Biology:Variovorax paradoxus

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Short description: Species of bacterium

Variovorax paradoxus
Scientific classification edit
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

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

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

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

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

File:Coordinated-surface-activities-in-Variovorax-paradoxus-EPS-1471-2180-9-124-S1.ogv 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

  1. ↑ 1.0 1.1 1.2 1.3 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. http://www.straininfo.net/strains/22223. 
  3. ↑ 3.0 3.1 3.2 3.3 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. ↑ 4.0 4.1 4.2 4.3 Satola, Barbara; Wübbeler, Jan Hendrik; Steinbüchel, Alexander (2012-11-29). "Metabolic characteristics of the species Variovorax paradoxus" (in en). Applied Microbiology and Biotechnology 97 (2): 541–560. doi:10.1007/s00253-012-4585-z. ISSN 0175-7598. PMID 23192768. 
  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" (in en). Applied Microbiology and Biotechnology 55 (2): 234–238. doi:10.1007/s002530000546. ISSN 0175-7598. PMID 11330720. 
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Han, Jong-In; Choi, Hong-Kyu; Lee, Seung-Won; Orwin, Paul M.; Kim, Jina; LaRoe, Sarah L.; Kim, Tae-gyu; O'Neil, Jennifer et al. (2011-03-01). "Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110" (in en). Journal of Bacteriology 193 (5): 1183–1190. doi:10.1128/JB.00925-10. ISSN 0021-9193. PMID 21183664. 
  7. ↑ 7.0 7.1 Han, Jong-In; Spain, Jim C.; Leadbetter, Jared R.; Ovchinnikova, Galina; Goodwin, Lynne A.; Han, Cliff S.; Woyke, Tanja; Davenport, Karen W. et al. (2013-10-31). "Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS" (in en). Genome Announcements 1 (5): e00843–13. doi:10.1128/genomeA.00843-13. ISSN 2169-8287. PMID 24158554. 
  8. ↑ 8.0 8.1 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" (in en). Environmental Microbiology 16 (11): 3370–3386. doi:10.1111/1462-2920.12340. ISSN 1462-2920. PMID 24245581. 
  9. ↑ 9.0 9.1 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. ↑ 10.0 10.1 10.2 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" (in en). Environmental Microbiology 10 (6): 1486–1500. doi:10.1111/j.1462-2920.2007.01564.x. ISSN 1462-2920. PMID 18279342. Bibcode: 2008EnvMi..10.1486S. 
  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." (in en). Applied and Environmental Microbiology 63 (6): 2266–2272. doi:10.1128/AEM.63.6.2266-2272.1997. ISSN 0099-2240. PMID 9172346. Bibcode: 1997ApEnM..63.2266K. 
  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" (in en). New Phytologist 181 (2): 413–423. doi:10.1111/j.1469-8137.2008.02657.x. ISSN 1469-8137. 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. doi:10.1016/j.watres.2010.07.027. ISSN 1879-2448. PMID 20705313. Bibcode: 2010WatRe..44.5050L. 
  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. doi:10.1080/01490450903408112. ISSN 0149-0451. Bibcode: 2010GmbJ...27...93G. 
  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. et al. (2008-12-01). "Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem". The ISME Journal 2 (12): 1231–1242. doi:10.1038/ismej.2008.75. ISSN 1751-7370. PMID 18754044. Bibcode: 2008ISMEJ...2.1231H. 
  16. ↑ 16.0 16.1 Northup, Diana E.; Barns, Susan M.; Yu, Laura E.; Spilde, Michael N.; Schelble, Rachel T.; Dano, Kathleen E.; Crossey, Laura J.; Connolly, Cynthia A. et al. (2003-11-01). "Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves". Environmental Microbiology 5 (11): 1071–1086. doi:10.1046/j.1462-2920.2003.00500.x. ISSN 1462-2912. PMID 14641587. Bibcode: 2003EnvMi...5.1071N. 
  17. ↑ 17.0 17.1 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. doi:10.1007/s10646-006-0093-1. ISSN 0963-9292. PMID 16955363. Bibcode: 2006Ecotx..15..549W. 
  18. ↑ 18.0 18.1 18.2 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. doi:10.1080/01490450600724282. ISSN 0149-0451. Bibcode: 2006GmbJ...23..201B. 
  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. 
  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. PMID 19121036. 
  23. ↑ Leadbetter, Jared R.; Greenberg, E. P. (2000-12-15). "Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus" (in en). Journal of Bacteriology 182 (24): 6921–6926. doi:10.1128/JB.182.24.6921-6926.2000. ISSN 0021-9193. 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. PMID 24065091. 
  25. ↑ 25.0 25.1 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" (in en). Environmental Science & Technology 38 (1): 104–111. doi:10.1021/es034455a. PMID 14740724. Bibcode: 2004EnST...38..104M. 
  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. doi:10.1371/journal.pone.0073778. PMID 24069232. Bibcode: 2013PLoSO...873778Y. 
  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" (in en). Plant and Soil 298 (1–2): 273–284. doi:10.1007/s11104-007-9379-1. ISSN 0032-079X. Bibcode: 2007PlSoi.298..273N. 
  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. doi:10.1016/j.chemosphere.2006.12.051. ISSN 0045-6535. PMID 17276484. Bibcode: 2007Chmsp..68..360A. 
  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. ↑ 34.0 34.1 34.2 34.3 Jamieson, W David; Pehl, Michael J; Gregory, Glenn A; Orwin, Paul M (2009-06-12). "Coordinated surface activities in Variovorax paradoxus EPS" (in En). BMC Microbiology 9 (1): 124. doi:10.1186/1471-2180-9-124. PMID 19523213. 
  35. ↑ 35.0 35.1 Pehl, Michael J.; Jamieson, William David; Kong, Karen; Forbester, Jessica L.; Fredendall, Richard J.; Gregory, Glenn A.; McFarland, Jacob E.; Healy, Jessica M. et al. (2012). "Genes That Influence Swarming Motility and Biofilm Formation in Variovorax paradoxus EPS". PLOS ONE 7 (2): e31832. doi:10.1371/journal.pone.0031832. PMID 22363744. Bibcode: 2012PLoSO...731832P. 

External links

Wikidata ☰ Q16993380 entry



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