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{{Short description|Species of bacterium}}
{{Taxobox
{{Speciesbox
| regnum = [[Bacteria]]
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| genus = Variovorax
| phylum = [[Proteobacteria]]
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| species = paradoxus
| classis = [[Betaproteobacteria]]
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| authority = <ref name=":0" />
| ordo = [[Burkholderiales]]
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| type_strain = 13-0-1D, ATCC 17713, BCRC 17070, CCM 4467, CCRC 17070, CCUG 1777, CIP 103459, DSM 30034, DSM 66, IAM 12373, IAM 13535, ICPB 3985, IFO 15149, JCM 20526, JCM 20895, KACC 10222, KCTC 1007, KCTC 12459, LGM 1797t1, LMG 11797 t1, LMG 1797, NBRC 15149, NCIB 11964, NCIMB 11964, VKM B-1329<ref>{{cite web|url=http://www.straininfo.net/strains/22223 |title=DSM 30034 Strain Passport |publisher=StrainInfo |access-date=2013-06-01}}</ref>
| familia = [[Comamonadaceae]]
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| genus = ''[[Variovorax]]''
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| species = '''''V. paradoxus'''''
| binomial = ''Variovorax paradoxus''
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| binomial_authority = <ref name=":0" />
| synonyms =
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| type_strain = 13-0-1D, ATCC 17713, BCRC 17070, CCM 4467, CCRC 17070, CCUG 1777, CIP 103459, DSM 30034, DSM 66, IAM 12373, IAM 13535, ICPB 3985, IFO 15149, JCM 20526, JCM 20895, KACC 10222, KCTC 1007, KCTC 12459, LGM 1797t1, LMG 11797 t1, LMG 1797, NBRC 15149, NCIB 11964, NCIMB 11964, VKM B-1329<ref>{{cite web|url=http://www.straininfo.net/strains/22223 |title=DSM 30034 Strain Passport |publisher=StrainInfo |date= |accessdate=2013-06-01}}</ref>
}}
}}


'''''Variovorax paradoxus''''' is a gram negative, beta proteobacterium from the genus ''Variovorax''.<ref name=":0">{{Cite journal|last=Willems|first=A.|last2=Ley|first2=J. De|last3=Gillis|first3=M.|last4=Kersters|first4=K.|date=1991-07-01|title=NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)|url=http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-41-3-445|journal=International Journal of Systematic Bacteriology|volume=41|issue=3|pages=445–450|doi=10.1099/00207713-41-3-445}}</ref> Strains of ''V. paradoxus'' can be categorized into two groups, hydrogen oxidizers and heterotrophic strains, both of which are aerobic.<ref name=":1">{{Cite journal|last=DAVIS|first=D. H.|last2=DOUDOROFF|first2=M.|last3=STANIER|first3=R. Y.|last4=MANDEL|first4=M.|date=1969-10-01|title=Proposal to reject the genus Hydrogenomonas: Taxonomic implications|url=http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-19-4-375|journal=International Journal of Systematic Bacteriology|volume=19|issue=4|pages=375–390|doi=10.1099/00207713-19-4-375}}</ref> The genus name Vario-vorax (various-voracious; devouring a variety of substrates) and species name para-doxus (contrary-to opinion) reflects both the dichotomy of ''V. paradoxus'' metabolisms, but also its ability to utilize a wide array of organic compounds.<ref name=":0" />
'''''Variovorax paradoxus''''' is a gram negative, beta proteobacterium from the genus ''Variovorax''.<ref name=":0">{{Cite journal|last1=Willems|first1=A.|last2=Ley|first2=J. De|last3=Gillis|first3=M.|last4=Kersters|first4=K.|date=1991-07-01|title=NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)|journal=International Journal of Systematic Bacteriology|volume=41|issue=3|pages=445–450|doi=10.1099/00207713-41-3-445|doi-access=free}}</ref> Strains of ''V. paradoxus'' can be categorized into two groups, hydrogen oxidizers and heterotrophic strains, both of which are aerobic.<ref name=":1">{{Cite journal|last1=DAVIS|first1=D. H.|last2=DOUDOROFF|first2=M.|last3=STANIER|first3=R. Y.|last4=MANDEL|first4=M.|date=1969-10-01|title=Proposal to reject the genus Hydrogenomonas: Taxonomic implications|journal=International Journal of Systematic Bacteriology|volume=19|issue=4|pages=375–390|doi=10.1099/00207713-19-4-375|doi-access=free}}</ref> The genus name Vario-vorax (various-voracious; devouring a variety of substrates) and species name para-doxus (contrary-opinion) reflects both the dichotomy of ''V. paradoxus'' metabolisms, but also its ability to utilize a wide array of organic compounds.<ref name=":0" />


== Morphology and physiology ==
== Morphology and physiology ==
''V. paradoxus'' cells are curved rods in shape, with dimensions of 0.3-0.6 x 0.7-3.0&nbsp;um in size and normally occur as either single or pairs of cells. Typically, cells have 1-3 peritrichous, non-polar flagella. Colonies of ''V. paradoxus'' are yellow-green in colour, due to the production of carotenoid pigments, and often has an iridescent sheen.<ref name=":2">{{Cite journal|last=Satola|first=Barbara|last2=Wübbeler|first2=Jan Hendrik|last3=Steinbüchel|first3=Alexander|date=2012-11-29|title=Metabolic characteristics of the species Variovorax paradoxus|url=http://link.springer.com/article/10.1007/s00253-012-4585-z|journal=Applied Microbiology and Biotechnology|language=en|volume=97|issue=2|pages=541–560|doi=10.1007/s00253-012-4585-z|issn=0175-7598}}</ref> Colony shape is normally convex, round and smooth, but can also have flat, undulate margins.<ref name=":0" /> ''V. paradoxus'' grows optimally at 30oC in most growth media, including M9-glucose. On nutrient agar and M9-glucose agar, colonies take 24–48 hours to grow to a few millimetres in size.
''V. paradoxus'' cells are curved rods in shape, with dimensions of 0.3-0.6 x 0.7-3.0&nbsp;μm in size and normally occur as either single or pairs of cells. Typically, cells have 1-3 peritrichous, degenerate flagella. Colonies of ''V. paradoxus'' are yellow-green in colour, due to the production of carotenoid pigments, and often have an iridescent sheen.<ref name=":2">{{Cite journal|last1=Satola|first1=Barbara|last2=Wübbeler|first2=Jan Hendrik|last3=Steinbüchel|first3=Alexander|date=2012-11-29|title=Metabolic characteristics of the species Variovorax paradoxus|journal=Applied Microbiology and Biotechnology|language=en|volume=97|issue=2|pages=541–560|doi=10.1007/s00253-012-4585-z|issn=0175-7598|pmid=23192768|s2cid=18656264}}</ref> Colony shape is normally convex, round and smooth, but can also display flat, undulate margins.<ref name=":0" /> ''V. paradoxus'' grows optimally at 30&nbsp;°C in most growth media, including M9-glucose. On nutrient agar and M9-glucose agar, colonies take 24–48 hours to grow to a few millimetres in size.


Pantothenate is a characteristic carbon source utilized by ''V. paradoxus''. Polyhydroxyalkanoates (PHA), including poly-3-hydroxybutyrate (3-PHB), are stored intracellularly by ''V. paradoxus'' cells when carbon is abundant and other factors limit growth.<ref name=":1" /><ref name=":2" />
Pantothenate is a characteristic carbon source utilized by ''V. paradoxus;'' it was the use of this sole carbon source that lead to the isolation of the first known strain of ''V. paradoxus''.<ref name=":1" /> Polyhydroxyalkanoates (PHA), including poly-3-hydroxybutyrate (3-PHB), are stored intracellularly by ''V. paradoxus'' cells when carbon is abundant and other factors limit growth<ref name=":1" /><ref name=":2" /><ref>{{Cite journal|last1=Maskow|first1=T.|last2=Babel|first2=W.|date=2001-03-01|title=A calorimetrically based method to convert toxic compounds into poly-3-hydroxybutyrate and to determine the efficiency and velocity of conversion|journal=Applied Microbiology and Biotechnology|language=en|volume=55|issue=2|pages=234–238|doi=10.1007/s002530000546|pmid=11330720|s2cid=40578199|issn=0175-7598}}</ref>


== Genome Sequences ==
== Genome Sequences ==
Two strains of ''V. paradoxus'' have been sequenced, S110<ref name=":3">{{Cite journal|last=Han|first=Jong-In|last2=Choi|first2=Hong-Kyu|last3=Lee|first3=Seung-Won|last4=Orwin|first4=Paul M.|last5=Kim|first5=Jina|last6=LaRoe|first6=Sarah L.|last7=Kim|first7=Tae-gyu|last8=O'Neil|first8=Jennifer|last9=Leadbetter|first9=Jared R.|date=2011-03-01|title=Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110|url=http://jb.asm.org/content/193/5/1183|journal=Journal of Bacteriology|language=en|volume=193|issue=5|pages=1183–1190|doi=10.1128/JB.00925-10|issn=0021-9193|pmc=3067606|pmid=21183664}}</ref> and EPS.<ref name=":4">{{Cite journal|last=Han|first=Jong-In|last2=Spain|first2=Jim C.|last3=Leadbetter|first3=Jared R.|last4=Ovchinnikova|first4=Galina|last5=Goodwin|first5=Lynne A.|last6=Han|first6=Cliff S.|last7=Woyke|first7=Tanja|last8=Davenport|first8=Karen W.|last9=Orwin|first9=Paul M.|date=2013-10-31|title=Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS|url=http://genomea.asm.org/content/1/5/e00843-13|journal=Genome Announcements|language=en|volume=1|issue=5|pages=e00843–13|doi=10.1128/genomeA.00843-13|issn=2169-8287|pmc=3813184|pmid=24158554}}</ref> S110 was isolated from the interior of a potato plant and was identified as a degrader of AHLs. This strain has two chromosomes (5.63 and 1.13Mb), a G+C content of 67.4% and a predicted number of 6279 open reading frames (ORF).<ref name=":3" /> EPS was isolated from the rhizosphere community of the sunflower (''Helianthus annuus''), and was initially studied for its motility. It has one chromosome (6.65Mb), a G+C content of 66.48% and a total of 6008 genes identified.<ref name=":4" />
The genomes of four strains of ''V. paradoxus'' have been sequenced, S110,<ref name=":3">{{Cite journal|last1=Han|first1=Jong-In|last2=Choi|first2=Hong-Kyu|last3=Lee|first3=Seung-Won|last4=Orwin|first4=Paul M.|last5=Kim|first5=Jina|last6=LaRoe|first6=Sarah L.|last7=Kim|first7=Tae-gyu|last8=O'Neil|first8=Jennifer|last9=Leadbetter|first9=Jared R.|date=2011-03-01|title=Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110|journal=Journal of Bacteriology|language=en|volume=193|issue=5|pages=1183–1190|doi=10.1128/JB.00925-10|issn=0021-9193|pmc=3067606|pmid=21183664}}</ref> EPS,<ref name=":4">{{Cite journal|last1=Han|first1=Jong-In|last2=Spain|first2=Jim C.|last3=Leadbetter|first3=Jared R.|last4=Ovchinnikova|first4=Galina|last5=Goodwin|first5=Lynne A.|last6=Han|first6=Cliff S.|last7=Woyke|first7=Tanja|last8=Davenport|first8=Karen W.|last9=Orwin|first9=Paul M.|date=2013-10-31|title=Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS|journal=Genome Announcements|language=en|volume=1|issue=5|pages=e00843–13|doi=10.1128/genomeA.00843-13|issn=2169-8287|pmc=3813184|pmid=24158554}}</ref> B4<ref name=":12">{{Cite journal|last1=Brandt|first1=Ulrike|last2=Hiessl|first2=Sebastian|last3=Schuldes|first3=Jörg|last4=Thürmer|first4=Andrea|last5=Wübbeler|first5=Jan Hendrik|last6=Daniel|first6=Rolf|last7=Steinbüchel|first7=Alexander|date=2014-11-01|title=Genome-guided insights into the versatile metabolic capabilities of the mercaptosuccinate-utilizing β-proteobacterium Variovorax paradoxus strain B4|journal=Environmental Microbiology|language=en|volume=16|issue=11|pages=3370–3386|doi=10.1111/1462-2920.12340|pmid=24245581|issn=1462-2920}}</ref> and TBEA6.<ref name=":13">{{Cite journal|last1=Wübbeler|first1=Jan Hendrik|last2=Hiessl|first2=Sebastian|last3=Meinert|first3=Christina|last4=Poehlein|first4=Anja|last5=Schuldes|first5=Jörg|last6=Daniel|first6=Rolf|last7=Steinbüchel|first7=Alexander|date=2015-09-10|title=The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3′-thiodipropionic acid and hence the production of polythioesters|journal=Journal of Biotechnology|volume=209|pages=85–95|doi=10.1016/j.jbiotec.2015.06.390|pmid=26073999}}</ref> S110 was isolated from the interior of a potato plant and was identified as a degrader of AHLs. This strain has two chromosomes (5.63 and 1.13Mb), a G+C content of 67.4% and a predicted number of 6279 open reading frames (ORF).<ref name=":3" /> EPS was isolated from the rhizosphere community of the sunflower (''Helianthus annuus''), and was initially studied for its motility. It has one chromosome (6.65Mb), a G+C content of 66.48% and a total of 6008 genes identified.<ref name=":4" /> The genomes of B4 and TBEA6 were sequenced with specific interest to better understand the strains abilities to degrade mercaptosuccinate and 3,3 -thiodipropionic acid respectively.<ref name=":12" /><ref name=":13" />


== Occurrence ==
== Occurrence ==
Found ubiquitously, ''V. paradoxus'' has been isolated from a diverse range of environments including soil,<ref name=":5">{{Cite journal|last=Schmalenberger|first=Achim|last2=Hodge|first2=Sarah|last3=Bryant|first3=Anna|last4=Hawkesford|first4=Malcolm J.|last5=Singh|first5=Brajesh K.|last6=Kertesz|first6=Michael A.|date=2008-06-01|title=The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimes|url=http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2007.01564.x/abstract|journal=Environmental Microbiology|language=en|volume=10|issue=6|pages=1486–1500|doi=10.1111/j.1462-2920.2007.01564.x|issn=1462-2920}}</ref> the rhizosphere of numerous plant species,<ref name=":3" /><ref name=":5" /><ref>{{Cite journal|last=Belimov|first=Andrey A.|last2=Dodd|first2=Ian C.|last3=Hontzeas|first3=Nikos|last4=Theobald|first4=Julian C.|last5=Safronova|first5=Vera I.|last6=Davies|first6=William J.|date=2009-01-01|title=Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling|url=http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02657.x/abstract|journal=New Phytologist|language=en|volume=181|issue=2|pages=413–423|doi=10.1111/j.1469-8137.2008.02657.x|issn=1469-8137}}</ref> ground water, freshwater iron seeps, ferromanganese deposits in both carbonate cave systems and shale rock cliffs, deep marine sediments, silver mine spoil, gold-arsenopyrite mine drainage water and rubber tyre leachate. In particularly, ''V. paradoxus'' is abundant in numerous environments that are contaminated with either recalcitrant organic compounds or heavy metals. ''V. paradoxus'' is also commonly found in plant rhizosphere communities and is a known plant growth-promoting bacterium (PGPB). It is from these two types of environments that ''V. paradoxus'' has been most extensively studied.
Found ubiquitously, ''V. paradoxus'' has been isolated from a diverse range of environments including soil,<ref name=":5">{{Cite journal|last1=Schmalenberger|first1=Achim|last2=Hodge|first2=Sarah|last3=Bryant|first3=Anna|last4=Hawkesford|first4=Malcolm J.|last5=Singh|first5=Brajesh K.|last6=Kertesz|first6=Michael A.|date=2008-06-01|title=The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimes|journal=Environmental Microbiology|language=en|volume=10|issue=6|pages=1486–1500|doi=10.1111/j.1462-2920.2007.01564.x|issn=1462-2920|pmid=18279342|bibcode=2008EnvMi..10.1486S }}</ref><ref>{{Cite journal|last1=Kamagata|first1=Y.|last2=Fulthorpe|first2=R. R.|last3=Tamura|first3=K.|last4=Takami|first4=H.|last5=Forney|first5=L. J.|last6=Tiedje|first6=J. M.|date=1997-06-01|title=Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria.|url= |journal=Applied and Environmental Microbiology|language=en|volume=63|issue=6|pages=2266–2272|doi=10.1128/AEM.63.6.2266-2272.1997|issn=0099-2240|pmc=168519|pmid=9172346|bibcode=1997ApEnM..63.2266K }}</ref> the rhizosphere of numerous plant species,<ref name=":3" /><ref name=":5" /><ref>{{Cite journal|last1=Belimov|first1=Andrey A.|last2=Dodd|first2=Ian C.|last3=Hontzeas|first3=Nikos|last4=Theobald|first4=Julian C.|last5=Safronova|first5=Vera I.|last6=Davies|first6=William J.|date=2009-01-01|title=Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling|journal=New Phytologist|language=en|volume=181|issue=2|pages=413–423|doi=10.1111/j.1469-8137.2008.02657.x|issn=1469-8137|pmid=19121036|pmc=2688299}}</ref> drinking water,<ref>{{Cite journal|last1=Lee|first1=J.|last2=Lee|first2=C. S.|last3=Hugunin|first3=K. M.|last4=Maute|first4=C. J.|last5=Dysko|first5=R. C.|date=2010-09-01|title=Bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study|journal=Water Research|volume=44|issue=17|pages=5050–5058|doi=10.1016/j.watres.2010.07.027|issn=1879-2448|pmid=20705313|bibcode=2010WatRe..44.5050L }}</ref> ground water,<ref>{{Cite journal|last1=Gao|first1=Weimin|last2=Gentry|first2=Terry J.|last3=Mehlhorn|first3=Tonia L.|last4=Carroll|first4=Susan L.|last5=Jardine|first5=Philip M.|last6=Zhou|first6=Jizhong|date=2010-01-26|title=Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater|journal=Geomicrobiology Journal|volume=27|issue=1|pages=93–100|doi=10.1080/01490450903408112|bibcode=2010GmbJ...27...93G |s2cid=12830074|issn=0149-0451}}</ref> freshwater iron seeps,<ref>{{Cite journal|last1=Haaijer|first1=Suzanne C. M.|last2=Harhangi|first2=Harry R.|last3=Meijerink|first3=Bas B.|last4=Strous|first4=Marc|last5=Pol|first5=Arjan|last6=Smolders|first6=Alfons J. P.|last7=Verwegen|first7=Karin|last8=Jetten|first8=Mike S. M.|last9=Op den Camp|first9=Huub J. M.|date=2008-12-01|title=Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem|journal=The ISME Journal|volume=2|issue=12|pages=1231–1242|doi=10.1038/ismej.2008.75|issn=1751-7370|pmid=18754044|bibcode=2008ISMEJ...2.1231H |doi-access=free|hdl=2066/71981|hdl-access=free}}</ref> ferromanganese deposits in carbonate cave systems,<ref name=":6">{{Cite journal|last1=Northup|first1=Diana E.|last2=Barns|first2=Susan M.|last3=Yu|first3=Laura E.|last4=Spilde|first4=Michael N.|last5=Schelble|first5=Rachel T.|last6=Dano|first6=Kathleen E. |author-link7= Laura J. Crossey |last7=Crossey|first7=Laura J.|last8=Connolly|first8=Cynthia A.|last9=Boston|first9=Penelope J.|date=2003-11-01|title=Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves|journal=Environmental Microbiology|volume=5|issue=11|pages=1071–1086|issn=1462-2912|pmid=14641587|doi=10.1046/j.1462-2920.2003.00500.x|bibcode=2003EnvMi...5.1071N }}</ref> deep marine sediments,<ref name=":7">{{Cite journal|last1=Wang|first1=Yu Ping|last2=Gu|first2=Ji-Dong|date=2006-08-01|title=Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomonas yanoikuyae DOS01 isolated from deep-ocean sediments|journal=Ecotoxicology (London, England)|volume=15|issue=6|pages=549–557|doi=10.1007/s10646-006-0093-1|issn=0963-9292|pmid=16955363|bibcode=2006Ecotx..15..549W |s2cid=7797546}}</ref> silver mine spoil,<ref name=":8">{{Cite journal|last1=Piotrowska-Seget|first1=Z.|last2=Cycoń|first2=M.|last3=Kozdrój|first3=J.|date=2005-03-01|title=Metal-tolerant bacteria occurring in heavily polluted soil and mine spoil|journal=Applied Soil Ecology|volume=28|issue=3|pages=237–246|doi=10.1016/j.apsoil.2004.08.001}}</ref> gold-arsenopyrite mine drainage water,<ref>{{Cite journal|last1=Battaglia-Brunet|first1=Fabienne|last2=Itard|first2=Yann|last3=Garrido|first3=Francis|last4=Delorme|first4=Fabian|last5=Crouzet|first5=Catherine|last6=Greffié|first6=Catherine|last7=Joulian|first7=Catherine|date=2006-07-01|title=A Simple Biogeochemical Process Removing Arsenic from a Mine Drainage Water|journal=Geomicrobiology Journal|volume=23|issue=3–4|pages=201–211|doi=10.1080/01490450600724282|bibcode=2006GmbJ...23..201B |s2cid=98629098|issn=0149-0451}}</ref> rubber tyre leachate<ref>{{Cite journal|last1=Vukanti|first1=R.|last2=Crissman|first2=M.|last3=Leff|first3=L. G.|last4=Leff|first4=A. A.|date=2009-06-01|title=Bacterial communities of tyre monofill sites: growth on tyre shreds and leachate|journal=Journal of Applied Microbiology|volume=106|issue=6|pages=1957–1966|doi=10.1111/j.1365-2672.2009.04157.x|issn=1365-2672|pmid=19239530|s2cid=20532920 |doi-access=}}</ref> and surface snow.<ref>{{Cite journal|last1=Ciok|first1=Anna|last2=Dziewit|first2=Lukasz|last3=Grzesiak|first3=Jakub|last4=Budzik|first4=Karol|last5=Gorniak|first5=Dorota|last6=Zdanowski|first6=Marek K.|last7=Bartosik|first7=Dariusz|date=2016-04-01|title=Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax|journal=FEMS Microbiology Ecology|volume=92|issue=4|doi=10.1093/femsec/fiw043|issn=1574-6941|pmid=26917781|pages=fiw043|doi-access=free}}</ref> In particularly, ''V. paradoxus'' is abundant in numerous environments that are contaminated with either recalcitrant organic compounds or heavy metals. ''V. paradoxus'' is also commonly found in plant rhizosphere communities and is a known plant growth-promoting bacterium (PGPB). It is from these two types of environments that ''V. paradoxus'' has been most extensively studied.<ref name=":2" />


== Role in the environment ==
== Role in the environment ==
''V. paradoxus''’s diverse metabolic capabilities enable it to degrade a wide array of recalcitrant organic pollutants including 2,4-dinitrotoluene, aliphatic polycarbonates and polychlorinated biphenyls. Both its catabolic and anabolic capabilities have been suggested for biotechnological use, such as to neutralise or degrade pollutants at contaminated sites.
''V. paradoxus''’s diverse metabolic capabilities enable it to degrade a wide array of recalcitrant organic pollutants including 2,4-dinitrotoluene, aliphatic polycarbonates and polychlorinated biphenyls. Both its catabolic and anabolic capabilities have been suggested for biotechnological use, such as to neutralise or degrade pollutants at contaminated sites.<ref name=":2" />


The role of ''V. paradoxus'' in the plant root rhizosphere and surrounding soil has been investigated in several plant species, with implicated growth promoting mechanisms including reducing plant stress, increasing nutrient availability and inhibiting growth of plant pathogens; many of these mechanisms relate to the species catabolic capabilities. In the rhizosphere of pea plants (''Pisum sativum''), ''V. paradoxus'' was shown to increase both growth and yield by degrading the ethylene precursor molecule 1-aminocyclopropane-1-carboxylate (ACC), using a secreted ACC deaminase. Strains of ''V. paradoxus'' have also been identified that can degrade N-acyl homoserine-lactones (AHL), microbial signalling molecules involved in quorum sensing. It is hypothesized that this ability could provide a host plant protection from pathogenic infection, with the impact of quorum quenching to reduce virulence in pathogenic strains present.
The role of ''V. paradoxus'' in the plant root rhizosphere and surrounding soil has been investigated in several plant species, with implicated growth promoting mechanisms including reducing plant stress, increasing nutrient availability and inhibiting growth of plant pathogens; many of these mechanisms relate to the species catabolic capabilities.<ref name=":3" /> In the rhizosphere of pea plants (''Pisum sativum''), ''V. paradoxus'' was shown to increase both growth and yield by degrading the ethylene precursor molecule 1-aminocyclopropane-1-carboxylate (ACC), using a secreted ACC deaminase.<ref>{{Cite journal|last1=Belimov|first1=Andrey A.|last2=Dodd|first2=Ian C.|last3=Hontzeas|first3=Nikos|last4=Theobald|first4=Julian C.|last5=Safronova|first5=Vera I.|last6=Davies|first6=William J.|date=2009-01-01|title=Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling|journal=The New Phytologist|volume=181|issue=2|pages=413–423|doi=10.1111/j.1469-8137.2008.02657.x|issn=1469-8137|pmid=19121036|pmc=2688299}}</ref> Strains of ''V. paradoxus'' have also been identified that can degrade N-acyl homoserine-lactones (AHL), microbial signalling molecules involved in quorum sensing.<ref>{{Cite journal|last1=Leadbetter|first1=Jared R.|last2=Greenberg|first2=E. P.|date=2000-12-15|title=Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus|journal=Journal of Bacteriology|language=en|volume=182|issue=24|pages=6921–6926|doi=10.1128/JB.182.24.6921-6926.2000|issn=0021-9193|pmid=11092851|pmc=94816}}</ref> It is hypothesized that this ability could provide a host plant protection from pathogenic infection, with the impact of quorum quenching to reduce virulence in pathogenic strains present.<ref>{{Cite journal|last1=Chen|first1=Fang|last2=Gao|first2=Yuxin|last3=Chen|first3=Xiaoyi|last4=Yu|first4=Zhimin|last5=Li|first5=Xianzhen|date=2013-08-26|title=Quorum Quenching Enzymes and Their Application in Degrading Signal Molecules to Block Quorum Sensing-Dependent Infection|journal=International Journal of Molecular Sciences|volume=14|issue=9|pages=17477–17500|doi=10.3390/ijms140917477|issn=1422-0067|pmc=3794736|pmid=24065091|doi-access=free}}</ref>


''V. paradoxus'' is involved in cycling numerous inorganic elements including arsenic,<ref name=":9">{{Cite journal|last1=Macur|first1=Richard E.|last2=Jackson|first2=Colin R.|last3=Botero|first3=Lina M.|last4=Mcdermott|first4=Timothy R.|last5=Inskeep|first5=William P.|date=2003-11-27|title=Bacterial Populations Associated with the Oxidation and Reduction of Arsenic in an Unsaturated Soil|journal=Environmental Science & Technology|language=en|volume=38|issue=1|pages=104–111|doi=10.1021/es034455a|pmid=14740724|bibcode=2004EnST...38..104M}}</ref><ref>{{Cite journal|last1=Bahar|first1=Md Mezbaul|last2=Megharaj|first2=Mallavarapu|last3=Naidu|first3=Ravi|date=2013-11-15|title=Kinetics of arsenite oxidation by Variovorax sp. MM-1 isolated from a soil and identification of arsenite oxidase gene|journal=Journal of Hazardous Materials|volume=262|pages=997–1003|doi=10.1016/j.jhazmat.2012.11.064|pmid=23290483}}</ref> sulfur,<ref name=":5" /> manganese<ref>{{Cite journal|last1=Yang|first1=Weihong|last2=Zhang|first2=Zhen|last3=Zhang|first3=Zhongming|last4=Chen|first4=Hong|last5=Liu|first5=Jin|last6=Ali|first6=Muhammad|last7=Liu|first7=Fan|last8=Li|first8=Lin|title=Population Structure of Manganese-Oxidizing Bacteria in Stratified Soils and Properties of Manganese Oxide Aggregates under Manganese–Complex Medium Enrichment|journal=PLOS ONE|volume=8|issue=9|doi=10.1371/journal.pone.0073778|pmc=3772008|pmid=24069232|pages=e73778|year=2013|bibcode=2013PLoSO...873778Y|doi-access=free}}</ref><ref>{{Cite journal|last1=Nogueira|first1=M. A.|last2=Nehls|first2=U.|last3=Hampp|first3=R.|last4=Poralla|first4=K.|last5=Cardoso|first5=E. J. B. N.|date=2007-08-28|title=Mycorrhiza and soil bacteria influence extractable iron and manganese in soil and uptake by soybean|journal=Plant and Soil|language=en|volume=298|issue=1–2|pages=273–284|doi=10.1007/s11104-007-9379-1|bibcode=2007PlSoi.298..273N |s2cid=43420007|issn=0032-079X}}</ref> and rare earth elements<ref>{{Cite journal|last1=Kamijo|first1=Manjiroh|last2=Suzuki|first2=Tohru|last3=Kawai|first3=Keiichi|last4=Murase|first4=Hironobu|date=1998-01-01|title=Accumulation of yttrium by Variovorax paradoxus|journal=Journal of Fermentation and Bioengineering|volume=86|issue=6|pages=564–568|doi=10.1016/S0922-338X(99)80007-5}}</ref> in a range of soil, freshwater and geological environments. In the case of arsenic, ''V. paradoxus'' is believed to oxidize As (III) to As (V) as a detoxification mechanism.<ref name=":9" /> ''V. paradoxus'' has been found in a range of rocky environments including carbonate caves, mine spoil and deep marine sediments, but the role of this organism within these environments is largely unstudied.<ref name=":6" /><ref name=":7" /><ref name=":8" /> The species is also tolerant of a large number of heavy metals including cadmium,<ref>{{Cite journal|last1=Belimov|first1=A. A.|last2=Hontzeas|first2=N.|last3=Safronova|first3=V. I.|last4=Demchinskaya|first4=S. V.|last5=Piluzza|first5=G.|last6=Bullitta|first6=S.|last7=Glick|first7=B. R.|date=2005-02-01|title=Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.)|journal=Soil Biology and Biochemistry|volume=37|issue=2|pages=241–250|doi=10.1016/j.soilbio.2004.07.033}}</ref> chromium, cobalt, copper, lead, mercury, nickel, silver,<ref name=":8" /> zinc<ref>{{Cite journal|last1=Malkoc|first1=Semra|last2=Kaynak|first2=Elif|last3=Guven|first3=Kıymet|date=2015-07-27|title=Biosorption of zinc(II) on dead and living biomass of Variovorax paradoxus and Arthrobacter viscosus|journal=Desalination and Water Treatment|volume=57|issue=33|pages=15445–15454|doi=10.1080/19443994.2015.1073181|issn=1944-3994|doi-access=free}}</ref> at mM concentrations.<ref>{{Cite journal|last1=Abou-Shanab|first1=R. a. I.|last2=van Berkum|first2=P.|last3=Angle|first3=J. S.|date=2007-06-01|title=Heavy metal resistance and genotypic analysis of metal resistance genes in gram-positive and gram-negative bacteria present in Ni-rich serpentine soil and in the rhizosphere of Alyssum murale|journal=Chemosphere|volume=68|issue=2|pages=360–367|doi=10.1016/j.chemosphere.2006.12.051|issn=0045-6535|pmid=17276484|bibcode=2007Chmsp..68..360A}}</ref> Despite this, very little is known about the physiological adaptions ''V. paradoxus'' uses to support this tolerance. The sequenced genome of the endophytic strain ''V. paradoxus'' S110 provides some clues to the organism's metal tolerance by identifying key molecular machinery in processing metals such as the arsenic reductase complex ArsRBC, metal transporting P1-type ATPases and a chemiosmotic antiporter efflux system similar to CzcCBA of ''Cupriavidus metallidurans''.<ref name=":3" /> ''Cupriavidus'' species, including ''C. metallidurans'', are well characterised in the field of microbe-metal interactions, and are found within the same order (Burkholderiales) as ''V. paradoxus''. Both the species ''C. necator and C. metallidurans'' (when not distinguished as separate species) were originally classified in the genera ''Alcaligenes'' along with ''V. paradoxus'' (''Alcaligenes eutrophus'' and ''Alicaligenes paradoxus'').<ref name=":1" /><ref>{{Cite journal|last1=Vandamme|first1=Peter|last2=Coenye|first2=Tom|date=2004-11-01|title=Taxonomy of the genus Cupriavidus: a tale of lost and found|journal=International Journal of Systematic and Evolutionary Microbiology|volume=54|issue=Pt 6|pages=2285–2289|doi=10.1099/ijs.0.63247-0|issn=1466-5026|pmid=15545472|doi-access=free}}</ref> This relationship with other heavy metal resistant species may help to partially explain the evolutionary history of ''V. paradoxus''<nowiki/>'s metal tolerance.
''V. paradoxus'' is involved in cycling numerous inorganic elements including arsenic, sulfur, manganese and rare earth elements in a range of soil, freshwater and geological environments. In the case of arsenic, ''V. paradoxus'' is believed to oxidize As (III) to As (V) as a detoxification mechanism. ''V. paradoxus'' has been found in a range of rocky environments including carbonate caves, shale rock, mine spoil and deep marine sediments, but the role of this organism within these environments is largely unstudied.
The species is also tolerant of a large number of heavy metals including cadmium, chromium, cobalt, copper, lead, mercury, nickel, silver, zinc at mM concentrations. Despite this, very little is known about the physiological adaptions ''V. paradoxus'' uses to support this tolerance. The sequenced genome of the endophytic strain ''V. paradoxus'' S110 provides some clues to the organism’s metal tolerance by identifying key molecular machinery in processing metals such as the arsenic reductase complex ArsRBC, metal transporting P1-type ATPases and a chemiosmotic antiporter efflux system similar to CzcCBA of ''Cupriavidus metallidurans''. ''Cupriavidus'' species, including ''C. metallidurans'', are well characterised in the field of microbe-metal interactions, and are found within the same order (Burkholderiales) as ''V. paradoxus''. The species ''Cupriavidus necator'' (''eutrophus'') was actually originally classified in the genera ''Alcaligenes'' along with ''V. paradoxus'' (''Alcaligenes eutrophus'' and ''Alicaligenes paradoxus'').


== Motility and biofilm formation ==
== Motility and biofilm formation ==
[[File:Coordinated-surface-activities-in-Variovorax-paradoxus-EPS-1471-2180-9-124-S1.ogv|thumb|''Variovorax paradoxus'' EPS swarming time-lapse video, swarming on FW-succinate-NH4Cl medium, taken 18 h after inoculation, 2 h time lapse, 3 m between frames.<ref name=":10"/>]]
The ''V. paradoxus'' strain EPS has been shown capable of swarming motility and biofilm formation. Jamieson ''et al.'' demonstrate that altering the carbon and nitrogen sources provided in the swarming agar causes variation in both swarm colony size and morphology. Mutagenesis studies have revealed that the swarming capability of ''V. paradoxus'' is largely dependent on a gene involved surfactant production, a type IV pili component and the ''ShkRS'' two component system. The ability of the organism to swim through agar has also been investigated. Dense biofilms of ''V. paradoxus'' can be grown in M9 medium with carbon sources including d-sorbitol, glucose, malic acid, mannitol and sucrose and casamino acids. Production of exopolysaccharide was hypothesized to be a controlling factor in biofilm formation. ''V. paradoxus'' biofilms take on a honeycomb morphology, as identified in many other species of biofilm forming bacteria.
The ''V. paradoxus'' strain EPS has been shown capable of swarming motility and [[biofilm]] formation.<ref name=":10">{{Cite journal|last1=Jamieson|first1=W David|last2=Pehl|first2=Michael J|last3=Gregory|first3=Glenn A|last4=Orwin|first4=Paul M|date=2009-06-12|title=Coordinated surface activities in Variovorax paradoxus EPS|journal=BMC Microbiology|language=En|volume=9|issue=1|doi=10.1186/1471-2180-9-124|pmc=2704215|pmid=19523213|pages=124 |doi-access=free }}</ref><ref name=":11">{{Cite journal|last1=Pehl|first1=Michael J.|last2=Jamieson|first2=William David|last3=Kong|first3=Karen|last4=Forbester|first4=Jessica L.|last5=Fredendall|first5=Richard J.|last6=Gregory|first6=Glenn A.|last7=McFarland|first7=Jacob E.|last8=Healy|first8=Jessica M.|last9=Orwin|first9=Paul M.|title=Genes That Influence Swarming Motility and Biofilm Formation in Variovorax paradoxus EPS|journal=PLOS ONE|volume=7|issue=2|doi=10.1371/journal.pone.0031832|pmc=3283707|pmid=22363744|pages=e31832|year=2012|bibcode=2012PLoSO...731832P|doi-access=free}}</ref> Jamieson ''et al.'' demonstrate that altering the carbon and nitrogen sources provided in the swarming agar causes variation in both swarm colony size and morphology.<ref name=":10" /> Mutagenesis studies have revealed that the swarming capability of ''V. paradoxus'' is largely dependent on a gene involved surfactant production, a type IV pili component and the ''ShkRS'' two component system.<ref name=":11" /> Dense biofilms of ''V. paradoxus'' can be grown in M9 medium with carbon sources including d-sorbitol, glucose, malic acid, mannitol and sucrose and casamino acids. Production of exopolysaccharide was hypothesized to be a controlling factor in biofilm formation. ''V. paradoxus'' biofilms take on a honeycomb morphology, as identified in many other species of biofilm forming bacteria.<ref name=":10" />


==References==
==References==
{{Reflist}}
{{Reflist}}

==External links==
*[http://bacdive.dsmz.de/index.php?search=3008&submit=Search Type strain of ''Variovorax paradoxus'' at Bac''Dive'' - the Bacterial Diversity Metadatabase]

{{Taxonbar|from=Q16993380}}


{{DEFAULTSORT:Variovorax paradoxus}}
{{DEFAULTSORT:Variovorax paradoxus}}
[[Category:Burkholderiales]]
[[Category:Comamonadaceae]]
[[Category:Bacteria described in 1991]]
[[Category:Bacteria described in 1991]]

Latest revision as of 22:24, 6 November 2024

Variovorax paradoxus
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Betaproteobacteria
Order: Burkholderiales
Family: Comamonadaceae
Genus: Variovorax
Species:
V. paradoxus
Binomial name
Variovorax paradoxus
Type strain
13-0-1D, ATCC 17713, BCRC 17070, CCM 4467, CCRC 17070, CCUG 1777, CIP 103459, DSM 30034, DSM 66, IAM 12373, IAM 13535, ICPB 3985, IFO 15149, JCM 20526, JCM 20895, KACC 10222, KCTC 1007, KCTC 12459, LGM 1797t1, LMG 11797 t1, LMG 1797, NBRC 15149, NCIB 11964, NCIMB 11964, VKM B-1329[2]

Variovorax paradoxus is a gram negative, beta proteobacterium from the genus Variovorax.[1] Strains of V. paradoxus can be categorized into two groups, hydrogen oxidizers and heterotrophic strains, both of which are aerobic.[3] The genus name Vario-vorax (various-voracious; devouring a variety of substrates) and species name para-doxus (contrary-opinion) reflects both the dichotomy of V. paradoxus metabolisms, but also its ability to utilize a wide array of organic compounds.[1]

Morphology and physiology

[edit]

V. paradoxus cells are curved rods in shape, with dimensions of 0.3-0.6 x 0.7-3.0 μm in size and normally occur as either single or pairs of cells. Typically, cells have 1-3 peritrichous, degenerate flagella. Colonies of V. paradoxus are yellow-green in colour, due to the production of carotenoid pigments, and often have an iridescent sheen.[4] Colony shape is normally convex, round and smooth, but can also display flat, undulate margins.[1] V. paradoxus grows optimally at 30 °C in most growth media, including M9-glucose. On nutrient agar and M9-glucose agar, colonies take 24–48 hours to grow to a few millimetres in size.

Pantothenate is a characteristic carbon source utilized by V. paradoxus; it was the use of this sole carbon source that lead to the isolation of the first known strain of V. paradoxus.[3] Polyhydroxyalkanoates (PHA), including poly-3-hydroxybutyrate (3-PHB), are stored intracellularly by V. paradoxus cells when carbon is abundant and other factors limit growth[3][4][5]

Genome Sequences

[edit]

The genomes of four strains of V. paradoxus have been sequenced, S110,[6] EPS,[7] B4[8] and TBEA6.[9] S110 was isolated from the interior of a potato plant and was identified as a degrader of AHLs. This strain has two chromosomes (5.63 and 1.13Mb), a G+C content of 67.4% and a predicted number of 6279 open reading frames (ORF).[6] EPS was isolated from the rhizosphere community of the sunflower (Helianthus annuus), and was initially studied for its motility. It has one chromosome (6.65Mb), a G+C content of 66.48% and a total of 6008 genes identified.[7] The genomes of B4 and TBEA6 were sequenced with specific interest to better understand the strains abilities to degrade mercaptosuccinate and 3,3 -thiodipropionic acid respectively.[8][9]

Occurrence

[edit]

Found ubiquitously, V. paradoxus has been isolated from a diverse range of environments including soil,[10][11] the rhizosphere of numerous plant species,[6][10][12] drinking water,[13] ground water,[14] freshwater iron seeps,[15] ferromanganese deposits in carbonate cave systems,[16] deep marine sediments,[17] silver mine spoil,[18] gold-arsenopyrite mine drainage water,[19] rubber tyre leachate[20] and surface snow.[21] In particularly, V. paradoxus is abundant in numerous environments that are contaminated with either recalcitrant organic compounds or heavy metals. V. paradoxus is also commonly found in plant rhizosphere communities and is a known plant growth-promoting bacterium (PGPB). It is from these two types of environments that V. paradoxus has been most extensively studied.[4]

Role in the environment

[edit]

V. paradoxus’s diverse metabolic capabilities enable it to degrade a wide array of recalcitrant organic pollutants including 2,4-dinitrotoluene, aliphatic polycarbonates and polychlorinated biphenyls. Both its catabolic and anabolic capabilities have been suggested for biotechnological use, such as to neutralise or degrade pollutants at contaminated sites.[4]

The role of V. paradoxus in the plant root rhizosphere and surrounding soil has been investigated in several plant species, with implicated growth promoting mechanisms including reducing plant stress, increasing nutrient availability and inhibiting growth of plant pathogens; many of these mechanisms relate to the species catabolic capabilities.[6] In the rhizosphere of pea plants (Pisum sativum), V. paradoxus was shown to increase both growth and yield by degrading the ethylene precursor molecule 1-aminocyclopropane-1-carboxylate (ACC), using a secreted ACC deaminase.[22] Strains of V. paradoxus have also been identified that can degrade N-acyl homoserine-lactones (AHL), microbial signalling molecules involved in quorum sensing.[23] It is hypothesized that this ability could provide a host plant protection from pathogenic infection, with the impact of quorum quenching to reduce virulence in pathogenic strains present.[24]

V. paradoxus is involved in cycling numerous inorganic elements including arsenic,[25][26] sulfur,[10] manganese[27][28] and rare earth elements[29] in a range of soil, freshwater and geological environments. In the case of arsenic, V. paradoxus is believed to oxidize As (III) to As (V) as a detoxification mechanism.[25] V. paradoxus has been found in a range of rocky environments including carbonate caves, mine spoil and deep marine sediments, but the role of this organism within these environments is largely unstudied.[16][17][18] The species is also tolerant of a large number of heavy metals including cadmium,[30] chromium, cobalt, copper, lead, mercury, nickel, silver,[18] zinc[31] at mM concentrations.[32] Despite this, very little is known about the physiological adaptions V. paradoxus uses to support this tolerance. The sequenced genome of the endophytic strain V. paradoxus S110 provides some clues to the organism's metal tolerance by identifying key molecular machinery in processing metals such as the arsenic reductase complex ArsRBC, metal transporting P1-type ATPases and a chemiosmotic antiporter efflux system similar to CzcCBA of Cupriavidus metallidurans.[6] Cupriavidus species, including C. metallidurans, are well characterised in the field of microbe-metal interactions, and are found within the same order (Burkholderiales) as V. paradoxus. Both the species C. necator and C. metallidurans (when not distinguished as separate species) were originally classified in the genera Alcaligenes along with V. paradoxus (Alcaligenes eutrophus and Alicaligenes paradoxus).[3][33] This relationship with other heavy metal resistant species may help to partially explain the evolutionary history of V. paradoxus's metal tolerance.

Motility and biofilm formation

[edit]
Variovorax paradoxus EPS swarming time-lapse video, swarming on FW-succinate-NH4Cl medium, taken 18 h after inoculation, 2 h time lapse, 3 m between frames.[34]

The V. paradoxus strain EPS has been shown capable of swarming motility and biofilm formation.[34][35] Jamieson et al. demonstrate that altering the carbon and nitrogen sources provided in the swarming agar causes variation in both swarm colony size and morphology.[34] Mutagenesis studies have revealed that the swarming capability of V. paradoxus is largely dependent on a gene involved surfactant production, a type IV pili component and the ShkRS two component system.[35] Dense biofilms of V. paradoxus can be grown in M9 medium with carbon sources including d-sorbitol, glucose, malic acid, mannitol and sucrose and casamino acids. Production of exopolysaccharide was hypothesized to be a controlling factor in biofilm formation. V. paradoxus biofilms take on a honeycomb morphology, as identified in many other species of biofilm forming bacteria.[34]

References

[edit]
  1. ^ a b c d Willems, A.; Ley, J. De; Gillis, M.; Kersters, K. (1991-07-01). "NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)". International Journal of Systematic Bacteriology. 41 (3): 445–450. doi:10.1099/00207713-41-3-445.
  2. ^ "DSM 30034 Strain Passport". StrainInfo. Retrieved 2013-06-01.
  3. ^ a b c d DAVIS, D. H.; DOUDOROFF, M.; STANIER, R. Y.; MANDEL, M. (1969-10-01). "Proposal to reject the genus Hydrogenomonas: Taxonomic implications". International Journal of Systematic Bacteriology. 19 (4): 375–390. doi:10.1099/00207713-19-4-375.
  4. ^ a b c d Satola, Barbara; Wübbeler, Jan Hendrik; Steinbüchel, Alexander (2012-11-29). "Metabolic characteristics of the species Variovorax paradoxus". Applied Microbiology and Biotechnology. 97 (2): 541–560. doi:10.1007/s00253-012-4585-z. ISSN 0175-7598. PMID 23192768. S2CID 18656264.
  5. ^ Maskow, T.; Babel, W. (2001-03-01). "A calorimetrically based method to convert toxic compounds into poly-3-hydroxybutyrate and to determine the efficiency and velocity of conversion". Applied Microbiology and Biotechnology. 55 (2): 234–238. doi:10.1007/s002530000546. ISSN 0175-7598. PMID 11330720. S2CID 40578199.
  6. ^ a b c d e Han, Jong-In; Choi, Hong-Kyu; Lee, Seung-Won; Orwin, Paul M.; Kim, Jina; LaRoe, Sarah L.; Kim, Tae-gyu; O'Neil, Jennifer; Leadbetter, Jared R. (2011-03-01). "Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110". Journal of Bacteriology. 193 (5): 1183–1190. doi:10.1128/JB.00925-10. ISSN 0021-9193. PMC 3067606. PMID 21183664.
  7. ^ a b Han, Jong-In; Spain, Jim C.; Leadbetter, Jared R.; Ovchinnikova, Galina; Goodwin, Lynne A.; Han, Cliff S.; Woyke, Tanja; Davenport, Karen W.; Orwin, Paul M. (2013-10-31). "Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS". Genome Announcements. 1 (5): e00843–13. doi:10.1128/genomeA.00843-13. ISSN 2169-8287. PMC 3813184. PMID 24158554.
  8. ^ a b Brandt, Ulrike; Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Wübbeler, Jan Hendrik; Daniel, Rolf; Steinbüchel, Alexander (2014-11-01). "Genome-guided insights into the versatile metabolic capabilities of the mercaptosuccinate-utilizing β-proteobacterium Variovorax paradoxus strain B4". Environmental Microbiology. 16 (11): 3370–3386. doi:10.1111/1462-2920.12340. ISSN 1462-2920. PMID 24245581.
  9. ^ a b Wübbeler, Jan Hendrik; Hiessl, Sebastian; Meinert, Christina; Poehlein, Anja; Schuldes, Jörg; Daniel, Rolf; Steinbüchel, Alexander (2015-09-10). "The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3′-thiodipropionic acid and hence the production of polythioesters". Journal of Biotechnology. 209: 85–95. doi:10.1016/j.jbiotec.2015.06.390. PMID 26073999.
  10. ^ a b c Schmalenberger, Achim; Hodge, Sarah; Bryant, Anna; Hawkesford, Malcolm J.; Singh, Brajesh K.; Kertesz, Michael A. (2008-06-01). "The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimes". Environmental Microbiology. 10 (6): 1486–1500. Bibcode:2008EnvMi..10.1486S. doi:10.1111/j.1462-2920.2007.01564.x. ISSN 1462-2920. PMID 18279342.
  11. ^ Kamagata, Y.; Fulthorpe, R. R.; Tamura, K.; Takami, H.; Forney, L. J.; Tiedje, J. M. (1997-06-01). "Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria". Applied and Environmental Microbiology. 63 (6): 2266–2272. Bibcode:1997ApEnM..63.2266K. doi:10.1128/AEM.63.6.2266-2272.1997. ISSN 0099-2240. PMC 168519. PMID 9172346.
  12. ^ Belimov, Andrey A.; Dodd, Ian C.; Hontzeas, Nikos; Theobald, Julian C.; Safronova, Vera I.; Davies, William J. (2009-01-01). "Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling". New Phytologist. 181 (2): 413–423. doi:10.1111/j.1469-8137.2008.02657.x. ISSN 1469-8137. PMC 2688299. PMID 19121036.
  13. ^ Lee, J.; Lee, C. S.; Hugunin, K. M.; Maute, C. J.; Dysko, R. C. (2010-09-01). "Bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study". Water Research. 44 (17): 5050–5058. Bibcode:2010WatRe..44.5050L. doi:10.1016/j.watres.2010.07.027. ISSN 1879-2448. PMID 20705313.
  14. ^ Gao, Weimin; Gentry, Terry J.; Mehlhorn, Tonia L.; Carroll, Susan L.; Jardine, Philip M.; Zhou, Jizhong (2010-01-26). "Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater". Geomicrobiology Journal. 27 (1): 93–100. Bibcode:2010GmbJ...27...93G. doi:10.1080/01490450903408112. ISSN 0149-0451. S2CID 12830074.
  15. ^ Haaijer, Suzanne C. M.; Harhangi, Harry R.; Meijerink, Bas B.; Strous, Marc; Pol, Arjan; Smolders, Alfons J. P.; Verwegen, Karin; Jetten, Mike S. M.; Op den Camp, Huub J. M. (2008-12-01). "Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem". The ISME Journal. 2 (12): 1231–1242. Bibcode:2008ISMEJ...2.1231H. doi:10.1038/ismej.2008.75. hdl:2066/71981. ISSN 1751-7370. PMID 18754044.
  16. ^ a b Northup, Diana E.; Barns, Susan M.; Yu, Laura E.; Spilde, Michael N.; Schelble, Rachel T.; Dano, Kathleen E.; Crossey, Laura J.; Connolly, Cynthia A.; Boston, Penelope J. (2003-11-01). "Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves". Environmental Microbiology. 5 (11): 1071–1086. Bibcode:2003EnvMi...5.1071N. doi:10.1046/j.1462-2920.2003.00500.x. ISSN 1462-2912. PMID 14641587.
  17. ^ a b Wang, Yu Ping; Gu, Ji-Dong (2006-08-01). "Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomonas yanoikuyae DOS01 isolated from deep-ocean sediments". Ecotoxicology (London, England). 15 (6): 549–557. Bibcode:2006Ecotx..15..549W. doi:10.1007/s10646-006-0093-1. ISSN 0963-9292. PMID 16955363. S2CID 7797546.
  18. ^ a b c Piotrowska-Seget, Z.; Cycoń, M.; Kozdrój, J. (2005-03-01). "Metal-tolerant bacteria occurring in heavily polluted soil and mine spoil". Applied Soil Ecology. 28 (3): 237–246. doi:10.1016/j.apsoil.2004.08.001.
  19. ^ Battaglia-Brunet, Fabienne; Itard, Yann; Garrido, Francis; Delorme, Fabian; Crouzet, Catherine; Greffié, Catherine; Joulian, Catherine (2006-07-01). "A Simple Biogeochemical Process Removing Arsenic from a Mine Drainage Water". Geomicrobiology Journal. 23 (3–4): 201–211. Bibcode:2006GmbJ...23..201B. doi:10.1080/01490450600724282. ISSN 0149-0451. S2CID 98629098.
  20. ^ Vukanti, R.; Crissman, M.; Leff, L. G.; Leff, A. A. (2009-06-01). "Bacterial communities of tyre monofill sites: growth on tyre shreds and leachate". Journal of Applied Microbiology. 106 (6): 1957–1966. doi:10.1111/j.1365-2672.2009.04157.x. ISSN 1365-2672. PMID 19239530. S2CID 20532920.
  21. ^ Ciok, Anna; Dziewit, Lukasz; Grzesiak, Jakub; Budzik, Karol; Gorniak, Dorota; Zdanowski, Marek K.; Bartosik, Dariusz (2016-04-01). "Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax". FEMS Microbiology Ecology. 92 (4): fiw043. doi:10.1093/femsec/fiw043. ISSN 1574-6941. PMID 26917781.
  22. ^ Belimov, Andrey A.; Dodd, Ian C.; Hontzeas, Nikos; Theobald, Julian C.; Safronova, Vera I.; Davies, William J. (2009-01-01). "Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling". The New Phytologist. 181 (2): 413–423. doi:10.1111/j.1469-8137.2008.02657.x. ISSN 1469-8137. PMC 2688299. PMID 19121036.
  23. ^ Leadbetter, Jared R.; Greenberg, E. P. (2000-12-15). "Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus". Journal of Bacteriology. 182 (24): 6921–6926. doi:10.1128/JB.182.24.6921-6926.2000. ISSN 0021-9193. PMC 94816. PMID 11092851.
  24. ^ Chen, Fang; Gao, Yuxin; Chen, Xiaoyi; Yu, Zhimin; Li, Xianzhen (2013-08-26). "Quorum Quenching Enzymes and Their Application in Degrading Signal Molecules to Block Quorum Sensing-Dependent Infection". International Journal of Molecular Sciences. 14 (9): 17477–17500. doi:10.3390/ijms140917477. ISSN 1422-0067. PMC 3794736. PMID 24065091.
  25. ^ a b Macur, Richard E.; Jackson, Colin R.; Botero, Lina M.; Mcdermott, Timothy R.; Inskeep, William P. (2003-11-27). "Bacterial Populations Associated with the Oxidation and Reduction of Arsenic in an Unsaturated Soil". Environmental Science & Technology. 38 (1): 104–111. Bibcode:2004EnST...38..104M. doi:10.1021/es034455a. PMID 14740724.
  26. ^ Bahar, Md Mezbaul; Megharaj, Mallavarapu; Naidu, Ravi (2013-11-15). "Kinetics of arsenite oxidation by Variovorax sp. MM-1 isolated from a soil and identification of arsenite oxidase gene". Journal of Hazardous Materials. 262: 997–1003. doi:10.1016/j.jhazmat.2012.11.064. PMID 23290483.
  27. ^ Yang, Weihong; Zhang, Zhen; Zhang, Zhongming; Chen, Hong; Liu, Jin; Ali, Muhammad; Liu, Fan; Li, Lin (2013). "Population Structure of Manganese-Oxidizing Bacteria in Stratified Soils and Properties of Manganese Oxide Aggregates under Manganese–Complex Medium Enrichment". PLOS ONE. 8 (9): e73778. Bibcode:2013PLoSO...873778Y. doi:10.1371/journal.pone.0073778. PMC 3772008. PMID 24069232.
  28. ^ Nogueira, M. A.; Nehls, U.; Hampp, R.; Poralla, K.; Cardoso, E. J. B. N. (2007-08-28). "Mycorrhiza and soil bacteria influence extractable iron and manganese in soil and uptake by soybean". Plant and Soil. 298 (1–2): 273–284. Bibcode:2007PlSoi.298..273N. doi:10.1007/s11104-007-9379-1. ISSN 0032-079X. S2CID 43420007.
  29. ^ Kamijo, Manjiroh; Suzuki, Tohru; Kawai, Keiichi; Murase, Hironobu (1998-01-01). "Accumulation of yttrium by Variovorax paradoxus". Journal of Fermentation and Bioengineering. 86 (6): 564–568. doi:10.1016/S0922-338X(99)80007-5.
  30. ^ Belimov, A. A.; Hontzeas, N.; Safronova, V. I.; Demchinskaya, S. V.; Piluzza, G.; Bullitta, S.; Glick, B. R. (2005-02-01). "Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.)". Soil Biology and Biochemistry. 37 (2): 241–250. doi:10.1016/j.soilbio.2004.07.033.
  31. ^ Malkoc, Semra; Kaynak, Elif; Guven, Kıymet (2015-07-27). "Biosorption of zinc(II) on dead and living biomass of Variovorax paradoxus and Arthrobacter viscosus". Desalination and Water Treatment. 57 (33): 15445–15454. doi:10.1080/19443994.2015.1073181. ISSN 1944-3994.
  32. ^ Abou-Shanab, R. a. I.; van Berkum, P.; Angle, J. S. (2007-06-01). "Heavy metal resistance and genotypic analysis of metal resistance genes in gram-positive and gram-negative bacteria present in Ni-rich serpentine soil and in the rhizosphere of Alyssum murale". Chemosphere. 68 (2): 360–367. Bibcode:2007Chmsp..68..360A. doi:10.1016/j.chemosphere.2006.12.051. ISSN 0045-6535. PMID 17276484.
  33. ^ Vandamme, Peter; Coenye, Tom (2004-11-01). "Taxonomy of the genus Cupriavidus: a tale of lost and found". International Journal of Systematic and Evolutionary Microbiology. 54 (Pt 6): 2285–2289. doi:10.1099/ijs.0.63247-0. ISSN 1466-5026. PMID 15545472.
  34. ^ a b c d Jamieson, W David; Pehl, Michael J; Gregory, Glenn A; Orwin, Paul M (2009-06-12). "Coordinated surface activities in Variovorax paradoxus EPS". BMC Microbiology. 9 (1): 124. doi:10.1186/1471-2180-9-124. PMC 2704215. PMID 19523213.
  35. ^ a b Pehl, Michael J.; Jamieson, William David; Kong, Karen; Forbester, Jessica L.; Fredendall, Richard J.; Gregory, Glenn A.; McFarland, Jacob E.; Healy, Jessica M.; Orwin, Paul M. (2012). "Genes That Influence Swarming Motility and Biofilm Formation in Variovorax paradoxus EPS". PLOS ONE. 7 (2): e31832. Bibcode:2012PLoSO...731832P. doi:10.1371/journal.pone.0031832. PMC 3283707. PMID 22363744.
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