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Cossa D, Infantes E, Dupont S. Hidden cost of pH variability in seagrass beds on marine calcifiers under ocean acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170169. [PMID: 38244616 DOI: 10.1016/j.scitotenv.2024.170169] [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: 09/03/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Coastal ecosystems experience large environmental variability leading to local adaptation. The key role of variability and adaptation in modulating the biological sensitivity to ocean acidification is increasingly acknowledged. Monitoring and understanding the ecological niche at the right spatio-temporal scale is key to understand the sensitivity of any organism and ecosystems. However, the role of the variability in relevant carbonate chemistry parameters as a driver is often overlooked. For example, the balance between photosynthesis and respiration over the day/night cycle is leading to high pH/pCO2 variability in seagrass beds. We hypothesized that (i) the calcifying larvae of the sea urchin Echinus esculentus exposed to seagrass-driven variability would have some physiological mechanisms to respond to such variability; and (ii) these mechanisms would reach their limit under ocean acidification. We compared the presence and absence of the seagrass Zostera marina in flow through mesocosms fed with seawater with 4 pHs. The carbonate chemistry was monitored and biological response of a sea urchin larvae was documented over 3 weeks. Growth and net calcification rates were measured twice a day to encompass diurnal variability. Our results show that larvae growth rate significantly decreased with decreasing average pHT in both absence and presence of seagrass. Moreover, sea urchin larvae showed a slower growth rate in presence of seagrass, only visible in the lowest pH conditions. In addition, larvae raised in presence of seagrass, maximized calcification during the day, and lower their calcification during the night. In contrast, no significant difference was observed between day and night for the net calcification rate in larvae raised in absence of seagrass. Our results demonstrate the limit of local adaptation to the present range of variability under ocean acidification conditions. It also demonstrates that photosynthetic ecosystems such as seagrass may not play a role of refuge against future ocean acidification.
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Affiliation(s)
- Damboia Cossa
- Department of Marine Sciences, University of Gothenburg, Kristineberg, 45178 Fiskebäckskil, Sweden; Department of Biological Sciences, Eduardo Mondlane University, 257 Maputo, Mozambique.
| | - Eduardo Infantes
- Department of Biological and Environmental Sciences, University of Gothenburg, Kristineberg, 45178 Fiskebäckskil, Sweden
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, Kristineberg, 45178 Fiskebäckskil, Sweden; Radioecology Laboratory, International Atomic Energy Agency (IAEA), Monaco
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2
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Estimation of functional diversity and species traits from ecological monitoring data. Proc Natl Acad Sci U S A 2022; 119:e2118156119. [PMID: 36256813 PMCID: PMC9618138 DOI: 10.1073/pnas.2118156119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The rampant loss of biodiversity is starting to be recognized as a global crisis rivaling the climate emergency. To address this crisis, scientists need robust methods to measure the diversity in a system. Importantly, these methods should not only count species but capture the variety of different functions that the species in a system can perform. In this paper, we propose a machine learning method by which existing data from ecosystem monitoring can be reanalyzed to reveal changes of functional biodiversity over time. The twin crises of climate change and biodiversity loss define a strong need for functional diversity monitoring. While the availability of high-quality ecological monitoring data is increasing, the quantification of functional diversity so far requires the identification of species traits, for which data are harder to obtain. However, the traits that are relevant for the ecological function of a species also shape its performance in the environment and hence, should be reflected indirectly in its spatiotemporal distribution. Thus, it may be possible to reconstruct these traits from a sufficiently extensive monitoring dataset. Here, we use diffusion maps, a deterministic and de facto parameter-free analysis method, to reconstruct a proxy representation of the species’ traits directly from monitoring data and use it to estimate functional diversity. We demonstrate this approach with both simulated data and real-world phytoplankton monitoring data from the Baltic Sea. We anticipate that wider application of this approach to existing data could greatly advance the analysis of changes in functional biodiversity.
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3
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Gajahin Gamage NT, Miyashita R, Takahashi K, Asakawa S, Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Proteomes 2022; 10:proteomes10030032. [PMID: 36136310 PMCID: PMC9505238 DOI: 10.3390/proteomes10030032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Affiliation(s)
- Nadeeka Thushari Gajahin Gamage
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Rina Miyashita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jayan Duminda Mahesh Senevirathna
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
- Correspondence:
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4
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Dalongeville A, Nielsen ES, Teske PR, Heyden S. Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Erica S. Nielsen
- Department of Evolution and Ecology University of California, Davis Davis California USA
| | - Peter R. Teske
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
| | - Sophie Heyden
- Department of Botany and Zoology Evolutionary Genomics Group Stellenbosch University Stellenbosch South Africa
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5
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Ballou L, Brankovits D, Chávez-Solís EM, Chávez Díaz JM, Gonzalez BC, Rohret S, Salinas A, Liu A, Simões N, Álvarez F, Miglietta MP, Iliffe TM, Borda E. An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatán Peninsula, Mexico. Sci Rep 2022; 12:5302. [PMID: 35351932 PMCID: PMC8961266 DOI: 10.1038/s41598-022-08779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/07/2022] [Indexed: 01/24/2023] Open
Abstract
The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (< 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.
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Affiliation(s)
- Lauren Ballou
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - David Brankovits
- Molecular Ecology Group, Water Research Institute, National Research Council of Italy (IRSA CNR), 28922, Pallanza, Italy
| | - Efraín M Chávez-Solís
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México, Mexico.,Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - José M Chávez Díaz
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, A.P. 70-153, 04510, Coyoacán, México D.F., Mexico
| | - Brett C Gonzalez
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington D.C., USA
| | - Shari Rohret
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Green Bldg., 77 Massachusetts Ave, Cambridge, MA, USA.,Geology & Geophysics Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS #52, Woods Hole, MA, USA
| | - Alexa Salinas
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, USA
| | - Arielle Liu
- School of Anthropology, University of Arizona, Emil W. Haury Anthropology Bldg., 1009 E South Campus Dr., Tucson, AZ, USA
| | - Nuno Simões
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo S/N, Sisal, Yucatán, Mexico.,National Coastal Resilience Laboratory (LANRESC), Puerto de Abrigo S/N, Sisal, Yucatán, Mexico.,International Chair for Ocean and Coastal Studies in Mexico, Harte Research Institute, Texas A&M at Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX, USA
| | - Fernando Álvarez
- Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, A.P. 70-153, 04510, Coyoacán, México D.F., Mexico
| | - Maria Pia Miglietta
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - Thomas M Iliffe
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Pkwy, Galveston, TX, USA
| | - Elizabeth Borda
- Department of Life Sciences, Texas A&M University San Antonio, One University Way, San Antonio, TX, USA.
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Ma X, Olsen JL, Reusch TBH, Procaccini G, Kudrna D, Williams M, Grimwood J, Rajasekar S, Jenkins J, Schmutz J, Van de Peer Y. Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass). F1000Res 2021; 10:289. [PMID: 34621505 PMCID: PMC8482049 DOI: 10.12688/f1000research.38156.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Seagrasses (Alismatales) are the only fully marine angiosperms.
Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass
Z.
marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved
Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.
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Affiliation(s)
- Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University - Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Jeanine L Olsen
- Groningen Institute of Evolutionary Life Sciences, Groningen, 9747 AG, The Netherlands
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, 24105, Germany
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, 80123, Italy
| | - Dave Kudrna
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona Tucson, Tucson, AZ, 85721, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University - Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,College of Horticulture, Nanjing Agricultural University, Nanjing, 210014, China
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7
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Peters K. The territories of governance: unpacking the ontologies and geophilosophies of fixed to flexible ocean management, and beyond. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190458. [PMID: 33131438 PMCID: PMC7662200 DOI: 10.1098/rstb.2019.0458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 01/31/2023] Open
Abstract
This paper offers a conceptual contribution to understanding ocean governance and the management of spaces for the protection of marine biodiversity, organization of extractive industries, the arrangement of global shipping and other 'blue-economy' uses. Rather than focus on one type of management technique (such as a Marine Protected Area (MPA) or example of Marine Spatial Planning), or a site- or species-specific case study of governance, this paper offers a theoretical tracking of the uncharted territories of governance that foreground ocean management approaches. The literature on ocean governance and management techniques predominantly derive from scientific disciplines (which provide the basis for planning) and policy-related social science fields, leaving a lacuna in more critical discussions of ways of knowing and understanding the world that drive it. The paper argues the need to critically understand the ontologies (the regimes of what we believe exists) and geophilosophies (the geographically informed modes of thinking) of territory that underscore ocean management to make sense of its past successes and failures, its present functioning and its future directions. This paper argues that without critical consideration of the kinds of thinking-the ontologies and geophilosophies-that drive ocean management, it will lack the transformative potential many hope it will achieve for sustainable development. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
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Affiliation(s)
- Kimberley Peters
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, 26129 Oldenburg, Germany
- Institute for Chemistry and Biology of Marine Environments [ICBM], University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26133 Oldenburg, Germany
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