読んだ本まとめ 2013年7月 Book memo (July. 2013)

2013年7月に読んだ本の一言感想とリンク、印象的な一節の記録。10冊。

『60年代日本SFベスト集成』（筒井康隆 編）

『わたしを離さないで』（カズオ・イシグロ 著）

『果しなき流れの果に』（小松左京 著）

『火星ダーク・バラード』（上田早夕里 著）

『ヴァリス』（フィリップ・K・ディック 著）

『てのひらの宇宙　星雲賞短編SF傑作選』（大森望 編）

『2001年宇宙の旅　決定版』（アーサー・C・クラーク 著）

『2010年宇宙の旅　新版』（アーサー・C・クラーク 著）

『アリの巣をめぐる冒険 未踏の調査地は足下に』（丸山宗利 著）

『われらをめぐる海』（レイチェル・カースン 著）

特に気になった新着論文 2013年6月 New Papers (June 2013)

1.    The acceleration of oceanic denitrification during deglacial warming

Galbraith, E.D., Kienast, M., Galbraith, E.D., Kienast, M., Albuquerque, A.L., et al.

Nature Geoscience. doi:10.1038/ngeo1832, Published online 02 June 2013

2.    Influence of sulfate reduction rates on the Phanerozoic sulfur isotope record

Leavitt, W.D., Halevy, I., Bradley, A.S., Johnston, D.T.

Proceedings of the National Academy of Sciences of the United States of America. Published online June 3, 2013, doi: 10.1073/pnas.1218874110

3.    Iron traps terrestrially derived dissolved organic matter at redox interfaces

Riedel, T., Zak, D., Biester, H., Dittmar, T.

Proceedings of the National Academy of Sciences of the United States of America. Published online before print June 3, 2013, doi: 10.1073/pnas.1221487110

4.    Evidence for reactive reduced phosphorus species in the early Archean ocean

Pasek, M.A., Harnmeijer, J.P., Buick, R., Gull, M., Atlas, Z.

Proceedings of the National Academy of Sciences of the United States of America. Published online before print June 3, 2013, doi: 10.1073/pnas.1303904110

5.    Life in the "Plastisphere": Microbial communities on plastic marine debris

Zettler, E.R., Mincer, T.J., Amaral-Zettler, L.A.

Environmental Science & Technology. Publication Date (Web): June 7, 2013, DOI: 10.1021/es401288x

6.    What Caused the Rise of Atmospheric O2?

Kasting, J.F.

Chemical Geology. Available online 7 June 2013, doi:10.1016/j.chemgeo.2013.05.039

7.    Intensification of open-ocean oxygen depletion by vertically migrating animals

Bianchi, D., Galbraith, E.D., Carozza, D.A., Mislan, K.A.S., Stock, C.A.

Nature Geoscience. Published online 09 June 2013, doi:10.1038/ngeo1837

8.    Functional and compositional succession of bacterioplankton in response to a gradient in bioavailable dissolved organic carbon

Dinasquet, J., Kragh, T., Schrøter, M.-L., Søndergaard, M., Riemann, L.

Environmental Microbiology. Accepted manuscript online: 11 JUN 2013, DOI: 10.1111/1462-2920.12178

9.    Gene expression in the deep biosphere

Orsi, W.D., Edgcomb, V.P., Christman, G.D., Biddle, J.F.

Nature. Published online 12 June 2013, doi:10.1038/nature12230

10.  Pan genome of the phytoplankton Emiliania underpins its global distribution

Read, B.A., Kegel, J., Klute, M.J., Kuo, A., Lefebvre, S.C., et al.

Nature. Published online 12 June 2013, doi:10.1038/nature12221

11.  Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs

Mayumi, D., Dolfing, J., Sakata, S., Maeda, H., Miyagawa, Y., Ikarashi, M., Tamaki, H., Takeuchi, M., Nakatsu, C.H., Kamagata, Y.

Nature Communications 4, 1998. Published 13 June 2013, doi:10.1038/ncomms2998

12.  Temperature effects on carbon-specific respiration rate and sinking velocity of diatom aggregates – potential implications for deep ocean export processes

Iversen, M.H., Ploug, H.

Biogeosciences 10, 4073–4085. Published: 20 June 2013

13.  Influence of bedrock mineral composition on microbial diversity in a subglacial environment

Mitchell, A.C., Lafreniere, M.J., Skidmore, M.L., Boyd, E.S.

Geology. First published online June 20, 2013, doi: 10.1130/G34194.1

14.  Smart Three-Dimensional Gas Chromatography

Chen, D., Seo, J.H., Liu, J., Kurabayashi, K., Fan, X.

Analytical Chemistry. Publication Date (Web): June 21, 2013, DOI: 10.1021/ac401152v

15.  Manganese-oxidizing photosynthesis before the rise of cyanobacteria

Johnson, J.E., Webb, S.M., Thomas, K., Ono, S., Kirschvink, J.L., Fischer, W.W.

Proceedings of the National Academy of Sciences of the United States of America. Published online before print June 24, 2013, doi: 10.1073/pnas.1305530110

16.  Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

Swan, B.K., Tupper, B., Sczyrba, A., Lauro, F.M., Martinez-Garcia, M., et al.

Proceedings of the National Academy of Sciences of the United States of America. Published online before print June 25, 2013, doi: 10.1073/pnas.1304246110

17.  On the potential role of marine calcifiers in glacial-interglacial dynamics

Omta, A.W., Van Voorn, G.A.K., Rickaby, R.E.M., Follows, M.J.

Global Biogeochemical Cycles. Accepted manuscript online: 29 JUN 2013, DOI: 10.1002/gbc.20060

18.  Taxon-specific response of marine nitrogen fixers to elevated carbon dioxide concentrations

Hutchins, D.A., Fu, F.-X., Webb, E.A., Walworth, N., Tagliabue, A.

Nature Geoscience. Published online 30 June 2013, doi:10.1038/ngeo1858

読んだ本まとめ 2013年6月 Book memo (June. 2013)

2013年6月に読んだ本の一言感想とリンク、印象的な一節の記録（Twitter＋追記）。渡米前後でドタバタしていたので、5冊だけ。今月では特に『逆転世界』がすごかった。プリーストの最高傑作という宣伝文句もうなずける。

『どんがらがん』（アヴラム・デイヴィッドスン 著）
『もうすぐ絶滅するという紙の書物について』（ウンベルト・エーコ／ジャン=クロード・カリエール 著）

『幸福の遺伝子』（リチャード・パワーズ 著）

『逆転世界』（クリストファー・プリースト 著）

『都市と都市』（チャイナ・ミエヴィル 著）

読んだ本まとめ 2013年5月 Book memo (May. 2013)

2013年5月に読んだ本の一言感想とリンク、印象的な一節の記録（Twitter＋追記）。7冊。今月は特に『極北』が収穫。読後しばらくぼーっとしてしまった。

『鳥類学者　無謀にも恐竜を語る』（川上和人 著）

『極北』（マーセル・セロー 著）

『ゴースト・オブ・ユートピア』（樺山三英 著）

『オープンサイエンス革命』（マイケル・ニールセン 著）

『チョッキー』（ジョン・ウィンダム 著）

『職業としての学問』（マックス・ウェーバー 著）

『読書について』（アルトゥール・ショーペンハウアー 著）

特に気になった新着論文 2013年5月 New Papers (May 2013)

1.    Widespread Production of Extracellular Superoxide by Heterotrophic Bacteria

Diaz, J.M., Hansel, C.M., Voelker, B.M., Mendes, C.M., Andeer, P.F., Zhang, T.

Science. Published Online May 2 2013, DOI: 10.1126/science.1237331

2.    Molecular biological and isotopic biogeochemical prognoses of the nitrification-driven dynamic microbial nitrogen cycle in hadopelagic sediments

Nunoura, T., Nishizawa, M., Kikuchi, T., Tsubouchi, T., Hirai, M., Koide, O., Miyazaki, J., Hirayama, H., Koba, K., Takai, K.

Environmental Microbiology. Accepted manuscript online: 6 MAY 2013, DOI: 10.1111/1462-2920.12152

3.    Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12

Vo, J., Inwood, W., Hayes, J.M., Kustu, S.

Proceedings of the National Academy of Sciences of the United States of America. Published online May 6, 2013, doi: 10.1073/pnas.1216683110

4.    Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene

Coolen, M.J.L., Orsi, W.D., Balkema, C., Quince, C., Harris, K., Sylva, S.P., Filipova-Marinova, M., Giosan, L.

Proceedings of the National Academy of Sciences of the United States of America. Published online before print May 6, 2013, doi: 10.1073/pnas.1219283110

5.    An Improved Cell Separation Technique for Marine Subsurface Sediments: Applications for High-throughput Analysis Using Flow Cytometry and Cell Sorting

Morono, Y., Terada, T., Kallmeyer, J., Inagaki, F.

Environmental Microbiology. Accepted manuscript online: 13 MAY 2013, DOI: 10.1111/1462-2920.12153

6.    Non-cyanobacterial nifH phylotypes in the North Pacific Subtropical Gyre detected by flow-cytometry cell sorting

Bombar, D., Turk-Kubo, K.A., Robidart, J., Carter, B.J., Zehr, J.P.

Environmental Microbiology Reports. Accepted manuscript online: 14 MAY 2013

7.    Role of sea ice in global biogeochemical cycles: emerging views and challenges

Vancoppenolle, M., Meiners, K.M., Michel, C., Bopp, L., Brabant, F., Carnat, G., Delille, B., Lannuzel, D., Madec, G., Moreau, S., Tison, J.-L., Van der Merwe, P.

Quaternary Science Reviews. Available online 15 May 2013

8.    Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

Von Bergen, M., Jehmlich, N., Taubert, M., Vogt, C., Bastida, F., Herbst, F.-A., Schmidt, F., Richnow, H.-H., Seifert, J.

The ISME Journal. Online publication 16 May 2013

9.    Synchrotron-based mass spectrometry to investigate the molecular properties of mineral-organic associations

Liu, S.Y., Kleber, M., Takahashi, L.K., Nico, P., Keiluweit, M., Ahmed, M.

Analytical Chemistry 85, 6100–6106. Publication Date (Web): May 16, 2013

10.  Biogeochemical effects of atmospheric oxygen concentration, phosphorus weathering, and sea-level stand on oceanic redox chemistry: Implications for greenhouse climates

Ozaki, K., Tajika, E.

Earth and Planetary Science Letters. Available online 17 May 2013

11.  Stable isotope probing of amino sugars - a promising tool to assess microbial interactions in soils

Bodé, S., Fancy, R., Boeckx, P.

Rapid Communications in Mass Spectrometry 27, 1367–1379. published online: 17 MAY 2013

12.  Natural Organic Matter as Global Antennae for Primary Production

Van Trump, J.I., Rivera Vega, F.J., Coates, J.D.

Astrobiology 13, 476–482. May 17, 2013

13.  Long term geological record of a global deep subsurface microbial habitat in sand injection complexes

Parnell, J., Boyce, A.J., Hurst, A., Davidheiser-Kroll, B., Ponicka, J.

Scientific Reports 3, 1828. Published 17 May 2013

14.  Degradation of terrestrially derived macromolecules in the Amazon River

Ward, N.D., Keil, R.G., Medeiros, P.M., Brito, D.C., Cunha, A.C., Dittmar, T., Yager, P.L., Krusche, A. V., Richey, J.E.

Nature Geoscience. Published online 19 May 2013, doi:10.1038/ngeo1817.

15.  Characterization of laboratory analogs of interstellar/cometary organic residues using very high resolution mass spectrometry

Danger, G., Orthous-Daunay, F.-R., De Marcellus, P., Modica, P., Vuitton, V., Duvernay, F., Flandinet, L., Le Sergeant d’Hendecourt, L., Thissen, R., Chiavassa, T.

Geochimica et Cosmochimica Acta 118, 184–201. Available online 21 May 2013

16.  Evidence and a conceptual model for the co‑occurrence of nitrogen fixation and denitrification in heterotrophic marine sediments

Fulweiler, R., Brown, S., Nixon, S., Jenkins, B.

Marine Ecology Progress Series 482, 57–68. Published May 22 2013.

17.  Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

Baker, B.J., Sheik, C.S., Taylor, C.A., Jain, S., Bhasi, A., Cavalcoli, J.D., Dick, G.J.

The ISME Journal. advance online publication 23 May 2013; doi: 10.1038/ismej.2013.85

18.  Hydrogen generation from low-temperature water–rock reactions

Mayhew, L.E., Ellison, E.T., McCollom, T.M., Trainor, T.P., Templeton, A.S.

Nature Geoscience 6, 478–484. Published online 26 May 2013

19.  Heme b in marine phytoplankton and particulate material from the North Atlantic Ocean

Honey, D., Gledhill, M., Bibby, T., Legiret, F., Pratt, N., Hickman, A., Lawson, T., Achterberg, E.

Marine Ecology Progress Series 483, 1–17. Published May 30 2013.

特に気になった新着論文 2013年4月 New Papers (Apr. 2013)

1.    Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

Nishizawa, M., Koba, K., Makabe, A., Yoshida, N., Kaneko, M., Hirao, S., Ishibashi, J., Yamanaka, T., Shibuya, T., Kikuchi, T., Hirai, M., Miyazaki, J., Nunoura, T., Takai, K., 2013.

Geochimica et Cosmochimica Acta. Available online 3 April 2013

2.    Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones

Purkamo, L., Bomberg, M., Nyyssönen, M., Kukkonen, I., Ahonen, L., Kietäväinen, R., Itävaara, M.

FEMS Microbiology Ecology. Accepted manuscript online: 8 APR 2013

3.    Zinc–amino acid complexes are more stable than free amino acids in saline and washed soils

Ghasemi, S., Khoshgoftarmanesh, A.H., Afyuni, M., Hadadzadeh, H., Schulin, R.

Soil Biology and Biochemistry 63, 73–79. Available online 9 April 2013

4.    Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs

Brazelton, W.J., Morrill, P.L., Szponar, N., Schrenk, M.O.

Applied and Environmental Microbiology. Published ahead of print 12 April 2013

5.    Abiotic methane on Earth

Etiope, G., Lollar, B., 2013.

Reviews of Geophysics. Accepted manuscript online: 12 APR 2013

6.    Marine denitrification rates determined from a global 3-D inverse model

DeVries, T., Deutsch, C., Rafter, P.A., Primeau, F.

Biogeosciences 10, 2481–2496. Published: 15 April 2013

7.    Biotic and abiotic degradation of alkenones and implications for paleoproxy applications: A review

Rontani, J.-F., Volkman, J.K., Prahl, F.G., Wakeham, S.G.

Organic Geochemistry 59, 95–113. Available online 16 April 2013

8.    Global Charcoal Mobilization from Soils via Dissolution and Riverine Transport to the Oceans

Jaffe, R., Ding, Y., Niggemann, J., Vahatalo, A. V., Stubbins, A., Spencer, R.G.M., Campbell, J., Dittmar, T.

Science 340, 345–347. 19 April 2013

9.    The effect of a quorum-quenching enzyme on leaf litter decomposition

Strickland, M.S., McCulley, R.L., Bradford, M.A.

Soil Biology and Biochemistry 64, 65–67. Available online 24 April 2013

10.  Long-term sedimentary recycling of rare sulphur isotope anomalies

Reinhard, C.T., Planavsky, N.J., Lyons, T.W., 2013.

Nature. Published online 24 April 2013

11.  Tracking the Fate of Microbially Sequestered Carbon Dioxide in Soil Organic Matter

Hart, K.M., Kulakova, A.N., Allen, C.C.R., Simpson, A.J., Oppenheimer, S.F., Masoom, H., Courtier-Murias, D., Soong, R., Kulakov, L.A., Flanagan, P. V, Murphy, B.T., Kelleher, B.P.

Environmental Science & Technology. April 24, 2013, DOI: 10.1021/es3050696

12.  Molecular level characterization of methyl sugars in marine high molecular weight dissolved organic matter

Panagiotopoulos, C., Repeta, D.J., Mathieu, L., Rontani, J.-F., Sempéré, R.

Marine Chemistry. Available online 25 April 2013

13.  Organophosphonates revealed: new insights into the microbial metabolism of ancient molecules

McGrath, J.W., Chin, J.P., Quinn, J.P.

Nature Reviews Microbiology 11, 412–419. Published online 29 April 2013

特に気になった新着論文 2013年3月 New Papers (Mar. 2013)

1.    Evidence for a persistent microbial seed bank throughout the global ocean

Gibbons, S.M., Caporaso, J.G., Pirrung, M., Field, D., Knight, R., Gilbert, J.A.

Proceedings of the National Academy of Sciences of the United States of America, Published online March 4, 2013, doi: 10.1073/pnas.1217767110

→”Everything is everywhere, but the environment selects” という海洋微生物学の有名な仮説を支持する兆候。海洋1地点について深くシーケンスして微生物群集組成を調べていくと、全球の海洋微生物群集データをカバーする率がどんどん上がっていく。シーケンス速度が現在のペースで上がっていけば、あと3年もすれば実際に検証可能らしい。

2.    Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater

Mailloux, B.J., Trembath-Reichert, E., Cheung, J., Watson, M., Stute, M., Freyer, G.A., Ferguson, A.S., Ahmed, K.M., Alam, M.J., Buchholz, B.A., Thomas, J., Layton, A.C., Zheng, Y., Bostick, B.C., Van Geen, A., 2013

Proceedings of the National Academy of Sciences of the United States of America 110, 5331–5335. Published online before print March 4, 2013

→バングラデシュの地下の微生物のDNAの放射性炭素濃度を測定すると、周囲の堆積物の有機物よりも何千年も若い。地上から溶存有機物が移流してきて、地下微生物の代謝を支えている？

3.    Dark inorganic carbon fixation sustains the functioning of benthic deep-sea ecosystems

Molari, M., Manini, E., Dell'Anno, A., 2013.

Global Biogeochemical Cycles 27, 212–221.

4.    Evidence for Microbial Carbon and Sulfur Cycling in Deeply Buried Ridge Flank Basalt

Lever, M.A., Rouxel, O., Alt, J.C., Shimizu, N., Ono, S., Coggon, R.M., Shanks, W.C., Lapham, L., Elvert, M., Prieto-Mollar, X., Hinrichs, K.-U., Inagaki, F., Teske, A.

Science 339, 1305–1308. 15 March 2013

5.    Anaerobic oxidation of methane in an iron-rich Danish freshwater lake sediment

Nordi, K.Á., Thamdrup, B., Schubert, C.J.

Limnology and Oceanography 58, 546–554. March 17 2013.

6.    Strong latitudinal patterns in the elemental ratios of marine plankton and organic matter

Martiny, A.C., Pham, C.T.A., Primeau, F.W., Vrugt, J.A., Moore, J.K., Levin, S.A., Lomas, M.W.

Nature Geoscience 6, 279–283 (2013) Published online 17 March 2013

7.    High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth

Glud, R.N., Wenzhöfer, F., Middelboe, M., Oguri, K., Turnewitsch, R., Canfield, D.E., Kitazato, H.

Nature Geoscience 6, 284–288. Published online 17 March 2013

8.    Using ammonium pore water profiles to assess stoichiometry of deep remineralization processes in methanogenic continental margin sediments

Burdige, D.J., Komada, T.

Geochemistry Geophysics Geosystems. Accepted manuscript online: 18 MAR 2013, DOI: 10.1002/ggge.20117

9.    Changes in global nitrogen cycling during the Holocene epoch

McLauchlan, K.K., Williams, J.J., Craine, J.M., Jeffers, E.S.

Nature 495, 352–355. Published online 20 March 2013

10.  Quantifying the degradation of organic matter in marine sediments: A review and synthesis

Arndt, S., Jørgensen, B.B., LaRowe, D.E., Middelburg, J.J., Pancost, R., Regnier, P.

Earth-Science Reviews. Available online 21 March 2013, doi:10.1016/j.earscirev.2013.02.008

11.  Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance

Kuzyakov, Y., Xu, X.

New Phytologist 198, 656–669. published online: 22 MAR 2013

12.  Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations

Xie, S., Lipp, J.S., Wegener, G., Ferdelman, T.G., Hinrichs, K.-U.

Proceedings of the National Academy of Sciences of the United States of America 110, 6010–6014. Published online before print March 25, 2013

13.  X-ray analysis on the nanogram to microgram scale using porous complexes

Inokuma, Y., Yoshioka, S., Ariyoshi, J., Arai, T., Hitora, Y., Takada, K., Matsunaga, S., Rissanen, K., Fujita, M.

Nature 495, 461–466. Published online 27 March 2013

14.  Predominant archaea in marine sediments degrade detrital proteins

Lloyd, K.G., Schreiber, L., Petersen, D.G., Kjeldsen, K.U., Lever, M.A., Steen, A.D., Stepanauskas, R., Richter, M., Kleindienst, S., Lenk, S., Schramm, A., Jørgensen, B.B.

Nature 496, 215–218. Published online 27 March 2013

15.  Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

Clemmensen, K.E., Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A., Wallander, H., Stenlid, J., Finlay, R.D., Wardle, D.A., Lindahl, B.D.

Science 339, 1615–1618. 29 March 2013