Abstract
A Gram-stain-negative and short rod-shaped bacterial strain designated GM2-3-6-6T was obtained from a mangrove sediment. Cells were light yellow-pigmented, catalase-positive and oxidase-positive. Carotenoid pigment was produced. Phylogeny of the 16S rRNA gene showed that strain GM2-3-6-6T was affiliated to the family Crocinitomicaceae, sharing maximum sequence similarities with Crocinitomix algicola 0182T, C. catalasitica IFO 15977T, and Putridiphycobacter roseus SM1701T of 93.8%, 93.6%, and 92.5%, respectively. The average nucleotide identity values, digital DNA-DNA hybridization estimates and average amino acid identity values between strain GM2-3-6-6T and the three close relatives were 68.6–68.8%, 18.5–19.2%, and 59.0–62.3%, respectively. The complete circular genome of strain GM2-3-6-6T was 4,365,762 bp in length with a DNA G + C content of 35.0%. The respiratory quinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, two unidentified phospholipids, one unidentified aminoglycolipid, one unidentified aminolipid and four other unidentified lipids. The major fatty acids were iso-C15:0, iso-C15:1 G, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and iso-C17:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain GM2-3-6-6T represents a novel species of a novel genus, for which the name Paracrocinitomix mangrovi gen. nov., sp. nov. is proposed. The type strain is GM2-3-6-6T (= MCCC 1K04831T = KCTC 82931T). Additionally, phylogenomic analysis of the type strains of the family Schleiferiaceae and family Cryomorphaceae related members including uncultivated bacteria, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk). Based on 16S rRNA gene phylogeny and genomic features, two novel families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov. are proposed. An emended description of the family Schleiferiaceae is also proposed.
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Data availability
The GenBank/EMBL/DDBJ accession numbers of the 16S rRNA gene sequence and genome sequences of strain GM2-3-6-6T are MT829391, and JAHXZQ000000000 (draft genome) and CP091819 (complete genome), respectively.
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Funding
This work was supported by the projects of the National Key Research and Development Program of China (No. 2018YFC0310705), National Science Foundation of Fujian Province (No. 2020J01789) and National Science and Technology Fundamental Resources Investigation Program of China (No. 2021FY100900).
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ZH conceived the study and wrote the manuscript. YH, QL and WW conducted the experiments. AO proposed names, wrote, and checked etymologies, and edited and corrected the manuscript. All authors reviewed the manuscript.
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10482_2022_1790_MOESM1_ESM.eps
Figure S1. Maximum-likelihood phylogenetic tree showing the relationship of strain GM2-3-6-6T and closely related species. Chitinophaga pinensis DSM 2588T was used as the outgroup. Bootstrap values are calculated using 1,000 replicates, and bootstrap values greater than 70 are shown. Paracrocinitomix mangrovi GM2-3-6-6T and the families Owenweeksiaceae and Phaeocystidibacteraceae were marked bold. Bar, 0.05, nucleotide substitution. (EPS 231 kb)
10482_2022_1790_MOESM4_ESM.docx
Figure S3. Polar lipid profile of GM2-3-6-6T. The plate was stained with ethanolic molybdophosphoric acid (a), ninhydrin (b), molybdenum blue (c), and α-naphthol-sulfuric acid (d). PE, phosphatidylethanolamine; PL, unidentified phospholipid; AGL, unidentified aminoglycolipid; AL, unidentified aminolipid; L, unidentified lipids. (DOCX 18 kb)
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Huang, Z., Huang, Y., Lai, Q. et al. Paracrocinitomix mangrovi gen. nov., sp. nov., isolated from a mangrove sediment: proposal of two new families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov., and emended description of the family Schleiferiaceae. Antonie van Leeuwenhoek 116, 171–184 (2023). https://doi.org/10.1007/s10482-022-01790-0
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DOI: https://doi.org/10.1007/s10482-022-01790-0