The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum.

Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA. The results showed that Delftia, Bordetella and norank_f_Xanthobacteraceae were the dominant bacteria in the roots of Geodorum, while norank_f_Xanthobacteraceae, Gaiella and norank_f_norank_o_Gaiellales were the dominant bacteria in the rhizosphere soil of Geodorum. In the roots, the proportion of Mycobacterium in GD_roadside was higher than that in GD_understory, on the contrary, the proportion of Fusarium, Delftia and Bordetella in GD_roadside was lower than that in GD_understory. Compared with the GD_understory, the roots of GD_roadside had lower microbial diversity. In the endangered species GE, Russula was the primary fungus in the roots and rhizosphere soil, with fungal diversity lower than in the more widespread species. Among the widespread species, the dominant fungal genera in the roots and rhizosphere soil were Neocosmospora, Fusarium and Coprinopsis. This study enhances our understanding of microbial composition and diversity, providing fundamental information for future research on microbial contributions to plant growth and ecosystem function in Geodorum.

Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum.

BACKGROUND: Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs. METHODS: In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level. RESULTS: The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization. CONCLUSIONS: Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.

Photosynthetic physiological characteristics, growth performance, and element concentrations reveal the calcicole-calcifuge behaviors of three Camellia species.

We grew three yellow Camellia species (the calcifuge C. nitidissima and C. tunghinensis, and the calcicole C. pubipetala) in acidic and calcareous soils for 7 months and assessed their photosynthetic physiological characteristics, growth performance, and element concentrations in this developmental context. The calcifuge C. nitidissima and C. tunghinensis species exhibited poor growth with leaf chlorosis, growth stagnation, and root disintegration in calcareous soils, and with their P n, G s, T r, F v/F m, ΦPSII, ETR, qP, leaf Chla, Chlb, and Chl(a + b) concentrations, and root, stem, leaf, and total biomass being significantly lower when grown in calcareous soils relative to in acidic soils. In contrast, the calcicole C. pubipetala grew well in both acidic and calcareous soils, with few differences in the above parameters between these two soil substrates. The absorption and/or transportation of nutrient elements such as N, K, Ca, Mg, and Fe by the two calcifuge Camellia species plants grown in calcareous soils were restrained. Soil type plays a major role in the failure of the two calcifuge Camellia species to establish themselves in calcareous soils, whereas other factors such as competition and human activity are likely more important limiting factors in the reverse case. This study furthers our understanding of the factors influencing the distribution of these rare and endangered yellow Camellia species, allowing for improved management of these species in conservation projects and horticultural production.

Combined analysis of metagenome and transcriptome revealed the adaptive mechanism of different golden Camellia species in karst regions.

Camellia sect. Chrysantha is an important rare and protected plant species. Some golden Camellia species grow in karst soil while others grow in acidic soil. In order to study the adaptation mechanism of golden Camellia to the karst environment, four species of golden Camellia growing in the karst soil (Camellia pubipetala, Camellia perpetua, Camellia grandis, and Camellia limonia) and four species growing in the acidic soil (Camellia nitidissima, Camellia euphlebia, Camellia tunghinensis, and Camellia parvipetala) were selected for this study. Combining the metagenome and transcriptome, the structure and function of the rhizosphere microbial communities and the gene expression in roots of golden Camellia were analyzed. The results showed that the rhizosphere microbial communities in different golden Camellia were significantly different in abundance of Acidobacteria, Actinobacteria, Candidatus_Rokubacteria, Nitrospirae, Planctomycetes, and Candidatus_Tectomicrobia. The proportion of Candidatus_Rokubacteria was significantly higher in the rhizosphere soil of four species of golden Camellia grown in karst areas, compared to C. nitidissima, C. euphlebia, and C. tunghinensis. The linear discriminant analysis Effect Size showed that C. parvipetala was similar to karst species in the enrichment of ABC transporters and quorum sensing. During the transcriptome analysis, numerous upregulated genes in four karst species, including CYP81E, CHS, F3H, C12RT1, NAS, and CAD, were found to be enriched in the secondary metabolite synthesis pathway in the KEGG library, when compared to C. tunghinensis. This study provides information for plant adaptation mechanisms on the rhizosphere soil microbial composition and gene expression in secondary metabolic pathways to karst habitats and its distribution in karst areas.