2011 Sediment Microbiology Meeting: Reference List

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Recommended readings for deep subsurface microbiology
Andreas Teske, Jennifer Biddle, Matt Schrenk

For participants who are not heavily involved in subsurface research, we have assembled the following list of key papers in the field. These papers provide a multifaceted introduction to deep sediment microbiology; they are by no means a complete reading list, but they include important recent papers and provide leads from multiple angles – biogeochemistry, microbial metabolism, microbial genomics – into this rapidly growing and maturing field. 

1. Expanding frontiers in deep subsurface microbiology. Jan P. Amend, Andreas Teske. 2005. Palaeogeography, Palaeoclimatology, Palaeoecology 219:131-155.
    
2. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Jennifer F. Biddle, Julius S. Lipp, Mark A. Lever, Karen G. Lloyd, Ketil B. Sørensen, Rika Anderson, Helen F. Fredricks, Marcus Elvert, Timothy J. Kelly, Daniel P. Schrag, Mitchell L. Sogin, Jean E. Brenchley, Andreas Teske, Christopher H. House, and Kai-Uwe Hinrichs. 2006. PNAS 103:3846-3851.
    
3. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Jennifer F. Biddle, Sorel Fitz-Gibbon, Stephan C. Schuster, Jean E. Brenchley, and Christopher H. House. 2008. PNAS 105:10583-10588.
    
4. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. Anna Blazejak and Axel Schippers. 2010. FEMS Microbiology Ecology 72:198-207.
    
5. Metabolic activity of subsurface life in deep-sea sediments. Steven D’Hondt, Scott Rutherford, Arthur J. Spivack. 2002. Science 295:2067-2070.
    
6. Distributions of microbial activities in deep subseafloor sediments. Steven D’Hondt, Bo Barker Jørgensen, D. Jay Miller, Anja Batzke, Ruth Blake, Barry A. Cragg, Heribert Cypionka, Gerald R. Dickens, Timothy Ferdelman, Kai-Uwe Hinrichs, Nils G. Holm, Richard Mitterer, Arthur Spivack, Guizhi Wang, Barbara Bekins, Bert Engelen, Kathryn Ford, Glen Gettemy, Scott D. Rutherford, Henrik Sass, C. Gregory Skilbeck, Ivano W. Aiello, Gilles Guèrin, Christopher H. House, Fumio Inagaki, Patrick Meister, Thomas Naehr, Sachiko Niitsuma, R. John Parkes, Axel Schippers, David C. Smith, Andreas Teske, Juergen Wiegel, Christian Naranjo Padilla, Juana Luz Solis Acosta. 2004. Science 306:2216-2221.
    
7. Exploring subseafloor life with the Integrated Ocean Drilling Program. Steven D’Hondt, Fumio Inagaki, Timothy Ferdelman, Bo Barker Jørgensen, Kenji Kato, Paul Kemp, Patricia Sobecky, Mitchell Sogin and Ken Takai. 2007. Scientific Drilling 5:26-37.
    
8. Subseafloor sedimentary life in the South Pacific Gyre. Steven D’Hondt, Arthur J. Spivack, Robert Pockalny, Timothy G. Ferdelman, Jan P. Fischer, Jens Kallmeyer, Lewis J. Abrams, David C. Smith, Dennis Graham, Franciszek Hasiuk, Heather Schrum, and Andrea M. Stancin. 2009. PNAS 106:11651-11656.
    
9. Marine subsurface eukaryotes: the fungal majority. Virginia P. Edgcomb, David Beaudoin, Rebecca Gast, Jennifer F. Biddle and Andreas Teske. 2010. Environmental Microbiology 13:172-183.
    
10. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. John C. Fry, R. John Parkes, Barry A. Cragg, Andrew J. Weightman, and Gordon Webster. 2008. FEMS Microbiology Ecology 66:181-196.
     
11. Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. Taiki Futagami, Yuki Morono, Takeshi Terada, Anna H. Kaksonen, and Fumio Inagaki. 2009. Applied and Environmental Microbiology 75:6905-6909.
     
12. Microbial metagenomics: beyond the genome. Jack A. Gilbert and Christopher L. Dupont. 2011. Annual Review of Marine Science 3:347-371.
     
13. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Fumio Inagaki, Takuro Nunoura, Satoshi Nakagawa, Andreas Teske, Mark Lever, Antje Lauer, Masae Suzuki, Ken Takai, Mark Delwiche, Frederick S. Colwell, Kenneth H. Nealson, Koki Horikoshi, Steven D’Hondt, and Bo B. Jørgensen. 2006. PNAS 103:2815-2820.
     
14. Feast and famine — microbial life in the deep-sea bed. Bo Barker Jørgensen and Antje Boetius. 2007. Nature Reviews Microbiology 5:770-781.
     
15. New cell extraction procedure applied to deep subsurface sediments. Jens Kallmeyer, David C. Smith, Arthur J. Spivack, Steven D’Hondt. 2008. Limnology and Oceanography: Methods 6:236-245.
     
16. Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge flank: a synthesis of geochemical, thermodynamic, and gene-based evidence. Lever, Mark A., Verena B. Heuer, Yuki Morono, Noriaki Masui, Frauke Schmidt, Marc J. Alperin, Fumio Inagaki, Kai-Uwe Hinrichs, and Andreas Teske. 2010. Geomicrobiology Journal 27:183-211.
     
17. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Julius S. Lipp, Yuki Morono, Fumio Inagaki, and Kai-Uwe Hinrichs. 2008. Nature 454:991-994.
     
18. Discriminative detection and enumeration of microbial life in marine subsurface sediments. Yuki Morono, Takeshi Terada, Noriaki Masui, and Fumio Inagaki. 2009. The ISME Journal 3:503-511.
     
19. Recent studies on bacterial populations and processes in subseafloor sediments: A review. R. John Parkes, Barry A. Cragg, Peter Wellsbury. 2000. Hydrogeology Journal 8:11-28.
     
20. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. R. John Parkes, Gordon Webster, Barry A. Cragg, Andrew J. Weightman, Carole J. Newberry, Timothy G. Ferdelman, Jens Kallmeyer, Bo B. Jørgensen, Ivano W. Aiello, and John C. Fry. 2005. Nature 436:390-394.
     
21. Who lives in the sea floor? Ann Pearson. 2008. Nature 454:952-953.
     
22. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Axel Schippers, Lev N. Neretin, Jens Kallmeyer, Timothy G. Ferdelman, Barry A. Cragg, R. John Parkes, and Bo B. Jørgensen. 2005. Nature 433:861-864.
     
23. Microbial provinces in the subseafloor. Matthew O. Schrenk, Julie A. Huber, and Katrina J. Edwards. 2010. Annual Review of Marine Science 2:279-304.
     
24. Exploration of life in deep subseafloor sediments. David C. Smith and Steven D’Hondt. 2006. Oceanography 19:58-70.
     
25. Stratified communities of active archaea in deep marine subsurface sediments. Ketil B. Sørensen and Andreas Teske. 2006. Applied and Environmental Microbiology 72:4596-4603.
     
26. Sedimentary lipids recycled by deep-sea benthic archaea. Yoshinori Takano, Yoshito Chikaraishi, Nakano O. Ogawa, Hideteka Nomaki, Yuki Morono, Fumio Inagaki, Hiroshi Kitazato, Kai-Uwe Hinrichs, Naohiko Ohkouchi. 2010. Nature Geoscience 3:858-861.
     
27. Uncultured archaea in deep marine subsurface sediments: have we caught them all? Andreas Teske and Ketil B Sørensen. 2008. The ISME Journal 2:3-18.
     
28. Central role of the cell in microbial ecology. Karsten Zengler. 2009. Microbiology and Molecular Biology Reviews 73:712-729.