Metabolic and metagenomic profiling of hydrocarbon-degrading microorganisms obtained from the deep biosphere of the Gulf of México

Abstract

Marine microbes are capable of degrading hydrocarbons; however, those inhabiting the deep biosphere (>1000 m) remain largely unexplored. Microbial metabolism could lead to the generation of diverse chemistries (some with therapeutic activities), but the impact of using hydrocarbons as the sole source of microbial energy in the synthesis of metabolites, remains obscure. Here, we investigated the metagenomic and metabolomic profile of two deep-marine sediments (>1 200 m deep, designated as A7 and B18) collected from the Gulf of México (GM) when grown for 28 days with a simple mixture of 4 hydrocarbons and complex hydrocarbon mixture (petroleum API 40) as their sole source of energy. State of the art techniques and analysis (e.g., Global Natural Products Social Molecular Networking, network annotation propagation [NAP], and MS2LDA) were used to describe the chemistries associated to the microbial utilization of hydrocarbons. The metagenomic sequencing analysis suggests a predominant abundance of Proteobacteria in environmental and API 40-enriched samples, while the abundance of Pseudomonas increased after microbial growth with API 40. The metabolomic analysis suggests the presence of diverse chemistries predominantly associated with lipid and lipid-like and phenyl propanoids and polyketides superclass (Classyfire annotation). Hydrocarbon derivatives were detected as carboxylic acids (e.g., azelaic and sebacic acid) or alcohols, while non-hydrocarbon related chemistries were also detected including tetracycline-related metabolites and sphinganines. Our study provides valuable chemical and microbiological information of microbes inhabiting one of the most understudied ecosystems in the earth, the deep marine biosphere.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

“…We expected the presence of diverse sequences related to hydrocarbon degradation as previous studies in the water and sediments in the GoM have shown the presence of PHDB (Godoy-Lozano et al, 2018;Moreno-Ulloa et al, 2019;Ramírez et al, 2020). It is important to note that some of the most abundant bacterial genera reported in this work are related to the biodegradation of contaminants and support the idea that microbial communities in deep-sea sediments of GoM have the potential to metabolize a variety of organic compounds, including oil, crude oil and its derivatives.…”

Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide

“…Notably, the results related to the presence of enzymes involved in oil degradation are consistent with previous works of our own and other groups that investigated the Mexican exclusive economic zone and identified oil-degrading microorganisms derived from 16S amplicon analysis (Fernanda Sánchez-Soto Jiménez et al, 2018;Godoy-Lozano et al, 2018;Hernández-López et al, 2019;Moreno-Ulloa et al, 2019;Raggi et al, 2020;Ramírez et al, 2020); isolated fractions related to petroleum (Moreno-Ulloa et al, 2019); isolated consortia and species capable of degrading petroleum under aerobic and anaerobic conditions (Muriel-Millán et al, 2019;Curiel-Maciel et al, 2021;Rosas-Díaz et al, 2021); and characterized petroleum-degrading enzymes (Rodríguez-Salazar et al, 2020), even in regions with no evidence of anthropogenic perturbation. A recent review illustrated the distribution of bacteria in the water column and sediments of the Mexican exclusive economic zone of the GoM (Rodríguez-Salazar et al, 2021).…”

Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments

“…Despite that Pseudoalteromonas sp. has a predominant role in hydrocarbon and heavy metal remediation, it is known to efficiently degrade hydrocarbons in association with other bacteria [33,43,44], and from our study co-culturing with Alcanivorax sp. SZN2 does not appear to result in the most efficient complementation.…”