Applied Microbiology and Biotechnology

, Volume 102, Issue 7, pp 3375–3386 | Cite as

Detection and cell sorting of Pseudonocardia species by fluorescence in situ hybridization and flow cytometry using 16S rRNA-targeted oligonucleotide probes

  • Mengyan Li
  • Yu Yang
  • Ya He
  • Jacques Mathieu
  • Cong Yu
  • Qilin Li
  • Pedro J. J. Alvarez
Environmental biotechnology


Pseudonocardia spp. are receiving increasing attention due to their ability to biodegrade recalcitrant cyclic ether pollutants (e.g., 1,4-dioxane and tetrahydrofuran), as well as for their distinctive ecological niches (e.g., symbiosis with ants/plants and production of antibiotics). Isolating and characterizing Pseudonocardia spp. is thus important to discern their metabolic and physiological idiosyncrasies and advance their potential applications. However, slow growth, low cell yield, and dissimilar colony morphology hinder efficient isolation of Pseudonocardia using conventional plating methods. Here, we develop the first fluorescent probe (Pse631) targeting the 16S rRNA of Pseudonocardia members. In combination with flow cytometry and cell sorting, in situ hybridization with this probe enables sensitive and specific detection of Pseudonocardia cells in mixed cultures and enriched environmental samples without significant false positives, using Escherichia coli, Bacillus subtilis, and Mycobacterium spp. as negative controls. Pseudonocardia dioxanivorans CB1190 cells labeled with Pse631 as a positive control were detected when their relative abundance in the total bacterial community was as low as 0.1%. Effective separation of Pseudonocardia cells from the mixed consortium was confirmed by quantitative PCR analysis of sorted cells. This study provides a culture-independent high-throughput molecular approach enabling effective separation of Pseudonocardia populations from complex microbial communities. This approach will not only facilitate subsequent molecular analyses including species identification and quantification, but also advance understanding of their catabolic capacities and functional molecular diversity.


Pseudonocardia Fluorescence in situ hybridization Flow cytometry 1,4-Dioxane Tetrahydrofuran 



The authors thank Joel M. Sederstrom (Baylor College of Medicine) for the assistance with flow cytometry.


This study was funded by SERDP (Grant # ER-2301).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

253_2018_8801_MOESM1_ESM.pdf (282 kb)
ESM 1 (PDF 282 kb)


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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Chemistry and Environmental ScienceNew Jersey Institute of TechnologyNewarkUSA
  2. 2.Department of Civil and Environmental EngineeringRice UniversityHoustonUSA

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