Similar mycorrhizal fungal communities associated with epiphytic and lithophytic orchids of Coelogyne corymbosa

Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation

Despite being the second largest family of flowering plants, orchids represent community structure variation in plant-microbial associations, contributes to niche partitioning in metacommunity assemblages. Yet, mycorrhizal communities and interactions remain unknown for orchids that are highly specialized or even obligated in their associations with their mycorrhizal partners. In this study, we sought to compare orchid mycorrhizal fungal (OMF) communities of three co-occurring hemiepiphytic Vanilla species (V. hartii, V. pompona, and V. trigonocarpa) in tropical forests of Costa Rica by addressing the identity of their OMF communities across species, root types, and populations, using high-throughput sequencing. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) yielded 299 fungal Operational Taxonomic Units (OTUs) from 193 root samples. We showed distinct segregation in the putative OMF (pOMF) communities of the three coexisting Vanilla hosts. We also found that mycorrhizal communities associated with the rare V. hartii varied among populations. Furthermore, we identified Tulasnellaceae and Ceratobasidiaceae as dominant pOMF families in terrestrial roots of the three Vanilla species. In contrast, the epiphytic roots were mainly dominated by OTUs belonging to the Atractiellales and Serendipitaceae. Furthermore, the pOMF communities differed significantly across populations of the widespread V. trigonocarpa and showed patterns of distance decay in similarity. This is the first report of different pOMF communities detected in roots of wild co-occurring Vanilla species using high-throughput sequencing, which provides evidence that three coexisting Vanilla species and their root types exhibited pOMF niche partitioning, and that the rare and widespread Vanilla hosts displayed diverse mycorrhizal preferences.

Gains and losses of the epiphytic lifestyle in epidendroid orchids: review and new analyses of succulence traits

BACKGROUND AND AIMS

Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Because water supply is generally erratic compared to that in soils, succulent forms in particular are widespread in epiphytic species. However, succulent organs also exist in terrestrial plants, and the question of the concomitant evolution of epiphytism and succulence has received little attention, not even in the epidendroid orchids, which account for 67.6 % of vascular epiphytes.

METHODS

We built a new time-calibrated phylogenetic tree of Epidendroideae with 203 genera treated in genus Orchidacearum, from which we reconstructed the evolution of epiphytism as well as traits related to water scarcity (stem and leaf succulence and the number of velamen layers), while testing for the correlated evolution between the two. Furthermore, we estimated the ancestral geographical ranges to evaluate the palaeoclimatic context in which epiphytism evolved.

KEY RESULTS

Epiphytism evolved at least three times: 39.0 million years ago (Mya) in the common ancestor of the Malaxideae and Cymbidieae that probably ranged from the Neotropics to Southeast Asia and Australia, 11.5 Mya in the Arethuseae in Southeast Asia and Australia, and 7.1 Mya in the neotropical Sobralieae, and it was notably lost in the Malaxidiinae, Collabieae, Calypsoeae, Bletiinae and Eulophiinae. Stem succulence is inferred to have evolved once, in a terrestrial ancestor at least 4.1 Mya before the emergence of epiphytic lineages. If lost, stem succulence was almost systematically replaced by leaf succulence in epiphytic lineages.

CONCLUSIONS

Epiphytism may have evolved in seasonally dry forests during the Eocene climatic cooling, among stem-succulent terrestrial orchids. Our results suggest that the emergence of stem succulence in early epidendroids was a key innovation in the evolution of epiphytism, facilitating the colonization of epiphytic environments that later led to the greatest diversification of epiphytic orchids.

Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism

Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29 Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.

Low Specificity but Dissimilar Mycorrhizal Communities Associating with Roots May Contribute to the Spatial Pattern of Four Co-Occurring Habenaria (Orchidaceae) Species

Fungi with orchid roots have been increasingly proven to play important roles in orchid growth, spatial distribution, and coexistence of natural communities. Here, we used 454 amplicon pyrosequencing with two different primer combinations to investigate the spatial variations in the community of OMF and endophytic fungi associates within the roots of four co-occurring Habenaria species. The results showed that all investigated Habenaria species were generalists and the different fungi communities may contribute to the spatial separation of the four Habenaria species. Firstly, the fungal OTUs identified in the roots of the four species overlapped but their presence differed amongst species and numerous distinct OMF families were unique to each species. Second, NMDS clustering showed samples clustered together based on associated species and PERMANOVA analyses indicated that fungi communities in the roots differed significantly between the Habenaria species, both for all endophytic fungi communities and for OMF communities. Third, the network structure of epiphytic fungi was highly specialized and modular but demonstrated lowly connected and anti-nested properties. However, it calls for more soil nutrition and soil fungal communities' studies to elucidate the contribution of habitat-specific adaptations in general and mycorrhizal divergence.

Dominant Dendrobium officinale mycorrhizal partners vary among habitats and strongly induce seed germination in vitro

Dendrobium officinale (Orchidaceae) is an endangered epiphytic orchid that has been well studied as a medicinal plant. Although previous studies have shown that various fungal isolates promote D. officinale seed germination and seedling development in vitro, mycorrhizal associations among its wild populations remain poorly understood. In this study, we identified mycorrhizal fungi associated with D. officinale (36 individuals from six sites) using Sanger sequencing and compared fungal communities among sites and habitats (lithophytic vs. epiphytic individuals). Among the obtained sequences, 76 belonged to orchid mycorrhizal fungi (OMF), among which Tulasnellaceae accounted for 45.8% and Serendipitaceae for 28.1%. The Serendipitaceae operational taxonomic unit (OTU) SE1 was the most dominant partner, accounting for 27.1% of all detected fungal sequences, followed by a Tulasnellaceae OTU, TU27, which accounted for 15.6%. The relative frequencies of Serendipitaceae and Tulasnellaceae differed greatly between lithophytic and epiphytic individuals. Serendipitaceae accounted for 47.3% of the OMF sequences among lithophytes, and Tulasnellaceae for 95.2% among epiphytes. Mycorrhizal community composition also varied among sites. We further conducted in vitro symbiotic culture from seeds with six fungal isolates. Two Serendipitaceae and two Tulasnellaceae isolates, including SE1 and TU27, significantly promoted seed germination and seedling development. These results indicate that D. officinale is mainly associated with Tulasnellaceae and Serendipitaceae as its main fungal partners, which strongly induced seed germination and seedling development in vitro, suggesting their association with D. officinale through its life cycle.

Orchid conservation in China from 2000 to 2020: Achievements and perspectives

We review achievements in the conservation of orchid diversity in China over the last 21 years. We provide updated information on orchid biodiversity and suggestions for orchid conservation in China. We outline national policies of biodiversity conservation, especially of orchid conservation, which provide general guidelines for orchid conservation in China. There are now approximately 1708 known species of Orchidaceae in 181 genera in China, including five new genera and 365 new species described over the last 21 years. The assessment of risk of extinction of all 1502 known native orchid species in China in 2013 indicated that 653 species were identified as threatened, 132 species were treated as data-deficient, and four species endemic to China were classified as extinct. Approximately 1100 species (ca. 65%) are protected in national nature reserves, and another ~66 species in provincial nature reserves. About 800 native orchid species have living collections in major botanical gardens. The pollination biology of 74 native orchid species and the genetic diversity and spatial genetic structure of 29 orchid species have been investigated at a local scale and/or across species distributions. The mycorrhizal fungal community composition has been investigated in many genera, such as Bletilla, Coelogyne, Cymbidium, Cypripedium, and Dendrobium. Approximately 292 species will be included in the list of national key protected wild plants this year. Two major tasks for near future include in situ conservation and monitoring population dynamics of endangered species.

How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics

Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.