2018 Geodynamics Program:

Guest Speaker Readings & Presentation
Jennifer Bowen's Talk Abstract and Suggested Readings

Talk Abstract

Microbial and Biogeochemical Responses to 15 years of Nutrient Enrichment in a New England Salt Marsh --Jennifer Bowen, Northeastern University, Boston

Linda A. Deegan et al.: Coastal eutrophication as a driver of salt marsh loss, NATURE, 388, Vol 490 | 18 October 2012

Required reading

Patrick J. Kearns et al.: Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments, NATURE COMMUNICATIONS, 7:12881 | DOI, Published 26 Sep 2016

Required Reading

Ashley Bulseco-McKim et al.: Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments, Global Change Biology, In Review, submitted April 29, 2018

Additional resource reading

Mary Ann Moran's Talk Abstract and Suggested Readings

Talk Abstract (pdf)

Chemical Currencies of the Surface Ocean Microbiome
Mary Ann Moran
University of Georgia

Bryndan P. Durham et al.: Cryptic carbon and sulfur cycling between surface ocean plankton, PNAS Early Edition 1 of 5 (2015)

Required reading for students

Bryndan P. Durham et al.: Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system, Environmental Microbiology, 19(9), 3500 - 3513 (2017)

Required reading for students

Daniel Segre's Talk Abstract and Suggested Readings

Talk Abstract

From Genome-scale to Ecosystem-level Models of Microbial Metabolism

Dan Segrè
Boston University

Ali R. Zomorrodi and Daniel Segre: Synthetic Ecology of Microbes: Mathematical Models and Applications,jmb, Volume 428, Issue 5, Part B, 27 February 2016, Pages 837 - 861

Required reading for students

William R. Harcombe et al.: Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports, Volume 7, Issue 4, p1104 - 1115, 22 May 2014

Required reading for students

Joshua E. Goldford and Daniel Segre: Modern views of ancient metabolic networks, Modern views of ancient metabolic networks, Current Opinion in Systems Biology, 2018, 8: 117 - 124

Additional resource article

Ben Twining's Talk Abstract and Suggested Readings

Talk Abstract

Constraining the Global Phytoplankton Metallome, One Cell at a Time
Ben Twining
Bigelow Laboratory for Ocean Sciences

Benjamin S. Twining and Stephen B. Baines: The Trace Metal Composition of Marine PhytoplanktonAnnu. Rev. Marine. Sci. 2013.5:191-215. Downloaded from www.annualreviews.org by 12.148.235.2 on 01/04/13. For personal use only.

Required reading

Philip W. Boyd et al.: Biotic and abiotic retention, recycling and remineralization of metals in the ocean NATURE GEOSCIENCE | VOL 10 | MARCH 2017

Required reading

Benjamin S. Twining et al.: Differential remineralization of major and trace elements in sinking diatoms Limnology and Oceanography, 59(3), 2014, 689 - 704

Additional resource reading

Robert Collier and John Edmond: The Trace Element Geochemistry of Marine Biogenic Particulate Matter Prog. Oceanog. Vo. 13, pp. 113-199, 1984

Additional resource reading

Alyson Santoro's Talk Abstract and Suggested Readings

Talk Abstract (pdf)

Nitrogen-fueled Chemoautotrophy in the Dark Ocean
Alyson Santoro
University of California, Santa Barbara

Alyson E. Santoro et al.: Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation Limnology and Oceanography , 62, 2017, 1984 – 200

Required reading for students

Alyson E. Santoro et al.: Genomic and proteomic characterization of Candidatus Nitrosopelagicus brevis: An ammonia-oxidizing archaeon from the open ocean, PNAS Early Edition, 2015, 6 pages

Required reading

Jack J. Middelburg: Chemoautotrophy in the ocean GEOPHYSICAL RESEARCH LETTERS VOL. 38, L24604, 2011

Additional resource reading

Rogier Braakman's Talk Abstract and Suggested Readings

Talk Abstract (pdf)

Reconstructing the Evolutionary Self-organization of the Oceanic Biogeochemical Cycles
Rogier Braakman
MIT

Rogier Braakman et al.: Metabolic evolution and the self-organization of ecosystems PNAS Published online March 27, 2017, e3091 - e3100

Required reading for students

Steven J. Biller et al.: Prochlorococcus the structure and function of collective diversity, NATURE REVIEWS | MICROBIOLOGY, VOLUME 13 | JANUARY 2015

Required reading for students

Jeffrey Morris et al.: The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene LossmBio, March/April 2012 Volume 3 Issue 2, e00036 - 12

Additional resource material

Steve Giovannoni's Talk Abstract and Suggested Readings

Talk Abstract

Outliers: Extreme Selection for Minimalism in Oligotrophic Bacterioplankton
Stephen Giovannoni
Department of Microbiology
Oregon State University

Stephen J Giovannoni1 et al.: Implications of streamlining theory for microbial ecology The ISME Journal, (2014), 1 - 13

Required reading for students

Jing Sun et al.: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol NATURE MICROBIOLOGY, Letters, Published: 16 May 2016 | Article Number: 16065

Required reading for students

Daniel P. Smith et al.: Proteome Remodeling in Response to Sulfur Limitation in Candidatus Pelagibacter ubique,American Society of Microbiology, mSystems, Volume 1, Issue 4, Published 12 July 2016

Additional resource material

Daniel P. Smith et al.: Proteomic and Transcriptomic Analyses of Candidatus Pelagibacter ubique" Describe the First PII-Independent Response to Nitrogen Limitation in a Free-Living AlphaproteobacteriummBio, November/December 2013 Volume 4 Issue 6

Additional resource material

Jing Sun et al.: Supplementary Information, The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Additional resource material

Mak Saito's Talk Abstract and Suggested Readings

Abstract (pdf)

Colonial Phaeocystis antarctica: a Marvelous Model Microbiome System
Mak Saito
WHOI

Bender, S. J. et al.: Iron triggers colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry, Biogeosciences Discuss, in review, 2018. (pdf)

Bender et al in open review: https://www.biogeosciences-discuss.net/bg-2017-558/

Required reading for students

G. R. DiTullio et al.: Rapid and early export of Phaeocystis antarctica blooms in the Ross Sea, Antarctica,NATURE |Vol. 404| 6 April 2000 |www.nature.com

Required reading for students

Harriet Alexander's Talk Abstract and Suggested Readings

Talk Abstract

Combining in situ and Culture-based Approaches to Characterize the Physiological Ecology of Blooming and Sinking Diatoms

Harriet Alexander
University of California, Davis
Tuesday, March 20, 2018
Clark Lab 507, WHOI

Durkin CA, Van Mooy BAS, Dyhrman ST, Buesseler KO. (2016). Sinking phytoplankton associated with carbon flux in the Atlantic Ocean. Limnol Oceanogr 61: 1172 - 1187

Reguired reading for students

Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, et al. (2016). Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 15: 6 - 20

Required reading for students

Ben Van Mooy's Talk Abstract, and Suggested Readings

Talk Abstract

The Trichodesmium Microbiome and its Role in the Marine Nitrogen and Phosphorus Cycles
Ben Van Mooy
Woods Hole Oceanographic Institution
Tuesday, March 6, 2018
1:30 – 2:30pm, Clark Lab 507, WHOI

Monica Rouco et al.: Microbial diversity within the Trichodesmium holobiont, Environmental Microbiology,(2016) 18 (12), 5151 - 5160

Required reading for students

Jill A. Sohmet al.: Emerging patterns of marine nitrogen fixation, NATURE REVIEWS | MICROBIOLOGY, VOLUME 9 | JULY 2011 | 499

Required reading for students

Benjamin AS Van Mooy et al.: Quorum sensing control of phosphorus acquisition in Trichodesmium consortia, The ISME Journal, (2012) 6, 422 - 429

Additional resource paper

Julie Huber's Talk Abstract, Suggested Readings and Presentation

Talk Abstract

Subseafloor Microbial Communities at Axial Seamount

Julie Huber
Woods Hole Oceanographic Institution

Caroline S Fortunato and Julie A Huber: Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent, The ISME Journal (2006) 10, 1925 - 1938

Required reading for students

Caroline S. Fortunato et al.: Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids Environmental Microbiology (2008) 20(2), 769 - 784

Required reading for students

Xavier Mayali's Talk Abstract, Suggested Readings, and Presentation

ABSTRACT (pdf)

NanoSIMS and Stable Isotope Probing for Quantitative Microbial Biogeochemistry

Xavier Mayali
Nuclear and Chemical Sciences Division
Lawrence Livermore National Laboratory, CA

Presentation (pdf)

NanoSIMS and Stable Isotope Probing for Quantitative Microbial Biogeochemistry

Xavier Mayali
Nuclear and Chemical Sciences Division
Lawrence Livermore National Laboratory, CA

Xavier Mayali et al.: High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use, The ISME Journal (2012) 6, 1210 - 1221

Required reading for students

Nestor Arandia-Gorostidi et al.: Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment, The ISME Journal (2017) 11, 641 - 650

Required reading for students