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Jokinen M, Sallinen S, Jones MM, Sirén J, Guilbault E, Susi H, Laine AL. The first arriving virus shapes within-host viral diversity during natural epidemics. Proc Biol Sci 2023; 290:20231486. [PMID: 37700649 PMCID: PMC10498040 DOI: 10.1098/rspb.2023.1486] [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: 02/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.
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Affiliation(s)
- Maija Jokinen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Mirkka M. Jones
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Jukka Sirén
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Emy Guilbault
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
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Kulikovskiy MS, Kociolek JP, Solak CN, Kuznetsova IV, Glushchenko AM. New and Interesting Taxa from the Diatom Genus Gomphonema Ehrenberg in Shallow, Nearshore Sites on the Eastern Coast of Lake Baikal. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091835. [PMID: 37176894 PMCID: PMC10181234 DOI: 10.3390/plants12091835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
During this investigation, sixteen species from the genus Gomphonema were found in a shallow bay (near Oimur, Kabansky District) located on the eastern shore of Lake Baikal. Eleven of these taxa have been described previously. Five species are described as new to science. We provide ecological information about these Gomphonema species, including their distribution within and outside Lake Baikal, and compare and contrast the new taxa with morphologically similar congeners. The diversity of morphologies present in Lake Baikal among the Gomphonema species suggests there has been both in-lake speciation as well as the introduction of various groups of species. The idea that Lake Baikal may support a high number of endemics by their partitioning niches based on depth is supported by the different groups of gomphonemoid diatoms present.
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Affiliation(s)
- Maxim S Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - John Patrick Kociolek
- Museum of Natural History, Henderson Building, 15th and Broadway, Boulder, CO 80309, USA
| | - Cüneyt Nadir Solak
- Department of Biology, Art & Science Faculty, Dumlupınar University, Kütahya 43100, Turkey
| | - Irina V Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Anton M Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
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Ngugi DK, Salcher MM, Andrei AS, Ghai R, Klotz F, Chiriac MC, Ionescu D, Büsing P, Grossart HP, Xing P, Priscu JC, Alymkulov S, Pester M. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. SCIENCE ADVANCES 2023; 9:eadc9392. [PMID: 36724220 PMCID: PMC9891703 DOI: 10.1126/sciadv.adc9392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
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Affiliation(s)
- David Kamanda Ngugi
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Corresponding author.
| | - Michaela M. Salcher
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Adrian-Stefan Andrei
- Microbial Evogenomics Lab, Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Franziska Klotz
- Department of Biology, University of Konstanz, D-78457 Constance, Germany
| | - Maria-Cecilia Chiriac
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, D-14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, D-14195 Berlin, Germany
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, 334 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek 720071, Kyrgyzstan
| | - Michael Pester
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, D-38108 Braunschweig, Germany
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Huang L, Timmermann A, Lee SS, Rodgers KB, Yamaguchi R, Chung ES. Emerging unprecedented lake ice loss in climate change projections. Nat Commun 2022; 13:5798. [PMID: 36184681 PMCID: PMC9527235 DOI: 10.1038/s41467-022-33495-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Seasonal ice in lakes plays an important role for local communities and lake ecosystems. Here we use Large Ensemble simulations conducted with the Community Earth System Model version 2, which includes a lake simulator, to quantify the response of lake ice to greenhouse warming and to determine emergence patterns of anthropogenic lake ice loss. Our model simulations show that the average duration of ice coverage and maximum ice thickness are projected to decrease over the next 80 years by 38 days and 0.23 m, respectively. In the Canadian Arctic, lake ice loss is accelerated by the cold-season polar amplification. Lake ice on the Tibetan Plateau decreases rapidly due to a combination of strong insolation forcing and ice-albedo feedbacks. Comparing the anthropogenic signal with natural variability represented by the Large Ensemble, we find that lake ecosystems in these regions may be exposed to no-analogue ice coverage within the next 4-5 decades. Many lakes on Earth are covered by seasonal ice, and as lake ice loss has been increasing, it is ever more important to quantify this. Here the authors present a fully coupled lake ice model projection as a part of the new CESM2 large ensemble modelling project and show that unprecedented lake ice loss is emerging globally as a result of anthropogenic-induced warming.
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Affiliation(s)
- Lei Huang
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea. .,Pusan National University, Busan, South Korea.
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Sun-Seon Lee
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Keith B Rodgers
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Ryohei Yamaguchi
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea.,Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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Response of Aquatic Organisms Communities to Global Climate Changes and Anthropogenic Impact: Evidence from Listvennichny Bay of Lake Baikal. BIOLOGY 2021; 10:biology10090904. [PMID: 34571780 PMCID: PMC8469207 DOI: 10.3390/biology10090904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary Lake Baikal is ranked first among the world’s lakes in terms of freshwater reserves (23,000 km3). It is a UNESCO World Heritage Site, and its biota is represented by unique fauna and flora, with endemics accounting for more than 60%. What is happening in the Baikal ecosystem in recent decades due to global climate change and anthropogenic impacts? In this paper, we studied this issue on the example of one of the few open bays on the western shore of Lake Baikal, as well as of some remote areas. It has been found that the plankton composition is dominated by thermophilic species; the role of endemic species in the formation of total biomass is decreasing, which confirms the ecosystem’s response to climate warming. As a result of human activity, filamentous algae bloom suppresses endemic algae species and reduces mollusk proportion. The coastal zone of Lake Baikal is taking on the features of common shallow freshwater lakes due to the predominance of cosmopolitan and widespread Palearctic species. It is necessary to monitor the Baikal ecosystem in the changing climate and to strengthen control over human activities on the shores of the lake. Abstract Recent studies have revealed how the freshwater biota of Lake Baikal responds to climate change and anthropogenic impacts. We studied phyto- and zooplankton, as well as phyto- and zoobenthos, in the open coastal waters of the southern basin of the lake and of Listvennichny Bay. A total of 180 aquatic organism taxa were recorded. The response of the Baikal ecosystem to climate change can be traced by changes in the species composition of planktonic communities of the lake’s open coasts in summer. The key species were thermophilic the Anabaena lemmermannii P. Richt. (Fij = +0.7) blue-green algae, the Asplanchna priodonta Gosse (Fij = +0.6) rotifers in 2016, the Rhodomonas pusilla (Bachm.) Javorn. (Fij = +0.5) cold-loving algae, and the Cyclops kolensis Lilljeborg (Fij = +0.9) copepods in the past century. The proportion of Chlorophyta decreased from 63% to 17%; the Cyanophyta increased from 3% to 11% in the total biomass of phytoplankton; and the proportion of Cladocera and Rotifera increased to 26% and 11% in the biomass of zooplankton, respectively. Human activity makes an additional contribution to the eutrophication of coastal waters. The Dinobryon species, the cosmopolitan Asterionella formosa Hass. and Fragilaria radians Kütz., dominated phytoplankton, and filamentous algae, Spirogyra, dominated at the bottom in the area with anthropogenic impact. The trophic level was higher than at the unaffected background site: the saprobity index varied from 1.45 to 2.17; the ratio of eutrophic species to oligotrophic species ranged from 1:2 to 3:1, and the ratio of mesosaprobiont biomass to endemics biomass ranged from 2:1 to 7:1. Currently, the boundaries of eutrophication zones of shallow waters in Lake Baikal are expanding, and its coastal zone has acquired features typical of freshwater bodies of the eutrophic type.
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