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Data from: Co-occurrence pattern and function prediction of bacterial community in Karst cave

Citation

Dong, Yiyi et al. (2020), Data from: Co-occurrence pattern and function prediction of bacterial community in Karst cave , Dryad, Dataset, https://doi.org/10.5061/dryad.m905qftxr

Abstract

Background: Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats.

Results: The bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed.

Conclusion: These results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.

Methods

non-metric multidimensional scaling) analysis and a test of significance among sample types of bacterial community;

The functional profiles of the bacteria were obtained by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis;

A co-occurrence network analysis;

Usage Notes

The data is from the OTU dataset or else community data, including row name and column name. The row represents the observations, the column means the variables.

Funding

the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province, Award: U1812401

Provincial Program on Platform and Talent Development of the Department of Science and Technology of Guizhou China*, Award: 2019-5661

Provincial Program on Platform and Talent Development of the Department of Science and Technology of Guizhou China*, Award: 2019-5617

the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province, Award: U1812401