A new approach for detection and quantification of microalgae in industrial-scale microalgal cultures
- 263 Downloads
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.
KeywordsMicroalgae 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.
- Arnon DI, McSwain BD, Tsujimoto HY, Wada K (1974) Photochemical activity and components of membrane preparations from blue-green algae. I. Coexistence of two photosystems in relation to chlorophyll a and removal of phycocyanin. BBA-Bioenerg 357:231–245. https://doi.org/10.1016/0005-2728(74)90063-2 CrossRefGoogle Scholar
- Carreres BM, de Jaeger L, Springer J, Barbosa MJ, Breuer G, van den End EJ, Kleinegris DMM, Schaffers I, Wolbert EJH, Zhang H, Lamers PP, Draaisma RB, dos Santos VAPM, Wijffels RH, Eggink G, Schaap PJ, Martens DE (2017) Draft genome sequence of the oleaginous green alga Tetradesmus obliquus UTEX 393. Am Soc Microbiol 5:1–2Google Scholar
- Coyne KJ, Handy SM, Demir E, Whereat EB, Hutchins DA, Portune KJ, Doblin MA, Cary SC (2005) Improved quantitative real-time PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard. Limnol Oceanogr Methods 3:381–391. https://doi.org/10.4319/lom.2005.3.381 CrossRefGoogle Scholar
- Handy SM, Demir E, Hutchins DA, Portune KJ, Whereat EB, Hare CE, Rose JM, Warner M, Farestad M, Cary SC, Coyne KJ (2008) Using quantitative real-time PCR to study competition and community dynamics among Delaware Inland Bays harmful algae in field and laboratory studies. Harmful Algae 7:599–613. https://doi.org/10.1016/j.hal.2007.12.018 CrossRefGoogle Scholar
- Maniatis T, Fritsch E, Sambrook J (1982) Molecular Cloning - A Laboratory Manual, First edit. Cold Spring Harbor Laboratory, New York Google Scholar
- Sánchez JF, Fernández-Sevilla JM, Acién FG, Cerón MC, Pérez-Parra J, Molina-Grima E (2008a) Biomass and lutein productivity of Scenedesmus almeriensis: influence of irradiance, dilution rate and temperature. Appl Microbiol Biotechnol 79:719–729. https://doi.org/10.1007/s00253-008-1494-2 CrossRefPubMedGoogle Scholar
- Starkenburg SR, Polle JEW, Hovde B, Daligault HE, Davenport KW, Huang A, Neofotis P, McKie-Krisberg Z (2017) Draft nuclear genome, chloroplast genome, and complete mitochondrial genome for the biofuel/bioproduct feedstock species Scenedesmus obliquus strain DOE0152z. Am Soc Microbiol 5:11–12Google Scholar
- White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, pp 315–322Google Scholar
- Woodman ME, Savage CR, Arnold WK, Stevenson B (2016) Direct PCR of intact bacteria (Colony PCR). Curr Protoc Microbiol 42. https://doi.org/10.1002/cpmc.14