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Eitel M, Osigus H, Brenzinger B, Wörheide G. Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics. Ecol Evol 2024; 14:e11220. [PMID: 38606341 PMCID: PMC11007570 DOI: 10.1002/ece3.11220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.
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Affiliation(s)
- Michael Eitel
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
| | - Hans‐Jürgen Osigus
- Institut für TierökologieStiftung Tierärztliche Hochschule HannoverHannoverDeutschland
- Present address:
Hochschulbibliothek, Stiftung Tierärztliche Hochschule HannoverHannoverDeutschland
| | - Bastian Brenzinger
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Zoologische StaatssammlungMünchenDeutschland
| | - Gert Wörheide
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Bayerische Staatssammlung für Paläontologie und GeologieMünchenDeutschland
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2
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van der Sprong J, de Voogd NJ, McCormack GP, Sandoval K, Schätzle S, Voigt O, Erpenbeck D, Wörheide G, Vargas S. A novel target-enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case. Mol Ecol Resour 2024; 24:e13891. [PMID: 38010340 DOI: 10.1111/1755-0998.13891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation and management efforts. Marine sponges are species-rich ecological key players on coral reefs, but their species diversity is still poorly understood. This is particularly true for the demosponge order Haplosclerida, whose systematic relationships are contentious due to the incongruencies between morphological and molecular phylogenetic hypotheses. The single gene markers applied in previous studies did not resolve these discrepancies. Hence, there is a high need for a genome-wide approach to derive a phylogenetically robust classification and understand this group's evolutionary relationships. To this end, we developed a target enrichment-based multilocus probe assay for the order Haplosclerida using transcriptomic data. This probe assay consists of 20,000 enrichment probes targeting 2956 ultraconserved elements in coding (i.e. exon) regions across the genome and was tested on 26 haplosclerid specimens from the Red Sea. Our target-enrichment approach correctly placed our samples in a well-supported phylogeny, in agreement with previous haplosclerid molecular phylogenies. Our results demonstrate the applicability of high-resolution genomic methods in a systematically complex marine invertebrate group and provide a promising approach for robust phylogenies of Haplosclerida. Subsequently, this will lead to biologically unambiguous taxonomic revisions, better interpretations of biological and ecological observations and new avenues for applied research, conservation and managing declining marine diversity.
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Affiliation(s)
- Joëlle van der Sprong
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicole Joy de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Grace Patricia McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, School of Natural Sciences & Ryan Institute, University of Galway, Galway, Ireland
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, School of Natural Sciences & Ryan Institute, University of Galway, Galway, Ireland
| | - Simone Schätzle
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Oliver Voigt
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Bavarian State Collections of Palaeontology and Geology, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
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3
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Popovic I, Bergeron LA, Bozec YM, Waldvogel AM, Howitt SM, Damjanovic K, Patel F, Cabrera MG, Wörheide G, Uthicke S, Riginos C. High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator. PLoS Genet 2024; 20:e1011129. [PMID: 38346089 PMCID: PMC10861045 DOI: 10.1371/journal.pgen.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.
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Affiliation(s)
- Iva Popovic
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lucie A. Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yves-Marie Bozec
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Samantha M. Howitt
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Frances Patel
- Australian Institute of Marine Science, Townsville, Australia
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
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4
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Conci N, Griesshaber E, Rivera-Vicéns RE, Schmahl WW, Vargas S, Wörheide G. Molecular and mineral responses of corals grown under artificial Calcite Sea conditions. Geobiology 2024; 22:e12586. [PMID: 38385602 DOI: 10.1111/gbi.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024]
Abstract
The formation of skeletal structures composed of different calcium carbonate polymorphs (e.g. aragonite and calcite) appears to be both biologically and environmentally regulated. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions-primarily in the molar ratio of magnesium and calcium during so-called 'Calcite' (mMg:mCa below 2) or 'Aragonite' seas (mMg:mCa above 2)-have had profound impacts on the distribution and performance of marine calcifiers throughout Earth's history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like mMg:mCa with various levels of magnesium and calcium concentration, and changes in both the mineralogy (i.e. CaCO3 polymorph) and gene expression were monitored. Both species maintained aragonite deposition at lower mMg:mCa ratios, while concurrent calcite presence was only detected in M. digitata. Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of the M. digitata skeleton organic matrix (SkOM), was found to consistently change at lower mMg:mCa. These results support the previously proposed involvements of the SkOM in counteracting decreases in seawater mMg:mCa. Although no consistent expression changes in calcium and magnesium transporters were observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at an mMg:mCa of 2.5, pointing to a possible active calcium uptake regulation by the corals under altered mMg:mCa.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Erika Griesshaber
- Department of Earth and Environmental Sciences, Crystallography, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ramón E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Crystallography, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität, Munich, Germany
- SNSB - Mineralogische Staatssammlung, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität, Munich, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Vargas S, Leiva L, Eitel M, Curdt F, Rohde S, Arnold C, Nickel M, Schupp P, Orsi WD, Adamska M, Wörheide G. Body-plan reorganization in a sponge correlates with microbiome change. Mol Biol Evol 2023:7191912. [PMID: 37288516 DOI: 10.1093/molbev/msad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e., bleaching) correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded species are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, TFG-β, and TLR-ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge post-embryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Laura Leiva
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Franziska Curdt
- Department of Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhemshaven, Germany
| | - Sven Rohde
- Department of Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhemshaven, Germany
| | - Christopher Arnold
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-Universität, Jena, Germany
| | - Michael Nickel
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-Universität, Jena, Germany
| | - Peter Schupp
- Department of Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhemshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Carl-von-Ossietzky University Oldenburg, 26129 Wilhemshaven, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Maja Adamska
- Research School of Biology, Australian National University, Canberra, Australia
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
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7
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Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, Wörheide G. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization. R Soc Open Sci 2023; 10:230423. [PMID: 37351491 PMCID: PMC10282587 DOI: 10.1098/rsos.230423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
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Affiliation(s)
- Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Catalina A. Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Deister
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jasmine L. Mah
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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8
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Erpenbeck D, VAN Soest RWM, Wörheide G, Kelly M. Genetic data confirms the enigmatic demosponge Janulum as haplosclerid. Zootaxa 2023; 5254:147-150. [PMID: 37044729 DOI: 10.11646/zootaxa.5254.1.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Indexed: 04/14/2023]
Abstract
Historically, sponge classification is based on the interpretation of morphological characters, whose phylogenetic information content is frequently limited, subject to homoplasies, or prone to environmental plasticity (e.g., Chombard et al. 1998). Therefore, the currently accepted order-level classification of its largest class, Demospongiae, has been largely revised with molecular phylogenetic data (Morrow & Cárdenas 2015). Nevertheless, numerous sponge genera with ambiguous or provisoric phylogenetic placement still await definite classification.
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Affiliation(s)
- Dirk Erpenbeck
- 1Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany .
| | | | - Gert Wörheide
- 1Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany Germany 4Bavarian State Collection of Palaeontology and Geology, Munich, Germany.
| | - Michelle Kelly
- 5National Institute of Water and Atmospheric Research Ltd., Auckland 1149, New Zealand.
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9
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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10
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Dohrmann M, Reiswig HM, Kelly M, Mills S, Schätzle S, Reverter M, Niesse N, Rohde S, Schupp P, Wörheide G. Expanded sampling of New Zealand glass sponges (Porifera: Hexactinellida) provides new insights into biodiversity, chemodiversity, and phylogeny of the class. PeerJ 2023; 11:e15017. [PMID: 37131989 PMCID: PMC10149058 DOI: 10.7717/peerj.15017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/17/2023] [Indexed: 05/04/2023] Open
Abstract
Glass sponges (Hexactinellida) constitute important parts of ecosystems on the deep-sea floor worldwide. However, they are still an understudied group in terms of their diversity and systematics. Here, we report on new specimens collected during RV Sonne expedition SO254 to the New Zealand region, which has recently emerged as a biodiversity hotspot for hexactinellids. Examination of the material revealed several species new to science or so far unknown from this area. While formal taxonomic descriptions of a fraction of these were published earlier, we here briefly report on the morphology of the remaining new species and use the collection to greatly expand the molecular phylogeny of the group as established with ribosomal DNA and cytochrome oxidase subunit I markers. In addition, we provide a chemical fingerprinting analysis on a subset of the specimens to investigate if the metabolome of glass sponges contains phylogenetic signal that could be used to supplement morphological and DNA-based approaches.
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Affiliation(s)
- Martin Dohrmann
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Henry M. Reiswig
- Biology Department, Natural History Section, University of Victoria, Victoria, British Columbia, Canada
| | - Michelle Kelly
- Coasts and Oceans National Centre, National Institute of Water & Atmospheric Research, Auckland, New Zealand
| | - Sadie Mills
- Invertebrate Collection, National Institute of Water & Atmospheric Research, Wellington, New Zealand
| | - Simone Schätzle
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miriam Reverter
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Natascha Niesse
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany
| | - Peter Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Bayerische Staatssammlung für Paläontologie und Geologie, Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB), Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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11
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Rivera-Vicéns RE, Garcia-Escudero CA, Conci N, Eitel M, Wörheide G. TransPi - a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly. Mol Ecol Resour 2022; 22:2070-2086. [PMID: 35119207 DOI: 10.1111/1755-0998.13593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/30/2022]
Abstract
The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available. In such organisms, studies of differential gene expression, DNA enrichment baits design, and phylogenetics can all be accomplished with de novo transcriptome assemblies. Multiple tools are available for transcriptome assembly, however, no single tool can provide the best assembly for all datasets. Therefore, a multi assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA-Seq data. However, most of these tools are designed for species where genome data is used as reference for the assembly process, limiting their use in non-model organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k-mer sets, read lengths, and read quantities were used for assessing the tool. Furthermore, a total of 49 non-model organisms, spanning different phyla, were also analysed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.
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Affiliation(s)
- R E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - C A Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,Graduate School for Evolution, Ecology and Systematics, Faculty of Biology, Ludwig-Maximilians-Universität München, Biozentrum Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - N Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - M Eitel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - G Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, München, Germany
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12
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Vargas S, Zimmer T, Conci N, Lehmann M, Wörheide G. Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress. Mol Ecol 2021; 31:798-810. [PMID: 34748669 DOI: 10.1111/mec.16266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Up to one-third of all described marine species inhabit coral reefs, but the future of these hyperdiverse ecosystems is insecure due to local and global threats, such as overfishing, eutrophication, ocean warming and acidification. Although these impacts are expected to have a net detrimental effect on reefs, it has been shown that some organisms such as octocorals may remain unaffected, or benefit from, anthropogenically induced environmental change, and may replace stony corals in future reefs. Despite their potential importance in future shallow-water coastal environments, the molecular mechanisms leading to the resilience to anthropogenically induced stress observed in octocorals remain unknown. Here, we use manipulative experiments, proteomics and transcriptomics to show that the molecular toolkit used by Pinnigorgia flava, a common Indo-Pacific gorgonian octocoral, to deposit its calcium carbonate skeleton is resilient to heat and seawater acidification stress. Sublethal heat stress triggered a stress response in P. flava but did not affect the expression of 27 transcripts encoding skeletal organic matrix (SOM) proteins. Exposure to seawater acidification did not cause a stress response but triggered the downregulation of many transcripts, including an osteonidogen homologue present in the SOM. The observed transcriptional decoupling of the skeletogenic and stress-response toolkits provides insights into the mechanisms of resilience to anthropogenically driven environmental change observed in octocorals.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Thorsten Zimmer
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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13
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Musser JM, Schippers KJ, Nickel M, Mizzon G, Kohn AB, Pape C, Ronchi P, Papadopoulos N, Tarashansky AJ, Hammel JU, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra CP, Achim K, Schieber NL, Pan L, Ruperti F, Francis WR, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider TR, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz LL, Arendt D. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 2021; 374:717-723. [PMID: 34735222 DOI: 10.1126/science.abj2949] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jacob M Musser
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Klaske J Schippers
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Nickel
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Friedrich-Schiller-Universität Jena, Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, 07743 Jena, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Andrea B Kohn
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nikolaos Papadopoulos
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Jörg U Hammel
- Friedrich-Schiller-Universität Jena, Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, 07743 Jena, Germany.,Institute for Materials Physics, Helmholtz-Zentrum Hereon, 21502 Geesthacht, Germany
| | - Florian Wolf
- Friedrich-Schiller-Universität Jena, Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, 07743 Jena, Germany
| | - Cong Liang
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China
| | - Ana Hernández-Plaza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Carlos P Cantalapiedra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Kaia Achim
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Leslie Pan
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences 69117 Heidelberg, Germany
| | - Warren R Francis
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Svenja Kling
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Maike Renkert
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Maxim Polikarpov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Hamburg, 22607 Germany.,Department of Information Technology and Electrical Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Hamburg, 22607 Germany
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Imre Gaspar
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Department of Totipotency, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Pawel Burkhardt
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Thomas R Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Hamburg, 22607 Germany
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gert Wörheide
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 München, Germany.,Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 München, Germany.,Bayerische Staatssammlung für Paläontologie und Geologie (SNSB), 80333 München, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Leonid L Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA.,Department of Neuroscience and Brain Institute, University of Florida, Gainesville, FL 32610, USA.,McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
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14
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Reiswig HM, Dohrmann M, Kelly M, Mills S, Schupp PJ, Wörheide G. Rossellid glass sponges (Porifera, Hexactinellida) from New Zealand waters, with description of one new genus and six new species. Zookeys 2021; 1060:33-84. [PMID: 34616203 PMCID: PMC8463523 DOI: 10.3897/zookeys.1060.63307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/04/2021] [Indexed: 11/12/2022] Open
Abstract
New Zealand's surrounding deep waters have become known as a diversity hotspot for glass sponges (Porifera: Hexactinellida) in recent years, and description and collection efforts are continuing. Here we report on eight rossellids (Hexasterophora: Lyssacinosida: Rossellidae) collected during the 2017 RV Sonne cruise SO254 by ROV Kiel 6000 as part of Project PoribacNewZ of the University of Oldenburg, Germany. The material includes six species new to science, two of which are assigned to a so far undescribed genus; we further re-describe two previously known species. The known extant rossellid diversity from the New Zealand region is thus almost doubled, from nine species in five genera to 17 species in eight genera. The specimens described here are only a small fraction of hexactinellids collected on cruise SO254. Unfortunately, the first author passed away while working on this collection, only being able to complete the nine descriptions reported here. The paper concludes with an obituary to him, the world-leading expert on glass sponge taxonomy who will be greatly missed.
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Affiliation(s)
- Henry M Reiswig
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
| | - Martin Dohrmann
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Michelle Kelly
- Coasts and Oceans National Centre, National Institute of Water and Atmospheric Research, Auckland, New Zealand
| | - Sadie Mills
- NIWA Invertebrate Collection, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Peter J Schupp
- ICBM Terramare, University of Oldenburg, Wilhelmshaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität, München, Germany
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15
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Galitz A, Nakao Y, Schupp PJ, Wörheide G, Erpenbeck D. A Soft Spot for Chemistry-Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution. Mar Drugs 2021; 19:448. [PMID: 34436287 PMCID: PMC8398655 DOI: 10.3390/md19080448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.
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Affiliation(s)
- Adrian Galitz
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
| | - Yoichi Nakao
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan;
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University Oldenburg, 26111 Wilhelmshaven, Germany;
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), 26129 Oldenburg, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- SNSB-Bavarian State Collection of Palaeontology and Geology, 80333 Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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16
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Conci N, Lehmann M, Vargas S, Wörheide G. Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification. Genome Biol Evol 2021; 12:1623-1635. [PMID: 32761183 PMCID: PMC7533068 DOI: 10.1093/gbe/evaa162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2020] [Indexed: 12/23/2022] Open
Abstract
Corals are the ecosystem engineers of coral reefs, one of the most biodiverse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO3) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for example, whether corals employ different molecular machineries to deposit different CaCO3 polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Martin Lehmann
- Department of Biology I-Botany, Biozentrum der LMU München, Planegg-Martinsried, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany.,GeoBio-Center LMU, Ludwig-Maximilians-Universität München, München, Germany
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17
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Abstract
The peer-reviewed journal Zootaxa has accelerated the rate of sponge (Porifera) species discoveries in 289 peer-reviewed papers published between 2002 up until the end of 2020, describing 725 new species, six new subspecies, 27 new genera, four new subgenera, and 123 new species and genus names needed to resolve existing homonyms. Zootaxa has been the most prolific of all taxonomic journals in its contributions to describing new taxa of Porifera in modern times. This present article analyses these taxonomic contributions over the past 20 years of Zootaxa, including their trends and highlights pertaining to sponge publications.
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Affiliation(s)
- John N A Hooper
- Queensland Museum, PO Box 3300, South Brisbane 4101, Brisbane, Queensland, Australia Griffith Institute for Drug Discovery, Griffith University, Brisbane 4111, Queensland, Australia.
| | - Gert Wörheide
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany SNSB-Bavarian State Collection of Palaeontology and Geology, Richard-Wagner Straße 10, 80333 Munich, Germany GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.
| | - Eduardo Hajdu
- Museu Nacional/UFRJ, TAXPO - Depto. Invertebrados, Quinta da Boa Vista, s/n 20940-040, Rio de Janeiro, RJ, BRASIL .
| | - Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.
| | - Nicole J DE Voogd
- Naturalis Biodiversity Center, Dept. Marine Biodiversity, P.O. Box 9617, 2300 RA Leiden, The Netherlands Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.
| | - Michelle Klautau
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Zoologia, Av. Carlos Chagas Filho, 373, CEP 21941-902, Rio de Janeiro, RJ, Brasil..
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18
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Conci N, Vargas S, Wörheide G. Corrigendum: The Biology and Evolution of Calcite and Aragonite Mineralization in Octocorallia. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.702511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Voigt O, Fradusco B, Gut C, Kevrekidis C, Vargas S, Wörheide G. Carbonic Anhydrases: An Ancient Tool in Calcareous Sponge Biomineralization. Front Genet 2021; 12:624533. [PMID: 33897759 PMCID: PMC8058475 DOI: 10.3389/fgene.2021.624533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Enzymes of the α-carbonic anhydrase gene family (CAs) are essential for the deposition of calcium carbonate biominerals. In calcareous sponges (phylum Porifera, class Calcarea), specific CAs are involved in the formation of calcite spicules, a unique trait and synapomorphy of this class. However, detailed studies on the CA repertoire of calcareous sponges exist for only two species of one of the two Calcarea subclasses, the Calcaronea. The CA repertoire of the second subclass, the Calcinea, has not been investigated so far, leaving a considerable gap in our knowledge about this gene family in Calcarea. Here, using transcriptomic analysis, phylogenetics, and in situ hybridization, we study the CA repertoire of four additional species of calcareous sponges, including three from the previously unsampled subclass Calcinea. Our data indicate that the last common ancestor of Calcarea had four ancestral CAs with defined subcellular localizations and functions (mitochondrial/cytosolic, membrane-bound, and secreted non-catalytic). The evolution of membrane-bound and secreted CAs involved gene duplications and losses, whereas mitochondrial/cytosolic and non-catalytic CAs are evidently orthologous genes. Mitochondrial/cytosolic CAs are biomineralization-specific genes recruited for biomineralization in the last common ancestor of calcareous sponges. The spatial-temporal expression of these CAs differs between species, which may reflect differences between subclasses or be related to the secondary thickening of spicules during biomineralization that does not occur in all species. With this study, we extend the understanding of the role and the evolution of a key biomineralization gene in calcareous sponges.
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Affiliation(s)
- Oliver Voigt
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Benedetta Fradusco
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carolin Gut
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Charalampos Kevrekidis
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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20
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Schuster A, Pomponi SA, Pisera A, Cárdenas P, Kelly M, Wörheide G, Erpenbeck D. Systematics of 'lithistid' tetractinellid demosponges from the Tropical Western Atlantic-implications for phylodiversity and bathymetric distribution. PeerJ 2021; 9:e10775. [PMID: 33859870 PMCID: PMC8020874 DOI: 10.7717/peerj.10775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Background Among all present demosponges, lithistids represent a polyphyletic group with exceptionally well-preserved fossils dating back to the Cambrian. Knowledge of their recent diversity, particularly in the Tropical Western Atlantic Ocean (TWA) where they are common in deep waters, is scarce making any comparison between present and past major 'lithistid' faunas difficult. In addition, the lack of sufficient molecular and morphological data hamper any predictions on phylogenetic relationships or phylodiversity from this region. The Harbor Branch Oceanographic Institute (HBOI, Fort Pierce, Florida) holds the largest collection of TWA lithistid sponges worldwide, however, the majority remain to be taxonomically identified and revised. Principal Findings In this study we provide sequences of 249 lithistid demosponges using two independent molecular markers (28S rDNA (C1-D2) and cox1 mtDNA). In addition, a morphological documentation of 70 lithistid specimens is provided in the database of the Sponge Barcoding Project (SBP). This integrated dataset represents the largest and most comprehensive of the TWA lithistids to date. The phylogenetic diversity of 'lithistid' demosponges in the Bahamas and Jamaica are high in comparison to other TWA regions; Theonellidae and Corallistidae dominate the fauna, while Neopeltidae and Macandrewiidae are rare. A proposed tetractinellid suborder, one undescribed genus and several undescribed species are recognized and the Pacific 'lithistid' genera, Herengeria and Awhiowhio, are reported from the TWA for the first time. The higher-taxa relationships of desma-bearing tetractinellids are discussed and topics for revision suggested. Conclusion This first integrative approach of TWA 'lithistid' demosponges contributes to a better understanding of their phylogenetic affinities, diversity and bathymetric distribution patterns within the TWA. As in the Pacific, the TWA 'lithistid' demosponges dominate deep-water habitats. Deeper taxonomic investigations will undoubtedly contribute to a better comparison between present major 'lithistid' faunas and their fossil record in the Mesozoic.
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Affiliation(s)
- Astrid Schuster
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,Current affiliation: Department of Biology, Nordcee, Southern University of Denmark, Odense, Denmark
| | - Shirley A Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft Pierce, FL, USA
| | - Andrzej Pisera
- Institute of Paleobiology, Polish Academy of Sciences, Warszawa, Poland
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Michelle Kelly
- National Centre for Coasts and Oceans, National Institute of Water and Atmospheric Research, Newmarket, Auckland, New Zealand
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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21
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Abstract
Octocorallia (class Anthozoa, phylum Cnidaria) is a group of calcifying corals displaying a wide diversity of mineral skeletons. This includes skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite). This represents a unique feature among anthozoans, as scleractinian corals (subclass Hexacorallia), main reef builders and focus of biomineralization research, are all characterized by an aragonite exoskeleton. From an evolutionary perspective, the presence of aragonitic skeletons in Octocorallia is puzzling as it is observed in very few species and has apparently originated during a Calcite sea (i.e., time interval characterized by calcite-inducing seawater conditions). Despite this, octocorals have been systematically overlooked in biomineralization studies. Here we review what is known about octocoral biomineralization, focusing on the evolutionary and biological processes that underlie calcite and aragonite formation. Although differences in research focus between octocorals and scleractinians are often mentioned, we highlight how strong variability also exists between different octocoral groups. Different main aspects of octocoral biomineralization have been in fact studied in a small set of species, including the (calcitic) gorgonian Leptogorgia virgulata and/or the precious coral Corallium rubrum. These include descriptions of calcifying cells (scleroblasts), calcium transport and chemistry of the calcification fluids. With the exception of few histological observations, no information on these features is available for aragonitic octocorals. Availability of sequencing data is also heterogeneous between groups, with no transcriptome or genome available, for instance, for the clade Calcaxonia. Although calcite represents by far the most common polymorph deposited by octocorals, we argue that studying aragonite-forming could provide insight on octocoral, and more generally anthozoan, biomineralization. First and foremost it would allow to compare calcification processes between octocoral groups, highlighting homologies and differences. Secondly, similarities (exoskeleton) between Heliopora and scleractinian skeletons, would provide further insight on which biomineralization features are driven by skeleton characteristics (shared by scleractinians and aragonitic octocorals) and those driven by taxonomy (shared by octocorals regardless of skeleton polymorph). Including the diversity of anthozoan mineralization strategies into biomineralization studies remains thus essential to comprehensively study how skeletons form and evolved within this ecologically important group of marine animals.
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22
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Vargas S, Leiva L, Wörheide G. Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes. Microb Ecol 2021; 81:213-222. [PMID: 32767091 PMCID: PMC7794106 DOI: 10.1007/s00248-020-01556-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Laura Leiva
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27498, Helgoland, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, Munich, Germany
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23
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Girard EB, Fuchs A, Kaliwoda M, Lasut M, Ploetz E, Schmahl WW, Wörheide G. Sponges as bioindicators for microparticulate pollutants? Environ Pollut 2021; 268:115851. [PMID: 33126031 DOI: 10.1016/j.envpol.2020.115851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/14/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Amongst other threats, the world's oceans are faced with man-made pollution, including an increasing number of microparticulate pollutants. Sponges, aquatic filter-feeding animals, are able to incorporate fine foreign particles, and thus may be a potential bioindicator for microparticulate pollutants. To address this question, 15 coral reef demosponges sampled around Bangka Island (North Sulawesi, Indonesia) were analyzed for the nature of their foreign particle content using traditional histological methods, advanced light microscopy, and Raman spectroscopy. Sampled sponges accumulated and embedded the very fine sediment fraction (<200 μm), absent in the surrounding sand, in the ectosome (outer epithelia) and spongin fibers (skeletal elements), which was confirmed by two-photon microscopy. A total of 34 different particle types were identified, of which degraded man-made products, i.e., polystyrene, particulate cotton, titanium dioxide and blue-pigmented particles, were incorporated by eight specimens at concentrations between 91 and 612 particle/g dry sponge tissue. As sponges can weigh several hundreds of grams, we conservatively extrapolate that sponges can incorporate on average 10,000 microparticulate pollutants in their tissue. The uptake of particles, however, appears independent of the material, which suggests that the fluctuation in material ratios is due to the spatial variation of surrounding microparticles. Therefore, particle-bearing sponges have a strong potential to biomonitor microparticulate pollutants, such as microplastics and other degraded industrial products.
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Affiliation(s)
- Elsa B Girard
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Adrian Fuchs
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Melanie Kaliwoda
- SNSB - Mineralogische Staatssammlung München, 80333, München, Germany
| | - Markus Lasut
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jalan Kampus Unsrat Bahu, Manado, 95115, Sulawesi Utara, Indonesia
| | - Evelyn Ploetz
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany; SNSB - Mineralogische Staatssammlung München, 80333, München, Germany; GeoBio-Center(LMU), Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany; GeoBio-Center(LMU), Ludwig-Maximilians-Universität München, 80333, Munich, Germany; SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, 80333, Munich, Germany.
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24
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Girard EB, Kaliwoda M, Schmahl WW, Wörheide G, Orsi WD. Biodegradation of textile waste by marine bacterial communities enhanced by light. Environ Microbiol Rep 2020; 12:406-418. [PMID: 32410317 DOI: 10.1111/1758-2229.12856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of biofilm formation on pollutants in the marine realm is expanding, but how communities respond to substrates during colonization remains poorly understood. Here, we assess community assembly and respiration in response to two different micropollutants, virgin high-density polyethylene (HDPE) microbeads and textile fibres under different light settings. Raman characterization, high-throughput DNA sequencing data, quantitative PCR, and respiration measurements reveal how a stimulation of aerobic respiration by micropollutants is translated into selection for significantly different communities colonizing the substrates. Despite the lack of evidence for biodegradation of HDPE, an increased abundance and respiration of bacterial taxa closely related to hydrocarbonoclastic Kordiimonas spp. and Alteromonas spp. in the presence of textile waste highlights their biodegradation potential. Incubations with textile fibres exhibited significantly higher respiration rates in the presence of light, which could be partially explained by photochemical dissolution of the textile waste into smaller bioavailable compounds. Our results suggest that the development and increased respiration of these unique microbial communities may potentially play a role in the bioremediation of the relatively long-lived textile pollutants in marine habitats, and that the respiration of heterotrophic hydrocarbon-degrading bacteria colonizing marine pollutants can be stimulated by light.
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Affiliation(s)
- Elsa B Girard
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Melanie Kaliwoda
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, 80333, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
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25
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Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nat Commun 2020; 11:3676. [PMID: 32719321 PMCID: PMC7385117 DOI: 10.1038/s41467-020-17397-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/23/2020] [Indexed: 11/09/2022] Open
Abstract
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.
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Affiliation(s)
- Nathan J Kenny
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK. .,Faculty of Health and Life Sciences, Oxford Brookes, Oxford, OX3 0BP, UK.
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Ramón E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Alex de Mendoza
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Luis A Bezares-Calderón
- College of Life and Environmental Sciences, University of Exeter, Stocker Rd, Exeter, EX4 4QD, UK
| | - Lauren Grombacher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Lael D Barlow
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Sara Camilli
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Joseph F Ryan
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL, 32080, USA
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - April L Hill
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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26
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Hertzer C, Kehraus S, Böhringer N, Kaligis F, Bara R, Erpenbeck D, Wörheide G, Schäberle TF, Wägele H, König GM. Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida). Beilstein J Org Chem 2020; 16:1596-1605. [PMID: 32704326 PMCID: PMC7356558 DOI: 10.3762/bjoc.16.132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 01/21/2023] Open
Abstract
Investigations on the biochemical relationship between Doriprismatica stellata (Chromodorididae, Doridoidea) nudibranchs, their egg ribbons, and the associated dietary sponge Spongia cf. agaricina (Demospongiae, Porifera) led to the isolation of the structurally new scalarane-type sesterterpene 12-deacetoxy-4-demethyl-11,24-diacetoxy-3,4-methylenedeoxoscalarin, with an unprecedented position of the cyclopropane ring annelated to the ring A. Unlike other scalaranes, which are most often functionalized at C-12 of ring C, it bears two acetoxy groups at C-11 and C-24 instead. The compound was present in all three samples, supporting the dietary relationship between chromodorid nudibranchs of the genus Doriprismatica and scalarane-containing dictyoceratid sponges of the Spongiidae family. The results also indicate that D. stellata passes the scalarane metabolite on to its egg ribbons, most likely for protective purposes. The scalarane showed antibacterial activity against the Gram-positive bacteria Arthrobacter crystallopoietes (DSM 20117) and Bacillus megaterium (DSM 32).
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Affiliation(s)
- Cora Hertzer
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University, Heinrich-Buff-Ring 26–32, 35392 Gießen, Germany
- Department for Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany
| | - Fontje Kaligis
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jl. Kampus UNSRAT Bahu, 95115 Manado, Sulawesi Utara, Indonesia
| | - Robert Bara
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jl. Kampus UNSRAT Bahu, 95115 Manado, Sulawesi Utara, Indonesia
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany
- SNSB – Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University, Heinrich-Buff-Ring 26–32, 35392 Gießen, Germany
- Department for Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany
| | - Heike Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
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27
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Steinert G, Busch K, Bayer K, Kodami S, Arbizu PM, Kelly M, Mills S, Erpenbeck D, Dohrmann M, Wörheide G, Hentschel U, Schupp PJ. Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida). Front Microbiol 2020; 11:716. [PMID: 32390977 PMCID: PMC7193145 DOI: 10.3389/fmicb.2020.00716] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/27/2020] [Indexed: 12/01/2022] Open
Abstract
In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.
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Affiliation(s)
- Georg Steinert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Kathrin Busch
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Kristina Bayer
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sahar Kodami
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Pedro Martinez Arbizu
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Michelle Kelly
- National Institute of Water and Atmospheric Research, Ltd., Auckland, New Zealand
| | - Sadie Mills
- National Institute of Water and Atmospheric Research, Ltd., Wellington, New Zealand
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Dohrmann
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrecht University of Kiel, Kiel, Germany
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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Erpenbeck D, Gholami A, Hesni MA, Ranjbar MS, Galitz A, Eickhoff B, Namuth L, Schumacher T, Esmaeili HR, Wörheide G, Teimori A. Molecular biodiversity of Iranian shallow water sponges. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1737978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Dirk Erpenbeck
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Aref Gholami
- Faculty of Sciences, Department of Biology, Shahid Bahonar University of Kerman, Kerman, 76169-14111, Iran
| | - Majid Askari Hesni
- Faculty of Sciences, Department of Biology, Shahid Bahonar University of Kerman, Kerman, 76169-14111, Iran
| | - Mohammad Sharif Ranjbar
- Faculty of Marine Sciences, Department of Marine Biology, Hormozgan University, Bandar Abbas, Iran
| | - Adrian Galitz
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Benjamin Eickhoff
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Leonard Namuth
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Tatjana Schumacher
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Hamid Reza Esmaeili
- Department of Biology, College of Sciences, Shiraz University, Shiraz, 71454, Iran
| | - Gert Wörheide
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, Munich, 80333, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, Munich, 80333, Germany
| | - Azad Teimori
- Faculty of Sciences, Department of Biology, Shahid Bahonar University of Kerman, Kerman, 76169-14111, Iran
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29
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Erpenbeck D, Galitz A, Ekins M, Cook SDC, Soest RWM, Hooper JNA, Wörheide G. Soft sponges with tricky tree: On the phylogeny of dictyoceratid sponges. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12351] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dirk Erpenbeck
- Department of Earth‐ and Environmental Sciences, Palaeontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
- GeoBio‐Center Ludwig‐Maximilians‐Universität München Munich Germany
| | - Adrian Galitz
- Department of Earth‐ and Environmental Sciences, Palaeontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
| | - Merrick Ekins
- Biodiversity Program Queensland Museum South Brisbane QLD Australia
- School of Biological Sciences University of Queensland St Lucia QLD Australia
| | - Steve de C. Cook
- Formerly Department of Zoology School of Biological Sciences University of Auckland Auckland New Zealand
| | | | - John N. A. Hooper
- Biodiversity Program Queensland Museum South Brisbane QLD Australia
- Griffith Institute for Drug Discovery Griffith University Nathan QLD Australia
| | - Gert Wörheide
- Department of Earth‐ and Environmental Sciences, Palaeontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
- GeoBio‐Center Ludwig‐Maximilians‐Universität München Munich Germany
- SNSB‐Bavarian State Collection of Palaeontology and Geology Munich Germany
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Abstract
A general trend observed in animal skeletomes-the proteins occluded in animal skeletons-is the copresence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend. However, distributions and phylogenetic analyses of biomineralization-related genes are often based on only a few species, with other anthozoan calcifiers such as octocorals (soft corals), not being fully considered. We de novo assembled the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs. calcitic sclerites) and data-mined published nonbilaterian transcriptome resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. Cnidaria shared no skeletome proteins with Placozoa or Ctenophora, but did share some skeletome proteins with Porifera, such as galaxin-related proteins. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes such as secreted acidic proteins, scleritin, and carbonic anhydrases, and propose an early, single biomineralization-recruitment event for galaxin sensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion into the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e., aragonite/calcite) with no differences in the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins such as galaxins and SCRiP-3a could represent instances of commonality.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
- SNSB—Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
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31
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Pett W, Adamski M, Adamska M, Francis WR, Eitel M, Pisani D, Wörheide G. The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content. Mol Biol Evol 2019; 36:643-649. [PMID: 30690573 DOI: 10.1093/molbev/msz013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
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Affiliation(s)
- Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Marcin Adamski
- Computational Biology and Bioinformatics Unit, Research School of Biology, The Australian National University, Canberra, Australia
| | - Maja Adamska
- Computational Biology and Bioinformatics Unit, Research School of Biology, The Australian National University, Canberra, Australia
| | - Warren R Francis
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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33
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Erpenbeck D, Steiner M, Schuster A, Genner MJ, Manconi R, Pronzato R, Ruthensteiner B, van den Spiegel D, van Soest RWM, Wörheide G. Minimalist barcodes for sponges: a case study classifying African freshwater Spongillida. Genome 2018; 62:1-10. [PMID: 30557098 DOI: 10.1139/gen-2018-0098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features. The discovery of additional cryptic species is very likely with the use of molecular techniques such as DNA barcoding. The Royal Museum of Central Africa (MRAC, Tervuren, Belgium) hosts one of the largest collections of (Central) African freshwater sponge type material. Type specimens in theory constitute ideal targets for molecular taxonomy; however, the success is frequently hampered by DNA degradation and deamination, which are a consequence of suboptimal preservation techniques. Therefore, we genotyped African demosponge holotype material of the MRAC with specific short primers suitable for degenerated tissue and compare the results with the current, morphology-based classification. Our results demonstrate the utility of minimalistic barcodes for identification of sponges, potentially enabling efficient identification of individuals in taxonomic or metabarcoding studies, and highlight inconsistencies in the current freshwater sponge classification.
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Affiliation(s)
- Dirk Erpenbeck
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany
| | - Markus Steiner
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Astrid Schuster
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin J Genner
- c School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Renata Manconi
- d Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Roberto Pronzato
- e Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Bernhard Ruthensteiner
- b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany.,f SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | | | | | - Gert Wörheide
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany.,i Bavarian State Collections of Palaeontology and Geology, Munich, Germany
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34
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Galitz A, Cook SDC, Ekins M, Hooper JNA, Naumann PT, de Voogd NJ, Abdul Wahab M, Wörheide G, Erpenbeck D. Identification of an aquaculture poriferan "Pest with Potential" and its phylogenetic implications. PeerJ 2018; 6:e5586. [PMID: 30280018 PMCID: PMC6160822 DOI: 10.7717/peerj.5586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/15/2018] [Indexed: 11/20/2022] Open
Abstract
Correct identification and classification of sponges is challenging due to ambiguous or misleading morphological features. A particular case is a blue keratose sponge occasionally referred to as the “Blue Photo Sponge” among aquarists, which appears frequently (and in several cases unintended) in private aquaria. This spicule-less species, occasionally specified as Collospongia auris Bergquist, Cambie & Kernan 1990, not only displays a high phenotypic plasticity in growth form and colour, it also proliferates in aquacultures under standard conditions unlike most other sponges. Therefore, this species is regarded as a pest for most aquarists. In turn, the ease of cultivation and propagation in aquacultures qualifies this species as a model organism for a wide array of scientific applications. For these purposes, correct identification and classification are indispensable. We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris, and corroborated by skeletal features. Additionally, the resulting phylogeny corroborated major shortcomings of the current Phyllospongiinae classification—its consequences are discussed.
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Affiliation(s)
- Adrian Galitz
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Steve de C Cook
- Department of Zoology, School of Biological Sciences, Formerly: University of Auckland, Auckland, New Zealand
| | - Merrick Ekins
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - John N A Hooper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland, Australia.,Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Peter T Naumann
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - Muhammad Abdul Wahab
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gert Wörheide
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bavarian State Collections of Palaeontology and Geology, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,Naturalis Biodiversity Center, Leiden, The Netherlands.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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35
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Correction: Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e3000032. [PMID: 30231017 PMCID: PMC6145499 DOI: 10.1371/journal.pbio.3000032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pbio.2005359.].
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Shimpi GG, Vargas S, Wörheide G. Modified parallel strategies for preparation of heteroduplex plasmids for in vitro mismatch repair assays. Anal Biochem 2018; 556:35-39. [PMID: 29940140 DOI: 10.1016/j.ab.2018.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/17/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022]
Abstract
We present efficient and reproducible parallel strategies for preparing large quantities of pure heteroduplex plasmids containing defined mismatches. The strategies described involve the use of synthetic oligonucleotides, the commercially available pGEM-T plasmid, and nicking enzymes to prepare prerequisite ssDNA. Alternatively, bacterial packaging cell lines containing an engineered phagemid construct to produce ssDNA without the need of a helper phage were utilized, hence providing added flexibility and choice. These integrated approaches help to construct different mismatch substrates of choice in large quantities, thus enhancing the usability of mismatch repair assays and extending their range and accessibility to wider research groups.
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Affiliation(s)
- Gaurav G Shimpi
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany; GeoBio-Center(LMU), Richard-Wagner-Str. 10, 80333, Munich, Germany; SNSB -Bavarian State Collections of Palaeontology and Geology, Richard-Wagner-Str. 10, 80333, Munich, Germany.
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37
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Renard E, Leys SP, Wörheide G, Borchiellini C. Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics: The disconnect between gene content and body plan evolution. Bioessays 2018; 40:e1700237. [PMID: 30070368 DOI: 10.1002/bies.201700237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Sponges are important but often-neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non-specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies.
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Affiliation(s)
- Emmanuelle Renard
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France.,Aix Marseille Univ., CNRS, UMR 7288, IBDM, Marseille, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
| | - Carole Borchiellini
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France
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38
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Schuster A, Vargas S, Knapp IS, Pomponi SA, Toonen RJ, Erpenbeck D, Wörheide G. Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model. BMC Evol Biol 2018; 18:114. [PMID: 30021516 PMCID: PMC6052604 DOI: 10.1186/s12862-018-1230-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Approximately 80% of all described extant sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions on the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils. Here, we calibrate the molecular data with the fossilized birth-death model, which compared to strict node dating, allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (~500 Ma), to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To infer a dated phylogeny of Demospongiae we assembled the mitochondrial genomes of six desma-bearing demosponges from reduced-representation genomic libraries. The total dataset included 33 complete demosponge mitochondrial genomes and 30 fossils. RESULTS Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed recent (~18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (~315 Ma), the Astrophorina (~240 Ma), the Spirophorina (~120 Ma) and the family Corallistidae (~188 Ma) all of which are considered as key groups for dating the Demospongiae due to their extraordinary rich and continuous fossil history. CONCLUSION This study provides novel insights into the evolution of Demospongiae. Observed discrepancies of our dated phylogeny with their putative first fossil appearance dates are discussed for selected sponge groups. For instance, a Carboniferous origin of the order Tetractinellida seems to be too late, compared to their first appearance in the fossil record in the Middle Cambrian. This would imply that Paleozoic spicule forms are not homologous to post-Paleozoic forms.
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Affiliation(s)
- Astrid Schuster
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Ingrid S. Knapp
- Hawai‘i Institute of Marine Biology, 46-007 Lilipuna Road, Kāne‘ohe, Hawai‘i 96744 USA
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute-Florida Atlantic University, 5600 U.S. 1 North, Ft Pierce, FL 34946 USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, 46-007 Lilipuna Road, Kāne‘ohe, Hawai‘i 96744 USA
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany
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39
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e2005359. [PMID: 30063702 PMCID: PMC6067683 DOI: 10.1371/journal.pbio.2005359] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.
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Affiliation(s)
- Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gray A. Williams
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology & Evolution, Yale University, New Haven, Connecticut, United States of America
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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40
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Abstract
One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.
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Affiliation(s)
- Warren R Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
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41
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Pichler M, Coskun ÖK, Ortega-Arbulú AS, Conci N, Wörheide G, Vargas S, Orsi WD. A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform. Microbiologyopen 2018; 7:e00611. [PMID: 29575567 PMCID: PMC6291791 DOI: 10.1002/mbo3.611] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 11/10/2022] Open
Abstract
High-throughput sequencing of the 16S rRNA gene on the Illumina platform is commonly used to assess microbial diversity in environmental samples. The MiniSeq, Illumina's latest benchtop sequencer, enables more cost-efficient DNA sequencing relative to larger Illumina sequencing platforms (e.g., MiSeq). Here we used a modified custom primer sequencing approach to test the fidelity of the MiniSeq for high-throughput sequencing of the V4 hypervariable region of 16S rRNA genes from complex communities in environmental samples. To this end, we designed additional sequencing primers that enabled application of a dual-index barcoding method on the MiniSeq. A mock community was sequenced alongside the environmental samples in four different sequencing runs as a quality control benchmark. We were able to recapture a realistic richness of the mock community in all sequencing runs, and identify meaningful differences in alpha and beta diversity in the environmental samples. Furthermore, rarefaction analysis indicated diversity in many environmental samples was close to saturation. These results show that the MiniSeq can produce similar quantities of high-quality V4 reads compared to the MiSeq, yet is a cost-effective option for any laboratory interested in performing high-throughput 16S rRNA gene sequencing.
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Affiliation(s)
- Monica Pichler
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ömer K Coskun
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ana-Sofia Ortega-Arbulú
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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42
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Schuster A, Cárdenas P, Pisera A, Pomponi SA, Kelly M, Wörheide G, Erpenbeck D. Seven new deep-water Tetractinellida (Porifera: Demospongiae) from the Galápagos Islands – morphological descriptions and DNA barcodes. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Astrid Schuster
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paco Cárdenas
- Department of Medicinal Chemistry, Division of Pharmacognosy, BioMedical Centre, Uppsala University, Uppsala, Sweden
| | - Andrzej Pisera
- Institute of Paleobiology, Polish Academy of Sciences, ul. Warszawa, Pol
| | - Shirley A Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft Pierce, FL, USA
| | - Michelle Kelly
- National Centre for Coasts and Oceans, National Institute of Water and Atmospheric Research, Auckland, New Zeal
| | - Gert Wörheide
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- SNSB – Bavarian State Collections of Palaeontology and Geology, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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43
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Schuster A, Pisera A, Kelly M, Bell LJ, Pomponi SA, Wörheide G, Erpenbeck D. New species and a molecular dating analysis of Vetulina Schmidt, 1879 (Porifera: Demospongiae: Sphaerocladina) reveal an ancient relict fauna with Tethys origin. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Astrid Schuster
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrzej Pisera
- Institute of Paleobiology, Polish Academy of Sciences, Warszawa, Poland
| | - Michelle Kelly
- Coasts and Oceans National Centre, National Institute of Water and Atmospheric Research, Newmarket, Auckland, New Zealand
| | - Lori J Bell
- Coral Reef Research Foundation, Koror, Palau, Western Caroline Islands
| | - Shirley A Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Gert Wörheide
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- SNSB – Bavarian State Collections of Palaeontology and Geology, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
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44
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Mills DB, Francis WR, Vargas S, Larsen M, Elemans CP, Canfield DE, Wörheide G. The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments. eLife 2018; 7:31176. [PMID: 29402379 PMCID: PMC5800844 DOI: 10.7554/elife.31176] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/21/2017] [Indexed: 12/30/2022] Open
Abstract
Animals have a carefully orchestrated relationship with oxygen. When exposed to low environmental oxygen concentrations, and during periods of increased energy expenditure, animals maintain cellular oxygen homeostasis by enhancing internal oxygen delivery, and by enabling the anaerobic production of ATP. These low-oxygen responses are thought to be controlled universally across animals by the hypoxia-inducible factor (HIF). We find, however, that sponge and ctenophore genomes lack key components of the HIF pathway. Since sponges and ctenophores are likely sister to all remaining animal phyla, the last common ancestor of extant animals likely lacked the HIF pathway as well. Laboratory experiments show that the marine sponge Tethya wilhelma maintains normal transcription under oxygen levels down to 0.25% of modern atmospheric saturation, the lowest levels we investigated, consistent with the predicted absence of HIF or any other HIF-like pathway. Thus, the last common ancestor of all living animals could have metabolized aerobically under very low environmental oxygen concentrations. Almost all animals need oxygen to live. This is because they use oxygen to release much of the energy locked up in their diets. Oxygen may have also played a crucial role in the early evolution of animal life. Animals evolved from single-celled ancestors in the ocean over 800 million years ago. Before then, it is debated whether the atmosphere and ocean had enough oxygen to permit animals to evolve. Oxygen levels are much higher now, but oxygen availability still varies in some environments. If oxygen becomes limited (a condition known as hypoxia), almost all animals react using a specific set of molecules known as the HIF pathway. This pathway – which is named after proteins called “hypoxia-inducible factors” – triggers changes that help the animal to maintain a stable level of oxygen in its cells. Yet it was not clear if the capacity to sense hypoxia and regulate oxygen demands within the body evolved in the ancestor of all animals, or if it evolved more recently. When trying to understand early evolution, scientists often turn to some living species that sit on the oldest branches of a group’s family tree. In the animal kingdom, sponges and comb jellies occupy those branches. Mills, Francis et al. have now searched the genomes of several of these animals to ask how oxygen sensing evolved. The genomes of the sponges and comb jellies surveyed lack key components of the HIF pathway, suggesting that the last common ancestor of living animals lacked the HIF pathway as well. This also implies that the ancestor of all animals probably did not respond to oxygen stress or used unknown mechanisms to deal with it instead. In laboratory experiments, Mills, Francis et al. saw that a marine sponge named Tethya wilhelma does not alter its gene activity even when the oxygen levels are reduced to 0.25% of modern levels. This is consistent with the predicted absence of a HIF pathway or anything similar. Together these finding may indicate that the last common ancestor of all living animals maintained normal gene activity even at very low concentrations of oxygen. These findings help scientists understand how life and the global environment have shaped each other since the origin of life over 3.5 billion years ago. This fundamental knowledge may provide the context needed to help society navigate through current and on-going environmental changes, including the dropping oxygen levels in the world’s oceans.
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Affiliation(s)
- Daniel B Mills
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Warren R Francis
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Morten Larsen
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Coen Ph Elemans
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Donald E Canfield
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Gert Wörheide
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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45
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Feuda R, Dohrmann M, Pett W, Philippe H, Rota-Stabelli O, Lartillot N, Wörheide G, Pisani D. Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals. Curr Biol 2017; 27:3864-3870.e4. [DOI: 10.1016/j.cub.2017.11.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/19/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
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46
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Poliseno A, Feregrino C, Sartoretto S, Aurelle D, Wörheide G, McFadden CS, Vargas S. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae). Mol Phylogenet Evol 2017; 115:181-189. [PMID: 28782594 DOI: 10.1016/j.ympev.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/05/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.
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Affiliation(s)
- Angelo Poliseno
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Christian Feregrino
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Stéphane Sartoretto
- IFREMER, Z.P: de Brègaillon, CS 20330, 83507 La Seyne-sur-mer Cedex, France.
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, 13007 Marseille, France.
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 München, Germany.
| | | | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
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47
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Witt V, Ayris PM, Damby DE, Cimarelli C, Kueppers U, Dingwell DB, Wörheide G. Volcanic ash supports a diverse bacterial community in a marine mesocosm. Geobiology 2017; 15:453-463. [PMID: 28256065 PMCID: PMC5413822 DOI: 10.1111/gbi.12231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
Shallow-water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post-burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well-characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate-specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement.
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Affiliation(s)
- V. Witt
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
- MWM‐Museum Witt MünchenMunichGermany
| | - P. M. Ayris
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
| | - D. E. Damby
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
- United States Geological SurveyMenlo ParkCAUSA
| | - C. Cimarelli
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
| | - U. Kueppers
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
| | - D. B. Dingwell
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
| | - G. Wörheide
- Department of Earth and Environmental SciencesLudwig‐Maximilians‐UniversitätMunichGermany
- GeoBio‐CenterMunichGermany
- SNSB‐Bavarian State Collections of Palaeontology und GeologyMunichGermany
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48
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Voigt O, Adamska M, Adamski M, Kittelmann A, Wencker L, Wörheide G. Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes. Sci Rep 2017; 7:45658. [PMID: 28406140 PMCID: PMC5390275 DOI: 10.1038/srep45658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/02/2017] [Indexed: 11/30/2022] Open
Abstract
The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin) or diactines (ARP2 or SciDiactinin). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes.
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Affiliation(s)
- Oliver Voigt
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Maja Adamska
- Research School of Biology, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, 46 Sullivans Creek Road, Acton ACT 2601, Australia
| | - Marcin Adamski
- Research School of Biology, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, 46 Sullivans Creek Road, Acton ACT 2601, Australia
| | - André Kittelmann
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Lukardis Wencker
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.,Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
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49
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Schuster A, Lopez JV, Becking LE, Kelly M, Pomponi SA, Wörheide G, Erpenbeck D, Cárdenas P. Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding. BMC Evol Biol 2017; 17:82. [PMID: 28320321 PMCID: PMC5360047 DOI: 10.1186/s12862-017-0928-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. RESULTS For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. CONCLUSION This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.
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Affiliation(s)
- Astrid Schuster
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004 USA
| | - Leontine E. Becking
- Marine Animal Ecology, Wageningen University & Research Centre, P.O. Box 3700, AH, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Marine Zoology Department, PO Box 9517, 2300 RA, Leiden, The Netherlands
| | - Michelle Kelly
- National Centre for Aquatic Biodiversity and Biosecurity, National Institute of Water and Atmospheric Research, P.O. Box 109–695, Newmarket, Auckland, New Zealand
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute-Florida Atlantic University, 5600 U.S. 1 North, Ft Pierce, FL 34946 USA
| | - Gert Wörheide
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Paco Cárdenas
- Department of Medicinal Chemistry, Division of Pharmacognosy, BioMedical Center, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
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Abstract
The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of diverse scientists, marked its second anniversary with a workshop in Munich, Germany, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritize taxonomic diversity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialized organism databases to globally advance invertebrate genomics. Therefore this article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.
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