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

Summary

Scientists extracted and analyzed ancient DNA from plant roots and soil samples stored in herbarium collections for over 120 years. The DNA showed typical signs of age and preserved microbial communities that originally lived in the soil around these plants. By comparing these ancient microbial communities to modern ones, researchers found that herbarium storage preserved the original characteristics of soil microbiomes, making these museum specimens valuable for studying how farming practices have changed soil ecosystems over time.

Background

Natural history herbarium collections contain century-old plant specimens that were involuntarily preserved with their associated soil microbiomes. These collections, encompassing over 400 million plant samples globally, were mostly established in the 19th and early 20th centuries, predating major global environmental changes. This offers a unique opportunity to study historical microbial communities before intensive agricultural practices altered soil ecosystems.

Objective

To validate the use of century-old herbarium plant roots and associated rhizospheric soils as sources for extracting ancient DNA and characterizing historical soil microbial communities. The study aimed to demonstrate that herbarium-extracted DNA reflects original plant-associated microbial composition and that preservation did not dramatically alter biodiversity features or assembly rules.

Results

DNA displayed typical ancient DNA features including cytosine deamination and fragments predominantly shorter than 50 bp. Herbarium microbial communities clustered with extant soil communities rather than other environments. Soil communities were richer in diversity than root communities, with clear separation based on sample type, collection site, and plant species, reflecting known soil microbiome assembly rules.

Conclusion

Herbarium-associated DNA retention of original microbiome characteristics validates using century-old herbarium specimens to investigate historical soil microbial diversity and temporal dynamics. This approach enables investigation of long-term responses of cultivated soil microbiomes to environmental changes, particularly the impact of intensive farming practices since the mid-20th century.
  • Published in:Molecular Ecology Resources,
  • Study Type:Experimental Research,
  • Source: PMID: 40411280, DOI: 10.1111/1755-0998.14122
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