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  Papers published with the support of the CMDE

2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007

2015

Gile, G. H., James, E. R., Okamoto, N., Carpenter, K. J., Burki, F., Scheffrahn, R. H., and Keeling, P. J. 2015. Molecular evidence for the polyphyly of Macrotrichomonas (Parabasalia: Cristamonadea) and a proposal for Macrotrichomonoides n. gen. J. Eukaryot. Microbiol., in press.

Janouškovec, J., Tikhonenhov, D. V., Burki, F., Howe, A. T., Kolisko, M., Mylnikov, A. P., and Keeling, P. J. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. Proc. Natl. Acad. Sic. USA, in press.

Worden, A. Z., Fellows, M. J., Giovannoni, S. J., Wilken, S. Zimmerman, A., and Keeling, P. J. 2015. Rethinking the marine carbon cycle: factoring in mutifarious lifestyles of microbes. Science 347, 1257594.

2014

Okamoto, N. and Keeling, P. J. 2014. A comparative overview of the flagellar apparatus of dinoflagellates, perkinsids, and colpodellids. Microorganisms 2, 73-91.

Hehenberger, E., Imanian, B., Burki, F., and Keeling, P. J. 2014. Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts. Gen. Biol. Evol. 6, 2321-2334.

Kolisko, M., Boscaro, V., Burki, F., Lynn, D. and Keeling, P. J. 2014. Single-cell transcriptomics for microbial eukaryotes. Curr. Biol. 17, R1081-10-82.

Burki, F. Imanian, B., Hehenberger, E., Hirakawa, Y. Maruyama, S., and Keeling, P. J. 2014. Endosymbiotic gene transfer in tertiary plastid containing dinoflagellates. Eukaryotic Cell, 13, 246-255. PDF

del Campo, J. Sieracki, M. E., Molestina, R., Keeling, P. J., Massana, R. and Ruiz-Trilo, I. 2014. The others: our biased perspectives of eukaryotes. Trends Ecol. Evol. 29, 252-259. PDF

Hirakawa, Y. Suzuki, S., Archibald, J. M., Keeling, P. J., and Ishida, K.-I. 2014. Over-expression of molecular chaperone genes in nucleomorph genomes. Mol. Biol. Evol. 31, 1437-1443. PDF

Keeling, P. J. et al (65 authors) 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol., 12, e1001889. PDF

Burki, F. and Keeling, P. J. 2014. Rhizaria. Curr. Biol., 24, R103-107. PDF

Okamoto, N. and Keeling, P. J. 2014. The 3D structure of the apical complex and its association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa. Plos ONE. 9, e84653. PDF

Keeling, P. J. 2014. The impact of history on our perception of evolutionary events: endosymbiosis and the origins of eukaryotic complexity. Cold Spring Harb. Perspect. Biol., 6, a016196. PDF

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2013

Yubuki, N. and Leander, B.S. 2013. Evolution of microtubule organizing centers across the tree of eukaryotes. The Plant Journal. In press.

Heger, T.J., Mitchell, E.A.D. and Leander, B.S. 2013. Holarctic phylogeography of the testate amoeba Hyalosphenia papilio (Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by climate than dispersal limitation. Molecular Ecology. In press.

Burki F., Corradi, N., Sierra, R., Pawlowski, J., Meyer, G. R., Abbott, C. L. and Keeling, P. J. Phylogenomics of the ‘amitochondriate’ intracellular parasite Mikrocytos mackini reveals first evidence for a mitosome in Rhizaria. 2013. Curr. Biol., 23, 1541-1547. PDF

Yubuki, N., Simpson, A.G.B. and Leander, B.S. 2013. Reconstruction of the feeding apparatus in Postgaardi mariagerensis provides evidence for character evolution in the Symbiontida (Euglenozoa). Europ. J. Protistol. 49:32-39.

Rundell, R.J. and Leander, B.S. 2013. Molecular phylogeny of kalyptorhynch turbellarians (Platyhelminthes: Rhabdocoela), including descriptions of five new meiofuanal species from the northeastern Pacific Ocean. Journal of the Marine Biological Association (UK). In press.

Chantangsi, C., Lynn, D.H., Rueckert, S., Prokopowicz, A.J., Panha, S. and Leander, B.S. 2013. Fusiforma themisticola n. gen., n. sp., a new species of apostome ciliate infecting the hyperiid amphipod Themisto libellula in the Canadian Beaufort Sea (Arctic Ocean), and establishment of the Pseudocolliniidae (Ciliophora, Apostomatia). Protist. In press.

An D., S. M. Caffrey, J. Soh, A. Agrawal, D. Brown, K. Budwill, X. Dong, P. F. Dunfield, J. Foght, L. M. Gieg, S. J. Hallam, N. W. Hanson, Z. He, T. R. Jack, J. Klassen, K. M. Konwar, E. Kuatsjah , C. Li, S. Larter, V. Leopatra, C. L. Nesbø, T. B. Oldenburg, A. P. Page, E. Ramos-Padron, F. Rochman, A. Saidi-Mehrabad, C. W. Sensen, P. Sipahimalani, Y. C. Song , S. Wilson, G. Wolbring, G. Wong, and G. Voordouw . 2013. Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol. In press.

Wright, J.J., K. Mewis, N. W. Hanson, K. M. Konwar, K. R. Mitchell and S. J. Hallam. 2013. A potential role for Marine Group A bacteria in the marine sulfur cycle. ISME Journal. In press.

Konwar, K. M., N. W. Hanson, A. P. Pagé, and S. J. Hallam. 2013. MetaPathways: A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information. BMC Bioinformatics 14:202.

Swan B.K., B. Tupper, A. Sczyrba, F. M. Lauro, M. Martinez-Garcia, J. M. González, H. Luo, J. J. Wright, Z. C. Landry, N. W. Hanson, B. P. Thompson, N. J. Poulton, P. Schwientek, S. G. Acinas, S. J. Giovannoni, M. A. Moran, S. J. Hallam, R. Cavicchioli, T. Woyke and R. Stepanauskas. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. PNAS 9;110(28):11463-8. doi: 10.1073/pnas.1304246110.

Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W. Liu, J. A. Eisen, S. J. Hallam, N. C. Kyrpides, R. Stepanauskas, E. M. Rubin, P. Hugenholtz and T. Woyke. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature (doi:10.1038/nature12352).

Durno E., N. W. Hanson, K. M. Konwar and S. J. Hallam. 2013. Expanding the boundaries of local similarity analysis. BMC Genomics 14 (Suppl 1), S3.

Labonté, J. and C.A. Suttle. 2013. Previously unknown and highly divergent ssDNA viruses populate the oceans. ISME Journal (online, ahead of print) doi:10.1038/ismej.2013.110.

Winter, C., B. Mathews and C.A. Suttle. 2013. Effects of environmental variation and spatial distance on Bacteria, Archaea, and viruses in sub-polar and arctic waters. ISME Journal 7, 1507–1518; doi:10.1038/ismej.2013.56.

Declerck, S.A.J., C. Winter, J.B. Shurin, C.A. Suttle and B. Matthews. 2013. Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses. ISME Journal 7: 533-542 (doi:10.1038/ismej.2012.138)

White, R.A. and C.A. Suttle. 2013. The draft genome of Sphingomonas paucimobilis strain HER1398 (Proteobacteria), host to the giant PAU phage, indicates that it is a member of the genus Sphingobacterium (Bacteroidetes). Genome Announcements 1(4):e00598-13. doi:10.1128/genomeA.00598-13.

White, R.A., III, C.J. Grassa and C.A. Suttle. 2013. Draft Genome Sequence of an Exiguobacterium Strain RW-2 with wide thermal, salinity, and pH tolerance, isolated from modern microbialites. Genome Announcements 1(4):e00597-13. doi:10.1128/genomeA.00597-13.

White, R.A., III, C.J. Grassa and C.A. Suttle. 2013. The first draft genome from the genus Agrococcus isolated from modern microbialites. Genome Announcements 1(4):e00391-13. doi:10.1128/genomeA.00391-13.

VanInsberghe, D., Hartmann, M., Stewart, G.R., Mohn, W.W. 2013. Isolation of a substantial proportion of bacterial forest soil communities as detected via pyrotag sequencing. Appl. Environ. Microbiol. 79:2096-2098.

Yubuki, N., Simpson, A.G.B. and Leander, B.S. 2013. Comprehensive ultrastructure of Kipferlia bialata provides evidence for character evolution within the Fornicata (Excavata). Protist. 164:423-439.

Rueckert, S., Wakeman, K. and Leander, B.S. 2013. Discovery of a diverse clade of gregarine apicomplexans from Pacific eunicid polychaetes, including descriptions of Paralecudina gen. n., Trichotokara japonica sp. n., and T. eunicae sp. n. J. Eukaryot. Microbiol. 60:121-136.

Breglia, S.A., Yubuki, N. and Leander, B.S. 2013. Ultrastructure and molecular phylogenetic position of Heteronema scaphurum: A eukaryovorous euglenid with a cytoproct. In press. J. Eukaryot. Microbiol. 60:107-120.

Hirakawa, Y. Burki, F., and Keeling, P. J. 2013. Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastids of chlorarachniophytes. J. Cell. Sci. 125, 6176-6184. PDF

James, E. R., Okamoto, N., Burki, F., Scheffrahn, R. and Keeling, P. J., 2013. Cthulhu macrofasciculumque n. g., n. sp. and Cthylla microfasciculumque n. g., n. sp., a newly identified lineage of parabasalian termite symbionts. Plos One 8, e58509. PDF

James, E. R., Burki, F., Harper, J. T., Scheffrahn, and Keeling, P. J. 2013. Molecular characterisation of parabasalian symbionts Coronympha clevelandii and Trichonympha subsquilla from the Hawaiian lowland tree termite Incisitermes immigrans. J. Eukaryot. Microbiol. 60, 313-316. PDF

Burki F., Corradi, N., Sierra, R., Pawlowski, J., Meyer, G. R., Abbott, C. L. and Keeling, P. J. Phylogenomics of the ‘amitochondriate’ intracellular parasite Mikrocytos mackini reveals first evidence for a mitosome in Rhizaria. Curr. Biol. 23, 1541-1547. PDF

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2012

Winter, C., J.P. Payet and C.A. Suttle. 2012. Modeling the Winter-to-Summer transition of prokaryotic and viral abundance in the Arctic Ocean. PLoS ONE 7 (12), e52794.

Curtis, B.A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., Arias, M.C., Ball, S.G., Gile, G.H., Hirakawa, Y., Hopkins, J.F., Kuo, A., Rensing, S.A., Schmutz, J., Symeonidi, A., Elias, M., Eveleigh, R.J., Herman, E.K., Klute, M.J., Nakayama, T., Oborník, M., Reyes-Prieto, A., Armbrust, E.V., Aves, S.J., Beiko, R.G., Coutinho, P., Dacks, J.B., Durnford, D.G., Fast, N.M., Green, B.R., Grisdale, C.J., Hempel, F., Henrissat, B., Höppner, M.P., Ishida, K., Kim, E., Kořený, L., Kroth, P.G., Liu, Y., Malik, S.B., Maier, U.G., McRose, D., Mock, T., Neilson, J.A., Onodera, N.T., Poole, A.M., Pritham, E.J., Richards, T.A., Rocap, G., Roy, S.W., Sarai, C., Schaack, S., Shirato, S., Slamovits, C.H., Spencer, D.F., Suzuki, S., Worden, A.Z., Zauner, S., Barry, K., Bell, C., Bharti, A.K., Crow, J.A., Grimwood, J., Kramer, R., Lindquist, E., Lucas, S., Salamov, A., McFadden, G.I., Lane, C.E., Keeling, P.J., Gray, M.W., Grigoriev, I.V., Archibald, J.M. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492, 59-65. (PDF)

Dimitriu, P.A., Boyce, G., Samarakoon, A., Hartmann, M., Johnson, P., Mohn, W.W. 2012. Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. Environ. Microbiol. 5:200-210. [Faculty of 1000 Recommended]

Hartmann, M., Howes, C.G., VanInsberghe, D., Yu, H., Bachar, D., Christen, R., Nilsson, R.H., Hallam, S.J., Mohn, W.W. 2012. Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. ISME J. 6:2199-2218. [Listed in the ISME Journal Top Ten]

Sze, M.A., Dimitriu, P.A., Hayashi, S., Elliott, W.M., Gosselink, J.V., Cooper, J., Sin, D.D., Mohn, W.W., Hog,g J.C. 2012. The lung tissue microbiome in chronic obstructive pulmonary disease. American Journal of Respiratory and Critical Care Medicine. 185:1073-1080.

Deslippe, J.R., Hartmann, M., Simard, S.W., Mohn, W.W. 2012. Long-term warming alters the composition of Arctic soil microbial communities. FEMS Microbiol. Ecol. 82:303-315.

Finlay, B.B., Russell, S., Gold, M., Hartmann, M., Willing, B., Thorson, L., Wlodarska, M., Gill, N., Blanchet, M.-R., Mohn, W.W., McNagny, K.M.. 2012. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Reports. 13(5):440-447.

Wright, J.J. K. Konwar, and S.J. Hallam. 2012. Microbial ecology of expanding oxygen minimum zones. Invited review for Nat. Rev. Microbiol. 10, 381-94.

Allers, E†., J. J. Wright†, K. M. Konwar, C. G. Howes, E. Beneze, S. J. Hallam* and Matthew J. Sullivan*. 2012. Diversity and population structure of Marine Group A bacteria in the oxygen minimum zone of the Northeast subarctic Pacific Ocean. ISME Journal 7(2):256-268.

Hartmann, M., C. G. Howes, D. VanInsberghe, H. Yu, D. Bachar, R. Christen, R. H. Nilsson, S. J. Hallam and W.W. Mohn. 2012. Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. ISME Journal. 6:2199-2218.

Leung, K., H. Zahn, T. Leaver, K. M. Konwar, N. W. Hanson, A.P. Pagé, C. Lo, P. S. Chain, S.J. Hallam, and C. L. Hansen. 2012. Programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl. Acad. Sci. USA 109(20):7665-70.

Janouškovec, J., Horák, A., Barott, K. L., Rohwer, F. L., and Keeling, P. J. 2012. Environmental distribution of a novel coral-associated eukaryote related to apicomplexan parasites. ISME J. 7, 444-447. (PDF)

Yubuki, N. and Leander, B.S. 2012. Reconciling the bizarre inheritance of microtubules in complex (euglenid) microeukaryotes. Protoplasma. 249:859-869. (PDF)

Pánek, T., Silberman, J.D., Yubuki, N., Leander, B.S. and Cepicka, I. 2012. Diversity, evolution and molecular systematics of the Psalteriomonadidae, the main lineage of anaerobic/microaerophilic heteroloboseans (Excavata: Discoba). Protist. 163:807-831.

Rundell, R.J. and Leander, B.S. 2012. Description and phylogenetic position of the first sand-dwelling entoproct species from the western coast of North America: Loxosomella vancouverensis sp. nov. Marine Biology Research. 8:294-291.

Kosakyan, A., Heger, T.J., Leander, B.S., Todorov, M., Mitchell, E.A.D. and Lara, E. 2012. COI barcoding of nebelid testate amoebae (Amoebozoa: Arcellinida): Extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze. Protist. 163:415-434.

Yamaguchi, A., Yubuki, N. and Leander, B.S. 2012. Morphostasis in a novel eukaryote illuminates the evolutionary transition from phagotrophy to phototrophy: Description of Rapaza viridis n. gen. et sp. (Euglenozoa, Euglenida). BMC Evolutionary Biology. 12:29 (16 pages).

Pombert, J.-F., Selman, M., Burki, F., Bardell, F. T., Farinelli, L., Solter, L.F., Whitman, D.W., Weiss, L.M., Corradi, N., and Keeling, P. J. 2012. Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc. Natl. Acad. Sci. USA 109, 12638-12643. PDF

Burki, F., Hirakawa, Y., and Keeling, P.J. 2012. Intragenomic spread of plastid-targeting presequences the coccolithophore Emiliania huxleyi. Mol. Biol. Evol. In press. (PDF)

Janouškovec, J. Horák, A., Barrot, K. L., Rohwer, F. L., and Keeling, P. J. 2012. Global analysis of plastid diversity reveals new apicomplexan-related lineages associated with coral reefs. Curr. Biol. R518-520. (PDF)

Burki, F., Felgontov, P. Obernik, M., Cihlar, J., Pain, A., Lukes, J., and Keeling, P.J. 2012. Re-evaluating the green vs. red signal in eukaryotes with secondary plastids of red algal origin. Genome Biol. Evol. 4, evs049. (PDF)

Okamoto, N.,Burki, F. and Keeling, P. J. 2012. Description of two species of early branching dinoflagellates, Psammosa pacifica n. g., n. sp. and P. atlantica n. sp. PLoS One 7, e34900. (PDF)

Burki, F. Okamoto, N. Pombert, J.-F., and Keeling, P. J. 2012. Phylogenomic evidence for a pholyphyletic origin of the cryptophytes, haptophytes, and associated heterotrophic lineages. Proc. Roy. Soc. B, 279, 2246-2254. (PDF)

Zhao, S., Burki, F., Brate, J., Keeling, P. J., Klaveness, D., and Shalchian-Tabrizi, K. 2012. Collodictyon – an ancient lineage in the tree of eukaryotes. Mol. Biol. Evol. 29, 1557-1568. (PDF)

Yuan, C.L., Krause, P., Keeling, P. J., Horák, A. Bent, S., Rollend, L., and Hua, X.G. 2012. A primitive apicomplexan-related parasitic infection in a woman with relapsing Babesia-like Illness. Emerg. Infect. Dis. 18, 125-1127. (PDF)

Hirakawa, Y. Burki, F., and Keeling, P. J. 2012. Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga. Eukaryot. Cell. 11:324-333 (PDF)

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2011

Fischer, M.G. and C.A. Suttle. 2011. A Virophage at the origin of large DNA transposons. Science 332: 231-234

Matthews, B., S. Hausch, C. Winter, C.A. Suttle and J.B. Shurin. 2011. Contrasting ecosystem effects of morphologically similar copepods. PLoS ONE 6(11): e26700

Deslippe, J.R., Hartmann, M., Mohn, W.W., Simard, S.W. 2011. Long-term experimental manipulation of climate alters the ectomycorrhizal community of Betula nana in Arctic tundra. Global Change Biology 17:1625-1636.

Saldarriaga, J. F., Gile, G. H., James, E. R., Horák, A., Scheffrahan, R. H., and Keeling, P. J. 2011. Morphology and molecular phylogeny of Pseudotrichonympha paulistana and Pseudotrichonympha hertwigi (Trichonymphea, Parabasalia) from neotropical rhinotermitids. J. Eukaryot. Microbiol. 58, 487-496. (PDF)

Hartmann M., C. G. Howes, V. Veldre, S. Schneider, P. A. Vaishampayan, A. C. Yannarell, C. Quince, P. Johansson, K. J. Björkroth, K. Abarenkov, S. J. Hallam, W. W. Mohn and R. H. Nilsson. 2011. V-RevComp: automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiol. Lett. Jun;319(2):140-5.

Mewis, K., M. Taupp and S.J. Hallam. A high-throughput screen for biomining cellulase activity from metagenomic libraries. J. Vis. Exp. 2011 Feb 1;(48). pii: 2461. doi: 10.3791/2461. [1 citation, 17, 081 views]

Walsh D.A. and S.J. Hallam. 2011. Bacterial community diversity and population dynamics in a seasonally anoxic fjord: Saanich Inlet, Chapter 25:253-267 Handbook of Molecular Microbial Ecology II: Metagenomics and Complementary Approaches, Wiley-Blackwell, Ed. Frans de Bruijn.

Taupp, M., K. Mewis and S.J. Hallam. 2011. The art and design of functional metagenomic screens. Curr. Opin. Biotechnol. 22(3):465-72, doi:10.1016/j.copbio.2011.02.010.

Rueckert, S., Simdyanov, T.G., Aleshin, V.V. and Leander, B.S. 2011. Identity of a divergent environmental DNA sequence clade using the phylogeny of gregarine parasites (Apicomplexa) from crustacean hosts. PLoS ONE. 6:e18163 (17 pages). (PDF)

Heger, T.J., Pawlowski, J., Lara, E., Todorov, M., Golemansky, V., Leander, B.S. and Mitchell, E.A.D. 2011. Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida). Protist. 162:131-141. (PDF)

Rueckert, S., Villette, P. and Leander, B.S. 2011. Species boundaries in gregarine apicomplexans: A case study comparison of morphometric and molecular variability in Lecudina cf. tuzetae (Eugregarina, Lecudinidae). J. Eukaryot. Microbiol. 58:275-283. (PDF)

Hartmann, M., Howes, C.G., Veldre, V., Schneider, S., Vaishampayan, P.A., Yannarell, A.C., Quince, C., Johansson, P., Björkroth, K.J., Abarenkov, K., Mohn, W.W., Nilsson, R.H.. 2011. V-RevComp: Automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiol. Ecol. 319:140-145.

Carpenter, K. J., Horák, A., Chow, L., and Keeling, P. J. 2011. Associations of cellulolytic parabasalid protests and their bacterial symbionts in the hindgut of the wood-feeding cockroach Cryptocercus punctulatus. J. Eukaryot. Microbiol. 58, 426-436..

Hirakawa, Y., Burki, F., and Keeling, P. J. 2011. Nucleus- and nucleomorph-targeted histone proteins in a cholarachniophyte alga. Mol. Microbiol. 80, 1339-1449. (PDF)

Smith, D.R., Burki, F., Yamada, T., Grimwood, J., Grigoriev, I.V., Van Etten, J.L., Keeling, P.J. 2011. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight onto the evolution of organelle DNA nucleotide landscape. PLoS One. 6, e23624. (PDF)

Slamovits, C. H., Okamoto, N., Burri, L., James, E. R., and Keeling, P. J. 2011. A bacterial proteorhodopsin proton pump in marine heterotrophic eukaryotes. Nat. Comm. 2, 183. (PDF)

Lowe, C. D., Keeling, P. J., Martin, L. E., Slamovits, C. H., Watts, P. C., Montangnes, D. J. S. 2011. Who is Oxyrrhis marina? Morphological and phylogenetic studies of an unusual dinoflagellate. J. Plankton Res. 33, 591-602.(PDF)

Slamovits, C. H., and Keeling, P. J. 2011. Contributions of Oxyrrhis marina to molecular biology, genomics, and organelle evolution of alveolates. J. Plankton Res. 33, 555-567. (PDF)

Montagnes, D. J. S., Lowe, C. D., Martin, L. E., Watts, P. C., Roberts, E. C., Wooton, E. C., Keeling, P. J., Slamovits, C. H., Kimmance, S. E., Davidson, K., Jeon, H. J., Breckels, M. N., Boakes, D. E., Steinke, M., and Yang, Z. 2011. Oxhrrhis marina, the “pink rat”: a model protozoon. J. Plankton Res. 33, 549-554. (PDF)

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2010

Hartmann, M., Howes, C.G., Abarenkov, K., Mohn, W.W., Nilsson, R.H., 2010. V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J. Microbiol. Meth. 83:250-253.

Zaikova, E., D. A. Walsh, C. P. Stilwell, W. W. Mohn, P. D. Tortell, and S. J. Hallam. 2010. Microbial community dynamics in a seasonally anoxic fjord: Sannich Inlet British Columbia. Env. Micro. 12(1):172-91.

Weidner, M.M., M. Taupp and S.J. Hallam. Expression of recombinant proteins in the methylotrophicyeast, Pichia pastoris. J. Vis. Exp. 2010 Feb 25;(36),p ii:1862. doi:10.3791/1862.

Taupp, M. and S.J. Hallam. 2010. The “meta-methanoxgenome” Part 23 in the Handbook of Hydrocarbon Microbiology, doi:10.1007/978-3-540-77587-4_162.

Taupp, M., L. Constan, S.J. Hallam. 2010. The biochemistry of anaerobic methane oxidation Part 17 in the Handbook of Hydrocarbon Microbiology, doi:10.1007/978-3-540-77587-4_63

Burki, F., Kudryavtsev, A., Matz, M. V., Aglyamova, G. V., Bulman, S., Fiers, M., Keeling, P. J., Pawlowski, J. 2010. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol. Biol. 10, 377. (PDF)

Rundell, R. J. and Leander, B. S. 2010. Masters of miniaturization: convergent evolution among interstitial eukaryotes. BioEssays. 32:430-437. (PDF)

Breglia, S. A., Yubuki, N., Hoppenrath, M. and Leander, B. S. 2010. Ultrastructure and molecular phylogenetic position of a novel euglenozoan with extrusive episymbiotic bacteria: Bihospites bacati n. gen. et sp. (Symbiontida). BMC Microbiology. 10:145 (21 pages). (PDF - 31.5 MB)

Edgcomb, V. P., Yubuki, N., Breglia, S., Leander, B. S., and Bernhard, J. 2010. Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine environments: evidence for symbiont and host co-evolution. The ISME Journal. doi:10.1038/ismej.2010.121. (PDF)

Yubuki, N., Céza, V., Cepicka, I., Yabuki, A., Inagaki, Y, Nakayama, T. Inouye, I. and Leander, B. S. 2010. Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. gen. et sp., as inferred from small subunit rDNA Sequences. J. Eukaryot. Microbiol. In press.

Heger, T. J., Mitchell, E. A. D., Todorov, M., Golemansky, V., Lara, E., Leander, B. S. and Pawlowski, J. 2010. Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent. Mol. Phylo. Evol. 55:113-122. (PDF)

Rueckert, S. and Leander, B. S. 2010. Description of Trichotokara nothriae n. gen. et sp. (Apicomplexa, Lecudinidae) - an intestinal gregarine of Nothria conchylega (Polychaeta, Onuphidae). J. Invert. Path. 104:172-179. (PDF) (Cover)

Yubuki, N., Leander, B. S. and Silberman, J. D. 2010. Ultrastructure and molecular phylogenetic position of a novel phagotrophic stramenopile from low oxygen environments: Rictus lutensis gen. et sp. nov. (Bicosoecida, incertae sedis). Protist. 161:264-278. (PDF)

Hoppenrath, M., Yubuki, N., Bachvaroff, S. and Leander, B. S. 2010. Re-classification of Pheopolykrikos hartmannii as Polykrikos (Dinophyceae) based partly on the ultrastructure of complex extrusomes. Europ. J. Protistol. 46:29-37. (PDF)

Keeling, P. J., Leander, B. S. and Lukes, J. 2010. Does complexity necessarily arise from selective advantage? Proceedings of the National Academy of Sciences, USA. 107:E26. (PDF)

Heger, T. J., Pawlowski, J., Lara, E., Todorov, M., Golemansky, V., Leander, B. S. and Mitchell, E. A. D. 2010. Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida). Protist. In press. (PDF)

Rueckert, S., Chantangsi, C. and Leander, B. S. 2010. Molecular systematics of marine gregarines (Apicomplexa) from North-eastern Pacific polychaetes and nemerteans, with descriptions of three new species: Lecudina phyllochaetopteri sp. nov., Difficilina tubulani sp. nov., and Difficilina paranemertis sp. nov. Int. J. Syst. Evol. Microbiol. In press. (Cover)

Kolisko, M., Silberman, J. D., Cepicka, I., Yubuki, N., Takishita, K., Yabuki, A., Leander, B. S., Inouye, I., Inagaki, Y., Roger, A. J. and Simpson, A. G. B. 2010. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environ. Microbiol. 12: In press. (PDF)

Prokopowicz, A., Rueckert, S., Leander, B. S., Michaud, J. and Fortier, L. 2010. Parasitic infection of the hyperiid amphipod Themisto libellula in the Canadian Beaufort Sea (Arctic Ocean), with a description of Ganymedes themistos sp. n. (Apicomplexa, Gregarinia). Polar Biology. 33: In press. (PDF)

Kim, E., Yubuki, N., Leander, B. S. and Graham, L. E. 2010. Ultrastructure and 18S rDNA phylogeny of Apoikia lindahlii comb. nov.(Chrysophyceae) and its epibiontic protists, Filos agilis gen. et sp. nov. (Bicosoecida) and Nanos amicus gen. et sp. nov. (Bicosoecida). Protist. 161:177-196. (PDF)

Stern, R.F., Horák, A., Andrew, R. L., Coffroth, M. A., Anderson, R. A., Kupper, F. C., Jameson, I., Hoppenrath, M., Veron, B., Kasai, F., Brand, J., James, E. R., and Keeling, P. J. 2010. Environmental barcoding reveals massive dinoflagellate diversity in marine environments. Plos One, in press.

Burki, F., Kudryavtsev, A., Matz, M.V., Aglyamova, G.V., Bulman, S., Fiers, M., Keeling, P.J., Pawlowski, J. 2010. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol. Biol., in press.

Fischer, M.G., M.J. Allen, W.H. Wilson and C.A. Suttle. 2010. A giant virus with a remarkable complement of genes infects marine zooplankton. Proceedings of the National Academy of Sciences 107: 19508-19513

Hirakawa Y., Gile G.H., Ota S., Keeling P.J., Ishida K.I. 2010. Characterization of periplastidal compartment targeting signals in chlorarachniophytes. Mol. Biol. Evol. 27, 1538-1545. (PDF)

Carpenter, K. J., Horák, A., and Keeling, P.J. 2010. Phylogenetic position and morphology of Spirotrichosomidae (Parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist 161, 122-132. (PDF)

Janouškovec J., Horák A., Obornik M., Lukeš J., Keeling P.J. 2010. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc. Natl. Acad. Sci. USA. 107, 10949-10954. (PDF)

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2009

Rueckert, S. and Leander, B. S. 2009. Phylogenetic position and description of Rhytidocystis cyamus sp. n. (Apicomplexa, Rhytidocystidae): A novel intestinal parasite of the North-eastern Pacific stink worm (Polychaeta, Opheliidae, Travisia pupa). Marine Biodiversity. 39:227-234. (PDF)

Walsh, D. A., E. Zaikova, C. G. Howes, Y. C. Song., J. J. Wright, S. Tringe, P. D. Tortell, and S. J. Hallam. 2010. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326(5952):578-82.

Zaikova, E., Walsh, D. A., Stilwell, C. P., Mohn, W. W., Tortell, P. D., and Hallam, S. J. 2009. Microbial community dynamics in a seasonally anoxic fjord: Sannich Inlet British Columbia. Environmental Microbiology, in press.

Burki, F., Inagaki, I. Brate, J., Archibald, J. M., Keeling, P. J., Cavalier-Smith, T. Horák, A., Sakaguchi, M. Hashimoto, T., Klaveness, D. Jokobsen, K. S., Pawlowski, J., and Shalchian-Tabrizi, K. 2009. Early evolution of eukaryotes: two enigmatic heterotrophic groups are related to photosynthetic chromalveolates. Genom. Biol. Evol., in press.

Keeling, P. J. 2009. The endosymbiotic origin, diversification, and fate of plastids. Proc. Roy Soc. Lond., in press. Carpenter, K. J., Horák, A., and Keeling, P. J. 2009. Phylogenetic position and morphology of Spirotrichosomidae (Parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist, in press.

Keeling, P. J. 2009. Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr. Opin. Genet. Dev., in press.

Hoppenrath, M., Yubuki, N., Bachvaroff, S. and Leander, B.S. 2009. Re-classification of Pheopolykrikos hartmannii as Polykrikos (Dinophyceae) based partly on the ultrastructure of complex extrusomes. Europ. J. Protistol., In press.

Kim, E., Yubuki, N., Leander, B.S. and Graham, L.E. 2009. Ultrastructure and 18S rDNA phylogeny of Apoikia lindahli comb. nov. (Chrysophyceae) and its epibionts, Filos agilis gen. et sp. nov. (Bicosoecida) and Nanos amicus gen. et sp. nov. (Bicosoecida). Protist, In press.

Hartmann, M., Lee, S., Hallam, S. J., and Mohn, W. W. 2009. Timber harvesting affects soil bacterial, achaeal and eukaryal communities in different soil strata. Environmental Microbiology. 11(6):1453-1462

Hartmann, M., S. Lee, S. J. Hallam and W. W. Mohn. 2009. Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Env. Micro. 11(12):3045-62.

Taupp, M., S. Lee, A. Hawley, J. Yang, S.J. Hallam. Large insert environmental genomic library production. J. Vis. Exp. 2009 Sep 23;(31),pii: 1387. doi:10.3791/1387.

Lee, S., and S.J. Hallam. Extraction of high molecular weight genomic DNA from soils and sediments. J. Vis. Exp. 2009 Nov 10;(33), pii:1569. doi:10.3791/1569.

Wright, J.J., S. Lee, E. Zaikova, D.A. Walsh and S.J. Hallam. DNA extraction from 0.22 micron Sterivex filters and cesium chloride density gradient centrifugation. J. Vis. Exp. 2009 Sep 18;(31). pii: 1352. doi:10.3791/1352.

Walsh, D.A., E. Zaikova, and S.J. Hallam. Small volume filtration of coastal seawater samples. J. Vis. Exp. 2009 Jun 19;(28). pii: 1163. doi: 10.3791/1163.

Walsh, D.A., E. Zaikova, and S.J. Hallam. Large volume filtration of coastal seawater samples. J. Vis. Exp. 2009 Jun 18;(28). pii: 1161. doi: 10.3791/1161.

Zaikova, E., A. Hawley, D.A. Walsh, and S.J. Hallam. Seawater sampling and collection. J. Vis. Exp. 2009 Jun 17;(28). pii: 1159. doi: 10.3791/1159.


The following papers summarize a symposium that took place July 28 in Halifax and was co- funded by the CMDE and CIFAR.

Keeling, P. J. 2009. Chromalveolates and the evolution of plastids by secondary endosymbiosis. J. Eukaryot. Microbiol. 56, 1-8. (PDF)

Bolte, K., Bullmann, L., Hempel, F., Bozarth, A., Zauner, S., and Maier, U.-G. 2009. Protein targeting into secondary plastids. J. Eukaryot. Microbiol. 56, 9-15. (PDF)

Pawlowski, J. and Burki, F. 2009. Untangling the phylogeny of amoeboid protists. J. Eukaryot. Microbiol. 56, 16-25. (PDF)

Cavalier-Smith, T. 2009. Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. J. Eukaryot. Microbiol. 56, 26-33. (PDF)


Yubuki, N., Edgcomb, V., Bernhard, J. and Leander, B.S. 2009. Ultrastructure and molecular phylogeny of Calkinsia aureus: Cellular identity of a novel clade of deep sea euglenozoans with epibiotic bacteria. BMC Microbiology 9, 16 (22 pages). (PDF)

Rueckert, S. and Leander, B.S. 2009. Molecular phylogeny and surface morphology of marine archigregarines (Apicomplexa) - Selenidium spp., Filipodium phascolosomae n. sp. and Platyproteus n. gen. et comb. - from North-eastern Pacific peanut worms (Sipuncula). J. Eukaryot. Microbiol. 56, 428-439. (PDF)

Okamoto, N., Chantangsi, C., Horák, A., Leander, B.S. and Keeling, P.J. 2009. Molecular phylogenetic position and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS ONE 17, e7080. (PDF)

Lukes, J., Leander, B.S. and Keeling, P.J. 2009. Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates. Proceedings of the National Academy of Sciences, USA 106, 9963-9970. (PDF)

Slamovits, C H. and Keeling, P.J. 2009. Evolution of ultrasmall introns in highly reduced nuclear genomes. Mol. Biol. Evol. 26, 1699-1705. (PDF)

Keeling, P.J. 2009. Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. Methods Mol. Biol. 532, 501-515. (PDF)

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2008

Leander, B.S. 2008. A hierarchical view of convergent evolution in microbial eukaryotes. J. Eukaryot. Microbiol. 55, 59-68. (PDF)

Yubuki, N. and Leander, B.S. 2008. Ultrastructure and molecular phylogeny of Stephanopogon minuta: an enigmatic microeukaryote from marine interstitial environments. Europ. J. Protistol. 44, 241-253. (PDF)

Leander, B.S. 2008. Different modes of convergent evolution reflect phylogenetic distances. Trends Ecol. Evol. 23, 481-482. (PDF)

Rueckert, S. and Leander, B.S. 2008. Morphology and molecular phylogeny of Haplozoon praxillellae n. sp. (Dinoflagellata): A novel intestinal parasite of the maldanid polychaete Praxillella pacifica Berkeley. Europ. J. Protistol. 44, 299-307. (PDF)

Leander, B.S. 2008. Marine gregarines - evolutionary prelude to the apicomplexan radiation? Trends Parasitol. 24, 60-67. (PDF)

Rueckert, S. and Leander, B.S. 2008. Morphology and phylogeny of two novel marine gregarines (Apicomplexa, Eugregarinorida) - Lankesteria chelyosomae n. sp. and Lankesteria cystodytae n. sp. -- from the intestines of North-eastern Pacific ascidians. Zoologica Scripta. 37, 637-645. (PDF)

McEwan, M. L., Humayun, R., Slamovits, C. H. and Keeling, P. J. 2008. Nuclear genome sequence survey of the dinoflagellate Heterocapsa triquetra. J. Eukaryot. Microbiol. 55, 530-535. (PDF)

Keeling, P. J. and Palmer, J. D. 2008. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9, 605-618. (PDF)

Slamovits, C. H. and Keeling, P. J. 2008. Widespread recycling of processed cDNAs in dinoflagellates. Curr. Biol. 18, R550-R552. (PDF)

Slamovits, C. H., Keeling, P. J. 2008. Plastid-derived genes in the non-photosynthetic alveolate Oxyrrhis marina. Mol. Biol. Evol. 25, 1297-1306. (PDF)

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2007

Slamovits, C. H., Saldarriaga, J. F., Larocque, A. and Keeling, P. J. 2007. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J. Mol. Biol. 372, 356-368. (PDF)

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