Background
Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.
Methods
The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.
Results
We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
Hydrogen, electric energy production, and metal toxic bioremediation are some of the biotechnological applications of sulfate-reducing organisms, which potentially depend on the sulfide produced. In this study, offshore of Yucatan, the capacity to produce hydrogen sulfide using microbial consortia from marine sediment (SC469, PD102, SD636) in batch reactors was evaluated. Kinetic tests were characterized by lactate oxidation to acetate, propionate, CO2 and methane. The inoculum SC469, located in open-ocean, differed strongly in microbial diversity and showed better performance in substrate utilization with the highest hydrogen sulfide production (246 mmolg−1 VSS) at a specific hydrogen sulfide rate of 113 mmol g−1 VSS d−1 with a 0.79 molar ratio of sulfate/lactate. Sulfate-reducing microbial consortia enriched in the laboratory from marine sediments collected offshore in Yucatan and with a moderate eutrophication index, differed strongly in microbial diversity with loss of microorganisms with greater capacity for degradation of organic macromolecules. The sulfate-reducing microorganisms were characterized using Illumina MiSeq technology and were mainly Desulfomicrobium, Clostridium and Desulfobacter.
ABSTRACT. Marine environments are a reservoir of relevant information on dangerous contaminants such as hydrocarbons, as well as microbial communities with probable degradation skills. However, to access microbial diversity, it is necessary to obtain high-quality DNA. An inexpensive, reliable, and effective metagenomic DNA (mgDNA) extraction protocol from marine sediments contaminated with petroleum hydrocarbons was established in this study from modifications to Zhou's protocol. The optimization included pretreatment of sediment with saline solutions for the removal of contaminants, a second precipitation and enzymatic degradation of RNA, followed by purification of mgDNA extracted by electroelution. The results obtained indicated that the modifications applied to 12 sediments with total petroleum hydrocarbon (TPH) concentrations from 22.6-174.3 (µg/g dry sediment) yielded 20.3-321.3 ng/µL mgDNA with A 260 /A 280 and A 260 /A 230 ratios of 1.75 ± 0.08 and 1.19 ± 0.22, respectively. The 16S rRNA amplification confirmed the purity of the mgDNA. The suitability of this mgDNA extraction protocol lies in the fact that all chemical solutions utilized are common in all molecular biology laboratories, and the use of dialysis membrane does not require any sophisticated or expensive equipment, only an electrophoretic chamber.
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