1 |
Colwell, F., A. Schwartz, and B. Briggs. 2011. Microbial community distribution in sediments from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope. Maine Petrol. Geol. 28: 404-410.
DOI
ScienceOn
|
2 |
D'Hondt, S., B. B. Jorgensen, D. J. Miller, A. Batzke, R. Blake, B. A. Cragg, et al. 2004. Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-2221.
DOI
ScienceOn
|
3 |
D'Hondt, S., F. Inagaki, T. Ferdelman, B. B. Jorgensen, K. Kato, P. Kemp, et al. 2007. Exploring subseafloor life with the integrated ocean drilling program. Scientific Drilling 5: 26-37.
|
4 |
DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685-5689.
DOI
ScienceOn
|
5 |
Etter, R. J. and J. F. Grassle. 1992. Patterns of species diversity in the deep sea as a function of sediment particle size diversity. Nature 360: 576-578.
DOI
|
6 |
Fry, J. C., R. J. Parkes, B. A. Cragg, A. J. Weightman, and G. Webster. 2008. Prokaryotic biodiversity and activity in the deep subseafoor biosphere. FEMS Microbiol. Ecol. 66: 181-196.
DOI
ScienceOn
|
7 |
Girvan, M. S., J. Bullimore, J. N. Pretty, A. M. Osborn, and A. S. Ball. 2003. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl. Environ. Microbiol. 69: 1800-1809.
DOI
ScienceOn
|
8 |
Heijs, S. K., G. Aloisi, I. Bouloubassi, R. D. Pancost, C. Pierre, J. S. S. Damste, et al. 2006. Microbial community structure in three deep-sea carbonate crusts. Microb. Ecol. 52: 451-462.
|
9 |
Glatz, R. E., P. W. Lepp, B. B. Ward, and C. A. Francis. 2006. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4: 53-67.
DOI
ScienceOn
|
10 |
Huneke, H. and T. Mulder (eds.). 2011. Deep-Sea Sediments, Vol. 63 (Developments in Sedimentology). Elsevier Science, Oxford.
|
11 |
Jiao, L., X. Su, F. Chen, Y. Zhang, H. Jiang, Y. Luo, and H. Dong. 2011. Microbial diversity in sediments of core HS-PC 500 from Shenhu Area, northern South China Sea. Wei Sheng Wu Xue Bao 51: 876-890.
|
12 |
Knittela, K., A. Boetius, A. Lemkea, H. Eilersa, K. Lochted, O. Pfannkuchee, et al. 2003. Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol. J. 20: 269-294.
DOI
ScienceOn
|
13 |
Kormas, K. A., D. C. Smith, V. Edgcomb, and A. Teske. 2003. Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol. Ecol. 45: 115-125.
DOI
ScienceOn
|
14 |
Marchesi, J. R., A. J. Weightman, B. A. Cragg, R. J. Parkes, and J. C. Fry. 2001. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34: 221-228.
DOI
|
15 |
Lopez-Garcia, P., S. Duperron, P. Philippot, J. Foriel, J. Susini, and D. Moreira. 2003. Bacterial diversity in hydrothermal sediment and epsilon-proteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5: 961-971.
DOI
ScienceOn
|
16 |
Li, T., P. Wang, and P. Wang. 2008. Bacterial and archaeal diversity in surface sediment from the south slope of the South China Sea. Wei Sheng Wu Xue Bao 48: 323-329.
|
17 |
Li, T., P. Wang, and P. Wang. 2008. Microbial diversity in surface sediments of the Xisha Trough, the South China Sea. Acta Ecol. Sin. 28: 1166-1173.
DOI
ScienceOn
|
18 |
Musata, N., U. Wernera, K. Knittela, S. Kolba, T. Dodenhofa, J. E. E. V. Beusekomb, et al. 2006. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Romo Basin, Wadden Sea. Syst. Appl. Microbiol. 29: 333-348.
DOI
ScienceOn
|
19 |
Neef, A., R. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: In situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144: 3257-3266.
DOI
ScienceOn
|
20 |
Schäfer, H., T. G. Ferdelman, H. Fossing, and G. Muyzer. 2007. Microbial diversity in deep sediments of the Benguela Upwelling System. Aquat. Microb. Ecol. 50: 1-9.
DOI
ScienceOn
|
21 |
Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida, and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68: 3759-3770.
DOI
ScienceOn
|
22 |
Rochelle, P. A., B. A. Cragg, J. C. Fry, R. J. Parkes, and A. J. Weightman. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S ribosomal-RNA gene sequence analysis. FEMS Microbiol. Ecol. 15: 215-225.
DOI
|
23 |
Sapp, M., E. R. Parker, L. R. Teal, and M. Schratzberger. 2010. Advancing the understanding of biogeography-diversity relationships of benthic microorganisms in the North Sea. FEMS Microbiol. Ecol. 74: 410-429.
DOI
ScienceOn
|
24 |
Schloss, P. D. and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501-1506.
DOI
ScienceOn
|
25 |
Sun, H., S. Dai, G. Wang, L. Xie, and X. Li. 2010. Phylogenetic diversity analysis of bacteria in the deep-sea sediments from the Bashi Channel by 16S rDNA BLAST. J. Trop. Oceanogr. 29: 41-46.
|
26 |
Swofford, D. L. (ed.). 1999. PAUP: Phylogenetic Analysis Using Parsimony ( other methods), Version 4.0. Sinauer Associates, Sunderland, Massachusetts.
|
27 |
Teske, A., K. U. Hinrichs, V. Edgcomb, A. V. Gomez, D. Kysela, S. P. Sylva, et al. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68: 1994-2007
DOI
ScienceOn
|
28 |
Wang, J., C. Jenkins, R. I. Webb, and J. A. Fuerst. 2002. Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater. Appl. Environ. Microbiol. 68: 417-422.
DOI
ScienceOn
|
29 |
Abulencia, C. B., D. L. Wyborski, J. A. Garcia, M. Podar, W. Chen, S. H. Chang, et al. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 72: 3291-3301.
DOI
|
30 |
Briee, C., D. Moreira, and P. Lopez-Garcia. 2007. Archaeal and bacterial community composition of sediment and plankton from asuboxic freshwater pond. Res. Microbiol. 158: 213-227.
DOI
ScienceOn
|
31 |
Bowman, J. P. and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within antarctic continental shelf sediment. Appl. Environ. Microbiol. 69: 2463-2483.
DOI
ScienceOn
|
32 |
Briggs, B. R., F. Inagaki, Y. Morono, T. Futagami, C. Huguet, A. Rosell-Mele, et al. 2012. Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol. Ecol. 81: 88-98.
DOI
ScienceOn
|
33 |
Cao, H., Y. Hong, M. Li, and J. Gu. 2011. Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the Western Pacific. Microb. Ecol. 62: 813-823.
DOI
|
34 |
Chao, A. and T. J. Shen. Program SPADE (Species prediction and diversity estimation). Program and user's guide. Available at http://chao.stat.nthu.edu.tw.
|
35 |
Dai, X., H. Zhou, Y. Chen, C. Cai, Y. Zhou, S. Zhou, and L. Qu. 2002. A preliminary study on 16S rDNA diversity of bacteria in the Nansha marine sediment, the South China Sea. Progress Natural Science 12: 479-484.
|
36 |
Wang, P. and Q. Li (eds.). 2009. The South China Sea: Paleoceanography and Sedimentology. Springer, Berlin.
|
37 |
Wagner, C., M. Mau, M. Schlomann, J. Heinicke, and U. Koch. 2007. Characterization of the bacterial flora in mineral waters in upstreaming fluids of deep igneous rock aquifers. J. Geophys. Res. 112: G01003.
|
38 |
Walker, A. W., J. D. Sanderson, C. Churcher, G. C. Parkes, B. N. Hudspith, N. Rayment, et al. 2011. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 11: 7.
DOI
ScienceOn
|
39 |
Wang, G., J. Dong, X. Li, and H. Sun. 2010. The bacterial diversity in surface sediment from the South China Sea. Acta Oceanol. Sin. 29: 98-105.
|
40 |
Wang, P., T. Li, A. Hu, Y. Wei, W. Guo, N. Jiao, and C. Zhang. 2010. Community structure of Archaea from deep-sea sediments of the South China Sea. Microb. Ecol. 60: 796-806.
DOI
ScienceOn
|
41 |
Webster, G., R. J. Parkes, B. A. Cragg, C. J. Newberry, A. J. Weightman, and J. C. Fry. 2006. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol. Ecol. 58: 65-85.
DOI
ScienceOn
|
42 |
Wegener, G., M. Shovitri, K. Knittel, H. Niemann, M. Hovland, and A. Boetius. 2008. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosci. Discuss. 5: 971-1015.
DOI
|
43 |
Xu, F., X. Dai, Y. Chen, H. Zhou, J. Cai, and L. Qu. 2004. Phylogenetic diversity of bacteria and archaea in the Nansha marine sediment, as determined by 16S rDNA analysis. Oceanol. Limnol. Sin. 35: 89-94.
|
44 |
Wei, Y., J. Wang, J. Liu, L. Dong, L. Li, H. Wang, et al. 2011. Spatial variations in archaeal lipids of surface water and coretop sediments in the South China Sea and their implications for paleoclimate studies. Appl. Environ. Microbiol. 77: 7479-7489.
DOI
ScienceOn
|
45 |
Wilms, R., B. Kopke, H. Sass, T. S. Chang, H. Cypionka, and B. Engelen. 2006. Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ. Microbiol. 8: 709-719.
DOI
ScienceOn
|
46 |
Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376.
|
47 |
Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70: 845-849.
DOI
|
48 |
Heijs, S. K., R. R. Haese, P. W. J. J. Wielen, L. J. Forney, and J. D. Elsas. 2007. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb. Ecol. 53: 384-398.
DOI
ScienceOn
|
49 |
Huber, J. A., H. P. Johnson, D. A. Butterfield, and J. A. Baross. 2006. Microbial life in ridge flank crustal fluids. Environ. Microbiol. 8: 88-99.
DOI
ScienceOn
|
50 |
Inagaki, F., M. M. M. Kuypers, U. Tsunogai, J.-I. Ishibashi, K.- I. Nakamura, T. Treude, et al. 2006. Microbial community in a sediment-hosted lake of the southern Okinawa Trough hydrothermal system. Proc. Natl. Acad. Sci. USA 103: 14164-14169.
DOI
ScienceOn
|
51 |
Jorgensen, B. B. and A. Boetius. 2007. Feast and famine - microbial life in the deep-sea bed. Nat. Rev. Microbiol. 5: 770-781.
DOI
ScienceOn
|
52 |
Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, et al. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA 103: 2815-2820.
DOI
ScienceOn
|
53 |
Inagaki, F., Y. Sakihama, A. Inoue, C. Kato, and K. Horikoshi. 2002. Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments. Environ. Microbiol. 4: 277-286.
DOI
ScienceOn
|
54 |
Inagaki, F., M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, et al. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69: 7224-7235.
DOI
ScienceOn
|
55 |
Niemann, H., T. Losekann, D. D. Beer, M. Elvert, T. Nadalig, K. Knittel, et al. 2006. Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443: 854-858.
DOI
ScienceOn
|
56 |
Nercessian, O., Y. Fouquet, C. Pierre, D. Prieur, and C. Jeanthon. 2005. Diversity of bacteria and archaea associated with a carbonate-rich metalliferous sediment sample from the rainbow vent field on the mid-atlantic ridge. Environ. Microbiol. 7: 698-714.
DOI
ScienceOn
|
57 |
Newberry, C. J., G. Webster, B. A. Cragg, R. J. Parkes, A. J. Weightman, and J. C. Fry. 2004. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6: 274-287.
DOI
ScienceOn
|
58 |
Parkes, R. J., B. A. Cragg, N. Banning, F. Brock, G. Webster, J. C. Fry, et al. 2007. Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ. Microbiol. 9: 1146-1161.
DOI
ScienceOn
|
59 |
Orcutt, B. N., J. B. Sylvan, N. J. Knab, and K. J. Edwards. 2011. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Molec. Biol. Rev. 75: 361-422.
DOI
ScienceOn
|
60 |
Pachiadaki, M. G., V. Lykousis, E. G. Stefanou, and K. A. Kormas. 2010. Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol. Ecol. 72: 429-444.
DOI
ScienceOn
|
61 |
Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, et al. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390-394.
DOI
ScienceOn
|
62 |
Penton, C. R., A. H. Devol, and J. M. Tiedje. 2006. Molecular evidence for the broad distribution of anaerobic ammoniumoxidizing bacteria in freshwater and marine sediments. Appl. Environ. Microbiol. 72: 6829-6832.
DOI
ScienceOn
|
63 |
Prell, W. L., P. Wang, P. Blum, D. K. Rea, and S. C. Clemens. 1999. Isotopic chemistry of organic carbon in sediments from Leg 184. In J. S. Leventhal (ed.). Proceedings of the Ocean Drilling Program, Scientific Results. Available at http://www.odp.tamu.edu/publications/184_SR/VOLUME/CHAPTERS/215.PDF.
|
64 |
Zhou, J., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143: 3913-3919.
DOI
ScienceOn
|
65 |
Wilms, R., H. Sass, B. Kopke, J. Koster, H. Cypionka, and B. Engelen. 2006. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl. Environ. Microbiol. 72: 2756-2764.
DOI
ScienceOn
|
66 |
Zeng, R., J. Zhao, R. Zhang, and N. Lin. 2004. Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment. Sci. China Ser. D Earth Sci. 42: 282-290.
|
67 |
Zhang, Y., X. Su, F. Chen, Y. Wang, L. Jiao, H. Dong, et al. 2012. Microbial diversity in cold seep sediments from the northern South China Sea. Geosci. Frontiers 3: 301-316.
DOI
ScienceOn
|