Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation

TL;DR

A new Pseudoalteromonas species from deep-sea water may help break down chitin, contributing to organic matter recycling.

Contribution

A novel Pseudoalteromonas species with potential chitin-degrading abilities is identified through a high-quality metagenome-assembled genome.

Findings

The MAG contains genes related to chitin degradation.

The species was recovered from deep-sea water at the South Mid-Atlantic Ridge.

Abstract

We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.

Figures

Maximum likelihood phylogenetic tree showing the relationship between Pseudoalteromonas SMAR (GCA_048515945.1) and closely related Pseudoalteromonas genomes. The tree was constructed using FastTree (v2.1.11) with the GTR model and 1,000 bootstrap replicates, based on the alignment of 120 conserved bacterial marker genes via GTDB-Tk. Node sizes correspond to bootstrap support values, with larger nodes indicating >75% support. Pseudoalteromonas SMAR is highlighted in red.

Tables

TABLE 1. Metagenome-assembled genome statistics for Pseudoalteromonas SMARa

Parameter	Data
Sequence read archive accession number	SRR32475513 (GenBank)NMDC10019562 (NMDC)
BioSample accession number	SAMN46958406 (GenBank)NMDC20366030 (NMDC)
MAG accession number	JBLWMW000000000 (GenBank)NMDC60209776 (NMDC)
No. of reads for assembly	228553006
Completion (%)	98.13
Contamination (%)	0.168
G + C content (%)	45.54
N50 (bp)	88369
No. of contigs	60
Genome size (bp)	3947538
No. of CDSs	3467
No. of tRNA	37
No. of tmRNA	1
Encoded rRNA	Not detected

Full text

ANNOUNCEMENT

Chitin is one of the most abundant biopolymers in marine ecosystems (1). Chitin-degrading bacteria play a crucial role in marine carbon and nitrogen cycling by breaking down chitin into bioavailable oligosaccharides and monomers, contributing to deep-sea biogeochemical cycles (2). Here, we report the draft MAG of a novel Pseudoalteromonas species from deep-sea water encoding chitinase genes, suggesting its potential role in chitin degradation and nutrient cycling in deep-sea ecosystems.

Deep-sea water was collected in February 2024 at 5,500 m depth from the South Mid-Atlantic Ridge (SMAR, 13°28′ W, 27°10′ S) using a CTD Rosette Sampler aboard the research vessel Deep Sea No. 1. Twenty liters of seawater was concentrated to 10 mL using a Large Volume Concentration Kit (Cat. No. CC01116, InnovaPrep, USA). The concentrated sample was diluted to approximately 1 × 10⁷ cells/mL in 2216E medium using a cell counting chamber (Cat. No. 177–112C, Watson, Japan) and then encapsulated as single cells into 30-pL droplets using a custom-built microfluidic device following laboratory-established protocols (3). Droplets were pooled and incubated at 25°C for 7 days and then demulsified with perfluorooctanol to collect enriched microbial cells.

Genomic DNA was extracted from 3 mL of demulsified droplet solution using the Bacterial DNA Extraction Kit (Cat. No. DZ314-03, FINDROP, China) following the manufacturer’s protocol. Sequencing libraries were prepared using the ALFA-SEQ DNA Library Prep Kit (Cat. No. NDI001E, FINDROP, China), and paired-end 150 bp reads were generated on the Illumina NovaSeq X Plus platform, yielding 37.59 Gbp of raw metagenomic data. Sequencing quality was assessed using Fastp (v0.23.2, default parameters) (4), and clean reads were assembled using SPAdes (v3.15.5) with the “--meta” option (5). MAGs were recovered using MetaWRAP (v1.3.2, default parameters) (6), and CheckM (v1.1.2) (7) identified eight high-quality MAGs (completeness >90%, contamination <5%). Taxonomic classification was performed via GTDB-Tk (v2.4.0, r220, default parameters) (8), and protein-coding sequences were predicted by PROKKA (v1.14.6, default parameters) (9). Predicted proteins were annotated against the KEGG database using DIAMOND BLASTp (v2.1.8, coverage >80%, identity >80%, e-value <1e-5) (10). Average nucleotide identity (ANI) was calculated using fastANI (v1.34) (11).

A MAG, designated Pseudoalteromonas SMAR (GCA_048515945.1), was identified, exhibiting high genome novelty and encoding genes associated with chitin degradation. GTDB-Tk classified it as an uncharacterized species within the genus Pseudoalteromonas, and its genomic features are summarized in Table 1. ANI analysis confirmed its novelty, with the highest similarity (78.37%) to Pseudoalteromonas shioyasakiensis. A phylogenetic tree illustrating its relationship to closely related species is presented in Fig. 1.

Maximum likelihood phylogenetic tree showing the relationship between Pseudoalteromonas SMAR (GCA_048515945.1) and closely related Pseudoalteromonas genomes. The tree was constructed using FastTree (v2.1.11) with the GTR model and 1,000 bootstrap replicates, based on the alignment of 120 conserved bacterial marker genes via GTDB-Tk. Node sizes correspond to bootstrap support values, with larger nodes indicating >75% support. Pseudoalteromonas SMAR is highlighted in red.

Functional annotation of the Pseudoalteromonas SMAR suggests a putative role in chitin degradation. The genome encodes key enzymes, including chitinase (chiA) and N-acetylglucosaminidase (nagZ), which may facilitate the conversion of chitin into oligomers and subsequently into monomeric N-acetylglucosamine (GlcNAc) (2), a bioavailable source of carbon and nitrogen. A nearly complete chitin degradation pathway suggests potential involvement in organic matter remineralization within deep-sea environments.