Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community
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Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community. / Bieker, Vanessa C.; Barreiro, Fatima Sanchez; Rasmussen, Jacob A.; Brunier, Marie; Wales, Nathan; Martin, Michael D.
In: Molecular Ecology Resources, Vol. 20, No. 5, 2020, p. 1206-1219.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community
AU - Bieker, Vanessa C.
AU - Barreiro, Fatima Sanchez
AU - Rasmussen, Jacob A.
AU - Brunier, Marie
AU - Wales, Nathan
AU - Martin, Michael D.
PY - 2020
Y1 - 2020
N2 - Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosiaartemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.
AB - Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosiaartemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.
KW - aDNA
KW - Ambrosia artemisiifolia
KW - Arabidopsis thaliana
KW - genomics
KW - historical herbarium collections
KW - metagenomics
KW - AMBROSIA-ARTEMISIIFOLIA
KW - ALTERNARIA-SOLANI
KW - GENETIC ANALYSES
KW - ANCIENT
KW - DNA
KW - SEQUENCE
KW - ILLUMINATE
KW - FRAMEWORK
KW - GENOMICS
KW - ECOLOGY
U2 - 10.1111/1755-0998.13174
DO - 10.1111/1755-0998.13174
M3 - Journal article
C2 - 32320134
VL - 20
SP - 1206
EP - 1219
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 5
ER -
ID: 246672921