Name: Pedobacter lusitanus NL19
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133123

Type strain:

Species: Pedobacter lusitanus

Strain Designation: NL19

Culture col. no.: LMG 29220, CECT 9028

NCBI tax ID(s): 1503925 (species)

Section

Pedobacter lusitanus NL19 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from sludge collected from a deactivated uranium; mine.

Gram-negative
rod-shaped
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter lusitanus**
	Full Scientific Name (LPSN)	Pedobacter lusitanus Covas et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25303]	Gram stain	negative

[Ref.: #25303]	Cell shape	rod-shaped

[Ref.: #25303]	Motility	no

[Ref.: #25303]	Colony color	light yellow
[Ref.: #25303]	Cultivation medium used	NA

[Ref.: #25303]	Colony color	light yellow
[Ref.: #25303]	Cultivation medium used	TSA

[Ref.: #25303]	Colony color	light yellow
[Ref.: #25303]	Cultivation medium used	MacConkey agar

[Ref.: #25303]	Colony color	pale white shiny
[Ref.: #25303]	Cultivation medium used	R2A

[Ref.: #25303]	Colony color	pale white shiny
[Ref.: #25303]	Cultivation medium used	minimal medium

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

minimal medium

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Culture medium growth

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Culture medium

TSB

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #25303]			growth	4-30 °C
[Ref.: #25303]			optimum	18-30 °C

	pH	Kind of pH		pH
[Ref.: #25303]			optimum	6-8

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25303]		NaCl	maximum	2	%(w/v)
[Ref.: #25303]		NaCl	optimum	0.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25303]	adipate ChEBI	-	assimilation
[Ref.: #25303]	amygdalin ChEBI	+	builds acid from
[Ref.: #25303]	arabinose ChEBI	-	fermentation
[Ref.: #25303]	casein	+	hydrolysis
[Ref.: #25303]	cellobiose ChEBI	+	builds acid from
[Ref.: #25303]	D-arabinose ChEBI	-	assimilation
[Ref.: #25303]	D-fructose ChEBI	+	builds acid from
[Ref.: #25303]	D-galactose ChEBI	+	builds acid from
[Ref.: #25303]	D-glucose ChEBI	-	fermentation
[Ref.: #25303]	D-glucose ChEBI	+	builds acid from
[Ref.: #25303]	D-glucose ChEBI	+	assimilation
[Ref.: #25303]	D-mannitol ChEBI	+	assimilation
[Ref.: #25303]	D-mannitol ChEBI	+	builds acid from
[Ref.: #25303]	D-mannose ChEBI	+	assimilation
[Ref.: #25303]	D-mannose ChEBI	+	builds acid from
[Ref.: #25303]	decanoate ChEBI	-	assimilation
[Ref.: #25303]	esculin ChEBI	+	hydrolysis
[Ref.: #25303]	esculin ferric citrate	+	builds acid from
[Ref.: #25303]	gelatin ChEBI	+	hydrolysis
[Ref.: #25303]	L-fucose ChEBI	+	builds acid from
[Ref.: #25303]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #25303]	L-xanthine	-	hydrolysis
[Ref.: #25303]	lactose ChEBI	-	fermentation
[Ref.: #25303]	lactose ChEBI	+	builds acid from
[Ref.: #25303]	malate ChEBI	-	assimilation
[Ref.: #25303]	maltose ChEBI	+	assimilation
[Ref.: #25303]	maltose ChEBI	+	builds acid from
[Ref.: #25303]	melibiose ChEBI	+	builds acid from
[Ref.: #25303]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #25303]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25303]	nitrate ChEBI	-	reduction
[Ref.: #25303]	phenylacetate ChEBI	-	assimilation
[Ref.: #25303]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25303]	ribitol ChEBI	-	fermentation
[Ref.: #25303]	salicin ChEBI	+	builds acid from
[Ref.: #25303]	sodium citrate ChEBI	-	assimilation
[Ref.: #25303]	sorbitol ChEBI	-	fermentation
[Ref.: #25303]	starch ChEBI	+	hydrolysis
[Ref.: #25303]	sucrose ChEBI	+	builds acid from
[Ref.: #25303]	trehalose ChEBI	+	builds acid from
[Ref.: #25303]	tween 20 ChEBI	+	hydrolysis
[Ref.: #25303]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25303]	amikacin ChEBI				yes	30	µg
[Ref.: #25303]	ampicillin ChEBI				yes	10	µg
[Ref.: #25303]	aztreonam ChEBI				yes	30	µg
[Ref.: #25303]	cefepime ChEBI				yes	30	µg
[Ref.: #25303]	cefoxitin ChEBI				yes	30	µg
[Ref.: #25303]	ceftazidime ChEBI				yes	10	µg
[Ref.: #25303]	cefuroxime ChEBI				yes	30	µg
[Ref.: #25303]	chloramphenicol ChEBI				yes	30	µg
[Ref.: #25303]	chlortetracyclin ChEBI				yes	30	µg
[Ref.: #25303]	ciprofloxacin ChEBI				yes	5	µg
[Ref.: #25303]	colistin sulfate				yes	10	µg
[Ref.: #25303]	gentamicin ChEBI				yes	10	µg
[Ref.: #25303]	imipenem ChEBI	yes	10	µg
[Ref.: #25303]	netilmycin ChEBI				yes	10	µg
[Ref.: #25303]	nitrofurantoin ChEBI	yes	100	µg
[Ref.: #25303]	penicillin g ChEBI				yes	10	µg
[Ref.: #25303]	piperacillin ChEBI				yes	30	µg
[Ref.: #25303]	streptomycin ChEBI				yes	10	µg
[Ref.: #25303]	ticarcillin ChEBI				yes	75	µg
[Ref.: #25303]	tobramycin ChEBI				yes	10	µg
[Ref.: #25303]	vancomycin ChEBI				yes	30	µg
	Only first 10 entries are displayed. Click here to see all.

	Group ID of combined antibiotics	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25303]	10	amoxicillin ChEBI				yes	30	µg
[Ref.: #25303]	10	clavulanic acid ChEBI				yes	30	µg
[Ref.: #25303]	22	piperacillin ChEBI				yes	30	µg
[Ref.: #25303]	26	sulfamethoxazole ChEBI	yes	25	µg
[Ref.: #25303]	22	tazobactam ChEBI				yes	60	µg
[Ref.: #25303]	26	trimethoprim ChEBI	yes	25	µg

	Metabolite	Production
[Ref.: #25303]	dinitrogen ChEBI	no
[Ref.: #25303]	hydrogen sulfide ChEBI	no
[Ref.: #25303]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25303]	acid phosphatase	+	3.1.3.2
[Ref.: #25303]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25303]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25303]	alpha-fucosidase	+	3.2.1.51
[Ref.: #25303]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25303]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25303]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25303]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25303]	beta-galactosidase	+	3.2.1.23
[Ref.: #25303]	beta-glucosidase	-	3.2.1.21
[Ref.: #25303]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25303]	catalase	+	1.11.1.6
[Ref.: #25303]	cystine arylamidase	-	3.4.11.3
[Ref.: #25303]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25303]	esterase (C 4)	+
[Ref.: #25303]	esterase Lipase (C 8)	+
[Ref.: #25303]	leucine arylamidase	+	3.4.11.1
[Ref.: #25303]	lipase (C 14)	-
[Ref.: #25303]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25303]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25303]	trypsin	-	3.4.21.4
[Ref.: #25303]	urease	-	3.5.1.5
[Ref.: #25303]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25303]

Fatty acid	Percentage	SD
C16:1ω7c	46.88	0.02
C14:1ω5c	18.78	0.01
C4:0	8.3	0.03
C17:0 iso	6.74	0.02
C16:0	4.01	0.01
C15:0 anteiso	2.36	0.01
C15:0 iso 3OH	1.84	0.01
C16:0 iso	0.9	0.07
C6:0	0.89	0.06
C8:0	0.85	0.02
C14:0	0.77	0.01
C15:0	0.52	0.02
C18:1ω7c	0.38	0.01
Cyclo-C17	0.36	0.01
C17:0 anteiso	0.28	0.01
C12:0 3OH	0.27	0.01
C14:0 iso	0.2	0.01
C17:0	0.18	0.01
C10:1	0.15	0.01
C14:0 2OH	0.14	0.01
C12:0 2OH	0.14	0.01
C14:0 3OH	0.13	0.01
C10:0 3OH	0.11	0.01
C18:0 iso	0.11	0.01
C16:1ω5t	0.1	0.01
C13:0 anteiso	0.09	0.01
C18:0	0.08	0.01
C10:0	0.08	0.01
C17:0 iso 2OH	0.08	0.01
C15:1ω5c	0.05	0.01

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

[Ref.: #25303]	Sample type/isolated from	sludge collected from a deactivated uranium mine
[Ref.: #25303]	Geographic location (country and/or sea, region)	Quinta do Bispo, District of Viseu, Portugal
[Ref.: #25303]	Country	Portugal
[Ref.: #25303]	Country ISO 3 Code	PRT
[Ref.: #25303]	Continent	Europe
[Ref.: #25303]	Geographic location	40.0000°/-7.0000°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KJ579161 (>99% sequence identity) for Pedobacter lusitanus from Microbeatlas

Aquatic Samples	200
Soil Samples	606
Animal Samples	282
Plant Samples	631
Total Samples	1719

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.: #25303]	16S rRNA gene sequences	KJ579161	1520	ENA	1503925 tax ID
[Ref.: #25303]	Pedobacter sp. NL19 clone 1 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	KT932318	874	ENA	1503925 tax ID
[Ref.: #25303]	Pedobacter sp. NL19 clone 2 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	KT932319	928	ENA	1503925 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter lusitanus NL19	GCA_000832545	contig	GenBank	1503925 tax ID	*
[Ref.: #66792]	Pedobacter lusitanus NL19	2639762777	draft	JGI IMG/M	1503925 tax ID	*

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GC-content

40.8 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

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Culture collection no.

LMG 29220, CECT 9028

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.	Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001814	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 )

#25303

C. C. Covas, T.,Cruz, A.,Santos, T.,Dias, L.,Klein, G.,Abdulmawjood, A.,Rodríguez-Alcalá, L. M.,Pimentel, L. L.,Gomes, A.,Freitas, A. C.,Garcia-Serrano, A.,Fontecha, J.,Mendo, S.: Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine. IJSEM 67: 1339 - 1348 2017 ( DOI 10.1099/ijsem.0.001814 , PubMed 28109203 )

#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) .

#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 .

* These data were automatically processed and therefore are not curated

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