Ex situ seed baiting to isolate germination-enhancing fungi for assisted colonization in Paphiopedilum spicerianum, a critically endangered orchid in China

Comparative transcriptomics and proteomics analysis of the symbiotic germination of Paphiopedilum barbigerum with Epulorhiza sp. FQXY019

Introduction

Paphiopedilum barbigerum is currently the rarest and most endangered species of orchids in China and has significant ornamental value. The mature seeds of P. barbigerum are difficult to germinate owing to the absence of an endosperm and are highly dependent on mycorrhizal fungi for germination and subsequent development. However, little is known about the regulation mechanisms of symbiosis and symbiotic germination of P. barbigerum seeds.

Methods

Herein, transcriptomics and proteomics were used to explore the changes in the P. barbigerum seeds after inoculation with (FQXY019 treatment group) or without (control group) Epulorhiza sp. FQXY019 at 90 days after germination.

Results

Transcriptome sequencing revealed that a total of 10,961 differentially expressed genes (DEGs; 2,599 upregulated and 8,402 downregulated) were identified in the control and FQXY019 treatment groups. These DEGs were mainly involved in carbohydrate, fatty acid, and amino acid metabolism. Furthermore, the expression levels of candidate DEGs related to nodulin, Ca2+ signaling, and plant lectins were significantly affected in P. barbigerum in the FQXY019 treatment groups. Subsequently, tandem mass tag-based quantitative proteomics was performed to recognize the differentially expressed proteins (DEPs), and a total of 537 DEPs (220 upregulated and 317 downregulated) were identified that were enriched in processes including photosynthesis, photosynthesis-antenna proteins, and fatty acid biosynthesis and metabolism.

Discussion

This study provides novel insight on the mechanisms underlying the in vitro seed germination and protocorm development of P. barbigerum by using a compatible fungal symbiont and will benefit the reintroduction and mycorrhizal symbiotic germination of endangered orchids.

Symbiotic seed germination and seedling growth of mycorrhizal fungi in Paphiopedilum hirsutissimun (Lindl.Ex Hook.) Stein from China

Similar to other orchid species, Paphiopedilum hirsutissimum (Lindl.ex Hook.) Stein, relies on nutrients provided by mycorrhizal fungus for seed germination and seedling development in the wild owing to a lack of endosperm in its seeds. Therefore, obtaining suitable and specialized fungi to enhance seed germination, seedling formation, and further development is considered a powerful tool for orchid seedling propagation, reintroduction, and species conservation. In this study, we investigated the diversity, abundance, and frequency of endophytic fungal strains in the root organs of P. hirsutissimum. One family and five genera of the fungi were isolated and identified through rDNA-ITS sequencing. The ability of isolated fungi to germinate in vitro from the seeds of this species was evaluated, and the development of P. hirsutissimum protocorm has been described. The findings showed that the treatments inoculated with endophytic fungal DYXY033 may successfully support the advanced developmental stage of seedlings up to stage 5. In addition, scanning electron microscopy (SEM) revealed that the mycelium of this strain began to invade from either end of the seeds up to the embryo, extending rapidly from the inside to the outside. Its lengthening resulted in the bursting of the seed coat to form protocorms, which developed into seedlings. The results showed that DYXY033 has a high degree of mycobiont specificity under in vitro symbiotic seed germination conditions and is a representative mycorrhizal fungus with ecological value for the species. In summary, this strain may particularly be significant for the protection of P. hirsutissimum species that are endangered in China. In the long run, it may also contribute to global efforts in reintroducing orchid species and in realizing in situ restorations of threatened orchid populations.

Habitat ecological characteristics and soil fungal community structure of Paphiopedilum subgenus Brachypetalum Hallier (Orchidaceae) plants in Southwest China

Species of the subgenus Brachypetalum are the most primitive, most ornamental and most threatened group in the Orchid. This study revealed the ecological characteristics, soil nutrient characteristics and soil fungal community structure of habitats of the subgenus Brachypetalum in Southwest China. Lays a foundation for research on the wild populations and conservation Brachypetalum. The results showed that species of the subgenus Brachypetalum preferred a cool and humid environment, grew in scattered or aggregated form in narrow negative terrain, mainly in humic soil. The soil physical and chemical properties and soil enzyme activity indexes of the habitats were significantly different among different species, and the soil properties of different distribution points of the same species also varied greatly. There were significant differences in the soil fungal community structure among the habitats of different species. Basidiomycetes and ascomycetes were the main fungi in habitats of subgenus Brachypetalum species, and their relative abundance varied among different species. The functional groups of soil fungi were mainly symbiotic fungi and saprophytic fungi. LEfSe analysis found that there were different numbers and species of biomarkers in the habitats of subgenus Brachypetalum species, indicating that the habitat preference characteristics of each species in subgenus Brachypetalum were reflected in the fungal community. It was found that environmental factors had an impact on the changes in soil fungal communities in the habitats of subgenus Brachypetalum species, with climatic factors having the highest explanation rate (20.96%). Soil properties were significantly positively or negatively correlated with a variety of dominant soil fungal groups. Conclusions: The results of this study lay the foundation for the study of the habitat characteristics of wild populations of subgenus Brachypetalum and provides data to support in situ and ex situ conservation in the future.

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.

A novel method to produce massive seedlings via symbiotic seed germination in orchids

Orchids produce large numbers of dust-like seeds that rely heavily on orchid mycorrhizal fungi (OMFs) for germination. Using OMFs to facilitate orchid proliferation is considered an effective method for orchid conservation but still presents challenges in practice. In this study, orchid seed-fungus complexes, in which orchid seeds and fungal mycelia were embedded together to form granules, were developed as platforms to facilitate seed germination and seedling production. Overall, seedlings were produced by seed-fungus complexes for five orchid species with large variations in the percentages of seedlings produced among species/treatments. For the different fungal treatments in Dendrobium officinale, Sebacinales LQ performed much better than the other fungal strains. At 90 days after sowing, 75.8±2.6% seedlings were produced in the LQ treatment, which was significantly higher than in the Tulasnella sp. JM (22.0±3.0%) and Tulasnella sp. TPYD-2 (5.3±1.0%) treatments, as well as in the LQ and TPYD-2 cocultured treatment (40.4±3.2%), while no seedlings were formed in the Tulasnella sp. SSCDO-5 or control treatments. For the other four orchid species, only one compatible fungus for each species was used, and the percentages of seedlings in epiphytic Dendrobium devonianum (67.2±2.9%) and D. nobile (38.9±2.8%) were much higher than those in terrestrial Paphiopedilum spicerianum (2.9±1.1%) and Arundina graminifolia (6.7±2.1%) at 90 days after sowing. Adding 1% polymer water-absorbent resin to the seed-fungus complexes of D. officinale seeds with fungal strain Sebacinales LQ significantly increased seedling formation, while other additional substances showed negative effects on seedling formation. For the storage of seed-fungus complexes, it is recommended to store the seed-fungus complexes in valve bags at room temperature for a short time and at a low temperature of 4°C for no more than 30 days. As a platform for symbiotic seed germination, the seed-fungus complex can facilitate seed germination, produce seedlings and support subsequent seedling growth, and its seedling productivity depends on seed germination characteristics, seed viability, and the efficiency of fungi. Seed-fungus complexes have great potential to be used as propagules in orchid conservation.

A comparative analysis of the past and present occurrences of some species of Paphiopedilum (Orchidaceae) in northeastern India using MaxEnt and GeoCAT

Members of the genus Paphiopedilum are well known for their long-lasting unique flowers. They are becoming rare due to over-collection and habitat loss because of human disturbances and deforestation. The present study aimed to compare the past and present occurrences of the genus Paphiopedilum in northeastern India using MaxEnt and GeoCAT. A historical occurrence model (HOM) was prepared using secondary data, and an actual occurrence model (AOM) was constructed with primary field data. The HOM and AOM revealed that bioclimatic factors, topography and precipitation play a significant role in the survival of Paphiopedilum populations in northeastern India in both the current and historical distributions. The other vital environmental variables were elevation (h_dem), mean diurnal range (bio_2), annual mean temperature (bio_1), temperature annual range (bio_5) and annual precipitation (bio_12). The results showed a sharp decline in the extent of occurrence and the area of occupancy of Paphiopedilum in the study area. The extent of occurrence and area of occupancy for HOM were 170,972 km2 and 18 km2. For the AOM, they were 125,315 km2 and 12 km2, respectively. The HOM model indicated that Paphiopedilum was earlier growing sporadically. On the other hand, the AOM result indicates that it is presently growing sparsely in isolated pockets that are more prone to extinction. Paphiopedilum can be conserved successfully using an integrative conservation approach, comprising ecological modeling techniques to search for additional locations, ex situ propagation techniques, and possible reintroduction in selected areas.

Epidendrumradicans Fungal Community during Ex Situ Germination and Isolation of Germination-Enhancing Fungi

Orchids exhibit varying specificities to fungi in different microbial environments. This pilot study investigated the preference of fungal recruitment during symbiotic germination of Epidendrum radicans Pav. ex Lindl. Two different orchid substrates were used for ex situ seed baiting: pine bark and rotten oak leaf, with Basidiomycota and Ascomycota as the respective dominant groups. Both substrates promoted seed germination, with a higher protocorm formation rate on pine bark (65.75%). High-throughput sequencing characterized the fungal communities of germinated protocorms. Basidiomycota was the dominant group in protocorms that symbiotically germinated on both substrates. The family-level community structures of endophytic fungi in protocorms that symbiotically germinated on both substrates were close to those of protocorms that germinated in vitro on MS1 medium. For protocorms, the dominant fungal groups recruited from substrates differed at the genus level; from pine bark, they were genera belonging to unclassified Sebacinales (41.34%), Thanatephorus (14.48%) and Fusarium (7.35%), while, from rotten oak leaf, they were Rhizoctonia (49.46%), Clitopilus (34.61%), and Oliveonia (7.96%). Four fungal isolates were successfully obtained and identified as belonging to the family Tulasnellaceae, genera Ceratobasidium and Peniophora, which could promote seed germination to the seedling stage. The data indicate that endophytic fungi for E. radicans germination on two different substrates are affected at the genus level by the substrate, with a degree of specificity at the family level.

What role does the seed coat play during symbiotic seed germination in orchids: an experimental approach with Dendrobium officinale

BACKGROUND

Orchids require specific mycorrhizal associations for seed germination. During symbiotic germination, the seed coat is the first point of fungal attachment, and whether the seed coat plays a role in the identification of compatible and incompatible fungi is unclear. Here, we compared the effects of compatible and incompatible fungi on seed germination, protocorm formation, seedling development, and colonization patterns in Dendrobium officinale; additionally, two experimental approaches, seeds pretreated with NaClO to change the permeability of the seed coat and fungi incubated with in vitro-produced protocorms, were used to assess the role of seed coat played during symbiotic seed germination.

RESULTS

The two compatible fungi, Tulasnella sp. TPYD-2 and Serendipita indica PI could quickly promote D. officinale seed germination to the seedling stage. Sixty-two days after incubation, 67.8 ± 5.23% of seeds developed into seedlings with two leaves in the PI treatment, which was significantly higher than that in the TPYD-2 treatment (37.1 ± 3.55%), and massive pelotons formed inside the basal cells of the protocorm or seedlings in both compatible fungi treatments. In contrast, the incompatible fungus Tulasnella sp. FDd1 did not promote seed germination up to seedlings at 62 days after incubation, and only a few pelotons were occasionally observed inside the protocorms. NaClO seed pretreatment improved seed germination under all three fungal treatments but did not improve seed colonization or promote seedling formation by incompatible fungi. Without the seed coat barrier, the colonization of in vitro-produced protocorms by TPYD-2 and PI was slowed, postponing protocorm development and seedling formation compared to those in intact seeds incubated with the same fungi. Moreover, the incompatible fungus FDd1 was still unable to colonize in vitro-produced protocorms and promote seedling formation.

CONCLUSIONS

Compatible fungi could quickly promote seed germination up to the seedling stage accompanied by hyphal colonization of seeds and formation of many pelotons inside cells, while incompatible fungi could not continuously colonize seeds and form enough protocorms to support D. officinale seedling development. The improvement of seed germination by seed pretreatment may result from improving the seed coat hydrophilicity and permeability, but seed pretreatment cannot change the compatibility of a fungus with an orchid. Without a seed coat, the incompatible fungus FDd1 still cannot colonize in vitro-produced protocorms or support seedling development. These results suggest that seed coats are not involved in symbiotic germination in D. officinale.

Spatio-temporal variation in potential habitats for rare and endangered plants and habitat conservation based on the maximum entropy model

Rare and endangered plants (REPs) act as key indicators for species habitat priorities, and can thus be critical in global biodiversity protection work. Human activities and climate change pose great threats to REPs, so protection should be a top priority. In this study, we used the maximum entropy model (Maxent) to identify current and future (2050) potential habitats of REPs in the Xishuangbanna tropical area of China. We compared potential habitats with existing protected areas (PAs) in gap analysis, and used a transfer matrix to quantify changes in potential habitats. By comparing the potential distribution obtained with existing land use and land cover, we analyzed the impact of human-dominated land use changes on potential habitats of REPs and identified the main habitat patch types of REPs. The results showed that the current potential habitat area of hotspots is 2989.85 km², which will be reduced to 247.93 km² by 2050, accounting for 15.60% and 1.29% of the total research area, respectively. Analysis of land use and land cover showed that rubber plantation was the human-dominated land use posing the greatest threat to potential habitats of REPs, occupying 23.40% and 21.62% of current and future potential habitats, respectively. Monsoon evergreen broad-leaved forest was identified as the main habitat patch type for REPs in Xishuangbanna and occupied the highest proportion of potential habitat area. Gap analysis showed that only 35.85% of habitat hotspots are currently included in existing PAs and that this will decrease to 32.26% by 2050. This emphasizes the importance of protecting current and future potential habitats of REPs in a dynamic conservation approach that can adapt to changes in future climate and human activities.

Different Strategies for Photosynthetic Regulation under Fluctuating Light in Two Sympatric Paphiopedilum Species

Fluctuating light can cause selective photoinhibition of photosystem I (PSI) in angiosperms. Cyclic electron flow (CEF) around PSI and electron flux from water via the electron transport chain to oxygen (the water-water cycle) play important roles in coping with fluctuating light in angiosperms. However, it is unclear whether plant species in the same genus employ the same strategy to cope with fluctuating light. To answer this question, we measured P700 redox kinetics and chlorophyll fluorescence under fluctuating light in two Paphiopedilum (P.) Pftzer (Orchidaceae) species, P. dianthum and P. micranthum. After transition from dark to high light, P. dianthum displayed a rapid re-oxidation of P700, while P. micranthum displayed an over-reduction of P700. Furthermore, the rapid re-oxidation of P700 in P. dianthum was not observed when measured under anaerobic conditions. These results indicated that photo-reduction of O₂ mediated by the water-water cycle was functional in P. dianthum but not in P. micranthum. Within the first few seconds after an abrupt transition from low to high light, PSI was highly oxidized in P. dianthum but was highly reduced in P. micranthum, indicating that the different responses of PSI to fluctuating light between P. micranthum and P. dianthum was attributed to the water-water cycle. In P. micranthum, the lack of the water-water cycle was partially compensated for by an enhancement of CEF. Taken together, P. dianthum and P. micranthum employed different strategies to cope with the abrupt change of light intensity, indicating the diversity of strategies for photosynthetic acclimation to fluctuating light in these two closely related orchid species.

In Vitro Symbiotic Germination: A Revitalized Heuristic Approach for Orchid Species Conservation

As one of the largest families of flowering plants, Orchidaceae is well-known for its high diversity and complex life cycles. Interestingly, such exquisite plants originate from minute seeds, going through challenges to germinate and establish in nature. Alternatively, orchid utilization as an economically important plant gradually decreases its natural population, therefore, driving the need for conservation. As with any conservation attempts, broad knowledge is required, including the species' interaction with other organisms. All orchids establish mycorrhizal symbiosis with certain lineages of fungi to germinate naturally. Since the whole in situ study is considerably complex, in vitro symbiotic germination study is a promising alternative. It serves as a tool for extensive studies at morphophysiological and molecular levels. In addition, it provides insights before reintroduction into its natural habitat. Here we reviewed how mycorrhiza contributes to orchid lifecycles, methods to conduct in vitro study, and how it can be utilized for conservation needs.