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  1. Article ; Online: Author Correction

    Takako Masuda / Keisuke Inomura / Naoto Takahata / Takuhei Shiozaki / Yuji Sano / Curtis Deutsch / Ondřej Prášil / Ken Furuya

    Communications Biology, Vol 6, Iss 1, Pp 1-

    Heterogeneous nitrogen fixation rates confer energetic advantage and expanded ecological niche of unicellular diazotroph populations

    2023  Volume 1

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin.

    Takuhei Shiozaki / Fumihiro Itoh / Yuu Hirose / Jonaotaro Onodera / Akira Kuwata / Naomi Harada

    PLoS ONE, Vol 16, Iss 2, p e

    2021  Volume 0245936

    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 ... ...

    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.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Investigating Algal Communities in Lacustrine and Hydro-Terrestrial Environments of East Antarctica Using Deep Amplicon Sequencing

    Yuu Hirose / Takuhei Shiozaki / Masahiro Otani / Sakae Kudoh / Satoshi Imura / Toshihiko Eki / Naomi Harada

    Microorganisms, Vol 8, Iss 497, p

    2020  Volume 497

    Abstract: Antarctica has one of the most extreme environments on Earth, with low temperatures and low nutrient levels. Antarctica’s organisms live primarily in the coastal, ice-free areas which cover approximately 0.18% of the continent’s surface. Members of ... ...

    Abstract Antarctica has one of the most extreme environments on Earth, with low temperatures and low nutrient levels. Antarctica’s organisms live primarily in the coastal, ice-free areas which cover approximately 0.18% of the continent’s surface. Members of Cyanobacteria and eukaryotic algae are important primary producers in Antarctica since they can synthesize organic compounds from carbon dioxide and water using solar energy. However, community structures of photosynthetic algae in Antarctica have not yet been fully explored at molecular level. In this study, we collected diverse algal samples in lacustrine and hydro-terrestrial environments of Langhovde and Skarvsnes, which are two ice-free regions in East Antarctica. We performed deep amplicon sequencing of both 16S ribosomal ribonucleic acid (rRNA) and 18S rRNA genes, and we explored the distribution of sequence variants (SVs) of these genes at single nucleotide difference resolution. SVs of filamentous Cyanobacteria genera, including Leptolyngbya , Pseudanabaena , Phormidium , Nodosilinea , Geitlerinama , and Tychonema , were identified in most of the samples, whereas Phormidesmis SVs were distributed in fewer samples. We also detected unicellular, multicellular or heterocyst forming Cyanobacteria strains, but in relatively small abundance. For SVs of eukaryotic algae, Chlorophyta, Cryptophyta, and Ochrophyta were widely distributed among the collected samples. In addition, there was a red colored bloom of eukaryotic alga, Geminigera cryophile (Cryptophyta), in the Langhovde coastal area. Eukaryotic SVs of Acutuncus antarcticus and/or Diphascon pingue of Tardigrada were dominant among most of the samples. Our data revealed the detailed structures of the algal communities in Langhovde and Skarvsnes. This will contribute to our understanding of Antarctic ecosystems and support further research into this subject.
    Keywords algae ; Antarctica ; lacustrine ; hydro-terrestrial ; Cyanobacteria ; microbiome ; Biology (General) ; QH301-705.5
    Subject code 550
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Stable isotopic evidence for the differential contribution of diazotrophs to the epipelagic grazing food chain in the mid‐Pacific Ocean

    Horii, Sachiko / Kazutaka Takahashi / Takuhei Shiozaki / Fuminori Hashihama / Ken Furuya

    Global ecology and biogeography. 2018 Dec., v. 27, no. 12

    2018  

    Abstract: AIM: Biological nitrogen fixation supports primary production in oligotrophic water, but its link to higher trophic levels has not been described fully on a biogeographical basis. Here, we determine the regional patterns of the contribution of the ... ...

    Abstract AIM: Biological nitrogen fixation supports primary production in oligotrophic water, but its link to higher trophic levels has not been described fully on a biogeographical basis. Here, we determine the regional patterns of the contribution of the combined nitrogen to biological production within the epipelagic layer of the mid‐Pacific Ocean using the isotopic signatures of nitrogen (δ¹⁵N) and carbon (δ¹³C) in the biological components. LOCATION: The mid‐Pacific Ocean along 170° W between the southern subtropical front and the Chukchi Sea. TIME PERIOD: Northern and austral summer in 2013 and 2014. MAJOR TAXA STUDIED: Planktonic and micronektonic biota in the euphotic layer. METHODS: We measured the geographical variations in δ¹⁵N and δ¹³C of the suspended particulate organic matter (POM), mesozooplankton assemblage and micronektonic fish. We analysed the relationships among these values and the environmental variables of temperature, nitrate concentration and biological nitrogen fixation activity along a 12,000‐km meridional transect. RESULTS: The POM δ¹⁵N at 0 m was negatively correlated with in situ N₂ fixation activity in the subtropical region, whereas that in the equatorial and high‐latitude regions was correlated with the nitrate concentration at 0 m. We found that the ratios of the increase in δ¹⁵N to δ¹³C along the grazing food chain were consistent throughout the equatorial and subtropical regions. Cluster analyses based on the stable isotopic signatures in the biotic components revealed that the food chains in the stations within the subtropical mid‐Pacific Ocean were separated into three groups based on the differential contributions of biological nitrogen fixation. MAIN CONCLUSIONS: Distinct food chains from primary to tertiary production sustained by different nitrogen sources, nitrate below the euphotic zone, and diazotrophic nitrogen occur within the same biogeographical provinces in the subtropical mid‐Pacific Ocean. The diazotroph‐dominant community contributes substantially to the apex predators in the central areas of the subtropical gyres.
    Keywords biogeography ; biological production ; carbon ; cluster analysis ; environmental factors ; euphotic zone ; fish ; food chain ; grazing ; latitude ; nitrates ; nitrogen ; nitrogen fixation ; nitrogen-fixing bacteria ; particulate organic matter ; predators ; primary productivity ; stable isotopes ; subtropics ; summer ; temperature ; trophic levels ; zooplankton ; Chukchi Sea
    Language English
    Dates of publication 2018-12
    Size p. 1467-1480.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2021283-5
    ISSN 1466-8238 ; 1466-822X ; 0960-7447
    ISSN (online) 1466-8238
    ISSN 1466-822X ; 0960-7447
    DOI 10.1111/geb.12823
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Nanomolar phosphate supply and its recycling drive net community production in the subtropical North Pacific

    Fuminori Hashihama / Ichiro Yasuda / Aki Kumabe / Mitsuhide Sato / Hiroshi Sasaoka / Yosuke Iida / Takuhei Shiozaki / Hiroaki Saito / Jota Kanda / Ken Furuya / Philip W. Boyd / Masao Ishii

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 8

    Abstract: Primary productivity in the oligotrophic ocean sustains Earth’s ecosystems, but nutrient concentrations are vanishingly low. Here the authors measure nanomolar macronutrient concentrations in the North Pacific and find that net community production is ... ...

    Abstract Primary productivity in the oligotrophic ocean sustains Earth’s ecosystems, but nutrient concentrations are vanishingly low. Here the authors measure nanomolar macronutrient concentrations in the North Pacific and find that net community production is sustained through high rates of phosphorus recycling.
    Keywords Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Utilization of ammonium by the hydrocarbon-producing microalga, Botryococcus braunii Showa

    Nakamura, Hiromasa / Ken Furuya / Natsuki Gonda / Shigeki Matsunaga / Shigeru Okada / Takuhei Shiozaki

    Algal research. 2017 July, v. 25

    2017  

    Abstract: As a prospective feedstock for sustainable biofuels, the green microalga Botryococcus braunii race B has attracted significant attention since this colony-forming alga has the ability to accumulate considerable amounts of triterpene hydrocarbons, ... ...

    Abstract As a prospective feedstock for sustainable biofuels, the green microalga Botryococcus braunii race B has attracted significant attention since this colony-forming alga has the ability to accumulate considerable amounts of triterpene hydrocarbons, botryococcenes, in its extracellular matrix. However, its primary metabolism, nutrient uptake and utilization relevant to growth, are still poorly understood in this alga. From this perspective, we investigated the utilization of ammonium by B. braunii as a more reduced form of nitrogen source compared to nitrate, which is generally used for cultures of the alga. Isotope-ratio mass spectrometry analyses indicated that the uptake rate of ammonium was higher than that of nitrate at a certain concentration. When ammonium was added to culture medium, however, it inhibited algal growth even in the presence of nitrate. Buffered culture media ameliorated the toxicity of ammonium, and the alga accumulated the same levels of hydrocarbons and secondary carotenoids, irrespective of nitrogen source. To characterize utilization of ammonium by B. braunii at the molecular level, putative ammonium transporter (AMT) genes were screened from a cDNA library and four isogenes (BbAMT1;1, 1;2, 1;3 and 1;4) were cloned. Two of them, BbAMT1;1 and 1;2, were upregulated under nitrogen deficient conditions. BbAMT1;1 complemented the growth of an ammonium uptake-defective yeast strain, showing it to be a functional gene coding for AMT. These results could pave the way for culturing B. braunii more efficiently using ammonium as a sole nitrogen source by improving ammonium uptake through our understanding of AMT.
    Keywords ammonium ; biofuels ; Botryococcus braunii ; carotenoids ; cDNA libraries ; complementary DNA ; culture media ; extracellular matrix ; feedstocks ; genes ; mass spectrometry ; metabolism ; microalgae ; nitrates ; nitrogen ; nutrient uptake ; toxicity ; triterpenoids ; yeasts
    Language English
    Dates of publication 2017-07
    Size p. 445-451.
    Publishing place Elsevier B.V.
    Document type Article
    ISSN 2211-9264
    DOI 10.1016/j.algal.2017.06.007
    Database NAL-Catalogue (AGRICOLA)

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