Archive BacDiveID:10.13145/bacdive7136.20230509.8.1

Strain identifier

BacDive ID: 7136

Type strain:

Species: Methanospirillum lacunae

Strain Designation: Ki8-1

Strain history: NBRC 104920 <-- T. Iino Ki8-1.

NCBI tax ID(s): 668570 (species)

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

General

@ref: 16493

BacDive-ID: 7136

DSM-Number: 22751

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

description: Methanospirillum lacunae Ki8-1 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from puddle soil.

NCBI tax id

NCBI tax id: 668570
Matching level: species

strain history

@ref	history
16493	<- K. Mori, NBRC <- T. Lino; Ki8-1 {2006}
67770	NBRC 104920 <-- T. Iino Ki8-1.

doi: 10.13145/bacdive7136.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanospirillaceae
genus: Methanospirillum
species: Methanospirillum lacunae
full scientific name: Methanospirillum lacunae Iino et al. 2010

@ref: 16493

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanomicrobiales

family: Methanospirillaceae

genus: Methanospirillum

species: Methanospirillum lacunae

full scientific name: Methanospirillum lacunae Iino et al. 2010

strain designation: Ki8-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29752	negative	11-25 µm	0.5-0.6 µm	rod-shaped	yes
69480	negative					99.952

colony morphology

@ref: 16493
incubation period: 3-7 days

pigmentation

@ref: 29752
production: yes

Culture and growth conditions

culture medium

@ref: 16493
name: METHANOSPIRILLUM LACUNAE MEDIUM (DSMZ Medium 1273)
growth: yes
link: https://mediadive.dsmz.de/medium/1273
composition: Name: METHANOSPIRILLUM LACUNAE MEDIUM (DSMZ Medium 1273) Composition: Na2CO3 0.98912 g/l Na-acetate 0.791296 g/l NH4Cl 0.534125 g/l Na2S x 9 H2O 0.49456 g/l L-Cysteine HCl x H2O 0.49456 g/l MgCl2 x 6 H2O 0.197824 g/l Yeast extract 0.197824 g/l KH2PO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16493	positive	growth	30	mesophilic
29752	positive	growth	5-37
29752	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

culture pH

@ref	ability	type	pH	PH range
29752	positive	growth	6-9.5	alkaliphile
29752	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
16493	anaerobe
29752	anaerobe
69480	anaerobe	99.999

spore formation

@ref	spore formation	confidence
29752	no
69481	no	100
69480	no	99.823

halophily

@ref	salt	growth	tested relation	concentration
29752	NaCl	positive	growth	0-1 %
29752	NaCl	positive	optimum	0-1 %

observation

@ref: 29752
observation: aggregates in chains

metabolite utilization

@ref: 29752
Chebi-ID: 15740
metabolite: formate
utilization activity: +
kind of utilization tested: carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16493	puddle soil	Chiba, Kisarazu	Japan	JPN	Asia
67770	Puddly soil in Kisarazu	Chiba	Japan	JPN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic
#Environmental	#Terrestrial	#Soil

taxonmaps

@ref: 69479
File name: preview.99_191496.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17807;96_70738;97_91863;98_124824;99_191496&stattab=map
Last taxonomy: Methanospirillum lacunae subclade
16S sequence: AB517986
Sequence Identity:
Total samples: 681
soil counts: 95
aquatic counts: 546
animal counts: 17
plant counts: 23

Safety information

risk assessment

@ref: 16493
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16493
description: Methanospirillum lacunae gene for 16S ribosomal RNA, partial sequence
accession: AB517986
length: 1260
database: ena
NCBI tax ID: 668570

Genome sequences

@ref: 67770
description: Methanospirillum lacunae Ki8-1
accession: GCA_003173355
assembly level: contig
database: ncbi
NCBI tax ID: 668570

GC content

@ref	GC-content	method
16493	45.3	high performance liquid chromatography (HPLC)
29752	45.3

Genome-based predictions

predictions

trait: spore-forming
prediction: no
confidence: 100
training_data: no

External links

@ref: 16493

culture collection no.: DSM 22751, JCM 16384, NBRC 104920

straininfo link

@ref: 76590
straininfo: 402920

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20008107	Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei.	Iino T, Mori K, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.020131-0	2009	Base Composition, DNA, Archaeal/genetics, Methane/metabolism, Methanospirillum/classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology	Metabolism
Phylogeny	24048867	Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature.	Parshina SN, Ermakova AV, Bomberg M, Detkova EN	Int J Syst Evol Microbiol	10.1099/ijs.0.056218-0	2013	Base Composition, Bioreactors/microbiology, Cold Temperature, DNA, Archaeal/genetics, Methanospirillum/classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Netherlands, Nucleic Acid Hybridization, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Temperature	Enzymology
Phylogeny	24158951	Methanospirillum psychrodurum sp. nov., isolated from wetland soil.	Zhou L, Liu X, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.057299-0	2013	Base Composition, China, DNA, Archaeal/genetics, Methane/biosynthesis, Methanospirillum/classification/genetics/isolation & purification, Molecular Sequence Data, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Wetlands	Enzymology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
16493	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22751)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22751
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
29752	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	26134	28776041
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		33211880	Nucleic Acids Res. 49: D498-D508 2020
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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
76590	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID402920.1	StrainInfo: A central database for resolving microbial strain identifiers