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Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile.

ABSTRACT: Alcaligenes aquatilis strain QD168 (= CCUG 69566) is a marine hydrocarbon-degrading bacterium isolated from crude oil-polluted sediment from Quintero Bay, Central Chile. Here, we present the 4.32-Mb complete genome sequence of strain QD168, with 3,892 coding sequences, 58 tRNAs, and a 56.3% G+C content.

SUBMITTER: Duran RE

PROVIDER: S-EPMC6357646 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Project description:Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic determinants and the physiological response of A. aquatilis QD168 to model environmental stressors (benzene, oxidizing agents, and salt). Phylogenomic analyses, using 35 housekeeping genes, clustered A. aquatilis QD168 with four other strains of Alcaligenes spp. (A. aquatilis BU33N, A. faecalis JQ135, A. faecalis UBA3227, and A. faecalis UBA7629). Genomic sequence analyses of A. aquatilis QD168 with 25 Alcaligenes spp., using ANIb, indicated that A. aquatilis BU33N is the closest related strain, with 96.8% ANIb similarity. Strain QD168 harbors 95 genes encoding proteins of seven central catabolic pathways, as well as sixteen peripheral catabolic pathways/reactions for aromatic compounds. A. aquatilis QD168 was able to grow on 3-hydroxybenzoate, 4-hydroxybenzoate, benzoate, benzene, 3-hydroxycinnamate, cinnamate, anthranilate, benzamide, 4-aminobenzoate, nicotinate, toluene, biphenyl and tryptophan, as sole carbon or nitrogen source. Benzene degradation was further analyzed by growth, metabolite identification and gene expression analyses. Benzene strongly induced the expression of the genes encoding phenol hydroxylase (dmpP) and catechol 1,2-dioxygenase (catA). Additionally, 30 genes encoding transcriptional regulators, scavenging enzymes, oxidative damage repair systems and isozymes involved in oxidative stress response were identified. Oxidative stress response of strain QD168 to hydrogen peroxide and paraquat was characterized, demonstrating that A. aquatilis QD168 is notably more resistant to paraquat than to H2O2. Genetic determinants (47 genes) for osmoprotective responses were identified, correlating with observed high halotolerance by strain QD168. The physiological adaptation of A. aquatilis QD168 to environmental stressors such as pollutants, oxidative stress and salinity may be exploited for bioremediation of oil-polluted saline sites.

Project description:The industrial park of Quintero Bay (QB) in the central coast of Chile was established in the 1960s, presents high levels of pollution due to the industrial activity, and it is known as one of the five Chilean "sacrifice zones". Lessonia spicata is the most important habitat-forming kelp species in the intertidal along the central and south shores of Chile, and currently there are no morphometric and population studies of L. spicata (or other seaweed species) nor studies about the effects of pollution on its development in QB and neighbouring sites. In this context, the aims of this study were (i) to register the abundance and morphological features of L. spicata populations from Ventanas, Horcón and Cachagua (sites with different pollution histories and located only up to 40 km from the QB); ii) to determine the heavy metals (HMs) concentration in seawater and marine sediments; and (iii) to evaluate in vitro the effects of exposure to seawater from the three sampling sites on spore release and early developmental stages, up to the juvenile sporophyte. Results showed that the chronically exposed Ventanas kelp population had the smallest adult individuals in comparison with the other sites. Ventanas and Horcón registered high HMs concentration in the seawater and marine sediments exceeding the international permissible limits (e.g in seawater Cu 20-859 μg L-1; sediments Cu > 50,000 μg kg-1). Unexpectedly in Cachagua, a site often considered unpolluted, high concentrations of Cu and As were also registered in the seawater (859 and 1,484 μg L-1, respectively) and of As in marine sediments (20,895 μg kg-1). Exposure of gametophytes to the seawater from Ventanas resulted in a developmental delay compared to the other treatments; however, low sporophyte production was determined in all treatments. Our results indicate that QB, more notably Ventanas, induce highly negative effects on individual development, and consequently on seaweed populations, which suggest a long-term negative impact on the community structure of these marine zones. Furthermore, the high concentrations of HMs reported here at Cachagua suggest a recent expansion of pollution along the central coast of Chile, evidencing effects on the marine ecosystem health even on sites far from the pollution source.

Dataset Information

Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile.

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