Complete genome sequence of Pseudomonas sp. gA1, a metabolically specialized deep-sea bacterium from abyssal sediment of the Western Pacific Ocean
Year: 2026
Type: article
Abstract: ABSTRACT The abyssal seafloor, exposed to extreme pressure, near-freezing temperatures, and severe carbon limitation, remains one of the least understood microbial habitats on Earth. Branched-chain amino acids (BCAAs) are an abundant but underexplored carbon source in abyssal sediments, yet the genomic basis for their use by deep-sea heterotrophs remains uncharacterized. Here, we report the complete genome of Pseudomonas sp. gA1, isolated from 6,000 m sediment in the Western Pacific Ocean by anaerobic enrichment with amino acids under 40 MPa. The 7.27 Mb circular chromosome encodes 6,827 protein-coding genes. Polyphasic taxonomy—including average nucleotide identity of 94.15% to P. yamanorum and digital DNA-DNA hybridization of 55.5%—confirmed strain gA1 as a novel species within the P. fluorescens group. We compared gA1 against 16 reference genomes from the P. fluorescens group and the marine Halopseudomonas and Stutzerimonas lineages. Under elevated hydrostatic pressure at 10 °C, which approximates selected aspects of the abyssal environment rather than the in situ pressure and temperature of the 6,000-m collection site, BCAAs accounted for 49% of total amino acid consumed, and growth increased by 50% at 40 MPa. Genome analysis revealed a largely represented BCAA degradation pathway (11 of 14 KEGG Orthology identifiers) conserved across the P. fluorescens group and a complete arginine deiminase (arcABC) pathway supporting anaerobic ATP generation by substrate-level phosphorylation. Denitrification and anaerobic respiratory genes were not detected, a trait shared with the marine Halopseudomonas lineage. Its most distinctive feature is expanded amino acid and peptide acquisition: 44 expanded orthogroups, including families involved in dipeptide, oligopeptide and amino acid acquisition, alongside a chaperone network and 17 biosynthetic gene clusters, including one similar to those associated with viscosinamide A/pseudodesmin A biosynthesis. These findings establish gA1 as a metabolically specialized deep-sea bacterium whose genomic architecture couples amino acid acquisition to piezotolerance. IMPORTANCE The abyssal seafloor is the largest and most energy-limited habitat on Earth, yet how its resident bacteria sustain growth where several canonical respiratory chains are not detected remains poorly understood. This study shows that a cultured abyssal isolate grows under elevated hydrostatic pressure on amino acids, and that its genome encodes a complete arginine deiminase pathway as a potential route to substrate-level phosphorylation, the contribution of which to energy metabolism remains to be measured. Through direct comparison with 16 related genomes, the same genomic configuration is shared across the sampled Halopseudomonas genomes rather than being confined to this isolate. The work carries a broader methodological message for deep-sea genomics: pathway-completeness scores and the presence or absence of individual genes are weak proxies for physiological capacity, and adaptation in these organisms appears to proceed through expansion of existing uptake systems rather than acquisition of novel functions. Because strain gA1 is both cultured and experimentally tractable under high pressure, it offers a testable model for linking genome content to function in the deep biosphere, and it identifies amino acid and peptide acquisition, rather than catabolism, as a point at which lineages adapted to cold, organic-poor sediments diverge.
Source: Microbiology Spectrum
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,500
OpenAlex ID: W7225632167