Background: Karst tiankengs serve as a reservoir of biodiversity in the degraded karst landscape areas. However, the microbial diversity of karst tiankengs is poorly understood. Here, we investigated the composition and function of the microbial community in a karst tiankeng. Results: We found that habitat differences inside and outside the karst tiankeng changed the composition and structure of the soil microbial communities, and the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. The Shannon–Wiener diversity of microbial communities inside and outside the tiankeng was significantly different, and it was higher inside the tiankeng (IT). Venn and LEfSe analysis found that the soil microbial communities inside the tiankeng had 640 more endemic species and 39 more biomarker microbial clades than those identified outside of the tiankeng (OT)..Functional prediction indicated that soil microorganisms in outside the tiankeng had a high potential for carbohydrate metabolism, translation and amino acid metabolism. There were biomarker pathways associated with several of human diseases at both IT and OT sites. Except for auxiliary activities (AA), other CAZy classes had higher abundance at IT sites, which can readily convert litter and fix carbon and nitrogen, thereby supporting the development of underground forests. The differences in microbial communities were mainly related to the soil water content and soil total nitrogen. Conclusions: Our results provide a metagenomic overview of the karst tiankeng system and provide new insights into habitat conservation and biodiversity restoration in the area.

Background: Karst tiankeng is a large-scale negative surface terrain, and slope aspects affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated. Methods: In this study, metagenomic sequencing technology was used to analyze the soil microbial community structure and functional potentials on the shady and sunny slopes of karst tiankeng. Results: The Shannon–Wiener diversity of microbial communities on shady slope (SHS) was significantly higher than that on sunny slope (SUS). Although the composition of dominant phyla on shady slope (SHS) and sunny slope (SUS) was similar, there were significant differences in beta-diversity. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOC and pH). Conclusions: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.

The underground forests developed on inverted stone slopes in degraded karst tiankengs are important areas for biodiversity conservation, but the microbial community profiles have not been sufficiently characterized. Thus, we investigated the soil microbial communities at four sites (at the bottom of the slope (BS), in the middle of the slope (MS), in the upper part of the slope (US) and outside the tiankeng (OT)) in the Shenxiantang tiankeng. The dominant phyla in the inverted stone slope were Proteobacteria, Actinobacteria, and Acidobacteria, and the relative abundance were different in different slope positions. The Shannon–Wiener diversity index of the microbial community was significantly greater for the US site than for the MS or BS sites. The metabolism functional pathways (including C/N cycle) were more abundant at the BS site. Total nitrogen and pH were the dominant factors in determining the distribution of the microbial community along an inverted stone slope. These results suggest that topographic heterogeneity can influence the variations in the soil microbial structure, diversity, and function in degraded karst tiankengs and emphasized the ecological value of inverted stone slopes within karst tiankengs.

Karst tiankengs, as one of the most magnificent negative topographies, are capable of forming a bank for species diversity conservation easily. More than 300 karst tiankengs have been discovered and identified worldwide. Given its treacherous terrain, although original karst tiankeng were identified as species refuges, the broader distribution of degraded karst tiankeng has not been systematically studied. Our study area comprised the degraded karst tiankeng cluster immersed in the fragmented karst forests of Yunnan, China. Fifty-eight plant samples were selected from karst tiankengs and surface. We compared species composition, and analyzed diversity indices and similarity coefficients to verify the isolation effect of karst tiankengs on floras. The results indicated that: (1) In the degraded karst tiankeng, there were 24 families, 37 genera and 48 species in the tree layer and 27 families, 43 genera and 49 species in the shrub layer. Outside the degraded karst tiankengs, 20 families, 31 genera and 39 species were in the tree layer, and the shrub layer included 26 families, 44 genera and 55 species. (2) The species composition reached significant differences within and outside degraded karst tiankeng (p < 0.05) based on the analysis of variance (ANOVA). (3) In the degraded karst tiankeng, species richness/diversity in trees were higher than those in the shrub layer, while at the surface, shrubs had higher richness and lower diversity than trees by Alpha-diversity index. And for Beta-diversity index, species similarity among degraded karst tiankengs (0.215) was extremely dissimilar, which was even lower than the contrast within and outside the degraded karst tiankengs (0.272). (4) Shared species ranged from 1 to 5 among the four habitats, with high variability in plant species across the habitat matrices. Through a comparative analysis of systematic biodiversity methods, we found that the degraded karst tiankengs, an independent type of karst tiankeng, are the unreported refugia. Species records in degraded karst tiankeng cluster will contribute to plant diversity conservation and resource management, and to the linkage with broader China’s karst floras. Karst tiankeng botanical habitats possess not only biodiversity value for in situ conservation, but will further support the ecological recovery of surface flora. While its mechanism needs to be further revealed.

Unmanned aerial vehicle (UAV) remote sensing technology is gradually playing a role alternative to traditional field survey methods in monitoring plant functional traits of forest ecology. Few studies focused on monitoring functional trait ecology of underground forests of inaccessible negative terrain with UAV. The underground forests of tiankeng were discovered and are known as the inaccessible precious ecological refugia of extreme negative terrain. The aim of this research proposal is to explore the suitability of UAV technology for extracting the stand parameters of underground forests’ functional traits in karst tiankeng. Based on the multi-scale segmentation algorithm and object-oriented classification method, the canopy parameters (crown width and densities) of underground forests in degraded karst tiankeng were extracted by UAV remote sensing image data and appropriate features collection. First, a multi-scale segmentation algorithm was applied to attain the optimal segmentation scale to obtain the single wood canopy. Second, feature space optimization was used to construct the optimal feature space set for the image and then the k-nearest neighbor(k-NN) classifier was used to classify the image features. The features were classified into five types: canopy, grassland, road, gap, and bare land. Finally, both the crown densities and average crown width of the trees were calculated, and their accuracy were verified. The results showed that overall accuracy of object-oriented image feature classification was 85.60%, with 0.72 of kappa coefficient. The accuracy of tree canopy density extraction was 82.34%, for which kappa coefficient reached 0.91. The average canopy width of trees in the samples from the tiankeng-inside was 5.38 m, while that of the outside samples was 4.83 m. In conclusion, the canopy parameters in karst tiankeng were higher than those outside the tiankeng. Stand parameters extraction of karst tiankeng underground forests based on UAV remote sensing was relatively satisfactory. Thus, UAV technology provides a new approach to explore forest resources in inaccessible negative terrain such as karst tiankengs. In the future, we need to consider UAVs with more bands of cameras to extract more plant functional traits to promote the application of UAV for underground forest ecology research of more inaccessible negative terrain.

Background: Karst tiankeng is a large-scale negative surface terrain, and slope aspect affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated. Methods: In this study, metagenomic sequencing technology was used to analyzed the soil microbial communities and metabolic function on the shady and sunny slopes of karst tiankeng. Results: The Shannon-Wiener diversity of microbial communities on shady slopes was significantly higher than that on shady slopes. Shady and sunny slopes have similar microbial community composition, but there are differences in abundance. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOM and pH). Conclusions: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.