Luis Demetrio Mora Hernández
An integrative approach to epilithic diatom diversity analysis in tropical streams from the Lerma-Chapala Basin, Central Mexico
Doctoral dissertation.
Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
Correspondencia: demetriomora@gmail.com
In most of the diatom studies of Mexican freshwaters, there seems to be low species diversity and high cosmopolitanism, contrary to what would be expected of a megadiverse country. This can be mainly because of 1) force-fitting identifications based on monographs from temperate regions and 2) the lone use of light microscopy for identifications, which not always differentiates between closely related species. In order to contribute to a better assessment of the diatom diversity of the country and to set an identification baseline for future bioindication studies with diatoms, this dissertation presents an integrative analysis (morphological, ecological, molecular and phylogenetic) to the diversity of epilithic diatoms in several streams from the Lerma-Chapala Basin, Central Mexico.
The morphological evaluation resulted in 274 infrageneric taxa, including the description of two new species, Brachysira altepetlensis and Sellaphora queretana. The ecological analysis revealed that community composition was mainly driven by the ionic composition of the water, with indicator taxa identified for the varying conditions in pH, conductivity and nutrients.
Under the premise that diatom identifications at species level in environmental DNA (eDNA) metabarcoding studies rely heavily on the completeness of barcode reference libraries, a regional barcode reference library was assembled based on diatom clonal cultivation. The eDNA metabarcoding approach tested here, which integrates molecular and tree-based phylogenetic methods based on the 18S V4 rRNA gene, revealed a larger diversity than the diversity recorded by morphological analysis. One quarter of the taxa assigned to species level in the eDNA metabarcoding approach was only possible due to the barcode reference library assembled for this study, supporting the aforementioned premise. Regional barcode reference libraries increase the success of species level identifications, particularly in poorly studied regions such as the tropics, whose species are poorly represented in INSDC (International Nucleotide Sequence Database Collaboration) databases. By comparing the diversity retrieved by morphology and eDNA metabarcoding, it was found that neither morphology nor eDNA metabarcoding were a better method than the other in recording the entire diversity, but they were rather complementary. Clonal cultivation of diatoms revealed a concealed diversity neither detected by morphology nor by eDNA metabarcoding, suggesting cultivation as a further method to unravel species diversity from environmental samples. The relative abundances recorded by morphology (diatom valves) and eDNA metabarcoding (sequence reads) showed large disparities, even after the application of correction factors. This suggests that further methodological improvements are needed in order to establish eDNA metabarcoding as a standard method for bioindication. Furthermore, the results presented here support the retrieval of DNA reference barcodes from High-Throughput Sequencing data.
Overall, this dissertation highlights the importance of integrative studies to better assess the diatom diversity in this biodiversity rich but environmentally threatened region of Mexico.
Keywords: epilithon, DNA barcoding, eDNA metabarcoding, barcode reference libraries, 18S V4 rRNA gene, High-Throughput Sequencing, Lerma-Chapala Basin, Central Mexico.
Texto completo disponible en: Refubium, the institutional repository of the University Library of Freie Universität Berlin: https://refubium.fu-berlin.de/handle/fub188/23033