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PLoS One
2022 Jan 01;178:e0271174. doi: 10.1371/journal.pone.0271174.
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Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.
Yamano R
,
Yu J
,
Jiang C
,
Harjuno Condro Haditomo A
,
Mino S
,
Sakai Y
,
Sawabe T
.
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A Gram-staining-negative, aerobic bacterium, designated strain PT3T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti KCTC 42154T and A. spongicola JCM 16668T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov. (type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.
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35947547
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Fig 1. A rooted ML tree based on 16S rRNA gene nucleotide sequences of strain PT3T and related type strains.Numbers shown on branches are bootstrap values (>50%) based on 1,000 replicated analysis from maximum-likelihood algorithm. Bar, 0.1 substitutions per nucleotide position. Sequences trimmed to 1,337 bp were compared (54–1,390 position in Al. ceti RA1T, KJ867528). Escherichia coli K-12 was used as an outgroup.
Fig 2. AAI matrix using Aliamphritea and related Oceanospirillaceae.Reference genomes were downloaded from NCBI database (S2 Table).
Fig 3. MLSA network.A list of strains and their assembly accession is provided in S2 Table.
Fig 4. Anvi’o representation of the pangenome of the Aliamphritea and Amphritea species.Layers represent each genome, and the bars represent the occurrence of gene clusters. The darker colored areas of the bars belong to one of the three bins: Core, Aliamphritea unique or Amphritea unique.
Fig 5. Syntenic dotplot comparison of Aliamphritea and Amphritea type strains.Dots closer to the diagonal line represents collinear arrangement between two homologous genes in two genomes. (A), (B) Intra-genus comparison of Aliamphritea species. (C), (D) Inter-genus comparison between Amphritea and Aliamphritea species. (E) Intra-genus comparison of Amphritea species.
Fig 6. Predicted fatty acid synthetic pathway in Amphritea and Aliamphritea species.Genes encoding each enzyme were present in all strains unless stated otherwise. *1: Only present in Al. hakodatensis, Al. ceti and Al. spongicola. *2: Only present in Al. ceti, A. atlantica, A. japonica, A. balenae and A. pacifica. ACP: acyl-carrier protein; AccABCD: acetyl-CoA carboxylase complex; FabD: malonyl-CoA: ACP transacylase; FabH/FabY: 3-ketoacyl-ACP synthase Ⅲ; FabB: 3-ketoacyl-ACP synthase Ⅰ; FabF: 3-ketoacyl-ACP synthase Ⅱ; FabG: 3-ketoacyl-ACP reductase; FabA: 3-hydroxyacyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase; enoyl-ACP reductase; FabZ: 3-hydroxyacyl-ACP dehydratase.
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