Taxonomic and Functional Profiling of Microbial Communities from Unexplored Karst Forest Soils of Guiuan Samar Province

Abstract

Numerous tropical karst landscapes are found in the Philippines, with the largest being located in Samar province. Despite the existence of these karst landscapes, research focusing on the soil microbiome remains limited. This study focused on the determination of the taxonomic and functional profile of the microbial community existing in karst forest soils in Guiuan, Samar Province. Metagenomic analysis was used to generate a taxonomic and functional profile of karst soil samples. To describe the taxonomic composition of the microbial communities present, MetaPhlan2 and MG-RAST servers were used, while the Level 1 subsystems from the SEED Subsystems database of MG-RAST were used to describe the functional potential. The SEED database utilizes subsystems, which are a set of functional roles that are related with each other, to provide functional annotation to the metagenomic reads. Taxonomic profiling using MetaPhlan2 showed that all members of the microbiome belonged to domain Bacteria, with dominance of the phylum Actinobacteria, followed by Proteobacteria, Acidobacteria, and Firmicutes, while the use of MG-RAST showed predominance of domain Bacteria, while members of domains Archaea, Eukaryota, and Viruses were also detected. MG-RAST results showed dominance of phylum Proteobacteria, Actinobacteria, Firmicutes, and Acidobacteria. Phyla Chloroflexi and Planctomycetes were also abundant. Functional profiling using the SEED Subsystems database revealed dominance of subsystems related to carbohydrates, clustering-based subsystems, amino acids and derivatives. Possible reasons are due to carbon-rich karst soils, presence of bacterial species involved in cycling of carbon and metabolism of carbohydrates, as well as the involvement of the soil microbiome in the different biogeochemical cycles. The results can be used as a basis for further studies that can elaborate more on specific taxa or subsystems of interest, most especially since there are phyla detected that have pathogenic members.