Bacterial and Fungal Community Profiling of Karst Ecosystem in Basey, Samar, Philippines Using Shotgun Metagenomic Approach

Abstract

The Philippines has an abundance of karst or forest over limestone landscapes, but only a small percentage of them have been studied and protected. Although the flora and fauna of karst forests are diverse and unique, little is known about the microflora that inhabits this ecosystem. The taxonomic and functional composition of bacteria and fungi in soil samples from three locations within three karst forest zones in Basey, Samar, Philippines were analyzed using Illumina shotgun metagenome sequencing. Proteobacteria and Actinobacteria bacterial sequences were most prevalent in the karst soil, followed by those of the Firmicutes, Acidobacteria, Chloroflexi, Planctomycetes, Cyanobacteria, Verrumicrobia, Bacteriodetes, and Deinococcus-Thermus. The most abundant fungal sequences belonged to Ascomycota, followed by Basidiomycota. An average of 33 million predicted protein features was detected across all sites. Enzyme pathways for nitrogen and sulfur metabolism, and several carbon fixation pathways, appeared nearly complete. To our knowledge, this is the first report to provide baseline information on the microbial community and their possible roles in karst forest ecosystem health in the Philippines, which may lead to identifying new microbes with specialized metabolism and promoting biodiversity conservation of karst forests in the Philippines. Furthermore, correlation analysis with plant diversity will reveal plant-microbe interaction leading to the understanding of the adaptation, abundance, survival, and diversity of microorganisms and plants.