Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Clio Der Sarkissian; Vianney Pichereau; Catherine Dupont; Peter Carsten Ilsøe; Mickael Perrigault; Paul Butler; Laurent Chauvaud; Jón Eiríksson; James Scourse; Christine Paillard; Ludovic Antoine Alexandre Orlando

doi:10.1111/1755-0998.12679

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter Carsten Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Antoine Alexandre Orlando^*

^*Corresponding author for this work

33 Citations (Scopus)

Abstract

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.

Original language	English
Journal	Molecular Ecology Resources
Volume	17
Issue number	5
Pages (from-to)	835-853
Number of pages	19
ISSN	1755-098X
DOIs	https://doi.org/10.1111/1755-0998.12679
Publication status	Published - Sept 2017

Keywords

ancient DNA
high-throughput DNA sequencing
marine mollusc shells
metagenomics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1111/1755-0998.12679

https://hal.archives-ouvertes.fr/hal-01624435/document

Cite this

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title = "Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past",

abstract = "Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.",

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author = "{Der Sarkissian}, Clio and Vianney Pichereau and Catherine Dupont and Ils{\o}e, {Peter Carsten} and Mickael Perrigault and Paul Butler and Laurent Chauvaud and J{\'o}n Eir{\'i}ksson and James Scourse and Christine Paillard and Orlando, {Ludovic Antoine Alexandre}",

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AU - Der Sarkissian, Clio

AU - Pichereau, Vianney

AU - Dupont, Catherine

AU - Ilsøe, Peter Carsten

AU - Perrigault, Mickael

AU - Butler, Paul

AU - Chauvaud, Laurent

AU - Eiríksson, Jón

AU - Scourse, James

AU - Paillard, Christine

AU - Orlando, Ludovic Antoine Alexandre

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Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Abstract

Keywords

UN SDGs

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