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Ekram MAE, Campbell M, Kose SH, Plet C, Hamilton R, Bijaksana S, Grice K, Russell J, Stevenson J, Vogel H, Coolen MJL. A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia). GEOBIOLOGY 2024; 22:e12599. [PMID: 38745401 DOI: 10.1111/gbi.12599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/24/2023] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.
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Affiliation(s)
- Md Akhtar-E Ekram
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Matthew Campbell
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Sureyya H Kose
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Chloe Plet
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Rebecca Hamilton
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Kliti Grice
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - James Russell
- Department of Earth, Environmental, and Planetary Sciences (DEEPS), Brown University, Providence, Rhode Island, USA
| | - Janelle Stevenson
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Marco J L Coolen
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
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Thorpe AC, Mackay EB, Goodall T, Bendle JA, Thackeray SJ, Maberly SC, Read DS. Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community. Mol Ecol Resour 2024; 24:e13903. [PMID: 37994249 DOI: 10.1111/1755-0998.13903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/26/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research.
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Affiliation(s)
- Amy C Thorpe
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | - Tim Goodall
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
| | - James A Bendle
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
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3
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Muschick M, Jemmi E, Lengacher N, Hänsch S, Wales N, Kishe MA, Mwaiko S, Dieleman J, Lever MA, Salzburger W, Verschuren D, Seehausen O. Ancient DNA is preserved in fish fossils from tropical lake sediments. Mol Ecol 2023; 32:5913-5931. [PMID: 37830773 DOI: 10.1111/mec.17159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.
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Affiliation(s)
- Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Eliane Jemmi
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Nicholas Lengacher
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Stephanie Hänsch
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Mary A Kishe
- Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Jorunn Dieleman
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | | | - Dirk Verschuren
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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5
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Picard M, Pochon X, Atalah J, Pearman JK, Rees A, Howarth JD, Moy CM, Vandergoes MJ, Hawes I, Khan S, Wood SA. Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes. Sci Rep 2022; 12:12810. [PMID: 35896561 PMCID: PMC9329365 DOI: 10.1038/s41598-022-14216-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.
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Affiliation(s)
- Maïlys Picard
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand. .,Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand.
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand.,Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Andrew Rees
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Christopher M Moy
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | | | - Ian Hawes
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand
| | - Samiullah Khan
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
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6
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Lake microbiome and trophy fluctuations of the ancient hemp rettery. Sci Rep 2022; 12:8846. [PMID: 35614182 PMCID: PMC9132974 DOI: 10.1038/s41598-022-12761-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply—hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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