Mangrovibacterium diazotrophicum (DSM 27148, JCM 19152, KCTC 32129)

Name: Mangrovibacterium diazotrophicum (DSM 27148, JCM 19152, KCTC 32129)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24811

Type strain

Culture col. no. DSM 27148 JCM 19152 KCTC 32129 SCSIO N0430

NCBI tax ID(s) 1261403

Special Collections DSMZ JCM KCTC

History <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO N0430 <- X.-F. Huang and X.-P. Tian X.-P. Tian SCSIO N0430.

Links

Mangrovibacterium diazotrophicum DSM 27148 is a mesophilic prokaryote that was isolated from mangrove sediment.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401038

KCTC 32129,JCM 19152,DSM 27148

@ref 20215

Last LPSN update 2025-12-16 09:52:57

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Prolixibacteraceae

Genus Mangrovibacterium

Species Mangrovibacterium diazotrophicum

Full scientific name Mangrovibacterium diazotrophicum Huang et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21318	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21318	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		91.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	pentose phosphate pathway	100	11 of 11
66794	vitamin K metabolism	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	100	14 of 14
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	starch degradation	100	10 of 10
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	pyrimidine metabolism	91.11	41 of 45
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	histidine metabolism	86.21	25 of 29
66794	purine metabolism	86.17	81 of 94
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	vitamin B6 metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	propionate fermentation	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	metabolism of disaccharids	72.73	8 of 11
66794	degradation of hexoses	72.22	13 of 18
66794	lysine metabolism	71.43	30 of 42
66794	citric acid cycle	71.43	10 of 14
66794	coenzyme M biosynthesis	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	cysteine metabolism	55.56	10 of 18
66794	lipid metabolism	54.84	17 of 31
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	butanoate fermentation	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	cyclohexanol degradation	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ethanol fermentation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	oxidative phosphorylation	48.35	44 of 91
66794	polyamine pathway	47.83	11 of 23
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	carotenoid biosynthesis	40.91	9 of 22
66794	3-phenylpropionate degradation	40	6 of 15
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Sediment
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21318	mangrove sediment	Sanya city, Bailu Park (18° 15' 04.43'' N 109° 31' 07.62'' E)	China	CHN	Asia	18.2512	109.519 18.2512/109.519
67770	Mangrove sediment at Bailu Park	Sanya City, on the south coast of China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX983191 (>99% sequence identity) for Mangrovibacterium diazotrophicum subclade from Microbeatlas

Aquatic Samples	776
Soil Samples	293
Animal Samples	142
Plant Samples	46
Total Samples	1257

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21318	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM361053v1 assembly for Mangrovibacterium diazotrophicum DSM 27148	scaffold	GCA_003610535	1261403.3	2695420982	1261403	75.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21318	Mangrovibacterium diazotrophicum strain SCSIO N0430 16S ribosomal RNA gene, partial sequence	JX983191	1417		1261403

GC content

@ref	GC-content (mol%)	Method
21318	43.28	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mangrovibacterium diazotrophicum DSM 27148
NCBI: GCA_003610535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.60	no
125439	motility	BacteriaNetⓘ	yes	58.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	82.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mangrovibacterium diazotrophicum strain DSM 27148
PATRIC: 1261403.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	88.35	no
125438	anaerobic	anaerobicⓘ	no	79.10	no
125438	spore-forming	spore-formingⓘ	no	86.76	no
125438	aerobic	aerobicⓘ	no	54.15	no
125438	thermophilic	thermophileⓘ	no	94.63	no
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic insights into the mangrove-associated cultivable bacteria and their ecological function.	Huang X, Jiang P, Yang X, Dong J, Liang T, Ling J, Chen H.	iScience	10.1016/j.isci.2025.113523	2025
Metabolism	Nitroreductase Activites in Giardia lamblia: ORF 17150 Encodes a Quinone Reductase with Nitroreductase Activity.	Muller J, Heller M, Uldry AC, Braga S, Muller N.	Pathogens	10.3390/pathogens10020129	2021
Phylogeny	Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment.	Yu WX, Liang QY, Xuan XQ, Du ZJ, Mu DS, Mu DS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005855	2023
	Gaoshiqia hydrogeniformans sp. nov., a novel hydrogen-producing bacterium isolated from a deep diatomaceous shale formation.	Ueno A, Sato K, Tamamura S, Murakami T, Inomata H, Tamazawa S, Amano Y, Miyakawa K, Naganuma T, Igarashi T.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006802	2025
Phylogeny	Mangrovibacterium marinum sp. nov., isolated from a coastal sediment.	Wu WJ, Zhou YX, Liu Y, Chen GJ, Du ZJ.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0452-0	2015
Phylogeny	Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment.	Sun C, Zeng X, Lai Q, Wang Z, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004305	2020
Phylogeny	Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov.	Huang XF, Liu YJ, Dong JD, Qu LY, Zhang YY, Wang FZ, Tian XP, Zhang S	Int J Syst Evol Microbiol	10.1099/ijs.0.052779-0	2013

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#21318	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27148
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Mangrovibacterium diazotrophicum (DSM 27148, JCM 19152, KCTC 32129)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003610535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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