Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples.
peer reviewed 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 whic...
Published in: | Frontiers in Ecology and Evolution |
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Format: | Article in Journal/Newspaper |
Language: | English |
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2018
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Online Access: | https://orbi.uliege.be/handle/2268/228129 https://orbi.uliege.be/bitstream/2268/228129/1/Heindler%20et%20al.%202018%20%28Front.%20Ecol.%20Evol.%29.pdf https://doi.org/10.3389/fevo.2018.00151 |
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ftorbi:oai:orbi.ulg.ac.be:2268/228129 2024-04-21T07:49:46+00:00 Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. Heindler, Franz M. Christiansen, Henrik Frederich, Bruno Dettaï, Agnes Lepoint, Gilles Maes, Gregory E. Van de Putte, Anton P. Volckaert, Filip A. M. FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège 2018-09-28 https://orbi.uliege.be/handle/2268/228129 https://orbi.uliege.be/bitstream/2268/228129/1/Heindler%20et%20al.%202018%20%28Front.%20Ecol.%20Evol.%29.pdf https://doi.org/10.3389/fevo.2018.00151 en eng Frontiers Media S.A. urn:issn:2296-701X https://orbi.uliege.be/handle/2268/228129 info:hdl:2268/228129 https://orbi.uliege.be/bitstream/2268/228129/1/Heindler%20et%20al.%202018%20%28Front.%20Ecol.%20Evol.%29.pdf doi:10.3389/fevo.2018.00151 scopus-id:2-s2.0-85091489141 open access http://purl.org/coar/access_right/c_abf2 info:eu-repo/semantics/openAccess Frontiers in Ecology and Evolution, 6, 151 (2018-09-28) Trematomus trophic ecology Southern Ocean metabarcoding biodiversity microbiome Notothenioidei Life sciences Environmental sciences & ecology Biochemistry biophysics & molecular biology Aquatic sciences & oceanology Zoology Sciences du vivant Sciences de l’environnement & écologie Biochimie biophysique & biologie moléculaire Sciences aquatiques & océanologie Zoologie journal article http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article peer reviewed 2018 ftorbi https://doi.org/10.3389/fevo.2018.00151 2024-03-27T14:53:43Z peer reviewed 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. Refugia and ecosystem tolerance in the Southern Ocean (RECTO) - Research project BR/154/A1/RECTO Article in Journal/Newspaper Antarc* Antarctic Southern Ocean University of Liège: ORBi (Open Repository and Bibliography) Frontiers in Ecology and Evolution 6 |
institution |
Open Polar |
collection |
University of Liège: ORBi (Open Repository and Bibliography) |
op_collection_id |
ftorbi |
language |
English |
topic |
Trematomus trophic ecology Southern Ocean metabarcoding biodiversity microbiome Notothenioidei Life sciences Environmental sciences & ecology Biochemistry biophysics & molecular biology Aquatic sciences & oceanology Zoology Sciences du vivant Sciences de l’environnement & écologie Biochimie biophysique & biologie moléculaire Sciences aquatiques & océanologie Zoologie |
spellingShingle |
Trematomus trophic ecology Southern Ocean metabarcoding biodiversity microbiome Notothenioidei Life sciences Environmental sciences & ecology Biochemistry biophysics & molecular biology Aquatic sciences & oceanology Zoology Sciences du vivant Sciences de l’environnement & écologie Biochimie biophysique & biologie moléculaire Sciences aquatiques & océanologie Zoologie Heindler, Franz M. Christiansen, Henrik Frederich, Bruno Dettaï, Agnes Lepoint, Gilles Maes, Gregory E. Van de Putte, Anton P. Volckaert, Filip A. M. Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
topic_facet |
Trematomus trophic ecology Southern Ocean metabarcoding biodiversity microbiome Notothenioidei Life sciences Environmental sciences & ecology Biochemistry biophysics & molecular biology Aquatic sciences & oceanology Zoology Sciences du vivant Sciences de l’environnement & écologie Biochimie biophysique & biologie moléculaire Sciences aquatiques & océanologie Zoologie |
description |
peer reviewed 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. Refugia and ecosystem tolerance in the Southern Ocean (RECTO) - Research project BR/154/A1/RECTO |
author2 |
FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège |
format |
Article in Journal/Newspaper |
author |
Heindler, Franz M. Christiansen, Henrik Frederich, Bruno Dettaï, Agnes Lepoint, Gilles Maes, Gregory E. Van de Putte, Anton P. Volckaert, Filip A. M. |
author_facet |
Heindler, Franz M. Christiansen, Henrik Frederich, Bruno Dettaï, Agnes Lepoint, Gilles Maes, Gregory E. Van de Putte, Anton P. Volckaert, Filip A. M. |
author_sort |
Heindler, Franz M. |
title |
Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
title_short |
Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
title_full |
Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
title_fullStr |
Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
title_full_unstemmed |
Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
title_sort |
historical dna metabarcoding of the prey and microbiome of trematomid fishes using museum samples. |
publisher |
Frontiers Media S.A. |
publishDate |
2018 |
url |
https://orbi.uliege.be/handle/2268/228129 https://orbi.uliege.be/bitstream/2268/228129/1/Heindler%20et%20al.%202018%20%28Front.%20Ecol.%20Evol.%29.pdf https://doi.org/10.3389/fevo.2018.00151 |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
Frontiers in Ecology and Evolution, 6, 151 (2018-09-28) |
op_relation |
urn:issn:2296-701X https://orbi.uliege.be/handle/2268/228129 info:hdl:2268/228129 https://orbi.uliege.be/bitstream/2268/228129/1/Heindler%20et%20al.%202018%20%28Front.%20Ecol.%20Evol.%29.pdf doi:10.3389/fevo.2018.00151 scopus-id:2-s2.0-85091489141 |
op_rights |
open access http://purl.org/coar/access_right/c_abf2 info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3389/fevo.2018.00151 |
container_title |
Frontiers in Ecology and Evolution |
container_volume |
6 |
_version_ |
1796933767769620480 |