Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify organic remains, including their morphological description. However, this is strongly constrained by the researcher's ability to identify residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions

Fracasso, I.; Zaccone, C.; Oskolkov, N.; Da Ros, L.; Dinella, A.; Belelli Marchesini, L.; Buzzini, P.; Sannino, C.; Turchetti, B.; Cesco, S.; Le Roux, G.; Tonon, G.; Vernesi, C.; Mimmo, T.; Ventura, M.; Borruso, L. (2024-11-01). Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. SCIENCE OF THE TOTAL ENVIRONMENT, 908: 168159. doi: 10.1016/j.scitotenv.2023.168159 handle: https://hdl.handle.net/10449/82935

Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA

Belelli Marchesini, Luca;Vernesi, Cristiano;
2024-11-01

Abstract

Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify organic remains, including their morphological description. However, this is strongly constrained by the researcher's ability to identify residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions
Ancient DNA
Climate change
Deamination patterns
Metagenomic
Paleobiodiversity
Soil ecology
Settore BIO/07 - ECOLOGIA
1-nov-2024
Fracasso, I.; Zaccone, C.; Oskolkov, N.; Da Ros, L.; Dinella, A.; Belelli Marchesini, L.; Buzzini, P.; Sannino, C.; Turchetti, B.; Cesco, S.; Le Roux, G.; Tonon, G.; Vernesi, C.; Mimmo, T.; Ventura, M.; Borruso, L. (2024-11-01). Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. SCIENCE OF THE TOTAL ENVIRONMENT, 908: 168159. doi: 10.1016/j.scitotenv.2023.168159 handle: https://hdl.handle.net/10449/82935
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