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Hu Y, Cai J, Song Y, Li G, Gong Y, Jiang X, Tang X, Shao K, Gao G. Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake. MICROBIAL ECOLOGY 2024; 87:68. [PMID: 38722447 PMCID: PMC11082002 DOI: 10.1007/s00248-024-02365-4] [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: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 05/12/2024]
Abstract
It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.
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Affiliation(s)
- Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jian Cai
- Xiangyang Polytechnic, Xiangyang, 441000, Hubei Province, China
| | - Yifu Song
- Nanjing Forestry University, Nanjing, 210008, China
| | | | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China.
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2
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Underwood JC, Hall NC, Mumford AC, Harvey RW, Bliznik PA, Jeanis KM. Relation between the relative abundance and collapse of Aphanizomenon flos-aquae and microbial antagonism in Upper Klamath Lake, Oregon. FEMS Microbiol Ecol 2024; 100:fiae043. [PMID: 38533659 PMCID: PMC11022654 DOI: 10.1093/femsec/fiae043] [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: 10/06/2023] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 03/28/2024] Open
Abstract
Aphanizomenon flos-aquae (AFA) is the dominant filamentous cyanobacterium that develops into blooms in Upper Klamath Lake, Oregon, each year. During AFA bloom and collapse, ecosystem conditions for endangered Lost River and shortnose suckers deteriorate, thus motivating the need to identify processes that limit AFA abundance and decline. Here, we investigate the relations between AFA and other members of the microbial community (photosynthetic and nonphotosynthetic bacteria and archaea), how those relations impact abundance and collapse of AFA, and the types of microbial conditions that suppress AFA. We found significant spatial variation in AFA relative abundance during the 2016 bloom period using 16S rRNA sequencing. The Pelican Marina site had the lowest AFA relative abundance, and this was coincident with increased relative abundance of Candidatus Sericytochromatia, Flavobacterium, and Rheinheimera, some of which are known AFA antagonists. The AFA collapse coincided with phosphorus limitation relative to nitrogen and the increased relative abundance of Cyanobium and Candidatus Sericytochromatia, which outcompete AFA when dissolved inorganic nitrogen is available. The data collected in this study indicate the importance of dissolved inorganic nitrogen combined with microbial community structure in suppressing AFA abundance.
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Affiliation(s)
- Jennifer C Underwood
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Natalie C Hall
- U.S. Geological Survey, Maryland–Delaware–D.C. Water Science Center, 5522 Research Park Dr, Catonsville, MD 21228, United States
| | - Adam C Mumford
- U.S. Geological Survey, Maryland–Delaware–D.C. Water Science Center, 5522 Research Park Dr, Catonsville, MD 21228, United States
| | - Ronald W Harvey
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Paul A Bliznik
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Kaitlyn M Jeanis
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
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3
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Lin Q, Zhang K, McGowan S, Huang S, Xue Q, Capo E, Zhang C, Zhao C, Shen J. Characterization of lacustrine harmful algal blooms using multiple biomarkers: Historical processes, driving synergy, and ecological shifts. WATER RESEARCH 2023; 235:119916. [PMID: 37003114 DOI: 10.1016/j.watres.2023.119916] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Harmful algal blooms (HABs) producing toxic metabolites are increasingly threatening environmental and human health worldwide. Unfortunately, long-term process and mechanism triggering HABs remain largely unclear due to the scarcity of temporal monitoring. Retrospective analysis of sedimentary biomarkers using up-to-date chromatography and mass spectrometry techniques provide a potential means to reconstruct the past occurrence of HABs. By combining aliphatic hydrocarbons, photosynthetic pigments, and cyanotoxins, we quantified herein century-long changes in abundance, composition, and variability of phototrophs, particularly toxigenic algal blooms, in China's third largest freshwater Lake Taihu. Our multi-proxy limnological reconstruction revealed an abrupt ecological shift in the 1980s characterized by elevated primary production, Microcystis-dominated cyanobacterial blooms, and exponential microcystin production, in response to nutrient enrichment, climate change, and trophic cascades. The empirical results from ordination analysis and generalized additive models support climate warming and eutrophication synergy through nutrient recycling and their feedback through buoyant cyanobacterial proliferation, which sustain bloom-forming potential and further promote the occurrence of increasingly-toxic cyanotoxins (e.g., microcystin-LR) in Lake Taihu. Moreover, temporal variability of the lake ecosystem quantified using variance and rate of change metrics rose continuously after state change, indicating increased ecological vulnerability and declined resilience following blooms and warming. With the persistent legacy effects of lake eutrophication, nutrient reduction efforts mitigating toxic HABs probably be overwhelmed by climate change effects, emphasizing the need for more aggressive and integrated environmental strategies.
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Affiliation(s)
- Qi Lin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ke Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Suzanne McGowan
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708PB Wageningen, Netherlands
| | - Shixin Huang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingju Xue
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Eric Capo
- Department of Marine Biology, Institut de Ciències del Mar, CSIC, DC 08003 Barcelona, Spain
| | - Can Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Cheng Zhao
- School of Geography and Oceanography Sciences, Nanjing University, Nanjing 210023, China
| | - Ji Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; School of Geography and Oceanography Sciences, Nanjing University, Nanjing 210023, China
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4
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Lin Y, Zhong W, Zhang X, Zhou X, He L, Lv J, Zhao Z. Environmental DNA metabarcoding revealed the impacts of anthropogenic activities on phytoplankton diversity in Dianchi Lake and its three inflow rivers. Ecol Evol 2023; 13:e10088. [PMID: 37214604 PMCID: PMC10196938 DOI: 10.1002/ece3.10088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Phytoplankton diversity is closely related to environmental variables and has been widely used in ecological health assessment of rivers and lakes. Combining advantages of DNA-based identification and high-throughput sequencing technology, environmental DNA (eDNA) metabarcoding permits a new measurement for biodiversity monitoring in aquatic ecosystems. However, it had rarely been used to explore the variability and similarity of phytoplankton diversity between lake and its inflow rivers and the effects of environmental variables on phytoplankton. This study utilized eDNA metabarcoding to investigate the spatial distribution of phytoplankton and the impacts of environmental variables on the phytoplankton diversity in Dianchi Lake (one of the most polluted urban lakes in China) and its main inflow rivers (Panlong River, Baoxiang River, and Chai River). A total of 243 distinct phytoplankton taxa were detected, covering 9 phyla, 30 classes, 84 orders, and 132 families, and the taxonomic richness of rivers was higher than that of Dianchi Lake. Distinct biodiversity patterns (e.g., community structure, dominant taxon, ɑ-diversity) were exhibited among Dianchi Lake and its three inflow rivers, but similar biodiversity patterns were also observed in Dianchi Lake and the estuarine sites. The patterns of phytoplankton diversity were closely related to environmental variables, which were associated with pollution sources from different anthropogenic activities (e.g., urbanization, water diversion, industrial and agricultural activities). The primary environmental variables correlated with phytoplankton diversity varied in different habitats. The total phosphorus (TP) and chemical oxygen demand (COD) positively correlated with the phytoplankton community structures in Dianchi Lake, whereas negatively correlated in Panlong River and Baoxiang River. The total nitrogen (TN) positively correlated with the phytoplankton community structures in Baoxiang River and Chai River but negatively correlated in Dianchi Lake. Overall, this study provides insights on the phytoplankton diversity monitoring and the conservation of its diversity and healthy management of Dianchi Lake.
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Affiliation(s)
- Yuanyuan Lin
- Academician Workstation for Ecological Health Assessment and Rehabilitation of Rivers and Lakes in Kunming, Key Laboratory of River and Lake Ecological Health Assessment and Restoration in Yunnan Province, Kunming Dianchi Lake Environmental Protection Collaborative Research CenterKunming UniversityKunmingChina
| | - Wenjun Zhong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the EnvironmentNanjing UniversityNanjingChina
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the EnvironmentNanjing UniversityNanjingChina
| | - Xiaohua Zhou
- Academician Workstation for Ecological Health Assessment and Rehabilitation of Rivers and Lakes in Kunming, Key Laboratory of River and Lake Ecological Health Assessment and Restoration in Yunnan Province, Kunming Dianchi Lake Environmental Protection Collaborative Research CenterKunming UniversityKunmingChina
| | - Liwei He
- Academician Workstation for Ecological Health Assessment and Rehabilitation of Rivers and Lakes in Kunming, Key Laboratory of River and Lake Ecological Health Assessment and Restoration in Yunnan Province, Kunming Dianchi Lake Environmental Protection Collaborative Research CenterKunming UniversityKunmingChina
| | - Jiacheng Lv
- Academician Workstation for Ecological Health Assessment and Rehabilitation of Rivers and Lakes in Kunming, Key Laboratory of River and Lake Ecological Health Assessment and Restoration in Yunnan Province, Kunming Dianchi Lake Environmental Protection Collaborative Research CenterKunming UniversityKunmingChina
| | - Zheng Zhao
- Academician Workstation for Ecological Health Assessment and Rehabilitation of Rivers and Lakes in Kunming, Key Laboratory of River and Lake Ecological Health Assessment and Restoration in Yunnan Province, Kunming Dianchi Lake Environmental Protection Collaborative Research CenterKunming UniversityKunmingChina
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5
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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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6
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Huo S, Zhang H, Monchamp ME, Wang R, Weng N, Zhang J, Zhang H, Wu F. Century-Long Homogenization of Algal Communities Is Accelerated by Nutrient Enrichment and Climate Warming in Lakes and Reservoirs of the North Temperate Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3780-3790. [PMID: 35143177 DOI: 10.1021/acs.est.1c06958] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Anthropogenic pressures can threaten lake and reservoir ecosystems, leading to harmful algal blooms that have become globally widespread. However, patterns of phytoplankton diversity change and community assembly over long-term scales remain unknown. Here, we explore biodiversity patterns in eukaryotic algal (EA) and cyanobacterial (CYA) communities over a century by sequencing DNA preserved in the sediment cores of seven lakes and reservoirs in the North Temperate Zone. Comparisons within lakes revealed temporal algal community homogenization in mesotrophic lakes, eutrophic lakes, and reservoirs over the last century but no systematic losses of α-diversity. Temporal homogenization of EA and CYA communities continued into the modern day probably due to time-lags related to historical legacies, even if lakes go through a eutrophication phase followed by a reoligotrophication phase. Further, algal community assembly in lakes and reservoirs was mediated by both deterministic and stochastic processes, while homogeneous selection played a relatively important role in recent decades due to intensified anthropogenic activities and climate warming. Overall, these results expand our understanding of global change effects on algal community diversity and succession in lakes and reservoirs that exhibit different successional trajectories while also providing a baseline framework to assess their potential responses to future environmental change.
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Affiliation(s)
- Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Marie-Eve Monchamp
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Quebec H3A 1B1, Canada
| | - Rong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jingtian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hong Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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7
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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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8
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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9
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Pawlowski J, Bonin A, Boyer F, Cordier T, Taberlet P. Environmental DNA for biomonitoring. Mol Ecol 2021; 30:2931-2936. [PMID: 34176165 PMCID: PMC8451586 DOI: 10.1111/mec.16023] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Jan Pawlowski
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
| | - Aurélie Bonin
- Department of Environmental Science and PolicyUniversità degli Studi di MilanoMilanItaly
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
| | - Tristan Cordier
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- NORCE ClimateNORCE Norwegian Research Centre ASBjerknes Centre for Climate ResearchBergenNorway
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
- Tromsø MuseumUiT – The Arctic University of NorwayTromsøNorway
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10
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Pearman JK, Thomson-Laing G, Howarth JD, Vandergoes MJ, Thompson L, Rees A, Wood SA. Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores. PLoS One 2021; 16:e0250783. [PMID: 33939728 PMCID: PMC8092796 DOI: 10.1371/journal.pone.0250783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Andrew Rees
- Victoria University of Wellington, Wellington, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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11
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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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12
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Capo E, Ninnes S, Domaizon I, Bertilsson S, Bigler C, Wang XR, Bindler R, Rydberg J. Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene. Microorganisms 2021; 9:microorganisms9020355. [PMID: 33670228 PMCID: PMC7916980 DOI: 10.3390/microorganisms9020355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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Affiliation(s)
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
- Correspondence:
| | - Sofia Ninnes
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Isabelle Domaizon
- UMR CARRTEL, INRAE, Université Savoie Mont Blanc, 74200 Thonon les Bains, France;
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, SLU, 75007 Uppsala, Sweden;
| | - Christian Bigler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Richard Bindler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Johan Rydberg
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
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