Applying high-throughput rRNA gene sequencing to assess microbial contamination of a 40-year old exposed archaeological profile

Daniel S. Jones, Gilliane Monnier, Aspen Cooper, Mile Baković, Goran Pajović, Nikola Borovinić, Gilbert Tostevin

Research output: Contribution to journalArticlepeer-review

Abstract

In recent years there has been a surge in the recovery of ancient organic molecules from archaeological contexts. These analyses are yielding unprecedented insights into human evolution and cultural practices, and are providing valuable data for reconstructing paleoenvironments. However, contamination of archaeological sediments by microorganisms can alter ancient biomolecular data. Furthermore, the extent to which microbes can penetrate ancient archaeological sediments once these are exposed by excavation is unknown. We tested this question at Crvena Stijena, a rock shelter in the Dinaric alps in Montenegro that contains archaeological deposits spanning more than 80,000 years. Excavations in the early 1960s exposed these profiles, which have been cleaned several times to permit sampling for archaeological, geological, and biomolecular analyses. The growth of green biofilms on the exposed profiles after cleaning has prompted the question of whether this surface contamination extends into the profile. To test this question, we examined five different geological layers by sampling sediments from the exposed surface and at 1 cm intervals horizontally into the profile. Results from 16S rRNA gene sequencing show that samples from sediment surfaces have distinct microbial communities from most samples collected more than 1 cm deep, and microbial biomass from the deeper samples is very low. Together, this evidence strongly indicates that microbial contamination is limited to the profile surfaces. This lowers the likelihood that ancient biomolecules in these sediments have been altered by recent changes to the in situ microbial community, and that cleaning of the profiles before sampling may not need to exceed 2 cm in depth. These results lend further support to the research utility of limited vertical sampling along archaeological profiles and witness sections, a strategy which conserves rare and limited archaeological deposits while helping to tackle key questions about the past.

Original languageEnglish (US)
Article number105308
JournalJournal of Archaeological Science
Volume126
DOIs
StatePublished - Feb 2021

Bibliographical note

Funding Information:
G. Monnier, G. Tostevin, M. Baković, G. Pajović, and N. Borovinić wish to thank Bob Whallon for his continued guidance and help; the villagers of Petrovići for their immense hospitality; Annie Melton, Samantha Porter, Vasilije Marojević, Đuro Pribilović, and the many other talented students and workers who assist with fieldwork and laboratory work; and the Montenegrin Ministry of Culture , Montenegro the Montenegrin Academy of Sciences, the United States National Science Foundation, United States ( NSF-BCS 1758285 ), the University of Minnesota's Office of the Vice President of Research Grant-in-Aid program, and the University of Minnesota's College of Liberal Arts Talle Faculty Research Award, for funding and support. Thanks to Kathryn Hobart for demonstrating the sample collection procedure, and to the staff at the University of Minnesota, United States Genomics Center for support with sequencing and handling of custom amplicon libraries.

Funding Information:
G. Monnier, G. Tostevin, M. Bakovi?, G. Pajovi?, and N. Borovini? wish to thank Bob Whallon for his continued guidance and help; the villagers of Petrovi?i for their immense hospitality; Annie Melton, Samantha Porter, Vasilije Marojevi?, ?uro Pribilovi?, and the many other talented students and workers who assist with fieldwork and laboratory work; and the Montenegrin Ministry of Culture, Montenegro the Montenegrin Academy of Sciences, the United States National Science Foundation, United States (NSF-BCS 1758285), the University of Minnesota's Office of the Vice President of Research Grant-in-Aid program, and the University of Minnesota's College of Liberal Arts Talle Faculty Research Award, for funding and support. Thanks to Kathryn Hobart for demonstrating the sample collection procedure, and to the staff at the University of Minnesota, United States Genomics Center for support with sequencing and handling of custom amplicon libraries.

Publisher Copyright:
© 2020 Elsevier Ltd

Keywords

  • 16S rRNA gene
  • Archaeological profile
  • Contamination
  • Crvena stijena
  • Microbial community
  • Paleolithic
  • Sediment

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