Biogeography and Ecology of Tulasnellaceae

Diversity of Mycorrhizal Fungi in Temperate Orchid Species: Comparison of Culture-Dependent and Culture-Independent Methods

Many orchid species are endangered due to anthropogenic pressures such as habitat destruction and overharvesting, meanwhile, all orchids rely on orchid mycorrhizal fungi (OMF) for seed germination and seedling growth. Therefore, a better understanding of this intimate association is crucial for orchid conservation. Isolation and identification of OMF remain challenging as many fungi are unculturable. In our study, we tested the efficiency of both culture-dependent and culture-independent methods to describe OMF diversity in multiple temperate orchids and assessed any phylogenetic patterns in cultivability. The culture-dependent method involved the cultivation and identification of single pelotons (intracellular hyphal coils), while the culture-independent method used next-generation sequencing (NGS) to identify root-associated fungal communities. We found that most orchid species were associated with multiple fungi, and the orchid host had a greater impact than locality on the variability in fungal communities. The culture-independent method revealed greater fungal diversity than the culture-dependent one, but despite the lower detection, the isolated fungal strains were the most abundant OMF in adult roots. Additionally, the abundance of NGS reads of cultured OTUs was correlated with the extent of mycorrhizal root colonization in orchid plants. Finally, this limited-scale study tentatively suggests that the cultivability character of OMF may be randomly distributed along the phylogenetic trees of the rhizoctonian families.

Culture age of Tulasnella affects symbiotic germination of the critically endangered Wyong sun orchid Thelymitra adorata (Orchidaceae)

Orchids (Orchidaceae) are dependent on mycorrhizal fungi for germination and to a varying extent as adult plants. We isolated fungi from wild plants of the critically endangered terrestrial orchid Thelymitra adorata and identified them using a multi-region barcoding approach as two undescribed Tulasnella species, one in each of phylogenetic group II and III (OTU1) of the Tulasnellaceae. Using symbiotic propagation methods, we investigated the role of Tulasnella identity (species and isolate) and age post isolation, on the fungus's ability and efficacy in germinating T. adorata. The group II isolate did not support germination. Seed germination experiments were conducted using either (i) three different isolates of OTU1, (ii) 4- and 12-week-old fungal cultures (post isolation) of a single isolate of OTU1, and (iii) T. subasymmetrica which is widespread and known to associate with other species of Thelymitra. Culture age and fungal species significantly (P < 0.05) affected the time to germination and percentage of seed germination, with greater and faster germination with 4-week-old cultures. Tulasnella subasymmetrica was able to germinate T. adorata to leaf stage, although at slightly lower germination percentages than OTU1. The ability of T. adorata to germinate with T. subasymmetrica may allow for translocation sites to be considered outside of its native range. Our findings on the age of Tulasnella culture affecting germination may have applications for improving the symbiotic germination success of other orchids. Furthermore, storage of Tulasnella may need to take account of the culture age post-isolation, with storage at - 80 °C as soon as possible recommended, post isolation.

Isolation of Tulasnella spp. from Cultivated Paphiopedilum Orchids and Screening of Germination-Enhancing Fungi

Ex situ conservation, an important way to increase the survival and sustainability of endangered species, is widely used in the conservation of endangered orchids. However, long-term ex situ conservation might affect the dominant group of orchid symbiotic fungi, which are crucial for orchid growth and reintroduction. This study investigated the culturable Tulasnella spp. associated with Paphiopedilum orchids after long-term greenhouse cultivation, and identified germination-enhancing isolates. A total of 44 Tulasnella isolates were obtained from the roots of 14 Paphiopedilum spp., and 29 of them were selected for phylogenetic analysis. They clustered mainly with Tulasnella deliquescens, Tulasnella calospora, Tulasnella bifrons, and Tulasnella irregularis, but included two potential new groups. Compared with published uncultured data, most of the isolates were grouped together with the reported types, and the dominant Tulasnella associated with P. armeniacum and P. micranthum could still be isolated after ten years of cultivation, most of which were the first isolation. In vitro symbiotic germination showed that certain root isolates could promote seed germination (e.g., parm152 isolated from P. armeniacum, Php12 from P. hirsutissimum, and prhi68 from P. rhizomatosum). These data indicated that the dominant Tulasnella types colonizing the roots of cultivated Paphiopedilum are stable over time, and germination-enhancing fungi colonizing the roots would benefit for seed reproduction after population reintroduction into the wild.

Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny

Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.

New species of Tulasnella associated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae

Tulasnella (Tulasnellaceae) is a genus of fungus that can form mycorrhizal associations with orchids (Orchidaceae). Here we used molecular phylogenetic analyses and morphological characteristics of pure cultures across four different media to support the description of five new Tulasnella species associated with commonly occurring and endangered Australian orchids. Tulasnella nerrigaensis associates with Calochilus; T. subasymmetrica and T. kiataensis with Thelymitra; and T. korungensis and T. multinucleata with Pyrorchis and Rimacola respectively. The newly described species were primarily delimited by analyses of five loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), C14436 (adenosine triphosphate [ATP] synthase), C4102 (glutamate synthase), C3304 (ATP helicase), and mt large subunit 16S rDNA (mtLSU). Tulasnella subasymmetrica is introduced for some isolates previously identified as T. asymmetrica, and this latter species is characterized from multilocus sequencing of a new isolate that matches ITS sequences from the ex-type culture. Morphological differences between the new species are slight. Tulasnella multinucleata has 6-12 nuclei per hyphal compartment which is the first instance of multinucleate rather than binucleate or trinucleate hyphal compartments in Tulasnella. The formal description of these species of Tulasnella will aid in future evolutionary and ecological studies of orchid-fungal interactions.

Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use

With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.

Progress and Prospects of Mycorrhizal Fungal Diversity in Orchids

Orchids form mycorrhizal symbioses with fungi in natural habitats that affect their seed germination, protocorm growth, and adult nutrition. An increasing number of studies indicates how orchids gain mineral nutrients and sometime even organic compounds from interactions with orchid mycorrhizal fungi (OMF). Thus, OMF exhibit a high diversity and play a key role in the life cycle of orchids. In recent years, the high-throughput molecular identification of fungi has broadly extended our understanding of OMF diversity, revealing it to be a dynamic outcome co-regulated by environmental filtering, dispersal restrictions, spatiotemporal scales, biogeographic history, as well as the distribution, selection, and phylogenetic spectrum width of host orchids. Most of the results show congruent emerging patterns. Although it is still difficult to extend them to all orchid species or geographical areas, to a certain extent they follow the "everything is everywhere, but the environment selects" rule. This review provides an extensive understanding of the diversity and ecological dynamics of orchid-fungal association. Moreover, it promotes the conservation of resources and the regeneration of rare or endangered orchids. We provide a comprehensive overview, systematically describing six fields of research on orchid-fungal diversity: the research methods of orchid-fungal interactions, the primer selection in high-throughput sequencing, the fungal diversity and specificity in orchids, the difference and adaptability of OMF in different habitats, the comparison of OMF in orchid roots and soil, and the spatiotemporal variation patterns of OMF. Further, we highlight certain shortcomings of current research methodologies and propose perspectives for future studies. This review emphasizes the need for more information on the four main ecological processes: dispersal, selection, ecological drift, and diversification, as well as their interactions, in the study of orchid-fungal interactions and OMF community structure.

New species of Tulasnella associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae

Many orchids have an obligate relationship with Tulasnella mycorrhizal fungi for seed germination and support into adulthood. Despite the importance of Tulasnella as mycorrhizal partners, many species remain undescribed. Here, we use multiple sequence locus phylogenetic analyses to delimit and describe six new Tulasnella species associated with Australian terrestrial orchids from the subtribes Cryptostylidinae and Drakaeinae. Five of the new species, Tulasnella australiensis, T. occidentalis, T. punctata, T. densa, and T. concentrica, all associate with Cryptostylis (Cryptostylidinae), whereas T. rosea associates with Spiculaea ciliata (Drakaeinae). Isolates representing T. australiensis were previously also reported in association with Arthrochilus (Drakaeinae). All newly described Tulasnella species were delimited by phylogenetic analyses of four loci (nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS], C14436 [ATP synthase], C4102 [glutamate synthase], and mt 16S rDNA [mtLSU]). The pairwise sequence divergence between species for the ITS region ranged from 5.6% to 25.2%, and the maximum sequence divergence within the newly described species ranged from 1.64% to 4.97%. There was a gap in the distribution of within- and between-species pairwise divergences in the region of 4-6%, with only one within-species value of 4.97% (for two T. australiensis isolates) and one between-species value of 5.6% (involving an isolate of T. occidentalis) falling within this region. Based on fluorescence staining, all six new Tulasnella species are binucleate and have septate, cylindrical hyphae. There was some subtle variation in culture morphology, but colony diameter as measured on 3MN+vitamin medium after 6 wk of growth did not differ among species. However, T. australiensis grew significantly (P < 0.02) slower than others on ½ FIM and ¼ potato dextrose agar (PDA) media. Formal description of these Tulasnella species contributes significantly to documentation of Tulasnella diversity and provides names and delimitations to underpin further research on the fungi and their relationships with orchids.

Specific mycorrhizal associations involving the same fungal taxa in common and threatened Caladenia (Orchidaceae): implications for conservation

BACKGROUND AND AIMS

In orchid conservation, quantifying the specificity of mycorrhizal associations, and establishing which orchid species use the same fungal taxa, is important for sourcing suitable fungi for symbiotic propagation and selecting sites for conservation translocation. For Caladenia subgenus Calonema (Orchidaceae), which contains 58 threatened species, we ask the following questions. (1) How many taxa of Serendipita mycorrhizal fungi do threatened species of Caladenia associate with? (2) Do threatened Caladenia share orchid mycorrhizal fungi with common Caladenia? (3) How geographically widespread are mycorrhizal fungi associated with Caladenia?

METHODS

Fungi were isolated from 127 Caladenia species followed by DNA sequencing of the internal transcibed spacer (ITS) sequence locus. We used a 4.1-6 % sequence divergence cut-off range to delimit Serendipita operational taxonomic units (OTUs). We conducted trials testing the ability of fungal isolates to support germination and plant growth. A total of 597 Serendipita isolates from Caladenia, collected from across the Australian continent, were used to estimate the geographic range of OTUs.

KEY RESULTS

Across the genus, Caladenia associated with ten OTUs of Serendipita (Serendipitaceae) mycorrhizal fungi. Specificity was high, with 19 of the 23 threatened Caladenia species sampled in detail associating solely with OTU A, which supported plants from germination to adulthood. The majority of populations of Caladenia associated with one OTU per site. Fungal sharing was extensive, with 62 of the 79 Caladenia sampled in subgenus Calonema associating with OTU A. Most Serendipita OTUs were geographically widespread.

CONCLUSIONS

Mycorrhizal fungi can be isolated from related common species to propagate threatened Caladenia. Because of high specificity of most Caladenia species, only small numbers of OTUs typically need to be considered for conservation translocation. When selecting translocation sites, the geographic range of the fungi is not a limiting factor, and using related Caladenia species to infer the presence of suitable fungal OTUs may be feasible.

Altered rhizoctonia assemblages in grasslands on ex-arable land support germination of mycorrhizal generalist, not specialist orchids

Species-rich seminatural grasslands in Central Europe have suffered a dramatic loss of biodiversity due to conversion to arable land, but vast areas are being restored. Population recovery of orchids, which depend on mycorrhizal fungi for germination, is however limited. We hypothesised that ploughing and fertilisation caused shifts in orchid mycorrhizal communities in soil and restricted orchid germination. We examined edaphic conditions in 60 restored and seminatural grasslands, and germination success in 10 restored grasslands. Using a newly designed primer, we screened the composition of rhizoctonias in soil, seedlings and roots of seven orchid species. Seminatural and restored grasslands differed significantly in nutrient amounts and rhizoctonia assemblages in soil. While Serendipitaceae prevailed in seminatural grasslands with a higher organic matter content, Ceratobasidiaceae were more frequent in phosphorus-rich restored grasslands with increased abundance on younger restored sites. Tulasnellaceae displayed no preference. Germination success in restored grasslands differed significantly between orchid species; two mycorrhizal generalist species germinated with a broad range of rhizoctonias at most restored grasslands, while germination success of specialists was low. Past agricultural practices have a long-lasting effect on soil conditions and orchid mycorrhizal communities. Altered mycorrhizal availability may be the main reason for low germination success of specialist orchid species.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

In situ Orchid Seedling-Trap Experiment Shows Few Keystone and Many Randomly Associated Mycorrhizal Fungal Species During Early Plant Colonization

Orchids are known for their vast diversity and dependency on mycorrhizal fungi. Under in situ conditions, the biotic and abiotic factors determining the composition and distribution of orchid mycorrhizal fungi (OMF) communities remain largely unexplored. Therefore in situ experiments are needed to better understand the interactions between orchids and fungi. A seedling-trap experiment was conducted in the Reserva Biológica San Francisco, a well-known biodiversity hotspot located in the Andes of southern Ecuador. The objective was to investigate the effect of orchid species, site, elevation or temporal variation on the assembly and structure of OMF associated with Cyrtochilum retusum and Epidendrum macrum. The OMF community composition was determined using the Illumina MiSeq sequencing of the internal transcribed spacer 2 (ITS2) region. The results exhibited 83 OMF operational taxonomic units belonging to Tulasnellaceae, Ceratobasidiaceae, Serendipitaceae and Atractiellales. It was observed that the composition of the OMF communities was different among orchid species and temporal variation but was not different among sites. The results further support that orchids have a core of keystone OMF that are ubiquitously distributed and stable across temporal change, whereas the majority of these fungi are randomly associated with the plants.