Name: Lysobacter aestuarii S2-C
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140892

Type strain:

Species: Lysobacter aestuarii

Strain Designation: S2-C

Culture col. no.: KACC 18502, JCM 31130

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; S2-C.

NCBI tax ID(s): 1706195 (species)

Section

Lysobacter aestuarii S2-C is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from An estuary sediment sample.

colony-forming
Gram-negative
rod-shaped
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter aestuarii**
	Full Scientific Name (LPSN)	Lysobacter aestuarii Jeong et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43724]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #43724]	Cell length	1-1 µm

[Ref.: #43724]	Cell width	0.4-0.6 µm

[Ref.: #43724]	Cell shape	rod-shaped

[Ref.: #43724]	Motility	no

[Ref.: #43724]	Colony color	Deep yellow cream
[Ref.: #43724]	Colony shape	circular
[Ref.: #43724]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43724]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #43724]

Culture medium growth

[Ref.: #43724]

Culture medium

Marine agar (MA)

[Ref.: #43724]

Culture medium growth

[Ref.: #43724]

Culture medium

Nutrient agar (NA)

[Ref.: #43724]

Culture medium growth

[Ref.: #43724]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43724]

Culture medium growth

[Ref.: #43724]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #43724]

Culture medium growth

		Temperature
[Ref.: #43724]	growth	15-40 °C
[Ref.: #43724]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43724]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43724]			optimum	6.5-7.5
[Ref.: #43724]			growth	5.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43724]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43724]		NaCl		growth	0-7	%(w/v)
[Ref.: #43724]		NaCl		optimum	0-2	%(w/v)

[Ref.: #43724]

Observation

Produces extracellular polysaccharides

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43724]	adipate ChEBI	-	assimilation
[Ref.: #43724]	casein	+	hydrolysis
[Ref.: #43724]	D-glucose ChEBI	+/-	assimilation
[Ref.: #43724]	D-mannitol ChEBI	-	assimilation
[Ref.: #43724]	D-mannose ChEBI	-	assimilation
[Ref.: #43724]	decanoate ChEBI	-	assimilation
[Ref.: #43724]	esculin ChEBI	+	hydrolysis
[Ref.: #43724]	gelatin ChEBI	+	hydrolysis
[Ref.: #43724]	L-arabinose ChEBI	-	assimilation
[Ref.: #43724]	malate ChEBI	-	assimilation
[Ref.: #43724]	maltose ChEBI	+/-	assimilation
[Ref.: #43724]	N-acetylglucosamine ChEBI	+/-	assimilation
[Ref.: #43724]	nitrate ChEBI	+	reduction
[Ref.: #43724]	phenylacetate ChEBI	-	assimilation
[Ref.: #43724]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43724]	sodium citrate ChEBI	-	assimilation
[Ref.: #43724]	starch ChEBI	-	hydrolysis
[Ref.: #43724]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43724]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43724]	tyrosine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43724]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43724]	acid phosphatase	+	3.1.3.2
[Ref.: #43724]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43724]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43724]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43724]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43724]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43724]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43724]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43724]	beta-galactosidase	-	3.2.1.23
[Ref.: #43724]	beta-glucosidase	-	3.2.1.21
[Ref.: #43724]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43724]	catalase	+	1.11.1.6
[Ref.: #43724]	cystine arylamidase	-	3.4.11.3
[Ref.: #43724]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43724]	esterase (C 4)	+
[Ref.: #43724]	esterase Lipase (C 8)	+/-
[Ref.: #43724]	leucine arylamidase	+	3.4.11.1
[Ref.: #43724]	lipase (C 14)	-
[Ref.: #43724]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43724]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43724]	trypsin	-	3.4.21.4
[Ref.: #43724]	urease	-	3.5.1.5
[Ref.: #43724]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43724]

Fatty acid	Percentage
C16:0 iso	21.6
C15:0 iso	19.1
C17:1 iso ω9c	11.6
C11:0 iso 3OH	7.1
C15:0 anteiso	6.8
C16:1ω7c-alcohol	5.8
C11:0 iso	5.4

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	oxidative phosphorylation	41.76	38 of 91
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43724]	Sample type/isolated from	An estuary sediment sample
[Ref.: #43724]	Geographic location (country and/or sea, region)	Asan
[Ref.: #43724]	Country	Republic of Korea
[Ref.: #43724]	Country ISO 3 Code	KOR
[Ref.: #43724]	Continent	Asia
[Ref.: #43724]	Geographic location	36.9440°/126.9900°

[Ref.: #67770]	Sample type/isolated from	Estuary sediment in Asan
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT583751 (>99% sequence identity) for Lysobacter from Microbeatlas

Aquatic Samples	37
Soil Samples	34
Animal Samples	15
Plant Samples	3
Total Samples	89

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43724]	16S rRNA gene sequence	KT583751		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysobacter aestuarii JCM 31130	GCA_006546775	contig	GenBank	1706195 tax ID	*
[Ref.: #66792]	Lysobacter aestuarii strain JCM 31130	1706195.3	wgs	PATRIC	1706195 tax ID	*
[Ref.: #66792]	Lysobacter aestuarii JCM 31130	2896281107	draft	JGI IMG/M	1706195 tax ID	*

[Ref.: #43724]	GC-content	63.8 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	63.8 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Lysobacter aestuarii strain JCM 31130 PATRIC: 1706195.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lysobacter aestuarii strain JCM 31130 PATRIC: 1706195.3
[Ref.: #69480]	motile	no	86.084	yes
[Ref.: #69480]	gram-positive	no	98.581	yes
[Ref.: #69480]	anaerobic	no	98.939	no
[Ref.: #69480]	aerobic	yes	96.637	yes
[Ref.: #69480]	halophile	no	87.052	no
[Ref.: #69480]	spore-forming	no	97.548	no
[Ref.: #69480]	thermophile	no	99.25	yes
[Ref.: #69480]	glucose-util	yes	90.015	no
[Ref.: #69480]	flagellated	no	95.973	yes
[Ref.: #69480]	glucose-ferment	no	91.189	no

Availability in culture collections External links

[Ref.: #43724]

Culture collection no.

KACC 18502, JCM 31130

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter penaei sp. nov., isolated from intestinal content of a Pacific white shrimp (Penaeus vannamei).	Xu S, Li A, Zhang MX, Yao Q, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004593	2021	*
Phylogeny	Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil.	Xu L, Huang XX, Fan DL, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003911	2020	*
Phylogeny	Lysobacter spongiae sp. nov., isolated from spongin.	Choi H, Im WT, Park JS	J Microbiol	10.1007/s12275-018-7462-3	2018	*
Phylogeny	Lysobacter aestuarii sp. nov., isolated from estuary sediment.	Jeong SE, Lee HJ, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.000884	2016	*

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 )

#43724

Sang Eun Jeong, Hyo Jung Lee, Che Ok Jeon: Lysobacter aestuarii sp. nov., isolated from estuary sediment. IJSEM 66: 1346 - 1351 2016 ( DOI 10.1099/ijsem.0.000884 , PubMed 26746421 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Lysobacter aestuarii strain JCM 31130

Lysobacter aestuarii strain JCM 31130

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