Xanthomonadales

The Xanthomonadales are a bacterial order within the Gammaproteobacteria. They are one of the largest groups of bacterial phytopathogens, harbouring species such as Xanthomonas citri, Xanthomonas euvesicatoria, Xanthomonas oryzae and Xylella fastidiosa.[1][2][3][4][5] These bacteria affect agriculturally important plants including tomatoes, bananas, citrus plants, rice, and coffee. Many species within the order are also human pathogens. Species within the genus Stenotrophomonas are multidrug resistant opportunistic pathogens that are responsible for nosocomial infections in immunodeficient patients.[6][7]

Xanthomonadales
Scientific classification
Kingdom:
Bacteria
Phylum:
Proteobacteria
Class:
Gammaproteobacteria
Families
  • Xanthomonadaceae Christensen and Cook 1978 emend. Naushad et al. 2015
  • Rhodanobacteraceae Naushad et al. 2015
Synonyms
  • Lysobacterales Christensen and Cook 1978

Characteristics

The Xanthomonadales are gram-negative, catalase positive, non-spore forming obligate aerobes.[8] Members belonging to the order are straight rods lacking prosthecae. While some members are non-motile, other species within the order are motile by means of flagella. Stenotrophomonas is the only genus capable of nitrate reduction within the Xanthomonadales.

Taxonomy

The Xanthomonadales consist of 28 validly named genera among two families: Xanthomonadaceae and Rhodanobacteraceae.[9][10][11] The Xanthomonadaceae consists of 13 genera while the Rhodanobacteraceae consist of 14 genera. The families can be distinguished from one another on the basis of conserved signature indels found among a variety of proteins, specific for each family.[10] These indels are in parallel with phylogenomic analysis that reveal two distinct clades that appear to be evolutionarily divergent. Lysobacterales and Lysobacteraceae are earlier synonyms of Xanthomonadales and Xanthomonadaceae, respectively.[10][12]

Phylogenetic position

The Xanthomonadales are early divergents of bacteria within the Gammaproteobacteria, and are often used to root phylogenetic trees created for the class.[13] Until recently, the Xanthomonodales order was inclusive of the families Xanthomonadaceae, Algiphilaceae, Solimonadaceae, Nevskiaceae and Sinobacteraceae. However, no molecular signatures were found that were inclusive of all families.[10] The organisms were taxonomically rearranged such that Xanthomonadales included Xanthomonadaceae, which was later divided into two families. The division was in accordance with CSIs that were found specifically for all members of the emended Xanthomonadales order, providing support for the currently accepted taxonomy. All other species were transferred to Nevskiales, which did not share CSIs with Xanthomonadales, but remain close relatives within the Gammaproteobacteria.[10] Cardiobacteriales, Chromatiales, Methylococcales, Legionellales and Thiotrichales are also deep branching orders that are phylogenetic neighbours of Xanthomonadales and Nevskiales members.[10][13] The Nevskiales order harbors a single family (Salinisphaeraceae) and six genera: Alkanibacter, Fontimonas, Hydrocarboniphaga, Nevskia, Solimonas and Steroidobacter.[10] Wohlfahrtiimonas chitiniclastica and Ignatzschineria larvae are two species that have historically been accepted as members of the Xanthomonadaceae family. However, they do not share conserved signatures with the family, or with the Xanthomonodales order.[10] These species form deep branching within neighbouring Gammaproteobacteria, and are monophyletic with Cardiobacteriales members. These species are thus currently labelled as incartae sedis.

Phylogeny

The currently accepted taxonomy is based on the National Center for Biotechnology Information (NCBI).[9]

References
  1. da Silva AC, Ferro JA, Reinach FC, et al. (2002). "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities". Nature. 417 (6887): 459–463. doi:10.1038/417459a. PMID 12024217.
  2. Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, et al. (2003). "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa". J Bacteriol. 185 (3): 1018–26. doi:10.1128/JB.185.3.1018-1026.2003. PMC 142809. PMID 12533478.
  3. Lee BM, Park YJ, Park DS, et al. (2005). "The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice". Nucleic Acids Res. 33 (2): 577–586. doi:10.1093/nar/gki206. PMC 548351. PMID 15673718.
  4. Ryan RP, Vorholter F, Potnis N, et al. (2005). "Pathogenomics of Xanthomonas: understanding bacterium–plant interactions". Nat Rev Microbiol. 9 (5): 344–355. doi:10.1038/nrmicro2558. PMID 21478901.
  5. Chen J, Xie G, Han S, Chertkov O, Sims D, Civerolo EL (2010). "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California". J Bacteriol. 192 (17): 4534. doi:10.1128/JB.00651-10. PMC 2937377. PMID 20601474.
  6. Crossman LC, Gould VC, Dow JM, et al. (2008). "The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants". Genome Biol. 9 (4): R74. doi:10.1186/gb-2008-9-4-r74. PMC 2643945. PMID 18419807.
  7. Looney WJ, Narita M, Mühlemann K (2009). "Stenotrophomonas maltophilia: an emerging opportunist human pathogen". Lancet Infect Dis. 9 (5): 312–323. doi:10.1016/S1473-3099(09)70083-0. PMID 19393961.
  8. Saddler GS, Bradbury JF (2005) Order III. Xanthomonadales ord. nov. In: Bergey’s Manual of Systematic Bacteriology. pp. 63-122. Eds Brenner DJ, Krieg NR, Staley JT, Garrity GM, Boone, Vos P, Goodfellow M, Rainey FA, Schleifer K-H Springer-: Austin.
  9. Sayers; et al. "Xanthomonadales". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-10-24.
  10. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS (2015). "A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives". Antonie van Leeuwenhoek. 107 (2): 467–485. doi:10.1007/s10482-014-0344-8. PMID 25481407.
  11. Oren A, Garrity GM (2015). "List of new names and new combinations previously effectively, but not validly, published". Int J Syst Evol Microbiol. 65 (7): 2017–2025. doi:10.1099/ijs.0.000317.
  12. Christensen P, Cook F (1978). "Lysobacter, a New Genus of Nonfruiting, Gliding Bacteria with a High Base Ratio". Int J Syst Evol Microbiol. 28 (3): 367–393. doi:10.1099/00207713-28-3-367.
  13. Cutiño-Jiménez AM, Martins-Pinheiro M, Lima WC, Martín-Tornet A, Morales OG, Menck CF (2010). "Evolutionary placement of Xanthomonadales based on conserved protein signature sequences". Mol Phylogenet Evol. 54 (2): 524–34. doi:10.1016/j.ympev.2009.09.026. PMID 19786109.
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