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Oliver T, Varghese N, Roux S, Schulz F, Huntemann M, Clum A, Foster B, Foster B, Riley R, LaButti K, Egan R, Hajek P, Mukherjee S, Ovchinnikova G, Reddy TBK, Calhoun S, Hayes RD, Rohwer RR, Zhou Z, Daum C, Copeland A, Chen IMA, Ivanova NN, Kyrpides NC, Mouncey NJ, Del Rio TG, Grigoriev IV, Hofmeyr S, Oliker L, Yelick K, Anantharaman K, McMahon KD, Woyke T, Eloe-Fadrosh EA. Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. Sci Data 2024; 11:966. [PMID: 39231974 DOI: 10.1038/s41597-024-03826-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.
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Affiliation(s)
- Tiffany Oliver
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Department of Biology, Spelman College, Atlanta, GA, 30314, USA.
| | - Neha Varghese
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bryce Foster
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Egan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Patrick Hajek
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Supratim Mukherjee
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Galina Ovchinnikova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sara Calhoun
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Richard D Hayes
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin R Rohwer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chris Daum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - I-Min A Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia N Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tijana Glavina Del Rio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Electrical Engineering and Computer Sciences Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Zhao Q, Van den Brink PJ, Xu C, Wang S, Clark AT, Karakoç C, Sugihara G, Widdicombe CE, Atkinson A, Matsuzaki SIS, Shinohara R, He S, Wang YXG, De Laender F. Relationships of temperature and biodiversity with stability of natural aquatic food webs. Nat Commun 2023; 14:3507. [PMID: 37316479 DOI: 10.1038/s41467-023-38977-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Temperature and biodiversity changes occur in concert, but their joint effects on ecological stability of natural food webs are unknown. Here, we assess these relationships in 19 planktonic food webs. We estimate stability as structural stability (using the volume contraction rate) and temporal stability (using the temporal variation of species abundances). Warmer temperatures were associated with lower structural and temporal stability, while biodiversity had no consistent effects on either stability property. While species richness was associated with lower structural stability and higher temporal stability, Simpson diversity was associated with higher temporal stability. The responses of structural stability were linked to disproportionate contributions from two trophic groups (predators and consumers), while the responses of temporal stability were linked both to synchrony of all species within the food web and distinctive contributions from three trophic groups (predators, consumers, and producers). Our results suggest that, in natural ecosystems, warmer temperatures can erode ecosystem stability, while biodiversity changes may not have consistent effects.
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Affiliation(s)
- Qinghua Zhao
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands.
- Research Unit of Environmental and Evolutionary Biology (URBE), University of Namur, Namur, Belgium.
- Institute of Complex Systems (naXys), University of Namur, Namur, Belgium.
- Institute of Life, Earth and the Environment (ILEE), University of Namur, Namur, Belgium.
| | - Paul J Van den Brink
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
- Wageningen Environmental Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
| | - Chi Xu
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 100871, Beijing, China
| | - Adam T Clark
- Institute of Biology, University of Graz, Holteigasse 6, 8010, Graz, Austria
| | - Canan Karakoç
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN, 47405, USA
| | - George Sugihara
- Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, USA
| | | | - Angus Atkinson
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL13DH, UK
| | | | | | - Shuiqing He
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Yingying X G Wang
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Frederik De Laender
- Research Unit of Environmental and Evolutionary Biology (URBE), University of Namur, Namur, Belgium
- Institute of Complex Systems (naXys), University of Namur, Namur, Belgium
- Institute of Life, Earth and the Environment (ILEE), University of Namur, Namur, Belgium
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Filazzola A, Mahdiyan O, Shuvo A, Ewins C, Moslenko L, Sadid T, Blagrave K, Imrit MA, Gray DK, Quinlan R, O'Reilly CM, Sharma S. A database of chlorophyll and water chemistry in freshwater lakes. Sci Data 2020; 7:310. [PMID: 32963248 PMCID: PMC7508946 DOI: 10.1038/s41597-020-00648-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/25/2020] [Indexed: 11/09/2022] Open
Abstract
Measures of chlorophyll represent the algal biomass in freshwater lakes that is often used by managers as a proxy for water quality and lake productivity. However, chlorophyll concentrations in lakes are dependent on many interacting factors, including nutrient inputs, mixing regime, lake depth, climate, and anthropogenic activities within the watershed. Therefore, integrating a broad scale dataset of lake physical, chemical, and biological characteristics can help elucidate the response of freshwater ecosystems to global change. We synthesized a database of measured chlorophyll a (chla) values, associated water chemistry variables, and lake morphometric characteristics for 11,959 freshwater lakes distributed across 72 countries. Data were collected based on a systematic review examining 3322 published manuscripts that measured lake chla, and we supplemented these data with online repositories such as The Knowledge Network for Biocomplexity, Dryad, and Pangaea. This publicly available database can be used to improve our understanding of how chlorophyll levels respond to global environmental change and provide baseline comparisons for environmental managers responsible for maintaining water quality in lakes.
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Affiliation(s)
| | | | - Arnab Shuvo
- Department of Biology, York University, Toronto, Canada
| | - Carolyn Ewins
- Department of Biology, York University, Toronto, Canada
| | - Luke Moslenko
- Department of Biology, York University, Toronto, Canada
| | - Tanzil Sadid
- Department of Biology, York University, Toronto, Canada
| | | | | | - Derek K Gray
- Department of Biology, Wilfrid Laurier University, Waterloo, Canada
| | | | | | - Sapna Sharma
- Department of Biology, York University, Toronto, Canada
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