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

特に気になった新着論文 2013年2月 New Papers (Feb. 2013)

ドタバタしていて更新が遅れていた新着論文紹介を復活させました。これまで月ごとの「特に気になった新着論文」は10本未満に抑えようとしていましたが、今後は、本数はあまり気にせず「これはちゃんと読んだ方がいいな」と個人的に思った論文を載せておくことにしました。

あと各論文の一言コメントも全部付けていると終わらなくて、いつまでも紹介を載せらなくなってしまうので、付けない場合も多くなります。各論文をちゃんと読んだら、随時追記するかも。

1.    Authigenic Carbonate and the History of the Global Carbon Cycle

Daniel P. Schrag, John. A. Higgins, Francis A. Macdonald, David T. Johnston

Science 1 February 2013: Vol. 339 no. 6119 pp. 540-543, DOI: 10.1126/science.1229578

→地球史における海洋溶存無機炭素（DIC）のd13Cの変動は、これまで海洋堆積物での有機炭素（低いd13C値を持つ）の埋没フラックスの変動が原因として考えられてきたけど、実は堆積物中自生炭酸塩の埋没フラックスも重要だという提案。特に嫌気的な海洋では、有機物が分解されて生成されたDIC（低いd13C値を持つ）が、堆積物中で自生炭酸塩を作りやすく、海洋DICの同位体マスバランスに有意に影響しうる。つまり、これまでの有機炭素埋没フラックスの復元は間違っている可能性がある。特に後期原生代や古生代、三畳紀などでは、極端に高いDICのd13C値が報告されており、その値は自生炭酸塩形成で説明できる？　有機炭素埋没フラックスの復元は、特に大気酸素濃度の復元に重要なので、この話が本当だとすると、地球史の描像が変わってくる可能性もあり、非常に重要。

（参考：東大TさんもBlogに解説記事を書いています）

2.    Anaerobic methane oxidation in low-organic content methane seep sediments

Pohlman, J.W., Riedel, M., Bauer, J.E., Canuel, E. a., Paull, C.K., Lapham, L., Grabowski, K.S., Coffin, R.B., Spence, G.D.

Geochimica et Cosmochimica Acta. Available online 4 February 2013

3.    The evolution of early diagenetic signals in Bering Sea subseafloor sediments in response to varying organic carbon deposition over the last 4.3Ma

Wehrmann, L.M., Arndt, S., März, C., Ferdelman, T.G., Brunner, B.

Geochimica et Cosmochimica Acta 109, 175–196. available online 8 February 2013

4.    Metaproteomic characterization of high molecular weight dissolved organic matter in surface seawaters in the South China Sea

Dong, H.-P., Wang, D.-Z., Xie, Z.-X., Dai, M.-H., Hong, H.-S.

Geochimica et Cosmochimica Acta 109, 51–61. available online 8 February 2013

5.    Abundant SAR11 viruses in the ocean

Zhao, Y., Temperton, B., Thrash, J.C., Schwalbach, M.S., Vergin, K.L., Landry, Z.C., Ellisman, M., Deerinck, T., Sullivan, M.B., Giovannoni, S.J.

Nature 494, 357–360. Published online 13 February 2013

→海洋に非常に優占するバクテリアであるSAR11グループ（Pelagibacter ubiqueなど）に感染するウイルスを単離。その遺伝子が海洋メタゲノムデータに多く存在することもわかった。SAR11が海洋中で非常に繁栄している理由として、これまで「ウイルス感染死を免れているから」という仮説があったが、今回の研究で棄却される。その代わりに、溶存態有機物の分解など、限られた資源を有効活用する能力に長けていることが、繁栄の理由と考えられる。

6.    Organic carbon export from the Greenland ice sheet

Bhatia, M.P., Das, S.B., Xu, L., Charette, M.A., Wadham, J.L., Kujawinski, E.B.

Geochimica et Cosmochimica Acta. Available online 14 February 2013

→グリーンランド氷床の融氷水の溶存態有機炭素（DOC）と懸濁態有機炭素（POC）。2010年にDOM組成の同定（by ESI-FT-ICR-MS）は報告していて（Bhatia et al., 2010, GCA）、今回はバルクで同位体組成分析。フラックスは大きな河川に匹敵するらしい。POCの方が多い。POCは濃度や放射性炭素濃度はあまり変わらないけれど、DOCはけっこう変わる。放射性炭素同位体的に“古い”けれど易分解性な有機炭素は、氷床の下の微生物が古い炭素を使って代謝しているのか、昔の有機物が氷床の下にそのまま残っているのか。

7.    Equatorial Upwelling Enhances Nitrogen Fixation in the Atlantic Ocean

Subramaniam, A., Mahaffey, C., Johns, W., Mahowald, N.

Geophysical Research Letters. DOI: 10.1002/grl.50250, Accepted manuscript online: 15 FEB 2013

8.    Directly coupled high-performance liquid chromatography-accelerator mass spectrometry measurement of chemically modified protein and peptides

Thomas, A.T., Stewart, B.J., Ognibene, T.J., Turteltaub, K.W., Bench, G.

Analytical Chemistry 85, 3644–3650. February 17, 2013

9.    Diatom microfossils from cretaceous and eocene sediments contain native silica precipitating long-chain polyamines

M. C. Bridoux, A. E. Ingalls

Geobiology, published online: 19 FEB 2013, DOI: 10.1111/gbi.12028

→珪藻のバイオマーカーである長鎖ポリアミン（LCPAs）を、白亜紀や始新世の地層から検出。LCPAsは、珪藻がシリカの殻を作るときに使う有機分子。しかも白亜紀の地層では、堆積物の全有機炭素や全窒素の大半を占めるらしく、海洋堆積物中での有機物の保存・埋没メカニズムとしても重要そう。殻に保護されて分解をまぬがれる？　古環境復元の新たなツールとして有望。Bさんはここ数年、分析法開発、現世珪藻群集の分析など、LCPAsに関する論文を立て続けに出している。1年前の学会ではさらに、LCPAsを単離して炭素・窒素同位体組成分析をやりたいようなことを言っていた。

10.  Microbial bioavailability regulates organic matter preservation in marine sediments

Koho, K. A., Nierop, K. G. J., Moodley, L., Middelburg, J. J., Pozzato, L., Soetaert, K., van der Plicht, J., and Reichart, G-J.

Biogeosciences, 10, 1131-1141, doi:10.5194/bg-10-1131-2013, 2013. Published: 20 February 2013

11.  Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

Kalvelage, T., Lavik, G., Lam, P., Contreras, S., Arteaga, L., Löscher, C.R., Oschlies, A., Paulmier, A., Stramma, L., Kuypers, M.M.M.

Nature Geoscience 6, 228–234. Published online 24 February 2013

12.  Methanogenic capabilities of ANME-archaea deduced from 13 C-labeling approaches

Bertram, S., Blumenberg, M., Michaelis, W., Siegert, M., Krüger, M., Seifert, R.

Environmental Microbiology. DOI: 10.1111/1462-2920.12112, Accepted manuscript online: 25 FEB 2013

→嫌気的メタン酸化アーキア（ANME）がメタン生成代謝を行えることの証拠？　黒海のANME-1とANME-2が優占する微生物マットを使って、13C同位体ラベル実験。二酸化炭素やメタノールを使ったメタン生成が検出された。特にANME-1はメタン無しでも生存可能らしい。嫌気的メタン酸化代謝がメタン生成代謝と同じ酵素システムを使う逆反応であることは最近実証されたけど、やはり同じ微生物が両方できるんだなー。メタノール絡みの代謝も面白そう。あと、ANME-1のバイオマーカーになる新しいGDGTs脂質も見つかったらしい。

13.  Deep-sea nutrient loss inferred from the marine dissolved N2/Ar ratio

Hamme, R.C., Emerson, S.R.

Geophysical Research Letters. Accepted manuscript online: 25 FEB 2013, DOI: 10.1002/grl.50275

14.  Dissolved organic nitrogen in the global surface ocean: Distribution and fate

Letscher, R.T., Hansell, D. A., Carlson, C. A., Lumpkin, R., Knapp, A. N.

Global Biogeochemical Cycles. DOI: 10.1029/2012GB004449, published online: 26 FEB 2013

15.  Dissolved organic carbon dynamics in anaerobic sediments of the Santa Monica Basin

Komada, T., Burdige, D.J., Crispo, S.M., Druffel, E.R.M., Griffin, S., Johnson, L., Le, D.

Geochimica et Cosmochimica Acta 110, 253–273. available online 27 February 2013

16.  Position-specific measurement of oxygen isotope ratios in cellulose: isotopic exchange during heterotrophic cellulose synthesis

Waterhouse, J.S., Cheng, S., Juchelka, D., Loader, N.J., Mccarroll, D., Roy Switsur, V., Gautam, L., 2013.

Geochimica et Cosmochimica Acta 112, 178–191. 27 February 2013.