Methanolobus zinderi (DSM 21339, ATCC BAA-1601, SD-1)

Name: Methanolobus zinderi (DSM 21339, ATCC BAA-1601, SD-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7082

Type strain

Strain Designation SD-1

Culture col. no. DSM 21339 ATCC BAA-1601 SD-1

NCBI tax ID(s) 536044

Special Collections DSMZ

History <- J. G. Ferry, Pennsylvania State Univ., University Park, USA; SD-1 <- S. Doerfert and M. Reichlen {2006}

Links

Methanolobus zinderi SD-1 is an anaerobe, mesophilic prokaryote that was isolated from coal formation water.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400257

ATCC BAA-1601,DSM 21339

@ref 20215

Last LPSN update 2026-02-09 11:19:23

Domain Archaea

Phylum Methanobacteriota

Class Methanosarcinia

Order Methanosarcinales

Family Methanosarcinaceae

Genus Methanolobus

Species Methanolobus zinderi

Full scientific name Methanolobus zinderi Doerfert et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	91.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15625	METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)		Medium recipe at MediaDive	Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c; with strain-specific modifications) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Methanol 3.87476 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15625	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

15625

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		93

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Engineered	#Waste	#Coalbed water
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15625	coal formation water	Louisiana, Monroe	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence EU711413 (>99% sequence identity) for Methanolobus from Microbeatlas

Aquatic Samples	76
Soil Samples	20
Animal Samples	1
Plant Samples	3
Total Samples	100

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15625	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1338825v1 assembly for Methanolobus zinderi DSM 21339	complete	GCA_013388255	536044.3	2883920249	536044	90.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15625	Methanolobus zinderi strain SD1 16S small subunit ribosomal RNA gene, complete sequence	EU711413	1480		536044

GC content

@ref	GC-content (mol%)	Method
15625	42	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanolobus zinderi DSM 21339
IMG: 2883920249

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.00	no
125439	motility	BacteriaNetⓘ	no	76.90	no
125439	gram_stain	BacteriaNetⓘ	negative	91.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	89.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanolobus zinderi DSM 21339
NCBI: GCA_013388255.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	66.97	no
125438	anaerobic	anaerobicⓘ	yes	87.25	yes
125438	aerobic	aerobicⓘ	no	89.95	yes
125438	spore-forming	spore-formingⓘ	no	86.63	no
125438	thermophilic	thermophileⓘ	no	84.74	yes
125438	flagellated	motile2+ⓘ	no	85.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern.	Bueno de Mesquita CP, Zhou J, Theroux SM, Tringe SG.	Genes (Basel)	10.3390/genes12101609	2021
Metabolism	Stable carbon isotope fractionation by methylotrophic methanogenic archaea.	Penger J, Conrad R, Blaser M.	Appl Environ Microbiol	10.1128/aem.01773-12	2012
Phylogeny	Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia.	Shen Y, Chen SC, Lai MC, Huang HH, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG	Int J Syst Evol Microbiol	10.1099/ijsem.0.004453	2020
Phylogeny	Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam.	Doerfert SN, Reichlen M, Iyer P, Wang M, Ferry JG	Int J Syst Evol Microbiol	10.1099/ijs.0.003772-0	2009

References

#15625	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21339
#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 )
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methanolobus zinderi (DSM 21339, ATCC BAA-1601, SD-1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013388255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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