Next Article in Journal
Sea Slugs (Mollusca, Gastropoda, Heterobranchia) from the Medes Islands (Costa Brava, NE Spain): Biodiversity and Ecological Study over a Decade
Previous Article in Journal
Species List and Temporal Trends of a Butterfly Community in an Urban Remnant in the Atlantic Forest
Previous Article in Special Issue
Insight into the Yeast Diversity of Hungarian Honeys
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Diversity
Volume 17
Issue 9
10.3390/d17090605
diversity-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions

by
Jingjing Du
1,
Shengqian Guo
2,
Xiaohang Li
2,
Zhonghu Geng
2,
Zhiliang Yuan
2 and
Xiqiang Song
1,*
1
College of Tropical Agriculture and Forestry, Hainan University, No. 58 Renmin Avenue, Meilan District, Haikou 570228, China
2
College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou 450002, China
*
Author to whom correspondence should be addressed.
Diversity 2025, 17(9), 605; https://doi.org/10.3390/d17090605
Submission received: 29 May 2025 / Revised: 23 July 2025 / Accepted: 24 July 2025 / Published: 28 August 2025
(This article belongs to the Special Issue Fungal Diversity)
Browse Figures
Versions Notes

Abstract

Orchidaceae is among the most diverse and widely distributed families of angiosperms, with significant ecological, ornamental, and medicinal value. However, the structure, function, and environmental associations of rhizosphere soil bacterial communities associated with Orchidaceae remain poorly characterized. This study selected five common Orchidaceae species in the transitional zone between the warm temperate and subtropical regions of China (Changnienia amoena, Cypripedium macranthos, Cremastra appendiculata, Cymbidium faberi, and Gastrodia elata). Using high-throughput sequencing technology, we characterized the bacterial diversity of the rhizosphere soil associated with these species and investigated their relationships with soil physicochemical properties. The results show significant differences in the structure of rhizosphere soil bacterial communities among the five Orchidaceae species. The principal environmental factors influencing these communities differ across species. Fermentation functional bacteria dominate the rhizosphere bacterial communities. The community assembly processes of specialized and generalized species are governed by deterministic and stochastic processes, respectively, indicating complex ecological mechanisms. This study clarifies the structural characteristics, functional differentiation, and environmental response mechanisms of rhizosphere soil bacterial communities across Orchidaceae species. It provides a theoretical foundation for the conservation and sustainable utilization of Orchidaceae from a microbiological perspective.

1. Introduction

The Orchidaceae family is recognized as one of the most diverse and widely distributed families among angiosperms, noted for its unique floral morphology, growth habits, and ecological adaptability. Globally, the family comprises approximately 880 genera and 25,000 species, found across tropical, subtropical, and temperate regions [1]. The Orchidaceae family fulfills crucial ecological roles within ecosystems [2]. Additionally, they possess high economic value in ornamental [3], medicinal, and cultural domains and represent a vital component of the horticultural industry [4,5]. These orchids, which employ the ‘opportunistic/generalist’ strategy, form symbiotic and synergistic relationships with local soil bacteria. However, most orchid species are very demanding in terms of their habitats.
The rhizosphere—the narrow soil zone directly influenced by root exudates—undergoes profound microbial and physicochemical transformations, including altered nutrient cycling, pH regulation, and pathogen suppression, which critically shape plant health and ecosystem functioning. Despite this, the rhizosphere effect in Orchidaceae remains underexplored, particularly regarding bacterial community assembly and functional differentiation. Rhizosphere bacterial diversity is closely related to the growth, development, and stress resistance of Orchidaceae [6,7]. Recent studies have demonstrated that the rhizosphere and endophytic bacterial communities associated with Orchidaceae can enhance plant growth through various mechanisms, including nitrogen (N) fixation, organic matter decomposition, secretion of plant growth hormones, and increased resistance to pathogens [8]. Furthermore, the symbiotic association between mycorrhizal bacteria and Orchidaceae significantly contributes to nutrient uptake and plant adaptation to environmental stress [9,10]. Therefore, comprehensive research on the bacterial diversity of Orchidaceae is vital for understanding their ecological adaptation mechanisms, conserving endangered species, and optimizing cultivation management [11].
Numerous studies have investigated the bacterial diversity of Orchidaceae, including the effects of soil bacteria on the germination of Orchidaceae seeds [12] and the bacterial communities present in the rhizosphere soil of Orchidaceae, as well as potential orchid mycorrhizal bacteria [13]. However, from an ecological perspective, the influence of soil bacterial composition, environmental factors, and soil bacterial functions on the structure of Orchidaceae soil bacterial communities remains inadequately understood [14].
China is abundant in Orchidaceae resources and harbors many species with unique ornamental and medicinal value [15]. For example, C. amoena and C. faberi are widely cultivated for their ornamental appeal, whereas G. elata is highly prized for its medicinal properties [16]. C. macranthos and C. appendiculata also possess significant ornamental value. All five of these Orchidaceae species are protected plants in China.
Based on a comprehensive survey of Orchidaceae in the north subtropical region of China [17], this study selected five common Orchidaceae species [18]. Utilizing high-throughput sequencing technology, we systematically analyzed the characteristics of rhizosphere soil bacterial diversity in Orchidaceae [19]. We explored the dominant bacterial groups, variations in diversity indices, and functional differences in soil bacterial communities among different Orchidaceae species, thereby providing a theoretical foundation for the conservation and sustainable use of Orchidaceae [20,21].

2. Materials and Methods

2.1. Overview of the Study Area

This study was conducted at the Funiu Mountain Nature Reserve in Henan Province, China [22]. The geographic coordinates of the reserve are 111°17′–112°17′ E longitude and 32°50′–33°54′ N latitude, covering a total area of 56,024 hectares (Attachment S2). The reserve occupies a transitional zone between the north subtropical and warm-temperate regions, exhibiting a continental monsoon climate characterized by four distinct seasons. Spring is dry and windy, summer is cool and humid, autumn is rainy, and winter is cold and dry. Most of the area has an elevation exceeding 1500 m.
The five Orchidaceae species selected for this study—C. amoena, C. macranthos, C. appendiculata, C. faberi, and G. elata—are typical and relatively common in Henan Province and are all nationally protected species [23].

2.2. Sampling Design

Following a review of the relevant literature and preliminary surveys of sampling sites (Table 1), we selected 10 representative Orchidaceae plants from a homogeneous population area in the Funiu Mountain Nature Reserve as study subjects in July 2023 [24]. The rhizosphere soil was defined as the soil within the 0–3 cm range surrounding the surface of the plant’s fibrous roots, excluding the surface humus layer, as well as the 5–15 cm soil layer. We employed a five-point composite sampling method. All soil samples were passed through a 2 mm sieve, thoroughly mixed in equal portions, and transported to the laboratory on the same day [3]. A portion of the soil samples was preserved at −80 °C for subsequent DNA analysis, while the remaining samples were stored at −4 °C for assessment of rhizosphere soil physicochemical properties [25].

2.3. Determination of Soil Bacterial Communities

Total DNA was extracted from 0.5 g of fresh soil sample using the Fast DNA SPIN extraction kit (Mobio Laboratories, Carlsbad, CA, USA) for bacterial analysis [26]. The DNA concentration was quantified using a spectrophotometer (Thermo Scientific, Wilmington, DE, USA); the samples were then stored at −80 °C. Subsequently, the V3–V4 region of the 16S rDNA was amplified and sequenced using primers 515F and 806R [27]. Sequencing was conducted on the Illumina HiSeq platform (Illumina Inc., San Diego, CA, USA), employing a paired-end sequencing strategy (2 × 150 bp). The sequencing and subsequent bioinformatics analysis were performed by Guangzhou Kidio Biotechnology Co., Ltd. (Guangzhou, China).

2.4. Determination of Soil Physicochemical Properties

Soil samples were air-dried, sieved through a 60-mesh sieve (0.25 mm aperture) to remove coarse fragments, and stored for analysis. The soil pH was measured potentiometrically using a 1 M KCl solution at a soil-to-solution ratio of 1:2.5. Soil Organic Matter (SOM) was quantified using the dichromate oxidation method. Available N was assessed using the alkaline hydrolysis diffusion method. Available phosphorus (P) was determined with the molybdenum blue method. Soil Moisture Content (SMC) was evaluated by drying the soil at 105 °C overnight. Available potassium (AK) was quantified using flame photometry [28].

2.5. Statistical Analysis

The VennDiagram package in R was utilized to generate Venn diagrams illustrating the number of unique and shared operational taxonomic units (OTUs) among the soils of different Orchidaceae species. Visualization was achieved through boxplots [29].
Stacked bar charts were employed to analyze the relative abundance of dominant bacterial communities in the rhizosphere soil of various Orchidaceae species [16]. Statistical analysis was conducted using the ggplot2 package in R. Redundancy analysis was employed to investigate the associations between environmental factors and soil bacterial communities across different Orchidaceae species [30]. Calculations were performed using the vegan package, and the envfit function was utilized to evaluate the effect of environmental factors on bacterial community distribution [31,32,33].
Null model methods were implemented to examine the relative significance of deterministic and stochastic processes in bacterial community assembly. The β nearest taxon index (βNTI) and the taxonomic diversity index (RCBray) were calculated to quantify variations in community phylogenetic and taxonomic diversity. A |βNTI| value greater than 2 indicates that deterministic processes, specifically environmental filtering, predominantly influence community turnover. A βNTI value exceeding 2 suggests heterogeneous selection (where differing environmental conditions lead to variations in communities), whereas a βNTI < 2 points to homogeneous selection (indicating similar environmental conditions foster community convergence). Conversely, a |βNTI| < 2 implies that stochastic processes, such as migration and dispersal, are the primary drivers of community assembly. For RCBray, values below 0.95 indicate homogeneous dispersal processes, whereas values exceeding 0.95 suggest dispersal-limited processes. A |βNTI| < 0.95 indicates the absence of a dominant process.
The neutral community model was employed to predict the association between the occurrence frequency of species across all samples and their relative abundance within the community [34]. The vegan package in R facilitated the fitting of the neutral model, the assessment of the association between species relative abundance and occurrence frequency, and the calculation of the R value (correlation coefficient) and N value (number of samples) to evaluate model fit and sample adequacy [35].
Bacterial functional prediction methods were utilized to reveal functional differences among the bacterial communities in the soils of the five Orchidaceae species. Using 16S rDNA gene sequence data, the Tax4Fun2 tool on the Biocloud platform was employed to perform OTU taxonomic annotation by comparing it with the SILVA database [36]. Functional annotations were integrated with information from the KEGG database (https://www.bioincloud.tech/standalone-task-ui/picrust2, accessed on 1 April 2024) to predict the metabolic functional profiles of the bacterial communities [37]. Finally, differences in the functional characteristics of the bacterial communities in the soils of the five Orchidaceae species were illustrated through the statistical analysis of the relative abundance of bacteria across various functional categories [38].

3. Results

3.1. Species Composition and Diversity of Soil Bacterial Communities

The Venn diagram results revealed that among all species, C. amoena exhibited the highest number of soil bacterial OTUs. In contrast, C. appendiculata displayed a lower number of soil bacterial OTUs and shared fewer OTUs with other plants (Figure 1). Among generalized and specialized species, C. faberi recorded the greatest number of soil bacterial OTUs.
Boxplot analysis indicated significant differences in the species richness of soil bacteria among the five different Orchidaceae species. C. amoena and G. elata demonstrated higher species richness of soil bacteria, whereas C. appendiculata exhibited lower species richness (Figure 1).
At the order level, Bacteroidales and Burkholderiales exhibited higher abundance in the rhizosphere soil of the five Orchidaceae species, with these order-level groups being particularly prevalent in samples of C. amoena and G. elata. At the family level, Chitinophagaceae and Sphingomonadaceae were dominant in the rhizosphere soil of the five Orchidaceae species. Notably, Pyrinomonadaceae was more prevalent in other soils but demonstrated lower abundance in the rhizosphere soil of C. appendiculata. At the genus level, Udaeobacter and Solibacter were predominant in the rhizosphere soil of the five Orchidaceae species. In addition, the RB41 and Pir4 lineages were more enriched in the rhizosphere soil of G. elata, while being relatively scarce in the rhizosphere soil of other Orchidaceae species (Figure 2).

3.2. Response of Bacterial Communities to Environmental Factors

The results of the RDA analysis indicated that the first and second axes accounted for 43.02% and 28.22% of the variation in bacterial communities, respectively, yielding a combined explanation rate of 61.24% (Figure 3). Soil pH significantly influenced the soil bacterial community of C. amoena. Total N was identified as the primary influencing factor for the soil bacterial community of C. macranthos. Available P and SMC were shown to significantly affect the soil bacterial communities of C. faberi and G. elata. The selected environmental factors had a relatively minor effect on the soil bacterial community of C. appendiculata.
For the generalized species, the RDA analysis revealed a cumulative explanation rate of 58.31%, with SMC identified as the primary environmental factor affecting the soil bacterial community of C. amoena. Total N significantly affected the soil bacterial communities of C. macranthos and C. appendiculata. In the case of specialized species, the RDA analysis indicated a cumulative explanation rate of 71.05%, with Available P, SOM, and AK significantly influencing the soil bacterial communities of C. amoena, G. elata, and C. faberi. Total N emerged as the principal environmental factor affecting the soil bacterial communities of C. macranthos and C. appendiculata.

3.3. Differences in Rhizosphere Soil Bacterial Community Assembly

The results of the NCM analysis indicated (Figure 4) that the fit of different bacterial communities to the neutral community model was as follows: all species (R2 = 0.804), neutral taxa (R2 = 0.792), specialized species (R2 = 0.759), and generalized species (R2 = 0.349). In the soil bacterial OTU data of the five different Orchidaceae species, the number of OTUs for all species, neutral taxa, specialized species, and generalized species were Nm = 8236, Nm = 3740, Nm = 1905, and Nm = 253, respectively.
During the assembly of rhizosphere soil bacterial communities, different species of Orchidaceae exhibited notable differences in their ecological strategies. The rhizosphere soils of C. amoena, C. macranthos, and C. faberi were primarily influenced by heterogeneous selection within deterministic processes. In contrast, in the rhizosphere soils of C. appendiculata and G. elata, non-dominant processes within stochastic frameworks were predominant. In the assembly of rhizosphere soil bacterial communities of generalized species, heterogeneous selection within deterministic processes was dominant across all five Orchidaceae species. In contrast, in the rhizosphere soil of C. macranthos for specialized species, homogeneous selection within stochastic processes was prevalent (Figure 5).

3.4. Functional Diversity of Soil Microorganisms in Different Orchidaceae

The pie charts representing metabolic functions indicate that fermentation predominates among the metabolic functional bacteria within the soils of the five Orchidaceae species. In the soil bacterial community of C. appendiculata, fermentation comprises as much as 81.15%. In the soil of G. elata, fermentation and chitinolysis are notably prevalent, accounting for 64.20% and 16.76% of the metabolic functional bacteria, respectively. In the soils of C. amoena and C. faberi, nitrate respiration is more pronounced (Figure 6A).
Nutritional bacteria are categorized into 12 types based on their nutritional strategies, which include interactions with hosts through phototrophy, parasitism, or symbiosis. Among these, aerobic chemoheterotrophy is the dominant nutritional strategy in the soil bacterial communities of the five Orchidaceae species. In C. amoena, nitrate respiration is particularly abundant. In contrast, the soil bacteria of C. macranthos and C. appendiculata exhibit a higher relative abundance of animal parasites or symbionts (Figure 6B).

4. Discussion

The structure of bacterial communities exhibits variation among different species of Orchidaceae, which may correlate with the specific plant species. The soil bacterial communities associated with G. elata and C. amoena demonstrate considerable richness, suggesting that these plants can sustain more diverse bacterial communities [39]. The higher number of shared OTUs in the rhizosphere soil of C. amoena and G. elata indicates that these two species may inhabit similar ecological environments or possess analogous requirements for bacterial community composition [40,41].
At the order level, Bacteroidales and Burkholderiales exhibit a higher relative abundance in the rhizosphere soil of the five different Orchidaceae species [28]. At the family level, Chitinophagaceae and Sphingomonadaceae are dominant, whereas at the genus level, Udaeobacter and Solibacter are the most prevalent. This highlights the universality and significance of these bacterial groups in the rhizosphere soil associated with the five species of Orchidaceae. However, certain bacteria, including Pyrinomonadaceae, RB41, and the Pir4 lineage, show a lower relative abundance in the rhizosphere soil of C. appendiculata. Overall, the structure of rhizosphere soil bacterial communities among different Orchidaceae species reveals significant variations, which may be attributed to plant species, growth environments, and the selective preferences of plants for bacterial communities.
The structure of rhizosphere soil bacterial communities across various Orchidaceae species is influenced by multiple physicochemical soil factors [42]. The bacterial community associated with C. amoena is primarily regulated by soil pH, whereas that of C. macranthos is mainly affected by total N content. The rhizosphere soil bacterial communities of C. faberi and G. elata are significantly driven by Available P and SMC. These findings indicate that the structure of rhizosphere soil bacterial communities in different Orchidaceae species is shaped by various physicochemical factors, with distinct plant species demonstrating varied responses to these influences. This variation may be closely associated with the ecological differentiation of Orchidaceae species, their strategies for resource utilization, and their symbiotic interactions with bacteria.
The results of the NCM analysis indicate that the fit of different bacterial communities to the neutral community model varies significantly. For all species, neutral taxa demonstrate a superior fit, indicating that stochastic processes have a substantial influence on community assembly. In contrast, specialized and generalized species exhibit lower fit values, indicating that deterministic processes play a more prominent role in shaping their communities.
In the assembly of the rhizosphere soil bacterial community associated with various Orchidaceae species, notable differences in ecological strategies are evident [43]. For the species studied, the rhizosphere soil of C. amoena, C. macranthos, and C. faberi is primarily shaped by heterogeneous selection within deterministic processes. This suggests that these plants selectively enrich specific bacterial taxa, enabling them to better adapt to their growth environments. Conversely, in the rhizosphere soil of C. appendiculata and G. elata, non-dominant processes within stochastic frameworks are more prevalent. This observation may be related to the adaptive evolution of these species in response to their environment. For generalized species, heterogeneous selection within deterministic processes predominates in the assembly of rhizosphere soil bacterial communities across all five Orchidaceae species, indicating a strong selectivity in bacterial community assembly. Overall, the assembly of rhizosphere bacterial communities in Orchidaceae species is influenced by both stochastic and deterministic processes. The varied assembly strategies observed among different Orchidaceae species are likely closely associated with their ecological niche differentiation and environmental adaptability [44].
Fermentation functional bacteria predominate in the rhizosphere soil bacterial communities associated with all five species of Orchidaceae, representing the primary metabolic type of bacteria [45]. This observation indicates that fermentation functions are likely vital to the rhizosphere soil bacterial communities of Orchidaceae [46]. These bacteria not only participate in the decomposition and transformation of organic matter but may also significantly affect soil nutrient cycling, plant health, and ecosystem stability. Notable differences in the relative abundance of metabolic and nutritional bacteria exist within the rhizosphere soil bacterial communities of various Orchidaceae species. For example, the rhizosphere soil of C. appendiculata exhibits a comparatively high abundance of bacteria associated with the degradation of aromatic compounds. In contrast, the rhizosphere soils of C. amoena and G. elata are characterized by a higher abundance of bacteria that contribute to chitin degradation. These variations likely correlate closely with the physiological characteristics of the respective plants and their rhizosphere environments. The rhizosphere soil of C. amoena and C. faberi supports a relatively high bacterial diversity, whereas C. macranthos, C. appendiculata, and G. elata exhibit lower bacterial numbers. Such differences may reflect varying strategies employed by different Orchidaceae species in constructing and maintaining their rhizosphere bacterial communities. These findings highlight the pivotal role of fermentation functional bacteria in the rhizosphere soil bacterial communities of Orchidaceae [32,47]. The observed differences in metabolic functions and bacterial abundance among the rhizosphere bacterial communities of different Orchidaceae species highlight their diverse ecological adaptation strategies [48].

5. Conclusions

This study provides a comprehensive analysis of the structure, function, and associations with environmental factors of the rhizosphere soil bacterial communities associated with five species of Orchidaceae [49]. The results indicate significant structural differences in the rhizosphere soil bacterial communities among the five Orchidaceae species. The primary environmental factors influencing these communities vary across different species. Fermentation functional bacteria dominate these communities and are crucial to the ecological functions of Orchidaceae rhizosphere ecosystems. Additionally, variations in the abundance of metabolic and nutritional bacteria are evident among the rhizosphere bacterial communities of different plants. The community assembly processes of specialized and generalized species are governed by deterministic and stochastic processes, respectively.
The five Orchidaceae species are not only protected plants in China but also possess significant ornamental and medicinal values. This study examines the structural characteristics, functional differences, and response mechanisms of the rhizosphere bacterial communities associated with various Orchidaceae species from the perspective of soil microbiology. This research offers a crucial theoretical foundation for the conservation and sustainable utilization of Orchidaceae.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/d17090605/s1. Attachment S1: Material sources and images of the five selected Orchidaceae species; Attachment S2: Abbreviations and their meanings.

Author Contributions

Conceptualization, J.D.; data curation, J.D. and S.G.; formal analysis, J.D., Z.Y. and X.L.; funding acquisition, Z.Y.; investigation, X.S.; methodology, J.D. and Z.G.; project administration, Z.Y.; resources, J.D.; software, Z.G.; supervision, S.G. and Z.Y.; validation, Z.Y. and S.G.; visualization, J.D.; writing—original draft, X.L.; writing—review and editing, X.S. and S.G. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the project “Survey of Endangered and Rare Medicinal Wild Plants in the Eastern Section of the Qinling Mountains in Henan Province in 2025” funded by the Science and Technology Office of Henan Agricultural University (Grant No. 111/30603204), the project “Survey, Collection and Monitoring of Agricultural Wild Plant Resources in Typical Areas” funded by the Social Service Office of Henan Agricultural University (Grant No. 330/30802105), and the project “Biodiversity Conservation Research” funded by Henan Agricultural University (Grant No. GZS2023006).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The raw data presented in this study are available on request from the corresponding author. The data are not publicly available due to the risk of potential threats to some endangered plant species.

Acknowledgments

We thank the staff members of the Urban Ecosystem Biodiversity Group at Henan Agricultural University for their technical guidance. We are grateful to Shengqian Guo, Zhonghu Geng, and Xiaohang Li from the College of Life Sciences of Henan Agricultural University for their contributions to data collection.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Bazzicalupo, M.; Calevo, J.; Smeriglio, A.; Cornara, L. Traditional, Therapeutic Uses and Phytochemistry of Terrestrial European Orchids and Implications for Conservation. Plants 2023, 12, 257. [Google Scholar] [CrossRef] [PubMed]
  2. Xie, X.; Shi, R.; Yan, X.; Zhang, A.; Wang, Y.; Jiao, J.; Yu, Y.; Horowitz, A.R.; Lu, J.; He, X. Changes in Soil Chemistry and Microbial Communities in Rhizospheres of Planted Gastrodia elata on a Barren Slope and under a Forest. Forests 2024, 15, 331. [Google Scholar] [CrossRef]
  3. Liu, J.; Zeng, D.; Huang, Y.; Zhong, L.; Liao, J.; Shi, Y.; Jiang, H.; Luo, Y.; Liang, Y.; Chai, S. The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum. BMC Genom. 2024, 25, 222. [Google Scholar] [CrossRef]
  4. Kaur, J.; Harder, C.B.; Sharma, J. Congeneric temperate orchids recruit similar-yet differentially abundant-endophytic bacterial communities that are uncoupled from soil, but linked to host phenology and population size. Am. J. Bot. 2023, 110, e16168. [Google Scholar] [CrossRef]
  5. Nargar, K.; Chen, J.-T. Orchid genomics and developmental biology, volume II. Front. Plant Sci. 2023, 14, 1136350. [Google Scholar] [CrossRef]
  6. Wang, T.; Chi, M.; Chen, J.; Liang, L.; Wang, Y.; Chen, Y. The Diversity and Growth-Promoting Potential of the Endophytic Fungi of Neuwiedia singapureana (Orchidaceae) in China. Diversity 2024, 16, 34. [Google Scholar] [CrossRef]
  7. Zhang, J.; Li, P.; Li, L.; Zhao, M.; Yan, P.; Liu, Y.; Li, W.; Ding, S.; Zhao, Q. Soil respiration and carbon sequestration response to short-term fertilization in wheat-maize cropping system in the North China Plain. Soil Tillage Res. 2025, 251, 106536. [Google Scholar] [CrossRef]
  8. Li, M.-H.; Zhang, G.-Q.; Liu, Z.-J.; Lan, S.-R. Subtribal relationships in Cymbidieae (Epidendroideae, Orchidaceae) reveal a new subtribe, Dipodiinae, based on plastid and nuclear coding DNA. Phytotaxa 2016, 246, 37–48. [Google Scholar] [CrossRef]
  9. Chamara, R.M.S.R.; Rammitsu, K.; Minobe, M.; Kinoshita, A.; Kotaka, N.; Yukawa, T.; Ogura-Tsujita, Y. Mycorrhizal Fungi of Phalaenopsis japonica (Orchidaceae) and Their Role in Seed Germination and Seedling Development. Diversity 2024, 16, 218. [Google Scholar] [CrossRef]
  10. Tawfiq, R.; Niu, K.; Hoehndorf, R.; Kulmanov, M. DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction. Sci. Rep. 2024, 14, 31813. [Google Scholar] [CrossRef] [PubMed]
  11. Yao, N.; Wang, T.; Jiang, J.; Yang, Y.; Cao, X. Coriolopsis strumosa as an Orchid Endophytic Fungus and Its Spatial Distribution in Epidendrum sp. (Orchidaceae). Microorganisms 2024, 12, 1054. [Google Scholar] [CrossRef]
  12. Nogueira, P.T.S.; Freitas, E.F.S.; Silva, J.A.R.; Kasuya, M.C.M.; Pereira, O.L. Efficiency of mycorrhizal fungi for seed germination and protocorms development of commercial Cattleya species (Orchidaceae). Braz. J. Microbiol. 2025, 56, 589–599. [Google Scholar] [CrossRef]
  13. Kambara, K.; Shimura, H.; Fujino, K.; Masuta, C. Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction Using Improved Assemble Tools. Methods Mol. Biol. 2024, 2732, 67–81. [Google Scholar] [CrossRef] [PubMed]
  14. Merckx, V.S.; Gomes, S.I. The Mycoheterotrophy. Curr. Biol. 2023, 33, R463–R465. [Google Scholar] [CrossRef]
  15. Lv, R.; Zhang, J.; Liao, H.; Yong, J.W.H.; Song, J. Study on the Soil Microbial Diversity of Cymbidium goeringii and Cymbidium faberi in the Qinling Mountains after Introduction and Domestication. Diversity 2023, 15, 951. [Google Scholar] [CrossRef]
  16. Hu, X.; Qi, X.; Ramírez, M.D.A.; Wu, Q.; Liu, S.; Deng, Z.; Li, X.; Zhang, N.; Zhang, H.; Dai, H.; et al. Analysis of the Fungal Community Composition in Endemic Orchids with Terrestrial Habitat in Subtropical Regions. Microorganisms 2024, 12, 1412. [Google Scholar] [CrossRef] [PubMed]
  17. Liu, W.; Shao, Y.; Guo, S.; Liu, F.; Tian, X.; Chen, Y.; Yuan, Z.; Ye, Q. Latitudinal gradient patterns and driving factors of the fruit types of woody plants based on multiple forest dynamic monitoring plots. J. Plant Ecology. 2025, 18, taf018. [Google Scholar] [CrossRef]
  18. Chen, Y.; Niu, S.; Li, P.; Jia, H.; Wang, H.; Ye, Y.; Yuan, Z. Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem. Front. Plant Sci. 2017, 8, 874. [Google Scholar] [CrossRef]
  19. Zhou, X.; Cheng, Z.; Liu, Q.; Zhang, J.; Hu, A.; Huang, M.; Hu, C.; Tian, H. An updated checklist of Orchidaceae for China, with two new national records. Phytotaxa 2016, 276, 1–148. [Google Scholar] [CrossRef]
  20. Zhao, Z.; Yang, L.; Wang, Y.; Qian, X.; Ding, G.; Jacquemyn, H.; Xing, X. Unlocking germination: The role of mycorrhizal strain and seed provenance in driving seed germination of a widespread terrestrial orchid. Mycorrhiza 2025, 35, 18. [Google Scholar] [CrossRef]
  21. Zhou, X.; Wang, Z.; Liu, W.; Fu, Q.; Shao, Y.; Liu, F.; Ye, Y.; Chen, Y.; Yuan, Z. Distribution Pattern of Woody Plants in a Mountain Forest Ecosystem Influenced by Topography and Monsoons. Forests 2022, 13, 957. [Google Scholar] [CrossRef]
  22. Tang, J.; Wang, H.; Cong, N.; Zu, J.; Yang, Y. Analysis of Changes in Forest Vegetation Peak Growth Metrics and Driving Factors in a Typical Climatic Transition Zone: A Case Study of the Funiu Mountain, China. Remote Sens. 2024, 16, 2921. [Google Scholar] [CrossRef]
  23. Li, S.; Li, X.; Ye, Y.; Chen, M.; Chen, H.; Yang, D.; Li, M.; Jiang, F.; Zhang, X.; Zhang, C. The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f. Bmc Plant Biol. 2024, 24, 409. [Google Scholar] [CrossRef]
  24. Xi, J.; Shao, Y.; Li, Z.; Zhao, P.; Ye, Y.; Li, W.; Chen, Y.; Yuan, Z. Distribution of Woody Plant Species Among Different Disturbance Regimes of Forests in a Temperate Deciduous Broad-Leaved Forest. Front. Plant Sci. 2021, 12, 618524. [Google Scholar] [CrossRef]
  25. Yuan, Y.; Li, X.; Liu, F.; Tian, X.; Shao, Y.; Yuan, Z.; Chen, Y. Differences in Soil Microbial Communities across Soil Types in China’s Temperate Forests. Forests 2024, 15, 1110. [Google Scholar] [CrossRef]
  26. Balducci, M.G.; Calevo, J.; Duffy, K.J. Orchid Mycorrhizal Communities Associated with Orchis italica Are Shaped by Ecological Factors and Geographical Gradients. J. Biogeogr. 2025, 52, 544–557. [Google Scholar] [CrossRef]
  27. Cuscó, A.; Catozzi, C.; Viñes, J.; Sanchez, A.; Francino, O. Microbiota profiling with long amplicons using Nanopore sequencing: Full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon [version 2; peer review: 2 approved, 3 approved with reservations]. F1000Research 2019, 7, 1755. [Google Scholar] [CrossRef]
  28. Bell, J.; Yokoya, K.; Kendon, J.P.; Sarasan, V. Diversity of root-associated culturable fungi of Cephalanthera rubra (Orchidaceae) in relation to soil characteristics. Peerj 2020, 8, e8695. [Google Scholar] [CrossRef]
  29. Tian, L.; An, M.; Liu, F.; Zhang, Y. Fungal community characteristics of the last remaining habitat of three paphiopedilum species in China. Sci. Rep. 2024, 14, 24737. [Google Scholar] [CrossRef]
  30. Volynchikova, E.A.; Khrenova, M.G.; Panova, T.V.; Rodin, V.A.; Zvereva, M.I.; Tsavkelova, E.A.; Pritchard, L. Complete genome sequence of new Microbacterium sp. strain ET2, isolated from roots of leafless orchid. Microbiol. Resour. Announc. 2024, 13, e0089923. [Google Scholar] [CrossRef]
  31. Mujica, M.I.; Pérez, M.F.; Jakalski, M.; Martos, F.; Selosse, M.A. Soil P reduces mycorrhizal colonization whereas favors fungal pathogens: Observational and experimental evidence in Bipinnula (Orchidaceae). Fems Microbiol. Ecol. 2020, 96, 178. [Google Scholar] [CrossRef]
  32. Yang, H.-X.; Guo, S.-X.; Liu, R.-J. Characteristics of arbuscular mycorrhizal fungal diversity and functions in saline-alkali land. Ying Yong Sheng Tai Xue Bao, J. Appl. Ecol. 2015, 26, 311–320. [Google Scholar]
  33. Yokoya, K.; Jacob, A.S.; Zettler, L.W.; Kendon, J.P.; Menon, M.; Bell, J.; Rajaovelona, L.; Sarasan, V. Fungal Diversity of Selected Habitat Specific Cynorkis Species (Orchidaceae) in the Central Highlands of Madagascar. Microorganisms 2021, 9, 792. [Google Scholar] [CrossRef]
  34. Liu, L.; Xia, A.; Tang, X.; Zhang, Y.; Meng, X.; Lei, S.; Wang, B.; Peng, S.; Liu, Y. Microbial diversity and prediction function profiling of microbial communities in rose jam. J. Food Saf. 2024, 44, e13102. [Google Scholar] [CrossRef]
  35. Novotná, A.; Suárez, J.P. Molecular detection of bacteria associated with Serendipita sp., a mycorrhizal fungus from the orchid Stanhopea connata Klotzsch in southern Ecuador. Bot. Lett. 2018, 165, 307–313. [Google Scholar] [CrossRef]
  36. Jung, S. Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data. J. Microbiol. 2025, 63, e.2411006. [Google Scholar] [CrossRef] [PubMed]
  37. Liu, J.-J.; Yang, X.-Q.; Li, Z.-Y.; Miao, J.-Y.; Li, S.-B.; Zhang, W.-P.; Lin, Y.-C.; Lin, L.-B. The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): A comprehensive review. Front. Plant Sci. 2024, 14, 1309038. [Google Scholar] [CrossRef]
  38. Zhou, Y.; Shi, Y.; Huang, Y.; Zhong, J. Microbes on the “peachy spots” of ancient Kaihua paper: Microbial community and functional analysis. Front. Microbiol. 2024, 14, 1326835. [Google Scholar] [CrossRef]
  39. Zuo, J.; Zu, M.; Liu, L.; Song, X.; Yuan, Y. Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium. BMC Plant Biol. 2021, 21, 127. [Google Scholar] [CrossRef]
  40. Kollmann, R.; Dörr, I. Fine structure of mycorrhiza in Neottia nidus-avis (L.) L. C. Rich. (Orchidaceae). Planta 1969, 89, 372–375. [Google Scholar] [CrossRef]
  41. Waud, M.; Busschaert, P.; Lievens, B.; Jacquemyn, H. Specificity and localised distribution of mycorrhizal fungi in the soil may contribute to co-existence of orchid species. Fungal Ecol. 2016, 20, 155–165. [Google Scholar] [CrossRef]
  42. Kaur, J.; Phillips, C.; Sharma, J. Host population size is linked to orchid mycorrhizal fungal communities in roots and soil, which are shaped by microenvironment. Mycorrhiza 2021, 31, 17–30. [Google Scholar] [CrossRef] [PubMed]
  43. Gao, J.; Sasse, J.; Lewald, K.M.; Zhalnina, K.; Cornmesser, L.T.; Duncombe, T.A.; Yoshikuni, Y.; Vogel, J.P.; Firestone, M.K.; Northen, T.R. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. Jove-J. Vis. Exp. 2018, 134, e57170. [Google Scholar] [CrossRef]
  44. Noguchi, M.; Toju, H. Mycorrhizal and endophytic fungi structure contrasting but interdependent assembly processes in forest below-ground symbiosis. BioRxiv 2024, 19, 84. [Google Scholar] [CrossRef]
  45. Li, X.; Qu, Z.; Zhang, Y.; Ge, Y.; Sun, H. Soil Fungal Community and Potential Function in Different Forest Ecosystems. Diversity 2022, 14, 520. [Google Scholar] [CrossRef]
  46. Li, Y.M.; Hu, J.C.; Wang, S.L. Function and application of soil microorganisms in forest ecosystem. Ying Yong Sheng Tai Xue Bao J. Appl. Ecol. 2004, 15, 1943–1946. [Google Scholar]
  47. Zhang, J.; Wang, C.; Guo, S.; Chen, J.; Xiao, P. Studies on the plant hormones produced by 5 species of endophytic fungi isolated from medicinal plants (Orchidacea). Zhongguo Yi Xue Ke Xue Yuan Xue Bao Acta Acad. Med. Sin. 1999, 21, 460–465. [Google Scholar]
  48. Egidi, E.; Delgado-Baquerizo, M.; Plett, J.M.; Wang, J.; Eldridge, D.J.; Bardgett, R.D.; Maestre, F.T.; Singh, B.K. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 2019, 10, 2369. [Google Scholar] [CrossRef] [PubMed]
  49. Tian, L.; An, M.; Wu, M.; Liu, F.; Zhang, Y. Habitat ecological characteristics and soil fungal community structure of Paphiopedilum subgenus Brachypetalum Hallier (Orchidaceae) plants in Southwest China. Plant Signal. Behav. 2023, 18, 2227365. [Google Scholar] [CrossRef]
Diversity 17 00605 g001
Figure 1. (a): Venn diagram of OTUs of rhizosphere soil bacteria of five orchid species, (b): boxplot of species richness of rhizosphere soil bacteria of five orchid species. DHL represents C. amoena, DHSL represents C. macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Figure 1. (a): Venn diagram of OTUs of rhizosphere soil bacteria of five orchid species, (b): boxplot of species richness of rhizosphere soil bacteria of five orchid species. DHL represents C. amoena, DHSL represents C. macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Diversity 17 00605 g001
Diversity 17 00605 g002
Figure 2. (a): Relative abundance of rhizosphere soil bacteria among all species for different orchids, (b): relative abundance of rhizosphere soil bacteria among generalist species for different orchids, (c): relative abundance of rhizosphere soil bacteria among specialist species for different orchids. DHL represents C. amoena, DHSL represents C. macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Figure 2. (a): Relative abundance of rhizosphere soil bacteria among all species for different orchids, (b): relative abundance of rhizosphere soil bacteria among generalist species for different orchids, (c): relative abundance of rhizosphere soil bacteria among specialist species for different orchids. DHL represents C. amoena, DHSL represents C. macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Diversity 17 00605 g002
Diversity 17 00605 g003
Figure 3. Redundancy analysis of rhizosphere soil bacterial community structure and environmental factors for different orchid species. (a): All species, (b): general species, (c): special species, SMC represents Soil Moisture Content, PH represents Potential of Hydrogen, AK represents Available Potassium (Attachment S2), AP represents Available P, SOM represents Soil Organic Matter, and TN represents Total Nitrogen. DHL represents C. amoena, DHSL represents Cypripedium macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Figure 3. Redundancy analysis of rhizosphere soil bacterial community structure and environmental factors for different orchid species. (a): All species, (b): general species, (c): special species, SMC represents Soil Moisture Content, PH represents Potential of Hydrogen, AK represents Available Potassium (Attachment S2), AP represents Available P, SOM represents Soil Organic Matter, and TN represents Total Nitrogen. DHL represents C. amoena, DHSL represents Cypripedium macranthos, DJL represents C. appendiculata, HL represents C. faberi, and TM represents G. elata.
Diversity 17 00605 g003
Diversity 17 00605 g004
Figure 4. Relative abundance distribution of rhizosphere soil microorganisms across different orchid species. (a) Total microbial community; (b) generalist species; (c) neutral taxa; (d) specialist species. Non-species represents the concept of neutral taxa. Cl represents Confidence Interval, Rsqr represents R-squared, and “Nm” represents Number of Measurements.
Figure 4. Relative abundance distribution of rhizosphere soil microorganisms across different orchid species. (a) Total microbial community; (b) generalist species; (c) neutral taxa; (d) specialist species. Non-species represents the concept of neutral taxa. Cl represents Confidence Interval, Rsqr represents R-squared, and “Nm” represents Number of Measurements.
Diversity 17 00605 g004
Diversity 17 00605 g005
Figure 5. Ecological processes of rhizosphere soil bacteria for five orchid species. The inner circle indicates whether deterministic or stochastic processes dominate community assembly. The outer circle illustrates the proportion of specific ecological processes within stochastic and deterministic frameworks. DHL represents C. amoena, DHSL represents C. macranthos, DJL denotes C. appendiculata, HL signifies C. faberi, and TM refers to G. elata.
Figure 5. Ecological processes of rhizosphere soil bacteria for five orchid species. The inner circle indicates whether deterministic or stochastic processes dominate community assembly. The outer circle illustrates the proportion of specific ecological processes within stochastic and deterministic frameworks. DHL represents C. amoena, DHSL represents C. macranthos, DJL denotes C. appendiculata, HL signifies C. faberi, and TM refers to G. elata.
Diversity 17 00605 g005
Diversity 17 00605 g006
Figure 6. Bacterial biological function in the soil of five orchid species. (A): Proportional circular diagram illustrating the different organic compound metabolism functions of soil bacteria in five orchid species, arranged from the inside out as follows: C. amoena (DHL), C. macranthos (DHSL), C. appendiculata (DJL), C. faberi (HL), and G. elata (TM). (B): Stacked bar chart depicting the relative abundance of phototrophic, parasitic, and symbiotic bacteria in the soil of the five orchid species in Funiu Mountain Nature Reserve.
Figure 6. Bacterial biological function in the soil of five orchid species. (A): Proportional circular diagram illustrating the different organic compound metabolism functions of soil bacteria in five orchid species, arranged from the inside out as follows: C. amoena (DHL), C. macranthos (DHSL), C. appendiculata (DJL), C. faberi (HL), and G. elata (TM). (B): Stacked bar chart depicting the relative abundance of phototrophic, parasitic, and symbiotic bacteria in the soil of the five orchid species in Funiu Mountain Nature Reserve.
Diversity 17 00605 g006
Table 1. Sampling sites of five orchid species.
Table 1. Sampling sites of five orchid species.
Species NamesElevation/mLongitudeLatitude
Cremastra appendiculata1258112.00536433.693947
Cremastra appendiculata1388112.00248333.697272
Changnienia amoena944111.91444733.574636
Changnienia amoena953111.9144533.5746
Cypripedium macranthos1205111.90509733.585867
Cypripedium macranthos1278111.90504233.585114
Gastrodia elata1248112.06769733.789036
Gastrodia elata1094111.913333333.57277778
Cymbidium faberi1009112.000277833.68416667
Cymbidium faberi1009112.0002933.68412
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Du, J.; Guo, S.; Li, X.; Geng, Z.; Yuan, Z.; Song, X. Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions. Diversity 2025, 17, 605. https://doi.org/10.3390/d17090605

AMA Style

Du J, Guo S, Li X, Geng Z, Yuan Z, Song X. Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions. Diversity. 2025; 17(9):605. https://doi.org/10.3390/d17090605

Chicago/Turabian Style

Du, Jingjing, Shengqian Guo, Xiaohang Li, Zhonghu Geng, Zhiliang Yuan, and Xiqiang Song. 2025. "Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions" Diversity 17, no. 9: 605. https://doi.org/10.3390/d17090605

APA Style

Du, J., Guo, S., Li, X., Geng, Z., Yuan, Z., & Song, X. (2025). Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions. Diversity, 17(9), 605. https://doi.org/10.3390/d17090605

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop