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Wang Q, Yang Q, Zhu L, Cui Z, Qu K, Wei Y. Environmental controls on the seasonal variations of diatoms and dinoflagellates in the Qingdao coastal region, the Yellow Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106524. [PMID: 38664079 DOI: 10.1016/j.marenvres.2024.106524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/29/2023] [Accepted: 04/20/2024] [Indexed: 06/11/2024]
Abstract
Diatoms and dinoflagellates are two typical functional groups of phytoplankton assemblages, which play a crucial role in the structure and functioning of most marine ecosystems. To date, a novel challenge in ecology and biogeochemistry is to address the influences of environmental changes associated with climate change and human activities on the dynamics of diatoms and dinoflagellates. However, the knowledge of the key environmental factors controlling the diatom-dinoflagellate dynamics remains to be improved, particularly in the coastal ecosystems. Therefore, we conducted four cruises along the Qingdao coastline in spring, summer, autumn, and winter 2022 to explore how diatoms and dinoflagellates varied in response to regional environmental changes. The results showed that the phytoplankton communities were dominated by diatoms and dinoflagellates in terms of abundance and species diversity throughout the year in the study region. Yet, there were significant seasonal variability of diatoms and dinoflagellates across the four seasons. For example, diatom species was the most diverse during autumn, and the higher average abundance was observed in the fall and winter. In contrast, the average abundance of dinoflagellates was maximum during the summer and minimum in the autumn season. Moreover, the abundance and species ratios of diatoms/dinoflagellates (dia/dino) also showed significant seasonal variations in the region. The dia/dino abundance ratio was lowest in summer, while the dia/dino species ratio showed an increasing trend from spring to fall and a slight descending trend during winter. Based on the redundancy analysis, we revealed that diatoms and dinoflagellates responded differently to various environmental variables in different seasons, of which temperature and nutrients (especially dissolved inorganic nitrogen, DIN) had highly significant correlations with both the dia/dino abundance and species ratios. Thus, we suggested that temperature and DIN were the key factors controlling the seasonal dynamics of diatoms and dinoflagellates in the Qingdao coastal area.
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Affiliation(s)
- Qingxuan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Qian Yang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Lin Zhu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhengguo Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Keming Qu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuqiu Wei
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
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2
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Behrenfeld MJ, Bisson KM. Neutral Theory and Plankton Biodiversity. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:283-305. [PMID: 37368954 DOI: 10.1146/annurev-marine-112122-105229] [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: 06/29/2023]
Abstract
The biodiversity of the plankton has been interpreted largely through the monocle of competition. The spatial distancing of phytoplankton in nature is so large that cell boundary layers rarely overlap, undermining opportunities for resource-based competitive exclusion. Neutral theory accounts for biodiversity patterns based purely on random birth, death, immigration, and speciation events and has commonly served as a null hypothesis in terrestrial ecology but has received comparatively little attention in aquatic ecology. This review summarizes basic elements of neutral theory and explores its stand-alone utility for understanding phytoplankton diversity. A theoretical framework is described entailing a very nonneutral trophic exclusion principle melded with the concept of ecologically defined neutral niches. This perspective permits all phytoplankton size classes to coexist at any limiting resource level, predicts greater diversity than anticipated from readily identifiable environmental niches but less diversity than expected from pure neutral theory, and functions effectively in populations of distantly spaced individuals.
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Affiliation(s)
- Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA; ,
| | - Kelsey M Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA; ,
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Anderson SI, Fronda C, Barton AD, Clayton S, Rynearson TA, Dutkiewicz S. Phytoplankton thermal trait parameterization alters community structure and biogeochemical processes in a modeled ocean. GLOBAL CHANGE BIOLOGY 2024; 30:e17093. [PMID: 38273480 DOI: 10.1111/gcb.17093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Phytoplankton exhibit diverse physiological responses to temperature which influence their fitness in the environment and consequently alter their community structure. Here, we explored the sensitivity of phytoplankton community structure to thermal response parameterization in a modelled marine phytoplankton community. Using published empirical data, we evaluated the maximum thermal growth rates (μmax ) and temperature coefficients (Q10 ; the rate at which growth scales with temperature) of six key Phytoplankton Functional Types (PFTs): coccolithophores, cyanobacteria, diatoms, diazotrophs, dinoflagellates, and green algae. Following three well-documented methods, PFTs were either assumed to have (1) the same μmax and the same Q10 (as in to Eppley, 1972), (2) a unique μmax but the same Q10 (similar to Kremer et al., 2017), or (3) a unique μmax and a unique Q10 (following Anderson et al., 2021). These trait values were then implemented within the Massachusetts Institute of Technology biogeochemistry and ecosystem model (called Darwin) for each PFT under a control and climate change scenario. Our results suggest that applying a μmax and Q10 universally across PFTs (as in Eppley, 1972) leads to unrealistic phytoplankton communities, which lack diatoms globally. Additionally, we find that accounting for differences in the Q10 between PFTs can significantly impact each PFT's competitive ability, especially at high latitudes, leading to altered modeled phytoplankton community structures in our control and climate change simulations. This then impacts estimates of biogeochemical processes, with, for example, estimates of export production varying by ~10% in the Southern Ocean depending on the parameterization. Our results indicate that the diversity of thermal response traits in phytoplankton not only shape community composition in the historical and future, warmer ocean, but that these traits have significant feedbacks on global biogeochemical cycles.
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Affiliation(s)
- Stephanie I Anderson
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clara Fronda
- Laboratoire de Physique, Ecole Normale Supérieure, Paris, France
| | - Andrew D Barton
- Scripps Institution of Oceanography and Department of Ecology, Behavior and Evolution, San Diego, California, USA
| | - Sophie Clayton
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Irit N, Hana B, Laura R, Arielle K, Mariela P, Esti KW, Guadalupe P, Katja S, Ariel K. Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166739. [PMID: 37673239 DOI: 10.1016/j.scitotenv.2023.166739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.
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Affiliation(s)
- Nir Irit
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Barak Hana
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rabbachin Laura
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kahn Arielle
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Pavan Mariela
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Kramarsky-Winter Esti
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Piñar Guadalupe
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Sterflinger Katja
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kushmaro Ariel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Wang Y, Cui Z, Ding D, Yang Q, Zhu L, Qu K, Sun J, Wei Y. Environmental forcing of phytoplankton carbon-to-diversity ratio and carbon-to-chlorophyll ratio: A case study in Jiaozhou Bay, the Yellow Sea. MARINE POLLUTION BULLETIN 2023; 197:115765. [PMID: 37988882 DOI: 10.1016/j.marpolbul.2023.115765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/22/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]
Abstract
The relationships between phytoplankton carbon (C) biomass and diversity (i.e., C-to-H' ratio) and chlorophyll a (i.e., C-to-Chl a ratio) are good indicators of marine ecosystem functioning and stability. Here we conducted four cruises spanning 2 years in Jiaozhou Bay to explore the dynamics of C-to-H' and C-to-Chl a ratios. The results showed that the phytoplankton C biomass and diversity were dominated by diatoms, followed by dinoflagellates. The average C-to-H' ratio ranged from 84.10 to 912.17, with high values occurring in the northern region of the bay. In contrast, the average C-to-Chl a ratio ranged between 15.55 and 89.47, and high values primarily appeared in the northern or northeastern part of the bay. In addition, the redundancy analysis showed that temperature and phosphate (DIP) were significantly correlated with both ratios in most cases, indicating that temperature and DIP may be key factors affecting the dynamics of C-to-H' and C-to-Chl a ratios.
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Affiliation(s)
- Yingzhe Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhengguo Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dongsheng Ding
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qian Yang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Lin Zhu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Keming Qu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China
| | - Yuqiu Wei
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
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6
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Gronniger JL, Gray PC, Niebergall AK, Johnson ZI, Hunt DE. A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters. PLoS One 2023; 18:e0293334. [PMID: 37943816 PMCID: PMC10635494 DOI: 10.1371/journal.pone.0293334] [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: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 phylotypes) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception. Additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.
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Affiliation(s)
| | - Patrick C. Gray
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
| | | | - Zackary I. Johnson
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Dana E. Hunt
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
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Burkart T, Willeke J, Frey E. Periodic temporal environmental variations induce coexistence in resource competition models. Phys Rev E 2023; 108:034404. [PMID: 37849086 DOI: 10.1103/physreve.108.034404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/13/2023] [Indexed: 10/19/2023]
Abstract
Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic population dynamics model to study how, and under what conditions, a periodic temporal environmental variation can alter an ecosystem's composition and biodiversity. We demonstrate that using timescale separation allows one to qualitatively predict the long-term population dynamics of interacting species in varying environments. We show that the notion of Tilman's R* rule, a well-known principle that applies for constant environments, can be extended to periodically varying environments if the timescale of environmental changes (e.g., seasonal variations) is much faster than the timescale of population growth (doubling time in bacteria). When these timescales are similar, our analysis shows that a varying environment deters the system from reaching a steady state, and stable coexistence between multiple species becomes possible. Our results posit that biodiversity can in part be attributed to natural environmental variations.
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Affiliation(s)
- Tom Burkart
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Jan Willeke
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 München, Germany
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Debeljak P, Baltar F. Fungal Diversity and Community Composition across Ecosystems. J Fungi (Basel) 2023; 9:jof9050510. [PMID: 37233221 DOI: 10.3390/jof9050510] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth's mycobiome.
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Affiliation(s)
- Pavla Debeljak
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
- SupBiotech, 94800 Villejuif, France
| | - Federico Baltar
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
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Rivera R, Escribano R, González CE, Pérez-Aragón M. Modeling present and future distribution of plankton populations in a coastal upwelling zone: the copepod Calanus chilensis as a study case. Sci Rep 2023; 13:3158. [PMID: 36823290 PMCID: PMC9950369 DOI: 10.1038/s41598-023-29541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Predicting species distribution in the ocean has become a crucial task to assess marine ecosystem responses to ongoing climate change. In the Humboldt Current System (HCS), the endemic copepod Calanus chilensis is one of the key species bioindicator of productivity and water masses. Here we modeled the geographic distribution of Calanus chilensis for two bathymetric ranges, 0-200 and 200-400 m. For the 0-200 m layer, we used the Bayesian Additive Regression Trees (BART) method, whereas, for the 200-400 m layer, we used the Ensembles of Small Models (ESMs) method and then projected the models into two future scenarios to assess changes in geographic distribution patterns. The models were evaluated using the multi-metric approach. We identified that chlorophyll-a (0.34), Mixed Layer Depth (0.302) and salinity (0.36) explained the distribution of C. chilensis. The geographic prediction of the BART model revealed a continuous distribution from Ecuador to the southernmost area of South America for the 0-200 m depth range, whereas the ESM model indicated a discontinuous distribution with greater suitability for the coast of Chile for the 200-400 m depth range. A reduction of the distribution range of C. chilensis is projected in the future. Our study suggests that the distribution of C. chilensis is conditioned by productivity and mesoscale processes, with both processes closely related to upwelling intensity. These models serve as a tool for proposing indicators of changes in the ocean. We further propose that the species C. chilensis is a high productivity and low salinity indicator at the HCS. We recommend further examining multiple spatial and temporal scales for stronger inference.
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Affiliation(s)
- Reinaldo Rivera
- Millennium Institute of Oceanography (IMO), University of Concepcion, 4030000, Concepcion, Chile.
| | - Rubén Escribano
- grid.5380.e0000 0001 2298 9663Millennium Institute of Oceanography (IMO), University of Concepcion, 4030000 Concepcion, Chile ,grid.5380.e0000 0001 2298 9663Department of Oceanography, Faculty of Natural and Oceanographic Sciences, University of Concepcion, 4030000 Concepcion, Chile
| | - Carolina E. González
- grid.5380.e0000 0001 2298 9663Millennium Institute of Oceanography (IMO), University of Concepcion, 4030000 Concepcion, Chile
| | - Manuela Pérez-Aragón
- grid.5380.e0000 0001 2298 9663Millennium Institute of Oceanography (IMO), University of Concepcion, 4030000 Concepcion, Chile ,grid.5380.e0000 0001 2298 9663Department of Oceanography, Faculty of Natural and Oceanographic Sciences, University of Concepcion, 4030000 Concepcion, Chile
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Phytoplankton Community Response to Environmental Factors along a Salinity Gradient in a Seagoing River, Tianjin, China. Microorganisms 2022; 11:microorganisms11010075. [PMID: 36677367 PMCID: PMC9864511 DOI: 10.3390/microorganisms11010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
A river-estuary ecosystem usually features a distinct salinity gradient and a complex water environment, so it is enormously valuable to study the response mechanism of living organisms to multiple abiotic factors under salinity stress. Phytoplankton, as an important part of aquatic microorganisms, has always been of concern for its crucial place in the aquatic ecosystem. In this study, phytoplankton data and 18 abiotic factors collected from 15 stations in Duliujian River, a seagoing river, were investigated in different seasons. The results showed that the river studied was of a Cyanophyta-dominant type. Salinity (SAL) was the key control factor for phytoplankton species richness, while water temperature (WT) was critical not only for species richness, but also community diversity, and the abundance and biomass of dominant species. Apart from WT, the abundance and biomass of dominant species were also driven by total nitrogen (TN), nitrate (NO3-), pH, and water transparency (SD). Moreover, total dissolved phosphorus (TDP), pH, and chemical oxygen demand (COD) were crucial for community diversity and evenness. The bloom of dominant species positively associated with TDP led to lower diversity and evenness in autumn. In addition, when available nitrogen was limited, Pseudoanabaena sp. could obtain a competitive advantage through the N2 fixation function. Increased available nitrogen concentration could favor the abundance of Chlorella vulgaris to resist the negative effect of WT. The results show that Oscillatoria limosa could serve as an indicator of organic contamination, and nutrient-concentration control must be effective to inhibit Microcystis bloom. This could help managers to formulate conservation measures.
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Fridman Y, Wang Z, Maslov S, Goyal A. Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments. PLoS Comput Biol 2022; 18:e1010244. [PMID: 36574450 PMCID: PMC9829172 DOI: 10.1371/journal.pcbi.1010244] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/09/2023] [Accepted: 12/05/2022] [Indexed: 12/28/2022] Open
Abstract
Recent observations have revealed that closely related strains of the same microbial species can stably coexist in natural and laboratory settings subject to boom and bust dynamics and serial dilutions, respectively. However, the possible mechanisms enabling the coexistence of only a handful of strains, but not more, have thus far remained unknown. Here, using a consumer-resource model of microbial ecosystems, we propose that by differentiating along Monod parameters characterizing microbial growth rates in high and low nutrient conditions, strains can coexist in patterns similar to those observed. In our model, boom and bust environments create satellite niches due to resource concentrations varying in time. These satellite niches can be occupied by closely related strains, thereby enabling their coexistence. We demonstrate that this result is valid even in complex environments consisting of multiple resources and species. In these complex communities, each species partitions resources differently and creates separate sets of satellite niches for their own strains. While there is no theoretical limit to the number of coexisting strains, in our simulations, we always find between 1 and 3 strains coexisting, consistent with known experiments and observations.
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Affiliation(s)
- Yulia Fridman
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Zihan Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sergei Maslov
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (SM); (AG)
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (SM); (AG)
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12
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Nef C, Madoui MA, Pelletier É, Bowler C. Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. PLoS Biol 2022; 20:e3001893. [PMID: 36441816 PMCID: PMC9731442 DOI: 10.1371/journal.pbio.3001893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Mohammed-Amin Madoui
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Éric Pelletier
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Metabolic Genomics, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Université Evry, Université Paris Saclay, Evry, France
| | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- * E-mail:
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13
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Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations. mSystems 2022; 7:e0147721. [PMID: 35695431 PMCID: PMC9239043 DOI: 10.1128/msystems.01477-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Some marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.” IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.
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14
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Controls and characteristics of biomass quantization in size-structured planktonic ecosystem models. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.109907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. Nat Commun 2022; 13:2448. [PMID: 35508497 PMCID: PMC9068609 DOI: 10.1038/s41467-022-30139-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities. Coastal upwelling sustains some of the most productive ocean regions. Here, the authors find that spatial patterns and temporal changes in nutrient supply explain marine microbial community structure and diversity in the Southern California Current region.
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16
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Robicheau BM, Tolman J, Bertrand EM, LaRoche J. Highly-resolved interannual phytoplankton community dynamics of the coastal Northwest Atlantic. ISME COMMUNICATIONS 2022; 2:38. [PMID: 37938666 PMCID: PMC9723599 DOI: 10.1038/s43705-022-00119-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/26/2022] [Accepted: 03/07/2022] [Indexed: 10/01/2023]
Abstract
Microbial observatories can track phytoplankton at frequencies that resolve monthly, seasonal, and multiyear trends in environmental change from short-lived events. Using 4-years of weekly flow cytometry along with chloroplast and cyanobacterial 16S rRNA gene sequence data from a time-series station in the coastal Northwest Atlantic (Bedford Basin, Nova Scotia, Canada), we analyzed temporal observations for globally-relevant genera (e.g., Bolidomonas, Teleaulax, Minidiscus, Chaetoceros, Synechococcus, and Phaeocystis) in an oceanic region that has been recognized as a likely hotspot for phytoplankton diversity. Contemporaneous Scotian Shelf data also collected during our study established that the major phytoplankton within the Bedford Basin were important in the Scotian Shelf during spring and fall, therefore pointing to their broader significance within the coastal Northwest Atlantic (NWA). Temporal trends revealed a subset of indicator taxa along with their DNA signatures (e.g., Eutreptiella and Synechococcus), whose distribution patterns make them essential for timely detection of environmentally-driven shifts in the NWA. High-resolution sampling was key to identifying important community shifts towards smaller phytoplankton under anomalous environmental conditions, while further providing a detailed molecular view of community compositions underpinning general phytoplankton succession within the coastal NWA. Our study demonstrates the importance of accessible coastal time-series sites where high-frequency DNA sampling allows for the detection of shifting baselines in phytoplankton communities.
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Affiliation(s)
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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17
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Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean. mBio 2022; 13:e0383221. [PMID: 35285696 PMCID: PMC9040759 DOI: 10.1128/mbio.03832-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.
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18
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Diao C, Jia H, Guo S, Hou G, Xian W, Zhang H. Biodiversity exploration in autumn using environmental DNA in the South China sea. ENVIRONMENTAL RESEARCH 2022; 204:112357. [PMID: 34774836 DOI: 10.1016/j.envres.2021.112357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/30/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The South China Sea (SCS) is an important part of the Indo-Pacific convergence zone, with high biodiversity and abundant marine resources. Traditional methods are primarily used to monitor biodiversity. However, a few studies have used environmental DNA (eDNA) metabarcoding to research the assemblage structure of the SCS. This study used eDNA metabarcoding to survey the SCS assemblage and its relationship with environmental factors over a month-long time-series (August 30th to September 30th, 2020) of seawater samples from the central part of the SCS (9°-20°86' N, 113°-118°47' E). 32 stations were divided into six groups (A, B, C, D, E, F) according to longitude. We collected water samples, extracted eDNA, and amplified 18S rRNA gene V4 region (18S V4), 18S rRNA gene V9 region (18S V9), and 12S rRNA gene (12S). Krona diagrams were used to show species composition. We identified 192 phytoplankton, 104 invertebrate, and 61 fish species from 18S V4, 18S V9, and 12S, respectively. Generally, the three assemblage structures exhibited an increase in species diversity with increasing longitude. Group E had the highest fish diversity. Groups F and C had the highest phytoplankton and invertebrate diversity, respectively. Canonical correspondence analysis showed that four factors (chlorophyll a, depth, salinity, and temperature) were correlated with assemblage structure. Chlorophyll a was the main environmental factor that affected fish, phytoplankton, and invertebrate assemblage structures; salinity was strongly correlated with fish and invertebrate assemblage structures; temperature was a key factor that impacted fish and invertebrate assemblage structures; and depth was strongly correlated with invertebrate assemblage structure. Our results revealed that eDNA metabarcoding is a powerful tool for improving detection rate and using multiple markers is an effective approach for monitoring biodiversity. This study provided information that can be used to enhance biodiversity protection efforts in the SCS.
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Affiliation(s)
- Caoyun Diao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Jia
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; China School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shujin Guo
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Gang Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, China
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Prochlorococcus Exudate Stimulates Heterotrophic Bacterial Competition with Rival Phytoplankton for Available Nitrogen. mBio 2022; 13:e0257121. [PMID: 35012332 PMCID: PMC8749424 DOI: 10.1128/mbio.02571-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study, we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and cocultures when nutrients were replete. However, in nitrogen-limited medium, Prochlorococcus outgrew Synechococcus but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen but only if stimulated by the exudate released by Prochlorococcus or if a proxy organic carbon source was provided. Genetic analysis of Alteromonas suggested that it outcompetes Synechococcus for nitrate and/or nitrite, during which cocultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in nutrient-limited regions of the ocean. IMPORTANCE In nutrient-poor habitats, competition for limited resources is thought to select for organisms with an enhanced ability to scavenge nutrients and utilize them efficiently. Such adaptations characterize the cyanobacterium Prochlorococcus, the most abundant photosynthetic organism in the nutrient-limited open ocean. In this study, the competitive superiority of Prochlorococcus over a rival cyanobacterium, Synechococcus, was captured in laboratory culture. Critically, this outcome was achieved only when key aspects of the open ocean were simulated: a limited supply of nitrogen and the presence of heterotrophic bacteria. The results indicate that Prochlorococcus promotes its numerical dominance over Synechococcus by energizing the heterotroph's ability to outcompete Synechococcus for available nitrogen. This study demonstrates how interactions between trophic groups can influence interactions within trophic groups and how these interactions likely contribute to the success of the most abundant photosynthetic microorganism.
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20
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Chen B. Thermal diversity affects community responses to warming. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2021.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean. mSystems 2022; 7:e0120321. [PMID: 35089068 PMCID: PMC8725599 DOI: 10.1128/msystems.01203-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.
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22
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Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics. Proc Natl Acad Sci U S A 2022; 119:2020956119. [PMID: 34969851 PMCID: PMC8740587 DOI: 10.1073/pnas.2020956119] [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] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
Persistently diverse microbial communities are one of biology’s great puzzles. Using a modeling framework that accommodates high mutation rates and a continuum of species traits, we studied microbial communities in which antagonistic interactions occur via the production of, inhibition of, and vulnerability to toxins (e.g., antibiotics). Mutation size and mobility enhanced microbial diversity and temporal persistence to extraordinarily high levels. These findings—including the discovery that the duration of the transient phase in community assembly provides a guide to equilibrial diversity—highlight the potentially critical role that antagonistic interactions play in promoting the diversity of bacterial systems. Such interactions, together with resource-driven interactions and spatial structure, may drive the enigmatic levels of biodiversity seen in microbial systems. The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involves cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities in which antibiotic-producing, sensitive, and resistant strains coexist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represent the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions—one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems.
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Wu P, Dutkiewicz S, Monier E, Zhang Y. Bottom-Heavy Trophic Pyramids Impair Methylmercury Biomagnification in the Marine Plankton Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15476-15483. [PMID: 34738802 DOI: 10.1021/acs.est.1c04083] [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: 06/13/2023]
Abstract
Methylmercury (CH3Hg+, MMHg) in the phytoplankton and zooplankton, which form the bottom of marine food webs, is a good predictor of MMHg in top predators, including humans. Therefore, evaluating the potential exposure of MMHg to higher trophic levels (TLs) requires a better understanding of relationships between MMHg biomagnification and plankton dynamics. In this study, a coupled ecological/physical model with 366 plankton types of different sizes, biogeochemical functions, and temperature tolerance is used to simulate the relationships between MMHg biomagnification and the ecosystem structure. The study shows that the MMHg biomagnification becomes more significant with increasing TLs. Trophic magnification factors (TMFs) in the lowest two TLs show the opposite spatial pattern to TMFs in higher TLs. The low TMFs are usually associated with a short food-chain length. The less bottom-heavy trophic pyramids in the oligotrophic oceans enhance the MMHg trophic transfer. The global average TMF is increased from 2.3 to 2.8 in the warmer future with a medium climate sensitivity of 2.5 °C. Our study suggests that if there are no mitigation measures for Hg emission, MMHg in the high-trophic-level plankton is increased more dramatically in the warming future, indicating greater MMHg exposure for top predators such as humans.
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Affiliation(s)
- Peipei Wu
- School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Center for Climate Change Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erwan Monier
- Department of Land, Air and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Yanxu Zhang
- School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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Cael BB, Dutkiewicz S, Henson S. Abrupt shifts in 21st-century plankton communities. SCIENCE ADVANCES 2021; 7:eabf8593. [PMID: 34714679 PMCID: PMC8555899 DOI: 10.1126/sciadv.abf8593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/10/2021] [Indexed: 05/28/2023]
Abstract
Marine microbial communities sustain ocean food webs and mediate global elemental cycles. These communities will change with climate; these changes can be gradual or foreseeable but likely have much more substantial consequences when sudden and unpredictable. In a complex virtual marine microbial ecosystem, we find that climate change–driven shifts over the 21st century are often abrupt, large in amplitude and extent, and unpredictable using standard early warning signals. Phytoplankton with unique resource needs, especially fast-growing species such as diatoms, are more prone to abrupt shifts. Abrupt shifts in biomass, productivity, and community structure are concentrated in Atlantic and Pacific subtropics. Abrupt changes in environmental variables such as temperature and nutrients rarely precede these ecosystem shifts, indicating that rapid community restructuring can occur in response to gradual environmental changes, particularly in nutrient supply rate ratios.
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Affiliation(s)
- B. B. Cael
- National Oceanography Centre, Southampton, UK
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25
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Landolfi A, Prowe AEF, Pahlow M, Somes CJ, Chien CT, Schartau M, Koeve W, Oschlies A. Can Top-Down Controls Expand the Ecological Niche of Marine N 2 Fixers? Front Microbiol 2021; 12:690200. [PMID: 34489886 PMCID: PMC8416505 DOI: 10.3389/fmicb.2021.690200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/05/2021] [Indexed: 01/12/2023] Open
Abstract
The ability of marine diazotrophs to fix dinitrogen gas (N2) is one of the most influential yet enigmatic processes in the ocean. With their activity diazotrophs support biological production by fixing about 100–200 Tg N/year and turning otherwise unavailable dinitrogen into bioavailable nitrogen (N), an essential limiting nutrient. Despite their important role, the factors that control the distribution of diazotrophs and their ability to fix N2 are not fully elucidated. We discuss insights that can be gained from the emerging picture of a wide geographical distribution of marine diazotrophs and provide a critical assessment of environmental (bottom-up) versus trophic (top-down) controls. We expand a simplified theoretical framework to understand how top-down control affects competition for resources that determine ecological niches. Selective mortality, mediated by grazing or viral-lysis, on non-fixing phytoplankton is identified as a critical process that can broaden the ability of diazotrophs to compete for resources in top-down controlled systems and explain an expanded ecological niche for diazotrophs. Our simplified analysis predicts a larger importance of top-down control on competition patterns as resource levels increase. As grazing controls the faster growing phytoplankton, coexistence of the slower growing diazotrophs can be established. However, these predictions require corroboration by experimental and field data, together with the identification of specific traits of organisms and associated trade-offs related to selective top-down control. Elucidation of these factors could greatly improve our predictive capability for patterns and rates of marine N2 fixation. The susceptibility of this key biogeochemical process to future changes may not only be determined by changes in environmental conditions but also via changes in the ecological interactions.
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Affiliation(s)
- Angela Landolfi
- Institute of Marine Sciences, National Research Council, Rome, Italy.,Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A E Friederike Prowe
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Markus Pahlow
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Christopher J Somes
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Chia-Te Chien
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Markus Schartau
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Wolfgang Koeve
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Andreas Oschlies
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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26
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Harke MJ, Frischkorn KR, Hennon GMM, Haley ST, Barone B, Karl DM, Dyhrman ST. Microbial community transcriptional patterns vary in response to mesoscale forcing in the North Pacific Subtropical Gyre. Environ Microbiol 2021; 23:4807-4822. [PMID: 34309154 DOI: 10.1111/1462-2920.15677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 07/18/2021] [Indexed: 11/30/2022]
Abstract
The physical and biological dynamics that influence phytoplankton communities in the oligotrophic ocean are complex, changing across broad temporal and spatial scales. Eukaryotic phytoplankton (e.g., diatoms), despite their relatively low abundance in oligotrophic waters, are responsible for a large component of the organic matter flux to the ocean interior. Mesoscale eddies can impact both microbial community structure and function, enhancing primary production and carbon export, but the mechanisms that underpin these dynamics are still poorly understood. Here, mesoscale eddy influences on the taxonomic diversity and expressed functional profiles of surface communities of microeukaryotes and particle-associated heterotrophic bacteria from the North Pacific Subtropical Gyre were assessed over 2 years (spring 2016 and summer 2017). The taxonomic diversity of the microeukaryotes significantly differed by eddy polarity (cyclonic versus anticyclonic) and between sampling seasons/years and was significantly correlated with the taxonomic diversity of particle-associated heterotrophic bacteria. The expressed functional profile of these taxonomically distinct microeukaryotes varied consistently as a function of eddy polarity, with cyclones having a different expression pattern than anticyclones, and between sampling seasons/years. These data suggest that mesoscale forcing, and associated changes in biogeochemistry, could drive specific physiological responses in the resident microeukaryote community, independent of species composition.
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Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Gloucester Marine Genomics Institute, Gloucester, MA, USA
| | - Kyle R Frischkorn
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,College of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, AK, USA
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Benedetto Barone
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
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27
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Zacaï A, Monnet C, Pohl A, Beaugrand G, Mullins G, Kroeck DM, Servais T. Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton. SCIENCE ADVANCES 2021; 7:eabd6709. [PMID: 33827811 PMCID: PMC8026127 DOI: 10.1126/sciadv.abd6709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
The latitudinal diversity gradient (LDG)-the decline in species richness from the equator to the poles-is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.
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Affiliation(s)
- Axelle Zacaï
- Evo-Eco-Paleo, UMR 8198, CNRS, Univ. Lille, F-59000 Lille, France.
- PALEVOPRIM, UMR 7262, CNRS, Université de Poitiers, 86073 Poitiers Cedex 9, France
| | - Claude Monnet
- Evo-Eco-Paleo, UMR 8198, CNRS, Univ. Lille, F-59000 Lille, France
| | - Alexandre Pohl
- Department of Earth and Planetary Sciences, University of California, Riverside, Riverside, CA, USA
- Biogéosciences, UMR 6282, CNRS, Université Bourgogne Franche-Comté, 6 boulevard Gabriel, F-21000 Dijon, France
| | - Grégory Beaugrand
- Laboratoire d'Océanologie et de Géosciences, UMR 8187, CNRS, Univ. Lille, F-59000 Lille, France
| | | | - David M Kroeck
- Evo-Eco-Paleo, UMR 8198, CNRS, Univ. Lille, F-59000 Lille, France
| | - Thomas Servais
- Evo-Eco-Paleo, UMR 8198, CNRS, Univ. Lille, F-59000 Lille, France
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28
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Kruk C, Piccini C, Devercelli M, Nogueira L, Accattatis V, Sampognaro L, Segura AM. A trait‐based approach predicting community assembly and dominance of microbial invasive species. OIKOS 2021. [DOI: 10.1111/oik.07694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Carla Kruk
- Limnología, IECA, Facultad de Ciencias UdelaR Uruguay
- Ecología Funcional de Sistemas Acuáticos, CURE UdelaR Uruguay
| | - Claudia Piccini
- Depto de Microbiología, Inst. de Investigaciones Biológicas Clemente Estable, MEC Uruguay
| | | | | | | | - Lía Sampognaro
- Ecología Funcional de Sistemas Acuáticos, CURE UdelaR Uruguay
- Modelación y Análisis de Recursos Naturales, CURE UdelaR Uruguay
| | - Angel M. Segura
- Modelación y Análisis de Recursos Naturales, CURE UdelaR Uruguay
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29
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Phoma BS, Makhalanyane TP. Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands. MICROBIAL ECOLOGY 2021; 81:396-409. [PMID: 32935183 DOI: 10.1007/s00248-020-01589-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.
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Affiliation(s)
- Boitumelo Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
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30
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Ramond P, Siano R, Schmitt S, de Vargas C, Marié L, Memery L, Sourisseau M. Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front. Sci Rep 2021; 11:2682. [PMID: 33514820 PMCID: PMC7846791 DOI: 10.1038/s41598-021-82071-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/26/2020] [Indexed: 01/30/2023] Open
Abstract
Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.
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Affiliation(s)
- Pierre Ramond
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS-UMR7144-Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France ,Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France ,grid.10914.3d0000 0001 2227 4609Department of Marine Microbiology and Biogeochemistry, NIOZ-Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands
| | - Raffaele Siano
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
| | - Sophie Schmitt
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
| | - Colomban de Vargas
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS-UMR7144-Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France ,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Louis Marié
- grid.503286.aLaboratoire d’Océanographie Physique et Spatiale (LOPS), UMR 6523 Univ. Brest, CNRS, IFREMER, IRD, Plouzané, France
| | - Laurent Memery
- grid.463763.30000 0004 0638 0577Laboratoire des Sciences de l’Environnement MARin (LEMAR), UMR 6539 Univ. Brest, CNRS, IFREMER, IRD, Plouzané, France
| | - Marc Sourisseau
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
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31
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Ukhurebor KE, Aigbe UO, Onyancha RB, Adetunji CO. Climate Change and Pesticides: Their Consequence on Microorganisms. MICROBIAL REJUVENATION OF POLLUTED ENVIRONMENT 2021. [DOI: 10.1007/978-981-15-7459-7_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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32
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Messer LF, Ostrowski M, Doblin MA, Petrou K, Baird ME, Ingleton T, Bissett A, Van de Kamp J, Nelson T, Paulsen I, Bodrossy L, Fuhrman JA, Seymour JR, Brown MV. Microbial tropicalization driven by a strengthening western ocean boundary current. GLOBAL CHANGE BIOLOGY 2020; 26:5613-5629. [PMID: 32715608 DOI: 10.1111/gcb.15257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change-driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k-strategist) signatures, to seasonally displace more copiotrophic (r-strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non-EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time-series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate-driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.
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Affiliation(s)
- Lauren F Messer
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martina A Doblin
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - Mark E Baird
- CSIRO Oceans and Atmosphere, Hobart, Tas., Australia
| | | | | | | | - Tiffanie Nelson
- Geelong Centre for Emerging Infectious Diseases, Deakin University, Melbourne, Vic., Australia
| | - Ian Paulsen
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
| | | | - Jed A Fuhrman
- University of Southern California, Los Angeles, CA, USA
| | - Justin R Seymour
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, NSW, Australia
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33
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Endo H, Blanc-Mathieu R, Li Y, Salazar G, Henry N, Labadie K, de Vargas C, Sullivan MB, Bowler C, Wincker P, Karp-Boss L, Sunagawa S, Ogata H. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat Ecol Evol 2020; 4:1639-1649. [DOI: 10.1038/s41559-020-01288-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022]
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34
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Sandhu SK, Morozov A, Juan L. Exploring the role of spatial and stoichiometric heterogeneity in the top-down control in eutrophic planktonic ecosystems. J Theor Biol 2020; 499:110311. [PMID: 32437709 DOI: 10.1016/j.jtbi.2020.110311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Understanding the impact of eutrophication on the dynamics of aquatic food webs, remains a long-term challenge in ecology. Mathematical models generally predict the destabilisation of such webs, under increasing eutrophication levels, with large oscillations of species densities that can result in their extinction. This is at odds with a number of ecological observations that show stable dynamics even for high nutrient loads. The apparent discrepancy between theory and observations is known as the Rosenzweig's 'paradox of enrichment' and various solutions to the problem have been proposed over the years. In this study, we explore the stabilisation of dynamics of a tri-trophic plankton model in a eutrophic environment which occurs as a result of interplay of space heterogeneity, ecological stoichiometry, and food taxis of predators. We build a variety of models of increasing complexity, to explore various scenarios of phytoplankton growth, zooplankton food-dependent vertical movement, and different stoichiometric limitations of zooplankton. We show that the synergy among the vertical gradient in phytoplankton growth, phytoplankton structuring in terms of their stoichiometric ratio, and food-dependent vertical movement of zooplankton, would result in a postponing of destabilisation of eutrophic systems as compared to a well-mixed system. Our approach reveals a high complexity of the bifurcation structure of the system when key model parameters, such as the degree of eutrophication and light shading, are varied. We find coexistence of limit cycles and stable equilibria and that the possibility of multiple attractors in the system can result in hysteresis phenomena when the nutrient load is manipulated. These results are relevant and should be taken into account in lake restoration programs.
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Affiliation(s)
| | - Andrew Morozov
- Department of Mathematics, University of Leicester, UK; Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia.
| | - Lourdes Juan
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX, USA
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35
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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36
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Wu Y, Zhang M, Li Z, Xu J, Beardall J. Differential Responses of Growth and Photochemical Performance of Marine Diatoms to Ocean Warming and High Light Irradiance. Photochem Photobiol 2020; 96:1074-1082. [DOI: 10.1111/php.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/20/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Yaping Wu
- College of Marine Life and Fisheries Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Mengjuan Zhang
- College of Marine Life and Fisheries Jiangsu Ocean University Lianyungang China
| | - Zhenzhen Li
- The Swire Institute of Marine Science and School of Biological Sciences The University of Hong Kong Hong Kong China
| | - Juntian Xu
- College of Marine Life and Fisheries Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - John Beardall
- School of Biological Sciences Monash University Clayton Vic. Australia
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Wu P, Zakem EJ, Dutkiewicz S, Zhang Y. Biomagnification of Methylmercury in a Marine Plankton Ecosystem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:5446-5455. [PMID: 32054263 DOI: 10.1021/acs.est.9b06075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylmercury is greatly bioconcentrated and biomagnified in marine plankton ecosystems, and these communities form the basis of marine food webs. Therefore, the evaluation of the potential exposure of methylmercury to higher trophic levels, including humans, requires a better understanding of its distribution in the ocean and the factors that control its biomagnification. In this study, a coupled physical/ecological model is used to simulate the trophic transfer of monomethylmercury (MMHg) in a marine plankton ecosystem. The model includes phytoplankton, a microbial community, herbivorous zooplankton (HZ), and carnivorous zooplankton (CZ). The model captures both shorter food chains in oligotrophic regions, with small HZ feeding on small phytoplankton, and longer chains in higher nutrient conditions, with larger HZ feeding on larger phytoplankton and larger CZ feeding on larger HZ. In the model, trophic dilution occurs in the food webs that involve small zooplankton, as the grazing fluxes of small zooplankton are insufficient to accumulate more MMHg in themselves than in their prey. The model suggests that biomagnification is more prominent in large zooplankton and that the microbial community plays an important role in the trophic transfer of MMHg. Sensitivity analyses show that with increasing body size, the sensitivity of the trophic magnification ratio to grazing, mortality rates, and food assimilation efficiency (AEC) increases, while the sensitivity to excretion rates decreases. More predation or a longer zooplankton lifespan may lead to more prominent biomagnification, especially for large species. Because lower AEC results in more predation, modeled ratios of MMHg concentrations between large plankton are doubled or even tripled when the AEC decreases from 50% to 10%. This suggests that the biomagnification of large zooplankton is particularly sensitive to food assimilation efficiency.
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Affiliation(s)
- Peipei Wu
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Emily J Zakem
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 United States
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Yanxu Zhang
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities. Microorganisms 2020; 8:microorganisms8040567. [PMID: 32326461 PMCID: PMC7232425 DOI: 10.3390/microorganisms8040567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Dinoflagellates and diatoms are among the most prominent microeukaryotic plankton groups, and they have evolved different functional traits reflecting their roles within ecosystems. However, links between their metabolic processes and functional traits within different environmental contexts warrant further study. The functional biodiversity of dinoflagellates and diatoms was accessed with metatranscriptomics using Pfam protein domains as proxies for functional processes. Despite the overall geographic similarity of functional responses, abiotic (i.e., temperature and salinity; ~800 Pfam domains) and biotic (i.e., taxonomic group; ~1500 Pfam domains) factors influencing particular functional responses were identified. Salinity and temperature were identified as the main drivers of community composition. Higher temperatures were associated with an increase of Pfam domains involved in energy metabolism and a decrease of processes associated with translation and the sulfur cycle. Salinity changes were correlated with the biosynthesis of secondary metabolites (e.g., terpenoids and polyketides) and signal transduction processes, indicating an overall strong effect on the biota. The abundance of dinoflagellates was positively correlated with nitrogen metabolism, vesicular transport and signal transduction, highlighting their link to biotic interactions (more so than diatoms) and suggesting the central role of species interactions in the evolution of dinoflagellates. Diatoms were associated with metabolites (e.g., isoprenoids and carotenoids), as well as lysine degradation, which highlights their ecological role as important primary producers and indicates the physiological importance of these metabolic pathways for diatoms in their natural environment. These approaches and gathered information will support ecological questions concerning the marine ecosystem state and metabolic interactions in the marine environment.
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Small phytoplankton dominate western North Atlantic biomass. ISME JOURNAL 2020; 14:1663-1674. [PMID: 32231247 PMCID: PMC7305139 DOI: 10.1038/s41396-020-0636-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 02/02/2023]
Abstract
The North Atlantic phytoplankton spring bloom is the pinnacle in an annual cycle that is driven by physical, chemical, and biological seasonality. Despite its important contributions to the global carbon cycle, transitions in plankton community composition between the winter and spring have been scarcely examined in the North Atlantic. Phytoplankton composition in early winter was compared with latitudinal transects that captured the subsequent spring bloom climax. Amplicon sequence variants (ASVs), imaging flow cytometry, and flow-cytometry provided a synoptic view of phytoplankton diversity. Phytoplankton communities were not uniform across the sites studied, but rather mapped with apparent fidelity onto subpolar- and subtropical-influenced water masses of the North Atlantic. At most stations, cells < 20-µm diameter were the main contributors to phytoplankton biomass. Winter phytoplankton communities were dominated by cyanobacteria and pico-phytoeukaryotes. These transitioned to more diverse and dynamic spring communities in which pico- and nano-phytoeukaryotes, including many prasinophyte algae, dominated. Diatoms, which are often assumed to be the dominant phytoplankton in blooms, were contributors but not the major component of biomass. We show that diverse, small phytoplankton taxa are unexpectedly common in the western North Atlantic and that regional influences play a large role in modulating community transitions during the seasonal progression of blooms.
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40
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Morris MM, Frixione NJ, Burkert AC, Dinsdale EA, Vannette RL. Microbial abundance, composition, and function in nectar are shaped by flower visitor identity. FEMS Microbiol Ecol 2020; 96:5700281. [DOI: 10.1093/femsec/fiaa003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/08/2020] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.
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Affiliation(s)
- Megan M Morris
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Natalie J Frixione
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Alexander C Burkert
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | | | - Rachel L Vannette
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
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41
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Hellweger FL. Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:267-289. [PMID: 31226029 DOI: 10.1146/annurev-marine-010419-010829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Advances in technologies for molecular observation are leading to novel types of data, including gene, transcript, protein, and metabolite levels, which are fundamentally different from the types traditionally compared with microbial ecosystem models, such as biomass (e.g., chlorophyll a) and nutrient concentrations. A grand challenge is to use these data to improve predictive models and use models to explain observed patterns. This article presents a framework that aligns observations and models along the dimension of abstraction or biological organization-from raw sequences to ecosystem patterns for observations, and from sequence simulators to ecological theory for models. It then reviews 16 studies that compared model results with molecular observations. Molecular data can and are being combined with microbial ecosystem models, but to keep up with and take advantage of the full scope of observations, models need to become more mechanistically detailed and complex, which is a technical and cultural challenge for the ecological modeling community.
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Affiliation(s)
- Ferdi L Hellweger
- Specialty Area of Water Quality Engineering (Wasserreinhaltung), Institute of Environmental Science and Engineering, Technical University of Berlin, 10623 Berlin, Germany;
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42
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Burson A, Stomp M, Mekkes L, Huisman J. Stable coexistence of equivalent nutrient competitors through niche differentiation in the light spectrum. Ecology 2019; 100:e02873. [PMID: 31463935 PMCID: PMC6916172 DOI: 10.1002/ecy.2873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 11/26/2022]
Abstract
Niche-based theories and the neutral theory of biodiversity differ in their predictions of how the species composition of natural communities will respond to changes in nutrient availability. This is an issue of major environmental relevance, as many ecosystems have experienced changes in nitrogen (N) and phosphorus (P) due to anthropogenic manipulation of nutrient loading. To understand how changes in N and P limitation may impact community structure, we conducted laboratory competition experiments using a multispecies phytoplankton community sampled from the North Sea. Results showed that picocyanobacteria (Cyanobium sp.) won the competition under N limitation, while picocyanobacteria and nonmotile nanophytoplankton (Nannochloropsis sp.) coexisted at equal abundances under P limitation. Additional experiments using isolated monocultures confirmed that Cyanobium sp. depleted N to lower levels than Nannochloropsis sp., but that both species had nearly identical P requirements, suggesting a potential for neutral coexistence under P-limited conditions. Pairwise competition experiments with the two isolates seemed to support the consistency of these results, but P limitation resulted in stable species coexistence irrespective of the initial conditions rather than the random drift of species abundances predicted by neutral theory. Comparison of the light absorption spectra indicates that coexistence of the two species was stabilized through differential use of the underwater light spectrum. Our results provide an interesting experimental example of modern coexistence theory, where species were equal competitors in one niche dimension but their competitive traits differed in other niche dimensions, thus enabling stable species coexistence on a single limiting nutrient through niche differentiation in the light spectrum.
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Affiliation(s)
- Amanda Burson
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Present address:
School of GeographyUniversity of NottinghamNottinghamUnited Kingdom
| | - Maayke Stomp
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Lisette Mekkes
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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43
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Xiao W, Laws EA, Xie Y, Wang L, Liu X, Chen J, Chen B, Huang B. Responses of marine phytoplankton communities to environmental changes: New insights from a niche classification scheme. WATER RESEARCH 2019; 166:115070. [PMID: 31525510 DOI: 10.1016/j.watres.2019.115070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/20/2019] [Accepted: 09/07/2019] [Indexed: 06/10/2023]
Abstract
Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes.
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Affiliation(s)
- Wupeng Xiao
- State Key Laboratory of Marine Environmental Science / Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies / College of the Environment and Ecology, Xiamen University, Xiamen, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Edward A Laws
- Department of Environmental Sciences, School of the Coast & Environment, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Yuyuan Xie
- State Key Laboratory of Marine Environmental Science / Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies / College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Xin Liu
- State Key Laboratory of Marine Environmental Science / Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies / College of the Environment and Ecology, Xiamen University, Xiamen, China.
| | - Jixin Chen
- State Key Laboratory of Marine Environmental Science / Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies / College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Bingzhang Chen
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Bangqin Huang
- State Key Laboratory of Marine Environmental Science / Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies / College of the Environment and Ecology, Xiamen University, Xiamen, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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44
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Ward BA, Collins S, Dutkiewicz S, Gibbs S, Bown P, Ridgwell A, Sauterey B, Wilson JD, Oschlies A. Considering the Role of Adaptive Evolution in Models of the Ocean and Climate System. JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS 2019; 11:3343-3361. [PMID: 32025278 PMCID: PMC6988444 DOI: 10.1029/2018ms001452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/24/2023]
Abstract
Numerical models have been highly successful in simulating global carbon and nutrient cycles in today's ocean, together with observed spatial and temporal patterns of chlorophyll and plankton biomass at the surface. With this success has come some confidence in projecting the century-scale response to continuing anthropogenic warming. There is also increasing interest in using such models to understand the role of plankton ecosystems in past oceans. However, today's marine environment is the product of billions of years of continual evolution-a process that continues today. In this paper, we address the questions of whether an assumption of species invariance is sufficient, and if not, under what circumstances current model projections might break down. To do this, we first identify the key timescales and questions asked of models. We then review how current marine ecosystem models work and what alternative approaches are available to account for evolution. We argue that for timescales of climate change overlapping with evolutionary timescales, accounting for evolution may to lead to very different projected outcomes regarding the timescales of ecosystem response and associated global biogeochemical cycling. This is particularly the case for past extinction events but may also be true in the future, depending on the eventual degree of anthropogenic disruption. The discipline of building new numerical models that incorporate evolution is also hugely beneficial in itself, as it forces us to question what we know about adaptive evolution, irrespective of its quantitative role in any specific event or environmental changes.
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Affiliation(s)
- B. A. Ward
- Ocean and Earth ScienceUniversity of SouthamptonSouthamptonUK
| | - S. Collins
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - S. Dutkiewicz
- Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. Gibbs
- Ocean and Earth ScienceUniversity of SouthamptonSouthamptonUK
| | - P. Bown
- Department of GeologyUniversity College LondonLondonUK
| | - A. Ridgwell
- Department of Earth SciencesUniversity of CaliforniaRiversideCAUSA
- School of Geographical SciencesUniversity of BristolBristolUK
| | - B. Sauterey
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - J. D. Wilson
- School of Geographical SciencesUniversity of BristolBristolUK
| | - A. Oschlies
- GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
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45
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Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP. Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. mSystems 2019; 4:e00392-19. [PMID: 31594828 PMCID: PMC6787564 DOI: 10.1128/msystems.00392-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.
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Affiliation(s)
- Eric Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rachel Cooper
- Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya Gomes
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jacquelyn S Meisel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - C David Mintz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven Connecticut, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, DC, USA
| | - Carly Muletz Wolz
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, USA
| | - Joseph P Zackular
- Department of Pathology and Laboratory Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Chopyk
- School of Public Health, University of Maryland, College Park, Maryland, USA
| | - Seth Commichaux
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Meghan Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Douglas Dluzen
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Sukirth M Ganesan
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Muyideen Haruna
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Dan Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Mary J Regan
- University of Maryland School of Nursing, Baltimore, Maryland, USA
| | - Saul Sarria
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Brook Stacy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Dylan Taylor
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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46
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Kraemer S, Ramachandran A, Colatriano D, Lovejoy C, Walsh DA. Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. ISME JOURNAL 2019; 14:79-90. [PMID: 31501503 DOI: 10.1038/s41396-019-0499-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/30/2019] [Accepted: 08/17/2019] [Indexed: 11/09/2022]
Abstract
The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.
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Affiliation(s)
- Susanne Kraemer
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - David Colatriano
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Connie Lovejoy
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Quebec City, QC, G1K 7P4, Canada
| | - David A Walsh
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada.
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47
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Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists' warning to humanity: microorganisms and climate change. Nat Rev Microbiol 2019; 17:569-586. [PMID: 31213707 PMCID: PMC7136171 DOI: 10.1038/s41579-019-0222-5] [Citation(s) in RCA: 640] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Abstract
In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Antje Boetius
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, and The Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | | | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Christine M Foreman
- Center for Biofilm Engineering, and Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - David A Hutchins
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science & Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David S Reay
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia I Rich
- Microbiology Department, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Department of Microbiology, and Department of Civil, Environmental and Geodetic Engineering, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Scott C Weaver
- Department of Microbiology and Immunology, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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48
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Liu J, Tu T, Gao G, Bartlam M, Wang Y. Biogeography and Diversity of Freshwater Bacteria on a River Catchment Scale. MICROBIAL ECOLOGY 2019; 78:324-335. [PMID: 30687882 DOI: 10.1007/s00248-019-01323-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
To illustrate how freshwater bacterial community changes with geographic gradient, we investigated the spatial changes of bacterial abundance and community structures from over 200 samples on a catchment scale in the Songhua River using heterotrophic plate counts, flow cytometry, denaturing gradient gel electrophoresis, and pyrosequencing analysis. The results showed that the mainstream had higher cultivable bacteria and total bacterial concentration than tributaries in the Songhua River catchment. Response model analysis demonstrated that the bacterial community exhibits a biogeographical signature even in an interconnected river network system, and the total bacterial concentration and biodiversity were significantly correlated to latitude (p < 0.001) and longitude (p < 0.001). Multivariate redundancy analysis indicated that temperature was the most important factor driving bacterial community structure in the Songhua River, which accounts for 35.30% variance of communities, then dissolved oxygen (17.60%), latitude (17.60%), longitude (11.80%), and pH (5.88%). High-throughput pyrosequencing revealed that at the phylum level, Proteobacteria was numerically dominant (89.6%) in river catchment, followed by Bacteroidetes (8.1%) and Cyanobacteria (1.2%). The overall results revealed that the bacterial community was driven by geographical distance regardless of the continuum of the river on a catchment scale.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
- Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Teng Tu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
- Center for Earth Environment and Resources, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology & College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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49
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Righetti D, Vogt M, Gruber N, Psomas A, Zimmermann NE. Global pattern of phytoplankton diversity driven by temperature and environmental variability. SCIENCE ADVANCES 2019; 5:eaau6253. [PMID: 31106265 PMCID: PMC6520023 DOI: 10.1126/sciadv.aau6253] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Despite their importance to ocean productivity, global patterns of marine phytoplankton diversity remain poorly characterized. Although temperature is considered a key driver of general marine biodiversity, its specific role in phytoplankton diversity has remained unclear. We determined monthly phytoplankton species richness by using niche modeling and >540,000 global phytoplankton observations to predict biogeographic patterns of 536 phytoplankton species. Consistent with metabolic theory, phytoplankton richness in the tropics is about three times that in higher latitudes, with temperature being the most important driver. However, below 19°C, richness is lower than expected, with ~8°- 14°C waters (~35° to 60° latitude) showing the greatest divergence from theoretical predictions. Regions of reduced richness are characterized by maximal species turnover and environmental variability, suggesting that the latter reduces species richness directly, or through enhancing competitive exclusion. The nonmonotonic relationship between phytoplankton richness and temperature suggests unanticipated complexity in responses of marine biodiversity to ocean warming.
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Affiliation(s)
- Damiano Righetti
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- Corresponding author.
| | - Meike Vogt
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Nicolas Gruber
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Achilleas Psomas
- Dynamic Macroecology, Landscape Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Niklaus E. Zimmermann
- Dynamic Macroecology, Landscape Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
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50
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Ramond P, Sourisseau M, Simon N, Romac S, Schmitt S, Rigaut-Jalabert F, Henry N, de Vargas C, Siano R. Coupling between taxonomic and functional diversity in protistan coastal communities. Environ Microbiol 2019; 21:730-749. [PMID: 30672084 DOI: 10.1111/1462-2920.14537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/19/2019] [Indexed: 01/11/2023]
Abstract
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the operational taxonomic units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade-offs) in order to build the best functional groups. Based on the annotated OTUs and our functional groups, we demonstrated that the functional diversity of marine protist communities varied in parallel with their taxonomic diversity. The coupling between functional and taxonomic diversity was conserved across different protist size classes. However, the smallest size-fraction was characterized by wider taxonomic and functional groups diversity, corroborating the idea that nanoplankton and picoplankton are part of a more stable ecological background on which larger protists and metazoans might develop.
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Affiliation(s)
- Pierre Ramond
- IFREMER, Dyneco Pelagos, BP 70, 29280 Plouzané, France.,Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | - Sarah Romac
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS - FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France
| | - Nicolas Henry
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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