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Research Interest

Selected Publications

[2025]
Nomaki H, Chikaraishi Y, Ogawa ON, Maki K, Shimanaga M, Suga H, Tsuchiya M, Nagata T, Ohkouchi N. 2025. Differential use of multiple food sources at a bathyal benthic ecosystem in the central Sagami Bay revealed by amino acid nitrogen isotopic compositions. Progress in Earth and Planetary Science 12, 6.

Isobe N, Tanaka K, Ishii S, Shimane Y, Okada S, Daicho K, Sakuma W, Uetani K, Yoshimura T, Kimoto K, Kimura S, Saito T, Nakajima R, Tsuchiya M, Ikuta T, Kawagucci S, Iwata T, Nomaki H. 2025. Fully-circular shapeable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea. Science Advances 11, eads2426.

Tsuchiya M, Kitahashi T, Taira Y, Saito H, Oguri K, Nakajima R, Lindsay DJ, Fujikura K. 2025. Rapid detection and quantification of Nile Red-stained microplastic particles in sediment samples. PeerJ 13, e19196.

Gooday AJ, Ishitani Y, Chen C, Holzmann M, Richirt J, Seike K, Yamashita M, Tsuchiya M, Nomaki H. 2025. Integrative taxonomy of new xenophyophores (Rhizaria, Foraminifera) from the abyssal northwest Pacific. European Journal of Taxonomy (in press).

[2024]
Hookabe N, Jimi N, Ogawa A, Tsuchiya M, Sluys R. 2024. The Abyssal Parasitic Flatworm Fecampia cf. abyssicola: New Records, Anatomy, and Molecular Phylogeny, with a Discussion on Its Systematic Position. The Biological Bulletin 245(2), 77–87.

Richirt J, Okada S, Ishitani Y, Uematsu K, Tame A, Oda K, Isobe N, Ishimura T, Tsuchiya M, Nomaki H. 2024. Composite calcite and opal test in Foraminifera (Rhizaria). Biogeosciences 21, 3271–3288.

Nakajima R, Nagano A, Osafune S, Tsuchiya M, Fujikura K. 2024. Aggregation and transport of microplastics by a cold-core ring in the southern recirculation of the Kuroshio Extension: the role of mesoscale eddies on plastic debris distribution. Ocean Dynamics 74, 773–782.

Omura T, Isobe N, Miura T, Ishii S, Mori M, Ishitani Y, Kimura S, Hidaka K, Komiyama K, Suzuki M, Kasuya K, Nomaki H, Nakajima R, Tsuchiya M, Kawagucci S, Mori H, Nakayama A, Kunioka M, Kamino K, Iwata T. 2024. Microbial Decomposition of Biodegradable Plastics on the Deep-Sea Floor. Nature Communications 15, 568.

Tsuchiya M, Kitahashi T, Nakajima R, Oguri K, Kawamura K, Nakamura A, Nakano K, Maeda Y, Murayama M, Chiba S, Fujikura K. 2024. Distribution of microplastics in bathyal- to hadal-depth sediments and transport process along the deep-sea canyon and the Kuroshio Extension in the Northwest Pacific. Marine Pollution Bulletin 199, 115466.

[2023]
Bernhard JM, Nomaki H, Shiratori T, Elmendorf A, Yabuki A, Kimoto K, Tsuchiya M, Shimanaga M. 2023. Hydrothermal vent chimney-base sediments as unique habitat for meiobenthos and nanobenthos: Observations on millimeter-scale distributions. Frontiers in Marine Science 9, 1033381.

Bouchet VMP, Seuront L, Tsujimoto A, Delaeter C, Richirt J, Frontalini F, Tsuchiya M, Matsuba M, Nomaki N. 2023. Foraminifera and plastic pollution: knowledge gaps and research opportunities. Environmental Pollution 324, 121365.

Matsuba M, Tsujimoto A, Tsuchiya M, Tanaka Y, Nomaki H. 2023. Effectiveness of hierarchical Bayesian models for citizen science data with missing values: A case study on the factors influencing beach litter in Shimane Prefecture, Japan. Marine Pollution Bulletin 191, 114948.

Tame A, Maruyama T, Ikuta T, Chikaraishi Y, Ogawa NO, Tsuchiya M, Takishita K, Tsuda M, Hirai M, Takaki Y, Ohkouchi N, Fujikura K, Yoshida T. 2023. mTORC1 regulates phagosome digestion of symbiotic bacteria for intracellular nutritional symbiosis in a deep-sea mussel. Science Advances 9, eadg8364.

Jimi N, Hookabe N, Fujimoto S, Kise H, Ogawa A, Tsuchiya M. 2023. Three species of Fauveliopsidae (Annelida) from the northwestern Pacific including a new species description. Plankton and Benthos Research 18(4), 178–184.
[2022]
Nakajima R, Miyama T, Kitahashi T, Isobe N, Nagano Y, Ikuta T, Oguri K, Tsuchiya M, Yoshida T, Aoki K, Maeda Y, Kawamura K, Suzukawa M, Yamauchi T, Ritchie H, Fujikura K, Yabuki A. 2022. Plastic after an extreme storm: The typhoon-induced response of micro- and mesoplastics in coastal waters. Frontiers in Marine Science 8, 806952.

Toue R, Fujita K, Tsuchiya M, Chikaraishi Y, Sasaki Y, Ohkouchi N, 2022. Trophic niche separation of two non-spinose planktonic foraminifers Neogloboquadrina dutertrei and Pulleniatina obliquiloculata. Progress in Earth and Planetary Science 9, 20.

[2021]
Hayward BW, Holzmann M, Pawlowski J, Parker J, Kaushik T, Toyofuku-Suzuki M, Tsuchiya M. 2021. Molecular and morphological taxonomy of living Ammonia and related taxa (Foraminifera) and their biogeography. Micropaleontology 67, 109–314.

Ikuta T, Nakajima R, Tsuchiya M, Chiba S, Fujikura K. 2021. Interdecadal distribution of persistent organic pollutants in deep-sea chemosynthetic bivalves. Frontiers in Marine Science 8, 751848.

Kitahashi T, Nakajima R, Nomaki H, Tsuchiya M, Yabuki A, Yamaguchi S, Zhu C, Kanaya Y, Lindsay DJ, Chiba S, Fujikura K. 2021. Development of robust models for rapid classification of microplastic polymer types based on near infrared hyperspectral images. Analytical Methods 13, 2215–2222.

Nakajima R, Tsuchiya M, Yabuki A, Masuda S, Kitahashi T, Nagano Y, Ikuta T, Isobe N, Nakata H, Ritchie H, Oguri K, Osafune S, Kawamura K, Suzukawa M, Yamauchi T, Iijima K, Yoshida T, Chiba S, Fujikura K. 2021. Massive occurrence of benthic plastic debris at the abyssal seafloor beneath the Kuroshio Extension, the Northwest Pacific. Marine Pollution Bulletin 166, 112188.

Nomaki H, Chen C, Oda K, Tsuchiya M, Tame A, Uematsu K, Isobe N. 2021. Abundant Chitinous Structures in Chilostomella (Foraminifera, Rhizaria) and Their Potential Functions. Journal of Eukaryotic Microbiology 68, e12828.

Nomaki H, Rastelli E, Alves A, Suga H, Ramos S, Kitahashi T, Tsuchiya M, Ogawa NO, Matsui Y, Seike K, Miyamoto N, Corinaldesi C, Manea E, Ohkouchi N, Danovaro R, Nunoura T, Amaro T. 2021. Abyssal fauna, benthic microbes, and organic matter quality across a range of trophic conditions in the western Pacific Ocean. Progress in Oceanography 195, 102591.

Nomaki H, Rastelli E, Ogawa NO, Matsui Y, Tsuchiya M, Manea E, Corinaldesi C, Hirai M, Ohkouchi N, Danovaro R, Nunoura T, Amaro T. 2021. In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change. Global Change Biology 27, 6139–6155.

Nurlatifah, Yamauchi T, Nakajima R, Tsuchiya M, Yabuki A, Kitahashi T, Nagano Y, Isobe N, Nakata H. 2021. Plastic additives in deep-sea debris collected from the western North Pacific and estimation for their environmental loads. Science of the Total Environment 768, 144537.

Salonen I, Chronopoulou P-M, Nomaki H, Langlet D, Tsuchiya M, Koho KA, 2021. 16S rRNA gene metabarcoding indicates characteristic microbiomes in different deep-sea benthic foraminiferal species. Fronitiers in Microbiology 12, 694406.

Tsuchiya M, Nomaki H. 2021. Rapid response of the giant protist xenophyophores (Foraminifera, Rhizaria) to organic matter supply at abyssal depths revealed by an in situ dual stable isotope labeling experiment. Deep Sea Research I 176, 103608.

Zhu C, Kanaya Y, Tsuchiya M, Nakajima R, Nomaki H, Kitahashi T, Fujikura K. 2021. Optimization of a hyperspectral imaging system for rapid detection of microplastics down to 100 μm. MethodsX 8, 101175.

[2020]
Tsuchiya M, Miyawaki S, Oguri K, Toyofuku T, Tame A, Uematsu K, Takeda K, Sakai Y, Miyake H, Maruyama T. 2020. Acquisition, Maintenance, and Ecological Roles of Kleptoplasts in Planoglabratella opercularis (Foraminifera, Rhizaria). Frontiers in Marine Science 7, 585.

Xing D, Choi B, Takizawa Y, Fan R, Sugaya S, Tsuchiya M, Ohkouchi N, Chikaraishi Y. 2020. Trophic hierarchy of coastal marine fish communities viewed via compound-specific isotopic analysis of amino acids. Marine Ecology Progresss Series 652, 137–144.

Zhu C, Kanaya Y, Nakajima R, Tsuchiya M, Nomaki H, Kitahashi T, Fujikura K. 2020. Characterization of marine microplastics on filter substrates based on hyperspectral imaging. Environment Pollution 263, 114296.

[2019]
Hayward BW, Holzmann M, Tsuchiya M. 2019. Combined molecular and morphological taxonomy of the beccarii/T3 clade of the foraminiferal genus Ammonia. Journal of foraminiferal Research 49, 367–389.

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. 2019. Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth. The ISME journal 13, 1899–1910.

Nakajima R, Lindsay DJ, Tsuchiya M, Matsui R, Kitahashi T, Fujikura K, Fukushima T. 2019. A small, stainless-steel sieve optimized for laboratory beaker-based extraction of microplastics from environmental samples. MethodsX 6, 1677–1682.

Nakajima R, Tsuchiya M, Lindsay DJ, Kitahashi T, Fujikura K, Fukushima T. 2019. A new small device made of glass for separating microplastics from marine and freshwater sediments. PeerJ, 7, e7915.

Tsuchiya M, Nomaki H, Kitahashi T, Nakajima R, Fujikura K. 2019. Sediment sampling with a core sampler equipped with aluminum tubes and an onboard processing protocol to avoid plastic contamination. MethodsX 6, 2662–2668.

[2018]
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.

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.

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.

Kitahashi T, Watanabe H, Tsuchiya M, Yamamoto Hideyuki, Yamamoto Hiroyuki. 2018. A new method for acquiring images of meiobenthic images using the FlowCAM. MethodsX 5, 1330–1335.

Tsuchiya M, Chikaraishi Y, Nomaki H, Sasaki Y, Tame A, Uematsu K, Ohkouchi N. 2018. Compound-specific isotope analysis of benthic foraminifer amino acids suggests microhabitat variability in rocky-shore environments. Ecology and Evolution 8, 8380–8395.

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.

[2017]
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 8, 14145.

[2016]
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.

[2015]
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.

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.

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]
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.

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.

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.

[2013]
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]
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.

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.

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.

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]
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]
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.

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]
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.

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]
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]
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.

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]
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.

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]
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.

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]
Kitazato H, Tsuchiya M, Takahara K. 2000. Recognition of breeding populations in foraminifera: an example using the genus Glabratella. Paleontological Research 4, 1‒15.

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.

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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