Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

Abstract

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 (Ambrosia artemisiifolia 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.

Genomics of natural history collections for understanding evolution in the wild

“…In a study using samples collected over 180 years of Ambrosia artemisifolia and Arabidopsis thaliana, Bieker and collaborators showed that some microbial species are exclusive to postmortem herbarium specimens and are not found in contemporary plant collections. These microbial species may compromise up to 7% of the historic samples' microbial DNA content (Bieker et al, 2020).…”

“…In the particular case of the invasive species Ambrosia artemisifolia, only after removing these contaminants, did researchers observe a shift in the microbial community over time (Bieker et al, 2020).…”

“…These microbial species may compromise up to 7% of the historic samples' microbial DNA content (Bieker et al, 2020). In the particular case of the invasive species Ambrosia artemisifolia, only after removing these contaminants, did researchers observe a shift in the microbial community over time (Bieker et al, 2020). Altogether, this study demonstrated that it is possible to obtain metagenomic profiles from herbarium samples and perform temporal studies to identify changes in the community, but incorporation of additional analysis specific to NHC metagenomics data may be necessary (Bieker et al, 2020).…”

“…In the particular case of the invasive species Ambrosia artemisifolia, only after removing these contaminants, did researchers observe a shift in the microbial community over time (Bieker et al, 2020). Altogether, this study demonstrated that it is possible to obtain metagenomic profiles from herbarium samples and perform temporal studies to identify changes in the community, but incorporation of additional analysis specific to NHC metagenomics data may be necessary (Bieker et al, 2020). Studies such as this could be further complemented by looking at environmental changes in association with shifts in the microbial community.…”

“…In a study using samples collected over 180 years of Ambrosia artemisifolia and Arabidopsis thaliana , Bieker and collaborators showed that some microbial species are exclusive to postmortem herbarium specimens and are not found in contemporary plant collections. These microbial species may compromise up to 7% of the historic samples' microbial DNA content (Bieker et al, 2020). In the particular case of the invasive species Ambrosia artemisifolia, only after removing these contaminants, did researchers observe a shift in the microbial community over time (Bieker et al, 2020).…”