Genomic analysis reveals the potential for hydrocarbon degradation of Rhodopirellula sp. MGV isolated from a polluted Brazilian mangrove

Abstract

Planctomycetes are bacteria found in several environments, such as mangroves. In the coastline of the State of Sao Paulo (Brazilian Southeast), mangroves occur in different stages of environmental contamination, promoted by the proximity to the city and industrial activities. One of these mangroves (located in the city of Bertioga) is characterized by the high impact due to past petroleum and ongoing urban contamination. We isolated five bacteria affiliated to Planctomycetes from this mangrove and further subjected them to phenotypical and genetic analysis. The tolerance for salinity was demonstrated by the cultivation under distinct concentrations of NaCl. The ability of this bacterium to use diverse carbon sources was revealed by the use of 30 C-sources from a total of 31 tests. We found the isolate Rhodopirellula sp. MGV very closely affiliated to species of the genus Rhodopirellula, harboring a genome with 7.16 Mbp and 55.3% of GC. The annotation of the 77 contigs resulted in 6.284 CDS, with a remarkable occurrence of sequences associated with aromatic carbon metabolism. In conclusion, we present the isolation and characterization of a Planctomycetes from mangroves, suggesting its participation in the degradation of hydrocarbons present in the contaminated mangroves studied.

Keywords: Bacterial cultivation; Degradation of hydrocarbons; Genome of Planctomycetes; Metabolic profile; PVC superphylum; Rhodopirellula sp. MGV.

Fig. 1

Morphological aspects of candidate colonies affiliated to the phylum Planctomycetes (a), and taxonomical affiliation of the isolate Rhodopirellula sp. MGV isolated from soil of a Brazilian mangrove (NPDI01000000) (b)

Fig. 2

Growth curves of the isolate Rhodopirellula sp. MGV, cultivated in the medium M13 under distinct concentrations of NaCl. Average values resulted from three replicates and bars indicates the standard deviation values

Fig. 3

Phylogenetic comparisons based on protein sequences codified by CDS of the genome of Rhodopirellula sp. MGV concerning the production of monooxygenases (salicylate via) (ID_VK1H96J1016) (a), 4-oxalocrotonatetautomerase (ID_VK1T39FV013) (b), meta-cleavage compound (2-hydroxy-6-oxohexa-2,4-dienoates)4-oxalocrotonate tautomerase (ID_VK20BRAW016) (c). Bootstrap support (>50) representing Neighbor-joining values using substitute model JTT (1000 replicates)