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Ensifer (bacterium)

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Ensifer (often referred to in literature by its synonym Sinorhizobium) is a genus of nitrogen-fixing bacteria (rhizobia), three of which (Ensifer meliloti,[22][23] Ensifer medicae[24] and Ensifer fredii[25][26]) have been sequenced.

Ensifer
Ensifer fredii USDA257 on an agar plate of typtone-yeast extract agar.
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Family: Rhizobiaceae
Genus: Ensifer
Casida, 1982
Type species
Ensifer adhaerens
Casida, 1982
Species[18][19][20][21]
Synonyms[19]
  • Sinorhizobium Chen et al. 1988

Etymology

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The generic epithet Ensifer derives from the Latin noun ensifer, "sword-bearer".[3] The synonym Sinorhizobium is a combination of Medieval Latin noun sino ("China"), the Classical Greek noun rhiza ("root"), and the Classical Greek noun bium ("life"). Thus, the Neo-Latin generic epithet of the synonym Sinorhizobium means "a Rhizobium isolated from China", in turn referring to the related genus Rhizobium ("root-associated life form").[18][9]

Proper name

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The name Ensifer was published in 1982 and the name Sinorhizobium was published in 1988 thus the latter is regarded as a later synonym and by the rules of the Bacteriological Code (1990 Revision) of the International Committee on Systematics of Prokaryotes (ICSP), the older name (Ensifer) takes priority.[27] In response to a request that the single extant species of Ensifer (Ensifer adhaerens) be moved to Sinorhizobium, a special ICSP subcommittee was formed to evaluate the request. It was ultimately ruled that Ensifer retained priority and that all Sinorhizobium species be transferred to the genus Ensifer.[28][29] However, both terms continue to be used in published scientific literature, with Sinorhizobium being the more common.[30]

Deprecated species

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Two species have been described which have since been reclassified into existing species: Sinorhizobium morelense (now Ensifer adhaerens)[27][31] and Sinorhizobium xinjiangense (now Ensifer fredii[32][33]—though some dissent exists[16][34]).

Phylogeny

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).[18][19] The following phylogeny is based on whole-genome analysis.[35]

This phylogeny is based on a constrained analysis of the 16S ribosomal RNA.[35]

References

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  1. ^ a b Ogasawara M, Suzuki T, Mutoh I, Annapurna K, Arora NK, Nishimura Y, Maheshwari DK (2003). "Sinorhizobium indiaense sp. nov. and Sinorhizobium abri sp. nov. isolated from tropical legumes, Sesbania rostrata and Abrus precatorius, respectively". Symbiosis. 34 (1): 53–68.
  2. ^ a b c d e Because no type strains have been submitted to international culture collections, these are not currently recognized as valid species.
  3. ^ a b Casida LE (1982). "Ensifer adhaerens gen. nov., sp. nov.: A bacterial predator of bacteria in soil". Int J Syst Bacteriol. 32 (3): 339–345. doi:10.1099/00207713-32-3-339.
  4. ^ Toledo I, Lloret L, Martínez-Romero E (March 2003). "Sinorhizobium americanus sp. nov., a new Sinorhizobium species nodulating native Acacia spp. in Mexico". Systematic and Applied Microbiology. 26 (1): 54–64. doi:10.1078/072320203322337317. PMID 12747410.
  5. ^ a b Nick G, de Lajudie P, Eardly BD, Suomalainen S, Paulin L, Zhang X, Gillis M, Lindström K (October 1999). "Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya". International Journal of Systematic Bacteriology. 49 (Pt. 4): 1359–68. doi:10.1099/00207713-49-4-1359. PMID 10555313.
  6. ^ Le Quéré A, Tak N, Gehlot HS, Lavire C, Meyer T, Chapulliot D, Rathi S, Sakrouhi I, Rocha G, Rohmer M, Severac D (2017). "Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts". BMC Genomics. 18 (1): 85. doi:10.1186/s12864-016-3447-y. PMC 5237526. PMID 28088165.
  7. ^ Rocha G, Le Quere A, Medina A, Cuellar A, Contreras JL, Carreno R, Bustillos R, Munoz-Rojas J, Villegas MD, Chaintreuil C, Dreyfus B, Munive JA (2020). "Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov". Arch Microbiol. 202 (2): 309–322. doi:10.1007/s00203-019-01744-7. PMC 7012998. PMID 31659382.
  8. ^ Rincón-Rosales R, Lloret L, Ponce E, Martínez-Romero E (January 2009). "Rhizobia with different symbiotic efficiencies nodulate Acaciella angustissima in Mexico, including Sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with Sinorhizobium mexicanum". FEMS Microbiology Ecology. 67 (1): 103–17. doi:10.1111/j.1574-6941.2008.00590.x. PMC 2784085. PMID 19120461.
  9. ^ a b Chen WX, Yan GH, Li JL (1988). "Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov". Int J Syst Bacteriol. 38 (4): 392–397. doi:10.1099/00207713-38-4-392.
  10. ^ a b Yan H, Yan J, Sui XH, Wang ET, Chen WX, Zhang XX, Chen WF (April 2016). "Ensifer glycinis sp. nov., an novel rhizobial species associated with Glycine spp". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 3): 2910–6. doi:10.1099/ijsem.0.001120. PMID 27125987.
  11. ^ Merabet C, Martens M, Mahdhi M, Zakhia F, Sy A, Le Roux C, Domergue O, Coopman R, Bekki A, Mars M, Willems A, de Lajudie P (March 2010). "Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 3): 664–74. doi:10.1099/ijs.0.012088-0. hdl:1854/LU-936490. PMID 19656922.
  12. ^ Wei GH, Wang ET, Tan ZY, Zhu ME, Chen WX (November 2002). "Rhizobium indigoferae sp. nov. and Sinorhizobium kummerowiae sp. nov., respectively isolated from Indigofera spp. and Kummerowia stipulacea". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 6): 2231–9. doi:10.1099/00207713-52-6-2231. PMID 12508892.
  13. ^ Rome S, Fernandez MP, Brunel B, Normand P, Cleyet-Marel JC (October 1996). "Sinorhizobium medicae sp. nov., isolated from annual Medicago spp". International Journal of Systematic Bacteriology. 46 (4): 972–80. doi:10.1099/00207713-46-4-972. PMID 8863426.
  14. ^ a b c de Lajudie P, Willems A, Pot B, Dewettinck D, Maestrojuan G, Neyra M, Collins MD, Dreyfus B, Kersters K, Gillis M (1994). "Polyphasic taxonomy of rhizobia: Emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov". Int J Syst Bacteriol. 44 (4): 715–733. doi:10.1099/00207713-44-4-715.
  15. ^ Lloret L, Ormeño-Orrillo E, Rincón R, Martínez-Romero J, Rogel-Hernández MA, Martínez-Romero E (June 2007). "Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico". Systematic and Applied Microbiology. 30 (4): 280–90. doi:10.1016/j.syapm.2006.12.002. PMID 17293074.
  16. ^ a b c Wang YC, Wang F, Hou BC, Wang ET, Chen WF, Sui XH, Chen WX, Li Y, Zhang YB (October 2013). "Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov". Systematic and Applied Microbiology. 36 (7): 467–73. doi:10.1016/j.syapm.2013.05.001. PMID 23759600.
  17. ^ Li QQ, Wang ET, Chang YL, Zhang YZ, Zhang YM, Sui XH, Chen WF, Chen WX (August 2011). "Ensifer sojae sp. nov., isolated from root nodules of Glycine max grown in saline-alkaline soils". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 8): 1981–8. doi:10.1099/ijs.0.025049-0. PMID 20851917.
  18. ^ a b c Euzéby JP. "Sinorhizobium". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2012-05-02.
  19. ^ a b c Euzéby JP. "Ensifer". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2012-05-02.
  20. ^ Balkwill DL (2005). "Ensifer Casida 1982, 343VP". In Brenner DJ, Krieg NR, Garrity GM, Staley JT, Boone DR, De Vos P, Goodfellow M, Rainey FA, Schleifer KH (eds.). Bergey's Manual of Systematic Bacteriology, Volume Two: The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. New York, New York: Springer. pp. 354–361. doi:10.1007/0-387-29298-5_87. ISBN 978-0-387-24145-6.
  21. ^ Kuykendall LD, Hashem FM, Wang ET (2005). "Sinorhizobium Chen, Yan and Li 1988b, 396VP emend. de Lajudie, Willems, Pot, Dewettinck, Maestrojuan, Neyra, Collins, Dreyfus, Kersters and Gillis 1994, 732". In Brenner DJ, Krieg NR, Garrity GM, Staley JT, Boone DR, De Vos P, Goodfellow M, Rainey FA, Schleifer KH (eds.). Bergey's Manual of Systematic Bacteriology, Volume Two: The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. New York, New York: Springer. pp. 358–361. doi:10.1007/0-387-29298-5_88. ISBN 978-0-387-24145-6.
  22. ^ Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, et al. (July 2001). "The composite genome of the legume symbiont Sinorhizobium meliloti". Science. 293 (5530): 668–72. doi:10.1126/science.1060966. PMID 11474104. S2CID 18580010.
  23. ^ "NCBI Genome Page for Sinorhizobium meliloti". National Center for Biotechnology Information (NCBI).
  24. ^ "NCBI Genome Page for Sinorhizobium medicae". National Center for Biotechnology Information (NCBI).
  25. ^ Schmeisser C, Liesegang H, Krysciak D, Bakkou N, Le Quéré A, Wollherr A, Heinemeyer I, Morgenstern B, Pommerening-Röser A, Flores M, Palacios R, Brenner S, Gottschalk G, Schmitz RA, Broughton WJ, Perret X, Strittmatter AW, Streit WR (June 2009). "Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems". Applied and Environmental Microbiology. 75 (12): 4035–45. Bibcode:2009ApEnM..75.4035S. doi:10.1128/AEM.00515-09. PMC 2698369. PMID 19376903.
  26. ^ "NCBI Genome Page for Sinorhizobium fredii". National Center for Biotechnology Information (NCBI).
  27. ^ a b Young JM (November 2003). "The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion". International Journal of Systematic and Evolutionary Microbiology. 53 (Pt 6): 2107–10. doi:10.1099/ijs.0.02665-0. PMID 14657154.
  28. ^ Lindström K, Martínez-Romero ME (2002). "International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium. Minutes of the meeting, 4 July 2001, Hamilton, Canada". Int J Syst Bacteriol. 52 (6): 2337. doi:10.1099/ijs.0.02524-0.
  29. ^ Judicial Commission of the International Committee on Systematics of Prokaryotes (August 2008). "The genus name Sinorhizobium Chen et al. 1988 is a later synonym of Ensifer Casida 1982 and is not conserved over the latter genus name, and the species name 'Sinorhizobium adhaerens' is not validly published. Opinion 84". International Journal of Systematic and Evolutionary Microbiology. 58 (Pt 8): 1973. doi:10.1099/ijs.0.2008/005991-0. PMID 18676490.
  30. ^ Young JPW. (February 9, 2013). "Rhizobium: Writing about bacteria and their genomes". WordPress.
  31. ^ Wang ET, Tan ZY, Willems A, Fernández-López M, Reinhold-Hurek B, Martínez-Romero E (September 2002). "Sinorhizobium morelense sp. nov., a Leucaena leucocephala-associated bacterium that is highly resistant to multiple antibiotics". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 5): 1687–93. doi:10.1099/ijs.0.01954-0. hdl:10261/109835. PMID 12361275.
  32. ^ Peng GX, Tan ZY, Wang ET, Reinhold-Hurek B, Chen WF, Chen WX (March 2002). "Identification of isolates from soybean nodules in Xinjiang Region as Sinorhizobium xinjiangense and genetic differentiation of S. xinjiangense from Sinorhizobium fredii". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 2): 457–62. doi:10.1099/00207713-52-2-457. PMID 11931157.
  33. ^ Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P, Willems A (January 2008). "Advantages of multilocus sequence analysis for taxonomic studies: A case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)". International Journal of Systematic and Evolutionary Microbiology. 58 (Pt 1): 200–14. doi:10.1099/ijs.0.65392-0. PMID 18175710.
  34. ^ Martens M, Delaere M, Coopman R, De Vos P, Gillis M, Willems A (March 2007). "Multilocus sequence analysis of Ensifer and related taxa". International Journal of Systematic and Evolutionary Microbiology. 57 (Pt 3): 489–503. doi:10.1099/ijs.0.64344-0. PMID 17329774.
  35. ^ a b Hördt, Anton; López, Marina García; Meier-Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus (7 April 2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
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