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Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [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: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
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Deshpande A, Rivera-Vicéns RE, Thakur NL, Wörheide G. Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition. Mol Ecol 2023. [PMID: 37715558 DOI: 10.1111/mec.17122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 06/15/2023] [Accepted: 07/28/2023] [Indexed: 09/17/2023]
Abstract
Spatial competition in the intertidal zones drives the community structure in marine benthic habitats. Organisms inhabiting these areas not only need to withstand fluctuations in temperature, water level, pH, and salinity but also need to compete for the best available space. Sponges are key members of the intertidal zones, and their life history processes (e.g. growth, reproduction, and regeneration) are affected by competition. Here, we used transcriptomics to investigate the effects of interspecific competition between the tetillid sponge Cinachyrella cf. cavernosa, the zoantharid Zoanthus sansibaricus and the macroalgae Dictyota ciliolata in the field. The analysis of differentially expressed genes showed that Z. sansibaricus was the more stressful competitor to C. cf. cavernosa, which showed an upregulation of cellular respiration under stress of competition. Similarly, an upregulation of energy metabolism, lipid metabolism and the heat-shock protein (HSP) 70 was also observed along with an increase in viral load and decreased ability to synthesize protein. A downregulation of purine and pyrimidine metabolism indicated a reduction in the physiological activities of the competing sponges. Moreover, a putative case of possible kleptocnidism, not previously reported in C. cf. cavernosa, was also observed. This study offers a glimpse into the inner workings of marine organisms competing for spatial resources using transcriptome data.
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Affiliation(s)
- Aabha Deshpande
- CSIR - National Institute of Oceanography, Dona Paula, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramón E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
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3
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Riesgo A, Santodomingo N, Koutsouveli V, Kumala L, Leger MM, Leys SP, Funch P. Molecular machineries of ciliogenesis, cell survival, and vasculogenesis are differentially expressed during regeneration in explants of the demosponge Halichondria panicea. BMC Genomics 2022; 23:858. [PMID: 36581804 PMCID: PMC9798719 DOI: 10.1186/s12864-022-09035-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/21/2022] [Indexed: 12/30/2022] Open
Abstract
Sponges are interesting animal models for regeneration studies, since even from dissociated cells, they are able to regenerate completely. In particular, explants are model systems that can be applied to many sponge species, since small fragments of sponges can regenerate all elements of the adult, including the oscula and the ability to pump water. The morphological aspects of regeneration in sponges are relatively well known, but the molecular machinery is only now starting to be elucidated for some sponge species. Here, we have used an explant system of the demosponge Halichondria panicea to understand the molecular machinery deployed during regeneration of the aquiferous system. We sequenced the transcriptomes of four replicates of the 5-day explant without an osculum (NOE), four replicates of the 17-18-day explant with a single osculum and pumping activity (PE) and also four replicates of field-collected individuals with regular pumping activity (PA), and performed differential gene expression analysis. We also described the morphology of NOE and PE samples using light and electron microscopy. Our results showed a highly disorganised mesohyl and disarranged aquiferous system in NOE that is coupled with upregulated pathways of ciliogenesis, organisation of the ECM, and cell proliferation and survival. Once the osculum is formed, genes involved in "response to stimulus in other organisms" were upregulated. Interestingly, the main molecular machinery of vasculogenesis described in vertebrates was activated during the regeneration of the aquiferous system. Notably, vasculogenesis markers were upregulated when the tissue was disorganised and about to start forming canals (NOE) and angiogenic stimulators and ECM remodelling machineries were differentially expressed once the aquiferous system was in place (PE and PA). Our results are fundamental to better understanding the molecular mechanisms involved in the formation of the aquiferous system in sponges, and its similarities with the early onset of blood-vessel formation in animal evolution.
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Affiliation(s)
- Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW5 7BD, UK.
| | - Nadia Santodomingo
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW5 7BD, UK
- Department of Earth Sciences, Oxford University, South Parks Road, Oxford, OX1 3AN, UK
| | - Vasiliki Koutsouveli
- Marine Symbioses Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Lars Kumala
- Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
- Marine Biological Research Center, University of Southern Denmark, Hindsholmvej 11, 5300, Kerteminde, Denmark
| | - Michelle M Leger
- Institute of Evolutionary Biology (CSIC-UPF), Paseo Marítimo de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2R3, Canada
| | - Peter Funch
- Department of Biology, Aarhus University, Ny Munkegade, 114-116, Aarhus C, Denmark
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Campana S, Riesgo A, Jongepier E, Fuss J, Muyzer G, de Goeij JM. Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter. BMC Genomics 2022; 23:674. [PMID: 36175840 PMCID: PMC9520939 DOI: 10.1186/s12864-022-08893-y] [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] [Received: 02/24/2022] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in different abundances and with different bioavailability to sponge holobionts, it is important to understand how the metabolic activity of the host and associated microbiota change in response to the exposure to both DOM sources. Here, we look at the differential gene expression of two sponge holobionts 6 hours after feeding on naturally sourced coral- and macroalgal-DOM using RNA sequencing and meta-transcriptomic analysis. Results We found a slight, but significant differential gene expression in the comparison between the coral- and macroalgal-DOM treatments in both the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Haliclona vansoesti. In the hosts, processes that regulate immune response, signal transduction, and metabolic pathways related to cell proliferation were elicited. In the associated microbiota carbohydrate metabolism was upregulated in both treatments, but coral-DOM induced further lipid and amino acids biosynthesis, while macroalgal-DOM caused a stress response. These differences could be driven by the presence of distinct organic macronutrients in the two DOM sources and of small pathogens or bacterial virulence factors in the macroalgal-DOM. Conclusions This work provides two new sponge meta-transcriptomes and a database of putative genes and genetic pathways that are involved in the differential processing of coral- versus macroalgal-DOM as food source to sponges with high and low abundances of associated microbes. These pathways include carbohydrate metabolism, signaling pathways, and immune responses. However, the differences in the meta-transcriptomic responses of the sponge holobionts after 6 hours of feeding on the two DOM sources were small. Longer-term responses to both DOM sources should be assessed to evaluate how the metabolism and the ecological function of sponges will be affected when reefs shift from coral towards algal dominance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08893-y.
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Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands.
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Evelien Jongepier
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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5
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Wu YC, Franzenburg S, Ribes M, Pita L. Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. Sci Rep 2022; 12:1307. [PMID: 35079031 PMCID: PMC8789774 DOI: 10.1038/s41598-022-05230-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
Upon injury, the homeostatic balance that ensures tissue function is disrupted. Wound-induced signaling triggers the recovery of tissue integrity and offers a context to understand the molecular mechanisms for restoring tissue homeostasis upon disturbances. Marine sessile animals are particularly vulnerable to chronic wounds caused by grazers that can compromise prey's health. Yet, in comparison to other stressors like warming or acidification, we know little on how marine animals respond to grazing. Marine sponges (Phylum Porifera) are among the earliest-diverging animals and play key roles in the ecosystem; but they remain largely understudied. Here, we investigated the transcriptomic responses to injury caused by a specialist spongivorous opisthobranch (i.e., grazing treatment) or by clipping with a scalpel (i.e., mechanical damage treatment), in comparison to control sponges. We collected samples 3 h, 1 d, and 6 d post-treatment for differential gene expression analysis on RNA-seq data. Both grazing and mechanical damage activated a similar transcriptomic response, including a clotting-like cascade (e.g., with genes annotated as transglutaminases, metalloproteases, and integrins), calcium signaling, and Wnt and mitogen-activated protein kinase signaling pathways. Wound-induced gene expression signature in sponges resembles the initial steps of whole-body regeneration in other animals. Also, the set of genes responding to wounding in sponges included putative orthologs of cancer-related human genes. Further insights can be gained from taking sponge wound healing as an experimental system to understand how ancient genes and regulatory networks determine healthy animal tissues.
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Affiliation(s)
- Yu-Chen Wu
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Soeren Franzenburg
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts University of Kiel, Kiel, Germany
| | - Marta Ribes
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Lucía Pita
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain.
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Sandoval K, McCormack GP. Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. Mar Drugs 2022; 20:md20010074. [PMID: 35049929 PMCID: PMC8778704 DOI: 10.3390/md20010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2021; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Ildiko Somorjai
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Oshrat Ben-Hamo
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Jardin du Pharo, 58 Boulevard Charles Livon, Marseille, 13007, France.,Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Ulitsa Vavilova, 26, Moscow, 119334, Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, Paris, F-75006, France
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Bygg 19, Gaustad Sykehus, Sognsvannsveien 21, Oslo, 0188, Norway
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, 06107, France.,Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), 28 Avenue de Valrose, Nice, 06103, France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06234 Villefranche-sur-Mer, Villefranche sur Mer, Cedex, France
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Technikerstr, Innsbruck, 256020, Austria
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Bideau L, Kerner P, Hui J, Vervoort M, Gazave E. Animal regeneration in the era of transcriptomics. Cell Mol Life Sci 2021; 78:3941-3956. [PMID: 33515282 PMCID: PMC11072743 DOI: 10.1007/s00018-021-03760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/27/2022]
Abstract
Animal regeneration, the ability to restore a lost body part, is a process that has fascinated scientists for centuries. In this review, we first present what regeneration is and how it relates to development, as well as the widespread and diverse nature of regeneration in animals. Despite this diversity, animal regeneration includes three common mechanistic steps: initiation, induction and activation of progenitors, and morphogenesis. In this review article, we summarize and discuss, from an evolutionary perspective, the recent data obtained for a variety of regeneration models which have allowed to identify key shared mechanisms that control these main steps of animal regeneration. This review also synthesizes the wealth of high-throughput mRNA sequencing data (bulk mRNA-seq) concerning regeneration which have been obtained in recent years, highlighting the major advances in the regeneration field that these studies have revealed. We stress out that, through a comparative approach, these data provide opportunities to further shed light on the evolution of regeneration in animals. Finally, we point out how the use of single-cell mRNA-seq technology and integration with epigenomic approaches may further help researchers to decipher mechanisms controlling regeneration and their evolution in animals.
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Affiliation(s)
- Loïc Bideau
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
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9
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Hudspith M, Rix L, Achlatis M, Bougoure J, Guagliardo P, Clode PL, Webster NS, Muyzer G, Pernice M, de Goeij JM. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis. MICROBIOME 2021; 9:44. [PMID: 33583434 PMCID: PMC7883440 DOI: 10.1186/s40168-020-00984-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/16/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. RESULTS The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. CONCLUSIONS Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.
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Affiliation(s)
- Meggie Hudspith
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Rix
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Michelle Achlatis
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
- The UWA Oceans Institute, The University of Western Australia, Perth, Australia
- The UWA School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, Australia
| | - Jasper M. de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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10
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Plese B, Kenny NJ, Rossi ME, Cárdenas P, Schuster A, Taboada S, Koutsouveli V, Riesgo A. Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Mol Phylogenet Evol 2020; 155:107011. [PMID: 33217579 DOI: 10.1016/j.ympev.2020.107011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/01/2022]
Abstract
The sponge class Demospongiae is the most speciose and morphologically diverse in the phylum Porifera, and the species within it are vital components of a range of ecosystems worldwide. Despite their ubiquity, a number of recalcitrant problems still remain to be solved regarding their phylogenetic inter-relationships, the timing of their appearance, and their mitochondrial biology, the latter of which is only beginning to be investigated. Here we generated 14 new demosponge mitochondrial genomes which, alongside previously published mitochondrial resources, were used to address these issues. In addition to phylogenomic analysis, we have used syntenic data and analysis of coding regions to forge a framework for understanding the inter-relationships between Demospongiae sub-classes and orders. We have also leveraged our new resources to study the mitochondrial biology of these clades in terms of codon usage, optimisation and gene expression, to understand how these vital cellular components may have contributed to the success of the Porifera. Our results strongly support a sister relationship between Keratosa and (Verongimorpha + Heteroscleromorpha), contradicting previous studies using nuclear markers. Our study includes one species of Clionaida, and show for the first time support for a grouping of Suberitida+(Clionaida+(Tethyida + Poecilosclerida). The findings of our phylogenetic analyses are supported by in-depth examination of structural and coding-level evidence from our mitochondrial data. A time-calibrated phylogeny estimated the origin of Demospongiae in the Cambrian (~529 Mya), and suggests that most demosponge order crown-groups emerged in the Mesozoic. This work therefore provides a robust basis for considering demosponge phylogenetic relationships, as well as essential mitochondrial data for understanding the biological basis for their success and diversity.
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Affiliation(s)
- Bruna Plese
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - Nathan James Kenny
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Faculty of Health and Life Sciences, Oxford Brookes University, Headington Rd, Oxford OX3 0BP, United Kingdom(2).
| | - Maria Eleonora Rossi
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; School of Earth Sciences, University of Bristol, Life Science Building, 24 Tyndall Ave, Bristol BS8 1TH, United Kingdom.
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Astrid Schuster
- Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark; CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
| | - Sergi Taboada
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Universidad de Alcalá de Henares, 28871 Alcalá de Henares, Spain; Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, C/ José Antonio Novais, 12, Ciudad Universitaria, 28040 Madrid, Spain.
| | - Vasiliki Koutsouveli
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales de Madrid (CSIC), c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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11
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Vad J, Dunnett F, Liu F, Montagner CC, Roberts JM, Henry TB. Soaking up the oil: Biological impacts of dispersants and crude oil on the sponge Halichondria panicea. CHEMOSPHERE 2020; 257:127109. [PMID: 32497834 DOI: 10.1016/j.chemosphere.2020.127109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Used during an oil spill to minimise the formation of an oil slick, dispersants have negative biological effects on marine model organisms. However, no study has investigated the impacts of dispersants on adult sponge individuals. Here, we examine the effects of water accommodated oil fraction (WAF - oil in seawater), chemically enhanced WAF (CEWAF - oil and dispersant in seawater) and Benzo[A]Pyrene on sponge Halichondria panicea at physiological and molecular levels. Sponge clearance rate decreased sharply when exposed to WAF and CEWAF but the oil loading at which the clearance rate was reduced by 50% (ED50) was 39-fold lower in CEWAF than in WAF. Transcriptomic analysis revealed a homogenous molecular response with the greatest number of differentially expressed genes identified in CEWAF samples (1,461 genes). Specifically, genes involved in stress responses were up-regulated. This study presents evidence that the use of dispersants should be considered carefully in areas where sponges are present.
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Affiliation(s)
- J Vad
- Changing Oceans Research Group, Grant Institute, School of Geosciences, The University of Edinburgh, Edinburgh, UK; Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK.
| | - F Dunnett
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK
| | - F Liu
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK; Scottish Association for Marine Science, Oban, UK
| | - C C Montagner
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | - J M Roberts
- Changing Oceans Research Group, Grant Institute, School of Geosciences, The University of Edinburgh, Edinburgh, UK
| | - T B Henry
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK; Center for Environmental Biotechnology, The University of Tennessee, Tennessee, USA
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12
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Hartigan A, Kosakyan A, Pecková H, Eszterbauer E, Holzer AS. Transcriptome of Sphaerospora molnari (Cnidaria, Myxosporea) blood stages provides proteolytic arsenal as potential therapeutic targets against sphaerosporosis in common carp. BMC Genomics 2020; 21:404. [PMID: 32546190 PMCID: PMC7296530 DOI: 10.1186/s12864-020-6705-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/27/2020] [Indexed: 01/24/2023] Open
Abstract
Background Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, and available genomic and transcriptomic datasets are limited. Some myxozoans are important aquaculture pathogens such as Sphaerospora molnari replicating in the blood of farmed carp before reaching the gills for sporogenesis and transmission. Proliferative stages cause a massive systemic lymphocyte response and the disruption of the gill epithelia by spore-forming stages leads to respiratory problems and mortalities. In the absence of a S. molnari genome, we utilized a de novo approach to assemble the first transcriptome of proliferative myxozoan stages to identify S. molnari proteases that are upregulated during the first stages of infection when the parasite multiplies massively, rather than in late spore-forming plasmodia. Furthermore, a subset of orthologs was used to characterize 3D structures and putative druggable targets. Results An assembled and host filtered transcriptome containing 9436 proteins, mapping to 29,560 contigs was mined for protease virulence factors and revealed that cysteine proteases were most common (38%), at a higher percentage than other myxozoans or cnidarians (25–30%). Two cathepsin Ls that were found upregulated in spore-forming stages with a presenilin like aspartic protease and a dipeptidyl peptidase. We also identified downregulated proteases in the spore-forming development when compared with proliferative stages including an astacin metallopeptidase and lipases (qPCR). In total, 235 transcripts were identified as putative proteases using a MEROPS database. In silico analysis of highly transcribed cathepsins revealed potential drug targets within this data set that should be prioritised for development. Conclusions In silico surveys for proteins are essential in drug discovery and understanding host-parasite interactions in non-model systems. The present study of S. molnari’s protease arsenal reveals previously unknown proteases potentially used for host exploitation and immune evasion. The pioneering dataset serves as a model for myxozoan virulence research, which is of particular importance as myxozoan diseases have recently been shown to emerge and expand geographically, due to climate change.
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Affiliation(s)
- Ashlie Hartigan
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czechia.
| | - Anush Kosakyan
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czechia
| | - Hana Pecková
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czechia
| | - Edit Eszterbauer
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czechia
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13
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Luter HM, Kenkel CD, Terzin M, Peirce T, Laffy PW, Gibb K, Webster NS. Gene correlation networks reveal the transcriptomic response to elevated nitrogen in a photosynthetic sponge. Mol Ecol 2020; 29:1452-1462. [PMID: 32223031 DOI: 10.1111/mec.15417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/08/2023]
Abstract
Nutrient levels in coastal environments have been increasing globally due to elevated inputs of sewage and terrigenous sediments carrying fertilizers. Yet, despite their immense filtering capacities, marine sponges appear to be less affected by elevated nutrients than sympatric benthic organisms, such as corals. While the molecular-level stress response of sponges to elevated seawater temperatures and other toxicants has been defined, this study represents the first global gene expression analysis of how sponges respond to elevated nitrogen. Gene correlation network analysis revealed that sponge gene modules, coded by colours, became either highly upregulated (Blue) or downregulated (Turquoise, Black, Brown) as nitrogen treatment levels increased. Gene Ontology enrichment analysis of the different modules revealed genes involved in cell signalling, immune response and flagella motility were affected by increasing nitrogen levels. Notably, a decrease in the regulation of NF-kappaB signalling and an increase in protein degradation was identified, which is comparable to metabolic pathways associated with the sponge thermal stress response. These results highlight that Cymbastela stipitata can rapidly respond to changes in the external environment and identifies pathways that probably contribute to the ability of C. stipitata to tolerate short-term nutrient pulses.
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Affiliation(s)
- Heidi M Luter
- NAMRA and the Research Institute for the Environment & Livelihoods, Charles Darwin University, Darwin, NT, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Carly D Kenkel
- Australian Institute of Marine Science, Townsville, QLD, Australia.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Marko Terzin
- Australian Institute of Marine Science, Townsville, QLD, Australia.,Marine Biology Research Group, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Tyler Peirce
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, James Cook University, Townsville, QLD, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Karen Gibb
- Research Institute for the Environment & Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - 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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14
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Costa ML, de Andrade Rosa I, Andrade L, Mermelstein C, C Coutinho C. Distinct interactions between epithelial and mesenchymal cells control cell morphology and collective migration during sponge epithelial to mesenchymal transition. J Morphol 2019; 281:183-195. [PMID: 31854473 DOI: 10.1002/jmor.21090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/19/2019] [Accepted: 12/09/2019] [Indexed: 11/10/2022]
Abstract
Epithelial and mesenchymal cell types are basic for animal multicellularity and they have complementary functions coordinated by cellular interactions. Sponges are especially important model organisms to address the evolutionary basis of morphogenetic programs for epithelial and mesenchymal organization in animals. Evolutionary studies in sponges can contribute to the understanding of the mechanisms that control tissue maintenance and tumor progression in humans. In the present study, sponge mesenchymal and epithelial cells were isolated from the demosponge Hymeniacidon heliophila, and aggregate formation was observed by video microscopy. Epithelial-mesenchymal interaction, epithelial transition, and cell migration led to sponge cell aggregation after drastic stress. Based on their different morphologies, adhesion specificities, and motilities, we suggest a role for different sponge cell types as well as complementary functions in cell aggregation. Micromanipulation under the microscope and cell tracking were also used to promote specific grafting-host interaction, to further test the effects of cell type interaction. The loss of cell polarity and flattened shape during the epithelial to mesenchymal cell transition generated small immobile aggregates of round/amoeboid cells. The motility of these transited epithelial-cell aggregates was observed by cell tracking using fluorescent dye, but only after interaction with streams of migratory mesenchymal cells. Cell motility occurred independently of morphological changes, indicating a progressive step in the transition toward a migratory mesenchymal state. Our data suggest a two-step signaling process: (a) the lack of interaction between mesenchymal and epithelial cells triggers morphological changes; and (b) migratory mesenchymal cells instruct epithelial cells for directional cell motility. These results could have an impact on the understanding of evolutionary aspects of metastatic cancer cells. HIGHLIGHTS: Morphogenetic movements observed in modern sponges could have a common evolutionary origin with collective cell migration of human metastatic cells. A sponge regenerative model was used here to characterize epithelial and mesenchymal cells, and for the promotion of grafting/host interactions with subsequent cell tracking. The transition from epithelial to mesenchymal cell type can be observed in sponges in two steps: (a) withdrawal of epithelial/mesenchymal cell interactions to trigger morphological changes; (b) migratory mesenchymal cells to induce epithelial cells to a collective migratory state.
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Affiliation(s)
- Manoel L Costa
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
| | - Ivone de Andrade Rosa
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
| | - Leonardo Andrade
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
| | - Claudia Mermelstein
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
| | - Cristiano C Coutinho
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
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15
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González-Aravena M, Kenny NJ, Osorio M, Font A, Riesgo A, Cárdenas CA. Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp. PeerJ 2019; 7:e8088. [PMID: 31824760 PMCID: PMC6896943 DOI: 10.7717/peerj.8088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.
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Affiliation(s)
| | - Nathan J Kenny
- Life Sciences, The Natural History Museum, London, London, UK.,Life Sciences, Oxford Brookes University, Oxford, UK
| | - Magdalena Osorio
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
| | - Ana Riesgo
- Life Sciences, The Natural History Museum, London, London, UK
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
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16
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Ribeiro RP, Ponz-Segrelles G, Bleidorn C, Aguado MT. Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process. BMC Genomics 2019; 20:855. [PMID: 31726983 PMCID: PMC6854643 DOI: 10.1186/s12864-019-6223-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/24/2019] [Indexed: 02/23/2023] Open
Abstract
Background Annelids exhibit remarkable postembryonic developmental abilities. Most annelids grow during their whole life by adding segments through the action of a segment addition zone (SAZ) located in front of the pygidium. In addition, they show an outstanding ability to regenerate their bodies. Experimental evidence and field observations show that many annelids are able to regenerate their posterior bodies, while anterior regeneration is often limited or absent. Syllidae, for instance, usually show high abilities of posterior regeneration, although anterior regeneration varies across species. Some syllids are able to partially restore the anterior end, while others regenerate all lost anterior body after bisection. Here, we used comparative transcriptomics to detect changes in the gene expression profiles during anterior regeneration, posterior regeneration and regular growth of two syllid species: Sphaerosyllis hystrix and Syllis gracilis; which exhibit limited and complete anterior regeneration, respectively. Results We detected a high number of genes with differential expression: 4771 genes in S. hystrix (limited anterior regeneration) and 1997 genes in S. gracilis (complete anterior regeneration). For both species, the comparative transcriptomic analysis showed that gene expression during posterior regeneration and regular growth was very similar, whereas anterior regeneration was characterized by up-regulation of several genes. Among the up-regulated genes, we identified putative homologs of regeneration-related genes associated to cellular proliferation, nervous system development, establishment of body axis, and stem-cellness; such as rup and JNK (in S. hystrix); and glutamine synthetase, elav, slit, Hox genes, β-catenin and PL10 (in S. gracilis). Conclusions Posterior regeneration and regular growth show no significant differences in gene expression in the herein investigated syllids. However, anterior regeneration is associated with a clear change in terms of gene expression in both species. Our comparative transcriptomic analysis was able to detect differential expression of some regeneration-related genes, suggesting that syllids share some features of the regenerative mechanisms already known for other annelids and invertebrates.
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Affiliation(s)
- Rannyele Passos Ribeiro
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
| | - Guillermo Ponz-Segrelles
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Christoph Bleidorn
- Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, 37073, Göttingen, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Maria Teresa Aguado
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain. .,Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, 37073, Göttingen, Germany. .,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, España.
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17
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Ereskovsky AV, Tokina DB, Saidov DM, Baghdiguian S, Le Goff E, Lavrov AI. Transdifferentiation and mesenchymal-to-epithelial transition during regeneration in Demospongiae (Porifera). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 334:37-58. [PMID: 31725194 DOI: 10.1002/jez.b.22919] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022]
Abstract
Origin and early evolution of regeneration mechanisms remain among the most pressing questions in animal regeneration biology. Porifera have exceptional regenerative capacities and, as early Metazoan lineage, are a promising model for studying evolutionary aspects of regeneration. Here, we focus on reparative regeneration of the body wall in the Mediterranean demosponge Aplysina cavernicola. The epithelialization of the wound surface is completed within 2 days, and the wound is completely healed within 2 weeks. The regeneration is accompanied with the formation of a mass of undifferentiated cells (blastema), which consists of archaeocytes, dedifferentiated choanocytes, anucleated amoebocytes, and differentiated spherulous cells. The main mechanisms of A. cavernicola regeneration are cell dedifferentiation with active migration and subsequent redifferentiation or transdifferentiation of polypotent cells through the mesenchymal-to-epithelial transformation. The main cell sources of the regeneration are archaeocytes and choanocytes. At early stages of the regeneration, the blastema almost devoid of cell proliferation, but after 24 hr postoperation (hpo) and up to 72 hpo numerous DNA-synthesizing cells appear there. In contrast to intact tissues, where vast majority of DNA-synthesizing cells are choanocytes, all 5-ethynyl-2'-deoxyuridine-labeled cells in the blastema are mesohyl cells. Intact tissues, distant from the wound, retains intact level of cell proliferation during whole regeneration process. For the first time, the apoptosis was studied during the regeneration of sponges. Two waves of apoptosis were detected during A. cavernicola regeneration: The first wave at 6-12 hpo and the second wave at 48-72 hpo.
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Affiliation(s)
- Alexander V Ereskovsky
- Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Aix Marseille University, CNRS, IRD, Station Marine d'Endoume, Rue de la Batterie des Lions, Avignon University, Marseille, France.,Department of Embryology, Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia.,Evolution of Morphogenesis Laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Daria B Tokina
- Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Aix Marseille University, CNRS, IRD, Station Marine d'Endoume, Rue de la Batterie des Lions, Avignon University, Marseille, France
| | - Danial M Saidov
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Emilie Le Goff
- ISEM, CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Andrey I Lavrov
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia.,Pertsov White Sea Biological Station, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
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18
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Kenny NJ, Plese B, Riesgo A, Itskovich VB. Symbiosis, Selection, and Novelty: Freshwater Adaptation in the Unique Sponges of Lake Baikal. Mol Biol Evol 2019; 36:2462-2480. [PMID: 31236592 PMCID: PMC6805232 DOI: 10.1093/molbev/msz151] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022] Open
Abstract
Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. Although spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan "Benchmarking Universal Single-Copy Orthologs" [BUSCO] set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication, and novelty in freshwater sponges compared with marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g., zinc transporter-2), transcription factors (aristaless-related homeobox), and structural proteins (e.g. actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (e.g., colonization and migration patterns) of these key species.
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Affiliation(s)
- Nathan J Kenny
- Life Sciences Department, The Natural History Museum, London, United Kingdom
| | - Bruna Plese
- Life Sciences Department, The Natural History Museum, London, United Kingdom
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, London, United Kingdom
| | - Valeria B Itskovich
- Limnological Institute, Siberian Branch of the Russian Academy of Science, Irkutsk, Russia
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Pozzolini M, Gallus L, Ghignone S, Ferrando S, Candiani S, Bozzo M, Bertolino M, Costa G, Bavestrello G, Scarfì S. Insights into the evolution of metazoan regenerative mechanisms: roles of TGF superfamily members in tissue regeneration of the marine sponge Chondrosia reniformis. ACTA ACUST UNITED AC 2019; 222:jeb.207894. [PMID: 31371401 DOI: 10.1242/jeb.207894] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/24/2019] [Indexed: 01/31/2023]
Abstract
Tissue repair is an adaptive and widespread metazoan response. It is characterised by different cellular mechanisms and complex signalling networks that involve numerous growth factors and cytokines. In higher animals, transforming growth factor-β (TGF-β) signalling plays a fundamental role in wound healing. In order to evaluate the involvement of TGF superfamily members in lower invertebrate tissue regeneration, sequences for putative TGF ligands and receptors were isolated from the transcriptome of the marine sponge Chondrosia reniformis We identified seven transcripts that coded for TGF superfamily ligands and three for TGF superfamily receptors. Phylogenetically, C. reniformis TGF ligands were not grouped into any TGF superfamily clades and thus presumably evolved independently, whereas the TGF receptors clustered in the Type I receptor group. We performed gene expression profiling of these transcripts in sponge regenerating tissue explants. Data showed that three ligands (TGF1, TGF3 and TGF6) were mainly expressed during early regeneration and seemed to be involved in stem cell maintenance, whereas two others (TGF4 and TGF5) were strongly upregulated during late regeneration and thus were considered pro-differentiating factors. The presence of a strong TGF inhibitor, SB431542, blocked the restoration of the exopinacoderm layer in the sponge explants, confirming the functional involvement of the TGF pathway in tissue regeneration in these early evolved animals.
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Affiliation(s)
- Marina Pozzolini
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Lorenzo Gallus
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection-Turin Unit (CNR), Viale Mattioli 25, 10125 Torino, Italy
| | - Sara Ferrando
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Simona Candiani
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Matteo Bozzo
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Marco Bertolino
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Gabriele Costa
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Giorgio Bavestrello
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Sonia Scarfì
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
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Lavrov AI, Bolshakov FV, Tokina DB, Ereskovsky AV. Sewing up the wounds : The epithelial morphogenesis as a central mechanism of calcaronean sponge regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:351-371. [PMID: 30421540 DOI: 10.1002/jez.b.22830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Sponges (Porifera) demonstrate prominent regeneration abilities and possess a wide variety of mechanisms, used during this process. In the current study, we combined in vivo observations with histological, immunohistochemical, and ultrastructural technics to elucidate the fine cellular mechanisms of the regeneration in the calcareous sponge Leucosolenia cf. variabilis. The regeneration of Leucosolenia cf. variabilis ends within 4-6 days. The crucial step of the process is the formation of the transient regenerative membrane, formed by the epithelial morphogenesis-spreading of the intact exopinacoderm and choanoderm. The spreading of the choanoderm is accompanied by the transdifferentiation of the choanocytes. The regenerative membrane develops without any contribution of the mesohyl cells. Subsequently, the membrane gradually transforms into the body wall. The cell proliferation is neither affected nor contributes to the regeneration at any stage. Thus, Leucosolenia cf. variabilis regeneration relies on the remodeling of the intact tissues through the epithelial morphogenesis, accompanied by the transdifferentiation of some differentiated cell types, which makes it similar to the regeneration in homoscleromorphs and eumetazoans.
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Affiliation(s)
- Andrey I Lavrov
- Pertsov White Sea Biological Station, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.,Department Embryology, Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Fyodor V Bolshakov
- Pertsov White Sea Biological Station, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.,Department Embryology, Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Daria B Tokina
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Station Marine d'Endoume, Marseille, France
| | - Alexander V Ereskovsky
- Department Embryology, Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Station Marine d'Endoume, Marseille, France
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Establishment of Transgenesis in the Demosponge Suberites domuncula. Genetics 2018; 210:435-443. [PMID: 30143594 PMCID: PMC6216596 DOI: 10.1534/genetics.118.301121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Sponges (Porifera) represent one of the most basally branching animal clades with key relevance for evolutionary studies, stem cell biology, and development. Despite a long history of sponges as experimental model systems, however, functional molecular studies are still very difficult to perform in these animals. Here, we report the establishment of transgenic technology as a basic and versatile experimental tool for sponge research. We demonstrate that slice explants of the demosponge Suberites domuncula regenerate functional sponge tissue and can be cultured for extended periods of time, providing easy experimental access under controlled conditions. We further show that an engineered expression construct driving the enhanced green fluorescence protein (egfp) gene under control of the Suberites domuncula β-actin locus can be transfected into such tissue cultures, and that faithfully spliced transcripts are produced from such transfected DNA. Finally, by combining fluorescence-activated cell sorting (FACS) with quantitative PCR, we validate that transfected cells can be specifically reisolated from tissue based on their fluorescence. Although the number of detected enhanced green fluorescent protein (EGFP)-expressing cells is still limited, our approach represents the first successful introduction and expression of exogenous DNA in a sponge. These results represent a significant advance for the use of transgenic technology in a cornerstone phylum, for instance for the use in lineage tracing experiments.
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Fields C, Levin M. Are Planaria Individuals? What Regenerative Biology is Telling Us About the Nature of Multicellularity. Evol Biol 2018. [DOI: 10.1007/s11692-018-9448-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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