Name: Paremcibacter congregatus ZYL
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159732

Type strain:

Species: Paremcibacter congregatus

Strain Designation: ZYL

Culture col. no.: KCTC 62328, JCM 32378, MCCC 1K03526

Strain history: <- Zhe Zhao, Zhejiang Univ.

NCBI tax ID(s): 2043170 (species)

Section

Paremcibacter congregatus ZYL is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from cultured in situ sediment sample.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Alphaproteobacteria*
	Order	*Emcibacterales*
	Family	*Emcibacteraceae*
	Genus	*Paremcibacter*
	Species	**Paremcibacter congregatus**
	Full Scientific Name (LPSN)	Paremcibacter congregatus (Zhao et al. 2018) Park et al. 2020

Synonym

Emcibacter congregatus

Information on morphological and physiological properties Morphology

[Ref.: #66640]	Gram stain	negative

[Ref.: #66640]	Cell length	1.4-2.6 µm

[Ref.: #66640]	Cell width	0.4-0.6 µm

[Ref.: #66640]	Cell shape	rod-shaped

[Ref.: #66640]	Motility	yes

[Ref.: #66640]	Colony color	pale yellow
[Ref.: #66640]	Colony shape	circular

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #66640]	optimum	25 °C
[Ref.: #66640]	growth	4-30 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #66640]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66640]			optimum	7
[Ref.: #66640]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66640]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #66640]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66640]		NaCl		growth	<7	%(w/v)
[Ref.: #66640]		NaCl		optimum	2	%(w/v)

[Ref.: #66640]	Observation	After prolonged incubation, the colonies become mucoid and irregular. Sticky filaments with a length of 1.0-4.0 µm between cells can be seen under transmission electron microscopy.
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66640]	cellobiose ChEBI	+	builds acid from
[Ref.: #66640]	D-arabinose ChEBI	+	builds acid from
[Ref.: #66640]	D-fructose ChEBI	+	builds acid from
[Ref.: #66640]	D-glucose ChEBI	+	builds acid from
[Ref.: #66640]	D-mannose ChEBI	+	builds acid from
[Ref.: #66640]	D-ribose ChEBI	+	builds acid from
[Ref.: #66640]	esculin ChEBI	-	hydrolysis
[Ref.: #66640]	gelatin ChEBI	-	hydrolysis
[Ref.: #66640]	glucose ChEBI	-	fermentation
[Ref.: #66640]	glycerol ChEBI	+	builds acid from
[Ref.: #66640]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #66640]	lactose ChEBI	+	builds acid from
[Ref.: #66640]	maltose ChEBI	+	builds acid from
[Ref.: #66640]	myo-inositol ChEBI	+	builds acid from
[Ref.: #66640]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #66640]	nitrate ChEBI	+	reduction
[Ref.: #66640]	potassium 2-dehydro-D-gluconate	+	builds acid from
[Ref.: #66640]	starch ChEBI	+	builds acid from
[Ref.: #66640]	starch ChEBI	-	hydrolysis
[Ref.: #66640]	tween 20 ChEBI	-	hydrolysis
[Ref.: #66640]	tween 40 ChEBI	-	hydrolysis
[Ref.: #66640]	tween 60 ChEBI	-	hydrolysis
[Ref.: #66640]	tween 80 ChEBI	-	hydrolysis
[Ref.: #66640]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66640]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #66640]	chloramphenicol ChEBI				yes	30	µg (disc)
[Ref.: #66640]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #66640]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #66640]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #66640]	ofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #66640]	penicillin ChEBI	yes	10	Unit (disc)
[Ref.: #66640]	piperacillin ChEBI	yes	100	µg (disc)
[Ref.: #66640]	streptomycin ChEBI	yes	10	µg (disc)

	Metabolite	Production
[Ref.: #66640]	acetoin ChEBI	yes
[Ref.: #66640]	hydrogen sulfide ChEBI	yes
[Ref.: #66640]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #66640]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #66640]	acid phosphatase	+	3.1.3.2
[Ref.: #66640]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66640]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66640]	alpha-glucosidase	-	3.2.1.20
[Ref.: #66640]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66640]	arginine dihydrolase	-	3.5.3.6
[Ref.: #66640]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #66640]	beta-galactosidase	-	3.2.1.23
[Ref.: #66640]	beta-glucosidase	-	3.2.1.21
[Ref.: #66640]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66640]	catalase	+	1.11.1.6
[Ref.: #66640]	chymotrypsin	+	3.4.4.5
[Ref.: #66640]	cystine arylamidase	+	3.4.11.3
[Ref.: #66640]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66640]	esterase (C 4)	+
[Ref.: #66640]	esterase Lipase (C 8)	-
[Ref.: #66640]	leucine arylamidase	+	3.4.11.1
[Ref.: #66640]	lipase (C 14)	-
[Ref.: #66640]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66640]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66640]	trypsin	+	3.4.21.4
[Ref.: #66640]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66640]

Fatty acid	Percentage
C18:1 w7c and/or C18:1 w6c	25.7
C15:0 iso 2OH and/or C16:1 w7c	22.7
C14:0 2OH	17.1
C14:0	11
C16:0	9
C17:1 w6c	5.8
C16:1 iso I and/or C14:0 3OH	1.3
C16:1 w5c	1.2
C19:0 cyclo w8c	1.1

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

[Ref.: #66640]	Sample type/isolated from	cultured in situ sediment sample
[Ref.: #66640]	Geographic location (country and/or sea, region)	coast in the East China Sea
[Ref.: #66640]	Country	China
[Ref.: #66640]	Country ISO 3 Code	CHN
[Ref.: #66640]	Continent	Asia
[Ref.: #66640]	Geographic location	29.9333°/122.0830°
[Ref.: #66640]	Enrichment culture	modified marine agar 2216
[Ref.: #66640]	Enrichment culture composition	replaced Na2SO4 with 6.64 g MgSO4 x 7H2O and decreased the amount of MgCl2 x 6H2O to 12.6 g.
[Ref.: #66640]	Enrichment culture duration	15 days
[Ref.: #66640]	Enrichment culture temperature	20 ̊C
[Ref.: #66640]	Isolation/enrichment procedure	We used YTP medium, which contained (per litre distilled water): 20 g NaCl, 0.5 g yeast extract, 1.0 g tryptone, 10 g peel of pemelo (Citrus maxima) and 20 g agar, pH 7.0. YTP agar medium was made and divided into 50 ml PP tubes sealed by gauze. After autoclaving, the gauze was replaced by single layer aseptic linen, and the tubes were placed into autoclaved barrels aseptically. We then buried this device on a coast in the East China Sea and dug it out after 1 year of culturing. For subsequent experiments, 1cm-thick medium on the upper layer was cut off. To isolate the strain, the standard dilution plating technique on modified marine agar 2216.

[Ref.: #67770]	Sample type/isolated from	Cultured in situ sediment sample collected on the coast of the East China Sea

[Ref.: #67771]	Sample type/isolated from	From marine sediment in the East China Sea
[Ref.: #67771]	Geographic location (country and/or sea, region)	Zhejiang Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

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.: #66640]	Emcibacter sp. strain ZYL 16S ribosomal RNA gene, partial sequence	MG051279	1490	ENA	2043170 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paremcibacter congregatus ZYLT	GCA_006385135	complete	GenBank	2043170 tax ID
[Ref.: #66792]	Paremcibacter congregatus ZYL	GCA_002740695	scaffold	GenBank	2043170 tax ID	*
[Ref.: #66792]	Paremcibacter congregatus ZYL	2786546679	draft	JGI IMG/M	2043170 tax ID	*

[Ref.: #67770]

GC-content

51.5 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paremcibacter congregatus ZYL NCBI: GCA_002740695.1
[Ref.: #69480]	flagellated	no	50.65	no
[Ref.: #69480]	gram-positive	no	97.728	yes
[Ref.: #69480]	anaerobic	no	99.1	yes
[Ref.: #69480]	aerobic	yes	88.569	yes
[Ref.: #69480]	halophile	yes	77.155	yes
[Ref.: #69480]	spore-forming	no	92.293	no
[Ref.: #69480]	glucose-util	yes	84.611	no
[Ref.: #69480]	thermophile	no	95.184	yes
[Ref.: #69480]	motile	yes	88.793	yes
[Ref.: #69480]	glucose-ferment	no	88.909	no

Availability in culture collections External links

[Ref.: #66640]

Culture collection no.

KCTC 62328, JCM 32378, MCCC 1K03526

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 )

#66640

Zhe Zhao, Xia Shen, Wu Chen, Xiao-yun Yu, Ge-yi Fu, Cong Sun, Min Wu: Emcibacter congregatus sp. nov., isolated from sediment cultured in situ. IJSEM 68: 2846 - 2850 2018 ( DOI 10.1099/ijsem.0.002906 , PubMed 30016229 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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) .

* These data were automatically processed and therefore are not curated

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