Selected Papers

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1. Matsumura, E*., Kato, H., Hara, S., Ohbayashi, T., Ito, K., Shingubara, R., Kawakami, T., Mitsunobu, S., Saeki, T., Tsuda, S., Minamisawa, K. and Wagai R.* (2025). "Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism." Frontiers in Microbiology Volume 16 - 2025.

2. Wang, Z., Wang, Y., Xing, D., Wagai R., Zheng, J., Zhang, H., Fan B. and Feng W. (2025). "Divergent effects of soil organic matter and carbonate on soil aggregation and structure in arid regions." CATENA 257: 109196.

3. Doetterl, S., Berhe, A. A., Heckman, K., Lawrence, C., Schnecker, J., Vargas, R., Vogel C. and Wagai, R. (2025). "A landscape-scale view of soil organic matter dynamics." Nature Reviews Earth & Environment 6(1): 67-81.

4. von Fromm, S. F., Jungkunst, H. F., Amenkhienan, B., Hall, S. J., Georgiou, K., Pries, C. H., Montaño-López, F., Quesada, C. A., Rasmussen, C., Schrumpf, M., Singh, B., Thompson, A., Wagai, R. and Fiedler, S. (2025). "Moisture and soil depth govern relationships between soil organic carbon and oxalate-extractable metals at the global scale." Biogeochemistry 168(1): 20.

5. Suzuki, A., Yanai, J., Paneru, P., Vista, S. P., Wagai, R., Tanaka, S., Arai, H., Tayasu, I. and Nakao A. (2025). "Effect of Elevation and Mineralogy on the Amount and Turnover of Fractionated Organic Carbon in Paddy Soils in Nepal." European Journal of Soil Science 76(2): e70073.

6. Mitsunobu, S*., Wagai, R*., Shimada, H., Kato, H., Ito, K., Sato, S., Hayatsu, M., Minamisawa, K. (2025) First microscale data on depth profiles of microbial N₂O reduction, O2 availability, and pore networks inside contrasting single soil aggregates. Soil Biology and Biochemistry 2025 Vol. 202 Pages 109684

7. Ichinose, Y., Matsui, K., Fukumasu, J., Matsuura, S., Takata, Y*., Wagai, R. (2024) How do reactive aluminum and iron phases control soil organic carbon and phosphate adsorption capacity in agricultural topsoils across Japan? Soil Science and Plant Nutrition

8. Arai, M., Ikazaki, K*., Anzai, T., Celestial, V. P., Tumbay, J. V., Santillana, I. S., Wagai, R. (2024) Protective role of reactive aluminum phases to stabilize soil organic matter against long-term cultivation in the humid tropics under volcanic influence. Soil Science and Plant Nutrition

9. Hara, S*., Kakizaki, K., Bamba, M., Itakura, M., Sugawara, M., Suzuki, A., Sasaki, Y., Takeda, M., Tago, K., Ohbayashi, T., Aono, T., Aoyagi, L. N., Shimada, H., Shingubara, R., Masuda, S., Shibata,  A., Shirasu, K., Wagai, R., Akiyama, H., Sato, S., Minamisawa K*. (2024) Does Rhizobial Inoculation Change the Microbial Community in Field Soils? A‍ ‍Comparison with Agricultural Land-use Changes. Microbes and Environments 39: Issue 3 Pages ME24006

10. Mizukami, C*., Mukai, M., Wagai, R., Kitayama, K. (2024) Intraspecific variations in activities of four classes of fine root phosphatases in Quercus serrata, a dominant deciduous oak, occurring across a wide soil phosphorus gradient in Japan. Plant and Soil: 1-17

11. Qin, Q*., Wagai, R., Aoyagi, R., Titin, J., Kitayama, K. (2024) Destructive selective logging in tropical forests causes soil carbon loss through forest degradation and soil redox change. Forest Ecology and Management 551: 121555. 

12. Pramono, A., Adriany, T. A., Viandari, A., Susilawati, N., Lina H., Wihardjaka, A., Sutriadi, M., Yusuf, W. A., Ariani, M., Wagai, R., Tokida, T. (2024). Higher rice yield and lower greenhouse gas emissions with cattle manure amendment is achieved by alternate wetting and drying. Soil Science and Plant Nutrition 70(2): 129-138.

13. Arai, M*., Wagai, R. (2023) Does rice paddy management increase soil organic carbon in the warm temperate and tropical regions? Geoderma Regional 36: e00738.

14. Hayashi, R*., Maie, N., Wagai, R., Hirano, Y., Matsuda, Y., Okamoto, T., Wada, R., Tanikawa, T. (2023). Soil acidity accelerates soil organic matter decomposition in Cryptomeria japonica stands and Chamaecyparis obtusa stands. Plant and Soil.

15. Wagai, R*., Yang, P-T., Kaiser, K. (2023) Interfacial reactions of microorganisms with minerals and organic matter. Encyclopedia of Soils in the Environment (Second Edition). M. J. Goss and M. Oliver. Oxford, Academic Press: 458-469. https://doi.org/10.1016/B978-0-12-822974-3.00232-9

16. Watanabe, T*., Harsh, J.B., Wagai, R. (2023). Short-range ordered aluminosilicates. Encyclopedia of Soils in the Environment (Second Edition). M. J. Goss and M. Oliver. Oxford, Academic Press: 121-134. https://doi.org/10.1016/B978-0-12-822974-3.00223-8

17. Zheng, J*., Fujii, K., Koba, K., Wanek, W., Müller, C., Jansen-Willems, A. B., Nakajima, Y., Wagai, R., Canarini, A. (2023) “Revisiting process-based simulations of soil nitrite dynamics: Tighter cycling between nitrite and nitrate than considered previously” Soil Biology and Biochemistry 178: 108958.

18. Shimada, H*., Ito, K., Kogure, T., Asano, M., Yamashita, S., Takeichi, Y., Takahashi, Y., Wagai, R. (2023). "Applicability of Focused-Ion-Beam-Based Thin Sectioning for STXM-NEXAFS Analysis of Carbon Species: Examination of Kaolinite-Bacteria Composite." Chemistry Letters.  https://www.journal.csj.jp/doi/abs/10.1246/cl.230098

19. Hayashi, R., Maie, N., Wagai, R., Hirano, Y., Matsuda, Y., Makita, N., Mizoguchi, T., Wada, R., Tanikawa, T*. (2023) “An increase of fine-root biomass in nutrient-poor soils increases soil organic matter but not soil cation exchange capacity” Plant and Soil, 1-22

20. Shimada*. H., Wagai, R., Inoue, Y., Tamura, K., Asano, M. (2022) “Millennium timescale carbon stability in an Andisol: How persistent are organo-metal complexes?” Geoderma 417, 115820

21. Nitzsche, K. N., Kayler, Z. E*., Premke, K., Gessler, A., Wagai, R. (2022) “Divergent roles of iron and aluminum in sediment organic matter association at the terrestrial–aquatic interface” Biogeochemistry 157 (3), 355-378

22. Heckman K*., Hicks Pries, C. E*., Lawrence, C. R., Rasmussen, C., Crow, S. E., Hoyt, A. M., von Fromm, S. F., Zheng S., Stoner S., McGrath, C., Beem‐Miller, J., Berhe, A. A., Blankinship, J. C., Keiluweit, M., Marín‐Spiotta, E., Monroe, J. G., Plante, A. F., Schimel, J., Sierra, C. A., Thompson, A., Wagai, R. (2022) “Beyond bulk: Density fractions explain heterogeneity in global soil carbon abundance and persistence” Global Change Biology 28 (3), 1178-1196

23. Iizumi, T*., Hosokawa, N., Wagai, R. (2021) “Soil carbon-food synergy: sizable contributions of small-scale farmers” CABI Agriculture and Bioscience 2 (1), 1-15

24. Takamoto, A., Hashimoto, Y., Asano, M., Noguchi, K., Wagai, R. (2021) Distribution and chemical species of phosphorus across density fractions in Andisols of contrasting mineralogy Geoderma 395: 115080.

25. Matsui, K., Takata,Y*., Matsuura, S., Wagai, R. (2021) Soil organic carbon was more strongly linked with soil phosphate fixing capacity than with clay content across 20,000 agricultural soils in Japan: a potential role of reactive aluminum revealed by soil database approach. Soil Science and Plant Nutrition 67(3): 233-242.

26. Wagai, R*., Kajiura, M, Asano, M. (2020). "Iron and aluminum association with microbially processed organic matter via meso-density aggregate formation across soils: organo-metallic glue hypothesis." SOIL 6(2): 597-627. doi.org/10.5194/soil-6-597-2020

27. Lawrence, C. R*., Beem-Miller, J., Hoyt, A. M., Monroe, G., Sierra, C. A., Stoner, S., Heckman, K., Blankinship, J. C., Crow, S. E., McNicol, G., Trumbore, S., Levine, P. A., Vindušková, O., Todd-Brown, K., Rasmussen, C., Hicks Pries, C. E., Schädel, C., McFarlane, K., Doetterl, S., Hatté, C., He, Y., Treat, C., Harden, J W., Torn, M. S., Estop-Aragonés, C., Asefaw Berhe, A., Keiluweit, M., Della Rosa Kuhnen, Á., Marin-Spiotta, E., Plante, A F., Thompson, A., Zheng, S., Schimel, J. P., Vaughn, L. JS., von Fromm, S. F., Wagai, R.(2020). "An open-source database for the synthesis of soil radiocarbon data: International Soil Radiocarbon Database (ISRaD) version 1.0." Earth Syst. Sci. Data 12(1): 61-76. doi.org/10.5194/essd-12-61-2020

28. Nakatsuka, H*., Karasawa, T., Ohkura, T., Wagai, R. (2020) Soil faunal effect on plant litter decomposition in mineral soil examined by two in-situ approaches: Sequential density-size fractionation and micromorphology. Geoderma 357. doi.org/10.1016/j.geoderma.2019.113910

29. Shimoda, S*., Wagai, R. (2020) Ecosystem Dynamics After Abandonment of Rice Paddy Fields: Does Alien Plant Invasion Enhance Carbon Storage? Ecosystems 23, 617–629. doi.org/10.1007/s10021-019-00426-1

30. Iizumi, T*., Wagai, R. (2019) Leveraging drought risk reduction for sustainable food, soil and climate via soil organic carbon sequestration. Scientific Report 9. https://doi.org/10.1038/s41598-019-55835-y

31. Arai, M., Uramoto, G-I, Asano, M., Uematsu, K., Uesugi, K., Takeuchi, A., Morono, Y*., Wagai, R.* (2019) An improved method to identify osmium-stained organic matter within soil aggregate structure by electron microscopy and synchrotron X-ray micro-computed tomography. Soil and Tillage Research 191: 275-281

32. Uramoto, G-I, 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(1): 400

33. Nakao, A*., Tomita, M., Wagai, R., Tanaka, R., Yanai, J., Kosaki, T. (2019) Asian dust increases radiocesium retention ability of serpentine soils in Japan. Journal of Environmental Radioactivity 204: 86-94

34. Blankinship, J.C., Crow, S.E., Berhe, A.A., Druhan, J.L., Heckman, K.A., Keiluweit, M., Lawrence, C.R., Marín-Spiotta, E., Plante, A.F., Rasmussen, C., Schädel, C., Schimel, J.P.,  Sierra, C.A., Thompson, A., Wagai, R., Wieder, W.R. (2018) Improving understanding of soil organic matter dynamics by triangulating theories, measurements, and models. Biogeochemistry 140 (1):1–13. https://doi.org/10.1007/s10533-018-0478-2

35. Asano, M*., Wagai, R*., Yamaguchi, N., Takeichi, Y., Maeda, M., Suga, H., Takahashi, Y. (2018) In search of a binding agent: nano-scale evidence of preferential carbon associations with poorly-crystalline mineral phases in physically-stable-clay-sized aggregates. Soil Systems 2(2), 32; https://doi.org/10.3390/soilsystems2020032

36. Wagai, R., Kajiura, M., Uchida, M., Asano, M. (2018) Distinctive Roles of Two Aggregate Binding Agents in Allophanic Andisols: Young Carbon and Poorly-Crystalline Metal Phases with Old Carbon. Soil Systems 2(2), 29. https://doi.org/10.3390/soilsystems2020029

37. Tashiro, Y., Nakao, A., Wagai, R., Yanai, J., Kosaki, T. (2018) Inhibition of radiocesium adsorption on 2:1 clay minerals under acidic soil environment: Effect of organic matter vs. hydroxy aluminum polymer. Geoderma 319: 52-60.

38. Rasmuusen, C., Heckman, K., Wieder, W., Keiluweit, M., Lawrence, C., Berhe, A. A., Blankinship, S., Crow, S., Druhan, J., Pries, C. H., Marin-Spiotta, E., Plante, A., Schadel, C., Schimel, J., Sierra, C., Thompson, A., Wagai, R. (2018) Beyond clay: towards an improved set of variables for predicting soil organic matter content. Biogeochemistry 137 (3): 297-306. https://doi.org/10.1007/s10533-018-0424-3

39. Kajiura, M*., Minamikawa, K., Tokida, T., Shirato, Y., Wagai, R. (2018) Methane and nitrous oxide emissions from paddy fields in Japan: An assessment of controlling factor using an intensive regional data set. Agriculture, Ecosystems & Environment 252: 51-60

40. Yokoyama, D*., Mori, T., Wagai, R., Hiradate, S., Kitayama, K. (2018) Characteristics of phosphorus fractions in the soils derived from sedimentary and serpentinite rocks in lowland tropical rain forests, Borneo, Soil Science and Plant Nutrition 64:2, 218-221, DOI: 10.1080/00380768.2017.1421018

41. Ito, A*., and Wagai, R. (2017) Global distribution of clay-size minerals on land surface for biogeochemical and climatological studies. Scientific Data 4, 170103.

42. Kaneda, S*., Ohkubo, S., Wagai, R. and Yagasaki, Y. (2016) Soil temperature and moisture-based estimation of rates of soil aggregate formation by the endogeic earthworm Eisenia japonica. Biology and Fertility of Soils 52 (6), 789-797.

43. Miyamoto, K*., Wagai, R., Aiba, S., Nilus, R. (2016) Variation in the aboveground stand structure and fine-root biomass of Bornean heath (kerangas) forests in relation to altitude and soil nitrogen availability. Trees 30 (2), 385-394

44. Zahn, G*., Wagai, R., and Yonemura, S. (2016) The effects of amoebal bacterivory on carbon and nitrogen dynamics depend on temperature and soil structure interactions. Soil Biology and Biochemistry 94: 133-137.

45. Wagai, R*., Kajiura, M., Asano, M., Hiradate, S. (2015) Nature of soil organo-mineral assemblage examined by sequential density fractionation with and without sonication: Is allophanic soil different? Geoderma 241-242: 295-305.

46. Asano, M*., and Wagai, R. (2015). Distinctive organic matter pools among particle-size fractions detected by solid-state 13C-NMR, d13C and d 15N analyses only after strong dispersion in an allophanic Andisol. Soil Science and Plant Nutrition 61: 242-248.

47. Kajiura, M*., Wagai, R., Hayashi, K. (2015) Optimal thermolysis conditions for soil carbon storage on plant residue burning: modeling the trade-off between thermal decomposition and subsequent biodegradation. Journal of Environmental Quality 44:1-8.

48. Minamikawa, K*., Wagai, R., Nishimura, S., Yagi, K. (2015). Heterotrophic denitrification constrains the upper limit of dissolved N2O-nitrate concentration ratio in agricultural groundwater. Nutrient Cycling in Agroecosystems. DOI 10.1007/s10705-014-9668-z

49. Asano, M*., and Wagai, R. (2014) Evidence of aggregate hierarchy at micro to submicron scales in an allophanic Andisol. Geoderma 216: 62-74.

50. Wagai, R*., Mayer, L.M., Kitayama, K., Shirato, Y. (2013) Association of organic matter with iron and aluminum across a range of soils determined via selective dissolution techniques coupled with dissolved nitrogen analysis. Biogeochemistry 112: 95-109.

51. Shirato, Y*., Jomura, M., Wagai, R., Kondo, M., Tanabe, K., Uchida, M. (2013) Deviations between observed and RothC‐simulated Δ14C values despite improved IOM initialization. European Journal of Soil Science 64: 576-585.

52. Wagai, R*., Kishimoto-Mo, A.W., Yonemura, S., Shirato, Y., Hiradate, S., Yagasaki, Y. (2013) Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and microbial physiology. Global Change Biology, 19: 1114-1125. DOI: 10.1111/gcb.12112

53. Wagai, R*., and Kitayama, K. (2012) Soil organic matter storage in the tropical forests of Borneo: pedogenic controls and ecological implications. In: International Symposia: Land Degradation and Pedology; Land Degradation and Management Pedologist 55(3): 392-402.

54. Fushimi, A*., Wagai, R., Uchida, M., Hasegawa, S., Takahashi, K., Kondo, M., Hirabayashi, M., Morino, Y., Shibata, Y., Ohara, T., Kobayashi, S., Tanabe K. (2011) Radiocarbon (14C) diurnal variations in fine particles at sites downwind from Tokyo, Japan in summer, Environmental Science and Technology 45: 6784-6792.

55. Wagai, R*., Kitayama, K., Satomura, T., Fujinuma, R. and Balser, T.C. (2011) Interactive influences of climate and parent material on soil microbial community structure in Bornean tropical forest ecosystems. Ecological Research 26: 627–636.

56. Wagai, R*., Mayer, L.M. and Kitayama, K. (2009) Nature of “occluded” low-density fraction in soil organic matter studies: a critical review. Soil Science and Plant Nutrition 55: 13-25.

57. Sollins, P*., Kramer, M.G., Swanston, C., Lajtha, K., Filley, T., Aufdenkampe, A.K., Wagai, R.  and Bowden, R.D. (2009) Organic C and N stabilization across soils of contrasting mineralogy: further evidence from sequential density fractionation. Biogeochemistry 96:209-231.

58. Moritz, L.K.*, Liang, C., Wagai, R., Kitayama, K. and Balser T.C. (2009) Vertical distribution and accumulation of microbial residues in tropical forest soils formed from distinct parent materials. Biogeochemistry 92:83-94.

59. Wagai, R*., Mayer, L.M. and Kitayama, K. (2009) Extent and nature of organic coverage of soil mineral surfaces assessed by a gas sorption approach. Geoderma 149: 152-160.

60. Ushio, M*., Wagai, R., Balser, T. and Kitayama K. (2008) Variations in the soil microbial community composition of a tropical montane forest ecosystem: does tree species matter? Soil Biology and Biochemistry 40: 2699-2702.

61. Wagai, R*., Mayer, L.M., Kitayama, K. and Knicker H. (2008) Climate and parent material controls on organic matter storage in surface soils: A three-pool, density-separation approach. Geoderma 147: 23-33.

62. Wagai, R*. and Mayer L.M. (2007) Significance of hydrous iron oxides for sorptive stabilization of organic carbon in a range of soils. Geochimica et Cosmochimica Acta 71: 25-35.

63. Mayer, L.M*., Schick, L.L., Hardy, K., Wagai, R. and McCarthy J.F. (2004) Organic matter content of small mesopores in sediments and soils. Geochimica et Cosmochimica Acta 68: 3863-3872.

64. Kitayama, K*., Aiba, S., Takyu, M., Majalap-Lee, N. and Wagai, R. (2004) Soil phosphorus fractionation and phosphorus-use efficiency of a Bornean tropical montane rain forest during soil ageing with podozolization. Ecosystems 7:259-274.

65. Wagai, R*. and Sollins, P. (2002) Biodegradation and regeneration of water-soluble organic carbon in a forest soil: leaching column study. Biology and Fertility of Soils 35:18-26.

66. Ohno, T*., Horesh, M.Y., Merritt, K. and Wagai, R. (2002) Calcium and pH effects on salicylic acid phytotoxicity. Allelopathy Journal 9: 19-25.

67. Norton, S*., Wagai, R., Navratil, T., Kaste, J.M. and Rissberger, F.A. (2000) Response of a first-order stream in Maine to short-term in-situ acidification.  Hydrology and Earth System Sciences 4: 383-391.

68. Wagai, R*., Brye, K., Gower, S.T., Norman, J.M. and Bundy, L. (1998) Land use and environmental factors influencing soil surface CO2 flux and microbial biomass in natural and managed ecosystems in southern Wisconsin. Soil Biology and Biochemistry 30: 1501-1509.