Applied Microbiology and Biotechnology

, Volume 102, Issue 19, pp 8429–8436 | Cite as

A new approach for detection and quantification of microalgae in industrial-scale microalgal cultures

  • Peter Beatrice-LindnerEmail author
  • Jose Antonio Garrido-Cardenas
  • Claudia Sepulveda
  • Francisco Gabriel Acien-Fernandez
Applied genetics and molecular biotechnology


In industrial-scale microalgal cultures, non-target microalgae compete with the desired species for nutrients and CO2, thus reducing the growth rate of the target species and the quality of the produced biomass. Microalgae identification is generally considered a complicated issue; although, in the last few years, new molecular methods have helped to rectify this problem. Among the different techniques available, DNA barcoding has proven very useful in providing rapid, accurate, and automatable species identification; in this work, it is used to assess the genomic identity of the microalga species Scenedesmus sp. ‘almeriensis’, a common strain in industrial-scale cultures. Barcode markers rbcL and ITS1-5.8S-ITS2 were sequenced and the obtained genomic information was used to design a quantitative PCR assay to precisely quantify the S. almeriensis concentration in microalgal cultures of industrial interest. TaqMan chemistry was used to quantify down to 1 μg/L dry weight of S. almeriensis cells, including in the presence of concentrated mixed cultures of other microalgae. A simple direct qPCR approach was also investigated to avoid classic DNA extraction and to reduce total assay time to approximately 2 h. The objective was to design strain-specific tools able to confirm and quantify the presence of different strains in whatever microalgae culture so as to achieve maximal productivity and quality of the produced biomass.


Microalgae Scenedesmus almeriensis Quantification Identification Direct qPCR 



This research received funding from the European Union’s Horizon 2020 Research and Innovation program under Grant Agreement No. 727874 SABANA.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal studies

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

Supplementary material

253_2018_9268_MOESM1_ESM.pdf (319 kb)
ESM 1 (PDF 318 kb)


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Copyright information

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

Authors and Affiliations

  1. 1.Department of EngineeringUniversity of AlmeriaAlmeriaSpain
  2. 2.Department of Biology and GeologyUniversity of AlmeriaAlmeriaSpain

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