Archive BacDiveID:10.13145/bacdive160492.20230509.8.1

Strain identifier

BacDive ID: 160492

Type strain:

Species: Methanohalophilus profundi

Strain Designation: SLHTYRO, SLHTYROT

Strain history: S. L'Haridon; Univ. of Brest, France; SLHTYRO.

NCBI tax ID(s): 2138083 (species)

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

General

@ref: 67400

BacDive-ID: 160492

DSM-Number: 108854

keywords: genome sequence, 16S sequence, Archaea, anaerobe, halophilic, methylotroph, mesophilic, Gram-negative, colony-forming

description: Methanohalophilus profundi SLHTYRO is an anaerobe, halophilic, methylotroph archaeon that forms circular colonies and was isolated from brine sample from deep hypersaline anoxic lake.

NCBI tax id

NCBI tax id: 2138083
Matching level: species

strain history

@ref	history
67400	<- S. L ´ Haridon, IUEM, Univ. Brest, Plouzané, France; SLHTYRO <- S. L ´ Haridon {2012}
67770	S. L'Haridon; Univ. of Brest, France; SLHTYRO.

doi: 10.13145/bacdive160492.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanohalophilus
species: Methanohalophilus profundi
full scientific name: Methanohalophilus profundi L'Haridon et al. 2021

@ref: 67400

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanohalophilus

species: Methanohalophilus profundi

full scientific name: Methanohalophilus profundi L'Haridon et al. 2020

strain designation: SLHTYRO, SLHTYROT

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence	cell shape	motility
69480	negative	99.993
69627			coccus-shaped	yes

colony morphology

@ref: 69627
colony size: 1-2 mm
colony color: mustard-colored
colony shape: circular
incubation period: 60 days

Culture and growth conditions

culture medium

@ref: 67400
name: METHANOHALOPHILUS PROFUNDI MEDIUM (DSMZ Medium 479a)
growth: yes
link: https://mediadive.dsmz.de/medium/479a
composition: Name: METHANOHALOPHILUS PROFUNDI MEDIUM (DSMZ Medium 479a) Composition: MgCl2 x 6 H2O 6.0 g/l HEPES 5.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l Trimethylamine-HCl 2.0 g/l KCl 1.5 g/l NH4Cl 1.0 g/l K2HPO4 x 3 H2O 0.4 g/l Na2S x 9 H2O 0.25 g/l 2-Mercaptoethanesulfonic acid 0.2 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
67400	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
69627	positive	growth	12-37
69627	positive	optimum	30	mesophilic

culture pH

@ref	ability	type	pH
69627	positive	growth	6.5-8.2
69627	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
69480	anaerobe	99.533
69627	anaerobe

nutrition type

@ref: 69627
type: methylotroph

spore formation

@ref	spore formation	confidence
69480	no	99.979
69481	no	100

halophily

@ref	halophily level	salt	growth	tested relation	concentration
69627	halophilic	NaCl	positive	growth	45-240 g/L
69627	halophilic	NaCl	positive	optimum	135 g/L

observation

@ref	observation
69627	Piezophilic growth 35 MPa
69627	occur singly or in pairs
69627	fluoresced blue-green under UV (420 nm)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date	latitude	longitude	enrichment culture composition	isolation date
67400	brine sample from deep hypersaline anoxic lake	Deep sea hypersaline Lake TYRO	Greece	GRC	Europe
67770	Deep hypersaline anoxic basin ("Tyro") located in the Eastern Mediterranean Sea
69627	Brine, deep sea hypersaline basin	Tyro	Greece	GRC	Europe	2011-09-17	33.5242	26.2196	see materials and methods section of paper	2012-10-16

Sequence information

16S sequences

@ref: 67770
description: Methanohalophilus sp. SLHTYRO 16S ribosomal RNA gene, partial sequence
accession: MH223463
length: 896
database: ena
NCBI tax ID: 2138083

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
67770	Methanohalophilus profundi SLHTYRO	GCA_004137855	scaffold	ncbi	2138083
69627	Whole genome shotgun	QBKB00000000		ncbi	2138083

GC content

@ref	GC-content	method
67400	42.7	sequence analysis
67770	42.7	genome sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
flagellated	no	97.465	no
gram-positive	no	97.042	no
anaerobic	yes	98.299	no
aerobic	no	94.135	no
halophile	no	63.957	no
spore-forming	no	95.861	no
glucose-util	yes	77.229	no
thermophile	no	63.293	yes
motile	no	92.085	no
glucose-ferment	no	71.546	no

External links

@ref: 67400

culture collection no.: DSM 108854, JCM 32768, UBOCC M-3308

straininfo link

@ref: 112736
straininfo: 398865

literature

topic: Phylogeny
Pubmed-ID: 32847782
title: Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin.
authors: L'Haridon S, Haroun H, Corre E, Roussel E, Chalopin M, Pignet P, Baliere C, la Cono V, Jebbar M, Yakimov M, Toffin L
journal: Syst Appl Microbiol
DOI: 10.1016/j.syapm.2020.126107
year: 2020
mesh: Anaerobiosis, Genes, Archaeal, Hydrogen-Ion Concentration, Hydrostatic Pressure, Mediterranean Sea, Methanol/metabolism, Methanosarcinaceae/*classification/cytology/*isolation & purification/physiology, Methylamines/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salinity, Seawater/*microbiology, Temperature, *Water Microbiology
topic2: Metabolism

Reference

@id	authors	title	doi/url	catalogue
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	10.1099/ijsem.0.004332
67400	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-108854	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108854)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	10.21203/rs.3.rs-2527258/v1
69627	Stéphane L'Haridon, Hani Haroun, Erwan Corre, Erwan Roussel, Morgane Chalopin, Patricia Pignet, Charlotte Balière, Violetta la Cono, Mohamed Jebbar, Michail Yakimov, Laurent Toffin	Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin	10.1016/j.syapm.2020.126107
112736	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	10.60712/SI-ID398865.1