Abstract
An aerobic, yellow-pigmented and Gram-stain-negative strain, designated as O-35 T, was isolated from a tidal flat sediment collected in Dangjiang Town, the southern China. Colonies of strain O-35 T were circular with 0.5–1.0 mm in diameter, convex and smooth. Cells of strain O-35 T were coccoid-shaped, non-spore forming, non-motile and the strain could reduce nitrate. Growth of strain O-35 T was observed at 15–40 °C (optimum 30 °C), at pH 6.0–9.5 (optimum 7.5–8.0) and in 0.5–5.0% NaCl (optimum 2%, w/v). Strain O-35 T showed 16S rRNA gene sequence identities of 97.3–97.5% with Sphingomicrobium lutaoense CC-TBT-3 T and Sphingomicrobium aestuariivivum AH-M8T, higher than the rest of Sphingomicrobium type strains. Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences demonstrated that strain O-35 T was affiliated within the genus Sphingomicrobium. Overall genome relatedness index calculations revealed that strain O-35 T had < 75.8% of average nucleotide identity and < 19.2% of digital DNA–DNA hybridization values with Sphingomicrobium type strains. The sole isoprenoid quinone was ubiquinone-10. The major fatty acids (> 10%) were summed feature 8, summed feature 3, C16:0 and C18:1 2-OH. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingoglycolipid, two unidentified glycolipids, one unidentified lipid and one unidentified phospholipid. On the basis of the phenotypic, chemotaxonomic and genomic properties, strain O-35 T represents a novel species in the genus Sphingomicrobium, for which the name Sphingomicrobium nitratireducens sp. nov. is proposed. The type strain is O-35 T (= KCTC 92308 T = MCCC 1K07589T).
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Abbreviations
- AL:
-
Aminolipid
- ANI:
-
Average nucleotide identity
- AAI:
-
Average amino acid identity
- COG:
-
Clusters of orthologous groups of proteins
- dDDH:
-
Digital DNA–DNA hybridization
- DPG:
-
Diphosphatidylglycerol
- DSM:
-
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
- GL:
-
Glycolipid
- JCM:
-
Japan collection of microorganisms
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- MA:
-
Marine 2216 agar
- MB:
-
Marine 2216 broth
- MCCC:
-
Marine culture collection of China
- NBRC:
-
Biological resource center, National Institute of Technology and evaluation
- OC:
-
Orthologous clusters
- PC:
-
Phosphatidylcholine
- PE:
-
Phosphatidylethanolamine
- PG:
-
Phosphatidylglycerol
- PL:
-
Phospholipid
- Q-10:
-
Ubiquinone-10
- RAST:
-
Rapid annotation using subsystem technology
- SGL:
-
Sphingoglycolipid
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Acknowledgements
We thank Zhi-Cheng Wu (Zhejiang University) for his help in collecting samples.
Funding
This study was funded by the National Science and Technology Fundamental Resources Investigation Program of China (2019FY100700, 2021FY100900) and the National Natural Science Foundation of China (32170005, 32000001).
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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by HY, Y-HK, CS and PZ. The first draft of the manuscript was written by HY, LX and X-WX and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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You, H., Xu, L., Kong, YH. et al. Sphingomicrobium nitratireducens sp. nov., isolated from a tidal flat in Guangxi. Arch Microbiol 204, 671 (2022). https://doi.org/10.1007/s00203-022-03273-2
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DOI: https://doi.org/10.1007/s00203-022-03273-2