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Okada S, Richirt J, Tame A, Nomaki H. Rapid Freezing and Cryo-SEM-EDS Imaging of Foraminifera (Unicellular Eukaryotes) Using a Conductive Viscous Cryogenic Glue. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:359-367. [PMID: 38578298 DOI: 10.1093/mam/ozae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/13/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
Spatial distribution of water-soluble molecules and ions in living organisms is still challenging to assess. Energy-dispersive X-ray spectroscopy (EDS) via cryogenic scanning electron microscopy (cryo-SEM) is one of the promising methods to study them without loss of dissolved contents. High-resolution cryo-SEM-EDS has challenges in sample preparation, including cross-section exposure and sample drift/charging due to insulative surrounding water. The former becomes problematic for large and inseparable organisms, such as benthic foraminifera, a unicellular eukaryote playing significant roles in marine ecosystems, which often exceed the size limit for the most reliable high-pressure freezing. Here we show graphite oxide dispersed in sucrose solution as a good glue to freeze, expose cross-section by cryo-ultramicrotome, and analyze elemental distribution owing to the glue's high viscosity, adhesion force, and electron conductivity. To demonstrate the effectiveness and applicability of the glue for cryo-SEM-EDS, deep-sea foraminifer Uvigerina akitaensis was sampled during a cruise and plunge frozen directly on the research vessel, where the liquid nitrogen supply is limited. The microstructures were preserved as faithfully in cryo-SEM images as those with the conventional resin-substituted transmission electron micrograph. We found elements colocalized within the cytoplasm originating from water-soluble compounds that can be lost with conventional dehydrative fixation.
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Affiliation(s)
- Satoshi Okada
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Julien Richirt
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Marine Works, Japan Ltd., 3-54-1 Oppama-Higashi-cho, Yokosuka, Kanagawa 237-0063, Japan
- Faculty of Medical Sciences, Life Science Research Laboratory, University of Fukui, 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui 910-1193, Japan
| | - Hidetaka Nomaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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Langer MR, Weinmann AE, Makled WA, Könen J, Gooday AJ. New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans. PeerJ 2022; 10:e12884. [PMID: 35211360 PMCID: PMC8862658 DOI: 10.7717/peerj.12884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m-2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
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Affiliation(s)
- Martin R. Langer
- Institute of Geoscience, Paleontology, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
| | - Anna E. Weinmann
- Geological-Paleontological Department, Natural History Museum Vienna, Vienna, Austria
| | - Walid A. Makled
- Exploration Department, Egyptian Petroleum Research Institute (EPRI), Cairo, Egypt
| | - Janine Könen
- Institute of Geoscience, Paleontology, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
| | - Andrew J. Gooday
- National Oceanography Centre, Southampton, United Kingdom,Life Sciences Department, Natural History Museum, London, United Kingdom
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Salonen IS, Chronopoulou PM, Nomaki H, Langlet D, Tsuchiya M, Koho KA. 16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera. Front Microbiol 2021; 12:694406. [PMID: 34385987 PMCID: PMC8353385 DOI: 10.3389/fmicb.2021.694406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.
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Affiliation(s)
- Iines S Salonen
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland.,SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Dewi Langlet
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, Université de Lille - CNRS, Université du Littoral Côte d'Opale, Station Marine de Wimereux, Lille, France.,Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC), Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Karoliina A Koho
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland
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