Draft genome sequences of hydrocarbon degrading Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 isolated from the estuarine sediments of Sundarban mangrove forests, India

Abstract

The present study reports the draft genomes of three hydrocarbon-degrading haloarchaeal strains Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 that were isolated from the estuarine sediments of Sundarban mangrove forests, India. All three genomes had a high GC content of around 60%, characteristic of the haloarchaea. The Haloferax sp. AB510 genome was around 3.9 Mb in size and consisted of 4567 coding sequences and 54 RNAs. The Haladaptatus sp. AB618 and Haladaptatus sp. AB643 genomes were comparatively larger and around 4.8 Mb each. The AB618 and AB643 genomes comprised 5279 and 5304 coding sequences and 60 and 59 RNAs, respectively. All three of the genomes encoded several genes that attributed to their survival in the presence of hydrocarbons in their native habitats. Functional annotation and curation of the sequenced genomes suggested that the Haloferax sp. AB510 strain utilized the gentisate pathway of aromatic compound degradation. While the Haladaptatus sp. AB618 and Haladaptatus sp. AB643 strains possessed the freedom of utilizing both the gentisate and the catechol pathways for degrading aromatic hydrocarbons.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03273-5.

Fig. 1

Neighbour-joining phylogenetic tree reconstructed on the basis of 16S rRNA gene sequence depicting the phylogenetic relationship between the three Haloarchaeal isolates Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 with other closely related species. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. This analysis involved 28 nucleotide sequences. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Evolutionary analyses were conducted in MEGA11 (Tamura et al. 2021)

Fig. 2

BRIG output image of Haloferax sp. AB510 along with other closely related Haloferax species. The innermost circle (black) represents the reference genome, Haloferax sp. AB510. The two skewed circles surrounding it on the outside represent the GC content (black) and the GC Skew (purple/green). The outer rings represent the shared identity (according to BLASTn +) with 11 other completed Haloferax genomes (refer to the colour-coded legend). BLASTn + matches between 50 and 100% nucleotide identity are coloured from lightest to darkest shade, respectively, according to the graduated scale on the right of the circular image. Matches with less than 50% identity, or Haloferax sp. AB510 regions with no BLAST matches, appear as blank spaces within each of the circles

Fig. 3

BRIG output image of Haladaptatus sp. AB618 along with other closely related Haladaptatus species. The innermost circle (black) represents the reference genome, Haladaptatus sp. AB618. The two skewed circles surrounding it on the outside represent the GC content (black) and the GC Skew (purple/green). The outer rings represent the shared identity (according to BLASTn +) with 5 other completed Haladaptatus genomes (refer to the colour-coded legend). BLASTn + matches between 50 and 100% nucleotide identity are coloured from lightest to darkest shade, respectively, according to the graduated scale on the right of the circular image. Matches with less than 50% identity, or Haladaptatus sp. AB618 regions with no BLAST matches, appear as blank spaces within each of the circles

Fig. 4

BRIG output image of Haladaptatus sp. AB643 along with other closely related Haladaptatus species. The innermost circle (black) represents the reference genome, Haladaptatus sp. AB643. The two skewed circles surrounding it on the outside represent the GC content (black) and the GC Skew (purple/green). The outer rings represent the shared identity (according to BLASTn +) with 5 other completed Haladaptatus genomes (refer to the colour-coded legend). BLASTn + matches between 50 and 100% nucleotide identity are coloured from lightest to darkest shade, respectively, according to the graduated scale on the right of the circular image. Matches with less than 50% identity, or Haladaptatus sp. AB643 regions with no BLAST matches, appear as blank spaces within each of the circles

Fig. 5

Schematic representation of the various hydrocarbon-degrading pathways operational in isolates Haloferax sp. AB510, Haladaptatus sp. AB618, and Haladaptatus sp. AB643. The stages of the pathways whose catalyzing enzymes could be traced to our three isolates’ genomes are marked in bold. The alphabet key legend is present in Table 3