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Burns JA, Daniels J, Becker KP, Casagrande D, Roberts P, Orenstein E, Vogt DM, Teoh ZE, Wood R, Yin AH, Genot B, Wood RJ, Katija K, Phillips BT, Gruber DF. Transcriptome sequencing of seven deep marine invertebrates. Sci Data 2024; 11:679. [PMID: 38914539 PMCID: PMC11196669 DOI: 10.1038/s41597-024-03533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
We present 4k video and whole transcriptome data for seven deep-sea invertebrate animals collected in the Eastern Pacific Ocean during a research expedition onboard the Schmidt Ocean Institute's R/V Falkor in August of 2021. The animals include one jellyfish (Atolla sp.), three siphonophores (Apolemia sp., Praya sp., and Halistemma sp.), one larvacean (Bathochordaeus mcnutti), one tunicate (Pyrosomatidae sp.), and one ctenophore (Lampocteis sp.). Four of the animals were sequenced with long-read RNA sequencing technology, such that the reads themselves define a reference assembly for those animals. The larvacean tissues were successfully preserved in situ and has paired long-read reference data and short read quantitative transcriptomic data for within-specimen analyses of gene expression. Additionally, for three animals we provide quantitative image data, and a 3D model for one siphonophore. The paired image and transcriptomic data can be used for species identification, species description, and reference genetic data for these deep-sea animals.
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Affiliation(s)
- John A Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.
| | - Joost Daniels
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, 95039, USA
| | - Kaitlyn P Becker
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David Casagrande
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI, 02882, USA
| | - Paul Roberts
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, 95039, USA
| | - Eric Orenstein
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, 95039, USA
| | - Daniel M Vogt
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | | | - Ryan Wood
- PA Consulting, Concord, MA, 01742, USA
| | - Alexander H Yin
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI, 02882, USA
| | - Baptiste Genot
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Robert J Wood
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Kakani Katija
- Monterey Bay Aquarium Research Institute, Research and Development, Moss Landing, 95039, USA
| | - Brennan T Phillips
- Department of Ocean Engineering, University of Rhode Island, 215 South Ferry Road, Narragansett, RI, 02882, USA
| | - David F Gruber
- Department of Natural Sciences, Baruch College, City University of New York and PhD Program in Biology, CUNY Graduate Center, New York, NY, 10010, USA.
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Ling F, Essock-Burns T, McFall-Ngai M, Katija K, Nawroth JC, Kanso E. Flow Physics Explains Morphological Diversity of Ciliated Organs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.12.528181. [PMID: 38168341 PMCID: PMC10760039 DOI: 10.1101/2023.02.12.528181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Organs that pump fluids by the coordinated beat of motile cilia through the lumen are integral to animal physiology. Such organs include the human airways, brain ventricles, and reproductive tracts. Although cilia organization and duct morphology vary drastically in the animal kingdom, ducts are typically classified as either carpet or flame designs. The reason behind this dichotomy and how duct design relates to fluid pumping remain unclear. Here, we demonstrate that two structural parameters -- lumen diameter and cilia-to-lumen ratio -- organize the observed duct diversity into a continuous spectrum that connects carpets to flames across all animal phyla. Using a unified fluid model, we show that carpet and flame designs maximize flow rate and pressure generation, respectively. We propose that convergence of ciliated organ designs follows functional constraints rather than phylogenetic distance, along with universal design rules for ciliary pumps.
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Hoving HJT, Neitzel P, Hauss H, Christiansen S, Kiko R, Robison BH, Silva P, Körtzinger A. In situ observations show vertical community structure of pelagic fauna in the eastern tropical North Atlantic off Cape Verde. Sci Rep 2020; 10:21798. [PMID: 33311534 PMCID: PMC7733502 DOI: 10.1038/s41598-020-78255-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/20/2020] [Indexed: 01/22/2023] Open
Abstract
Distribution patterns of fragile gelatinous fauna in the open ocean remain scarcely documented. Using epi-and mesopelagic video transects in the eastern tropical North Atlantic, which features a mild but intensifying midwater oxygen minimum zone (OMZ), we established one of the first regional observations of diversity and abundance of large gelatinous zooplankton. We quantified the day and night vertical distribution of 46 taxa in relation to environmental conditions. While distribution may be driven by multiple factors, abundance peaks of individual taxa were observed in the OMZ core, both above and below the OMZ, only above, or only below the OMZ whereas some taxa did not have an obvious distribution pattern. In the eastern eropical North Atlantic, OMZ expansion in the course of global climate change may detrimentally impact taxa that avoid low oxygen concentrations (Beroe, doliolids), but favour taxa that occur in the OMZ (Lilyopsis, phaeodarians, Cydippida, Colobonema, Haliscera conica and Halitrephes) as their habitat volume might increase. While future efforts need to focus on physiology and taxonomy of pelagic fauna in the study region, our study presents biodiversity and distribution data for the regional epi- and mesopelagic zones of Cape Verde providing a regional baseline to monitor how climate change may impact the largest habitat on the planet, the deep pelagic realm.
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Affiliation(s)
- H J T Hoving
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - P Neitzel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - H Hauss
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
- Christian Albrecht University Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
| | - S Christiansen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
- University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - R Kiko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
- Laboratoire dOcéanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | - B H Robison
- Monterey Bay Aquarium Research Institute, Sandholtroad 7700, Moss Landing, USA
| | - P Silva
- Ocean Science Centre Mindelo & Instituto do Mar (IMAR), Cova de Inglesa, C.P. 132, Mindelo, São Vicente, Republic of Cabo Verde
| | - A Körtzinger
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
- Christian Albrecht University Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
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Katija K, Troni G, Daniels J, Lance K, Sherlock RE, Sherman AD, Robison BH. Revealing enigmatic mucus structures in the deep sea using DeepPIV. Nature 2020; 583:78-82. [DOI: 10.1038/s41586-020-2345-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/19/2020] [Indexed: 11/09/2022]
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Abstract
Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.
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Affiliation(s)
- Julien Pichon
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.,Université de Paris, Paris, France
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.,The Francis Crick Institute, London, NW1 1AT, UK.,Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
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Choy CA, Robison BH, Gagne TO, Erwin B, Firl E, Halden RU, Hamilton JA, Katija K, Lisin SE, Rolsky C, S Van Houtan K. The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column. Sci Rep 2019; 9:7843. [PMID: 31171833 PMCID: PMC6554305 DOI: 10.1038/s41598-019-44117-2] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Plastic waste has been documented in nearly all types of marine environments and has been found in species spanning all levels of marine food webs. Within these marine environments, deep pelagic waters encompass the largest ecosystems on Earth. We lack a comprehensive understanding of the concentrations, cycling, and fate of plastic waste in sub-surface waters, constraining our ability to implement effective, large-scale policy and conservation strategies. We used remotely operated vehicles and engineered purpose-built samplers to collect and examine the distribution of microplastics in the Monterey Bay pelagic ecosystem at water column depths ranging from 5 to 1000 m. Laser Raman spectroscopy was used to identify microplastic particles collected from throughout the deep pelagic water column, with the highest concentrations present at depths between 200 and 600 m. Examination of two abundant particle feeders in this ecosystem, pelagic red crabs (Pleuroncodes planipes) and giant larvaceans (Bathochordaeus stygius), showed that microplastic particles readily flow from the environment into coupled water column and seafloor food webs. Our findings suggest that one of the largest and currently underappreciated reservoirs of marine microplastics may be contained within the water column and animal communities of the deep sea.
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Affiliation(s)
- C Anela Choy
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California, 95039, USA. .,Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0218, USA.
| | - Bruce H Robison
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California, 95039, USA
| | - Tyler O Gagne
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, California, 93940, USA
| | - Benjamin Erwin
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California, 95039, USA
| | - Evan Firl
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, California, 93940, USA
| | - Rolf U Halden
- Arizona State University, Tempe, Arizona, 85287, USA
| | - J Andrew Hamilton
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California, 95039, USA
| | - Kakani Katija
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California, 95039, USA
| | - Susan E Lisin
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, California, 93940, USA
| | | | - Kyle S Van Houtan
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, California, 93940, USA. .,Nicholas School of the Environment, Duke University, PO Box 90328, Durham, NC, 27708, USA.
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Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements. Curr Biol 2019; 29:1161-1168.e6. [DOI: 10.1016/j.cub.2019.01.080] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 11/26/2018] [Accepted: 01/31/2019] [Indexed: 01/08/2023]
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Katija K, Sherlock RE, Sherman AD, Robison BH. New technology reveals the role of giant larvaceans in oceanic carbon cycling. SCIENCE ADVANCES 2017; 3:e1602374. [PMID: 28508058 PMCID: PMC5415331 DOI: 10.1126/sciadv.1602374] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/08/2017] [Indexed: 05/29/2023]
Abstract
To accurately assess the impacts of climate change on our planet, modeling of oceanic systems and understanding how atmospheric carbon is transported from surface waters to the deep benthos are required. The biological pump drives the transport of carbon through the ocean's depths, and the rates at which carbon is removed and sequestered are often dependent on the grazing abilities of surface and midwater organisms. Some of the most effective and abundant midwater grazers are filter-feeding invertebrates. Although the impact of smaller, near-surface filter feeders is generally known, efforts to quantify the impact of deeper filter feeders, such as giant larvaceans, have been unsuccessful. Giant larvaceans occupy the upper 400 m of the water column, where they build complex mucus filtering structures that reach diameters greater than 1 m. Because of the fragility of these structures, direct measurements of filtration rates require in situ methods. Hence, we developed DeepPIV, an instrument deployed from a remotely operated vehicle that enables the direct measurement of in situ filtration rates. The rates measured for giant larvaceans exceed those of any other zooplankton filter feeder. Given these filtration rates and abundance data from a 22-year time series, the grazing impact of giant larvaceans far exceeds previous estimates, with the potential for processing their 200-m principal depth range in Monterey Bay in as little as 13 days. Technologies such as DeepPIV will enable more accurate assessments of the long-term removal of atmospheric carbon by deep-water biota.
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