Name: Glycocaulis profundi ZYF765
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164440

Type strain:

Species: Glycocaulis profundi

Strain Designation: ZYF765

Culture col. no.: JCM 33028, MCCC 1K03554

Strain history: M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; ZYF765.

NCBI tax ID(s): 2518983 (species)

Special Collections

Section

Glycocaulis profundi ZYF765 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Seawater sampled at a depth of 4000 m in the Mariana Trench.

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	*Alphaproteobacteria*
	Order	*Caulobacterales*
	Family	*Maricaulaceae*
	Genus	*Glycocaulis*
	Species	**Glycocaulis profundi**
	Full Scientific Name (LPSN)	Glycocaulis profundi Sun et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69525]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.796

[Ref.: #69525]	Cell length	0.5-2.0 µm

[Ref.: #69525]	Cell width	0.2-0.3 µm

[Ref.: #69525]	Cell shape	rod-shaped

[Ref.: #69525]	Motility	no

[Ref.: #69525]	Colony size	0.5-1.0 mm
[Ref.: #69525]	Colony color	faint yellow
[Ref.: #69525]	Colony shape	circular
[Ref.: #69525]	Incubation period	3 days
[Ref.: #69525]	Cultivation medium used	MA 2216E

Information on culture and growth conditions Culture and growth conditions

[Ref.: #69525]

Culture medium

MA 2216E

[Ref.: #69525]

Culture medium growth

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #69525]	growth	16.0-37.0 °C
[Ref.: #69525]	optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #69525]			optimum	7.0-8.0
[Ref.: #69525]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69525]

Oxygen tolerance

obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69525]		NaCl		growth	1.0-15.0	%(w/v)
[Ref.: #69525]		NaCl		optimum	4	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69525]	alginate ChEBI	-	hydrolysis
[Ref.: #69525]	casein	+	hydrolysis
[Ref.: #69525]	cellulose ChEBI	-	hydrolysis
[Ref.: #69525]	chitin ChEBI	-	hydrolysis
[Ref.: #69525]	dna ChEBI	-	hydrolysis
[Ref.: #69525]	esculin ferric citrate	+	builds acid from
[Ref.: #69525]	gelatin ChEBI	-	hydrolysis
[Ref.: #69525]	starch ChEBI	-	hydrolysis
[Ref.: #69525]	tween 20 ChEBI	+	hydrolysis
[Ref.: #69525]	tween 40 ChEBI	+	hydrolysis
[Ref.: #69525]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #69525]		acetoin ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #69525]	acid phosphatase	+	3.1.3.2
[Ref.: #69525]	alkaline phosphatase	+	3.1.3.1
[Ref.: #69525]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #69525]	alpha-galactosidase	-	3.2.1.22
[Ref.: #69525]	alpha-mannosidase	-	3.2.1.24
[Ref.: #69525]	beta-fucosidase	-
[Ref.: #69525]	beta-galactosidase	-	3.2.1.23
[Ref.: #69525]	beta-glucosidase	-	3.2.1.21
[Ref.: #69525]	beta-glucuronidase	-	3.2.1.31
[Ref.: #69525]	catalase	+	1.11.1.6
[Ref.: #69525]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #69525]	cytochrome oxidase	+	1.9.3.1
[Ref.: #69525]	esterase (C 4)	+
[Ref.: #69525]	esterase Lipase (C 8)	+/-
[Ref.: #69525]	leucine arylamidase	+	3.4.11.1
[Ref.: #69525]	lipase (C 14)	-
[Ref.: #69525]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #69525]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #69525]	trypsin	+	3.4.21.4
[Ref.: #69525]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #69525]

Fatty acid	Percentage
C18:1 w7c	46.2
C18:0	14.1
C19:0 cyclo w8c	9.7
C17:0	8.5
11-methyl C18:1 w7c	4.3
C17:1 w6c	3.9
C12:0	3.5
C16:1 w7c / C16:1 w6c	3.2
C16:0	1.5
C14:0	0.4
ECL 18.846 / C19:1 w6c	0.4
C12:0 3OH	0.2

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

[Ref.: #67770]	Sample type/isolated from	Seawater sampled at a depth of 4000 m in the Mariana Trench

[Ref.: #69525]	Sample type/isolated from	deepsea water sample from 4000m depth
[Ref.: #69525]	Sampling date	2016-09-02
[Ref.: #69525]	Geographic location (country and/or sea, region)	Station L9 Mariana Trench
[Ref.: #69525]	Country	Pacific Ocean
[Ref.: #69525]	Geographic location	11.3333°/142.1920°
[Ref.: #69525]	Enrichment culture	MA 2216E
[Ref.: #69525]	Enrichment culture temperature	28 ̊C
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MH010196 (>99% sequence identity) for Glycocaulis profundi from Microbeatlas

Aquatic Samples	102
Soil Samples	95
Animal Samples	250
Plant Samples	17
Total Samples	464

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.: #67770]	Glycocaulis profundi 16S ribosomal RNA gene, partial sequence	MH010196	1429	GenBank ENA	2518983 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Glycocaulis profundi ZYF765	GCA_007050995	contig	GenBank ENA	2518983 tax ID
[Ref.: #69525]	genome sequence	VJOU00000000		GenBank ENA	2518983 tax ID

[Ref.: #67770]

GC-content

67.7 mol%

genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Glycocaulis profundi ZYF765 NCBI: GCA_007050995.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.796	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.245	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.274	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.53	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.396	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	72.693	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33028, MCCC 1K03554

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.	Sun H, Hu Y, Zhou S, Zheng Y, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003830	2020	*

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 )

#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) .

#69525

Hao Sun, Yuyao Hu, Shun Zhou, Yanfen Zheng, Xiao-Hua Zhang: Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. IJSEM 70: 2019 ( DOI 10.1099/ijsem.0.003830 )

* These data were automatically processed and therefore are not curated

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