DCO/Deep Life Community Publications – updated February 2015

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DCO/Deep Life Community Publications – updated February 2015; 2010 and younger (N=133;
partly with relevance statements)
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2. Anderson RE, Brazelton WJ, Baross J. 2011. Is the genetic landscape of the deep subsurface
biosphere affected by viruses? Front. Microbiol. 2:doi: 10.3389/fmicb.2011.00219.
Little studied subsurface viriome and the conditions that dictate the distribution and diversity
of viruses in the subsurface. DG#1&3. [13]
3. Anderson RE, Brazelton WJ, Baross JA. 2013. The Deep Viriosphere: Assessing the Viral
Impact on Microbial Community Dynamics in the Deep Subsurface. Rev. Min. Geochem. 75.
Little studied subsurface viriome and the conditions that dictate the distribution and diversity
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seeps, Nature Geosci. 6, 725-734 (2013).
Quantitative constraints on carbon fluxes in the form of methane from subsurface and its
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5. Borgonie G, Garcıa-Moyano A, Litthauer D, Bert W, Bester A, van Heerden E, Moller C,
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Rare observation of eukaryotes in the deep subsurface. DG#1) - This is the first sighting of
metazoans in the deep subsurface and it also reports a novel species of nematode. (Incidentally,
the work was done before DCO started but published afterward. Borgonie was supported by
DCO funds for later work.
6. Bowles, M. W., J. M. Mogollón, S. Kasten, M. Zabel, and K. U. Hinrichs, Global rates of
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Modeling of the global distribution of microbial sulfate reduction in the ocean floor and
implication for the modes of carbon cycling in the subseafloor (DG #1 and 3).
7. Brazelton, W., Ludwig, K., Sogin, M., Andreishcheva, E.N., Kelley, D.S., Shen, C-C, Edwards,
R.L., Baross, J. (2010) Archaea and bacteria with surprising microdiversity show shifts in
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Macroscopic biofilms of the anaerobic oxidation of methane consortia in subseafloor sediment
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Description of unique biofilms involved in the methane oxidation and occurring in subsurface
fractures DG#1 and 3
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12. Cardace, D., T. Hoehler, T. McCollom, M. Schrenk, D. Carnevale, M. Kubo, M., & K. Twing
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Comprehensive consideration of current state of subseafloor and sub-continental microbiology
including a proposed prioritization for future studies
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T.G., Kuypers, M.M.M., Jørgensen, B.B. (2013) Strong 100-kyr migration of sub-seafloor
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18. D’Hondt, S. (2013) Geochemistry: Subsurface sustenance. Nature Geoscience. DOI:
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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.,
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23. Feseker T, Boetius A, Wenzhöfer F, Blandin J, Olu K, Yoerger DR, Camilli R, German CR, de
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24. Futagami, T., Morono, Y., Terada, T., Kaksonen, A. H., and Inagaki, F. * (2013) Distribution of
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25. Gagen, E.J., Huber, H., Meador, T., Hinrichs, K.-U., Thomm, M. (2013) A novel cultivationbased approach for understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea
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26. Georget, E., S. Kapoor, R. Winter, K. Reineke, Y. Song, M. Callanan, E. Ananta, V. Heinz, A.
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inactivation mechanisms under moderate high pressure. Food Microbiology. DOI:
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27. Grobelny, S., M. Erlkamp, J. Möller, M. Tolan, and R. Winter. (2014) Intermolecular
Interactions in Highly Concentrated Protein Solutions upon Compression and the Role of the
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28. Hazael R, Foglia F, Kardzhaliyska L, Daniel I, Meersman F and McMillan P (2014) Laboratory
investigation of high pressure survival in Shewanella oneidensis MR-1 into the gigapascal
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29. Hinrichs, K.-U. *, and Inagaki, F. (2012) Downsizing the deep biosphere. Science, 338, 204205. [10]
30. Hirayama, H. *, Suzuki, Y., Abe, M., Miyazaki, M., Makita, H., Inagaki, F., Uematsu, K., and
Takai, K. (2011) Methylothermus subterraneus sp. nov., a moderately thermophilic
methanotrophic bacterium from a terrestrial subsurface hot aquifer in Japan. Int. J. Syst. Evol.
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31. Hoshino, T., Morono, Y., Terada, T., Imachi, H., Ferdelman, T. G., and Inagaki, F. * (2011)
Comparative study of subseafloor microbial community structures in deeply buried coral fossils
and sediment matrices from the Challenger Mound of the Porcupine Seabight. Front.
Microbio., 2, Article no. 231. [10]
32. Hoshino, T. *, and Inagaki, F. (2012) Molecular quantification of environmental DNA using
microfluidics and digital PCR. Syst. Appl. Microbiol., 35, 390-395. [13]
33. Hoshino, T. *, and Inagaki, F. (2013) A comparative study of microbial diversity and community
structure in marine sediments using poly(A) tailing and reverse transcription PCR Front.
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34. Ijiri, A. *, Ohtomo, Y., Morono, Y., Ikehara, M., and Inagaki, F. (2013) Increase in acetate
concentrations during sediment sample onboard storage: a caution for pore-water geochemical
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35. Imachi, H. *, Aoi, K., Tasumi, E., Saito, Y., Yamanaka, Y., Saito, Y., Yamaguchi, T., Tomaru, H.,
Takeuchi, R., Morono, Y., Inagaki, F., and Takai, K. (2011) Cultivation of methanogenic
community from subseafloor sediments using a continuous-flow bioreactor. ISME J., 5, 17511925. [25]
Subseafloor methanogenic microbial communities, which contribute to the degradation of
organic matter and the formation of methane hydrates during the sediment burial, are
successfully cultivated in the laboratory using a continuous bioreactor cultivation technique.
36. Imachi, H. *, Sakai, S., Lipp, J. S., Miyazaki, M., Saito, Y., Yamanaka, Y., Hinrichs, K.-U.,
Inagaki, F., and Takai, K. (2014) Pelolinea submarina gen. nov., an anaerobic filamentous
bacterium of the phylum Chloroflexi isolated from subseafloor sediment offshore Shimokita,
Japan. Int. J. Syst. Evol. Microbiol., 64, 812-818. [0]
37. Ishibashi, J. *, Noguchi, T., Toki, T., Miyabe, S., Yamagami, S., Onishi, Y., Yamanaka, T.,
Yokoyama, Y., Omori, R., Takahashi, Y., Hatada, K., Nakaguchi, J., Yoshizaki, M., Konno, U.,
Shibuya, T., Takai, K., Inagaki, F., and Kawagucci, S. (2014) Diversity of fluid geochemistry
affected by processes during fluid upwelling in active hydrothermal fields in the Izena Hole, the
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38. Kapoor, S., M. Berghaus, S. Suladze, D. Prumbaum, S. Grobelny, P. Degan, S. Raunser, and R.
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39. Kallmeyer, J., R. Pockalny, R. R. Adhikari, D. C. Smith, and S. D'Hondt, Global distribution of
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correlated with biomass (DG 1, 2, 3)
40. Kallmeyer, J., T.L. Kieft. The Ubiquitous Hidden Biosphere. In: Unraveling the Compelxities
of Planet Earth: Science Plan for 2014-2019. International Continental Scientific Drilling
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41. Kawai, M., Futagami, T., Toyoda, A., Takaki, Y., Nishi, S., Hori, S., Arai, W., Tsubouchi, T.,
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frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep
subseafloor sedimentary metagenomes. Front. Microbiol., 5, Article no. 80,
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42. Kawai, M., Uchiyama, I., Takami, H., and Inagaki, F. * (2015) Low frequency of endosporespecific genes in subseafloor sedimentary metagenomes. Environ. Microbiol. Rept., in press.
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43. Kieft, T.L., and T.C. Onstott. Developing Deep Life Continental Drilling Projects. Eos (in
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44. Kieft, T.L. Microbiology of the deep continental biosphere. Ch. 6 In:Volume 1 of Advances in
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45. Kieft, T.L. Sampling the subsurface. In: Hydrocarbons and Lipid Microbiology (editors:
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46. Kellermann, M.Y., Wegener, G., Elvert, M., Yoshinaga, M.Y., Lin, Y.S., Holler, T., Mollar,
X.P., Knittel, K., Hinrichs, K.-U. (2012) Autotrophy as predominant mode of carbon fixation in
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47. Kouduka, M., Suko, T., Morono, Y., Inagaki, F., Ito, K, and Suzuki, Y. * (2012) A new DNA
extraction method by controlled alkaline treatments from consolidated subsurface sediments.
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48. Kubota, K. *, Morono, Y., Ito, M., Terada, T., Itezono, S., Harada, H., and Inagaki, F. (2014)
Gold-ISH: A nano-size gold particle-based phylogenetic identification compatible with
NanoSIMS. Syst. Appl. Microbiol., 37, 261-266. [0]
49. Langerhuus, A. T., Røy, H., Lever, M. A., Morono, Y., Inagaki, F., Jørgensen, B. B., and
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50. Lau, M.C.Y., C. Cameron, F., Schilkey, S. Grim, C. Magnabosco, C.T. Brown, S. Hendrickson,
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genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial
evolutionary relationships. Front. Microbiol. 5:531. doi: 10.3389/fmicb.2014.00531
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51. Lavalleur H.J., and F. Colwell. 2013. Microbial characterization of basalt formation waters targeted for
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54. Lever, M. A., O. Rouxel, J. C. Alt, N. Shimizu, S. Ono, R. M. Coggon, W. C. Shanks III, L.
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Documentation of microbial life in crust (DG# 1 and 3)
55. Lin, Y.S., Heuer, V.B., Goldhammer, T., Kellermann, M.Y., Zabel, M., Hinrichs, K.-U. (2012)
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56. Lin, Y.S., Lipp, J.S., Elvert, M., Holler, T., Hinrichs, K.-U. (2013) Assessing production of the
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sediment core retrieved from a potential hydrate-bearing region offshore southwestern
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58. Liu, X.L., Summons, R.E., Hinrichs, K.-U. (2012) Extending the known range of glycerol ether
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59. Lloyd, K. G., May, M. K., Kevorkian, R. T., & Steen, A. D. (2013). Meta-analysis of
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60. Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever, M. A., Steen, A. D., ... &
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Constraints on the function of members of one of the most abundant uncultured microbial
groups in Earth’s subsurface (DG #3)
61. Magnabosco, C., C.Y.M. Lau, T.L. Kieft, Memory Tekere, Jana Olivier, B. Linage, O. Kuloyo,
M. Erasmus, E. Cason, E. van Heerden, G. Borgonie, and T.C. Onstott. 2014. Comparisons of
the composition and biogeographic distribution of the bacterial communities occupying South
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62. Makita, H. *, Nakagawa, S., Miyazaki, M., Nakamura, K., Inagaki, F., and Takai, K. (2012)
Thiofractor thiocaminus gen. nov., sp. nov., a novel hydrogen-oxidizing sulfur-reducing
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63. Marteinsson V.T., A. Runarsson, A. Stefansson, T. Thorsteinsson, T. Johannesson, S.H.
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64. (Study of low diversity, microbial communities in a subglacial lake. Phylogenetic relationships
of the communities suggest that this is a lithoautotrophic microbial ecosystem. May have
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65. Mayhew, L.E., E.T. Ellison, T. M. McCollom, T.P. Trainor, A. Templeton. (2013) Hydrogen
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68. Meersman, F., I. Daniel, D. Bartlett, R. Winter, R. Hazael, P. McMillan. (2013) High-pressure
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69. Méhay, S., G. L. Früh-Green, S. Q. Lang, S.M. Bernasconi, W.J. Brazelton, M. O. Schrenk, P.
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70. Ménez, B., V. Pasini, and D. Brunelli, Life in the hydrated suboceanic mantle, Nature Geosci.
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71. Identification of biosignatures in serpentinized peridotites, DG #1 and 3.
72. Mills, H. J. *, Reese, B. K., Shepard, A. K., Riedinger, N., Dowd, S. E., Morono, Y., and
Inagaki, F. (2012) Characterization of metabolically active bacterial populations in subseafloor
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73. Miyazaki, M. *, Koide, O., Kobayashi, T., Mori, K., Shimamura, S., Nunoura, T., Imachi, H.,
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74. Moller, J., S. Grobelny, J. Schulze, S. Bieder, A. Steffen, M. Erlkamp, M. Paulus, M. Tolan, R.
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77. Morono, Y. *, Yamamoto, K., and Inagaki, F. (2012) Radical gas-based DNA decontamination
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79. This study demonstrates the incorporation of isotopically labeled-substrates into deeply
buried microbial cells in sediments by NanoSIMS, suggesting that most
subseafloor sedimentary cells are physiologically active and standby for the energy supply.
80. Morono, Y. *, Terada, T., Kallmeyer, J., and Inagaki, F. (2013) An improved cell separation
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81. A new cell separation technique lowered the minimum detection limit for cell counts down to
~100 cells per cm3 of sediment, which is at least 2 orders of magnitude lower than the
conventional microscopic cell count and allows analyses of single cells or target cells in the
combined use of flow cytometry and cell sorter.
82. Morono, Y. *, Terada, T., Hoshino, T., and Inagaki, F. (2014) Hot-alkaline DNA extraction
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83. Morono, Y. *, Terada, T., Hoshino, T., and Inagaki, F. (2014) Correction for Morono et al., Hotalkaline DNA extraction method for deep-subseafloor archaeal communities. Appl. Environ.
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