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Zimmermann HH, Stoof-Leichsenring KR, Dinkel V, Harms L, Schulte L, Hütt MT, Nürnberg D, Tiedemann R, Herzschuh U. Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 2023; 14:1650. [PMID: 36964154 PMCID: PMC10039020 DOI: 10.1038/s41467-023-36845-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.
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Affiliation(s)
- Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), DK-1350, Copenhagen, Denmark
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Viktor Dinkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Lars Harms
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Data Science Support, D-27568, Bremerhaven, Germany
| | - Luise Schulte
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Marc-Thorsten Hütt
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Ocean circulation and climate dynamics, D-24148, Kiel, Germany
| | - Ralf Tiedemann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Marine Geology, D-27568, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, D-28334, Bremen, Germany
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, D-14476, Potsdam, Germany.
- University of Potsdam, Institute of Environmental Sciences and Geography, D-14476, Potsdam, Germany.
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2
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Yuan D, Mao Z, Chen P, He Y, Pan D. Remote sensing of seawater optical properties and the subsurface phytoplankton layer in coastal waters using an airborne multiwavelength polarimetric ocean lidar. OPTICS EXPRESS 2022; 30:29564-29583. [PMID: 36299129 DOI: 10.1364/oe.463146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/29/2022] [Indexed: 06/16/2023]
Abstract
The vertical profiles of the seawater optical properties and subsurface phytoplankton layer observed during an airborne lidar flight experiment carried out on 29 January 2021 in the coastal waters near Qionghai city were studied. We employed a hybrid inversion model combining the Klett and perturbation retrieval methods to estimate the seawater optical properties, while the vertical subsurface phytoplankton layer profiles were obtained by an adaptive evaluation. The airborne lidar data preprocessing scheme and inversion of the seawater optical properties were described in detail, and the effects of water environment parameters on the airborne lidar detection performance in coastal waters were discussed. The obtained seawater optical properties and phytoplankton layer profiles exhibit characteristic spatiotemporal distributions. The vertical stratification of seawater optical properties along a flight track from 19.19°N to 19.27°N is more pronounced than that from 19.27°N to 19.31°N. The subsurface phytoplankton layer appears along the flight track at water depths of 5-14 m with a thickness of 2-8.3 m. The high concentrations of chlorophyll, colored dissolved organic matter (CDOM), and suspended particulate matter (SPM) in coastal waters are the main factors leading to the shallower detection depth for airborne lidar. A 532 nm laser emission wavelength is more suitable than 486 nm for investigating coastal waters. The 532 nm receiving channel with 25 mrad receiving field of view achieves a better detection performance than that with 6 mrad. These results indicate that lidar technology has great potential for the wide-range and long-term monitoring of coastal waters.
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Hirose Y, Shiozaki T, Hamano I, Yoshihara S, Tokumoto H, Eki T, Harada N. A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform. DNA Res 2021; 27:5893952. [PMID: 32810209 PMCID: PMC7547650 DOI: 10.1093/dnares/dsaa017] [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: 05/13/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
Amplicon sequencing is a powerful approach in microbiome studies as it detects live organisms with high sensitivity. This approach determines the composition of sequence variants of marker genes using high-throughput DNA sequencers. The use of dual index adaptors is the fundamental technique for pooling DNA libraries for Illumina sequencers and is believed not to affect the results. However, here, we observed a decrease of sequence quality in samples containing a specific combination of indexes, namely N704 and S507 in Nextera kits, in multiple runs on the Illumina MiSeq sequencer operated in different facilities. This decrease was also observed when sequencing randomly fragmented DNA of Escherichia coli and was not observed when either individual adaptor was used. Each end of the DNA library with this index combination contains a complementary sequence motif, which potentially inhibits proper cluster generation and/or subsequent sequencing. Community analysis of the 16S and 18S rRNA amplicons using QIIME2 revealed significant decreases in α-diversity in the samples containing the N704/S507 index combination, resulting from loss of low-abundance sequence variants during denoising. Our data underscore the importance of quality validation of sequence reads in developing dual index techniques and suggest cautious interpretation of microbiome data containing low-quality sequence reads.
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Affiliation(s)
- Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Itsuki Hamano
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Shizue Yoshihara
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Hayato Tokumoto
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Harada
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
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Makita Y, Suzuki S, Fushimi K, Shimada S, Suehisa A, Hirata M, Kuriyama T, Kurihara Y, Hamasaki H, Okubo-Kurihara E, Yoshitake K, Watanabe T, Sakuta M, Gojobori T, Sakami T, Narikawa R, Yamaguchi H, Kawachi M, Matsui M. Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nat Commun 2021; 12:3593. [PMID: 34135337 PMCID: PMC8209157 DOI: 10.1038/s41467-021-23741-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Aya Suehisa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Manami Hirata
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidefumi Hamasaki
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Watanabe
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tomoko Sakami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan.
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Micro-size plankton abundance and assemblages in the western North Pacific Subtropical Gyre under microscopic observation. PLoS One 2021; 16:e0250604. [PMID: 33901250 PMCID: PMC8075241 DOI: 10.1371/journal.pone.0250604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/11/2021] [Indexed: 11/28/2022] Open
Abstract
While primary productivity in the oligotrophic North Pacific Subtropical Gyre (NPSG) is changing, the micro-size plankton community has not been evaluated in the last 4 decades, prompting a re-evaluation. We collected samples over three years (2016–2018) from depths of 10 to 200 m (n = 127), and the micro-size plankton were identified and counted to understand the heterogeneity of micro-size plankton community structure. The assemblages were consistent to the those of 4 decades ago. Dinophyceae (dinoflagellates) were the most numerically abundant, followed by Cryptophyceae and Bacillariophyceae (diatoms). The other micro-size plankton classes (Cyanophyceae, Haptophyceae, Dictyochophyceae, Euglenophyceae, and Prasinophyceae) were not always detected, whereas only Trichodesmium spp. was counted in the Cyanophyceae. Other unidentified autotrophic and heterotrophic flagellates were also significantly present, and their numeric abundance was higher than or at the same level as was that of the Dinophyceae. In the Dinophyceae, Gymnodiniaceae and Peridiniales were abundant. The chlorophyll a concentration and these class-level assemblages suggested micro-size plankton is not a major primary producer in this area. We applied generalized additive models (GAMs) and principal coordination analyses (PCoAs) to evaluate the habitats of every plankton group and the heterogeneity of the assemblages. The GAMs suggested that every classified plankton abundance showed a similar response to salinity, and we observed differences in habitats in terms of temperature and nitrate concentrations. Based on the PCoAs, we observed unique communities at the 200 m depth layer compared with those at the other sampling layers. The site scores of PCoAs indicated that the micro-size plankton assemblages are most heterogeneous at the 10 m depth layer. At such depth, diazotrophic Cyanophyceae (Trichodesmium spp.) are abundant, particularly in less-saline water. Therefore, nitrogen fixation may contribute to the heterogeneity in the abundance and assemblages in the western NPSG.
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Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada N. A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLoS One 2021; 16:e0245936. [PMID: 33596231 PMCID: PMC7888612 DOI: 10.1371/journal.pone.0245936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 01/04/2023] Open
Abstract
Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.
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Affiliation(s)
- Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- * E-mail:
| | - Fumihiro Itoh
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Jonaotaro Onodera
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Naomi Harada
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience 2020; 24:102002. [PMID: 33490910 PMCID: PMC7811142 DOI: 10.1016/j.isci.2020.102002] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022] Open
Abstract
The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics. Eukaryotic virus community composition is shown to predict carbon export efficiency Tens of viruses are highly important in the prediction of the efficiency These viruses are inferred to infect ecologically important hosts
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