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. 2025 Jul 31;14(9):e00524-25. doi: 10.1128/mra.00524-25

Complete genome sequences of two dye-decolorizing aeromonads isolated from a stormwater drain in Hong Kong

P S K Leung 1, K M Leung 1, G K K Lai 1, S D J Griffin 1,✉
Editor: J Cameron Thrash2
PMCID: PMC12424365  PMID: 40741739

ABSTRACT

Aeromonas hydrophila subsp. hydrophila PSKL.DP and Aeromonas dhakensis PSKL.DM were isolated from a stormwater drain in Hong Kong. Their complete genomes—single chromosomes of 4,844,288 bp (61.50% G+C) and 4,820,799 bp (61.49% G+C), respectively—were established through hybrid assembly.

KEYWORDS: Aeromonas hydrophila, Aeromonas dhakensis, dye-degradation, bioremediation

ANNOUNCEMENT

Aeromonas species comprise Gram-negative facultative anaerobes found as non-spore forming, flagellated rods, that are ubiquitous in freshwater and brackish environments (1). They have been isolated from drinking water, soil, raw meats, and agricultural produce (2–4); from the gastrointestinal tracts of aquatic animals, including birds (5–7); and even from microplastics (8). While Aeromonas spp. may be linked to cases of human infection, likely through untreated water (2), their versatile biochemistry has been applied to the bioremediation of triarylmethane dyes (9) and heavy metals (10). They are also useful as producers of industrial enzymes and polyhydroxyalkanoate (11).

Here, two aeromonads were isolated from a stormwater drain in Hong Kong (22.264420°N, 114.130481°E; 2022-06-02). A 1 mL sample of rainwater from a collector drain was serial diluted to 0.1% v:v in 0.9% w:v saline before spreading a 100 µL aliquot onto CHROMagar Vibrio plates and incubating for 48 h at 27°C (this temperature was used throughout). PDKL.DP and PSKL.DM appear, respectively, as purple and white colonies on this medium, and these were picked and transferred to a minimal salts agar (12) containing either methylene blue (0.0005%), malachite green (25 ng/mL), or azure blue (0.0125 g/L). Isolates producing decolorized zones around colonies on all three dye-containing media were purified by single-colony streaking on Luria agar (13). For DNA extraction, using a PureLink Genomic DNA Mini Kit (Invitrogen) following the manufacturer’s protocol, a single colony was transferred to Luria broth and incubated overnight.

Paired-end short-read sequencing libraries were prepared using the NovaSeqX Series 10B Reagent Kit and sequenced via the Illumina NovaSeq 6000 platform (SP flowcell PE250, v1.5 Reagent Kit) with reads quality-filtered and trimmed using Trimmomatic v0.32 (14). Long-read libraries, prepared from the same extracted DNA using the Rapid Barcoding Kit SQK-RBK004 (without shearing or size selection), were sequenced using a Spot-ON Flow Cell (vR9), MinION sequencer, and MinKNOW v3.1.8 software, with base-calling by Guppy v2.1.3 (all by Oxford Nanopore Technologies plc). The final long-read data set was trimmed by Porechop v0.2.4 (15). Default parameters were used for all software unless otherwise specified.

NovaSeq and MinION data sets were combined using Unicycler v0.4.8-beta (16) to yield single chromosomes of 4,844,288 bp (61.50% G+C) and 4,820,799 bp (61.49% G+C) for PSKL.DP and PSKL.DM respectively, which were submitted to NCBI PGAP v6.5 (17) for annotation. Using GenomesDB (18), JSpeciesWS v.5.0.1 (19) found PSKL.DP and PSKL.DM to share average nucleotide identities (ANIb by BLAST+ [20]) of 96.84% and 97.04% with type strain Aeromonas hydrophila subsp. hydrophila ATCC7966 (CP000462) and with Aeromonas dhakensis 1706-28330 (CP054854) respectively. Sequencing and assembly data are given in Table 1.

TABLE 1.

Sequencing, assembly, and analysis for PSKL.DP and PSKL.DM, including the loci of putative dye-degrading genes

PSKL.DP PSKL.DM
Sequencing method Illumina NovaSeq Nanopore MinION Illumina NovaSeq Nanopore MinION
Raw reads 6,317,280 607,929 7,142,248 1,427,792
Mean length bp 250 4,892 250 5,942
Total Gbp 1.58 2.97 1.79 8.48
N50 250 8,648 250 10,900
SRA (raw) SRX28704585 SRX21625239 SRX28776443 SRX21353834
Filtered reads 6,303,476 110,340 7,131,554 46,964
Mean length 250 13,594 232 31,940
N50 250 13,767 250 31,423
Total Gbp 1.55 1.50 1.65 1.50
Assembly
 Species Aeromonas hydrophila subsp. hydrophila Aeromonas dhakensis
 GenBank accession CP117918 CP117919
 Topology Circular Circular
 Size (bp) 4,844,288 4,820,799
 G+C % 61.50 61.49
 Coverage 310× 311×
 Rotated to begin Not rotated dnaA (A0KEC3)
 CDs (coding)a 4,260 4,213
 Pseudogenesa 23 27
 rRNA (5S-16S-23S)a 11-10-10 11-10-10
 tRNAa 126 124
Analysis (loci of dye degradation-linked genes)
    Triphenylmethane oxygenase
    (tpmD) (20, 21)		 [not found] PUB92_03280
    FMN-dependent NADH: quinone
    azoreductase (azoR) (22)		 PUB83_20410
PUB83_06035		 PUB92_10075
PUB92_03145
 Dyp-type peroxidase (23) PUB83_13030 PUB92_02640
    Laccase (lacA)/multicopper
    oxidase (cueO) (24, 25)		 PUB83_20335 PUB92_17505
 Tyrosinase (26) PUB83_11010 PUB92_16400
 Xenobiotic reductase
 (xenB) (27)		 [not found] PUB83_12610
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a

Found by NCBI PGAP v6.5 (PSKL.DP)/v6.4 (PSKL.DM).

NCBI PGAP and NCBI BLASTp (21) were used to identify proteins encoded in PSKL.DP and PSKL.DM similar to those reported as dye-degrading in strains of Aeromonas. Loci of putative homologs—i.e. for triphenylmethane oxygenase (tpmD) (22, 23), azoreductase (azoR) (24), Dyp-type peroxidase (25), laccase (lacA) (26, 27), tyrosinase (28), and xenobiotic reductase (xenB) (29)—are given Table 1.

Contributor Information

S. D. J. Griffin, Email: sgriffin@isf.edu.hk.

J. Cameron Thrash, University of Southern California, Los Angeles, California, USA.

DATA AVAILABILITY

The complete genome sequences and raw sequence data for PSKL.DP and PSKL.DM are available through NCBI under BioProjects PRJNA933919 and PRJNA933921, respectively, with GenBank and SRA accession numbers given in Table 1.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The complete genome sequences and raw sequence data for PSKL.DP and PSKL.DM are available through NCBI under BioProjects PRJNA933919 and PRJNA933921, respectively, with GenBank and SRA accession numbers given in Table 1.

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