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Chew XZ, Cobcroft J, Hutson KS. Fish ectoparasite detection, collection and curation. ADVANCES IN PARASITOLOGY 2024; 125:105-157. [PMID: 39095111 DOI: 10.1016/bs.apar.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Fish parasitology is a dynamic and internationally important discipline with numerous biological, ecological and practical applications. We reviewed optimal fish and parasite sampling methods for key ectoparasite phyla (i.e. Ciliophora, Platyhelminthes, Annelida and Arthropoda) as well as recent advances in molecular detection of ectoparasites in aquatic environments. Ideally, fish capture and anaesthesia as well as parasite recovery methods should be validated to eliminate potential sampling bias and inaccuracy in determining ectoparasite population parameters. There are considerable advantages to working with fresh samples and live parasites, when combined with appropriate fixation methods, as sampling using dead or decaying materials can lead to rapid decomposition of soft-bodied parasites and subsequent challenges for identification. Sampling methods differ between target phyla, and sometimes genera, with optimum techniques largely associated with identification of parasite microhabitat and the method of attachment. International advances in fish parasitology can be achieved through the accession of whole specimens and/or molecular voucher specimens (i.e. hologenophores) in curated collections for further study. This approach is now critical for data quality because of the increased application of environmental DNA (eDNA) for the detection and surveillance of parasites in aquatic environments where the whole organism may be unavailable. Optimal fish parasite sampling methods are emphasised to aid repeatability and reliability of parasitological studies that require accurate biodiversity and impact assessments, as well as precise surveillance and diagnostics.
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Affiliation(s)
- Xian Zhe Chew
- James Cook University Singapore, Singapore City, Singapore
| | - Jennifer Cobcroft
- James Cook University Singapore, Singapore City, Singapore; College of Science and Engineering, Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kate S Hutson
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia; Cawthron Institute, Nelson, New Zealand.
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2
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Laine J, Mak SST, Martins NFG, Chen X, Gilbert MTP, Jones FC, Pedersen MW, Romundset A, Foote AD. Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Curr Biol 2024; 34:1142-1147.e6. [PMID: 38350445 DOI: 10.1016/j.cub.2024.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.
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Affiliation(s)
- Jan Laine
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Nuno F G Martins
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Xihan Chen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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3
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Von Eggers JM, Wisnoski NI, Calder JW, Capo E, Groff DV, Krist AC, Shuman B. Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environ Microbiol 2024; 26:e16607. [PMID: 38477387 DOI: 10.1111/1462-2920.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes-like dispersal limitation-contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.
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Affiliation(s)
- Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
| | - Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, Wyoming, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - John W Calder
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Dulcinea V Groff
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
| | - Amy C Krist
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Bryan Shuman
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
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Yang Q, Yan Y, Huang J, Wang Z, Feng M, Cheng H, Zhang P, Zhang H, Xu J, Zhang M. The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms. Microorganisms 2023; 11:2807. [PMID: 38004818 PMCID: PMC10672829 DOI: 10.3390/microorganisms11112807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.
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Affiliation(s)
- Qian Yang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Yifeng Yan
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Jinhe Huang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Zhaolei Wang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Mingjun Feng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Haowu Cheng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Peiyu Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Huan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Min Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
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5
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Pantel JH, Becks L. Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics. Trends Ecol Evol 2023; 38:760-772. [PMID: 37437547 DOI: 10.1016/j.tree.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 07/14/2023]
Abstract
While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.
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Affiliation(s)
- Jelena H Pantel
- Ecological Modelling, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45117 Essen, Germany.
| | - Lutz Becks
- University of Konstanz, Aquatic Ecology and Evolution, Limnological Institute University of Konstanz Mainaustraße 252 78464, Konstanz/Egg, Germany
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6
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Tornabene BJ, Smalling KL, Givens CE, Oja EB, Hossack BR. Energy-related wastewater contamination alters microbial communities of sediment, water, and amphibian skin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163160. [PMID: 37003337 DOI: 10.1016/j.scitotenv.2023.163160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 05/27/2023]
Abstract
To inform responsible energy development, it is important to understand the ecological effects of contamination events. Wastewaters, a common byproduct of oil and gas extraction, often contain high concentrations of sodium chloride (NaCl) and heavy metals (e.g., strontium and vanadium). These constituents can negatively affect aquatic organisms, but there is scarce information for how wastewaters influence potentially distinct microbiomes in wetland ecosystems. Additionally, few studies have concomitantly investigated effects of wastewaters on the habitat (water and sediment) and skin microbiomes of amphibians or relationships among these microbial communities. We sampled microbiomes of water, sediment, and skin of four larval amphibian species across a gradient of chloride contamination (0.04-17,500 mg/L Cl) in the Prairie Pothole Region of North America. We detected 3129 genetic phylotypes and 68 % of those phylotypes were shared among the three sample types. The most common shared phylotypes were Proteobacteria, Firmicutes, and Bacteroidetes. Salinity of wastewaters increased dissimilarity within all three microbial communities, but not the diversity or richness of water and skin microbial communities. Strontium was associated with lower diversity and richness of sediment microbial communities, but not those of water or amphibian skin, likely because metal deposition occurs in sediment when wetlands dry. Based on Bray Curtis distance matrices, sediment microbiomes were similar to those of water, but neither had substantial overlap with amphibian microbiomes. Species identity was the strongest predictor of amphibian microbiomes; frog microbiomes were similar but differed from that of the salamander, whose microbiome had the lowest richness and diversity. Understanding how effects of wastewaters on the dissimilarity, richness, and diversity of microbial communities also influence the ecosystem function of communities will be an important next step. However, our study provides novel insight into the characteristics of, and associations among, different wetland microbial communities and effects of wastewaters from energy production.
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Affiliation(s)
- Brian J Tornabene
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT 59812, USA.
| | - Kelly L Smalling
- U.S. Geological Survey, New Jersey Water Science Center, 3450 Princeton Pike, Suite 110, Lawrenceville, NJ 08648, USA
| | - Carrie E Givens
- U.S. Geological Survey, Upper Midwest Water Science Center, 5840 Enterprise Drive, Lansing, MI 48911, USA
| | - Emily B Oja
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT 59812, USA
| | - Blake R Hossack
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT 59812, USA; Wildlife Biology Program, W. A. Franke College of Forestry & Conservation, University of Montana, Missoula, MT 59812, USA
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7
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Everett R, Cribdon B. MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.888421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
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8
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The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA. Int J Mol Sci 2022; 23:ijms232213690. [PMID: 36430193 PMCID: PMC9698649 DOI: 10.3390/ijms232213690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
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Strugnell JM, McGregor HV, Wilson NG, Meredith KT, Chown SL, Lau SCY, Robinson SA, Saunders KM. Emerging biological archives can reveal ecological and climatic change in Antarctica. GLOBAL CHANGE BIOLOGY 2022; 28:6483-6508. [PMID: 35900301 PMCID: PMC9826052 DOI: 10.1111/gcb.16356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Anthropogenic climate change is causing observable changes in Antarctica and the Southern Ocean including increased air and ocean temperatures, glacial melt leading to sea-level rise and a reduction in salinity, and changes to freshwater water availability on land. These changes impact local Antarctic ecosystems and the Earth's climate system. The Antarctic has experienced significant past environmental change, including cycles of glaciation over the Quaternary Period (the past ~2.6 million years). Understanding Antarctica's paleoecosystems, and the corresponding paleoenvironments and climates that have shaped them, provides insight into present day ecosystem change, and importantly, helps constrain model projections of future change. Biological archives such as extant moss beds and peat profiles, biological proxies in lake and marine sediments, vertebrate animal colonies, and extant terrestrial and benthic marine invertebrates, complement other Antarctic paleoclimate archives by recording the nature and rate of past ecological change, the paleoenvironmental drivers of that change, and constrain current ecosystem and climate models. These archives provide invaluable information about terrestrial ice-free areas, a key location for Antarctic biodiversity, and the continental margin which is important for understanding ice sheet dynamics. Recent significant advances in analytical techniques (e.g., genomics, biogeochemical analyses) have led to new applications and greater power in elucidating the environmental records contained within biological archives. Paleoecological and paleoclimate discoveries derived from biological archives, and integration with existing data from other paleoclimate data sources, will significantly expand our understanding of past, present, and future ecological change, alongside climate change, in a unique, globally significant region.
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Affiliation(s)
- Jan M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Securing Antarctica's Environmental FutureJames Cook UniversityTownsvilleQueenslandAustralia
| | - Helen V. McGregor
- Securing Antarctica's Environmental Future, School of Earth, Atmospheric and Life SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Nerida G. Wilson
- Securing Antarctica's Environmental FutureWestern Australian MuseumWestern AustraliaAustralia
- Research and CollectionsWestern Australian MuseumWestern AustraliaAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Karina T. Meredith
- Securing Antarctica's Environmental FutureAustralian Nuclear Science and Technology OrganisationLucas HeightsNew South WalesAustralia
| | - Steven L. Chown
- Securing Antarctica's Environmental Future, School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Sally C. Y. Lau
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Securing Antarctica's Environmental FutureJames Cook UniversityTownsvilleQueenslandAustralia
| | - Sharon A. Robinson
- Securing Antarctica's Environmental Future, School of Earth, Atmospheric and Life SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Krystyna M. Saunders
- Securing Antarctica's Environmental Future, School of Earth, Atmospheric and Life SciencesUniversity of WollongongWollongongNew South WalesAustralia
- Securing Antarctica's Environmental FutureAustralian Nuclear Science and Technology OrganisationLucas HeightsNew South WalesAustralia
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasmaniaAustralia
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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Barouillet C, Vasselon V, Keck F, Millet L, Etienne D, Galop D, Rius D, Domaizon I. Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes. Sci Rep 2022; 12:7899. [PMID: 35551223 PMCID: PMC9098483 DOI: 10.1038/s41598-022-12041-7] [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: 11/30/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.
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Affiliation(s)
- Cécilia Barouillet
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France. .,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.
| | - Valentin Vasselon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France.,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.,OFB, Site INRAE UMR CARRTEL, 74200, Thonon-les-Bains, France
| | - François Keck
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France.,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France
| | | | - David Etienne
- Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 73370, Le Bourget du Lac, France
| | - Didier Galop
- GEODE UMR 5602 CNRS, Université de Toulouse, 31058, Toulouse, France.,Labex DRIIHM, OHM Pyrénées, CNRS/INEE, Toulouse, France
| | - Damien Rius
- CNRS, Chrono Environnement, 25000, Besançon, France
| | - Isabelle Domaizon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France. .,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.
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12
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Isanta-Navarro J, Klauschies T, Wacker A, Martin-Creuzburg D. A sterol-mediated gleaner-opportunist trade-off underlies the evolution of grazer resistance to cyanobacteria. Proc Biol Sci 2022; 289:20220178. [PMID: 35538780 PMCID: PMC9091858 DOI: 10.1098/rspb.2022.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The human-caused proliferation of cyanobacteria severely impacts consumers in freshwater ecosystems. Toxicity is often singled out as the sole trait to which consumers can adapt, even though cyanobacteria are not necessarily toxic and the lack of nutritionally critical sterols in cyanobacteria is known to impair consumers. We studied the relative significance of toxicity and dietary sterol deficiency in driving the evolution of grazer resistance to cyanobacteria in a large lake with a well-documented history of eutrophication and oligotrophication. Resurrecting decades-old Daphnia genotypes from the sediment allowed us to show that the evolution and subsequent loss of grazer resistance to cyanobacteria involved an adaptation to changes in both toxicity and dietary sterol availability. The adaptation of Daphnia to changes in cyanobacteria abundance revealed a sterol-mediated gleaner-opportunist trade-off. Genotypes from peak-eutrophic periods showed a higher affinity for dietary sterols at the cost of a lower maximum growth rate, whereas genotypes from more oligotrophic periods showed a lower affinity for dietary sterols in favour of a higher maximum growth rate. Our data corroborate the significance of sterols as limiting nutrients in aquatic food webs and highlight the applicability of the gleaner-opportunist trade-off for reconstructing eco-evolutionary processes.
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Affiliation(s)
| | - Toni Klauschies
- Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Alexander Wacker
- Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Dominik Martin-Creuzburg
- Department of Aquatic Ecology, Research Station Bad Saarow, BTU Cottbus-Senftenberg, 15526 Bad Saarow, Germany
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13
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Lezcano MÁ, Sánchez-García L, Quesada A, Carrizo D, Fernández-Martínez MÁ, Cavalcante-Silva E, Parro V. Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses. Front Microbiol 2022; 13:799360. [PMID: 35928160 PMCID: PMC9345047 DOI: 10.3389/fmicb.2022.799360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.
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Affiliation(s)
- María Ángeles Lezcano
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- *Correspondence: María Ángeles Lezcano,
| | | | - Antonio Quesada
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
| | | | | | - Víctor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
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14
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Evolution of Phytoplankton as Estimated from Genetic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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15
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Tsugeki N, Nakane K, Doi H, Ochi N, Kuwae M. Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA. Sci Rep 2022; 12:1741. [PMID: 35110566 PMCID: PMC8810866 DOI: 10.1038/s41598-021-03899-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/10/2021] [Indexed: 11/09/2022] Open
Abstract
Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.
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Affiliation(s)
- Narumi Tsugeki
- Faculty of Law, Matsuyama University, Matsuyama, 790-8578, Ehime, Japan.
| | - Kai Nakane
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, 650-0047, Hyogo, Japan
| | - Natsuki Ochi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
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16
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Cuenca-Cambronero M, Courtney-Mustaphi CJ, Greenway R, Heiri O, Hudson CM, King L, Lemmen KD, Moosmann M, Muschick M, Ngoepe N, Seehausen O, Matthews B. An integrative paleolimnological approach for studying evolutionary processes. Trends Ecol Evol 2022; 37:488-496. [DOI: 10.1016/j.tree.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
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17
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Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA. Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
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18
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Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment. Appl Environ Microbiol 2021; 88:e0184521. [PMID: 34818108 DOI: 10.1128/aem.01845-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.
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19
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O'Grady CJ, Dhandapani V, Colbourne JK, Frisch D. Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs. Mol Ecol Resour 2021; 22:946-961. [PMID: 34672105 DOI: 10.1111/1755-0998.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.
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Affiliation(s)
- Christopher James O'Grady
- School of Life Sciences, University of Warwick, Coventry, UK.,Cell and Gene Therapy Catapult, London, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Dagmar Frisch
- School of Biosciences, University of Birmingham, Birmingham, UK.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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20
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Tardy V, Etienne D, Masclaux H, Essert V, Millet L, Verneaux V, Lyautey E. Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France). FEMS Microbiol Ecol 2021; 97:6362600. [PMID: 34472595 DOI: 10.1093/femsec/fiab126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/31/2021] [Indexed: 11/15/2022] Open
Abstract
Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.
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Affiliation(s)
- Vincent Tardy
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - David Etienne
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - Hélène Masclaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valentin Essert
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Laurent Millet
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valérie Verneaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Emilie Lyautey
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
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21
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From Water into Sediment-Tracing Freshwater Cyanobacteria via DNA Analyses. Microorganisms 2021; 9:microorganisms9081778. [PMID: 34442857 PMCID: PMC8400057 DOI: 10.3390/microorganisms9081778] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 01/04/2023] Open
Abstract
Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.
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22
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Brasell KA, Howarth J, Pearman JK, Fitzsimons SJ, Zaiko A, Pochon X, Vandergoes MJ, Simon K, Wood SA. Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances. Mol Ecol 2021; 30:5137-5150. [PMID: 34379827 DOI: 10.1111/mec.16110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1,100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, c. 50 yrs) phases directly after the earthquakes and more stable (interseismic, c. 250 yr) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrates communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase likely represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.
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Affiliation(s)
- Katie A Brasell
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - Kevin Simon
- University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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23
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Wood SM, Kremp A, Savela H, Akter S, Vartti VP, Saarni S, Suikkanen S. Cyanobacterial Akinete Distribution, Viability, and Cyanotoxin Records in Sediment Archives From the Northern Baltic Sea. Front Microbiol 2021; 12:681881. [PMID: 34211448 PMCID: PMC8241101 DOI: 10.3389/fmicb.2021.681881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria of the order Nostocales, including Baltic Sea bloom-forming taxa Nodularia spumigena, Aphanizomenon flosaquae, and Dolichospermum spp., produce resting stages, known as akinetes, under unfavorable conditions. These akinetes can persist in the sediment and germinate if favorable conditions return, simultaneously representing past blooms and possibly contributing to future bloom formation. The present study characterized cyanobacterial akinete survival, germination, and potential cyanotoxin production in brackish water sediment archives from coastal and open Gulf of Finland in order to understand recent bloom expansion, akinete persistence, and cyanobacteria life cycles in the northern Baltic Sea. Results showed that cyanobacterial akinetes can persist in and germinate from Northern Baltic Sea sediment up to >40 and >400 years old, at coastal and open-sea locations, respectively. Akinete abundance and viability decreased with age and depth of vertical sediment layers. The detection of potential microcystin and nodularin production from akinetes was minimal and restricted to the surface sediment layers. Phylogenetic analysis of culturable cyanobacteria from the coastal sediment core indicated that most strains likely belonged to the benthic genus Anabaena. Potentially planktonic species of Dolichospermum could only be revived from the near-surface layers of the sediment, corresponding to an estimated age of 1–3 years. Results of germination experiments supported the notion that akinetes do not play an equally significant role in the life cycles of all bloom-forming cyanobacteria in the Baltic Sea. Overall, there was minimal congruence between akinete abundance, cyanotoxin concentration, and the presence of cyanotoxin biosynthetic genes in either sediment core. Further research is recommended to accurately detect and quantify akinetes and cyanotoxin genes from brackish water sediment samples in order to further describe species-specific benthic archives of cyanobacteria.
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Affiliation(s)
- Steffaney M Wood
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Anke Kremp
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Henna Savela
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Sultana Akter
- Biotechnology, Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Saija Saarni
- Department of Geography and Geology, University of Turku, Turku, Finland
| | - Sanna Suikkanen
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
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24
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Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Cordellier M, Wojewodzic MW, Wessels M, Kuster C, von Elert E. Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment. ZOOLOGY 2021; 145:125895. [PMID: 33561655 DOI: 10.1016/j.zool.2021.125895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/25/2023]
Abstract
Hatching resting stages of ecologically important organisms such as Daphnia from lake sediments, referred to as resurrection ecology, is a powerful approach to assess changes in alleles and traits over time. However, the utility of the approach is constrained by a few obstacles, including low and/or biased hatching among genotypes. Here, we eliminated such bottlenecks by investigating DNA sequences isolated directly (i.e. without hatching) from resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. While we expected genome-wide changes, we specifically expected changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise FST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances. In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.
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Affiliation(s)
- Mathilde Cordellier
- Universität Hamburg, Biozentrum Grindel, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
| | - Marcin W Wojewodzic
- Cancer Registry of Norway (Kreftregisteret), Institute of Population-Based Cancer Research, Etiology Group, NO-0304, Oslo, Norway; School of Biosciences, University of Birmingham, B15 2TT, United Kingdom.
| | - Martin Wessels
- Institute for Lake Research at the Agency for Environment Baden-Württemberg, 88085, Langenargen, Germany.
| | - Christian Kuster
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
| | - Eric von Elert
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
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Jalili F, Trigui H, Guerra Maldonado JF, Dorner S, Zamyadi A, Shapiro BJ, Terrat Y, Fortin N, Sauvé S, Prévost M. Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant? Toxins (Basel) 2021; 13:toxins13010025. [PMID: 33401450 PMCID: PMC7823770 DOI: 10.3390/toxins13010025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 02/05/2023] Open
Abstract
Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). Aphanothece clathrata brevis, Microcystis aeruginosa, Dolichospermum spiroides
, and Chroococcus minimus were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the Dolichospermum bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that Synechococcus, Microcystis
, and Dolichospermum were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of Microcystis and Dolichospermum. Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1-13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.
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Affiliation(s)
- Farhad Jalili
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
- Correspondence:
| | - Hana Trigui
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Juan Francisco Guerra Maldonado
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Sarah Dorner
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Arash Zamyadi
- Water Research Australia, Adelaide SA 5001, Australia;
| | - B. Jesse Shapiro
- Department of Biological Sciences, University of Montréal, Montréal, QC H2V 0B3, Canada; (B.J.S.); (Y.T.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- McGill Genome Center, McGill University, Montréal, QC H3A 0G1, Canada
| | - Yves Terrat
- Department of Biological Sciences, University of Montréal, Montréal, QC H2V 0B3, Canada; (B.J.S.); (Y.T.)
| | - Nathalie Fortin
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC H4P 2R2, Canada;
| | - Sébastien Sauvé
- Department of Chemistry, University of Montréal, Montréal, QC H3C 3J7, Canada;
| | - Michèle Prévost
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
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Dane M, Anderson NJ, Osburn CL, Colbourne JK, Frisch D. Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability. Ecol Evol 2020; 10:14178-14188. [PMID: 33391708 PMCID: PMC7771157 DOI: 10.1002/ece3.7012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Climate and environmental condition drive biodiversity at many levels of biological organization, from populations to ecosystems. Combined with paleoecological reconstructions, palaeogenetic information on resident populations provides novel insights into evolutionary trajectories and genetic diversity driven by environmental variability. While temporal observations of changing genetic structure are often made of sexual populations, little is known about how environmental change affects the long-term fate of asexual lineages. Here, we provide information on obligately asexual, triploid Daphnia populations from three Arctic lakes in West Greenland through the past 200-300 years to test the impact of environmental change on the temporal and spatial population genetic structure. The contrasting ecological state of the lakes, specifically regarding salinity and habitat structure may explain the observed lake-specific clonal composition over time. Palaeolimnological reconstructions show considerable regional environmental fluctuations since 1,700 (the end of the Little Ice Age), but the population genetic structure in two lakes was almost unchanged with at most two clones per time period. Their local populations were strongly dominated by a single clone that has persisted for 250-300 years. We discuss possible explanations for the apparent population genetic stability: (a) persistent clones are general-purpose genotypes that thrive under broad environmental conditions, (b) clonal lineages evolved subtle genotypic differences unresolved by microsatellite markers, or (c) epigenetic modifications allow for clonal adaptation to changing environmental conditions. Our results motivate research into the mechanisms of adaptation in these populations, as well as their evolutionary fate in the light of accelerating climate change in the polar regions.
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Affiliation(s)
- Maison Dane
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | | | - Christopher L. Osburn
- Department of Marine, Earth, and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | | | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
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Møller TE, van der Bilt WGM, Roerdink DL, Jørgensen SL. Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions. Front Microbiol 2020; 11:1520. [PMID: 32903319 PMCID: PMC7396534 DOI: 10.3389/fmicb.2020.01520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.
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Affiliation(s)
- Tor Einar Møller
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Willem G M van der Bilt
- Department of Earth Science, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, Bergen, Norway
| | - Desiree L Roerdink
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Steffen L Jørgensen
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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