Strain identifier

BacDive ID: 133113

Type strain: Yes

Species: Pedobacter jamesrossensis

NCBI tax ID(s): 1908238 (species)

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General

@ref: 25302

BacDive-ID: 133113

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Pedobacter jamesrossensis LMG 29684 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from stone fragments.

NCBI tax id

  • NCBI tax id: 1908238
  • Matching level: species

doi: 10.13145/bacdive133113.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter jamesrossensis
  • full scientific name: Pedobacter jamesrossensis Švec et al. 2017

@ref: 25302

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter jamesrossensis

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25302negative1.0-1.2 µm0.5 µmrod-shapedno
25302negative0.9-1.4 µm0.4-0.5 µmrod-shapedno
25302negative1.0-1.3 µm0.5 µmrod-shapedno
25302negative1.2-1.6 µm0.6 µmrod-shapedno

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
253021-2 mmreddishcircular5 daysR2A agar
253021-2 mmreddishcircular5 daysR2A
253021-2 mmpinkcircular5 daysR2A

Culture and growth conditions

culture medium

@refnamegrowth
25302Reasoner's 2A agar (R2A)yes
25302nutritient agaryes
25302tryptone soy agar (TSA)yes
25302brain heart infusion agaryes
25302nutritient agar (NA)yes
25302MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
25302positivegrowth1-30
25302nogrowth35mesophilic
25302positiveoptimum20psychrophilic

culture pH

@refabilitytypepHPH range
25302positivegrowth6-10alkaliphile
25302positivegrowth6-8
25302inconsistentgrowth9
25302nogrowth10
25302positivegrowth6-9
25302inconsistentgrowth10
25302nogrowth5
25302nogrowth11
25302positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 25302
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25302
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25302NaClpositivegrowth0-1 %(w/v)
25302NaClnogrowth2 %(w/v)
25302NaClpositivegrowth0-2 %(w/v)
25302NaClpositivegrowth1-2 %(w/v)
25302NaClnogrowth3 %(w/v)
25302NaCloptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2530227856acetamide-growth
25302casein-hydrolysis
2530216947citrate-carbon source
2530216991dna-hydrolysis
253025291gelatin-hydrolysis
2530261995lecithin-hydrolysis
2530217632nitrate-reduction
2530216301nitrite-reduction
2530262983sodium malonate-growth
2530228017starch-hydrolysis
2530253426tween 80-hydrolysis
2530218186tyrosine-hydrolysis
25302casein+hydrolysis
2530216991dna+hydrolysis
253024853esculin+hydrolysis
253025291gelatin+hydrolysis
2530228017starch+hydrolysis
2530253426tween 80+hydrolysis
253024853esculin+/-hydrolysis
2530253426tween 80+/-hydrolysis

metabolite production

  • @ref: 25302
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25302
  • Chebi-ID: 16947
  • metabolite: citrate
  • citrate test: -

enzymes

@refvalueactivityec
25302alpha-galactosidase-3.2.1.22
25302cystine arylamidase+/-3.4.11.3
25302naphthol-AS-BI-phosphohydrolase+/-
25302alpha-fucosidase+/-3.2.1.51
25302cystine arylamidase+3.4.11.3
25302esterase (C 4)+/-
25302alpha-fucosidase+3.2.1.51
25302acid phosphatase+3.1.3.2
25302alkaline phosphatase+3.1.3.1
25302alpha-fucosidase-3.2.1.51
25302alpha-galactosidase+3.2.1.22
25302alpha-glucosidase+3.2.1.20
25302alpha-mannosidase+3.2.1.24
25302arginine dihydrolase-3.5.3.6
25302beta-galactosidase+3.2.1.23
25302beta-glucosidase+3.2.1.21
25302beta-glucuronidase-3.2.1.31
25302catalase+1.11.1.6
25302chymotrypsin-3.4.4.5
25302cystine arylamidase-3.4.11.3
25302cytochrome oxidase+1.9.3.1
25302esterase (C 4)-
25302esterase Lipase (C 8)+
25302leucine arylamidase+3.4.11.1
25302lipase (C 14)-
25302lysine decarboxylase-4.1.1.18
25302N-acetyl-beta-glucosaminidase+3.2.1.52
25302naphthol-AS-BI-phosphohydrolase+
25302ornithine decarboxylase-4.1.1.17
25302trypsin+3.4.21.4
25302urease-3.5.1.5
25302valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25302C11:0 anteiso1.5
    25302C15:0 anteiso7.6
    25302C17:1 anteiso ω9c1.3
    25302C15:0 2OH1.1
    25302C16:0 10-methyl / iso-C17:1ω9c2.9
    25302C16:0 3OH1.9
    25302C16:1ω5c4
    25302C16:1ω7c / C16:1ω6c34.7
    25302C17:0 2OH6.6
    25302C15:0 iso12
    25302C15:0 iso 3OH1.4
    25302C16:0 iso1.8
    25302C16:0 iso 3OH6.6
    25302C16:1 iso H1.2
    25302C17:0 iso 3OH11.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A (Oxoid)
  • agar/liquid: agar
  • incubation temperature: 20
  • incubation time: 2
  • software version: Sherlock 6.2
  • library/peak naming table: RTSBA 6.21
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 25302
  • sample type: stone fragments
  • geographic location: Devils Rocks, James Ross Island
  • country: Antarctica
  • origin.country: ATA
  • continent: Australia and Oceania
  • latitude: -63
  • longitude: -57
  • enrichment culture: R2A agar
  • enrichment culture duration: 5-7 days
  • enrichment culture temperature: 15

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25302Pedobacter sp. RP02016a strain CCM 8689 16S ribosomal RNA gene, partial sequenceKX6114671474nuccore1908238
25302Pedobacter sp. RP02016b strain CCM 8691 16S ribosomal RNA gene, partial sequenceKX6114751483nuccore1908239
25302Pedobacter sp. RP02016c strain CCM 8685 16S ribosomal RNA gene, partial sequenceKX6114771474nuccore1908240
25302Pedobacter sp. RP02016d strain CCM 8687 16S ribosomal RNA gene, partial sequenceKX6114811472nuccore1908241

GC content

@refGC-contentmethod
2530236.2high performance liquid chromatography (HPLC)
2530235.6high performance liquid chromatography (HPLC)
2530235.5high performance liquid chromatography (HPLC)
2530238.8high performance liquid chromatography (HPLC)

External links

@ref: 25302

culture collection no.: LMG 29684, CCM 8689

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27995868Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment.Svec P, Kralova S, Busse HJ, Kleinhagauer T, Pantucek R, Maslanova I, Cnockaert M, Vandamme P, Stankova E, Gelbicova T, Holochova P, Bartak M, Kyrova K, Sedlacek IInt J Syst Evol Microbiol10.1099/ijsem.0.0017492017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35819898Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0054482022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25302P. K. Svec, S.,Busse, H. J.,Kleinhagauer, T.,Pantucek, R.,Maslanová, I.,Cnockaert, M.,Vandamme, P.,Stanková, E.,Gelbícová, T.,Holochová, Pavla,Barták, M.,Kýrová, Kamila,Sedlácek, I.Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment10.1099/ijsem.0.001749IJSEM 67: 1499-1507 201727995868