Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast

Abstract

Oil spills are among the most catastrophic events to marine ecosystems and current remediation techniques are not suitable for ecological restoration. Bioremediation approaches can take advantage of the activity of microorganisms with biodegradation capacity thus helping to accelerate the recovery of contaminated environments. The use of native microorganisms can increase the bioremediation efficiency since they have higher potential to survive in the natural environment while preventing unpredictable ecological impacts associated with the introduction of non-native organisms. In order to know the geographical scale to which a native bioremediation consortium can be applied, we need to understand the spatial heterogeneity of the natural microbial communities with potential for hydrocarbon degradation. In the present study, we aim to describe the genetic diversity and the potential of native microbial communities to degrade petroleum hydrocarbons, at an early stage of bioremediation, along the NW Iberian Peninsula coast, an area particularly susceptible to oil spills. Seawater samples collected in 47 sites were exposed to crude oil for 2 weeks, in enrichment experiments. Seawater samples collected in situ, and samples collected after the enrichment with crude oil, were characterized for prokaryotic communities by using 16S rRNA gene amplicon sequencing and predictive functional profiling. Results showed a drastic decrease in richness and diversity of microbial communities after the enrichment with crude oil. Enriched microbial communities were mainly dominated by genera known to degrade hydrocarbons, namely Alcanivorax, Pseudomonas, Acinetobacter, Rhodococcus, Flavobacterium, Oleibacter, Marinobacter, and Thalassospira, without significant differences between geographic areas and locations. Predictive functional profiling of the enriched microbial consortia showed a high potential to degrade the aromatic compounds aminobenzoate, benzoate, chlorocyclohexane, chlorobenzene, ethylbenzene, naphthalene, polycyclic aromatic compounds, styrene, toluene, and xylene. Only a few genera contributed for more than 50% of this genetic potential for aromatic compounds degradation in the enriched communities, namely Alcanivorax, Thalassospira, and Pseudomonas spp. This work is a starting point for the future development of prototype consortia of hydrocarbon-degrading bacteria to mitigate oil spills in the Iberian NW coast.

Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus

“…Oceanobacter -related bacteria (ORB) are clearly an ecologically important microbial clade in marine environments and are particularly involved in hydrocarbon metabolism. Notably, Thalassolituus and Oleibacter frequently occurred as predominant members in hydrocarbon-spiking microcosms of temperate seawater and sediment ( Yakimov et al, 2005 ; McKew et al, 2007 ; Tremblay et al, 2017 ; Lofthus et al, 2018 ; Bôto et al, 2021 ), tropical seawater ( Teramoto et al, 2009 ), oil plumes and seawater collected from the vicinity of the Deepwater Horizon blowout site ( Hazen et al, 2010 ; Liu et al, 2017 ), Arctic and subarctic seawater ( Dong et al, 2014 ; Suja et al, 2017 ; Shtratnikova et al, 2018 ) and sediment ( Murphy et al, 2021 ), as well as in the in situ sediment after oil-spills ( Lee et al, 2017 ; Thomas et al, 2020 ). Recently, they were identified as key hydrocarbon degraders not only in the ocean sunlight zone ( Love et al, 2021 ) but also in the dark hadal zone ( Liu et al, 2019 ; Jian et al, 2021 ).…”

Study on the Changes in Immobilized Petroleum–Degrading Bacteria Beads in a Continuous Bioreactor Related to Physicochemical Performance, Degradation Ability, and Microbial Community

“…Except for the genus Shewanella , many bacteria, not being abundant in seawater, could be detected in the immobilized petroleum–degrading bacteria beads, which indicated that the immobilized petroleum–degrading bacteria beads provided shelter for these bacteria and improved their growth and reproduction. The genera Alcanivorax , Shewanella , Thalassospira , Alteromonas , Tenacibaculum , and Lutibacter , were abundant in the interior of the immobilized petroleum–degrading bacteria beads, and these bacteria were all petroleum–degrading bacteria [ 27 , 28 , 29 ]. Plenty of holes in the immobilized petroleum–degrading bacteria beads could absorb diesel (shown in Figure 2 c); thus, the immobilized petroleum–degrading bacteria beads attracted many petroleum–degrading bacteria to migrate into the interior of the immobilized petroleum–degrading bacteria beads [ 30 , 31 ].…”

Exploiting bacterial isolates for diesel degrading potential under in vitro conditions

“…Enumeration of bacterial population was performed by plating 0.1 ml of serially diluted soil sample on nutrient agar. Diesel degrading bacterial strains were screened by streaking them over Bushnell Haas (BH) Agar supplemented with 1% (v/v) filter sterilized diesel as carbon source using the standard methods (14,17,18). The soil samples after physical and analytical characterization were subjected to the microbiological analysis.…”

“…In order to find out the microbial isolates possessing hydrocarbon degrading capabilities (13,19). Primary and secondary screenings (17,18,20) of hydrocarbon degrading microbes were performed. Soil suspension was made by mixing with 1 g soil in 10 ml Bushnell and Hass Broth (BH broth) conditioned with 1% (v/v) filter-sterilized diesel as the sole source of carbon.…”

“…After 48 hrs of incubation of pure single isolates, colonies were subjected to microbiological identification (cultural, microscopic and biochemi-cal characterization) of all the gram positive and gramnegative isolates. All the identified microbial isolates were transferred to agar slants and glycerol stocks for further use (2,13,14,18). Primary screening, soil suspension was inoculated in Bushnell Hass broth supplemented with 1% filter sterilized diesel incubated on orbital shaker incubator for 24 hrs.…”