Dataset Information

High-Throughput DNA sequencing of ancient wood.

ABSTRACT: Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.

SUBMITTER: Wagner S

PROVIDER: S-EPMC5896730 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Publications

High-Throughput DNA sequencing of ancient wood.

Wagner Stefanie S Lagane Frédéric F Seguin-Orlando Andaine A Schubert Mikkel M Leroy Thibault T Guichoux Erwan E Chancerel Emilie E Bech-Hebelstrup Inger I Bernard Vincent V Billard Cyrille C Billaud Yves Y Bolliger Matthias M Croutsch Christophe C Čufar Katarina K Eynaud Frédérique F Heussner Karl Uwe KU Köninger Joachim J Langenegger Fabien F Leroy Frédéric F Lima Christine C Martinelli Nicoletta N Momber Garry G Billamboz André A Nelle Oliver O Palomo Antoni A Piqué Raquel R Ramstein Marianne M Schweichel Roswitha R Stäuble Harald H Tegel Willy W Terradas Xavier X Verdin Florence F Plomion Christophe C Kremer Antoine A Orlando Ludovic L

Molecular ecology 20180303 5

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to ...[more]

PMID: 29412519

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Project description:Wood-inhabiting fungi (WIF) are pivotal to wood decomposition, which in turn strongly influences nutrient dynamics in forest soils. However, their dispersal mechanisms remain unclear. We hypothesized that the majority of WIF are soil-borne. For this reason, the presented research aimed to quantify the contribution of soil as a source and medium for the dispersal of WIF to deadwood using high-throughput sequencing. We tested effects of tree species (specifically Schima superba and Pinus massoniana) on the percentage of WIF shared between soil and deadwood in a Chinese subtropical forest ecosystem. We also assessed the taxonomic and ecological functional group affiliations of the fungal community shared between soil and deadwood. Our results indicate that soil is a major route for WIF colonization as 12%-15% (depending on the tree species) of soil fungi were simultaneously detected in deadwood. We also demonstrate that tree species (p < 0.01) significantly shapes the composition of the shared soil and deadwood fungal community. The pH of decomposing wood was shown to significantly correspond (p < 0.01) with the shared community of wood-inhabiting (of both studied tree species) and soil fungi. Furthermore, our data suggest that a wide range of fungal taxonomic (Rozellida, Zygomycota, Ascomycota, and Basidiomycota) and ecological functional groups (saprotrophs, ectomycorrhizal, mycoparasites, and plant pathogens) may use soil as a source and medium for transport to deadwood in subtropical forest ecosystem. While 12%-62% of saprotrophic, ectomycorrhizal, and mycoparasitic WIF may utilize soil to colonize deadwood, only 5% of the detected plant pathogens were detected in both soil and deadwood, implying that these fungi use other dispersal routes. Animal endosymbionts and lichenized WIF were not detected in the soil samples. Future studies should consider assessing the relative contributions of other possible dispersal mechanisms (e.g. wind, water splash, water dispersal, animal dispersal, and mycelial network) in the colonization of deadwood by soil fungi.

Dataset Information

High-Throughput DNA sequencing of ancient wood.

Publications

High-Throughput DNA sequencing of ancient wood.

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