Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples

• Published in: Frontiers in Ecology and Evolution
• Main Authors: Heindler, Franz M., Christiansen, Henrik, Frédérich, Bruno, Dettai, Agnes, Lepoint, Gilles, Maes, Gregory E., Putte, Anton P., van De, Volckaert, Filip A. M.
• Other Authors: Catholic University of Leuven = Katholieke Universiteit Leuven (KU Leuven), Université de Liège, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut Royal des Sciences Naturelles de Belgique = Royal Belgian Institute of Natural Sciences (IRSNB / RBINS)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2018
• Subjects: natural history museum; notothenioidei; 16S rRNA; COI; Southern Ocean; Antarctica; [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology; Antarc*; Antarctic
• Online Access: https://hal.science/hal-03868078; https://hal.science/hal-03868078/document; https://hal.science/hal-03868078/file/doi_321467.pdf; https://doi.org/10.3389/fevo.2018.00151

International audience Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean.