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Saran A, Kim HM, Manning I, Hancock MA, Schmitz C, Madej M, Potempa J, Sola M, Trempe JF, Zhu Y, Davey ME, Zeytuni N. Unveiling the Molecular Mechanisms of the Type-IX Secretion System's Response Regulator: Structural and Functional Insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594396. [PMID: 38798656 PMCID: PMC11118453 DOI: 10.1101/2024.05.15.594396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The Type-IX secretion system (T9SS) is a nanomachinery utilized by bacterial pathogens to facilitate infection. The system is regulated by a signaling cascade serving as its activation switch. A pivotal member in this cascade, the response regulator protein PorX, represents a promising drug target to prevent the secretion of virulence factors. Here, we provide a comprehensive characterization of PorX both in vitro and in vivo . First, our structural studies revealed PorX harbours a unique enzymatic effector domain, which, surprisingly, shares structural similarities with the alkaline phosphatase superfamily, involved in nucleotide and lipid signaling pathways. Importantly, such pathways have not been associated with the T9SS until now. Enzymatic characterization of PorX's effector domain revealed a zinc-dependent phosphodiesterase activity, with active site dimensions suitable to accommodate a large substrate. Unlike typical response regulators that dimerize via their receiver domain upon phosphorylation, we found that zinc can also induce conformational changes and promote PorX's dimerization via an unexpected interface. These findings suggest that PorX can serve as a cellular zinc sensor, broadening our understanding of its regulatory mechanisms. Despite the strict conservation of PorX in T9SS-utilizing bacteria, we demonstrate that PorX is essential for virulence factors secretion in Porphyromonas gingivalis and affects metabolic enzymes secretion in the non-pathogenic Flavobacterium johnsoniae , but not for the secretion of gliding adhesins. Overall, this study advances our structural and functional understanding of PorX, highlighting its potential as a druggable target for intervention strategies aimed at disrupting the T9SS and mitigating virulence in pathogenic species.
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Madeira P, Reddy MM, Assis J, Bolton JJ, Rothman MD, Anderson RJ, Kandjengo L, Kreiner A, Coleman MA, Wernberg T, De Clerck O, Leliaert F, Bandeira S, Ada AM, Neiva J, Pearson GA, Serrão EA. Cryptic diversity in southern African kelp. Sci Rep 2024; 14:11071. [PMID: 38745036 PMCID: PMC11093989 DOI: 10.1038/s41598-024-61336-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/04/2024] [Indexed: 05/16/2024] Open
Abstract
The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution ~ 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.
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Affiliation(s)
- Pedro Madeira
- CCMAR, University of Algarve, Gambelas, Faro, Portugal.
| | - Maggie M Reddy
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
| | - Jorge Assis
- CCMAR, University of Algarve, Gambelas, Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway
| | - John J Bolton
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
| | - Mark D Rothman
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
- Department of Environment, Forestry and Fisheries, Private Bag X2, Vlaeberg, 8012, South Africa.
| | - Robert J Anderson
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - Lineekela Kandjengo
- Department of Fisheries and Ocean Sciences, University of Namibia, Sam Nujoma Campus, Henties Bay, Namibia
| | - Anja Kreiner
- National Marine Information and Research Centre, Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | - Melinda A Coleman
- New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
- National Marine Science Centre, Southern Cross University, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Thomas Wernberg
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Olivier De Clerck
- Biology Department, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
| | | | - Salomão Bandeira
- Department of Biological Sciences, Eduardo Mondlane University, Maputo, Mozambique
| | - Abdul M Ada
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - João Neiva
- CCMAR, University of Algarve, Gambelas, Faro, Portugal
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Vafeiadou A, Fragkopoulou E, Assis J. A global dataset of demosponge distribution records. Data Brief 2024; 53:110200. [PMID: 38435734 PMCID: PMC10907141 DOI: 10.1016/j.dib.2024.110200] [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: 11/20/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Biodiversity information in the form of species occurrence records is key for monitoring and predicting current and future biodiversity patterns, as well as for guiding conservation and management strategies. However, the reliability and accuracy of this information are frequently undermined by taxonomic and spatial errors. Additionally, biodiversity information facilities often share data in diverse incompatible formats, precluding seamless integration and interoperability. We provide a comprehensive quality-controlled dataset of occurrence records of the Class Demospongiae, which comprises 81% of the entire Porifera phylum. Demosponges are ecologically significant as they structure rich habitats and play a key role in nutrient cycling within marine benthic communities. The dataset aggregates occurrence records from multiple sources, employs dereplication and taxonomic curation techniques, and is flagged for potentially incorrect records based on expert knowledge regarding each species' bathymetric and geographic distributions. It yields 417,626 records of 1,816 accepted demosponge species (of which 321,660 records of 1,495 species are flagged as potentially correct), which are provided under the FAIR principle of Findability, Accessibility, Interoperability and Reusability in the Darwin Core Standard. This dataset constitutes the most up-to-date baseline for studying demosponge diversity at the global scale, enabling researchers to examine biodiversity patterns (e.g., species richness and endemicity), and forecast potential distributional shifts under future scenarios of climate change.
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Affiliation(s)
- Ariadni Vafeiadou
- Centre of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
| | - Eliza Fragkopoulou
- Centre of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
| | - Jorge Assis
- Centre of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Postboks 1490, Bodø, Norway
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Assis J, Alberto F, Macaya EC, Castilho Coelho N, Faugeron S, Pearson GA, Ladah L, Reed DC, Raimondi P, Mansilla A, Brickle P, Zuccarello GC, Serrão EA. Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scales. Sci Rep 2023; 13:12046. [PMID: 37491385 PMCID: PMC10368654 DOI: 10.1038/s41598-023-38944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
The paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following ~ 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.
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Affiliation(s)
- Jorge Assis
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal.
- Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway.
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin, Milwaukee, USA
| | - Erasmo C Macaya
- Centro Fondap IDEAL and Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Nelson Castilho Coelho
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal
- University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Sylvain Faugeron
- Núcleo Milenio MASH and IRL3614 Evolutionary Biology and Ecology of Algae, Facultad de Ciencias Biológicas, CNRS, Sorbonne Université, Universidad Austral de Chile, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | | | - Lydia Ladah
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Daniel C Reed
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | | | - Andrés Mansilla
- Cape Horn International Center (CHIC), Universidad de Magallanes, Punta Arenas, Chile
| | - Paul Brickle
- South Atlantic Environmental Research Institute, Stanley, Falkland Islands
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Ester A Serrão
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal
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Balogh V, Fragkopoulou E, Serrão EA, Assis J. A dataset of cold-water coral distribution records. Data Brief 2023; 48:109223. [PMID: 37383736 PMCID: PMC10293957 DOI: 10.1016/j.dib.2023.109223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 06/30/2023] Open
Abstract
Species distribution data are key for monitoring present and future biodiversity patterns and informing conservation and management strategies. Large biodiversity information facilities often contain spatial and taxonomic errors that reduce the quality of the provided data. Moreover, datasets are frequently shared in varying formats, inhibiting proper integration and interoperability. Here, we provide a quality-controlled dataset of the diversity and distribution of cold-water corals, which provide key ecosystem services and are considered vulnerable to human activities and climate change effects. We use the common term cold-water corals to refer to species of the orders Alcyonacea, Antipatharia, Pennatulacea, Scleractinia, Zoantharia of the subphylum Anthozoa, and order Anthoathecata of the class Hydrozoa. Distribution records were collated from multiple sources, standardized using the Darwin Core Standard, dereplicated, taxonomically corrected and flagged for potential vertical and geographic distribution errors based on peer-reviewed published literature and expert consulting. This resulted in 817,559 quality-controlled records of 1,170 accepted species of cold-water corals, openly available under the FAIR principle of Findability, Accessibility, Interoperability and Reusability of data. The dataset represents the most updated baseline for the global cold-water coral diversity, and it can be used by the broad scientific community to provide insights into biodiversity patterns and their drivers, identify regions of high biodiversity and endemicity, and project potential redistribution under future climate change. It can also be used by managers and stakeholders to guide biodiversity conservation and prioritization actions against biodiversity loss.
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Affiliation(s)
- Viktória Balogh
- Center of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
| | - Eliza Fragkopoulou
- Center of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
| | - Ester A. Serrão
- Center of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
| | - Jorge Assis
- Center of Marine Sciences (CCMAR-CIMAR), University of the Algarve, 8005-139 Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Postboks 1490, Bodø, Norway
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Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales. Sci Rep 2022; 12:21064. [PMID: 36473926 PMCID: PMC9726941 DOI: 10.1038/s41598-022-25565-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).
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Liconti A, Pittman SJ, Rees SE, Mieszkowska N. Identifying conservation priorities for gorgonian forests in Italian coastal waters with multiple methods including citizen science and social media content analysis. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Arianna Liconti
- School of Biological and Marine Sciences Plymouth University Plymouth UK
- The Marine Biological Association The Laboratory Plymouth UK
| | - Simon J. Pittman
- School of Biological and Marine Sciences Plymouth University Plymouth UK
- Oxford Seascape Ecology Lab School of Geography and the Environment, University of Oxford Oxford UK
| | - Sian E. Rees
- School of Biological and Marine Sciences Plymouth University Plymouth UK
| | - Nova Mieszkowska
- The Marine Biological Association The Laboratory Plymouth UK
- School of Environmental Sciences University of Liverpool Liverpool UK
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8
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Anderson AB, Assis J, Batista MB, Serrão EA, Guabiroba HC, Delfino SDT, Pinheiro HT, Pimentel CR, Gomes LEO, Vilar CC, Bernardino AF, Horta P, Ghisolfi RD, Joyeux JC. Global warming assessment suggests the endemic Brazilian kelp beds to be an endangered ecosystem. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105307. [PMID: 33984550 DOI: 10.1016/j.marenvres.2021.105307] [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: 11/24/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Kelps are canopy-forming brown seaweed sustaining critical ecosystem services in coastal habitats, including shelter, nursery grounds, and providing food resources to a myriad of associated species. This study modeled the fundamental niche of Laminaria abyssalis along the Brazilian continental margin, an endemic species of the South Atlantic, to anticipate potential distributional range shifts under two contrasting scenarios of future environmental changes (RCP2.6 and RCP8.5). The model for fundamental niche predictions considering the "present scenario" has shown a wider potential area than the realized niche (i.e., the area where the species actually occurs) along the Brazilian coast. In both future scenarios, the models have shown niche erosion on the northern portion of the Brazilian coast and niche gains towards the south. In both scenarios, L. abyssalis populations tend to shift to deeper regions of the reef. The restricted range of occurrence (33,000 km2), intense anthropic activities along these beds (e.g., trawling fisheries, oil/gas mining, or removal for agricultural purposes) acting synergically with global warming, may drive this ecosystem to collapse faster than kelp species' ability to adapt. We propose to classify L. abyssalis as Endangered - (EN) under IUCN criteria, and highlight that long-term monitoring of kelp beds is an urgent need to develop effective conservation initiatives to protect such rare and invaluable ecosystem.
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Affiliation(s)
- A B Anderson
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil.
| | - J Assis
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - M B Batista
- Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil
| | - E A Serrão
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - H C Guabiroba
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - S D T Delfino
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - H T Pinheiro
- Ichthyology Section, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - C R Pimentel
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - L E O Gomes
- Benthic Ecology Group, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - C C Vilar
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - A F Bernardino
- Benthic Ecology Group, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - P Horta
- Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil
| | - R D Ghisolfi
- Laboratory of Oceanography, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - J-C Joyeux
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
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Krause-Jensen D, Archambault P, Assis J, Bartsch I, Bischof K, Filbee-Dexter K, Dunton KH, Maximova O, Ragnarsdóttir SB, Sejr MK, Simakova U, Spiridonov V, Wegeberg S, Winding MHS, Duarte CM. Imprint of Climate Change on Pan-Arctic Marine Vegetation. FRONTIERS IN MARINE SCIENCE 2020; 7. [PMID: 0 DOI: 10.3389/fmars.2020.617324] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The Arctic climate is changing rapidly. The warming and resultant longer open water periods suggest a potential for expansion of marine vegetation along the vast Arctic coastline. We compiled and reviewed the scattered time series on Arctic marine vegetation and explored trends for macroalgae and eelgrass (Zostera marina). We identified a total of 38 sites, distributed between Arctic coastal regions in Alaska, Canada, Greenland, Iceland, Norway/Svalbard, and Russia, having time series extending into the 21st Century. The majority of these exhibited increase in abundance, productivity or species richness, and/or expansion of geographical distribution limits, several time series showed no significant trend. Only four time series displayed a negative trend, largely due to urchin grazing or increased turbidity. Overall, the observations support with medium confidence (i.e., 5–8 in 10 chance of being correct, adopting the IPCC confidence scale) the prediction that macrophytes are expanding in the Arctic. Species distribution modeling was challenged by limited observations and lack of information on substrate, but suggested a current (2000–2017) potential pan-Arctic brown macroalgal distribution area of 655,111 km2(140,433 km2intertidal, 514,679 km2subtidal), representing an increase of about 45% for subtidal- and 8% for intertidal macroalgae since 1940–1950, and associated polar migration rates averaging 18–23 km decade–1. Adjusting the potential macroalgal distribution area by the fraction of shores represented by cliffs halves the estimate (340,658 km2). Warming and reduced sea ice cover along the Arctic coastlines are expected to stimulate further expansion of marine vegetation from boreal latitudes. The changes likely affect the functioning of coastal Arctic ecosystems because of the vegetation’s roles as habitat, and for carbon and nutrient cycling and storage. We encourage a pan-Arctic science- and management agenda to incorporate marine vegetation into a coherent understanding of Arctic changes by quantifying distribution and status beyond the scattered studies now available to develop sustainable management strategies for these important ecosystems.
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The Genome Sequence of the Octocoral Paramuricea clavata - A Key Resource To Study the Impact of Climate Change in the Mediterranean. G3-GENES GENOMES GENETICS 2020; 10:2941-2952. [PMID: 32660973 PMCID: PMC7467007 DOI: 10.1534/g3.120.401371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change.
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Assis J, Fragkopoulou E, Frade D, Neiva J, Oliveira A, Abecasis D, Faugeron S, Serrão EA. A fine-tuned global distribution dataset of marine forests. Sci Data 2020; 7:119. [PMID: 32286314 PMCID: PMC7156423 DOI: 10.1038/s41597-020-0459-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 03/19/2020] [Indexed: 11/08/2022] Open
Abstract
Species distribution records are a prerequisite to follow climate-induced range shifts across space and time. However, synthesizing information from various sources such as peer-reviewed literature, herbaria, digital repositories and citizen science initiatives is not only costly and time consuming, but also challenging, as data may contain thematic and taxonomic errors and generally lack standardized formats. We address this gap for important marine ecosystem-structuring species of large brown algae and seagrasses. We gathered distribution records from various sources and provide a fine-tuned dataset with ~2.8 million dereplicated records, taxonomically standardized for 682 species, and considering important physiological and biogeographical traits. Specifically, a flagging system was implemented to signal potentially incorrect records reported on land, in regions with limiting light conditions for photosynthesis, and outside the known distribution of species, as inferred from the most recent published literature. We document the procedure and provide a dataset in tabular format based on Darwin Core Standard (DwC), alongside with a set of functions in R language for data management and visualization.
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Affiliation(s)
- Jorge Assis
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal.
| | - Eliza Fragkopoulou
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - Duarte Frade
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - João Neiva
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - André Oliveira
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - David Abecasis
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - Sylvain Faugeron
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique, Roscoff, France
| | - Ester A Serrão
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
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12
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Cerrano C, Bastari A, Calcinai B, Di Camillo C, Pica D, Puce S, Valisano L, Torsani F. Temperate mesophotic ecosystems: gaps and perspectives of an emerging conservation challenge for the Mediterranean Sea. EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1677790] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- C. Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - A. Bastari
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - B. Calcinai
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - C. Di Camillo
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - D. Pica
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - S. Puce
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - L. Valisano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - F. Torsani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Pilczynska J, Cocito S, Boavida J, Serrão EA, Assis J, Fragkopoulou E, Queiroga H. Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean. PeerJ 2019; 7:e6794. [PMID: 31179167 PMCID: PMC6536111 DOI: 10.7717/peerj.6794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background In the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata. Methods We used five polymorphic microsatellite markers to infer differences in genetic diversity and differentiation, and to detect bottleneck signs between shallow and deeper populations across the Atlantic Ocean and the Mediterranean Sea. We further explored the potential relationship between depth and environmental gradients (temperature, ocean currents, productivity and slope) on the observed patterns of diversity by means of generalized linear mixed models. Results An overall pattern of higher genetic diversity was found in the deeper sites of the Atlantic Ocean and the Mediterranean Sea. This pattern was largely explained by bottom temperatures, with a linear pattern of decreasing genetic diversity with increasing thermal stress. Genetic differentiation patterns showed higher gene flow within sites (i.e., shallow vs. deeper populations) than between sites. Recent genetic bottlenecks were found in two populations of shallow depths. Discussion Our results highlight the role of deep refugial populations safeguarding higher and unique genetic diversity for marine structuring species. Theoretical regression modelling demonstrated how thermal stress alone may reduce population sizes and diversity levels of shallow water populations. In fact, the examination of time series on a daily basis showed the upper water masses repeatedly reaching lethal temperatures for P. clavata. Differentiation patterns showed that the deep richer populations are isolated. Gene flow was also inferred across different depths; however, not in sufficient levels to offset the detrimental effects of surface environmental conditions on genetic diversity. The identification of deep isolated areas with high conservation value for the red gorgonian represents an important step in the face of ongoing and future climate changes.
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Affiliation(s)
- Joanna Pilczynska
- Departamento de Biologia and CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal.,Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Silvia Cocito
- Italian Agency for New Technologies, Energy and Sustainable Economic Development-ENEA, Marine Environment Research Centre, La Spezia, Italy
| | - Joana Boavida
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.,Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Ester A Serrão
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Jorge Assis
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Eliza Fragkopoulou
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Henrique Queiroga
- Departamento de Biologia and CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
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Ramilo DW, Nunes T, Madeira S, Boinas F, da Fonseca IP. Geographical distribution of Culicoides (DIPTERA: CERATOPOGONIDAE) in mainland Portugal: Presence/absence modelling of vector and potential vector species. PLoS One 2017; 12:e0180606. [PMID: 28683145 PMCID: PMC5500329 DOI: 10.1371/journal.pone.0180606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 06/19/2017] [Indexed: 12/24/2022] Open
Abstract
Vector-borne diseases are not only accounted responsible for their burden on human health-care systems, but also known to cause economic constraints to livestock and animal production. Animals are affected directly by the transmitted pathogens and indirectly when animal movement is restricted. Distribution of such diseases depends on climatic and social factors, namely, environmental changes, globalization, trade and unplanned urbanization. Culicoides biting midges are responsible for the transmission of several pathogenic agents with relevant economic impact. Due to a fragmentary knowledge of their ecology, occurrence is difficult to predict consequently, limiting the control of these arthropod vectors. In order to understand the distribution of Culicoides species, in mainland Portugal, data collected during the National Entomologic Surveillance Program for Bluetongue disease (2005-2013), were used for statistical evaluation. Logistic regression analysis was preformed and prediction maps (per season) were obtained for vector and potentially vector species. The variables used at the present study were selected from WorldClim (two climatic variables) and CORINE databases (twenty-two land cover variables). This work points to an opposite distribution of C. imicola and species from the Obsoletus group within mainland Portugal. Such findings are evidenced in autumn, with the former appearing in Central and Southern regions. Although appearing northwards, on summer and autumn, C. newsteadi reveals a similar distribution to C. imicola. The species C. punctatus appears in all Portuguese territory throughout the year. Contrary, C. pulicaris is poorly caught in all areas of mainland Portugal, being paradoxical present near coastal areas and higher altitude regions.
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Affiliation(s)
- David W. Ramilo
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Telmo Nunes
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Sara Madeira
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Fernando Boinas
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- * E-mail:
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