Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves.

Suprokash Koner,Chao-Wen Tan,Bashir Hussain,Cheng-Wei Fan,Bing-Mu Hsu,Jung-Sheng Chen,Viji Nagarajan,Tsung-Hsien Chen

doi:10.3390/microorganisms9081789

Abstract

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Highlights

Microbes-associated biomineralization is a widespread phenomenon in regions rich in limestone, and leads to the precipitation of calcium carbonate [1]
Previous studies reported that the growth of bacteria cells and their metabolism are strongly influenced by diverse carbon source catabolism activity, because it may deliver the building block metabolites and energy for them [6,7]
The microbial community in this area indicated that they have a shorter lag phase period of cell growth

Summary

Introduction

Microbes-associated biomineralization is a widespread phenomenon in regions rich in limestone, and leads to the precipitation of calcium carbonate [1]. Previous studies reported that the growth of bacteria cells and their metabolism are strongly influenced by diverse carbon source catabolism activity, because it may deliver the building block metabolites and energy for them [6,7]. In this aspect, the pool of SOC might be different according to the variations of natural earth crust structures, which are promotionally allied with the amount of soil microbial biomass [8,9]. The assimilation or uptake of carbon from the environment is considered the key factor for microbial-mediated calcification in limestone [10]

Methods

Results

Discussion

Conclusion