Name: Hoyosella subflava DQS3-9A1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8593

Type strain:

Species: Hoyosella subflava

Strain Designation: DQS3-9A1

Culture col. no.: DSM 45089, CGMCC 4.3532, JCM 17490, NBRC 109087

Strain history: CGMCC 4.3532 <-- Y.-N. Wang et al. DQS3-9A1.

NCBI tax ID(s): 639313 (species)

SI-ID 406859

DSM 45089

Section

Hoyosella subflava DQS3-9A1 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from oil-polluted saline soil.

coccus-shaped
colony-forming
Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Hoyosella*
	Species	**Hoyosella subflava**
	Full Scientific Name (LPSN)	Hoyosella subflava (Wang et al. 2010) Hamada et al. 2016

Synonym

Amycolicicoccus subflavus

Information on morphological and physiological properties Morphology

[Ref.: #24974]	Gram stain	positive
[Ref.: #29301]	Gram stain	positive

[Ref.: #24974]	Cell length	1.1-1.2 µm
[Ref.: #29301]	Cell length	0.975 µm

[Ref.: #24974]	Cell shape	coccus-shaped
[Ref.: #29301]	Cell shape	coccus-shaped

[Ref.: #29301]	Cell width	0.8 µm

[Ref.: #29301]	Motility	no

[Ref.: #24974]	Colony color	cream
[Ref.: #24974]	Colony shape	circular
[Ref.: #24974]	Incubation period	2 days
[Ref.: #24974]	Cultivation medium used	BHI agar plate

[Ref.: #29301]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12331]

Culture medium

PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)

[Ref.: #12331]

Culture medium growth

[Ref.: #12331]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12331]

Culture medium composition

expand / minimize

[Ref.: #12331]

Culture medium

MYCOBACTERIUM MEDIUM (DSMZ Medium 219)

[Ref.: #12331]

Culture medium growth

[Ref.: #12331]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12331]

Culture medium composition

expand / minimize

[Ref.: #24974]

Culture medium

BHI agar plate

[Ref.: #24974]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #12331]		growth	28 °C
[Ref.: #24974]		growth	20.0-37.0 °C
[Ref.: #24974]	no	growth	5.0-15.0 °C
[Ref.: #24974]	no	growth	45 °C
[Ref.: #24974]	no	growth	60 °C
[Ref.: #24974]		optimum	28.0-37.0 °C
[Ref.: #29301]		growth	15-42 °C
[Ref.: #29301]		optimum	37 °C
[Ref.: #67770]		growth	37 °C

[Ref.: #12331]	Temperature range	mesophilic
[Ref.: #24974]	Temperature range	psychrophilic
[Ref.: #24974]	Temperature range	thermophilic
[Ref.: #24974]	Temperature range	mesophilic
[Ref.: #29301]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

		pH
[Ref.: #24974]	optimum	7.0-9.0
[Ref.: #29301]	optimum	8
[Ref.: #24974]	growth	7.0-11.0
[Ref.: #29301]	growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24974]	Oxygen tolerance	aerobe
[Ref.: #29301]	Oxygen tolerance	aerobe

[Ref.: #24974]	Ability of spore formation	no
[Ref.: #29301]	Ability of spore formation	no

	Salt	Tested relation		Salt conc.
[Ref.: #24974]	NaCl		growth	0.0-7.0	%(w/v)
[Ref.: #24974]	NaCl		growth	10	%(w/v)
[Ref.: #24974]	NaCl	no	growth	15	%(w/v)
[Ref.: #29301]	NaCl		growth	01-12	%
[Ref.: #29301]	NaCl		optimum	8	%

[Ref.: #24974]	Murein short key	A31
[Ref.: #24974]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67770]

Observation

quinones: MK-8, MK-7, MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29301]	cellobiose ChEBI	+	carbon source
[Ref.: #24974]	D-fructose ChEBI	+	assimilation
[Ref.: #24974]	D-glucose ChEBI	-	assimilation
[Ref.: #24974]	D-mannitol ChEBI	-	assimilation
[Ref.: #29301]	dextrin ChEBI	+	carbon source
[Ref.: #29301]	fucose ChEBI	+	carbon source
[Ref.: #29301]	glucose ChEBI	+	carbon source
[Ref.: #24974]	L-arabinose ChEBI	-	assimilation
[Ref.: #29301]	malate ChEBI	+	carbon source
[Ref.: #29301]	maltose ChEBI	+	carbon source
[Ref.: #29301]	mannitol ChEBI	+	carbon source
[Ref.: #29301]	mannose ChEBI	+	carbon source
[Ref.: #24974]	myo-inositol ChEBI	-	assimilation
[Ref.: #29301]	nitrate ChEBI	+	reduction
[Ref.: #29301]	proline ChEBI	+	carbon source
[Ref.: #29301]	sorbitol ChEBI	+	carbon source
[Ref.: #29301]	succinate ChEBI	+	carbon source
[Ref.: #29301]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29301]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #24974]	acid phosphatase	+	3.1.3.2
[Ref.: #24974]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24974]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #24974]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24974]	alpha-galactosidase	-	3.2.1.22
[Ref.: #24974]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24974]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24974]	beta-galactosidase	-	3.2.1.23
[Ref.: #24974]	beta-glucosidase	+	3.2.1.21
[Ref.: #24974]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24974]	catalase	+	1.11.1.6
[Ref.: #24974]	cystine arylamidase	-	3.4.11.3
[Ref.: #24974]	cytochrome oxidase	-	1.9.3.1
[Ref.: #24974]	esterase (C 4)	+
[Ref.: #24974]	esterase Lipase (C 8)	+
[Ref.: #24974]	leucine arylamidase	+	3.4.11.1
[Ref.: #24974]	lipase (C 14)	-
[Ref.: #24974]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #24974]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24974]	trypsin	-	3.4.21.4
[Ref.: #24974]	valine arylamidase	-
	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.: #12331]	Sample type/isolated from	oil-polluted saline soil
[Ref.: #12331]	Geographic location (country and/or sea, region)	Shengli Oilfield
[Ref.: #12331]	Country	China
[Ref.: #12331]	Country ISO 3 Code	CHN
[Ref.: #12331]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Saline soil contaminated with crude oil in the Daqing Oilfield
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF564379 (>99% sequence identity) for Hoyosella from Microbeatlas

Aquatic Samples	567
Soil Samples	948
Animal Samples	1015
Plant Samples	155
Total Samples	2685

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #12331]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #12331]	Amycolicicoccus subflavus DQS3-9A1 16S ribosomal RNA gene, partial sequence	EF564379	1486	ENA	443218 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hoyosella subflava DQS3-9A1	GCA_000214175	complete	GenBank	443218 tax ID	*
[Ref.: #66792]	Hoyosella subflava DQS3-9A1	443218.12	plasmid	PATRIC	443218 tax ID	*
[Ref.: #66792]	Hoyosella subflava DQS3-9A1	443218.13	plasmid	PATRIC	443218 tax ID	*
[Ref.: #66792]	Hoyosella subflava DQS3-9A1	650716009	complete	JGI IMG/M	443218 tax ID	*

[Ref.: #12331]	GC-content	62.2 mol%
[Ref.: #24974]	GC-content	62.2 mol%	genome sequence analysis
[Ref.: #29301]	GC-content	60.04 mol%
[Ref.: #67770]	GC-content	60.04 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	62.24 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: Hoyosella subflava DQS3-9A1 DQS3-9A1 NCBI: GCA_000214175.1
[Ref.: #69480]	motile	no	94.583	no
[Ref.: #69480]	flagellated	no	98.293	no
[Ref.: #69480]	gram-positive	yes	91.959	yes
[Ref.: #69480]	anaerobic	no	99.236	yes
[Ref.: #69480]	aerobic	yes	92.993	yes
[Ref.: #69480]	halophile	no	63.412	no
[Ref.: #69480]	spore-forming	no	77.549	no
[Ref.: #69480]	thermophile	no	99.343	no
[Ref.: #69480]	glucose-util	yes	89.094	no
[Ref.: #69480]	glucose-ferment	no	88.77	no

Availability in culture collections External links

[Ref.: #12331]

Culture collection no.

DSM 45089, CGMCC 4.3532, JCM 17490, NBRC 109087

[Ref.: #77977]

SI-ID 406859

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hoyosella suaedae sp. nov., a novel bacterium isolated from rhizosphere soil of Suaeda aralocaspica (Bunge) Freitag & Schutze.	Liu DF, Chen SQ, Wang HF, Xie YG, Gao R, Song JQ, Gao YL, Xiao M, Li QL, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005117	2021	*
Phylogeny	Hoyosella rhizosphaerae sp. nov., a halotolerant actinobacterium isolated from rhizosphere soil of Suaeda salsa, and emended description of the genus Hoyosella.	Li XJ, Liu SW, Jiang ZK, Wu G, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001416	2016	*
Phylogeny	Reclassification of Amycolicicoccus subflavus as Hoyosella subflava comb. nov. and emended descriptions of the genus Hoyosella and Hoyosella altamirensis.	Hamada M, Shibata C, Sakurai K, Hosoyama A, Oji S, Teramoto K, Tamura T	Int J Syst Evol Microbiol	10.1099/ijsem.0.001415	2016	*
Genetics	The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1(T) reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment.	Nie Y, Fang H, Li Y, Chi CQ, Tang YQ, Wu XL	PLoS One	10.1371/journal.pone.0070986	2013	*
Genetics	Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil.	Cai M, Chen WM, Nie Y, Chi CQ, Wang YN, Tang YQ, Li GY, Wu XL	J Bacteriol	10.1128/JB.05388-11	2011	*
Phylogeny	Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil.	Wang YN, Chi CQ, Cai M, Lou ZY, Tang YQ, Zhi XY, Li WJ, Wu XL, Du X	Int J Syst Evol Microbiol	10.1099/ijs.0.010546-0	2009	*
	Bioemulsification and Microbial Community Reconstruction in Thermally Processed Crude Oil.	Hu B, Zhao JY, Nie Y, Qin XY, Zhang KD, Xing JM, Wu XL	Microorganisms	10.3390/microorganisms9102054	2021	*

References

#12331

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45089

#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 )

#24974

M. S. Hamada, Chiyo,Sakurai, Kenta,Hosoyama, Akira,Oji, Syoko,Teramoto, Kanae,Tamura, Tomohiko: Reclassification of Amycolicicoccus subflavus as Hoyosella subflava comb. nov. and emended descriptions of the genus Hoyosella and Hoyosella altamirensis. IJSEM 66: 4711 - 4715 2016 ( DOI 10.1099/ijsem.0.001415 , PubMed 27514929 )

#29301

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25715 (see below)

#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;

#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) .

#77977

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406859.1 )

#25715

IJSEM 638 2010 ( DOI 10.1099/ijs.0.010546-0 , PubMed 19654348 )

* These data were automatically processed and therefore are not curated

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Hoyosella subflava DQS3-9A1 DQS3-9A1

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