Syntrophotalea carbinolica (DSM 2380, NBRC 103641, Bd1)

Name: Syntrophotalea carbinolica (DSM 2380, NBRC 103641, Bd1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4218

Type strain

Strain Designation Bd1, GraBd1

Culture col. no. DSM 2380 NBRC 103641 Bd1 GraBd1

NCBI tax ID(s) 338963 19

Special Collections DSMZ

Links

Syntrophotalea carbinolica Bd1 is an anaerobe, mesophilic prokaryote that was isolated from mud.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 47605

DSM 2380,NBRC 103641

@ref 20215

Last LPSN update 2025-12-16 09:47:45

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfuromonadia

Order Desulfuromonadales

Family Syntrophotaleaceae

Genus Syntrophotalea

Species Syntrophotalea carbinolica

Full scientific name Syntrophotalea carbinolica (Schink 1984) Waite et al. 2020

Synonyms (1)

Pelobacter carbinolicus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.673
125439	negative	99.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1062	PROPIONIGENIUM MODESTUM MEDIUM (MARINE) (DSMZ Medium 293)		Medium recipe at MediaDive	Name: PROPIONIGENIUM MODESTUM MEDIUM (MARINE) (DSMZ Medium 293; with strain-specific modifications) Composition: NaCl 19.98 g/l MgCl2 x 6 H2O 2.997 g/l Na2CO3 1.24875 g/l 2,3-butanediol 0.899101 g/l KCl 0.499501 g/l Na2S x 9 H2O 0.35964 g/l NH4Cl 0.24975 g/l KH2PO4 0.1998 g/l CaCl2 x 2 H2O 0.14985 g/l HCl 0.0024975 g/l FeCl2 x 4 H2O 0.0014985 g/l Sodium resazurin 0.0004995 g/l CoCl2 x 6 H2O 0.00018981 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l Na2MoO4 x 2 H2O 3.5964e-05 g/l NiCl2 x 6 H2O 2.3976e-05 g/l H3BO3 5.99401e-06 g/l CuCl2 x 2 H2O 1.998e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1062	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

1062

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1062	mud	Venice, Canale Grande	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence X79413 (>99% sequence identity) for Syntrophotalea carbinolica subclade from Microbeatlas

Aquatic Samples	275
Soil Samples	20
Animal Samples	5
Plant Samples
Total Samples	300

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1062	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	ASM1288v1 assembly for Syntrophotalea carbinolica DSM 2380	complete	GCA_000012885	338963.6	637000204	338963	97.08
66792	Syntrophotalea carbinolica DSM 2380	complete			2518285547	338963	13.4
66792	Syntrophotalea carbinolica DSM 2380	complete			2518285546	338963

Genome browser: GCA_000012885

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Pelobacter carbinolicus 16S ribosomal RNA gene, partial sequence	U23141	1414		19
20218	P.carbinolicus 16S rDNA	X79413	1476		338963

GC content

@ref	GC-content (mol%)	Method
1062	55.1	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Syntrophotalea carbinolica DSM 2380
NCBI: GCA_000012885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	88.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	61.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Syntrophotalea carbinolica DSM 2380 DSM 2380
NCBI: GCA_000012885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.67	no
125438	anaerobic	anaerobicⓘ	yes	67.68	no
125438	aerobic	aerobicⓘ	no	76.77	yes
125438	spore-forming	spore-formingⓘ	no	82.66	no
125438	thermophilic	thermophileⓘ	no	83.18	no
125438	flagellated	motile2+ⓘ	yes	72.57	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Desulfuromonas sp. 'CSMB_57', isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals.	McLeish AG, Greenfield P, Midgley DJ, Paulsen IT.	Microb Genom	10.1099/mgen.0.000857	2022
	Simultaneous Genome Sequencing of Prosthecochloris ethylica and Desulfuromonas acetoxidans within a Syntrophic Mixture Reveals Unique Pili and Protein Interactions.	Kyndt JA, Van Beeumen JJ, Meyer TE.	Microorganisms	10.3390/microorganisms8121939	2020
	Reconstructing horizontal gene flow network to understand prokaryotic evolution.	Sengupta S, Azad RK.	Open Biol	10.1098/rsob.220169	2022
	Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.	Akob DM, Sutton JM, Bushman TJ, Baesman SM, Klein E, Shrestha Y, Andrews R, Fierst JL, Kolton M, Gushgari-Doyle S, Oremland RS, Freeman JL.	Appl Environ Microbiol	10.1128/aem.01219-22	2022
Phylogeny	Diversity and Evolution of Myxobacterial Type IV Pilus Systems.	Sharma G, Burrows LL, Singer M.	Front Microbiol	10.3389/fmicb.2018.01630	2018
Metabolism	Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes.	Yee MO, Rotaru AE.	Sci Rep	10.1038/s41598-019-57206-z	2020
Metabolism	Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri.	Rotaru AE, Shrestha PM, Liu F, Markovaite B, Chen S, Nevin KP, Lovley DR.	Appl Environ Microbiol	10.1128/aem.00895-14	2014
	Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus.	Sharma G, Narwani T, Subramanian S.	PLoS One	10.1371/journal.pone.0148593	2016
Metabolism	Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.	Alvarez-Carreno C, Becerra A, Lazcano A.	PLoS One	10.1371/journal.pone.0157904	2016
Metabolism	Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus.	Wawrousek K, Noble S, Korlach J, Chen J, Eckert C, Yu J, Maness PC.	PLoS One	10.1371/journal.pone.0114551	2014
Metabolism	Ethanolamine utilization in Vibrio alginolyticus.	Khatri N, Khatri I, Subramanian S, Raychaudhuri S.	Biol Direct	10.1186/1745-6150-7-45	2012
Metabolism	Carbon isotope fractionation of 11 acetogenic strains grown on H2 and CO2.	Blaser MB, Dreisbach LK, Conrad R.	Appl Environ Microbiol	10.1128/aem.03203-12	2013
Metabolism	Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae.	Wagner DD, Hug LA, Hatt JK, Spitzmiller MR, Padilla-Crespo E, Ritalahti KM, Edwards EA, Konstantinidis KT, Loffler FE.	BMC Genomics	10.1186/1471-2164-13-200	2012
Metabolism	Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens.	Rotaru AE, Shrestha PM, Liu F, Ueki T, Nevin K, Summers ZM, Lovley DR.	Appl Environ Microbiol	10.1128/aem.01946-12	2012
Metabolism	RcoM: a new single-component transcriptional regulator of CO metabolism in bacteria.	Kerby RL, Youn H, Roberts GP.	J Bacteriol	10.1128/jb.00033-08	2008
	Dissemination of 6S RNA among bacteria.	Wehner S, Damm K, Hartmann RK, Marz M.	RNA Biol	10.4161/rna.29894	2014
Genetics	Genome evolution and the emergence of fruiting body development in Myxococcus xanthus.	Goldman B, Bhat S, Shimkets LJ.	PLoS One	10.1371/journal.pone.0001329	2007
Metabolism	Degradation of acetaldehyde and its precursors by Pelobacter carbinolicus and P. acetylenicus.	Schmidt A, Frensch M, Schleheck D, Schink B, Muller N.	PLoS One	10.1371/journal.pone.0115902	2014
Metabolism	The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.	Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR.	BMC Genomics	10.1186/1471-2164-13-690	2012
Metabolism	Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production.	Haveman SA, DiDonato RJ, Villanueva L, Shelobolina ES, Postier BL, Xu B, Liu A, Lovley DR.	Appl Environ Microbiol	10.1128/aem.02901-07	2008
Phylogeny	Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.	Shulse CN, Allen EE.	PLoS One	10.1371/journal.pone.0020146	2011
Genetics	Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression.	McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F, Paul JH.	PLoS One	10.1371/journal.pone.0003263	2008
Metabolism	A novel Giardia lamblia nitroreductase, GlNR1, interacts with nitazoxanide and other thiazolides.	Muller J, Wastling J, Sanderson S, Muller N, Hemphill A.	Antimicrob Agents Chemother	10.1128/aac.01548-06	2007
Metabolism	Constraint-based modeling analysis of the metabolism of two Pelobacter species.	Sun J, Haveman SA, Bui O, Fahland TR, Lovley DR.	BMC Syst Biol	10.1186/1752-0509-4-174	2010
Metabolism	Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters.	Bevers LE, Hagedoorn PL, Krijger GC, Hagen WR.	J Bacteriol	10.1128/jb.00548-06	2006
Enzymology	Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.	Wilms R, Sass H, Kopke B, Koster J, Cypionka H, Engelen B.	Appl Environ Microbiol	10.1128/aem.72.4.2756-2764.2006	2006
	Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes.	Bohlin J, Skjerve E, Ussery DW.	BMC Genomics	10.1186/1471-2164-9-104	2008
Metabolism	Predicting the pathway involved in post-translational modification of elongation factor P in a subset of bacterial species.	Bailly M, de Crecy-Lagard V.	Biol Direct	10.1186/1745-6150-5-3	2010
Genetics	Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.	Saeed I, Tang SL, Halgamuge SK.	Nucleic Acids Res	10.1093/nar/gkr1204	2012
Metabolism	Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea.	Cherif-Zahar B, Durand A, Schmidt I, Hamdaoui N, Matic I, Merrick M, Matassi G.	J Bacteriol	10.1128/jb.01089-07	2007
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
Metabolism	Fe(III) and S0 reduction by Pelobacter carbinolicus.	Lovley DR, Phillips EJ, Lonergan DJ, Widman PK.	Appl Environ Microbiol	10.1128/aem.61.6.2132-2138.1995	1995
Enzymology	Purification and characterization of acetoin:2,6-dichlorophenolindophenol oxidoreductase, dihydrolipoamide dehydrogenase, and dihydrolipoamide acetyltransferase of the Pelobacter carbinolicus acetoin dehydrogenase enzyme system.	Oppermann FB, Schmidt B, Steinbuchel A.	J Bacteriol	10.1128/jb.173.2.757-767.1991	1991
Metabolism	Evidence for oxidative thiolytic cleavage of acetoin in Pelobacter carbinolicus analogous to aerobic oxidative decarboxylation of pyruvate.	Oppermann FB, Steinbuchel A, Schlegel HG	FEMS Microbiol Lett	10.1016/0378-1097(89)90087-6	1989
	The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov.	Spring S, Lunsdorf H, Fuchs BM, Tindall BJ.	PLoS One	10.1371/journal.pone.0004866	2009
Phylogeny	Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments.	Baesman SM, Sutton JM, Fierst JL, Akob DM, Oremland RS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004698	2021

References

#1062	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2380
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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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Syntrophotalea carbinolica (DSM 2380, NBRC 103641, Bd1)

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_000012885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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