A Research Paper: Royal Belum Soils Dissolved Organic Matters and Bacterial Community Profiling Via Shotgun Metagenomics Approach

  • Mohd Fadzli Ahmad Universiti Selangor
  • Nor Suhaila Yaacob Universiti Selangor
Keywords: Royal Belum., Soil Bacterium., Illumina Paired-End Sequencing., Metagenomics., Metavelvet., Dissolved Organic Matters.

Abstract

Purpose: This research project initiated to investigate the complex of microbiomes that resides in the soils from the oldest pristine rain forest in the world Royal Belum Reserved Forest through high-throughput sequencing technology combined with several computational pipelines consists of shotgun metagenomics method, Metavelvet assembly and contigs analysis to understand the functions of specific strains from these communities that interact with each other synergistically and antagonistically.  

Design/Methodology/Approach: Soils collected from three distinct locations from Royal Belum Forest Reserved and preserved accordingly to maintain both quality and accuracy of metagenomics data. Site A soil sample has been collected at Sungai Kooi while site B located at Sungai Papan and site C soil sample was located at Sungai Ruok. For dissolved organioc matters (DOM) charcterization soil samples have been extracted by using autoclaves method at 121˚C twice and the concentration of TDN and TDP were analysed using Lovibond MD600 /MaxiDirect photometer system and TOC was determined by using Shimadzu TOC-L series of TOC analyser whereas for metagenomics study the samples extracted by using DNeasy PowerSoil Kit and undergone three quality controls (QC) procedure by Nanodrop spectrophotometer at UV lenght A260/280, gel electrophoresis profiling and Qubit fluorescent dye to ensure the intactness of the DNA samples. Samples were sequenced by using Illumina NGS Paired-end technology and reads were align and analysed with Rarefaction, Velvet, MetaVelvet and MgRast bioinformatics software to analyse the genetic repertoire of the microbiome. 

Results/Findings: Based on the findings on comparison of the three designated sites the reading of DOC level of site A is 169.269 mg/L C, site B 133.155 mg/L C and site C 169.976 mg/L C; whereas, the TDP concentration for site A is 1.40 mg/L P, site B 0.23 mg/L P and site C 0.49 mg/L P. On the TDN measurement the reading showed that site A is 1.00 mg/L N, site B 6.90 mg/L N and site C 12.20 mg/L N. The findings showed that site C had the highest concentration of total dissolved carbon and nitrogen among the designated sites whereas site A has the highest recovery for total dissolved phosphorus.

Conclusion and Implications:  The study has successfully revealed that difference site of samples have their own uniqueness of physical and chemical characteristic by few factors that can change the value of the concentrations of TDN, TDP, and DOC. Mineralization, temperature, site condition, moisture, are the factors that effects the chemical concentration and more over the bacterial communities that resides within the soils may directly affected the chemical concentration. Soil microbial metabolic interactions during degradation of cellulose and other C compounds, as well as the myriads of other soil processes that result in the differences of N and P compound, are not well known. Soil metagenomes, is one of the latest technology that can revealed on how the physiology of the interacting organisms respond to these environmental conditions that contributed to the variability of dissolved organic matters concentrations within the designated sites.

Published
2020-01-06
How to Cite
Ahmad, M. F., & Yaacob, N. S. (2020). A Research Paper: Royal Belum Soils Dissolved Organic Matters and Bacterial Community Profiling Via Shotgun Metagenomics Approach. Postgraduate Research Symposium - January 2020, 1(1). Retrieved from http://ojs.journals.unisel.edu.my/index.php/prsj20/article/view/91