Archive BacDiveID:10.13145/bacdive5977.20230509.8.1

Strain identifier

BacDive ID: 5977

Type strain:

Species: Halarchaeum acidiphilum

Strain Designation: MH1-52-1

Strain history: H. Minegishi MH1-52-1.

NCBI tax ID(s): 1261545 (strain), 489138 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16336

BacDive-ID: 5977

DSM-Number: 22442

keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, ovoid-shaped

description: Halarchaeum acidiphilum MH1-52-1 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from solar salt.

NCBI tax id

NCBI tax id	Matching level
489138	species
1261545	strain

strain history

@ref	history
16336	<- H. Minegishi, Bio-Nano Electronics Res. Centre, Toyo Univ., Kawagoe, Japan; MH1-52-1
67770	H. Minegishi MH1-52-1.

doi: 10.13145/bacdive5977.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Halobacteria
order: Halobacteriales
family: Halobacteriaceae
genus: Halarchaeum
species: Halarchaeum acidiphilum
full scientific name: Halarchaeum acidiphilum Minegishi et al. 2010

@ref: 16336

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halobacteriaceae

genus: Halarchaeum

species: Halarchaeum acidiphilum

full scientific name: Halarchaeum acidiphilum Minegishi et al. 2010

strain designation: MH1-52-1

type strain: yes

Morphology

cell morphology

@ref: 29468
gram stain: negative
cell width: 2 µm
cell shape: ovoid-shaped
motility: no

pigmentation

@ref: 29468
production: no

Culture and growth conditions

culture medium

@ref: 16336
name: HALOARCHAEAL MEDIUM MH-1 (DSMZ Medium 1396)
growth: yes
link: https://mediadive.dsmz.de/medium/1396
composition: Name: HALOARCHAEAL MEDIUM MH-1 (DSMZ Medium 1396) Composition: NaCl 249.377 g/l Agar 24.9377 g/l K2SO4 6.23441 g/l Casamino acids 4.98753 g/l L-Glutamic acid 2.49377 g/l Trisodium citrate x 2 H2O 2.49377 g/l Yeast extract 2.49377 g/l NH4Cl 1.24688 g/l KH2PO4 1.24688 g/l Na2S2O3 x 5 H2O 0.00498753 g/l FeSO4 x 6 H2O 0.00498753 g/l CaCl2 x 2 H2O 0.00249377 g/l CoCl2 x 6 H2O 0.00074813 g/l Na2MoO4 x 2 H2O 0.000249377 g/l MnCl2 x 4 H2O 0.000249377 g/l ZnCl2 0.000249377 g/l NiCl2 x 6 H2O 0.000249377 g/l AlCl3 9.97506e-05 g/l H3BO4 4.98753e-05 g/l Na2WO4 x 2 H2O 4.98753e-05 g/l CuCl2 x 6 H2O 2.49377e-05 g/l BaCl2 x 2 H2O 2.49377e-05 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16336	positive	growth	37	mesophilic
29468	positive	growth	15-45
29468	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH	PH range
29468	positive	growth	04-06	acidophile
29468	positive	optimum	4.4.-4.5

Physiology and metabolism

oxygen tolerance

@ref: 29468
oxygen tolerance: anaerobe

spore formation

@ref: 29468
spore formation: no

halophily

@ref	salt	growth	tested relation	concentration
29468	NaCl	positive	growth	18-30 %
29468	NaCl	positive	optimum	21-24 %

observation

@ref: 29468
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29468	22599	arabinose	+	carbon source
29468	17057	cellobiose	+	carbon source
29468	28757	fructose	+	carbon source
29468	28260	galactose	+	carbon source
29468	17234	glucose	+	carbon source
29468	17754	glycerol	+	carbon source
29468	16634	raffinose	+	carbon source
29468	17992	sucrose	+	carbon source
29468	18222	xylose	+	carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16336	solar salt	solar salt imported into Japan from Australia	Australia	AUS	Australia and Oceania
67770	Commercially available salt imported from Australia into Japan

isolation source categories

Cat1: #Condition
Cat2: #Saline

taxonmaps

@ref: 69479
File name: preview.99_187212.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17659;96_68866;97_89513;98_121794;99_187212&stattab=map
Last taxonomy: Halarchaeum acidiphilum
16S sequence: AB371717
Sequence Identity:
Total samples: 8
aquatic counts: 2
animal counts: 4
plant counts: 2

Safety information

risk assessment

@ref: 16336
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Halarchaeum acidiphilum gene for 16S rRNA, complete sequence, strain: JCM 16109	AB663350	1474	ena	1261545
16336	Halarchaeum acidiphilum gene for 16S ribosomal RNA, partial sequence	AB371717	1474	ena	1261545

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Halarchaeum acidiphilum JCM 16109	2648501819	draft	img	1261545
66792	Halarchaeum acidiphilum MH1-52-1	2648501790	draft	img	1261545
67770	Halarchaeum acidiphilum MH1-52-1	GCA_000400975	contig	ncbi	1261545
67770	Halarchaeum acidiphilum MH1-52-1 JCM 16109	GCA_000474235	contig	ncbi	1261545
66792	Halarchaeum acidiphilum MH1-52-1	1261545.10	wgs	patric	1261545
66792	Halarchaeum acidiphilum MH1-52-1	1261545.11	wgs	patric	1261545

GC content

@ref	GC-content	method
16336	61.4	high performance liquid chromatography (HPLC)
29468	61.4

External links

@ref: 16336

culture collection no.: DSM 22442, CECT 7534, JCM 16109

straininfo link

@ref: 75466
straininfo: 371184

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19965997	Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt.	Minegishi H, Echigo A, Nagaoka S, Kamekura M, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.013722-0	2009	Acids/metabolism, DNA, Archaeal/genetics, Halobacteriaceae/classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism	Metabolism
Phylogeny	22753525	Halarchaeum salinum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt.	Yamauchi Y, Minegishi H, Echigo A, Shimane Y, Shimoshige H, Kamekura M, Itoh T, Doukyu N, Inoue A, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.044693-0	2012	Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/classification/genetics/isolation & purification, Indonesia, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Philippines, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sodium Chloride	Genetics
Phylogeny	23435243	Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples.	Yamauchi Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Doukyu N, Inoue A, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.049262-0	2013	Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/classification/genetics/isolation & purification, Indonesia, Japan, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Philippines, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride	Genetics
Phylogeny	23771625	Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt.	Minegishi H, Yamauchi Y, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.054668-0	2013	Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/classification/genetics/isolation & purification, Indonesia, Japan, Lipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sodium Chloride	Genetics
Phylogeny	28875923	Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample.	Shimane Y, Minegishi H, Echigo A, Kamekura M, Itoh T, Ohkuma M, Tsubouchi T, Usui K, Maruyama T, Usami R, Hatada Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000501	2015

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
16336	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22442)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22442
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
29468	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information		28776041	25871
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
75466	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID371184.1	StrainInfo: A central database for resolving microbial strain identifiers