Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing

Abstract

Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples. Bacterial genera were identified for their potential hydrocarbon bioremediation activity. These included generalist genera commonly reported in hydrocarbon-polluted areas and petroleum reservoirs, as well as specialists such as Alcanivorax and Cycloclasticus. The highest readings for bacteria with potential hydrocarbon bioremediation activity were for the genera Vibrio, Alteromonas, Pseudomonas, Acinetobacter, Burkholderia, Acidovorax and Pseudoalteromonas from different environments in the study area. Some genera were identified only in specific sites; for example, Aquabacterium and Polaromonas were found only in freshwater upwellings. Variation in genera distribution was probably due to differences in environmental conditions in the sampled zones. Bacterial diversity was high in the study area and included numerous genera with known bioremediation activity. Functional prediction of the metagenome indicated that the studied bacterial communities would most probably degrade toluene, naphthalene, chloroalkane and chloroalkene, with lower degradation proportions for aromatic hydrocarbons, fluorobenzoate and xylene. Differences in predicted degradation existed between sediments and water, and between different locations.

Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils

“…In treatments amended with digestate also an increase of taxa containing recognized TPH degraders was observed. In S1 soil for treatments CDA and CDBI Mycobacterium species were still present, however new dominant genera appeared including Arenimonas which was previously observed in hydrocarbon degrading cultures and associated with oil degradation (Reyes-Sosa et al, 2018;Wang et al, 2016), Arthrobacter (for CDA only) able to degrade crude oil components (Reyes-Sosa et al, 2018) and Thermomonas which was observed in microbial communities under intensive oil degradation (Al-Kharusi et al, 2016).…”

“…Acinetobacter (alkB genes expression) (Barra Caracciolo et al, 2015;Liu et al, 2011;Nie et al, 2014;Pepi et al, 2011;Reyes-Sosa et al, 2018). Species belonging to Thiobacillus were also found in control soil, presence of this bacteria was already detected in petroleum reservoirs (Reyes-Sosa et al, 2018). Within genera present in digestate and consequently in amended soils at the beginning, Psychrobacter was the most abundant.…”

“…In S2 soil, microbial diversity evolved differently and the most abundant genera detected after 30 days were: Dietzia, known to express alkB like genes and having ability to degrade a wide range of hydrocarbons (Wang et al, 2011), Halomonas with ability to degrade aliphatic hydrocarbons (Reyes-Sosa et al, 2018), Stenotrophomonas which was previously observed in soils amended with digestate (Wolters et al, 2018), Microbacterium previously described as phenanthrene degrader (Reyes-Sosa et al, 2018) and Mycobacterium. At the end of the treatment, we have also observed increase of other bacterial genera connected with hydrocarbon degradation.…”

Functional potential of sewage sludge digestate microbes to degrade aliphatic hydrocarbons during bioremediation of a petroleum hydrocarbons contaminated soil

“…In the control (B1), the most abundant genera at the beginning of the experiment were Pseudomonas (46.8%). Pseudomonas genus is a common soil bacterial taxa and contains many well-known PHCs degrading species (Liu et al, 2011;Reyes-Sosa et al, 2018). After 30 days, the population of Pseudomonas decreased to 1.6% and other species associated with PHCs degradation were promoted including Pseudoxanthomonas, Microbacterium and Nocardioides (Liu et al, 2011;Reyes-Sosa et al, 2018;Yu et al, 2018).…”

“…In soil amended with digestate (B3), the most common genera at the beginning were Pseudomonas (33%), Acinetobacter (32.3%) and Rhodococcus (12.4%), all of these genera contain species with known ability to degrade PHCs (Liu et al, 2011;Reyes-Sosa et al, 2018;Yu et al, 2018). Interestingly, in the middle part of the process, Alkanindiges reached a peak abundance of 17.5% and almost totally disappeared after the next 30 days (0.2%).…”