Publications

Teehara, K. B., S. P. Jungbluth, T. E. Acosta, E. Hellebrand, A. K. Misra, P. B. Onac, A. Pflitsch, M. S. Rappé, S. M. Smith, M. Telus, and N. Schorghofer (2017) Cryogenic minerals in Hawaiian lava tubes: Geochemical and microbiological exploration. Geobiology. In review.

Jungbluth, S. P., T. Glavina del Rio, S. Tringe, R. Stepanauskas, and M. S. Rappé (2017) Characteristics of a bacterial lineage that inhabits both marine and terrestrial subsurface systems. PeerJ, 5:e3134. doi:10.7717/peerj.3134  OPEN

Jungbluth, S. P., J. P. Amend, and M. S. Rappé (2017) Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Scientific Data, 4:170037. doi:10.1038/sdata.2017.37  OPEN

Nigro, O. D., S. P. Jungbluth, H.-T. Lin, C.-C. Hsieh, J. A. Miranda, C. R. Schvarcz, M. S. Rappé, and G. F. Steward (2017) Viruses in the oceanic basement. mBio, 8:e02129-16. doi:10.1128/mBio.02129-16. OPEN

Salerno, J. L., B. W. Bowen, and M. S. Rappé (2016) Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago. FEMS Microbiology Ecology, 92:fiw109. doi:10.1093/femsec/fiw109.  PDF

Robador, A., D. E. LaRowe, S. P. Jungbluth, H. T. Lin, M. S. Rappé, K.H. Nealson, and J. P. Amend (2016) Nanocalorimetric characterization of microbial activity in deep subsurface oceanic crustal fluids. Frontiers in Microbiology, 7:454. doi:10.3389/fmicb.2016.00454. OPEN

Jungbluth, S. P., R. M. Bowers, H. T. Lin, J. P. Cowen, and M. S. Rappé (2016) Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt. The ISME Journal, 10:2033-2047. doi:10.1038/ismej.2015.248. OPEN

Saito, M. A., A. Dorsk, A. F. Post, M. R. McIlvin, M. S. Rappé, G. R. DiTullio, and D. M. Moran (2015) Needles in the blue sea: Sub‐species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome. Proteomics, 15:3521-3531. doi:10.1002/pmic.201400630. OPEN

Lin, H.-T., C.-C. Hsieh, J. P. Cowen, and M. S. Rappé (2015) Dissolved and particulate organic carbon in the deep sediments of U1363 near Grizzly Bare Seamount. Proceedings of the Integrated Ocean Drilling Program 327: doi:10.2204/iodp.proc.327.202.2015. OPEN

Robador, A., S. P. Jungbluth, D. E. LaRowe, R. M. Bowers, M. S. Rappé, J. P. Amend, & J. P. Cowen (2015) Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust. Frontiers in Microbiology, 5:748. doi:10.3389/fmicb.2014.00748. OPEN

Lin, H.-T., J. P. Cowen, E. J. Olson, M. D. Lilley, S. P. Jungbluth, S. T. Wilson, and M. S. Rappé (2014) Dissolved hydrogen and methane in the oceanic basaltic biosphere. Earth and Planetary Science Letters 405:62-73. doi:10.1016/j.epsl.2014.07.037. PDF

Jungbluth, S., H. T. Lin, J. Cowen, B. T. Glazer, and M. S. Rappé (2014) Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank. Frontiers in Microbiology, 5, 119.

Durham, B. P., J. Grote, K. A. Whittaker, S. J. Bender, H. Luo, S. L. Grim, J. M. Brown, J. R. Casey, A. Dron, L. Florez-Leiva, A. Krupke, C. M. Luria, A. H. Mine, O. D. Nigro, S. Pather, A. Talarmin, E. K. Wear, T. S. Weber, J. M. Wilson, M. J. Church, E. F. DeLong, D. M. Karl, G. F. Steward, J. M. Eppley, N. C. Kyrpides, S. Schuster and M. S. Rappé (2014) Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Standards in Genomic Sciences, 9(3), p.632.

Rappé, M. S. (2013). Stabilizing the foundation of the house that ‘omics builds: the evolving value of cultured isolates to marine microbiology. Current Opinion in Microbiology, 16(5), 618-624.

Yeo, S. K., M. J. Huggett, A. Eiler and M. S. Rappé (2013) Coastal bacterioplankton community dynamics in response to a natural disturbance.PLoS One, 8(2), e56207.

Jungbluth, S. P., J. Grote, H. T. Lin, J. P. Cowen, and M. S. Rappé (2013) Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. The ISME Journal, 7(1), 161-172.

Grote, J., J. C. Thrash, M. J. Huggett, Z. C. Landry, P. Carini, S. J. Giovannoni, and M. S. Rappé (2012) Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio, 3(5), e00252-12.

Apprill, A., H. Q. Marlow, M. Q. Martindale, and M. S. Rappé (2012) Specificity of associations between bacteria and the coral Pocillopora meandrina during early development. Applied and Environmental Microbiology, 78(20), 7467-7475.

Huggett, M.J., D. H. Hayakawa and M. S. Rappé (2012) Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria. Standards in Genomic Sciences, 6(1), p.11.

Huggett, M.J. and M. S. Rappé (2012) Genome sequence of strain HIMB55, a novel marine Gammaproteobacterium of the OM60/NOR5 Clade. Journal of Bacteriology, 194(9), pp.2393-2394.

Huggett, M.J. and M. S. Rappé (2012) Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria. Journal of Bacteriology, 194(3), pp.732-733.

Grote, J., C. Bayindirli, K. Bergauer, P. C. de Moraes, H. Chen, L. D’Ambrosio, B. Edwards, B. Fernández-Gómez, M. Hamisi, R. Logares, D. Nguyen, Y. M. Rii, E. Saeck, C. Schutte, B. Widner, M. J. Church, G. F. Steward, D. M. Karl, E. F. DeLong, J. M. Eppley, S. C. Schuster, N. C. Kyrpides, and M. S. Rappé (2011) Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Standards in Genomic Sciences, 5(3), p.269.

Thrash, J.C., A. Boyd, M. J. Huggett, J. Grote, P. Carini, R. J. Yoder, B. Robbertse, J. W. Spatafora, M. S. Rappé and S. J. Giovannoni (2011) Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific reports, 1, p.13.

Eiler, A., D. H. Hayakawa and M. S. Rappé (2011) Non-random assembly of bacterioplankton communities in the subtropical North Pacific Ocean. Frontiers in microbiology, 2, p.140.

Apprill, A., T. A. Mooney, E. Lyman, A. K. Stimpert and M. S. Rappé (2011) Humpback whales harbour a combination of specific and variable skin bacteria. Environmental microbiology reports, 3(2), pp.223-232.

Van Mooy, B.A., H. F. Fredricks, B. E. Pedler, S. T. Dyhrman, D. M. Karl, M. Koblížek, M. W. Lomas, T. J. Mincer, L. R. Moore, T. Moutin, and M. S. Rappé (2009) Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature, 458(7234), pp.69-72.

Eiler, A., D. H. Hayakawa, M. J. Church, D. M. Karl, and M. S. Rappé (2009) Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre. Environmental microbiology, 11(9), pp.2291-2300.

Apprill, A., H. Q. Marlow, M. Q. Martindale, and M. S. Rappé (2009) The onset of microbial associations in the coral Pocillopora meandrina. The ISME journal, 3(6), pp.685-699.

Giovannoni, S. J., D. H. Hayakawa, U. Stingl, H. J. Tripp, S. Givan, J.-C. Cho, H.-M. Oh, J. Kitner, K. L. Vergin and M. S. Rappé (2008) The small genome of an abundant coastal ocean methylotroph.  Environmental Microbiology, 10:1771-1782.

Brandon, M. L., J. W. Becker and M. S. Rappé (2008) Isolation of aquatic microorganisms via high throughput cultivation methods.  Molecular Microbial Ecology Manual, 3rd Edition.

Vergin, K. L., H. J. Tripp, L. J. Wilhelm, D. R. Denver, M. S. Rappé, and S. J. Giovannoni (2007) High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11).  Environmental Microbiology, 9:2430–2440.

Benitez-Nelson, C. R., R. R. Bidigare, T. Dickey, M. R. Landry, C. L. Leonard, S. L. Brown, F. Nencioli, Y. M. Rii, K. Maiti, J. W. Becker, T. S. Bibby, W. Black, W.-J. Cai, C. Carlson, F.Z. Chen, V. S. Kuwahara, C. Mahaffey, P. M. McAndrew, P. D. Quay, M. S. Rappé, K. E. Selph, M. E. Simmons, and E. J. Yang (2007) Eddy-induced diatom bloom drives increased biogenic silica flux, but inefficient carbon export in the subtropical North Pacific Ocean.  Science, 316:1017-1021.

Steward, G. F. and M. S. Rappé (2007) What’s the “meta” with metagenomics? The ISME Journal, 1:100-102.

Becker, J. W., M. L. Brandon, and M. S. Rappé (2007) Cultivating microorganisms from dilute aquatic environments:  melding traditional methodology with new cultivation techniques and molecular methods.  In C. J. Hurst et al. [eds], Manual of Environmental Microbiology, 3rdEdition.  ASM Press, pp. 399-406.

Giovannoni, S. J., R. A. Foster, M. S. Rappé, and S. Epstein (2007) New cultivation strategies bring more microbial plankton species into the laboratory.  Oceanography 20:24-30.

Giovannoni, S. J., L. Bibbs, J.-C. Cho, M. D. Staples, R. Desiderio, K. L. Vergin, M. S. Rappé, S. Laney, D. F. Barofsky, and E. Mathur (2005) Proteorhodopsin phototrophy in the ubiquitous marine bacterium SAR11.  Nature 438:82-85.

Giovannoni, S. J., H. J. Tripp, S. Givan, M. Podar, K. L. Vergin, D. Baptista, L. Bibbs, J. Eads, T. H. Richardson, M. Noordewier, M. S. Rappé, J. M. Short, J. C. Carrington and E. J. Mathur (2005) Genome streamlining in a cosmopolitan oceanic bacterium.  Science 309:1242-1245.

Morris, R. M., J.-C. Cho, K. L. Vergin, M. S. Rappé, C. A. Carlson, and S. J. Giovannoni (2005) Temporal and spatial response of bacterioplankton lineages to annual convective overturn at BATS.  Limnology and Oceanography  50:1687-1696.

Lodge-Ivey, S. L., M. S. Rappé, W. H. Johnston, R.E. Bohlken, and A. M. Craig (2005) Molecular analysis of a consortium of ruminal microbes that detoxify pyrrolizidine alkaloids.  Canadian Journal of Microbiology 51:455-465.

Morris, R. M., M. S. Rappé, S. A. Connon, E. Urbach, and S. J. Giovannoni (2004) Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean.  Applied and Environmental Microbiology  70:2836-2842.

Rappé, M. S., and S. J. Giovannoni (2003) The uncultured microbial majority.  Annual Review of Microbiology 57:369-394.

Cowen, J. P, S. J. Giovannoni, F. Kenig, H. P. Johnson, D. Butterfield, M. S. Rappé, M. Hutnak, and P. Lam (2003) Fluids from aging ocean crust that support microbial life.  Science  299:120-123.

Zengler, K., G. Toledo, M. Rappé, J. Elkins, E. Mathur, J. Short, and M. Keller (2002) Cultivating the uncultured.  Proceedings of the National Academy of Sciences, USA  99:15681-15686.

Morris, R. M., M. S. Rappé, S. A. Connon, K. L. Vergin, W. A. Siebold, C. Carlson, and S. J. Giovannoni (2002) SAR11 clade dominates ocean surface bacterioplankton communities.  Nature  420:806-810.

Rappé, M. S., S. A. Connon, K. L. Vergin, and S. J. Giovannoni (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.  Nature  418:630-633.

Hold, G. L., E. A. Smith, M. S. Rappé, E. W. Maas, E. R. B. Moore, C. Stroempl, J. R. Stephen, J. I. Prosser, T. H. Birkbeck, and S. Gallacher (2001) Characterization of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea.  FEMS Microbiology Ecology  37:161-173.

Vergin, K. L., M. S. Rappé, and S. J. Giovannoni (2001) Streamlined method to analyze 16S rRNA gene clone libraries.  BioTechniques  30:938-944.

Brinkmeyer, R., M. Rappé, S. Gallacher, and L. Medlin (2000) Development of clade (Roseobacter and Alteromonas) and taxon-specific oligonucleotide probes to study bacterial/toxic algal interactions in toxic dinoflagellate cultures.  European Journal of Phycology  35:315-329.

Giovannoni, S. J., and M. S. Rappé (2000) Evolution, diversity and molecular ecology of marine prokaryotes.  In D. L. Kirchman [ed.], Microbial Ecology of the Oceans.  Wiley and Sons, pp. 47-84.

Rappé, M. S., K. Vergin, and S. J. Giovannoni (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems.  FEMS Microbiology Ecology  33:219-232.

Giovannoni, S., and M. Rappé (1999) Microbial diversity: it’s a new world. The NEB Transcript  10:1-4.

Rappé, M. S., D. Gordon, K. Vergin, and S. J. Giovannoni (1999) Phylogeny of Actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton.  Systematic and Applied Microbiology  22:106-112.

Suzuki, M. T., M. S. Rappé, and S. J. Giovannoni (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity.  Applied and Environmental Microbiology  64:4522-4529.

Rappé, M. S., M. T. Suzuki, K. Vergin, and S. J. Giovannoni (1998) Phylogenetic diversity of ultraphytoplankton plastid SSU rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States.  Applied and Environmental Microbiology  64:294-303.

Rappé, M. S., P. F. Kemp, and S. J. Giovannoni (1997) Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina.  Limnology and Oceanography  42:811-826.

Suzuki, M. T., M. S. Rappé, Z. W. Haimberger, H. Winfield, N. Adair, J. Ströbel, and S. J. Giovannoni (1997) Bacterial diversity among SSU rDNA gene clones and cellular isolates from the same seawater sample.  Applied and Environmental Microbiology  63:983-989.

Field, K. G., D. Gordon, M. S. Rappé, E. Urbach, T. Wright, and S. J. Giovannoni (1997) Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.  Applied and Environmental Microbiology  63:63-70.

Giovannoni, S. J., M. S. Rappé, D. Gordon, E. Urbach, M. Suzuki, and K. G. Field.  Ribosomal RNA and the evolution of bacterial diversity (1996) In Roberts, D. McL., P. Sharp, G. Alderson, and M. Collins [eds], Evolution of microbial life.  Society for General Microbiology Symposium 54.  Cambridge University Press, pp. 63-85.

Giovannoni, S. J., M. S. Rappé, K. Vergin, and N. Adair (1996) 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria.  Proceedings of the National Academy of Sciences, USA  93:7979-7984.

Rappé, M. S., P. F. Kemp, and S. J. Giovannoni (1995) Abundant chromophyte plastid 16S ribosomal RNA genes found in a clone library from Atlantic Ocean seawater.  Journal of Phycology  31:979-988.

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