Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Abstract

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

“…In turn, de Menezes et al (2012) demonstrated an increased number of dioxygenase-associated transcripts belonging to Mycobacterium while investigating soil bacterial community responses to pollution with phenanthrene. Mukherjee et al (2017) showed the presence of both n-alkane and aromatic hydrocarbon utilization genes of Mycobacterium in the soil samples collected from Chinese refineries. They suggested that bacteria of this genus were among the most important hydrocarbon degraders in the tested soils.…”

“…To develop a successful bioremediation strategy, a detailed knowledge is required regarding the microbiome of a given habitat together with a deep understanding of bacterial ecological status. Several studies revealed the presence of the mentioned genera or occurrence of catabolic genes related to these taxa in hydrocarbon-polluted environments (Margesin et al 2003;Leys et al 2005;de Menezes et al 2012;Yergeau et al 2013;Mukherjee et al 2017). Margesin et al (2003) found that microorganisms containing hydrocarbon-degradative genotypes related to Pseudomonas proliferated following oil contamination.…”

Dietary lysozyme supplement alters serum biochemical makers and milk metabolite profile of sows via gut microbiota

“…Functional categories at different levels were computed with the script categorize by function.py. Functional differences within groups were explored using LEfSe and specific analysis was performed through the Galaxy server [38]. Output files from the PICRUSt analysis were collected and analyzed by R software (v3.5.1) for further statistical interrogation and graphical depictions of all predicted functional datasets.…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…Disrupted ecosystems can also present shifts in particular taxa or overall biodiversity (Nogales et al, 2011;Mason et al, 2014;Mukherjee et al, 2017), opening the possibility to evaluate ecological status according to such metrics. Toward this goal, Aylagas et al (2017) developed two composite indicators: (1) a sediment quality index that included organic matter content, redox potential, and metal, PAH and PCB concentrations; and (2) a bacterial index of environmental quality adapted from the AMBI.…”