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Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China

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Abstract

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4–63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

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Data availability

The 16S rRNA gene sequence of strain CJK-A8-3T has been deposited in GenBank under the accession number MZ520614. Whole Genome Shotgun project of strain CJK-A8-3T has been deposited at GenBank under accession number JAIEZN000000000.

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Acknowledgements

We thank Dr. Huirong Li from Polar Research Institute of China for providing Devosia strain D. beringensis S02T. We also appreciated Dr. Aharon Oren for the help with the consultation of species name. Samples were collected onboard of R/V Zheyuke II implementing the open research cruise NORC2019-03-03 supported by NSFC Shiptime Sharing Project. The work was supported by the National Natural Science Foundation of China (grants No. 42176038), Science Foundation of Donghai Laboratory (No. DH-2022KF0211), Scientific Research Fund of the Second Institute of Oceanography, MNR (No. JG1521) and the Project of State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography (No. SOEDZZ2204).

Funding

The funding was provided by National Natural Science Foundation of China (Grant No 42176038), Science Foundation of Donghai Laboratory (Grant No DH-2022KF0211), the Scientific Research Fund of the Second Institute of Oceanography, MNR (Grant No. JG1521), Project of State Key Laboratory of Satellite Ocean Environment Dynamics,Second Institute of Oceanography (Grant No SOEDZZ2204).

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  1. Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People’s Republic of China

    Mingyan Lai, Yurong Qian, Yue-Hong Wu & Qian Liu

  2. Ocean College, Zhejiang University, Hangzhou, 310012, Zhejiang, People’s Republic of China

    Yue-Hong Wu & Qian Liu

  3. Institute of Polar and Ocean Technology, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People’s Republic of China

    Chenhua Han

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Contributions

QL designed research. YRQ, MYL, YHW and CHH performed isolation, deposition and polyphasic taxonomy. YRQ and QL conducted the growth experiment on nitrogen substrates. MYL, YRQ and QL performed the genome analysis. MYL, YRQ and QL drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Qian Liu.

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Supplementary file1 (DOCX 34 KB)

10482_2023_1924_MOESM2_ESM.tif

Supplemental Fig. 1 Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship of strain CJK-A8-3Tand other isolated Devosia strains. Caulobacter vibrioides CB51T was used as an outgroup. Bootstrap values (>50.0%) based on 1000 replications were shown at branch nodes. Bar, 0.01 substitutions per nucleotide position (TIF 11381 KB)

10482_2023_1924_MOESM3_ESM.tif

Supplemental Fig. 2 Polar lipid diagram of strain CJK-A8-3T, a, total lipid; b, amino lipid; c, glycolipid; d, phospholipid. These abbreviations indicate phosphatidic acid (PA), phosphatidylglycerol (PG), a combination of phospholipids and glycolipids (PGL) and two unidentified glycolipids (GL1, GL2) (TIF 1061 KB)

10482_2023_1924_MOESM4_ESM.tif

Supplemental Fig. 3 Growth curves of strain CJK-A8-3T in modified marine agar 2216 (MA) media individually added with different concentrations (50, 200, 500 and 1000 nM) of six nitrogen substrates: (a) putrescine, (b) spermidine, (c) spermine, (d) glutamic acids, (e) urea and (f) ammonium chloride. Error bars represent the standard errors of three replicates of each treatment. Asterisks indicate the significant differences (One-Way ANOVA; p<0.05) between cell densities at the stationary phase cultured in modified MA with nitrogen compounds and those in modified MA without extra substrate addition (control) (TIF 939 KB)

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Lai, M., Qian, Y., Wu, YH. et al. Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China. Antonie van Leeuwenhoek 117, 29 (2024). https://doi.org/10.1007/s10482-023-01924-y

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