Soil Metagenomics Analysis Reveals the Compositions of Bacteria Communities in The World’s Oldest Tropical Rainforest

Abstract

This study was initiated to investigate the complex of soil microbiomes that resides in three different pristine ecosystems in the world's oldest tropical rainforest, Royal Belum Reserved Forest (RB). 27 soil samples from 3 sites have been collected and classified as Lithosol formed on loess material. The composition of the bacterial communities was determined via Shotgun Whole Genome Sequencing (WGS) by Illumina technology and undergone data pre-processing that includes alignments and quality trimming with Solexa QA++, contigs assembly with Metaspades before functionally analyzed by MgRast server in order to extract the genetic repertoire of the microbiomes. Each gene sequence that consists of the whole genome data was assigned to its specific roles and functions and clustered into OTU based on a 99% similarity threshold. The RB soils tested were distinctly dominated by α-Proteobacteria made up of 30.57% abundance in Sungai Kooi (SK), 34.75% in Sungai Papan (SP), and 26.14% in Sungai Ruok (SR). Bacteria from Actinobacteria class and Solibacteres class were subdominants in every sample but slightly different in genus level where SK top 3 most abundant genus other than Candidatus solibacter and Candidatus koribacter were Bradyrhizobium (6.42%), Streptomyces (4.59%) and Acidobacterium (3.59%) while SP shows Mycobacterium appearance for 4.26% abundances. For SR samples, the Variovorax, Chthoniobacter and Bradyrhizobium were among of the 5 most abundant genus with 6.75%, 4.26% and 3.38% respectively. A total of 620 different bacterial species from 269 genus were detected, of which 588 were present in all three sites. Among all the genus found relatively, SK showed higher statistical differences compared to other sites except for Acidovorax, Delftia, Polaromonas, Stenotrophomonas, Variovorax, Xanthomonas, Xylella and Methylophilales which were more abundance in SR sample.