Afifella pfennigii (DSM 17143, ATCC BAA-1145, AR2102)

Name: Afifella pfennigii (DSM 17143, ATCC BAA-1145, AR2102)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13876

Type strain

Strain Designation AR2102

Culture col. no. DSM 17143 ATCC BAA-1145 AR2102

NCBI tax ID(s) 1120956 209897

Special Collections DSMZ Literature strains

History DSMZ <- ATCC <- R. Guyoneaud, Lab. d’Ecologie Moléculaire-Microbiol., EA3525, Univ. Pau et Pays de l’Adour, France; AR2102

Links

Afifella pfennigii AR2102 is a Gram-negative, motile, rod-shaped bacterium that was isolated from benthic microbial mat in a brackish pond located on the rim of the Rangiroa atoll.

Gram-negative motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404089

ATCC BAA-1145,DSM 17143

@ref 20215

Last LPSN update 2026-05-29 08:28:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Afifellaceae

Genus Afifella

Species Afifella pfennigii

Full scientific name Afifella pfennigii (Caumette et al. 2007) Urdiain et al. 2009

Synonyms (1)

Rhodobium pfennigii

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31992	negative	01-02 µm	0.6 µm	rod-shaped
125438	negative					99.4

Pigmentation

31992

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6788	RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)		Medium recipe at MediaDive	Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: NaCl 10.0 g/l Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Resazurin 0.005 g/l Fe(III) citrate 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6788	positive	growth	28
31992	positive	growth	30-35
31992	positive	optimum	32.5

Culture pH

@ref	Ability	Type	PH	PH range
31992	positive	optimum	7.2-7.5
31992	positive	growth	6.3-8.5	alkaliphile

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.461

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31992	NaCl	positive	growth	0-5 %
31992	NaCl	positive	optimum	01-02 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31992	30089 ChEBI	acetate	+	carbon source
31992	35391 ChEBI	aspartate	+	carbon source
31992	24996 ChEBI	lactate	+	carbon source
31992	25115 ChEBI	malate	+	carbon source
31992	17272 ChEBI	propionate	+	carbon source
31992	15361 ChEBI	pyruvate	+	carbon source
31992	30031 ChEBI	succinate	+	carbon source
31992	31011 ChEBI	valerate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Tidal flat
#Host	#Microbial	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6788	benthic microbial mat in a brackish pond (R2) located on the rim of the Rangiroa atoll	Tuamotu Islands	French Polynesia	PYF	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence FR733717 (>99% sequence identity) for Afifella pfennigii from Microbeatlas

Aquatic Samples	604
Soil Samples	1125
Animal Samples	85
Plant Samples	52
Total Samples	1866

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6788	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	ASM68851v1 assembly for Afifella pfennigii DSM 17143	scaffold	GCA_000688515	1120956.3	2556921008	1120956	66.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Afifella pfennigii partial 16S rRNA gene, type strain DSM17143T	FR733717	1455		209897
6788	Rhodobium pfennigii partial 16S rRNA gene, type strain AR2102T	AJ510235	858		1120956

GC content

@ref	GC-content (mol%)	Method
6788	67.5	high performance liquid chromatography (HPLC)
31992	67.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM68851v1 assembly for Afifella pfennigii DSM 17143
NCBI: GCA_000688515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	89.21	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.81	no
125439	motility	BacteriaNetⓘ	yes	46.72	no
125439	spore_formation	BacteriaNetⓘ	no	98.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Afifella pfennigii DSM 17143 DSM 17143
NCBI: GCA_000688515.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.40	no
125438	anaerobic	anaerobicⓘ	no	86.60	no
125438	aerobic	aerobicⓘ	yes	75.42	no
125438	spore-forming	spore-formingⓘ	no	86.89	no
125438	thermophilic	thermophileⓘ	no	91.92	no
125438	flagellated	motile2+ⓘ	yes	72.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Automated orthogonal tRNA generation.	Spinck M, Guppy A, Chin JW.	Nat Chem Biol	10.1038/s41589-024-01782-3	2025
Metabolism	Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria.	LaSarre B, Kysela DT, Stein BD, Ducret A, Brun YV, McKinlay JB.	mBio	10.1128/mbio.00780-18	2018
Metabolism	Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase-tRNA pairs.	Cervettini D, Tang S, Fried SD, Willis JCW, Funke LFH, Colwell LJ, Chin JW.	Nat Biotechnol	10.1038/s41587-020-0479-2	2020
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
Phylogeny	Afifella aestuarii sp. nov., a phototrophic bacterium.	Buddhi S, G S, Gupta D, Ch S, Ch V R	Int J Syst Evol Microbiol	10.1099/ijsem.0.003756	2020
Phylogeny	Rhodobium pfennigii sp. nov., a phototrophic purple non-sulfur bacterium with unusual bacteriochlorophyll a antennae, isolated from a brackish microbial mat on Rangiroa atoll, French Polynesia.	Caumette P, Guyoneaud R, Duran R, Cravo-Laureau C, Matheron R	Int J Syst Evol Microbiol	10.1099/ijs.0.64775-0	2007

References

#6788	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17143
#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 )
#28246	IJSEM 1250 2007 ( DOI 10.1099/ijs.0.64775-0 , PubMed 17551038 )
#31992	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28246
#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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Afifella pfennigii (DSM 17143, ATCC BAA-1145, AR2102)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000688515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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