Name: Herbaspirillum robiniae HZ10
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158710

Type strain:

Species: Herbaspirillum robiniae

Strain Designation: HZ10

Culture col. no.: JCM 31754, CCTCC AB 2014352

Strain history: Y. Lin; Northwest A&F Univ., China; HZ10.

NCBI tax ID(s): 2014887 (species)

Section

Herbaspirillum robiniae HZ10 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County.

colony-forming
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Herbaspirillum*
	Species	**Herbaspirillum robiniae**
	Full Scientific Name (LPSN)	Herbaspirillum robiniae Fan et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65452]	Gram stain	negative

[Ref.: #65452]	Cell length	0.3-2.0 µm

[Ref.: #65452]	Cell shape	rod-shaped

[Ref.: #65452]	Flagellum arrangement	polar

[Ref.: #65452]	Colony size	3-5 mm
[Ref.: #65452]	Colony color	brownish
[Ref.: #65452]	Colony shape	circular
[Ref.: #65452]	Incubation period	2 days
[Ref.: #65452]	Cultivation medium used	Yeast Mannitol Agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

Tryptic Soy Agar

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Culture medium growth

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Culture medium

Yeast Mannitol Agar

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Culture medium growth

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Culture medium

nitrogen-free medium

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Culture medium growth

		Temperature
[Ref.: #65452]	growth	4-45 °C
[Ref.: #65452]	optimum	25-30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #65452]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65452]			optimum	7-8
[Ref.: #65452]			growth	5-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65452]		NaCl		growth	0-1	%(w/v)

[Ref.: #65452]	Observation	quinone type is Q-8
[Ref.: #65452]	Observation	major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65452]	2-oxopentanoate ChEBI	+	assimilation
[Ref.: #65452]	4-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #65452]	adipate ChEBI	-	assimilation
[Ref.: #65452]	arginine ChEBI	+	assimilation
[Ref.: #65452]	cellobiose ChEBI	+	assimilation
[Ref.: #65452]	citrate ChEBI	+	assimilation
[Ref.: #65452]	D-arabinose ChEBI	-	assimilation
[Ref.: #65452]	D-arabitol ChEBI	+	assimilation
[Ref.: #65452]	D-fructose ChEBI	+	assimilation
[Ref.: #65452]	D-galactose ChEBI	+	assimilation
[Ref.: #65452]	D-galacturonic acid ChEBI	+	assimilation
[Ref.: #65452]	D-glucosaminic acid ChEBI	+	assimilation
[Ref.: #65452]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #65452]	D-lyxose ChEBI	+	assimilation
[Ref.: #65452]	D-mannitol ChEBI	+	assimilation
[Ref.: #65452]	D-mannose ChEBI	+	assimilation
[Ref.: #65452]	D-serine ChEBI	+	assimilation
[Ref.: #65452]	ethanolamine ChEBI	+	assimilation
[Ref.: #65452]	formate ChEBI	+	assimilation
[Ref.: #65452]	gamma-aminobutyric acid ChEBI	+	assimilation
[Ref.: #65452]	glycerol ChEBI	+	assimilation
[Ref.: #65452]	glycerol 1-phosphate ChEBI	+	assimilation
[Ref.: #65452]	glycerol 3-phosphate ChEBI	+	assimilation
[Ref.: #65452]	glycogen ChEBI	+	assimilation
[Ref.: #65452]	glycyl L-aspartic acid ChEBI	+	assimilation
[Ref.: #65452]	L-arabinose ChEBI	+	assimilation
[Ref.: #65452]	L-arabitol ChEBI	-	assimilation
[Ref.: #65452]	L-fucose ChEBI	+	assimilation
[Ref.: #65452]	L-rhamnose ChEBI	+	assimilation
[Ref.: #65452]	L-threonine ChEBI	+	assimilation
[Ref.: #65452]	leucine ChEBI	+	assimilation
[Ref.: #65452]	methylmalonic acid ChEBI	+	assimilation
[Ref.: #65452]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #65452]	phenylacetate ChEBI	-	assimilation
[Ref.: #65452]	rhamnose ChEBI	+	assimilation
[Ref.: #65452]	ribitol ChEBI	-	assimilation
[Ref.: #65452]	salicin ChEBI	+	assimilation
[Ref.: #65452]	sorbitol ChEBI	-	assimilation
[Ref.: #65452]	tyrosine ChEBI	+	assimilation
[Ref.: #65452]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65452]	ceftazidime ChEBI				yes	30	µg (disc)
[Ref.: #65452]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65452]	streptomycin ChEBI	yes	10	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #65452]		sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65452]	beta-glucosidase	+	3.2.1.21
[Ref.: #65452]	catalase	+	1.11.1.6
[Ref.: #65452]	esterase Lipase (C 8)	+

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65452]

Fatty acid	Percentage
C16:1ω7c and/or C16:1ω6c	36.6
C18:1ω7c and/or C18:1ω6c	23.1
C16:0	20.9
C12:0	3.4
C12:0 3OH	3.2
C17:0 cyclo	2.1
C10:0 3OH	1.5
C18:00	1.4
C14:00	0.6
C12:0 2OH	0.5
C14:0 3-OH and/or C16:1 iso	0.1

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

[Ref.: #65452]	Sample type/isolated from	root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County
[Ref.: #65452]	Geographic location (country and/or sea, region)	Shaanxi Province
[Ref.: #65452]	Country	China
[Ref.: #65452]	Country ISO 3 Code	CHN
[Ref.: #65452]	Continent	Asia
[Ref.: #65452]	Geographic location	33.1148°/106.7920°
[Ref.: #65452]	Enrichment culture duration	3-5 days
[Ref.: #65452]	Enrichment culture temperature	28 ̊C
[Ref.: #65452]	Isolation/enrichment procedure	The surfaces of the root nodules were sterilized by immersing them in 95 % ethanol and 0.2 % HgCl 2 and rinsing them six times with distilled water, as described previously. Next, the surface-sterilized nodules were crushed and streaked on a yeast-mannitol agar (YMA) medium.

[Ref.: #67770]	Sample type/isolated from	Root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County
[Ref.: #67770]	Host species	Robinia pseudoacacia
[Ref.: #67770]	Geographic location (country and/or sea, region)	Shaanxi Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Heavy metal
#Engineered	#Other	#Mine
#Host Body-Site	#Plant	#Root nodule
#Host	#Plants	#Tree

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP276241 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	704
Soil Samples	738
Animal Samples	249
Plant Samples	614
Total Samples	2305

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.: #65452]	16S rRNA gene sequence	KP276241		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Herbaspirillum robiniae HZ10	GCA_002213415	contig	GenBank	2014887 tax ID
[Ref.: #66792]	Herbaspirillum robiniae HZ10	2839094727	draft	JGI IMG/M	2014887 tax ID	*

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GC-content

64.9 mol%

sequence analysis

Availability in culture collections External links

[Ref.: #65452]

Culture collection no.

JCM 31754, CCTCC AB 2014352

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead-zinc mine.	Fan MC, Guo YQ, Zhang LP, Zhu YM, Chen WM, Lin YB, Wei GH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002666	2018	*

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 )

#65452

Miao-Chun Fan, Yan-Qing Guo, Li-Ping Zhang, Ya-Min Zhu, Wei-Min Chen, Yan-Bing Lin, Ge-Hong Wei: Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead–zinc mine. IJSEM 68: 1300 - 1306 2018 ( DOI 10.1099/ijsem.0.002666 , PubMed 29485397 )

#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 .

* These data were automatically processed and therefore are not curated

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