Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico

Abstract

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.

Insights into coastal microbial antibiotic resistome through a meta-transcriptomic approach in Yucatan

“…The identification of the ARGs present in the sediments of Yucatan coast was carried out at four sites: two sites with anthropic impact, and two state ecological reserves. The selected wetlands with anthropic impact were the swamps in the towns of Sisal (21°09′43.6″ N 90°02′27.2″ W) and Progreso (21°16′37.6″ N 89°40′35.6″ W); these locations are contaminated with organic and inorganic garbage, septic tank sedimentation sludge, sanitary waste, insecticides, and petroleum hydrocarbons with the concentration of total petroleum hydrocarbons (TPH) exceeding the permissible level in coastal sediments of 70 μg/g ( Suárez-Moo et al, 2020 ). The preserved wetlands were those located in El Palmar (21°08′56.4″ N 90°06′07.0″ W) and Bocas de Dzilam (21°27′22.2″ N 88°40′53.7″ W), which are Reserves State Ecological, in addition to Ramsar sites ( Figure 1 ).…”

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

“…To carry out the description of the microbial communities present in the sediments of four wetlands of the Yucatan state, the wetland of Sisal (21°09′43.6″ N 90°02′27.2″ W) and Progreso (21°16′37.6″ N 89°40′35.6″ W) locations were selected because they are contaminated with organic and inorganic garbage, septic tank sedimentation sludge, sanitary waste, insecticides, and petroleum hydrocarbons ( Supplementary Figure S1 ). Indeed, the concentration of total petroleum hydrocarbons (TPH) in Progreso and Sisal is exceeding the permissible level in coastal sediments of 70 μg/g [ 8 ]. By other side, two locations with not perturbations were sampled.…”

Changes in the sediment microbial community structure of coastal and inland sinkholes of a karst ecosystem from the Yucatan peninsula

“…Some of these phyla (Chloroflexi, Proteobacteria, and Bacteroidetes) have been reported in sediments from freshwater karst sinkholes from Lake Huron 25 in water and sediments from other sinkholes in the Yucatan peninsula 6 , and in the karst caves bacteriome from southwest China 21 . A study that included coastal marine sediments from two sites in the Yucatan peninsula, showed high abundances of Spirochaeta , Desulfococcus , Clostridium, Psychrobacter 26 , four genera that were abundant in the coastal sinkhole. However, Desulfococcus , Synechococcus were also abundant in the inland sinkhole.…”

“…A comparative analysis of published data with other studies in the Yucatan peninsula (sinkholes and marine environments, Supplementary Table S5 ) using 16S rRNA amplicons was performed considering a rarefaction to 3490 reads per sample. An nMDS with Bray–Curtis distance analysis was created using VEGAN package in R 37 and used to visualize the similarities between samples of the different studies 2 , 13 , 26 . To visualize families shared among the six different environment an Upsetplot was constructed using R package UpsetR 46 .…”