Metagenomic binning to recover functional and taxonomical information from environmental engineering biological systems

Great value can be added to the study of biological processes with having a broader view of microbial community structure, functions, and interactions in ecosystems important to environmental engineering. Advances in cellular and molecular biology are providing overtures to new ways of studying microbial communities holistically. Metagenomics, for example, is a method for analysis of the entire genomic contents of a microbial community. Metagenomics circumvents the challenges of lab culturing by using genomic sequencing to study the diversity of microorganisms in an environment (even if they were previously unknown or difficult to culture). Although there are still several obstacles yet to be overcome for interpretation of metagenomic data, metagenomic binning (i.e., clustering of metagenomic raw data) is an approach to subset metagenomic sequencing reads into microbial populations. Metagenomic binning therefore provides a method for studying the taxonomical classification and functional annotations of microbial populations to interpret interactions among microbial populations that compose a microbial community. This study aims to perform metagenomic binning to enhance taxonomical classification, functional potentials, and interactions among microbial populations in environmental systems. For this reason, a metagenomic data processing pipeline is developed to evaluate metagenomic data from three environmental engineering projects including: (1) a 2,4,6-Trinitrotoluene (TNT) contaminated site remediation project; (2) a bench scale reactor study of Enhanced Biological Phosphorous Removal (EBPR); and (3) a bench scale study of Algae-bacteria bioreactor designed for nitrogen removal from wastewater. This customized pipeline which is comprised of a series of genomic/metagenomic tools designed to recover better quality results to have more accurate and reliable interpretation of the system dynamics for the given systems. The successful pipeline hopefully, not only would help to uncover new information from aforementioned environmental engineering studies, but also, could be applicable to any other metagenomic studies across various disciplines.