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Peer-Reviewed Papers 2019 Peer-reviewed papers 2019 1. Kashiyama Y, Yokoyama A, Shiratori T, Bachy C, Gutierrez-Rodriguez A, Not F, Hess S, Wang M, Chen M, Gong Y, Seto K, Kagami M, Hamamoto Y, Honda D, Umetani T, Shihongi A, Kayama M, Matsuda T, Taira J, Yabuki A, Tsuchiya M, Hirakawa Y, Kawaguchi A, Nomura M, Nakamura A, Namba N, Matsumoto M, Tanaka T, Yoshino T, Higuchi R, Yamamoto A, Maruyama T, Yamaguchi A, Uzuka A, Miyagishima S, Kawahara J, Suzaki T, Nakazawa M, Ishikawa T, Maruyama M, Tanifuji G, Kinoshita Y, Tamiaki H, Taming chlorophylls allowed eukaryotes to prosper on the oxygenated Earth. The ISME journal (submitted: 17Feb2018, 19Jan2019) 10.1038/s41396-019-0377-0 2018 2. Bernhard JM, Tsuchiya M, Nomaki H, 2018, Ultrastructural observations on prokaryotic associates of benthic foraminifera: food, mutualistic symbionts, or parasites? Marine Micropaleontology, 138, 33-45. (Accepted 6th Sep 2017, available online 6th Oct 2017, published Jan 2018) 3. Jauffrais T, LeKieffre C, Koho K, Tsuchiya M, Schweizer M, Bernhard JM, Meibom A, Geslin E, 2018, Ultrastructure and distribution of sequestered chloroplasts in benthic foraminiferafrom shallow-water (photic) habitats. Marine Micropaleontology, 138, 46-62. (Accepted 16th Oct 2017, available online 22nd Oct 2017, published Jan 2018) 4. Tsuchiya M, Chikaraishi Y, Nomaki H, Sasaki Y, Tame A, Uematsu K, Ohkouchi N, Compound-specific isotope analysis of benthic foraminifer amino acids suggests microhabitat variability in rocky-shore environments. Ecology and Evolution, DOI: 10.1002/ece3.4358 (major revision, submission of revised manuscript: 20 Apr 2018, accepted 20 Jun 2018, 24 July, 2018) 5. Ishikawa NF, Chikaraishi Y, Takano Y, Sasaki Y, Takizawa Y, Tsuchiya M, Tayasu I, Nagata T, Ohkouchi N, 2018, A new analytical method for determination of the nitrogen isotopic composition of methionine: Its application to aquatic ecosystems with mixed resources. Limnology & Oceanography: Methods 16, 607-620 (submitted: 22 Jan 2018, accepted 24 Jul 2018, published 10 Sept 2018) doi: 10.1002/lom3.10272 6. Voltski I, Weiner AKM, Tsuchiya M, Kitazato H, 2018, Morphological and genetic description of Syringammina limosa sp. nov., the first xenophyophore (Foraminifera) from the deep Sea of Okhotsk. Deep-Sea Research Part II, 154, 32-46, doi.org/10.1016/j.dsr2.2017.12.001 (Accepted-online published 14th Dec 2017, published Aug 2018) 7. Kitahashi T, Watanabe H, Tsuchiya M, Yamamoto Hideyuki, Yamamoto Hiroyuki, 2018, A new method for acquiring images of meiobenthic images using the FlowCAM. Methods X, 5, 1330-1335 (submitted: 10 Aug 2018, accepted 20 Oct 2018, published 23 Oct 2018) 2017 8. Toyofuku T, Matsuo MY, de Nooijer LJ, Nagai Y, Kawada S, Fujita K, Reichart G-J, Nomaki H, Tsuchiya M, Sakaguchi H, Kitazato H, 2017, Proton pumping accompanies calcification in foraminifera. Nature Communications, DOI: 10.1038/ncomms14145 |www.nature.com/naturecommunications (accepted 1st Dec.) 2016 9. Nomaki H, Bernhard JM, Ishida A, Tsuchiya M, Uematsu K, Tame A, Kitahashi T, Takahata N, Sano Y, Toyofuku T, 2016, Intracellular isotope localization in Ammonia sp. (Foraminifera) of oxygen-depleted environments: results of nitrate and sulfate labeling experiments. Frontiers in Microbiology. 7:163. doi: 10.3389/fmicb.2016.00163 2015 10. Nomaki H, Chikaraishi Y, Tsuchiya M, Toyofuku T, Suga H, Sasaki Y, Uematsu K, Tame A, Ohkouchi N, 2015, Variation in the nitrogen isotopic composition of amino acids in benthic foraminifera: implications for their adaptation to oxygen-depleted environments. Limnology and Oceanography. 6, 1906-1916, doi: 10.1002/lno.10140 (online: 25 Jul, 2015) 11. Nomaki H, Toyofuku T, Tsuchiya M, Matsuzaki T, Uematsu K, Tame A, 2015, Three-dimensional observation of foraminiferal cytoplasmic morphology and internal structures by using uranium–osmium staining and micro X-ray computed tomography. Marine Micropaleontology: 121, 32-40. 12. Tsuchiya M, Toyofuku T, Uematsu K, Brüchert V, Collen J, Yamamoto H, Kitazato H, 2015, Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera). Journal of Eukaryotic Microbiology: 62, 454-469. 2014 13. Chikaraishi Y, Steffan SA, Ogawa ON, Ishikawa NF, Sasaki Y, Tsuchiya M, Ohkouchi N, 2014, High-resolution food webs based on nitrogen isotopic composition of amino acids. Ecology and Evolution 4: 2423-2449. doi: 10.1002/ece3.1103 14. Nomaki H, Chikaraishi Y, Tsuchiya M, Toyofuku T, Ohkouchi N, Uematsu K, Tame A, Kitazato H, 2014, Nitrate uptake by foraminifera and use in conjunction with endobionts under anoxic conditions. Limnology and Oceanography 59: 1897-1888. 15. Tsuchiya M, Takahara K, Aizawa M, Suzuki-Kanesaki H, Toyofuku T, Kitazato H, 2014, How has foraminiferal genetic diversity developed? A case study of Planoglabratella opercularis and the species concept inferred from its ecology, distribution, genetics, and breeding behavior. Pp. 133-162 in H. Kitazato, J. M. Bernhard, eds. Experimental Approaches in Foraminifera: Collection, Maintenance and Experiments. Environmental Science Series. Springer, Tokyo, Japan. DOI 10.1007/978-4-431-54388-6_9 2013 16. Tsuchiya M, Gooday AJ, Nomaki H, Oguri K, Kitazato H, 2013, Genetic diversity and environmental preferences of monothalamous foraminifers revealed through clone analysis of environmental small-subunit ribosomal DNA sequences. Journal of Foraminiferal Research: 43, 3-13. 2012 17. Hori S, Tsuchiya M, Nishi S, Arai W, Yoshida T, Takami H, 2013, Active bacterial flora surrounding foraminifera (xenophyophorea) living on the deep-sea floor. Bioscience, Biotechnology, and Biochemistry: 77, 381-384. 18. Ishitani Y, Kamikawa R, Yabuki A, Tsuchiya M, Inagaki Y, Takishita K, 2012, Evolution of Elongation Factor-Like (EFL) Protein in Rhizaria Is Revised by Radiolarian EFL Gene Sequences. Journal of Eukaryotic Microbiology: 59, 367-373. 19. Maeda T, Hirose E, Chikaraishi Y, Kawato M, Takishita K, Yoshida T, Verbruggen H, Tanaka J, Shimamura S, Takaki Y, Tsuchiya M, Iwai K, Maruyama T, 2012, Algivore or phototroph? Plakobranchus ocellatus (Gastropoda) continuously acquires kleptoplasts and nutrition from multiple algal species in nature. PLosOne: 7, e42024. 20. Takahashi Y, Sasaki Y, Chikaraishi Y, Tsuchiya M, Watanabe H, Asahida T, Maruyama T, Fujikura K, 2012, Does the symbiotic scale—worm feed on the host mussel in deep-sea vent field? Research in Organic Geochemistry, 28, 23-26. 2011 21. Ishitani Y, Ishikawa SA, Inagaki Y, Tsuchiya M, Takahashi K, Takishita K, 2011, Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis - the sister relationship of Radiolaria and Foraminifera. Marine Micropaleontology: 81, 32-42. 2009 22. Lecroq B, Gooday AJ, Tsuchiya M, Pawlowski J, 2009, A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis. The Zoological Journal of the Linnean Society: 156, 455-464. 23. Tsuchiya M, Grimm GW, Heinz P, Stögerer K, Ertan KT, Collen J, Brüchert V, Hemleben C, Hemleben V, Kitazato H, 2009, Ribosomal DNA shows extremely low genetic divergence in a world-wide distributed, but disjunct and highly adapted marine protozoan (Virgulinella fragilis, Foraminiferida). Marine Micropaleontology: 70, 8-19. 2008 24. Kuroyanagi A, Tsuchiya M, Kawahata H, Kitazato H, 2008, The occurrence of two genotypes of the planktonic foraminifer Globigerinoides ruber (white) and paleo-environmental implications, Marine Micropaleontology: 68, 236-243. 25. Tsuchiya M, Tazume M, Kitazato H, 2008, Molecular characterization of the non-costate morphotypes of buliminid foraminifers based on internal transcribed region of ribosomal DNA (ITS rDNA) sequence data. Marine Micropaleontology: 69, 212-224. 2007 26. Takishita K, Tsuchiya M, Kawato M, Oguri K, Kitazato H, Maruyama T, 2007, Genetic Diversity of Microbial Eukaryotes in Anoxic Sediment of the Saline Meromictic Lake Namako-ike (Japan): On the Detection of Anaerobic or Anoxic-tolerant Lineages of Eukaryotes. Protist: 158, 51-64. 2006 27. Nozawa F, Kitazato H, Tsuchiya M, Gooday AJ, 2006, ‘Live’ benthic foraminifera at an abyssal site in the equatorial Pacific nodule province: Abundance, diversity and taxonomic composition. Deep-Sea Research I; 53, 1406–1422. 28. Takishita K, Tsuchiya M, Reimer JD, Maruyama T, 2006, Molecular evidence demonstrating the basidiomycetous fungus Cryptococcus curvatus is the dominant microbial eukaryote in sediment at the Kuroshima Knoll methane seep. Extremophiles: 10, 165-169. 2005 29. Takishita K, Inagaki Y, Tsuchiya M, Sakaguchi M, Maruyama T, 2005, A close relationship between Cerocozoa and Foraminifera supported by phylogenetic analysis based on combined amino acid sequences of three cytoskeletal proteins (actin, α-tubulin, and β-tubulin). Gene: 362, 153-160. 30. Toyofuku-Suzuki M, Kitazato H, Tsuchiya M, 2005, Phylogenetic relationships among genus Ammonia (Foraminifera) based on ribosomal DNA sequences, which are distributed in the vicinity of the Japanese Islands. Frontier Research on Earth Evolution: 2, 1-9. 2003 31. Kitazato H, Tazume M, Tsuchiya M, 2003, Phylogenetic relationships among the species of genus Bulimina (Foraminifera) inferred from ribosomal DNA sequences. Frontier Research on Earth Evolution: 1, 233-238. 32. Tsuchiya M, Kitazato H, Pawlowski J, 2003, Analysis of internal transcribed spacer of ribosomal DNA reveals cryptic speciation in Planoglabratella opercularis. Journal of Foraminiferal Research: 33, 285-293. 2000 33. Kitazato H, Tsuchiya M, Takahara K, 2000, Recognition of breeding populations in foraminifera: an example using the genus Glabratella. Paleontological Research: 4, 1-15. 34. Toyofuku T, Kitazato H, Kawahata H, Tsuchiya M, Nohara M, 2000, Evaluation of Mg/Ca thermometry in foraminifera: Comparison of experimental results and measurements in nature. Paleoceanography: 15, 456-464. 35. Tsuchiya M, Kitazato H, Pawlowski J, 2000, Phylogenetic relationships among species of Glabratellidae (Foraminifera) inferred from ribosomal DNA sequences: Comparison with morphological and reproductive data. In Lee, J.J. and Hallock, P. (eds.), Advances in the Biology of Foraminifera. Micropaleontology: 46, 13-20. .
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