The Neolithic site “La Marmotta”: DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood

Abstract

IntroductionThe evaluation of biological degradation of waterlogged archeological wood is crucial to choose the conservative and protective treatments to be applied to the wooden material. The waterlogged environmental conditions are characterized by oxygen scarcity, only allowing the growth of adapted microbes capable to degrade the organic wooden material, mainly erosion bacteria and soft-rot fungi. In this work, we characterized and evaluated the biodegradation state and the microbial communities of wooden fragments preserved in storage tanks. These were preserved by waterlogging within the Neolithic village “La Marmotta,” currently found under the Bracciano Lake (Lazio, Italy).MethodsThe waterlogged wood samples were first identified taxonomically with an optical microscope, also allowing an evaluation of their preservation state. The microbial community was then evaluated through the sequencing of Internal Transcribed Spacer sequences for fungi and 16S for bacteria with the Oxford Nanopore Technologies (ONT) MinION platform.ResultsThe identified microbial community appears to be consistent with the waterlogged samples, as many bacteria attributable to the erosion of wood and ligninolytic fungi have been sequenced.DiscussionThe reported results highlight the first use of targeted metabarcoding by ONT applied to study the biodeterioration of waterlogged archeological wood.

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

“…Beccaccioli and colleagues [29] targeted the ITS and 16S rDNA regions to understand the microbial communities contributing to the deterioration of waterlogged wooden fragments from pirogues. The authors also developed and tested a custom pipeline for their bioinformatics analysis.…”

Experimental waterlogging of grape seeds, impact on seed shape and geometrical reversing for morphometric inference

“…However, under anaerobic conditions complex microbial processes will still result in some decomposition of organic matter through fermentation reactions and anaerobic respiration (Herndon et al, 2015;Keller and Takagi, 2013). On waterlogged plant remains these processes more especially involve bacteria over fungal species (Beccaccioli et al, 2023). Chemical factors also impact organic decomposition in combination with micro-organisms.…”