Resolving a bioindicator diatom species complex using genomic approaches for freshwater biomonitoring

Ciftci, O. (2023)

Doctoral Thesis

This thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to highlight their strengths and limitations; (ii) unraveling the evolutionary history of Nitzschia palea and investigating species delimitation within the species complex; (iii) identifying silica genes in N. palea for insights into ecology and evolution; and (iv) assessing a genome-scale quantification method for diatom biomonitoring to improve accuracy and scalability in estimating abundances. The review (Chapter 2) emphasizes disparities between molecular and morphology-based approaches and introduces the challenges in accurately estimating species abundances. Chapter 3 explores N. palea's evolutionary history using transcriptome data and reveals reticulate evolutionary patterns resulting in a putative hybrid between populations with different morphological characteristics. Chapter 4 pinpoints silica genes in N. palea and reveals variations among different populations that may lead to differences in silica metabolism. Chapter 5 introduces a genome-scale quantification approach that provides a promising alternative for molecular diatom biomonitoring due to its improved taxonomic resolution and quantification accuracy. In summary, this thesis underscores that genome-scale methods' have a critical role in diatom identification and quantification, and in advancing our understanding of microalgal taxonomy, ecology, and evolution.

• Evolution
• Ecology
• Biomonitoring
• Bioindicators
• Freshwater
• Diatom
• Genomics
• Transcriptomics
• Phylogenetics
• Hybridization

• All authors: Ciftci, O.
• Supervisor: Bodegom, P.M. van
• Co-supervisor: Gravendeel, B.
• Committee: Alverson, A.; Mann, D.; Kooistra, W.H.C.F.; Stewart, K.A.; Vijver, M.; Voogd, N.J. de
• Qualification: Doctor (dr.)
• Awarding Institution: Institute of Environmental Sciences (CML), Faculty of Science, Leiden University
• Date: 2023-10-17
• Sponsorship: H2020 MSCA-ITN-ETN, Grant Agreement No:765000, Plant.ID