Archive BacDiveID:10.13145/bacdive1656.20230509.8.1

Strain identifier

BacDive ID: 1656

Type strain:

Species: Methylocapsa acidiphila

Strain Designation: B2

Strain history: <- S. N. Dedysh; B2

NCBI tax ID(s): 133552 (species)

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

General

@ref: 5202

BacDive-ID: 1656

DSM-Number: 13967

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped

description: Methylocapsa acidiphila B2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sphagnum peat bog.

NCBI tax id

NCBI tax id: 133552
Matching level: species

strain history

@ref: 5202
history: <- S. N. Dedysh; B2

doi: 10.13145/bacdive1656.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Beijerinckiaceae
genus: Methylocapsa
species: Methylocapsa acidiphila
full scientific name: Methylocapsa acidiphila Dedysh et al. 2002

@ref: 5202

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Beijerinckiaceae

genus: Methylocapsa

species: Methylocapsa acidiphila

full scientific name: Methylocapsa acidiphila Dedysh et al. 2002

strain designation: B2

type strain: yes

Morphology

cell morphology

@ref: 23147
gram stain: negative
cell length: 0.8-1.2 µm
cell width: 0.7-1.0 µm
cell shape: coccus-shaped
motility: no

colony morphology

@ref: 23147
colony color: colourless

Culture and growth conditions

culture medium

@ref: 5202
name: METHYLOSINUS MEDIUM MM2 (DSMZ Medium 1423)
growth: yes
link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1423.pdf

culture temp

@ref	growth	type	temperature	range
23147	positive	maximum	30	mesophilic
23147	positive	minimum	10	psychrophilic
23147	positive	optimum	20-24	psychrophilic
5202	positive	growth	20	psychrophilic

culture pH

@ref	ability	type	pH
23147	positive	optimum	5.0-5.5
23147	positive	growth	4.2-7.2

Physiology and metabolism

oxygen tolerance

@ref: 5202
oxygen tolerance: aerobe

halophily

@ref	salt	growth	tested relation	concentration
23147	NaCl	positive	growth	0-0.5
23147	NaCl	no	growth	>0.5 %(w/v)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
23147	16183	methane	+	carbon source
23147	17790	methanol	+	carbon source
23147	16183	methane	+	energy source
23147	17790	methanol	+	energy source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
5202	sphagnum peat bog	West Siberia, 56N, 82E	Russia	RUS	Europe	56	82
23147	from Sphagnum-Carex peat of Bakchar bog					56	82

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Wetland (Swamp)
#Host	#Plants	#Peat moss

Safety information

risk assessment

@ref: 5202
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5202
description: Methylocapsa acidiphila partial 16S rRNA gene, type strain strain B2
accession: AJ278726
length: 1415
database: ena
NCBI tax ID: 395964

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methylocapsa acidiphila B2	GCA_000427445	scaffold	ncbi	395964
66792	Methylocapsa acidiphila B2	395964.6	wgs	patric	395964
66792	Methylocapsa acidiphila B2	2510065046	draft	img	395964

GC content

@ref: 5202
GC-content: 63.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	69.54	no
flagellated	no	78.788	no
gram-positive	no	98.064	no
anaerobic	no	96.83	yes
aerobic	yes	87.794	yes
halophile	no	94.058	no
spore-forming	no	87.311	no
glucose-util	yes	74.88	no
glucose-ferment	no	93.034	no
thermophile	no	98.217	no

External links

@ref: 5202

culture collection no.: DSM 13967, NCIMB 13765

straininfo link

@ref: 71303
straininfo: 60975

literature

topic: Phylogeny
Pubmed-ID: 11837310
title: Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.
authors: Dedysh SN, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Liesack W, Tiedje JM
journal: Int J Syst Evol Microbiol
DOI: 10.1099/00207713-52-1-251
year: 2002
mesh: Bryopsida/*microbiology, DNA, Ribosomal/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Methane/*metabolism, Molecular Sequence Data, Nitrogen Fixation/*physiology, Oxidation-Reduction, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/enzymology/genetics/physiology/ultrastructure, Sequence Analysis, DNA, *Soil Microbiology
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5202	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13967)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-13967
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
23147	Svetlana N Dedysh, Valentina N Khmelenina, Natalia E Suzina, Yuri A Trotsenko, Jeremy D Semrau, Werner Liesack, James M Tiedje		10.1099/00207713-52-1-251	Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog	IJSEM 52: 251-261 2002	11837310
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)
71303	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID60975.1	StrainInfo: A central database for resolving microbial strain identifiers