Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil

Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.