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

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.

Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility

“…This functional diversity is evidenced in the type and abundance of carbon utilized in the soil (Habig and Swanepoel, 2015;Zhao et al, 2019). Carbon source utilization at di erent growth stages of bambara groundnut Average well color development observed in carbon sources inoculated with soil samples reflects the ability of the microbes to utilize them and it is directly related to the number of species present in the soil as observed in this study and previous studies (Chen et al, 2008;Yang et al, 2013;Koner et al, 2021).…”

The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities—a case study of Zhijin Cave in Southwest China

“…Gaiella and Nitrospira were dominant in the surface sediments, of which Nitrospira can fix carbon and act as the primary producer in the cave ecosystem (Ortiz et al 2013). In virgin limestone caves, Cyanobacteria only existed in the soil outside the cave (Suprokash et al 2021), which further illustrated that tourism activities could change microbial community structure in the cave. There were few researches about the composition and structure of the archaeal communities in caves, but evidences showed that the Crenarchaeota accounted for 99% of the archaeal community in the bat and bird feces in primitive caves of Domica in Slovakia (Chroňáková et al 2009).…”

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

“…Apparently, microbial communities from these low-temperature and oligotrophic habitats are readily exploiting chemically heterogeneous organic matter. Koner et al (2021) noted that the non-ionic detergents were the fastest metabolized polymers by the rock microbiota. Utilization of carbon by bacterial communities is a key factor in the process of biomineralization in karst areas, and the efficiency of carbon catabolism is associated with the availability of different C-sources.…”

“…Taxonomic diversity of microbial communities including uncultivated fraction can be directly derived from the 16S rRNA gene sequences. Furthermore, functional information could be predicted from 16S rRNA gene amplicon-sequencing datasets by computational methods such as phylogenetic investigation of communities by the reconstruction of unobserved states (PICRUSt; Koner et al, 2021 ). By combining these approaches with community-level physiological profiling (e.g., BIOLOG ® EcoPlate™), a clearer picture of microbial diversity and metabolic potential could be drawn ( Koner et al, 2021 ).…”