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Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States).

Davenport EJ, Neudeck MJ, Matson PG, Bullerjahn GS, Davis TW, Wilhelm SW, Denney MK, Krausfeldt LE, Stough JMA, Meyer KA, Dick GJ, Johengen TH, Lindquist E, Tringe SG, McKay RML.

Front Microbiol. 2019 Sep 10;10:2081. doi: 10.3389/fmicb.2019.02081. eCollection 2019.


The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally.

Dick GJ.

Nat Rev Microbiol. 2019 May;17(5):271-283. doi: 10.1038/s41579-019-0160-2. Review.


A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales.

Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW.

Harmful Algae. 2018 Jul;77:93-107. doi: 10.1016/j.hal.2018.05.009. Epub 2018 Jun 29.


Nitrogen limitation, toxin synthesis potential, and toxicity of cyanobacterial populations in Lake Okeechobee and the St. Lucie River Estuary, Florida, during the 2016 state of emergency event.

Kramer BJ, Davis TW, Meyer KA, Rosen BH, Goleski JA, Dick GJ, Oh G, Gobler CJ.

PLoS One. 2018 May 23;13(5):e0196278. doi: 10.1371/journal.pone.0196278. eCollection 2018.


Sulfide inhibition of nitrite oxidation in activated sludge depends on microbial community composition.

Delgado Vela J, Dick GJ, Love NG.

Water Res. 2018 Jul 1;138:241-249. doi: 10.1016/j.watres.2018.03.047. Epub 2018 Mar 17.


Interactions between nitrogen form, loading rate, and light intensity on Microcystis and Planktothrix growth and microcystin production.

Chaffin JD, Davis TW, Smith DJ, Baer MM, Dick GJ.

Harmful Algae. 2018 Mar;73:84-97. doi: 10.1016/j.hal.2018.02.001. Epub 2018 Feb 8.


Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment.

Stadler LB, Delgado Vela J, Jain S, Dick GJ, Love NG.

Microb Biotechnol. 2018 Nov;11(6):995-1007. doi: 10.1111/1751-7915.12870. Epub 2017 Oct 27.


Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms.

Meyer KA, Davis TW, Watson SB, Denef VJ, Berry MA, Dick GJ.

PLoS One. 2017 Oct 11;12(10):e0183859. doi: 10.1371/journal.pone.0183859. eCollection 2017.


Ecophysiological Examination of the Lake Erie Microcystis Bloom in 2014: Linkages between Biology and the Water Supply Shutdown of Toledo, OH.

Steffen MM, Davis TW, McKay RML, Bullerjahn GS, Krausfeldt LE, Stough JMA, Neitzey ML, Gilbert NE, Boyer GL, Johengen TH, Gossiaux DC, Burtner AM, Palladino D, Rowe MD, Dick GJ, Meyer KA, Levy S, Boone BE, Stumpf RP, Wynne TT, Zimba PV, Gutierrez D, Wilhelm SW.

Environ Sci Technol. 2017 Jun 20;51(12):6745-6755. doi: 10.1021/acs.est.7b00856. Epub 2017 Jun 8.


Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

Sharrar AM, Flood BE, Bailey JV, Jones DS, Biddanda BA, Ruberg SA, Marcus DN, Dick GJ.

Front Microbiol. 2017 May 8;8:791. doi: 10.3389/fmicb.2017.00791. eCollection 2017.


Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes.

Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ, Sarnelle O, Denef VJ.

Front Microbiol. 2017 Mar 8;8:365. doi: 10.3389/fmicb.2017.00365. eCollection 2017.


Cyanobacterial harmful algal blooms are a biological disturbance to Western Lake Erie bacterial communities.

Berry MA, Davis TW, Cory RM, Duhaime MB, Johengen TH, Kling GW, Marino JA, Den Uyl PA, Gossiaux D, Dick GJ, Denef VJ.

Environ Microbiol. 2017 Mar;19(3):1149-1162. doi: 10.1111/1462-2920.13640. Epub 2017 Feb 16.


Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems.

Marcus DN, Pinto A, Anantharaman K, Ruberg SA, Kramer EL, Raskin L, Dick GJ.

Environ Microbiol Rep. 2017 Apr;9(2):120-128. doi: 10.1111/1758-2229.12508. Epub 2017 Jan 25.


Embracing the mantra of modellers and synthesizing omics, experiments and models.

Dick GJ.

Environ Microbiol Rep. 2017 Feb;9(1):18-20. doi: 10.1111/1758-2229.12491. Epub 2016 Nov 28. No abstract available.


Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

Kinsman-Costello LE, Sheik CS, Sheldon ND, Allen Burton G, Costello DM, Marcus D, Uyl PA, Dick GJ.

Geobiology. 2017 Mar;15(2):225-239. doi: 10.1111/gbi.12215. Epub 2016 Sep 27.


Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes.

Li M, Jain S, Dick GJ.

Front Microbiol. 2016 Jul 27;7:1125. doi: 10.3389/fmicb.2016.01125. eCollection 2016.


Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture.

Den Uyl PA, Richardson LL, Jain S, Dick GJ.

PLoS One. 2016 Jun 23;11(6):e0157953. doi: 10.1371/journal.pone.0157953. eCollection 2016.


Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System.

Pinto AJ, Marcus DN, Ijaz UZ, Bautista-de Lose Santos QM, Dick GJ, Raskin L.

mSphere. 2015 Dec 30;1(1). pii: e00054-15. doi: 10.1128/mSphere.00054-15. eCollection 2016 Jan-Feb.


Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity.

Flood BE, Fliss P, Jones DS, Dick GJ, Jain S, Kaster AK, Winkel M, Mußmann M, Bailey J.

Front Microbiol. 2016 May 3;7:603. doi: 10.3389/fmicb.2016.00603. eCollection 2016.


Deciphering the Complex Chemistry of Deep-Ocean Particles Using Complementary Synchrotron X-ray Microscope and Microprobe Instruments.

Toner BM, German CR, Dick GJ, Breier JA.

Acc Chem Res. 2016 Jan 19;49(1):128-37. doi: 10.1021/acs.accounts.5b00282. Epub 2015 Dec 4.


Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments.

Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP.

Environ Microbiol. 2016 Apr;18(4):1200-11. doi: 10.1111/1462-2920.13142. Epub 2016 Jan 18.


Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.

Li M, Baker BJ, Anantharaman K, Jain S, Breier JA, Dick GJ.

Nat Commun. 2015 Nov 17;6:8933. doi: 10.1038/ncomms9933.


Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center.

Anantharaman K, Breier JA, Dick GJ.

ISME J. 2016 Jan;10(1):225-39. doi: 10.1038/ismej.2015.81. Epub 2015 Jun 5.


Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time.

Sheik CS, Stevenson EI, Den Uyl PA, Arendt CA, Aciego SM, Dick GJ.

Front Microbiol. 2015 May 20;6:495. doi: 10.3389/fmicb.2015.00495. eCollection 2015.


Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET-743.

Schofield MM, Jain S, Porat D, Dick GJ, Sherman DH.

Environ Microbiol. 2015 Oct;17(10):3964-75. doi: 10.1111/1462-2920.12908. Epub 2015 Jul 21.


Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.

Baker BJ, Lazar CS, Teske AP, Dick GJ.

Microbiome. 2015 Apr 13;3:14. doi: 10.1186/s40168-015-0077-6. eCollection 2015.


Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents.

Reed DC, Breier JA, Jiang H, Anantharaman K, Klausmeier CA, Toner BM, Hancock C, Speer K, Thurnherr AM, Dick GJ.

ISME J. 2015 Aug;9(8):1857-69. doi: 10.1038/ismej.2015.4. Epub 2015 Feb 6.


Ecological and genetic interactions between cyanobacteria and viruses in a low-oxygen mat community inferred through metagenomics and metatranscriptomics.

Voorhies AA, Eisenlord SD, Marcus DN, Duhaime MB, Biddanda BA, Cavalcoli JD, Dick GJ.

Environ Microbiol. 2016 Feb;18(2):358-71. doi: 10.1111/1462-2920.12756. Epub 2015 Mar 4.


Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin.

Sheik CS, Anantharaman K, Breier JA, Sylvan JB, Edwards KJ, Dick GJ.

ISME J. 2015 Jun;9(6):1434-45. doi: 10.1038/ismej.2014.228. Epub 2014 Dec 9.


Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen E, Mackey KR, DeLong EF.

Stand Genomic Sci. 2014 Mar 15;9(3):1252-8. doi: 10.4056/sigs.5749944. eCollection 2014 Jun 15.


Sulfur oxidation genes in diverse deep-sea viruses.

Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ.

Science. 2014 May 16;344(6185):757-60. doi: 10.1126/science.1252229. Epub 2014 May 1.


Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol.

Vorobev A, Jagadevan S, Jain S, Anantharaman K, Dick GJ, Vuilleumier S, Semrau JD.

Appl Environ Microbiol. 2014 May;80(10):3044-52. doi: 10.1128/AEM.00218-14. Epub 2014 Mar 7.


Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents.

Li M, Toner BM, Baker BJ, Breier JA, Sheik CS, Dick GJ.

Nat Commun. 2014;5:3192. doi: 10.1038/ncomms4192.


Gene-centric approach to integrating environmental genomics and biogeochemical models.

Reed DC, Algar CK, Huber JA, Dick GJ.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1879-84. doi: 10.1073/pnas.1313713111. Epub 2014 Jan 21.


Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume.

Li M, Jain S, Baker BJ, Taylor C, Dick GJ.

Environ Microbiol. 2014 Jan;16(1):60-71. doi: 10.1111/1462-2920.12182. Epub 2013 Jul 4.


Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics.

Sheik CS, Jain S, Dick GJ.

Environ Microbiol. 2014 Jan;16(1):304-17. doi: 10.1111/1462-2920.12165. Epub 2013 Jun 30.


The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS.

Front Microbiol. 2013 May 21;4:124. doi: 10.3389/fmicb.2013.00124. eCollection 2013.


Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling.

Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD, Dick GJ.

ISME J. 2013 Oct;7(10):1962-73. doi: 10.1038/ismej.2013.85. Epub 2013 May 23. Erratum in: ISME J. 2013 Oct;7(10):2060.


Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria.

Anantharaman K, Breier JA, Sheik CS, Dick GJ.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):330-5. doi: 10.1073/pnas.1215340110. Epub 2012 Dec 20.


Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume.

Baker BJ, Lesniewski RA, Dick GJ.

ISME J. 2012 Dec;6(12):2269-79. doi: 10.1038/ismej.2012.64. Epub 2012 Jun 14.


The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs.

Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ.

ISME J. 2012 Dec;6(12):2257-68. doi: 10.1038/ismej.2012.63. Epub 2012 Jun 14.


Cyanobacterial life at low O(2): community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat.

Voorhies AA, Biddanda BA, Kendall ST, Jain S, Marcus DN, Nold SC, Sheldon ND, Dick GJ.

Geobiology. 2012 May;10(3):250-67. doi: 10.1111/j.1472-4669.2012.00322.x. Epub 2012 Mar 8.


Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray.

Lee PK, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L.

ISME J. 2011 Jun;5(6):1014-24. doi: 10.1038/ismej.2010.202. Epub 2011 Jan 13.


Enigmatic, ultrasmall, uncultivated Archaea.

Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF.

Proc Natl Acad Sci U S A. 2010 May 11;107(19):8806-11. doi: 10.1073/pnas.0914470107. Epub 2010 Apr 26.


Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

Dick GJ, Tebo BM.

Environ Microbiol. 2010 May;12(5):1334-47. doi: 10.1111/j.1462-2920.2010.02177.x. Epub 2010 Feb 25.


Community-wide analysis of microbial genome sequence signatures.

Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF.

Genome Biol. 2009;10(8):R85. doi: 10.1186/gb-2009-10-8-r85. Epub 2009 Aug 21.


Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.

Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2009 Jul;75(13):4599-615. doi: 10.1128/AEM.02943-08. Epub 2009 May 8.


Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.

Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM.

Appl Environ Microbiol. 2008 May;74(9):2646-58. doi: 10.1128/AEM.01656-07. Epub 2008 Mar 14.

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