Microbial Diversity Publications | Marine Biological Laboratory

Thesis

Meredith, L. K. (2013). Field measurement of the fate of atmospheric H₂ in a forest environment : from canopy to soil [Massachusetts Institute of Technology]. https://dspace.mit.edu/handle/1721.1/79283

Preprints

Urtecho, G., Campbell, D. E., Hershey, D. M., Whitaker, R. J., & O’Toole, G. A. (2020). Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18. BioRxiv, 2020.04.13.038638. https://doi.org/10.1101/2020.04.13.038638

Mitchison-Field, L. M. Y., Vargas-Muñiz, J. M., Stormo, B. M., Vogt, E. J. D., Van Dierdonck, S., Ehrlich, C., Lew, D. J., Field, C. M., & Gladfelter, A. S. (2019). Unconventional cell division cycles from marine-derived yeasts. BioRxiv, 657254. https://doi.org/10.1101/657254

Fiebig, A. (2019). The role of Caulobacter cell surface structures in colonization of the air-liquid interface. BioRxiv, 524058. https://doi.org/10.1101/524058

Journal articles

Mickol, R. L., Louyakis, A. S., Kee, H. L., Johnson, L. K., Dawson, S. C., Hargreaves, K. R., Chadwick, G. L., Newman, D. K., Leadbetter, J. R., & Brown, C. T. (2021). Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR. Microbiology Resource Announcements, 10(1). https://doi.org/10.1128/MRA.01302-20

Bhatnagar, S., Cowley, E. S., Kopf, S. H., Pérez Castro, S., Kearney, S., Dawson, S. C., Hanselmann, K., & Ruff, S. E. (2020). Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome, 15(1), 3. https://doi.org/10.1186/s40793-019-0348-0

Urtecho, G., Campbell, D. E., Hershey, D. M., Hussain, F. A., Whitaker, R. J., & O’Toole, G. A. (2020). Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18. MSphere, 5(6). https://doi.org/10.1128/mSphere.00898-20

Yang, T., Teske, A., Ambrose, W., Salman-Carvalho, V., Bagnell, R., & Nielsen, L. P. (2019). Intracellular calcite and sulfur dynamics of Achromatium cells observed in a lab-based enrichment and aerobic incubation experiment. Antonie van Leeuwenhoek, 112(2), 263–274. https://doi.org/10.1007/s10482-018-1153-2

Mitchison-Field, L. M. Y., Vargas-Muñiz, J. M., Stormo, B. M., Vogt, E. J. D., Van Dierdonck, S., Pelletier, J. F., Ehrlich, C., Lew, D. J., Field, C. M., & Gladfelter, A. S. (2019). Unconventional Cell Division Cycles from Marine-Derived Yeasts. Current Biology, 29(20), 3439-3456.e5. https://doi.org/10.1016/j.cub.2019.08.050

Fiebig, A. (2019). Role of Caulobacter Cell Surface Structures in Colonization of the Air-Liquid Interface. Journal of Bacteriology, 201(18). https://doi.org/10.1128/JB.00064-19

Guzman, M. S., Kuse, J. C., Santiago-Merced, N., & Bose, A. (2019). Draft Genome Sequences of Two Closely Related Marichromatium Isolates, Photosynthetic Gammaproteobacteria from Marine Ecosystems. Microbiology Resource Announcements, 8(2). https://doi.org/10.1128/MRA.01510-18

Kee, H. L., Mikheyeva, I. V., Mickol, R. L., Dawson, S. C., Newman, D. K., & Leadbetter, J. R. (2019). Draft Genome Sequence of the Iridescent Marine Bacterium Tenacibaculum discolor Strain IMLK18. Microbiology Resource Announcements, 8(5). https://doi.org/10.1128/MRA.01683-18

Perry, E. K., & Newman, D. K. (2019). The transcription factors ActR and SoxR differentially affect the phenazine tolerance of Agrobacterium tumefaciens. Molecular Microbiology, mmi.14263. https://doi.org/10.1111/mmi.14263

Huang, Y. Y., Martínez-del Campo, A., & Balskus, E. P. (2018). Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity. Gut Microbes, 1–16. https://doi.org/10.1080/19490976.2018.1435244

Wilbanks, E. G., Salman-Carvalho, V., Jaekel, U., Humphrey, P. T., Eisen, J. A., Buckley, D. H., & Zinder, S. H. (2017). The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.01623

Guzman, M. S., McGinley, B., Santiago-Merced, N., Gupta, D., & Bose, A. (2017). Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur Bacterium Rhodovulum sulfidophilum. Genome Announcements, 5(11). https://doi.org/10.1128/genomeA.00029-17

Alexiev, A., Krusor, M. L., Jospin, G., Lang, J. M., Eisen, J. A., & Coil, D. A. (2016). Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina. Genome Announcements, 4(2). https://doi.org/10.1128/genomeA.00116-16

Liu, X.-L., De Santiago Torio, A., Bosak, T., & Summons, R. E. (2016). Novel archaeal tetraether lipids with a cyclohexyl ring identified in Fayetteville Green Lake, NY, and other sulfidic lacustrine settings. Rapid Communications in Mass Spectrometry, 30(10), 1197–1205. https://doi.org/10.1002/rcm.7549

Alexiev, A., Krusor, M. L., Jospin, G., Lang, J. M., Eisen, J. A., & Coil, D. A. (2016). Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina. Genome Announcements, 4(1). https://doi.org/10.1128/genomeA.00010-16

Thauer, R. K. (2015). My Lifelong Passion for Biochemistry and Anaerobic Microorganisms. Annual Review of Microbiology, 69(1), 1–30. https://doi.org/10.1146/annurev-micro-091014-104344

Pepe-Ranney, C., & Hall, E. K. (2015). The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.00703

Rowe, A. R., Chellamuthu, P., Lam, B., Okamoto, A., & Nealson, K. H. (2015). Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00784

Mariita, R. M., Bhatnagar, S., Hanselmann, K., Hossain, M. J., Korlach, J., Boitano, M., Roberts, R. J., Liles, M. R., Moss, A. G., Leadbetter, J. R., Newman, D. K., & Dawson, S. C. (2015). Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. Genome Announcements, 3(6). https://doi.org/10.1128/genomeA.01504-15

Mariita, R. M., Bhatnagar, S., Hanselmann, K., Hossain, M. J., Korlach, J., Boitano, M., Roberts, R. J., Liles, M. R., Moss, A. G., Leadbetter, J. R., Newman, D. K., & Dawson, S. C. (2015). Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. Genome Announcements, 3(6). https://doi.org/10.1128/genomeA.01506-15

Jones, D. S., Bailey, J. V., & Flood, B. E. (2015). Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens. International Journal of Systematic and Evolutionary Microbiology, 65(8), 2522–2530. https://doi.org/10.1099/ijs.0.000295

Kleindienst, S., Seidel, M., Ziervogel, K., Grim, S., Loftis, K., Harrison, S., Malkin, S. Y., Perkins, M. J., Field, J., Sogin, M. L., Dittmar, T., Passow, U., Medeiros, P. M., & Joye, S. B. (2015). Chemical dispersants can suppress the activity of natural oil-degrading microorganisms. Proceedings of the National Academy of Sciences, 112(48), 14900–14905. https://doi.org/10.1073/pnas.1507380112

Salman, V., Yang, T., Berben, T., Klein, F., Angert, E., & Teske, A. (2015). Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh. The ISME Journal, 9(11), 2503–2514. https://doi.org/10.1038/ismej.2015.62

Bräuer, S. L., Vuono, D., Carmichael, M. J., Pepe-Ranney, C., Strom, A., Rabinowitz, E., Buckley, D. H., & Zinder, S. H. (2014). Microbial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds. Current Microbiology. https://doi.org/10.1007/s00284-014-0643-3

Wilbanks, E. G., Jaekel, U., Salman, V., Humphrey, P. T., Eisen, J. A., Faccioti, M. T., Buckley, D. H., Zinder, S. H., Druschel, G. K., Fike, D. A., & Orphan, V. J. (2014). Microscale sulfur cycling in the phototrophic pink berry consortia of the sippewissett salt marsh. Environmental Microbiology, 16(11), 3398–3415. https://doi.org/10.1111/1462-2920.12388

Meredith, L. K., Rao, D., Bosak, T., Klepac-Ceraj, V., Tada, K. R., Hansel, C. M., Ono, S., & Prinn, R. G. (2014). Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria. Environmental Microbiology Reports, 6(3), 226–238. https://doi.org/10.1111/1758-2229.12116

Blasiak, L. C., Zinder, S. H., Buckley, D. H., & Hill, R. T. (2014). Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis. The ISME Journal, 8(2), 309–320. https://doi.org/10.1038/ismej.2013.156

McNulty, N. P., Wu, M., Erickson, A. R., Pan, C., Erickson, B. K., Martens, E. C., Pudlo, N. A., Muegge, B. D., Henrissat, B., Hettich, R. L., & Gordon, J. I. (2013). Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome. PLoS Biology, 11(8). https://doi.org/10.1371/journal.pbio.1001637

Armitage, D. W., Gallagher, K. L., Youngblut, N. D., Buckley, D. H., & Zinder, S. H. (2012). Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. Frontiers in Microbiology, 3(AUG). https://doi.org/10.3389/fmicb.2012.00293

Adebusoye, S. A., & Miletto, M. (2011). Characterization of multiple chlorobenzoic acid-degrading organisms from pristine and contaminated systems: Mineralization of 2,4-dichlorobenzoic acid. Bioresource Technology, 102(3), 3041–3048. https://doi.org/10.1016/j.biortech.2010.10.026

Shapiro, O. H., Hatzenpichler, R., Buckley, D. H., Zinder, S. H., & Orphan, V. J. (2011). Multicellular photo-magnetotactic bacteria. Environmental Microbiology Reports, 3(2), 233–238. https://doi.org/10.1111/j.1758-2229.2010.00215.x

Burgin, A. J., & Hamilton, S. K. (2008). NO(3)(-)-driven SO(4)(2-) production in freshwater ecosystems: Implications for N and S cycling. ECOSYSTEMS, 11(6), 908–922. https://doi.org/10.1007/s10021-008-9169-5

Breznak, J. A., & Warnecke, F. (2008). Spirochaeta cellobiosiphila sp. nov., a facultatively anaerobic, marine spirochaete. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58(12), 2762–2768. https://doi.org/10.1099/ijs.0.2008/001263-0

Lennon, J. T. (2007). Diversity and Metabolism of Marine Bacteria Cultivated on Dissolved DNA. Applied and Environmental Microbiology, 73(9), 2799–2805. https://doi.org/10.1128/AEM.02674-06

Saltikov, C. W., Cifuentes, A., Venkateswaran, K., & Newman, D. K. (2003). The ars Detoxification System Is Advantageous but Not Required for As(V) Respiration by the Genetically Tractable Shewanella Species Strain ANA-3. Applied and Environmental Microbiology, 69(5), 2800–2809. https://doi.org/10.1128/aem.69.5.2800-2809.2003

Whittle, G., Whitehead, T. R., Hamburger, N., Shoemaker, N. B., Cotta, M. A., & Salyers, A. A. (2003). Identification of a New Ribosomal Protection Type of Tetracycline Resistance Gene, tet(36), from Swine Manure Pits. Applied and Environmental Microbiology, 69(7), 4151–4158. https://doi.org/10.1128/aem.69.7.4151-4158.2003

Zaar, A., Fuchs, G., Golecki, J. R., & Overmann, J. (2003). A new purple sulfur bacterium isolated from a littoral microbial mat, Thiorhodococcus drewsii sp. nov. Archives of Microbiology, 179(3), 174–183. https://doi.org/10.1007/s00203-002-0514-3

Rajagopal, S., Eis, N., & Nickerson, K. W. (2003). Eight Gram-negative bacteria are 10 000 times more sensitive to cationic detergents than to anionic detergents. Canadian Journal of Microbiology, 49(12), 775–779. https://doi.org/10.1139/w03-100

Niggemyer, A., Spring, S., Stackebrandt, E., & Rosenzweig, R. F. (2001). Isolation and Characterization of a Novel As(V)-Reducing Bacterium: Implications for Arsenic Mobilization and the Genus Desulfitobacterium. Applied and Environmental Microbiology, 67(12), 5568–5580. https://doi.org/10.1128/aem.67.12.5568-5580.2001

Whittle, G., Hund, B. D., Shoemaker, N. B., & Salyers, A. A. (2001). Characterization of the 13-KilobaseermF Region of the BacteroidesConjugative Transposon CTnDOT. Applied and Environmental Microbiology, 67(8), 3488–3495. https://doi.org/10.1128/aem.67.8.3488-3495.2001

Shoemaker, N. B., Vlamakis, H., Hayes, K., & Salyers, A. A. (2001). Evidence for Extensive Resistance Gene Transfer among Bacteroides spp. and among Bacteroides and Other Genera in the Human Colon. Applied and Environmental Microbiology, 67(2), 561–568. https://doi.org/10.1128/aem.67.2.561-568.2001

Whittle, G., Hund, B. D., Shoemaker, N. B., & Salyers, A. A. (2001). Characterization of the 13-KilobaseermF Region of the BacteroidesConjugative Transposon CTnDOT. Applied and Environmental Microbiology, 67(8), 3488 LP – 3495. https://doi.org/10.1128/AEM.67.8.3488-3495.2001

Barbieri, E., Paster, B. J., Hughes, D., Zurek, L., Moser, D. P., Teske, A., & Sogin, M. L. (2001). Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda: Loliginidae). Environmental Microbiology, 3(3), 151–167. https://doi.org/10.1046/j.1462-2920.2001.00172.x

Christner, B. C., Mosley‐Thompson, E., Thompson, L. G., & Reeve, J. N. (2001). Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environmental Microbiology, 3(9), 570–577. https://doi.org/10.1046/j.1462-2920.2001.00226.x

Spear, J. R., Figueroa, L. A., & Honeyman, B. D. (2000). Modeling Reduction of Uranium U(VI) under Variable Sulfate Concentrations by Sulfate-Reducing Bacteria. Applied and Environmental Microbiology, 66(9), 3711–3721. https://doi.org/10.1128/aem.66.9.3711-3721.2000

Plugge, C. M., Zoetendal, E. G., & Stams, A. J. (2000). Caloramator coolhaasii sp. nov., a glutamate-degrading, moderately thermophilic anaerobe. International Journal of Systematic and Evolutionary Microbiology, 50(3), 1155–1162. https://doi.org/10.1099/00207713-50-3-1155

Glaeser, J., & Overmann, J. (1999). Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Archives of Microbiology, 171(6), 405–416. https://doi.org/10.1007/s002030050727

Salyers, A. (1999). Microbial diversity – the past and future of microbiology. In recognition of the centennial of the American Society for Microbiology. Environmental Microbiology, 1(1), 5–7. https://doi.org/10.1046/j.1462-2920.1999.00015.x

Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt, E., & Nealson, K. H. (1999). Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. International Journal of Systematic and Evolutionary Microbiology, 49(4), 1341–1351. https://doi.org/10.1099/00207713-49-4-1341

Vetriani, C., Reysenbach, A.-L., & DorÃ©, J. (1998). Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiology Letters, 161(1), 83–88. https://doi.org/10.1111/j.1574-6968.1998.tb12932.x

Sackett, M. J., Armitage, J. P., Sherwood, E. E., & Pitta, T. P. (1997). Photoresponses of the purple nonsulfur bacteria Rhodospirillum centenum and Rhodobacter sphaeroides. Journal of Bacteriology, 179(21), 6764–6768. https://doi.org/10.1128/jb.179.21.6764-6768.1997

Ochs, C. A. (1997). Effects of UV radiation on grazing by two marine heterotrophic nanoflagellates on autotrophic picoplankton. Journal of Plankton Research, 19(10), 1517–1536. https://doi.org/10.1093/plankt/19.10.1517

Lie, T. J., Pitta, T., Leadbetter, E. R., Godchaux III., W., & Leadbetter, J. R. (1996). Sulfonates: novel electron acceptors in anaerobic respiration. Archives of Microbiology, 166(3), 204–210. https://doi.org/10.1007/s002030050376