Employing a modified cultivation method, we studied two bacterial strains, UC10 and UC38T, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0–2 % (w/v) NaCl, at pH 4–9 and a temperature range of 4–35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to Variovorax guangxiensis GXGD002T, with 98.6 % similarity. Strains UC10 and UC38T were 98.0 % similar to V.ariovorax soli GH9-3T; 97.8 % to V.ariovorax dokdonensis DS-43T; 97.3–97.7 % to V.ariovorax ginsengisoli Gsoil 3165T; 97.7–98.0 % to V.ariovorax paradoxus IAM 12373T; 97.4–97.6 % to V.ariovorax defluvii 2C1-bT; and 97.3–97.4 % to V.ariovorax boronicumulans BAM-48T. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. DNA–DNA hybridization assays indicated 89.2–91.4 % genomic DNA similarity between strains UC10 and UC38T. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus Variovoraxwas less than the 70 %. Based on these results, strain UC38T was designated a representative of a novel species of the genus Variovorax, with the proposed name Variovorax humicola sp. nov. The type strain is UC38T (=KACC 18501T=NBRC 111520T).
BelimovA. A.,
HontzeasN.,
SafronovaV. I.,
DemchinskayaS. V.,
PiluzzaG.,
BullittaS.,
GlickB. R.2005; Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L.Czern.). Soil Biol Biochem 37:241–250[CrossRef]
BelimovA. A.,
DoddI. C.,
HontzeasN.,
TheobaldJ. C.,
SafronovaV. I.,
DaviesW. J.2009; Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling. New Phytol 181:413–423 [View Article][PubMed]
BlümelS.,
BusseH. J.,
StolzA.,
KämpferP.2001; Xenophilus azovorans gen. nov., sp. nov., a soil bacterium that is able to degrade azo dyes of the Orange II type. Int J Syst Evol Microbiol 51:1831–1837 [View Article][PubMed]
BrulandN.,
BatheS.,
WillemsA.,
SteinbüchelA.2009; Pseudorhodoferax soli gen. nov., sp. nov. and Pseudorhodoferax caeni sp. nov., two members of the class Betaproteobacteria belonging to the family Comamonadaceae
. Int J Syst Evol Microbiol 59:2702–2707 [View Article][PubMed]
CollinsM. D.,
GoodfellowM.1979; Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 41:81–95
Da CostaM. S.,
AlbuquerqueL.,
NobreM. F.,
WaitR.2011; The extraction and identification of respiratory lipoquinones of Prokaryotes and their use in taxonomy. In Methods in Microbiology, 1st edn. vol. 38 pp 197–206 Edited by
Rainey.F.,
OrenA.
Elsevier: Academic Press;
DavisD. H.,
DoudoroffM.,
StanierR. Y.,
MandelM.1969; Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol 19:375–390[CrossRef]
DingL.,
YokotaA.2004; Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol 54:2223–2230 [View Article][PubMed]
EzakiT.,
HashimotoY.,
YabuuchiE.1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229[CrossRef]
FisherP. R.,
AppletonJ.,
PembertonJ. M.1978; Isolation and characterization of the pesticide-degrading plasmid pJP1 from Alcaligenes paradoxus
. J Bacteriol 135:798–804[PubMed]
FrankJ. A.,
ReichC. I.,
SharmaS.,
WeisbaumJ. S.,
WilsonB. A.,
OlsenG. J.2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470 [View Article][PubMed]
MergaertJ.,
WebbA.,
AndersonC.,
WoutersA.,
SwingsJ.1993; Microbial degradation of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in soils. Appl Environ Microbiol 59:3233–3238[PubMed]
MesbahM.,
PremachandranU.,
WhitmanW. B.1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167[CrossRef]
MinnikinD. E.,
O’DonnellA. G.,
GoodfellowM.,
AldersonG.,
AthalyeM.,
SchaalA.,
ParlettJ. H.1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241[CrossRef]
PitcherD. G.,
SaundersN. A.,
OwenR. J.1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [View Article]
SierraG.1957; A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie Van Leeuwenhoek 23:15–22 [View Article][PubMed]
SunJ .,
MatsumotoK .,
NdukoJ. M.,
OoiT.,
TaguchiS.2014; Enzymatic characterization of a depolymerase from the isolated bacterium Variovorax sp. C34 that degrades poly (enriched lactate-co-3-hydroxybutyrate). Polym Degrad Stab 110:44–49[CrossRef]
TaliaP.,
SedeS. M.,
CamposE.,
RorigM.,
PrincipiD.,
TostoD.,
HoppH. E.,
GrassoD.,
CataldiA.2012; Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes. Res Microbiol 163:221–232 [View Article][PubMed]
ThompsonJ. D.,
GibsonT. J.,
PlewniakF.,
JeanmouginF.,
HigginsD. G.1997; The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
WayneL. G.,
BrennerD. J.,
ColwellR. R.,
GrimontP. A. D.,
KandlerO.,
KrichevskyM. I.,
MoorL. H.,
MooreW. E. C.,
MurrayR. G. E. et al.1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464[CrossRef]
WiddelF.,
KohringG.-W.,
MayerF.1983; Studies on Dissimilatory Sulfate-reducing bacteria that decompose fatty acids III. characterization of the Filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134:286–294[CrossRef]
WillemsA.,
LeyJ. D.,
GillisM.,
KerstersK.1991; NOTES: Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Evol Microbiol 41:445–450
WillemsA.,
MergaertJ.,
SwingsJ.2005; Genus X. Variovorax Willems, De Ley, Gillis and Kersters 1991a, 446VP
. In Bergey's Manual of Systematic Bacteriologyvol. 2, 2nd edn. Part C pp 732–735 Edited by
BrennerD. J.,
Krieg.N. R.,
Staley.J. T.
Springer; [CrossRef]