Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation
2.2. Morphological, Physiological, and Biochemical Studies
2.3. 16S rRNA Gene Analysis
2.4. Chemotaxonomy
2.5. Whole-Genome Analysis
2.6. Secondary Metabolite Production and Antimicrobial Activity
2.7. Chromatogram and Mass Analysis for Extraction of WHA3T
3. Result and Discussion
3.1. Morphological, Physiological, and Biochemical Results
3.2. 16S rRNA Gene Analysis
3.3. Chemotaxonomic Characterization
3.4. Genomic Characteristics and Phylogenomic Analysis
3.5. Chromatogram and Mass Analysis for Extraction of WHA3T
4. Conclusions
Description of Pacificimonas pallium sp. nov.
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Culture Media | Pacificimonas pallium WHA3T | Pacificimonas flava DSM 107612T | Pacificimonas aurantium DSM 107782T |
---|---|---|---|
MB 514f | RAL2003 Pastel orange | RAL1037 Sun yellow | RAL1032 Broom yellow |
CSY-3 | RAL2008 Bright red orange | RAL1002 Sand yellow | RAL1002 Sand yellow |
1.5 LBM | RAL2003 Pastel orange | RAL1033 Dahlia yellow | RAL1037 Sun yellow |
YED | RAL2000 Yellow orange | RAL1002 Sand yellow | RAL1005 Honey yellow |
TSA | NG | RAL2000 Yellow orange | NG |
SSM + T | NG | RAL1011 Brown beige | NG |
SSM-T | NG | RAL1002 Sand yellow | NG |
YTSS | RAL1017 Saffron yellow | RAL1003 Signal yellow | RAL1003 Signal yellow |
ASG + Cycloheximide | NG | NG | RAL1015 Light ivory |
YEA | NG | RAL1023 Traffic yellow | NG |
Enzyme | Observation | Enzyme | Observation |
---|---|---|---|
Phosphatase alkaline | ++ | Naphtol-AS-BI-phosphohydrolase | (+) |
Esterase (C4) | + | α-galactosidase | - |
Esterase lipase (C8) | + | β-galactosidase | - |
Lipase (C14) | (+) | β-glucurunidase | - |
Leucin arylamidase | ++ | α-glucosidase | - |
Valine arylamidase | (+) | β-glucosidase | - |
Cystine arylamidase | (+) | N-acetyl-beta- glucosaminidase | - |
Trypsin | + | α-mannosidase | - |
Chymotrypsin | ++ | α-fucosidase | - |
Phosphatase acid | (+) |
Characteristics | 1 | 2 | 3 |
---|---|---|---|
Color of colony | orange | orange | orange |
Temperature range for growth (°C) | 15–40 | 20–30 * | 10–40 † |
pH spectrum for growth | 5–11 | 5–12 * | 5–10 † |
NaCl optimum for growth (%) | 2.5–5 | 0.5–7 * | 0.5–4 † |
Trypsin | + | + | (+) |
α-Chymotrypsin | ++ | (+) | - |
Acid phosphatase | (+) | ++ | (+) |
Naphthol-AS-BI-phosphohydrolase | (+) | + | (+) |
N-acetyl-β-glucosaminidase | - | (+) | (+) |
gelatine (hydrolysis) | - | + | + |
Oxidation of (Biolog GN2) | |||
Acetic acid | + | + * | - † |
Methyl pyruvate | - | + * | - † |
D-galactose | - | ND * | + † |
D-raffinose | - | - * | + † |
D-trehalose | - | - * | + † |
D-Turanose | - | - * | + † |
α -keto glutaric acid | - | - * | + † |
L-alanine | + | - * | + † |
L-glutamic acid | - | - * | + † |
L-aspartic acid | - | - * | + † |
γ-amino butyric acid | - | ND * | + † |
Dextrin | - | + * | + † |
D-fructose | - | + * | + † |
α-D-glucose | (+) | + * | + † |
Tween 40 | - | + * | + † |
Susceptibility to | |||
Ampicillin | - | - * | + † |
Gentamycin | + | - * | + † |
Kanamycin | + | - * | + † |
Polar lipids | DPG-PE-PG-SGL-PL-GL-L | DPG-PE-PG-SGL-L | DPG-PE-PG-SGL † |
Major fatty acid | C18:1ω7c C16:1ω7c | C18:1ω7c C14:02-OH | C18:1ω7c C14:02-OH Unknown fatty acid |
Contigs | 11 | 32 | 12 |
No. of proteins | 2794 | 2908 | 3104 |
rRNA | 3 | 4 | 3 |
tRNA | 44 | 45 | 45 |
No. of Genes | 2859 | 3038 | 3185 |
Other RNA | 3 | 4 | 4 |
Pseudogenes | 15 | 77 | 29 |
G + C content (%) | 61.69 | 64.2 * | 65.5 † |
Total sequence length (Mbp) | 3.01 | 3.25 | 3.34 |
Pacificimonas pallium WHA3T | Pacificimonas flava DSM 107612T | Pacificimonas aurantium DSM 107782T | |
---|---|---|---|
Fatty acid | |||
C14:0 | -- | 5.0 | -- |
C15:0 | -- | 2.2 | -- |
C16:0 | 4.2 | 9.1 | 9.8 |
C17:0 | -- | -- | 5.2 |
C19:0 | -- | 2.4 | 8.3 |
anteiso-C15:0 | -- | 5.7 | -- |
anteiso-C17:0 | -- | 1.9 | -- |
iso-C16:0 | -- | 4.1 | -- |
C16:1ω7c | 20.5 | 5.8 | -- |
C17:1ω6c | 5.1 | 4.0 | 5.3 |
C18:1ω7c | 50.6 | 26.9 | 22.0 |
C14:02-OH | 8.4 | 22.8 | 27.6 |
C16:02-OH | 3.6 | -- | -- |
cyclo-C19:0d8,9 | 1.3 | 5.7 | 4.0 |
Unknown fatty acid | 6.3 | 4.4 | 17.8 |
Strain | 1 | 2 | 3 | 4 | ||||
---|---|---|---|---|---|---|---|---|
POCP (%) | AAI (%) | POCP (%) | AAI (%) | POCP (%) | AAI (%) | POCP (%) | AAI (%) | |
Pacificimonas pallium WHA3T (JAGSPA000000000) | 60.36 | 66.00 | 60.55 | 64.48 | 49.96 | 54.47 | 33.01 | 46.38 |
Pacificimonas flava DSM 107612T (JACHGC010000001) | 100 | 100 | 63.39 | 69.22 | 46.92 | 55.02 | 32.12 | 46.42 |
Pacificimonas aurantium DSM 107782T (JAGSGB000000000) | 63.39 | 69.22 | 100 | 100 | 47.20 | 54.58 | 33.63 | 46.85 |
Strain | 1 | 2 | 3 | 4 | ||||
---|---|---|---|---|---|---|---|---|
Ortho ANIu (%) | dDDH (%) | Ortho ANIu (%) | dDDH (%) | Ortho ANIu (%) | dDDH (%) | Ortho ANIu (%) | dDDH (%) | |
Pacificimonas pallium WHA3T (JAGSPA000000000) | 71.95 | 19.20 | 72.25 | 18.40 | 68.84 | 19.00 | 66.73 | 17.90 |
Pacificimonas flava DSM 107612T (JACHGC010000001) | 74.36 | 20.30 | 100 | 100 | 69.17 | 19.20 | 67.15 | 16.30 |
Pacificimonas aurantium DSM 107782T (JAGSGB000000000) | 100 | 100 | 74.36 | 20.30 | 69.13 | 18.90 | 67.05 | 18.30 |
Genes for C1 Oxidation and Methylotrophy | 1 | 2 | 3 | |
---|---|---|---|---|
THF-linked oxidation | ||||
Methylene -THF methylenetetrahydrofolate reductase metF | + | - | - | |
Bifunctional methylene-THF dehydrogenase-methenyl-THF cyclohydrolase folD | + | - | - | |
AMTs | ||||
Glycine system cleavage T-protein gcvT | + | - | - | |
Glycine cleavage system H protein gcvH | + | - | - | |
GSH-dependent pathway | ||||
S-formyl-glutathione hydrolase (FGH) fghA | + | - | - | |
methylamine oxidation | ||||
Sarcosine oxidase subunit beta soxB | + | - | - |
Genes TonB-Dependent Transporters (TBDTs) | 1 | 2 | 3 |
---|---|---|---|
btuB_1 btuB_3 btuB_4 btuB_6 btuB_8 btuB_9 btuB_10 btuB_12 btuB_13 btuB_14 btuB_15 btuB_17 btuB_19 btuB_20 btuB_21 btuB_23 | btuB | btuB | |
fyuA_1 fyuA_2 | TonB | TonB | |
putative TonB-dependent receptor BfrD | + | - | - |
TonB-dependent hemin and ferrichrome receptor hemR | + | - | - |
TonB-dependent receptor and iron siderophore receptor protein btuB_7 | + | - | - |
1 | 2 | 3 | |
Vitamin B12 transporter btuB | + | - | - |
Outer membrane vitamin B12 receptor btuB | + | + | + |
Biopolymer transport protein | exbD_1 exbD_2 exbD_3 | exbD | exbD |
Fe(3+) ions import ATP-binding protein FbpC | + | - | - |
Ferric uptake regulation protein fur | + | + | + |
Fe(2+) transporter FeoB | + | + | + |
Superoxide dismutase [Fe] sodB | + | - | - |
Lipopolysaccharide ABC transporter, ATP-binding protein lptB | + | + | + |
Capsular polysaccharide ABC transporter, ATP-binding protein kpsT | + | + | - |
Lipopolysaccharide export system protein lptA | + | - | + |
Lipopolysaccharide export system permease protein lptF-lptG | + | + | + |
Capsular polysaccharide export system protein kpsS | + | + | - |
Capsular polysaccharide ABC transporter, permease protein kpsM | + | + | - |
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Pira, H.; Risdian, C.; Müsken, M.; Schupp, P.J.; Wink, J. Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism. Diversity 2022, 14, 181. https://doi.org/10.3390/d14030181
Pira H, Risdian C, Müsken M, Schupp PJ, Wink J. Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism. Diversity. 2022; 14(3):181. https://doi.org/10.3390/d14030181
Chicago/Turabian StylePira, Hani, Chandra Risdian, Mathias Müsken, Peter J. Schupp, and Joachim Wink. 2022. "Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism" Diversity 14, no. 3: 181. https://doi.org/10.3390/d14030181
APA StylePira, H., Risdian, C., Müsken, M., Schupp, P. J., & Wink, J. (2022). Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism. Diversity, 14(3), 181. https://doi.org/10.3390/d14030181