Pseudothioclava nitratireducens (MCCC 1A06955, LMG 29616, DL5-4)

Name: Pseudothioclava nitratireducens (MCCC 1A06955, LMG 29616, DL5-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140990

Type strain

Strain Designation DL5-4

Culture col. no. MCCC 1A06955 LMG 29616 DL5-4

NCBI tax ID(s) 1928646

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Pseudothioclava nitratireducens DL5-4 is a facultative aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from surface seawater of Dalian Bay, PR China.

Gram-negative rod-shaped colony-forming facultative aerobe 16S sequence

Name and taxonomic classification

SI-ID 267239

LMG 29616

@ref 20215

Last LPSN update 2025-12-16 10:03:44

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Pseudothioclava

Species Pseudothioclava nitratireducens

Full scientific name Pseudothioclava nitratireducens (Liu et al. 2017) Huang et al. 2024

Synonyms (1)

Defluviimonas nitratireducens

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43877	negative	0.9-1.3 µm	0.7-0.8 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43877	0.5-1.0 mm	brown	circular	3 days	Marine agar 2216

Culture and growth conditions

Culture medium

@ref	Name	Growth
43877	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43877	positive	growth	8-40
43877	positive	optimum	28-30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43877	positive	optimum	7
43877	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

43877

Oxygen tolerancefacultative aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43877	NaCl	positive	growth	0-7 %(w/v)
43877	NaCl	positive	optimum	1-3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43877	64552 ChEBI	2-hydroxybutyrate	+	carbon source
43877	30916 ChEBI	2-oxoglutarate	+	carbon source
43877	30089 ChEBI	acetate	+	carbon source
43877	17128 ChEBI	adipate	-	carbon source
43877	17925 ChEBI	alpha-D-glucose	+	carbon source
43877	27613 ChEBI	amygdalin	-	builds acid from
43877	22599 ChEBI	arabinose	-	builds acid from
43877	8295 ChEBI	beta-hydroxybutyrate	+	carbon source
43877	17057 ChEBI	cellobiose	+	builds acid from
43877	17057 ChEBI	cellobiose	+	carbon source
43877	16947 ChEBI	citrate	+	carbon source
43877	18333 ChEBI	D-arabitol	+	builds acid from
43877	18333 ChEBI	D-arabitol	+	carbon source
43877	15824 ChEBI	D-fructose	+	builds acid from
43877	15824 ChEBI	D-fructose	+	carbon source
43877	28847 ChEBI	D-fucose	+	builds acid from
43877	17634 ChEBI	D-glucose	+	builds acid from
43877	17634 ChEBI	D-glucose	+	carbon source
43877	17634 ChEBI	D-glucose	+/-	fermentation
43877	16899 ChEBI	D-mannitol	+	builds acid from
43877	16899 ChEBI	D-mannitol	+	carbon source
43877	16899 ChEBI	D-mannitol	+/-	builds acid from
43877	16024 ChEBI	D-mannose	-	carbon source
43877	27605 ChEBI	D-psicose	+	carbon source
43877	17924 ChEBI	D-sorbitol	+	builds acid from
43877	17924 ChEBI	D-sorbitol	+	carbon source
43877	27689 ChEBI	decanoate	-	carbon source
43877		esculin ferric citrate	+	hydrolysis
43877	495056 ChEBI	gamma-cyclodextrin	+	carbon source
43877	5291 ChEBI	gelatin	-	hydrolysis
43877	17234 ChEBI	glucose	-	builds acid from
43877	17754 ChEBI	glycerol	+	carbon source
43877	28087 ChEBI	glycogen	+	carbon source
43877		L-alanine 4-nitroanilide	+	carbon source
43877	30849 ChEBI	L-arabinose	-	carbon source
43877	17203 ChEBI	L-proline	+	carbon source
43877	24996 ChEBI	lactate	+	carbon source
43877	17716 ChEBI	lactose	+	carbon source
43877	25115 ChEBI	malate	+	builds acid from
43877	25115 ChEBI	malate	+	carbon source
43877	17306 ChEBI	maltose	+	builds acid from
43877	17306 ChEBI	maltose	+	carbon source
43877		maltose hydrate	+	builds acid from
43877	29864 ChEBI	mannitol	-	builds acid from
43877	28053 ChEBI	melibiose	-	builds acid from
43877	51850 ChEBI	methyl pyruvate	+	carbon source
43877	75146 ChEBI	monomethyl succinate	+	carbon source
43877	17268 ChEBI	myo-inositol	-	builds acid from
43877	17268 ChEBI	myo-inositol	+	carbon source
43877	506227 ChEBI	N-acetylglucosamine	-	carbon source
43877	506227 ChEBI	N-acetylglucosamine	+	carbon source
43877	17632 ChEBI	nitrate	+	reduction
43877	18401 ChEBI	phenylacetate	-	carbon source
43877	32032 ChEBI	potassium gluconate	-	carbon source
43877	17272 ChEBI	propionate	+	carbon source
43877	26490 ChEBI	quinate	+	carbon source
43877	26546 ChEBI	rhamnose	-	builds acid from
43877	17814 ChEBI	salicin	+/-	builds acid from
43877	53258 ChEBI	sodium citrate	+	builds acid from
43877	53258 ChEBI	sodium citrate	+	carbon source
43877	30911 ChEBI	sorbitol	-	builds acid from
43877	28017 ChEBI	starch	+	builds acid from
43877	143136 ChEBI	succinamate	+	carbon source
43877	30031 ChEBI	succinate	+	carbon source
43877	17992 ChEBI	sucrose	-	builds acid from
43877	17992 ChEBI	sucrose	+	builds acid from
43877	17992 ChEBI	sucrose	+	carbon source
43877	27082 ChEBI	trehalose	+	builds acid from
43877	27082 ChEBI	trehalose	+	carbon source
43877	32528 ChEBI	turanose	+	builds acid from
43877	32528 ChEBI	turanose	+	carbon source
43877	53426 ChEBI	tween 80	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43877	28971	ampicillin	10 µg (disc)
43877	3393	carbenicillin	100 µg (disc)
43877	474053	cefazolin	30 µg (disc)
43877	29007	ceftriaxone	30 µg (disc)
43877	3534	cephalexin	30 µg (disc)
43877	3547	cephradine	30 µg (disc)
43877	100241	ciprofloxacin	5 µg (disc)
43877	3745	clindamycin		2 µg (disc)
43877	3770	co-trimoxazole		25 µg (disc)
43877	48923	erythromycin		15 µg (disc)
43877	5195	furazolidone	15 µg (disc)
43877	17833	gentamicin	10 µg (disc)
43877	6104	kanamycin	30 µg (disc)
43877	100246	norfloxacin		10 µg (disc)
43877	7731	ofloxacin	5 µg (disc)
43877	7809	oxacillin	1 µg (disc)
43877	18208	penicillin g	10 µg (disc)
43877	8232	piperacillin	100 µg (disc)
43877	8309	polymyxin b	30 Unit (disc)
43877	28077	rifampicin	5 µg (disc)
43877	17076	streptomycin		10 µg (disc)
43877	27902	tetracycline	30 µg (disc)
43877	28001	vancomycin		30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite
43877	15688 ChEBI	acetoin
43877	16136 ChEBI	hydrogen sulfide
43877	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43877	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
43877	6-phospho-beta-galactosidase	-	3.2.1.85
43877	acid phosphatase	+	3.1.3.2
43877	alkaline phosphatase	+	3.1.3.1
43877	alpha-chymotrypsin	-	3.4.21.1
43877	alpha-fucosidase	-	3.2.1.51
43877	alpha-galactosidase	-	3.2.1.22
43877	alpha-glucosidase	-	3.2.1.20
43877	alpha-mannosidase	-	3.2.1.24
43877	arginine dihydrolase	-	3.5.3.6
43877	beta-galactosidase	-	3.2.1.23
43877	beta-glucosidase	-	3.2.1.21
43877	beta-glucuronidase	-	3.2.1.31
43877	catalase	+	1.11.1.6
43877	cystine arylamidase	+	3.4.11.3
43877	cytochrome oxidase	+	1.9.3.1
43877	esterase (C 4)	+
43877	esterase Lipase (C 8)	+
43877	gelatinase	-
43877	leucine arylamidase	+	3.4.11.1
43877	lipase	+
43877	lysine decarboxylase	-	4.1.1.18
43877	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43877	naphthol-AS-BI-phosphohydrolase	+/-
43877	ornithine decarboxylase	-	4.1.1.17
43877	trypsin	-	3.4.21.4
43877	tryptophan deaminase	-	4.1.99.1
43877	urease	-	3.5.1.5
43877	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43877

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	90.3
C18:0	3.4
C16:1ω7c / C16:1ω6c	2.2
C16:0	1.5
unknown 18.846 / C19:1ω6c	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43877	surface seawater of Dalian Bay, PR China	Dalian Bay	China	CHN	Asia	38.9667	124.767 38.9667/124.767

Taxonmaps

69479

Global distribution of 16S sequence KF146513 (>99% sequence identity) for Defluviimonas nitratireducens subclade from Microbeatlas

Aquatic Samples	105
Soil Samples	9
Animal Samples	11
Plant Samples	2
Total Samples	127

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43877	Thioclava pacifica strain DL5-4 16S ribosomal RNA gene, partial sequence	KF146513
124043	Defluviimonas nitratireducens strain DL5-4 16S ribosomal RNA gene, partial sequence.	KY081665	1433		1928646

GC content

@ref	GC-content (mol%)	Method
43877	63.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006452	2024
Phylogeny	Defluviimonas nitratireducens sp. nov., isolated from surface seawater.	Liu Y, Lai Q, Wang W, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002015	2017

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 )
#43877	Yang Liu, Qiliang Lai, Wanpeng Wang, Zongze Shao: Defluviimonas nitratireducens sp. nov., isolated from surface seawater. IJSEM 67: 2752 - 2757 2017 ( DOI 10.1099/ijsem.0.002015 , PubMed 28809144 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Pseudothioclava nitratireducens (MCCC 1A06955, LMG 29616, DL5-4)

Name and taxonomic classification