{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T05:57:26Z","timestamp":1785563846088,"version":"3.56.0"},"reference-count":34,"publisher":"Japanese Society of Microbial Ecology","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microb. Environ.","Microbes Environ.","Microbes and environments"],"published-print":{"date-parts":[[2026]]},"DOI":"10.1264\/jsme2.me26008","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T22:11:30Z","timestamp":1785363090000},"page":"n\/a","source":"Crossref","is-referenced-by-count":0,"title":["Oxic Subseafloor Microbial Communities Retain Anabolic Capacity under both Oxic and Oxygen-depleted Conditions"],"prefix":"10.1264","volume":"41","author":[{"given":"Mako","family":"Takada","sequence":"first","affiliation":[{"name":"Atmosphere and Ocean Research Institute, The University of Tokyo"},{"name":"Graduate School of Frontier Sciences, The University of Tokyo"},{"name":"Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Motoo","family":"Ito","sequence":"additional","affiliation":[{"name":"Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu Ying","family":"Wee","sequence":"additional","affiliation":[{"name":"University of Southern California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason B.","family":"Sylvan","sequence":"additional","affiliation":[{"name":"Texas A&amp;M University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosalind M.","family":"Coggon","sequence":"additional","affiliation":[{"name":"University of Southampton"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily R.","family":"Estes","sequence":"additional","affiliation":[{"name":"Texas A&amp;M University"},{"name":"Now at National Science Foundation"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William P.","family":"Gilhooly III","sequence":"additional","affiliation":[{"name":"Indiana University Indianapolis"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Tulane University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masataka","family":"Aizawa","sequence":"additional","affiliation":[{"name":"Hokkaido University of Education"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susumu","family":"Yoshizawa","sequence":"additional","affiliation":[{"name":"Atmosphere and Ocean Research Institute, The University of Tokyo"},{"name":"Graduate School of Frontier Sciences, The University of Tokyo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Morono","sequence":"additional","affiliation":[{"name":"Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"336","reference":[{"key":"1","doi-asserted-by":"crossref","unstructured":"Bar-On, Y.M., Phillips, R., and Milo, R. (2018) The biomass distribution on Earth. Proc Natl Acad Sci U S A               115: 6506\u20136511.","DOI":"10.1073\/pnas.1711842115"},{"key":"2","doi-asserted-by":"crossref","unstructured":"Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., et al. (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol               37: 852\u2013857.","DOI":"10.1038\/s41587-019-0209-9"},{"key":"3","doi-asserted-by":"crossref","unstructured":"Bradley, J.A., Arndt, S., Amend, J.P., Burwicz, E., Dale, A.W., Egger, M., et al. (2020) Widespread energy limitation to life in global subseafloor sediments. Sci Adv               6: eaba0697.","DOI":"10.1126\/sciadv.aba0697"},{"key":"4","doi-asserted-by":"crossref","unstructured":"Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., and Holmes, S.P. (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods               13: 581\u2013583.","DOI":"10.1038\/nmeth.3869"},{"key":"5","doi-asserted-by":"crossref","unstructured":"Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J               6: 1621\u20131624.","DOI":"10.1038\/ismej.2012.8"},{"key":"6","doi-asserted-by":"crossref","unstructured":"Coggon, R.M., Teagle, D.A.H., Sylvan, J.B., Reece, J., Estes, E.R., Williams, T.J., et al. (2024a) Expedition 390\/393 methods. In <i>Proceedings of the International Ocean Discovery Program<\/i>. International Ocean Discovery Program. https:\/\/doi.org\/10.14379\/iodp.proc.390393.102.2024","DOI":"10.14379\/iodp.proc.390393.102.2024"},{"key":"7","doi-asserted-by":"crossref","unstructured":"Coggon, R.M., Teagle, D.A.H., Sylvan, J.B., Reece, J., Estes, E.R., Williams, T.J., et al. (2024b) Site U1559. In <i>Proceedings of the International Ocean Discovery Program<\/i>. International Ocean Discovery Program. https:\/\/doi.org\/10.14379\/iodp.proc.390393.109.2024","DOI":"10.14379\/iodp.proc.390393.109.2024"},{"key":"8","doi-asserted-by":"crossref","unstructured":"D\u2019Hondt, S., Inagaki, F., Zarikian, C.A., Abrams, L.J., Dubois, N., Engelhardt, T., et al. (2015) Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments. Nat Geosci               8: 299\u2013304.","DOI":"10.1038\/ngeo2387"},{"key":"9","doi-asserted-by":"crossref","unstructured":"Dixon, P. (2003) VEGAN, a package of R functions for community ecology. J Veg Sci               14: 927\u2013930.","DOI":"10.1111\/j.1654-1103.2003.tb02228.x"},{"key":"10","doi-asserted-by":"crossref","unstructured":"Estes, E.R., Pockalny, R., D\u2019Hondt, S., Inagaki, F., Morono, Y., Murray, R.W., et al. (2019) Persistent organic matter in oxic subseafloor sediment. Nat Geosci               12: 126\u2013131.","DOI":"10.1038\/s41561-018-0291-5"},{"key":"11","doi-asserted-by":"crossref","unstructured":"Fuchs, G. (2011) Alternative pathways of carbon dioxide fixation: insights into the early evolution of life?               Annu Rev Microbiol               65: 631\u2013658.","DOI":"10.1146\/annurev-micro-090110-102801"},{"key":"12","doi-asserted-by":"crossref","unstructured":"Goethals, V., Vanwinsen, N., Mermans, F., De Gand, S., Boon, N., Van de Wiele, T., et al. (2025) An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting and extraction bias in sorted microbial communities. bioRxiv.               https:\/\/doi.org\/10.1101\/2025.11.13.688239","DOI":"10.1101\/2025.11.13.688239"},{"key":"13","doi-asserted-by":"crossref","unstructured":"Gormanns, P., Reckow, S., Poczatek, J.C., Turck, C.W., and Lechene, C. (2012) Segmentation of multi-isotope imaging mass spectrometry data for semi-automatic detection of regions of interest. PLoS One               7: e30576.","DOI":"10.1371\/journal.pone.0030576"},{"key":"14","doi-asserted-by":"crossref","unstructured":"Hoshino, T., Doi, H., Uramoto, G.-I., W\u00f6rmer, L., Adhikari, R.R., Xiao, N., et al. (2020) Global diversity of microbial communities in marine sediment. Proc Natl Acad Sci U S A               117: 27587\u201327597.","DOI":"10.1073\/pnas.1919139117"},{"key":"15","doi-asserted-by":"crossref","unstructured":"H\u00fcgler, M., and Sievert, S.M. (2011) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann Rev Mar Sci               3: 261\u2013289.","DOI":"10.1146\/annurev-marine-120709-142712"},{"key":"16","doi-asserted-by":"crossref","unstructured":"Jalaluddin, F.M., Ahmerkamp, S., Marchant, H.K., Meyer, V., Koren, K., and Kuypers, M.M.M. (2025) Microenvironments on individual sand grains enhance nitrogen loss in coastal sediments. Sci Rep               15: 16384.","DOI":"10.1038\/s41598-025-00755-3"},{"key":"17","doi-asserted-by":"crossref","unstructured":"Kallmeyer, J., Pockalny, R., Adhikari, R.R., Smith, D.C., and D\u2019Hondt, S. (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci U S A               109: 16213\u201316216.","DOI":"10.1073\/pnas.1203849109"},{"key":"18","doi-asserted-by":"crossref","unstructured":"Lever, M.A., Rogers, K.L., Lloyd, K.G., Overmann, J., Schink, B., Thauer, R.K., et al. (2015) Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev               39: 688\u2013728.","DOI":"10.1093\/femsre\/fuv020"},{"key":"19","doi-asserted-by":"publisher","unstructured":"Lipp, J.S., Morono, Y., Inagaki, F., and Hinrichs, K.-U. (2008) Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature               454: 991\u2013994.","DOI":"10.1038\/nature07174"},{"key":"20","doi-asserted-by":"crossref","unstructured":"Magnabosco, C., Lin, L.-H., Dong, H., Bomberg, M., Ghiorse, W., Stan-Lotter, H., et al. (2018) The biomass and biodiversity of the continental subsurface. Nat Geosci               11: 707\u2013717.","DOI":"10.1038\/s41561-018-0221-6"},{"key":"21","doi-asserted-by":"crossref","unstructured":"McMurdie, P.J., and Holmes, S. (2013) phyloseq: an R package for reproducible interactive anal\u00adysis and graphics of microbiome census data. PLoS One               8: e61217.","DOI":"10.1371\/journal.pone.0061217"},{"key":"22","doi-asserted-by":"crossref","unstructured":"Morono, Y., Terada, T., Masui, N., and Inagaki, F. (2009) Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J               3: 503\u2013511.","DOI":"10.1038\/ismej.2009.1"},{"key":"23","doi-asserted-by":"crossref","unstructured":"Morono, Y., and Inagaki, F. (2010) Automatic slide-loader fluorescence microscope for discriminative enumeration of subseafloor life. Sci Drill               9: 32\u201336.","DOI":"10.5194\/sd-9-32-2010"},{"key":"24","doi-asserted-by":"crossref","unstructured":"Morono, Y., Terada, T., Nishizawa, M., Ito, M., Hillion, F., Takahata, N., et al. (2011) Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci U S A               108: 18295\u201318300.","DOI":"10.1073\/pnas.1107763108"},{"key":"25","doi-asserted-by":"crossref","unstructured":"Morono, Y., Terada, T., Kallmeyer, J., and Inagaki, F. (2013) An improved cell separation technique for marine subsurface sediments: applications for high-throughput anal\u00adysis using flow cytometry and cell sorting: Counting and sorting cells from marine sediments. Environ Microbiol               15: 2841\u20132849.","DOI":"10.1111\/1462-2920.12153"},{"key":"26","doi-asserted-by":"crossref","unstructured":"Morono, Y., Terada, T., Hoshino, T., and Inagaki, F. (2014) Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities. Appl Environ Microbiol               80: 1985\u20131994.","DOI":"10.1128\/AEM.04150-13"},{"key":"27","doi-asserted-by":"crossref","unstructured":"Morono, Y., Ito, M., Hoshino, T., Terada, T., Hori, T., Ikehara, M., et al. (2020) Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years. Nat Commun               11: 3626.","DOI":"10.1038\/s41467-020-17330-1"},{"key":"28","doi-asserted-by":"crossref","unstructured":"Orsi, W.D., Coolen, M.J.L., Wuchter, C., He, L., More, K.D., Irigoien, X., et al. (2017) Climate oscillations reflected within the microbiome of Arabian Sea sediments. Sci Rep               7: 6040.","DOI":"10.1038\/s41598-017-05590-9"},{"key":"29","doi-asserted-by":"crossref","unstructured":"Orsi, W.D. (2018) Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol               16: 671\u2013683.","DOI":"10.1038\/s41579-018-0046-8"},{"key":"30","doi-asserted-by":"crossref","unstructured":"Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., et al. (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods               9: 676\u2013682.","DOI":"10.1038\/nmeth.2019"},{"key":"31","doi-asserted-by":"crossref","unstructured":"Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods               9: 671\u2013675.","DOI":"10.1038\/nmeth.2089"},{"key":"32","doi-asserted-by":"crossref","unstructured":"Tengberg, A., Hovdenes, J., Andersson, H.J., Brocandel, O., Diaz, R., Hebert, D., et al. (2006) Evaluation of a lifetime-based optode to measure oxygen in aquatic systems. Limnol Oceanogr Methods               4: 7\u201317.","DOI":"10.4319\/lom.2006.4.7"},{"key":"33","doi-asserted-by":"crossref","unstructured":"Trembath-Reichert, E., Morono, Y., Ijiri, A., Hoshino, T., Dawson, K.S., Inagaki, F., et al. (2017) Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proc Natl Acad Sci U S A               114: E9206\u2013E9215.","DOI":"10.1073\/pnas.1707525114"},{"key":"34","doi-asserted-by":"crossref","unstructured":"Whitman, W.B., Coleman, D.C., and Wiebe, W.J. (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A               95: 6578\u20136583.","DOI":"10.1073\/pnas.95.12.6578"}],"container-title":["Microbes and Environments"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/jsme2\/41\/3\/41_ME26008\/_pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T05:01:28Z","timestamp":1785560488000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/jsme2\/41\/3\/41_ME26008\/_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":34,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026]]}},"URL":"https:\/\/doi.org\/10.1264\/jsme2.me26008","relation":{},"ISSN":["1342-6311","1347-4405"],"issn-type":[{"value":"1342-6311","type":"print"},{"value":"1347-4405","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"article-number":"ME26008"}}