Beijerinckia indica (DSM 1715, ATCC 9039, NCIB 8712)

Name: Beijerinckia indica (DSM 1715, ATCC 9039, NCIB 8712)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1665

Type strain

Culture col. no. DSM 1715 ATCC 9039 NCIB 8712

NCBI tax ID(s) 533 31994

Special Collections DSMZ

History DSMZ <- NCIB <- C.B. van Niel

Links

Beijerinckia indica DSM 1715 is a bacterium of the family Beijerinckiaceae.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1222

LMG 2817,ATCC 9039,LMG 3901,LMG 3910,NCIB 8712,NCIMB 8712,LMD 38.7,CECT 840,KCTC 12011,NCCB 38007,HAMBI 2265,CCUG 53672,DSM 1715

@ref 20215

Last LPSN update 2026-05-29 08:25:18

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Beijerinckiaceae

Genus Beijerinckia

Species Beijerinckia indica

Full scientific name Beijerinckia indica (Starkey and De 1939) Derx 1950 (Approved Lists 1980)

Synonyms (1)

"Azotobacter indicum"

BacDive ID	Other strains from **Beijerinckia indica** (2)	Type strain
1663	B. indica B.102.C, DSM 591
1664	B. indica DSM 724, ATCC 9037, IFO 3744, NBRC 3744, ...

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97
125439	negative	94.111

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
872	BEIJERINCKIA MEDIUM (DSMZ Medium 111)		Medium recipe at MediaDive	Name: BEIJERINCKIA MEDIUM (DSMZ Medium 111) Composition: Agar 15.7895 g/l Glucose 10.5263 g/l K2HPO4 0.842105 g/l KH2PO4 0.210526 g/l MgSO4 x 7 H2O 0.105263 g/l FeSO4 x 7 H2O 0.0210526 g/l ZnSO4 x 6 H2O 0.00526316 g/l Na2MoO4 x 2 H2O 0.00526316 g/l CuSO4 x 6 H2O 0.00421053 g/l MnSO4 x 6 H2O 0.00210526 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
872	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		97.257

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence AJ563930 (>99% sequence identity) for Beijerinckia from Microbeatlas

Aquatic Samples	99
Soil Samples	101
Animal Samples	14
Plant Samples	9
Total Samples	223

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
872	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	ASM1984v1 assembly for Beijerinckia indica subsp. indica ATCC 9039	complete	GCA_000019845	395963.13	641522606	395963	98.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Beijerinckia indica ribosomal RNA small subunit	M59060	1436		533
872	Beijerinckia indica subsp. indica partial 16S rRNA gene, strain ATCC 9039	AJ563930	1411		395963

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1984v1 assembly for Beijerinckia indica subsp. indica ATCC 9039
BV-BRC: 395963.13

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	50.30	no
125439	gram_stain	BacteriaNetⓘ	negative	94.11	no
125439	motility	BacteriaNetⓘ	yes	48.90	no
125439	spore_formation	BacteriaNetⓘ	no	97.26	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Beijerinckia indica subsp. indica ATCC 9039 ATCC 9039
NCBI: GCA_000019845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	89.00	no
125438	aerobic	aerobicⓘ	yes	79.90	no
125438	spore-forming	spore-formingⓘ	no	84.93	no
125438	thermophilic	thermophileⓘ	no	97.79	no
125438	flagellated	motile2+ⓘ	yes	69.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Footprint area analysis of binary imaged Cupriavidus necator cells to study PHB production at balanced, transient, and limited growth conditions in a cascade process.	Vadlja D, Koller M, Novak M, Braunegg G, Horvat P.	Appl Microbiol Biotechnol	10.1007/s00253-016-7844-6	2016
	Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.	Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A.	Front Microbiol	10.3389/fmicb.2019.02896	2019
Genetics	Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.	Dai Z, Guo X, Yin H, Liang Y, Cong J, Liu X.	PLoS One	10.1371/journal.pone.0087976	2014
Phylogeny	Complete genome sequence of Beijerinckia indica subsp. indica.	Tamas I, Dedysh SN, Liesack W, Stott MB, Alam M, Murrell JC, Dunfield PF.	J Bacteriol	10.1128/jb.00656-10	2010
	Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp.	Zervas A, Zeng Y, Madsen AM, Hansen LH.	Genome Biol Evol	10.1093/gbe/evz204	2019
	Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.	Wiech EM, Cheng HP, Singh SM.	Protein Sci	10.1002/pro.2616	2015
Enzymology	Extent and variation of phage-borne bacterial 16S rRNA gene sequences in wastewater environments.	Del Casale A, Flanagan PV, Larkin MJ, Allen CC, Kulakov LA.	Appl Environ Microbiol	10.1128/aem.00457-11	2011
Metabolism	Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil.	Wang X, Sharp CE, Jones GM, Grasby SE, Brady AL, Dunfield PF.	Appl Environ Microbiol	10.1128/aem.00055-15	2015
Metabolism	Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria.	Marassi FM.	Proteins	10.1002/prot.23151	2011
Enzymology	Isoaurostatin, a novel topoisomerase inhibitor produced by Thermomonospora alba.	Suzuki K, Yahara S, Maehata K, Uyeda M.	J Nat Prod	10.1021/np0004606	2001
	Whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens.	Zhou Y, Call DR, Broschat SL.	Pathogens	10.3390/pathogens2040627	2013
Genetics	Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil.	Salam LB.	3 Biotech	10.1007/s13205-020-02219-z	2020
	Topostatin, a novel inhibitor of topoisomerases I and II produced by Thermomonospora alba strain No. 1520. III. Inhibitory properties.	Suzuki K, Yamaizumi M, Tateishi S, Monnai Y, Uyeda M.	J Antibiot (Tokyo)	10.7164/antibiotics.52.460	1999
	Topostatin, a novel inhibitor of Topoisomerases I and II produced by Thermomonospora alba strain No. 1520. II. Physico-chemical properties and structure elucidation.	Suzuki K, Yahara S, Kido Y, Nagao K, Hatano Y, Uyeda M.	J Antibiot (Tokyo)	10.7164/antibiotics.51.999	1998
Pathogenicity	Topostatin, a novel inhibitor of topoisomerases I and II produced by Thermomonospora alba strain No. 1520. I. Taxonomy, fermentation, isolation and biological activities.	Suzuki K, Nagao K, Monnai Y, Yagi A, Uyeda M.	J Antibiot (Tokyo)	10.7164/antibiotics.51.991	1998
Metabolism	Symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation.	Ciccolella CO, Raynard NA, Mei JH, Church DC, Ludwig RA.	PLoS One	10.1371/journal.pone.0012094	2010
	An alternative path for the evolution of biological nitrogen fixation.	Boyd ES, Hamilton TL, Peters JW.	Front Microbiol	10.3389/fmicb.2011.00205	2011
Genetics	DOOR: a database for prokaryotic operons.	Mao F, Dam P, Chou J, Olman V, Xu Y.	Nucleic Acids Res	10.1093/nar/gkn757	2009
Phylogeny	A comprehensive phylogenetic analysis of copper transporting P_1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes.	Cubillas C, Miranda-Sanchez F, Gonzalez-Sanchez A, Elizalde JP, Vinuesa P, Brom S, Garcia-de Los Santos A.	Microbiologyopen	10.1002/mbo3.452	2017
	High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA.	Lau E, Iv EJ, Dillard ZW, Dague RD, Semple AL, Wentzell WL.	Microorganisms	10.3390/microorganisms3020113	2015
Phylogeny	Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.	Shulse CN, Allen EE.	PLoS One	10.1371/journal.pone.0020146	2011
	Type IVB Secretion Systems of Legionella and Other Gram-Negative Bacteria.	Nagai H, Kubori T.	Front Microbiol	10.3389/fmicb.2011.00136	2011
Phylogeny	Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales.	Heavner ME, Qiu WG, Cheng HP.	PLoS One	10.1371/journal.pone.0135655	2015
	REGEN: Ancestral Genome Reconstruction for Bacteria.	Yang K, Heath LS, Setubal JC.	Genes (Basel)	10.3390/genes3030423	2012
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
	Distribution of genes encoding nucleoid-associated protein homologs in plasmids.	Takeda T, Yun CS, Shintani M, Yamane H, Nojiri H.	Int J Evol Biol	10.4061/2011/685015	2011
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Metabolism	Novel toxin-antitoxin system composed of serine protease and AAA-ATPase homologues determines the high level of stability and incompatibility of the tumor-inducing plasmid pTiC58.	Yamamoto S, Kiyokawa K, Tanaka K, Moriguchi K, Suzuki K.	J Bacteriol	10.1128/jb.00124-09	2009
	Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.	Puri V, Goyal A, Sankaranarayanan R, Enright AJ, Vaidya T.	BMC Evol Biol	10.1186/1471-2148-11-334	2011
Genetics	An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.	Thiergart T, Landan G, Schenk M, Dagan T, Martin WF.	Genome Biol Evol	10.1093/gbe/evs018	2012
Biotechnology	Detection of Salmonella spp. in oysters by PCR.	Bej AK, Mahbubani MH, Boyce MJ, Atlas RM.	Appl Environ Microbiol	10.1128/aem.60.1.368-373.1994	1994
Metabolism	Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria.	Kamagata Y, Fulthorpe RR, Tamura K, Takami H, Forney LJ, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.63.6.2266-2272.1997	1997
Enzymology	Coffea arabica L., a new host plant for Acetobacter diazotrophicus, and isolation of other nitrogen-fixing acetobacteria.	Jimenez-Salgado T, Fuentes-Ramirez LE, Tapia-Hernandez A, Mascarua-Esparza MA, Martinez-Romero E, Caballero-Mellado J.	Appl Environ Microbiol	10.1128/aem.63.9.3676-3683.1997	1997
	Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis.	Laguerre G, van Berkum P, Amarger N, Prevost D.	Appl Environ Microbiol	10.1128/aem.63.12.4748-4758.1997	1997
Phylogeny	Phylogenetic analysis of the bacterial communities in marine sediments.	Gray JP, Herwig RP.	Appl Environ Microbiol	10.1128/aem.62.11.4049-4059.1996	1996
Phylogeny	Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol.	Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.02481-0	2003

References

#872	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1715
#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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Beijerinckia indica (DSM 1715, ATCC 9039, NCIB 8712)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000019845

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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