Novosphingobium pokkalii (DSM 28827, KCTC 42224, LMG 28916)

Name: Novosphingobium pokkalii (DSM 28827, KCTC 42224, LMG 28916)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158235

Type strain

Strain Designation L3E4

Culture col. no. DSM 28827 KCTC 42224 LMG 28916 MTCC 12357 L3E4

NCBI tax ID(s) 1770194

Special Collections DSMZ KCTC

History <- N. Ramesh Kumar, Nat. Inst. of Interdisciplinary Science and Technol., Thiruvananthapuram, Kerala, India; L3E4

Links

Novosphingobium pokkalii L3E4 is a bacterium that was isolated from rhizosphere of saline-tolerant pokkali rice.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 272355

LMG 28916,KCTC 42224

@ref 20215

Last LPSN update 2026-02-09 11:38:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Novosphingobium

Species Novosphingobium pokkalii

Full scientific name Novosphingobium pokkalii Krishnan et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.206
125439	negative	98.3

Multimedia

@ref:	64874
multimedia content:	DSM_28827.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_28827.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.7

Spore formation

@ref	Spore formation	Confidence
125438		90.638
125439		97

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64874	rhizosphere of saline-tolerant pokkali rice	Kerala	India	IND	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465285v1 assembly for Novosphingobium pokkalii KCTC 42224	scaffold	GCA_014652855	1770194.3	2996096088	1770194	62.08
124043	ASM4264882v1 assembly for Novosphingobium pokkalii KCTC 42224	scaffold	GCA_042648825			1770194	57.22
124043	ASM4268576v1 assembly for Novosphingobium pokkalii KCTC 42224	contig	GCA_042685765			1770194	34.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Novosphingobium pokkalii KCTC 42224
NCBI: GCA_014652855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.00	no
125439	motility	BacteriaNetⓘ	yes	65.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Novosphingobium pokkalii KCTC 42224
NCBI: GCA_014652855.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.21	no
125438	anaerobic	anaerobicⓘ	no	94.42	no
125438	aerobic	aerobicⓘ	yes	87.92	no
125438	spore-forming	spore-formingⓘ	no	90.64	no
125438	thermophilic	thermophileⓘ	no	97.08	no
125438	flagellated	motile2+ⓘ	yes	66.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	List of new names and new combinations previously effectively, but not validly, published.	Oren A, Garrity GM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002278	2017
Phylogeny	Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice.	Krishnan R, Menon RR, Likhitha, Busse HJ, Tanaka N, Krishnamurthi S, Rameshkumar N	Res Microbiol	10.1016/j.resmic.2016.09.001	2016

References

#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 )
#64874	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28827
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Novosphingobium pokkalii (DSM 28827, KCTC 42224, LMG 28916)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014652855

Genome-based predictions

Predictions

Literature

Literature

References

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