Japanese/ English

Fumito Shiraishi

Dr. rer. nat. (University of Göttingen)

Research areas:
Geomicrobiology, Geochemistry, Sedimentology, Paleontology,
etc.

Contact:
Earth and Planetary Systems Science Program,
Graduate School of Advanced Science and Engineering,
Hiroshima University

Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima,
739-8526 Japan

Sutdy career
1998-2002 Bachelor, Department of Earth and Planetary Systems Science, Hiroshima University
2002-2004 Master, Department of Earth and Planetary Systems Science, Hiroshima University
2004-2005 Doctor, Department of Earth and Planetary Systems Science, Hiroshima University
2005-2008 Doctor, Department of Geoscience and Geography, University of Göttingen
2008 Dr. rer. nat. (summa cum laude), University of Göttingen

Job career
2005-2008 Doctoral research fellow, University of Göttingen
2008-2009 Postdoctoral fellow, Hiroshima University
2009-2011 JSPS research fellow
2011-2014 JAMSTEC invited researcher
2011-2020 Assistant Professor, Hiroshima University
2020-recent Associate Professor, Hiroshima University

Research activity

Publication (peer-reviewed)

[1] Shiraishi F., Kano A. (2004) Composition and spatial distribution of microencrusters and microbial crusts in upper Jurassic-lowermost Cretaceous reef limestone (Torinosu Limestone, Southwest Japan). Facies 50, 217-227.

[2] Shiraishi F., Yoshidomi K. (2005) Depositional environment of the upper Jurassic-lower Cretaceous reef limestone in western Yamaguchi Prefecture, Southwest Japan. The Journal of the Geological Society of Japan 111, 21-28. (Japanese with English abstract)

[3] Shiraishi F., Tanimizu M., Ishikawa T., Matsuoka J., Murayama M., Kano A. (2005) Strontium isotopic age of the Torinosu Limestone in Niyodo Village, Kochi Prefecture, SW Japan. The Journal of the Geological Society of Japan 111, 610-623 (Japanese with English abstract)

[4] Shiraishi F., Bissett A., de Beer D., Reimer A., Arp G. (2008) Photosynthesis, respiration and exopolymer calcium-binding in biofilm calcification (Westerhöfer and Deinschwanger Bach, Germany). Geomicrobiology Journal 25, 83-94. <Top 10 Most-Cited Articles from Geomicrobiology Journal 2007-2009>

[5] Bissett A., de Beer D., Schoon R., Shiraishi F., Reimer A., Arp G. (2008) Microbial mediation of stromatolite formation in karst-water creeks. Limnology and Oceanography 53, 1159–1168.

[6] Shiraishi F., Reimer A., Bissett A., de Beer D., Arp G. (2008) Microbial effects on biofilm calcification, ambient water chemistry and stable isotope records (Westerhöfer Bach, Germany). Palaeogeography, Palaeoclimatology, Palaeoecology 262, 91-106.

[7] Shiraishi F., Zippel B., Neu T.R., Arp G. (2008) In situ detection of bacteria in calcified biofilms using FISH and CARD–FISH. Journal of Microbiological Methods 75, 103-108.

[8] Bissett A., Reimer A., de Beer D., Shiraishi F., Arp G. (2008) Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH. Applied and Environmental Microbiology 74, 6306-6312.

[9] Arp G., Bissett A., Brinkmann N., Cousin S., de Beer D., Friedl T., Mohr K., Neu T., Reimer A., Shiraishi F., Stackebrandt E., Zippel B. (2010) Tufa-forming biofilms of German karstwater creeks: Microorganisms, exopolymers, hydrochemistry and calcification. Geological Society, London, Special Publications 336, 83-118.

[10] Shiraishi F., Okumura T., Takahashi Y., Kano A. (2010) Influence of microbial photosynthesis on tufa stromatolite formation and ambient water chemistry, SW Japan. Geochimica et Cosmochimica Acta 74, 5289-5304.

[11] Shiraishi F. (2011) Photosynthesis-induced stromatolite formation in the freshwater creeks. In: Reitner J., Queric N., Arp G. (eds.) Advances in Geobiology of Stromatolite Formation, Lecture Notes in Earth Sciences 131, 135-140.

[12] Okumura T., Takashima C., Shiraishi F., Nishida S., Yukimura K., Naganuma T., Koike H., Arp G., Kano A. (2011) Microbial processes forming daily lamination in an aragonite travertine, Nagano-yu hot spring, southwest Japan. Geomicrobiology Journal 28, 135-148.

[13] Kano A., Kunimitsu Y., Togo T., Takashima T., Shiraishi F., Wang W. (2011) The evolution of animal multicellularity stimulated by dissolved organic carbon in early Ediacaran ocean: DOXAM hypothesis. Island Arc 20, 280-293.

[14] Shiraishi F. (2012) Chemical conditions favoring photosynthesis-induced CaCO3 precipitation and implications for microbial carbonate formation in the ancient ocean. Geochimica et Cosmochimica Acta 77, 157-174.

[15] Mitsunobu S., Shiraishi F., Makita H., Orcutt B.N., Kikuchi S., Jørgensen B.B., Takahashi Y. (2012) Bacteriogenic Fe(III) (oxyhydr)oxides characterized by synchrotron microprobe coupled with spatially-resolved phylogenetic analysis. Environmental Science & Technology 46, 3304-3311.

[16] Okumura T., Takashima C., Shiraishi F., Akmaluddin, Kano A. (2012) Textural transition in an aragonite travertine formed under various flow conditions at Pancuran Pitu, Central Java, Indonesia. Sedimentary Geology 265-266, 195-209.

[17] Zhang G., Smith-Duque C., Tang S., Li H., Zarikian C., D'Hondt S., Inagaki F., IODP Expedition 329 Scientists (2012) Geochemistry of basalts from IODP site U1365: Implications for magmatism and mantle source signatures of the mid-Cretaceous Osbourn Trough. Lithos 144-145, 73-87.

[18] D’Hondt S., Inagaki F., Alvarez Zarikian C.A., the IODP Expedition 329 Scientific Party (2013) IODP Expedition 329: Life and habitability beneath the seafloor of the South Pacific Gyre. Scientific Drilling 15, 4-10.

[19] Mitsunobu S., Hamamura N., Kataoka T., Shiraishi F. (2013) Arsenic attenuation in geothermal streamwater coupled with biogenic arsenic(III) oxidation. Applied Geochemistry 35, 154-160.

[20] Okumura T., Takashima C., Shiraishi F., Nishida S., Kano A. (2013) Processes forming daily lamination in a microbe-rich travertine under low flow condition at the Nagano-yu Hot Spring, Southwestern Japan. Geomicrobiology Journal 30, 910-927.

[21] D'Hondt S., Inagaki F., Alvarez Zarikian C.A., Abrams L.J., Dubois N., Engelhardt T., Evans H., Ferdelman T., Gribsholt B., Harris R.N., Hoppie B.W., Hyun J.-H., Kallmeyer J., Kim J., Lynch J.E., McKinley C.C., Mitsunobu S., Morono Y., Murray R.W., Pockalny R., Sauvage J., Shimono T., Shiraishi F. Smith D.C., Smith-Duque C.E., Spivack A.J., Steinsbu B.O., Suzuki Y., Szpak M., Toffin L., Uramoto G., Yamaguchi Y.T., Zhang G., Zhang X.-H., Ziebis W. (2015) Presence of oxygen and aerobic communities from seafloor to basement in deep-sea sediments. Nature Geoscience 8, 299-304.

[22] Kikuchi S., Makita H., Konno U., Shiraishi F., Ijiri A., Takai K., Maeda M., Takahashi Y. (2016) Limited reduction of ferrihydrite encrusted by goethite in a freshwater sediment. Geobiology 14, 374–389.

[23] Shiraishi F., Mitsunobu S., Suzuki K., Hoshino T., Morono Y., Inagaki F. (2016) Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles, Earth and Planetary Science Letters 447, 10-20.

[24] Shiraishi F., Hanzawa Y., Okumura T., Tomioka N., Kodama Y., Suga H., Takahashi Y., Kano A. (2017) Cyanobacterial exopolymer properties differentiate microbial carbonate fabrics. Scientific Reports 7, 11805.

[25] Shiraishi F., Nakao K., Takashima C., Kano A., Itai T. (2018) Fe(II) oxidation processes at the surface of bacterially colonized iron deposits. Chemical Geology 476, 161-170.

[26] Tsukiji Y., Azuma Y., Shiraishi F., Shibata M., Noda Y. (2018) New ornithopod footprints from the Lower Cretaceous Kitadani Formation, Fukui, Japan: ichnotaxonomical implications. Cretaceous Research84, 510-514.

[27] Shiraishi F., Eno Y., Nakamura Y., Hanzawa Y., Asada J., Bahniuk A.M. (2019) Relative influence of biotic and abiotic processes on travertine fabrics, Satono-yu hot spring, Japan. Sedimentology 66, 459-479.

[28] Shiraishi F., Ohnishi S., Hayasaka Y., Hanzawa Y., Takashima C., Okumura T., Kano A. (2019) Potential photosynthetic impact on phosphate stromatolite formation after the Marinoan glaciation: Paleoceanographic implications. Sedimentary Geology 380, 65-82.

[29] Tsukiji Y., Shiraishi F., Shibata M., Azuma Y. (2019) A diverse theropod footprint assemblage from the Lower Cretaceous Kitadani Formation, Tetori Group, central Japan. Cretaceous Research 97, 16−33.

[30] Sakai S., Yang D., Yasuda T., Akiyama K., Kuga T., Kano A., Shiraishi F., Amekawa S., Ohtsuka S., Nakaguchi K., Yamaguchi S. (2019) Pulsed terahertz radiation for sensitive quantification of carbonate minerals.ACS Omega 4, 2702−2707.

[31] Uramoto G., Morono Y., Tomioka N., Wakaki S., Nakada R., Wagai R., Uesugi K., Takeuchi A., Hoshino M., Suzuki Y., Shiraishi F., Mitsunobu S., Suga H., Takeichi Y., Takahashi Y., Inagaki F. (2019) Significant contribution of subseafloor microparticles to the global manganese budget. Nature Communications 10, 400.

[32] Shiraishi F., Matsumura Y., Chihara R., Okumura T., Itai T., Kashiwabara T., Kano A., Takahashi Y. (2019) Depositional processes of microbially colonized manganese crusts, Sambe hot spring, Japan. Geochimica et Cosmochimica Acta 258, 1−18.

[33] Yanagawa K., Shiraishi F., Tanigawa Y., Maeda T., Mustapha N.A., Owari S., Tomaru H., Matsumoto R., Kano A. (2019) Endolithic microbial habitats hosted in carbonate nodules currently forming within sediment at a high methane flux site in the Japan Sea. Geosciences 9, 463.

[34] Mitsunobu S., Toda M., Hamamura N., Shiraishi F., Tominaga Y., Sakata M. (2020) Millimeter-scale topsoil layer blocks arsenic migration in flooded paddy soil. Geochimica et Cosmochimica Acta 274, 211-227.

[35] Paul P.P., Chakraborty P.P., Shiraishi F., Das K., Kamei A., Bhattacharya S. (2020) Clue on ocean redox condition from trace element and rare earth element (REE) composition of iron formation and carbonate rocks from the late Paleoproterozoic Morar Formation, Gwalior Group, central India. Journal of Mineralogical and Petrological Sciences 115, 175-191.

[36] Shiraishi F., Morikawa A., Kuroshima K., Amekawa S., Yu T.-L., Shen C.-C., Kakizaki Y., Kano A., Asada J., Bahniuk A.M. (2020) Genesis and diagenesis of travertine, Futamata hot spring, Japan. Sedimentary Geology 405, 105706.

[37] Shiraishi F., Omori T., Tomioka N., Motai S., Suga H., Takahashi Y. (2020) Characteristics of CaCO3 nucleated around cyanobacteria: implications for calcification process. Geochimica et Cosmochimica Acta 285, 55-69.

[38] Shiraishi F., Hanzawa Y., Nakamura Y., Eno Y., Morikawa A., de Mattos R.F., Asada J., Cury L.F., Bahniuk A.M. (2021) Abiotic and biotic processes controlling travertine deposition: Insights from eight hot springs in Japan. Sedimentology 69, 592-623.

[39] Shiraishi F., Hanzawa Y., Asada J., Cury L.F., Bahniuk A.M. (2022) Microbial influences on tufa deposition in a tropical climate. Sedimentary Geology 427, 106045.

[40] Koyano S., Shiraishi F., Miyairi Y., Yokoyama Y., Fujita K. (2022) Microscale evolution of reefal microbialites. IAS Special Publication, 49, 39-67.

[41] Kuroshima K., Fujita M., Kakizaki Y., Shiraishi F. (2022) Relationship among paleosol types, depositional settings, and paleoclimates in Tetori group (Lower Cretaceous, central Japan). Island Arc 31, e12445.

[42] Shiraishi F., Chihara R., Tanimoto R., Tanaka K., Takahashi Y. (2022) Microbial influences on manganese deposit formation at Yunotaki Fall, Japan. Island Arc 31, e12448.

[43] Sharma A., Das K., Chakraborty P., Shiraishi F., Kayama M. (2022) U-Pb zircon geochronology of a pyroclastic rock from the Parsoi Formation, Mahakoshal Group: Implications towards basin age and related tectonics in Central Indian Tectonic Zone. Geological Journal, in press.

[44] Shiraishi F., Hanzawa Y., Asada J., Cury L.F., Bahniuk A.M. (2023) Decompositional processes of microbial carbonates in Lagoa Vermelha, Brazil. Journal of Sedimentary Research 93, 202-211.

[45] Shiraishi F., Akimoto T., Tomioka N., Takahashi Y., Matsumoto R., Snyder G.T. (2023) Microbial traces found in microdolomite associated with seep-related shallow gas hydrate. Frontiers in Earth Science 11, 1188142.

[46] Shiraishi F., Akimoto T., Tomioka N., Motai S., Takahashi Y. (2023) Formation processes of paper-thin raft and coated bubble: calcium carbonate deposition at gas-water interface. Sedimentary Geology 456, 106514.

Other publications

[1] Reitner J., Shiraishi F., Schumann G. (2006) Biosignetures in rocks and minerals. Sediment2006: 21th Meeting of Sedimentologists/4th Meeting of SEPM Central European Section, Short Course W3.

[2] Arp G., Shiraishi F., Hoffmann F., Reitner J. (2006) Biomineralization and microbialites - Frontiers in carbonate sedimentology. 17th International Sedimentological Congress, Short Course 2, 16 p.

[3] Kano A., Kakizaki Y., Shiraishi F., Kawai T., Matsuoka J. (2006) Uppermost Jurassic limestone mounds and the recent tufa deposits in southern Shikoku Province. ISC 2006 Excursion guidebook B08. 13 p.

[4] Expedition 329 Scientists (2011) South Pacific Gyre: Subseafloor life and habitability in the South Pacific Gyre. IODP Preliminary Report 329, doi:10.2204/iodp.pr.329.2011.

[5] Dubois N., Smith-Duque C., IODP Expedition 329 Shipboard Science Party (2011) IODP Expedition 329: South Pacific Gyre Microbiology. UK IODP Newsletter 36, 7-11.

[6] D'Hondt S., Inagaki F., Alvarez Zarikian C.A., the Expedition 329 Scientists (2011) South Pacific Gyre Subseafloor Life. The Proceedings of the Integrated Ocean Drilling Program 329, doi:10.2204/iodp.proc.329.109.2011.

[7] Mitsunobu S., Shiraishi F. A new method to observe in situ microbe-metal-mineral interaction by micro-XAFS-FISH technique, SPring-8 Research Frontiers 2012, in press.

Talks in congresses

[1] Shiraishi F., Kano A. (2003) The spatial distribution and microenvironment of calcareous microbes in uppermost Jurassic-lowermost Cretaceous Torinosu Group. Abstracts of the 110th Annual Meeting of Geological Society of Japan (Shizuoka), 241. (Poster)

[2] Shiraishi F., Yoshidomi K., Kano A. (2004) Depositional environment of the uppermost Jurassic-lowermost Cretaceous reef limestone in western Yamaguchi Prefecture, Southwest Japan. Abstracts of the Meeting of the Chapter of Southeast Japan, Geological Society of Japan (Higashi-hiroshima), 10.

[3] Shiraishi F. (2004) Quantitative analysis and depositional environments of the microbialite in the Torinosu Limestone. Abstracts of the 111th Annual Meeting of Geological Society of Japan (Chiba), 203. (poster)

[4] Shiraishi F., Tanimizu M., Ishikawa T., Matsuoka J., Murayama M. (2005) Strontium isotopic age of the Torinosu Limestone in Niyodo Village, Kochi Prefecture, SW Japan. Abstracts of the Meeting of the Chapter of Southeast Japan, Geological Society of Japan (Kagoshima), 21.

[5] Shiraishi F., Kano A. (2005) Microbialites and microencrusters in uppermost Jurassic-lowermost Cretaceous Torinosu Limestone (SW Japan). Abstracts of "System Earth-Biosphere Coupling", International Conference and Annual Meeting, Geologische Vereinigung (GV) Deutsche Gesellschaft für Geowissenschaften (DGG), Erlangen, Germany, 358.

[6] Shiraishi F., Reimer A., Bissett A., Bruns S., Mohr K., Cousin S., Päuker O., Brambilla E., Jonkers H., de Beer D., Stackebrandt E., Friedl T., Arp G. (2006) Microbial communities and tufa formation in karst-water creeks of Germany. Abstract of Sediment2006: 21th Meeting of Sedimentologists/4th Meeting of SEPM Central European Section, Göttingen, Germany, 155.

[7] Shiraishi F., Reimer A., Bissett A., Bruns S., Mohr K., Cousin S., Päuker O., Brambilla E., Jonkers H., de Beer D., Stackebrandt E., Friedl T., Arp G. (2006) Microbial communities and tufa formation in karst-water creeks of Germany. Abstract of 17th International Sedimentological Congress, Fukuoka, Japan, 135.

[8] Shiraishi F., Reimer A., Bissett A., Bruns S., Mohr K., Cousin S., Päuker O., Brambilla E., Jonkers H., de Beer D., Stackebrandt E., Friedl T., Arp G. (2006) Microbial communities and tufa formation in karst-water creeks of Germany. Abstracts of the 113th Annual Meeting of Geological Society of Japan (Kochi), 81.

[9] Shiraishi F. (2008) Stromatolite formation by photosynthesis. Abstracts of the 55th Annual Meeting of Geochemical Society of Japan (Tokyo), 291.

[10] Shiraishi F., Bissett A., de Beer D., Zippel B., Neu T.R., Reimer A., Arp G. (2008) Photosynthesis-induced stromatolite formation. Abstract of International Kalkowsky-Symposium, Göttingen, Germany, 122-123.

[11] Shiraishi F., Bissett A., de Beer D., Reimer A., Arp G. (2008) Photosynthesis-induced stromatolite formation. Abstract of 7th International Symposium for Subsurface Microbiology, Shizuoka, Japan, 40. (poster)

[12] Shiraishi F. (2009) Photosynthesis-induced calcite precipitation recognized from freshwater stromatolite. Abstracts of the 116th Annual Meeting of Geological Society of Japan (Okayama), 213. (poster)

[13] Shiraishi F. (2010) Calcite precipitation and stromatolite formation induced by photosynthetic bacteria. Japan Geoscience Union Meeting 2010 (Chiba), BBG005-21.

[14] Shiraishi F. (2011) Experimental paleontology of stromatolite. Abstracts of the Meeting of the Chapter of Southeast Japan, Geological Society of Japan (Hiroshima), 19.

[15] Shiraishi F. (2011) Role(s) of oxygenic photosynthesis in Precambrian stromatolite formation. Japan Geoscience Union Meeting 2011 (Chiba), U020-20.

[16] Shiraishi F. (2011) Experimental paleontology of stromatolite. Abstracts of the 118th Annual Meeting of Geological Society of Japan (Ibaraki), 105.

[17] Shiraishi F. (2012) Composition of carbonate chemical species in the Phanerozoic ocean estimated from fossil cyanobacteria. Japan Geoscience Union Meeting 2012 (Chiba), U04-18.

[18] Shiraishi F. (2012) Chemical conditions favoring photosynthesis-induced CaCO3 precipitation. 2012 ASLO Aquatic Sciences Meeting (Lake Biwa), 149.

[19] Shiraishi F. (2012) <Invited>Formation prosesses and appearance of microbialites. 1st meeting of Carbonate Subdivision in 2012, Exploration Technology Committee, The Japanese Association for Petroleum Technology (Tokyo).

Thesis

Professional Societies
The Geological Society of Japan, Palaeontological Society of Japan