Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies

Abstract

18 Microbial remediation of oil polluted habitats remains one of the foremost methods for 19 restoration of petroleum hydrocarbon contaminated environments. The development of 20 effective bioremediation strategies however, require an extensive understanding of the 21 36 37 38 39 40 41 42 43 48 during production, operational use, and transportation. The development, effectiveness and 49 availability of technologies and strategies pose a significant challenge for the remediation, 50 rehabilitation and restoration of these contaminated environments. Many of the 51 technologies developed and in use for the restoration of oil contaminated environments 52 exploit the potential of biological systems, in particular microbial systems, to use these toxic 53 compounds as substrates for growth. Hence, much of the research conducted on 54 bioremediation has concentrated on the capabilities of a single or couple of microbes 55 exhibiting robust and effective growth using petroleum hydrocarbons. However, in the 56 environment, bioremediation is often a complex process involving co-metabolism, cross-57 induction, inhibition and non-interaction among microbes 1-3 , possibly as petroleum 58 hydrocarbons are a mixture of organic pollutants and therefore are used differently by 59 different microbes. These findings, along with others, established bioremediation as a 60 process mediated by a consortium of microbes rather than a few. Thus, characterization of 61 microbial communities of oil contaminated environments could potentially provide 62 guidelines for effective remediation and restoration of such environments. 63 Until recently, it was only possible to study a handful of microorganisms of interest 64 isolated from source materials (as blood, soil, water or air), given the restrictions of the 65 composition of culture media which cannot reflect and mimic the dynamic nutrient fluxes of 66 the source environment. Indeed, only 1% of microorganisms were found to be cultivable 67 4 using a set of media from the highly characterized soil rhizosphere 4 . The advent of high 68 throughput massively-parallel sequencing methods has however, allowed us to investigate 69 the entire complement of organisms inhabiting a certain environment. These next-70 generation sequencing methods (NGS) include a variety of methods to holistically study any 71 biological system such as amplicon sequencing (for variant identification and phylogenetic 72 surveys), whole genome shotgun sequencing (single organism genome and metagenomes) 73 and RNA-Seq (transcriptomes, metatranscriptomes and identification of non-regular RNAs). 74 These powerful methods have ushered in rapid advances in bioinformatics approaches 75 leading to development of software capable of handling huge amounts of data and offering 76 meaningful biological interpretations of the same. Although a technological breakthrough in 77 modern science, a number of NGS methods as metagenomic and transcriptomic/ 78 metatranscriptomic sequencing are still expensive and hence, most studies on ecologic...

Metagenomics insight into microbial dynamics in field-scale remediation of crude oil-polluted soil

“…The reduction in abundance of these degradation pathways during the later stages of Landfarming and a subsequent resurgence of Alphaproteobacteria (day-56) is also a con rmation of the important role these pathways play during bioremediation. Several studies have employed the use of predictive methods to pro le crude oil polluted soils and several other environments [38][39][40][41]. Using predictive functional pro ling, Bao et al [38] was able to reveal that majority of differentially detected functional genes responsible for both saturates and aromatic hydrocarbon degradation in their study were associated with oil polluted soils.…”

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

“…Taxonomic composition of bacterial communities through the use of 16S rRNA gene profiling is useful in showing differences in community composition between sites, as well as providing understanding regarding taxonomic response to the presence of fish cages in the harbour. However, evidence on potential functional composition can provide important insights into the interaction between metabolic pathways and environmental stress (Mukherjee et al, 2017;Wu et al, 2019;Laroche et al, 2021;Raes et al, 2021). PICRUSt2 is a computational approach to predict the functional composition of a metagenome from the 16S rRNA sequence (Douglas et al, 2020), and has been used widely in previous studies on aquaculture environmental impact (Hornick and Buschmann, 2017;Ortiz-Estrada et al, 2019;Vargas-Albores et al, 2019;Laroche et al, 2021;Qu et al, 2021).…”

Metagenomics insight into microbial dynamics in field-scale remediation of crude oil-polluted soil

“…The reduction in abundance of these degradation pathways during the later stages of Landfarming and a subsequent resurgence of Alphaproteobacteria (day 36-56) is also a confirmation of the important role these pathways play during bioremediation. Several studies have employed the use of predictive methods to profile crude oil polluted soils and several other environments [38][39][40][41].…”