stress. We characterized root-associated fungal endophytes in cereal grains and their progenitors grown on two different soil-types. We aimed at determining how clay and desert soil affects the colonization of root fungal community. Both culture-dependent and culture-independent methods were employed to identify endophytes that successfully colonized greenhouse-grown host plants. The Internal Transcriber Spacer region of fungal ribosomal DNA was utilized for identification purposes. This study revealed soil as a prominent factor influencing the composition of microfungal communities inhabiting the roots of maize (Zea mays subsp. mays) and its conspecific progenitor, teosinte (Zea mays subsp. parviglumis). Similar results were found in wheat (Triticum aestivum subsp. aestivum) and its progenitor (Triticum monococcum subsp. monococcum). The multidimensional comparisons of Morisita-Horn similarity values of fungal colonists of various host plant taxa indicated that soil plays a primary role in shaping the root fungal community; a secondary effect was plant host identity, even when the plant host is a conspecific. Future studies focused on characterizing root endophytes in other cereal grains, and studying the effect of edaphic factors on fungal colonization, can ultimately contribute to crop productivity.

Precipitation increases the abundance of some groups of root-associated fungal endophytes in a semiarid grassland

Diverse communities of Root-Associated Fungal (RAF) species, including Dark Septate Endophytes (DSE), inhabit grasses in semiarid soils. These aridlands are often distinguished by large but variable precipitation events (monsoons). We sought to compare the composition and fungal load of the RAF community inhabiting the roots of Sporobolus cryptandrus, a dominant forage grass, exposed to variable precipitation events. We used a rainfall manipulation experiment at the Sevilleta National Wildlife Refuge (SNWR) to examine the abundance and composition of the RAF communities using molecular and microscopic techniques. Molecular data reveals that the RAF communities are dominated by Ascomycetes and few sequences were related to Arbuscular Mycorrhizal Fungi (AMF). The most dominant group (Paraphaeosphaeria spp.) clearly increased in abundance in response to water amendments and the addition of similar volumes of water appeared to increase similarity among the RAF communities, irrespective of size and distribution of precipitation events. Microscopic examinations of the roots also revealed an increased fungal load when exposed to elevated moisture, irrespective of rainfall frequency. We suggest that the increase in these cosmopolitan and abundant groups of Ascomycete fungi, in part, represents a common but complicated strategy of water translocation in a variety of soil types, similar to that proposed and shown in the arbuscular mycorrhizal fungi (AMF). Additional work should examine whether many (or most) members of the Ascomycete RAF also can facultatively broker water in the larger biological network in the soil.

Molecular Characterization of Coprophilous Fungal Communities Reveals Sequences Related to Root-Associated Fungal Endophytes

This paper reports the use of molecular methods to characterize the coprophilous fungal communities (CFC) that inhabit the dung of four species of mammalian herbivores at two sites, Sevilleta National Wildlife Refuge (SNWR) in New Mexico and Wind Cave National Park (WCNP) in South Dakota. Results reveal that CFC from domesticated cattle (Bos taurus) at SNWR, and bison (Bison bison) and black-tailed prairie dogs (Cynomys ludovicianus) at WCNP were diverse but dominated primarily by members within eight taxonomic orders, including the rarely cultured and anaerobic order Neocallimastigales. In addition, 7.7% (138 of 1,788) of the sequences obtained from all dung samples were at least 97% similar to root-associated fungal (RAF) sequences previously described from blue grama (Bouteloua gracilis), a common forage grass found throughout North America and growing at both study sites. In contrast, 95.8% (295 of 308) of the sequences and four of the total seven operational taxonomic units obtained from pronghorn antelope (Antilocapra americana) dung belonged to the Pleosporalean order. We hypothesize that some herbivore vectors disperse non-systemic (non-clavicipitaceous) fungal endophytes. These dispersal events, it is argued, are most likely to occur via herbivores that occasionally forage and masticate root tissue, especially in arid regions where aboveground vegetation is sparse. The results of this study suggest that some (possibly many) members of the RAF community can expand their ecological role to include colonizing dung.

Diversity of root-associated fungal endophytes in Rhododendron fortunei in subtropical forests of China

To investigate the diversity of root endophytes in Rhododendron fortunei, fungal strains were isolated from the hair roots of plants from four habitats in subtropical forests of China. In total, 220 slow-growing fungal isolates were isolated from the hair roots of R. fortunei. The isolates were initially grouped into 17 types based on the results of internal transcribed spacer-restriction fragment length polymorphism (ITS-RFLP) analysis. ITS sequences were obtained for representative isolates from each RFLP type and compared phylogenetically with known sequences of ericoid mycorrhizal endophytes and selected ascomycetes or basidiomycetes. Based on phylogenetic analysis of the ITS sequences in GenBank, 15 RFLP types were confirmed as ascomycetes, and two as basidiomycetes; nine of these were shown to be ericoid mycorrhizal endophytes in experimental cultures. The only common endophytes of R. fortunei were identified as Oidiodendron maius at four sites, although the isolation frequency (3-65%) differed sharply according to habitat. Phialocephala fortinii strains were isolated most abundantly from two habitats which related to the more acidic soil and pine mixed forests. A number of less common mycorrhizal RFLP types were isolated from R. fortunei at three, two, or one of the sites. Most of these appeared to have strong affinities for some unidentified root endophytes from Ericaceae hosts in Australian forests. We concluded that the endophyte population isolated from R. fortunei is composed mainly of ascomycete, as well as a few basidiomycete strains. In addition, one basidiomycete strain was confirmed as a putative ericoid mycorrhizal fungus.

Genetic diversity of root-associated fungal endophytes from Calluna vulgaris at contrasting field sites.

A total of 107 putative ericoid mycorrhizal endophytes were isolated from hair roots of Calluna vulgaris from two abandoned arsenic/copper mine sites and a natural heathland site in southwest England. The endophytes were initially grouped as 14 RFLP types, based on the results of ITS-RFLP analysis using the restriction endonucleases Hinf I, Rsa I and Hae III. ITS sequences were obtained for representative isolates from each RFLP type and compared phylogenetically with sequences for known ericoid mycorrhizal endophytes and selected ascomycetes. The majority of endophyte isolates (62-92%) from each site were identified as Hymenoscyphus ericae, but a number of other less common mycorrhizal RFLP types were also identified, all of which appear to have strong affinities with the order Leotiales. None of the less common RFLP types was isolated from C. vulgaris at more than one field site. Neighbour-joining analysis indicated similarities between the endophytes from C. vulgaris and mycorrhizal endophytes isolated from other Ericaceae and Epacridaceae hosts in North America and Australia.