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

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 ribulosebisphosphate 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. Cooccurring 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 coexistence 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.

Metagenome-assembled genomes fromMonte CristoCave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars

“…The prevalent lineages were classified within Nitrososphaeria, Chloroflexota, Acidobacteriota, Nitrospirota, Dormibacterota and Methylomirabilota. These groups were also described in other karst caves, such as in Chapada Diamantina (Brazil) (Marques et al, 2018), Ozark cave (USA) (Oliveira et al, 2017), Mizoram (India) (De Mandal et al, 2017) and Zhijin cave (China) (Dong et al, 2020). In this site, it was found the higher diversity of metabolic processes, mainly involved with chemolithotrophy, such as ammonia oxidation, sulfur oxidation, sulfate reduction, iron oxidation, nitrate reduction and anaerobic methane oxidation.…”

Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession

“…Most other published metabarcoding studies have surveyed soil and speleothems ( Porca et al, 2012 ; Ortiz et al, 2013 ; Wu et al, 2015 ; Mendoza et al, 2016 ; Lavoie et al, 2017 ; Vardeh, Woodhouse & Neilan, 2018 ; Wisechart et al, 2018 , 2019 ; Thompson et al, 2019 ; Dong et al, 2020 ). The most abundant phyla identified in these studies were also found in the Panel Cave water samples.…”

“…When combined with deep-sequencing technologies, metabarcoding gives researchers the ability to screen millions of individual DNAs and identify thousands of unique sequences from an environmental sample ( Handelsman, 2004 ; Wooley, Godzik & Friedberg, 2010 ). To date, this technique has been used to survey microbes in cave soils, speleothems, water, and biofilms in temperate and extreme environments ( Ortiz et al, 2013 ; Wu et al, 2015 ; Lavoie et al, 2017 ; Pfendler et al, 2018 ; Wisechart et al, 2018 , 2019 ; Thompson et al, 2019 ; Burow et al, 2019 ; D’Angeli et al, 2019 ; Zhu et al, 2019 ; Dong et al, 2020 ).…”

Enhanced Metabolic Potentials and Functional Gene Interactions of Microbial Stress Responses to a 4,100-m Elevational Increase in Freshwater Lakes

“…This finding was consistent with that of acidic mining lakes, in which harsh conditions such as low pH, high concentrations of sulfate and metals, and limited carbon, nitrogen, and phosphorus sources resulted in more complex microbial functional gene networks ( Ren et al, 2018 ). These discoveries may be attributed to the fact that to survive in harsh environments, microorganisms cooperate by participating in diverse metabolic pathways of the microbial food chain, such as degrading (complex) organics or metabolizing carbon, nitrogen, and phosphorus ( Dong et al, 2020 ). Similarly, to adapt to the high elevation and its related factors, some microorganisms in the HELs enhanced their potentials of recalcitrant carbon degradation genes (such as cellobiase_bact_arch , chitinaseb , and hyaluronidase ; Figure 3B ) to provide carbon sources for other microorganisms.…”