Nocardia

Cultured colonies of Nocardia pseudobrasiliensis, from Stamos et al. (2023).

Belongs within: Nocardiaceae.

Nocardia pseudovaccinii
Published 16 August 2020

As noted on this site before, the Actinobacteria are one of the most significant groups of bacteria in the terrestrial environment. Among the more diverse genera of Actinobacteria is Nocardia, members of which produce fine, branching mycelia that often fragment into individual rod-shaped or coccoid segments, each of which is capable of developing into a new mycelium (Goodfellow et al. 2012). As is the way of things, Nocardia species are usually soil dwellers but are more commonly studied as facultative pathogens. Nevertheless, recent years have seen the recognition of an increasing number of species isolated from soil samples with one such species being Nocardia pseudovaccinii.

Nocardia pseudovaccinii was described as a new species by Kim et al. (2002). In culture, N. pseudovaccinii grows a beige-red substrate mycelium supported a scarce, white aerial mycelium. Kim et al. (2002) identified the species as able to utilise a wide range of organic substrates such as ribose and glucosaminic acid though it could not break down others such as sucrose or citrate. Molecular analyses of Nocardia in Kim et al. (2002) and Goodfellow et al. (2012) do not really indicate a clear association of N. pseudovaccinii with any other species. Bacterial systematists apparently still maintain that neighbour-joining analyses are something more than a complete waste of time. I do not support this view.

The strains assigned to N. pseudovaccinii by Kim et al. (2002) had previously been identified as another species, N. vaccinii, hence the new species’ name (‘vaccinii‘, in case you were wondering, has no direct connection to vaccines but refers to Vaccinium, the plant genus including blueberries and from which N. vaccinii was first isolated). Nocardia vaccinii has been known to act as a facultative plant pathogen but I am not aware of this role being identified for N. pseudovaccinii. The original isolates were cultured from soil (though Kim et al. say nothing about what kind of soil or even where it was sampled). Nocardia pseudovaccinii has also been found forming part of the microbiome of wireworms of the genus Agriotes, beetle larvae that feed on plant roots. It may form a symbiotic association with these grubs that provides the latter with antibiotic protection from the pathogenic fungus Metarhizium brunneum (Kabaluk et al. 2017). A good thing for the wireworms but perhaps not so good for agriculturists who would like to keep them under control.

Systematics of Nocardia
<==Nocardia Trevis. 1889 [incl. Proactinomyces (Lehm. & Haag) Jensen 1934]KC01
|--+--+--+--N. otitidiscaviarum Snijders 1924NC18
| | | `--N. uniformis (ex Marton & Szabó 1959) Isik et al. 1999NC18
| | `--+--N. crassostreae Friedman et al. 1998ABM03, NC18
| | `--+--+--N. acidivoransNC18
| | | `--N. pseudobrasiliensisNC18
| | `--+--+--N. inohanensis Kageyama et al. 2004NC18
| | | `--N. yamanashiensis Kageyama et al. 2004NC18
| | `--+--N. jejuensis Lee 2006NC18
| | `--+--N. niigatensis Kageyama et al. 2004NC18
| | `--+--N. concavaNC18
| | `--N. seriolaeNC18
| `--+--+--+--N. blacklockiaeNC18
| | | `--+--N. transvalensis Pijper & Pullinger 1927NC18
| | | `--N. wallaceiNC18
| | `--+--+--N. aciditoleransNC18
| | | `--N. vaccinii Demaree & Smith 1952NC18
| | `--+--N. rayongensisNC18
| | `--+--N. jiangxiensis Cui et al. 2005NC18
| | `--N. miyunensisNC18
| `--+--N. vermiculataNC18
| `--+--N. elegansNC18
| `--+--N. veterana Gürtler et al. 2001NC18
| `--+--+--N. africana Hamid, Maldonado et al. 2001VP NC18, IJSEM01
| | `--N. nova Tsukamura 1983NC18
| `--+--N. cerradoensis Albuquerque de Barros, Manfio et al. 2003NC18, ABM03
| `--+--N. kruczakiae Conville et al. 2005NC18
| `--+--N. aobensisNC18
| `--+--N. mikamiiNC18
| `--+--N. casuarinaeNC18
| `--N. shinanonensisNC18
`--+--+--N. thailandicaNC18
| `--+--N. asteroides (Eppinger 1891) Blanchard 1896NC18
| `--+--+--N. neocaledoniensisNC18
| | `--N. rhizosphaeraeNC18
| `--+--N. camponotiNC18
| `--+--+--N. coubleaeNC18
| | `--N. ignorataNC18
| `--+--N. fluminea Maldonado et al. 2001NC18
| `--+--N. lasiiNC18
| `--N. salmonicidaNC18
| |--N. s. ssp. salmonicidaNC18
| `--N. s. ssp. cummidelens (Maldonado et al.) Nouioui, Carro et al. 2018 (see below for synonymy)NC18
`--+--+--N. cyriacigeorgicaNC18
| `--+--+--N. brevicatena (Lechevalier et al. 1961) Goodfellow & Pirouz 1982ABM03, NC18 (see below for synonymy)
| | `--N. paucivoransABM03
| `--+--N. flavoroseaNC18
| |--N. pigrifrangensNC18
| `--+--N. carnea (Rossi Doria 1891) Castellani & Chalmers 1913ABM03, NC18
| `--+--N. sienataNC18
| `--+--N. rhamnosiphila Everest et al. 2012NC18
| `--N. testaceaNC18
`--+--+--+--N. takedensisNC18
| | `--+--N. harenaeNC18
| | `--N. jiangsuensisNC18
| `--+--+--N. farcinica Trevisan 1889NC18
| | `--N. kroppenstedtiiNC18
| `--+--N. shimofusensis Kageyama et al. 2004NC18
| `--+--N. higoensisNC18
| `--N. purisNC18
`--+--+--N. amikacinitolerans Ezeoke et al. 2013NC18
| `--+--N. xishanensisNC18
| `--+--+--N. lijiangensisNC18
| | `--N. polyresistensNC18
| `--+--N. artemisiaeNC18
| `--+--N. mexicanaNC18
| `--N. thraciensisNC18
`--+--+--+--N. halotoleransNC18
| | `--+--N. albaNC18
| | `--N. ninaeNC18
| `--+--N. sungurluensisNC18
| `--+--N. goodfellowiiNC18
| `--+--N. caishijiensisNC18
| `--+--N. anaemiaeNC18
| `--+--N. pseudovaccinii Kim et al. 2002NC18
| `--N. vinacea Kinoshita et al. 2002NC18, JC08
`--+--+--+--N. iowensisNC18
| | `--N. tenerifensisNC18
| `--+--N. brasiliensis (Lindenberg 1909) Pinoy 1913NC18
| `--+--N. altamirensisNC18
| `--N. vulnerisNC18
`--+--+--N. amamiensisNC18
| `--N. pneumoniaeNC18
`--+--+--N. abscessusNC18
| `--N. asiatica Kageyama, Poonwan et al. 2004NC18
`--+--+--N. araoensisNC18
| `--+--N. beijingensisNC18
| `--‘Streptomyces’ gardneriNC18
`--+--+--N. bhagyanarayanaeNC18
| `--N. niwaeNC18
`--+--N. arthritidisNC18
`--+--N. exalbidaNC18
`--N. gamkensisNC18

Nocardia incertae sedis:
N. amaraeK-WK92
N. callitridisNC18
N. corallinaNL03
N. endophyticaNC18
N. erythropolisAS92
N. grenadensisNC18
N. jinanensisNC18
N. opaca (den Dooren de Jong) Waksman & Henrici 1948 [=Mycobacterium opacum den Dooren de Jong 1927]AS92
N. rubraBV16
N. speluncaeNC18
N. terpenicaNC18
N. zapadnayensisNC18

Nocardia brevicatena (Lechevalier et al. 1961) Goodfellow & Pirouz 1982ABM03, NC18 [=*Micropolyspora brevicatenaE92]

Nocardia salmonicida ssp. cummidelens (Maldonado et al.) Nouioui, Carro et al. 2018 [=N. cummidelens Maldonado et al. 2000; incl. N. soli Maldonado et al. 2001]NC18

*Type species of generic name indicated

References

[ABM03] Albuquerque de Barros, E. V. S., G. P. Manfio, V. R. Maitan, L. A. Mendes Bataus, S. B. Kim, L. A. Maldonado & M. Goodfellow. 2003. Nocardia cerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil. International Journal of Systematic and Evolutionary Microbiology 53: 29–33.

[AS92] Aragno, M., & H. G. Schlegel. 1992. The mesophilic hydrogen-oxidizing (knallgas) bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 344–384. Springer-Verlag: New York.

[BV16] Barka, E. A., P. Vatsa, L. Sanchez, N. Gaveau-Vaillant, C. Jacquard, J. P. Meier-Kolthoff, H.-P. Klenk, C. Clément, Y. Ouhdouch & G. P. van Wezel. 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews 80 (1): 1–43.

[E92] Embley, T. M. 1992. The family Pseudonocardiaceae. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 996–1027. Springer-Verlag: New York.

Goodfellow, M., P. Kämpfer, H.-J. Busse, M. E. Trujillo, K. Suzuki, W. Ludwig & W. B. Whitman (eds) 2012. Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 5. The Actinobacteria, Part A and B. Springer.

[IJSEM01] IJSEM. 2001. Validation list no. 81: Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 51: 1229.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

Kabaluk, T., E. Li-Leger & S. Nam. 2017. Metarhizium brunneum—an enzootic wireworm disease and evidence for its suppression by bacterial symbionts. Journal of Invertebrate Pathology 150: 82–87.

Kim, K. K., A. Roth, S. Andrees, S. T. Lee & R. M. Kroppenstedt. 2002. Nocardia pseudovaccinii sp. nov. International Journal of Systematic and Evolutionary Microbiology 52: 1825–1829.

[KC01] Kirk, P. M., P. F. Cannon, J. C. David & J. A. Stalpers. 2001. Ainsworth & Bisby’s Dictionary of the Fungi 9th ed. CAB International: Wallingford (UK).

[K-WK92] Korn-Wendisch, F., & H. J. Kutzner. 1992. The family Streptomycetaceae. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 921–995. Springer-Verlag: New York.

[NL03] Notomista, E. A. Lahm, A. Di Donato & A. Tramontano. 2003. Evolution of bacterial and archaeal multicomponent monooxygenases. Journal of Molecular Evolution 56: 435–445.

[NC18] Nouioui, I., L. Carro, M. García-López, J. P. Meier-Kolthoff, T. Woyke, N. Kyrpides, C., R. Pukall, H.-P. Klenk, M. Goodfellow & M. Göker. 2018. Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology 9: 2007.

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