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 -