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Volume 14
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10.3390/microorganisms14030582
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Article

Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights

by
Alexandros Ntzouvaras
1,
Aikaterini Koletti
1,
Maria Eleftheria Zografaki
1,
Sofia Marka
1,
Dimitrios Skliros
1,
Gabriel Vasilakis
2,
Ioannis Karavidas
3,
Adonis Konstantinos Koukouvinis
4,
Rodica C. Efrose
1,5,
Chrysanthi Kalloniati
1,6,
Ioannis Tzovenis
7 and
Emmanouil Flemetakis
1,*
1
Laboratory of Environmental Biotechnology, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
2
Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece
3
Laboratoty of Vegetable Crops, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
4
Sector of Ecology & Systematics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
5
Department of Chemistry, Physics and Environment, Faculty of Sciences and Environment, “Dunarea de Jos” University of Galati, 47 Domneasca, 800008 Galati, Romania
6
Department of Marine Sciences, University of the Aegean, 81100 Mytilene, Greece
7
Microphykos Aquaculture Systems & Services, Halandri, 15238 Athens, Greece
*
Author to whom correspondence should be addressed.
Microorganisms 2026, 14(3), 582; https://doi.org/10.3390/microorganisms14030582
Submission received: 30 December 2025 / Revised: 10 February 2026 / Accepted: 15 February 2026 / Published: 4 March 2026
(This article belongs to the Section Environmental Microbiology)
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Abstract

Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1–PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.
Keywords: hydroponic effluent; microalgal isolates; metagenomics; characterization hydroponic effluent; microalgal isolates; metagenomics; characterization

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MDPI and ACS Style

Ntzouvaras, A.; Koletti, A.; Zografaki, M.E.; Marka, S.; Skliros, D.; Vasilakis, G.; Karavidas, I.; Koukouvinis, A.K.; Efrose, R.C.; Kalloniati, C.; et al. Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights. Microorganisms 2026, 14, 582. https://doi.org/10.3390/microorganisms14030582

AMA Style

Ntzouvaras A, Koletti A, Zografaki ME, Marka S, Skliros D, Vasilakis G, Karavidas I, Koukouvinis AK, Efrose RC, Kalloniati C, et al. Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights. Microorganisms. 2026; 14(3):582. https://doi.org/10.3390/microorganisms14030582

Chicago/Turabian Style

Ntzouvaras, Alexandros, Aikaterini Koletti, Maria Eleftheria Zografaki, Sofia Marka, Dimitrios Skliros, Gabriel Vasilakis, Ioannis Karavidas, Adonis Konstantinos Koukouvinis, Rodica C. Efrose, Chrysanthi Kalloniati, and et al. 2026. "Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights" Microorganisms 14, no. 3: 582. https://doi.org/10.3390/microorganisms14030582

APA Style

Ntzouvaras, A., Koletti, A., Zografaki, M. E., Marka, S., Skliros, D., Vasilakis, G., Karavidas, I., Koukouvinis, A. K., Efrose, R. C., Kalloniati, C., Tzovenis, I., & Flemetakis, E. (2026). Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights. Microorganisms, 14(3), 582. https://doi.org/10.3390/microorganisms14030582

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