Microbial Diversity Course Reports

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Reports from past students’ research projects in the Microbial Diversity Course held at the Marine Biological Laboratory, Woods Hole, MA can be found here. Reports are browsable by year.

The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, as well as how to perform molecular and computational analyses relevant to their study.

Launched in 1971 by Holger Jannasch, the Microbial Diversity summer course at the Marine Biological Laboratory has trained generations of scientists from diverse backgrounds. The course is an intense immersion experience for 20 students that lasts 6.5 weeks. The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, as well as how to perform molecular and computational analyses relevant to their study. While microbial isolation techniques form the essential core of the course, each new set of directors brings an additional focus that reflects their interests/expertise. We have introduced basic genetic methods to the course for the first time to enable students to study how microbes catalyze interesting reactions and exhibit interesting behaviors. In addition, we emphasize state-of-the-art imaging techniques and training in quantitative microscopy to study microbial cell biology and single-cell gene expression. Genetically-tractable strains isolated in the course are sequenced by Pacific Biosystems, and students learn how to annotate and analyze their genomes. Given the wealth of DNA, RNA and protein sequences now available from isolated microbes and environmental samples, these tools are important for students to master so they may understand what these sequences mean and in which context they are expressed—be it in the marine environment, soils, or plant and animal hosts. We also emphasize quantitative approaches to microbial diversity, including teaching students how to describe the energetic potential of diverse metabolisms. A dedicated team of resident course instructors as well as guest-lecturers participate in the course every summer, allowing students to be exposed to exciting current research. The opportunity to interact one-on-one with these individuals is a tremendous opportunity, often leading to future collaborations.

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Recent Submissions

Now showing 1 - 11 of 11
  • Article
    Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in “Pink Berry” marine microbial aggregates
    (American Society for Microbiology, 2023-07-05) Kosmopoulos, James C. ; Campbell, Danielle E. ; Whitaker, Rachel J. ; Wilbanks, Elizabeth G.
    Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the “pink berry” consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system.
  • Article
    Microbial Diversity: Marine Biological Laboratory 2011 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Armitage, David W. ; Aruda, Amalia ; Blasiak, Leah ; Buchwald, Carly ; Cregger, Melissa ; Cappelletti, Martina ; Cordero, Otto X. ; Gallagher, Kim ; Glass, Jennifer ; Holmes, Jeff ; Hurley, Sarah ; Hemp, James ; Ma, Peijun ; Rampersaud, Ryan ; Ruff, Emil ; Salman, Verena ; Schick, Michael ; Shade, Ashley ; Vuono, David ; Youngblut, Nicholas
    "Ecological investigations into the causes and consequences of cyanobacterial diversity" by David W. Armitage
  • Article
    Microbial Diversity: Marine Biological Laboratory 2012 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Abreu, Fernanda ; Behrendt, Thomas ; Brigham, Brian ; El Khawand, Myriam ; Gerardin, Ylaine ; Gravuer, Kelly ; Greenspan, Alex ; Hausladen, Debra ; Kav, Aya Brown ; Kraft, Beate ; Larsen, Steffen ; Schubotz, Florence ; Smith, Heidi ; Suter, Elizabeth ; Thiele, S. ; Torti, Andrea ; Whitman, Thea ; Wolfson, Sarah ; Zhang, Ying
    "Metal corrosion and biological H2S cycling in closed systems" by Fernanda Abreu
  • Article
    Microbial Diversity: Marine Biological Laboratory 2013 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Abramovich, Reut Sorek ; Blanton, Jessica ; Buckner, Caroline ; Cardarelli, Emily ; Donaldson, Teraya ; García, Diego Giao ; Heyward, Christa ; Jácome, Luz Adriana Puentes ; Jesus, Ederson da Conceicao ; Kotlarz, Nadine ; Mathai, Prince ; Mukherjee, Dishari ; Neubauer, Cajetan ; Pishchany, Gleb ; Rangel, Lorena ; Saleska, Scott ; Starnawski, Piotr ; Tapilatu, Yosmina ; Weisenhorn, Pamela ; Yang, Tingting
    "Anaerobic nitrogen fixing in microbial mats from Little Sippewisset Marsh, Woods Hole, MA" by Reut Sorek Abramovich
  • Article
    Microbial Diversity: Marine Biological Laboratory 2014 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Berben, Tom ; Boidi, Flavia Jaquelina ; Cheng, Bingran ; Cohen, Jacob W. ; Conner, Jenna ; Gazitúa, María Consuelo ; Hestrin, Rachel ; Jangir, Yamini ; Kiang, Nancy Y. ; Krusor, Megan ; Mariita, Richard M. ; Murali, Ranjani ; Naughton, Hannah R. ; Omairi-Nasser, Amin ; Peng, Xuefeng "Nick" ; Roller, Ben ; Sarno, Analissa F. ; Stacy, Apollo ; Szoboszlay, Márton ; Tien, Matthew
    "Intracellular calcium carbonate crystals as a possible protection against acidification in Achromatium spp." by Tom Berben
  • Article
    Microbial Diversity: Marine Biological Laboratory 2015 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Abdul Halim, Mohd Farid ; Buck, Moritz ; Choi, Jessica K. ; Dabrowska, Alicja ; Enke, Tim Niklas ; Ettinger, Cassie ; Graham, Emily B. ; Hargreaves, Katherine R. ; Huang, Yolanda ; Kearney, Sean ; Krause, David J. ; Lagostina, Lorenzo ; Liu, Xiaolei ; Reese, Aspen T. ; Rivera Pérez, Jessica ; Russell, James ; Scholz, Rebecca ; Tikhonov, Mikhail ; Van Steendam, Caroline ; Wu, Yunji
    "The diversity of microbial community involved in the iron cycling" by Mohd Farid Abdul Halim
  • Article
    Microbial Diversity: Marine Biological Laboratory 2016 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Braus, Michael ; Brown, C. Titus ; Enalls, Brandon C. ; Grond, Kirsten ; Happel, Elisabeth Münster ; Holland-Moritz, Hannah ; Jelen, Benjamin ; Kee, Lynn ; Mayer, Marisa ; Mayr, Magdalena ; McHugh, Theresa ; Meirelles, Lucas A. ; Mickol, Rebecca ; Mikheyeva, Irina ; Rhim, Jeemin H. ; Sousoni, Despoina ; Thorup, Casper ; Villa, Max ; Zhou, Zhichao
    "Responses of bacillus spore germination to soil extracts" by Michael Braus
  • Article
    Microbial Diversity: Marine Biological Laboratory 2017 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Barnett, Samuel ; Bar-On, Yinon ; Busck, Mette ; Chittor, Achala ; Demko, Alyssa ; Dykes, Gretchen ; Grießmeier, Victoria ; Herrera, Nadia ; Hussain, Fatima ; Kardish, Melissa ; Lin, Jonathan Y. ; Maguffin, Scott C. ; Moynihan, Molly A. ; Nguyen, Chi ; Perry, Elena K. ; Shafiee, Roxana ; Sharma, Indu ; Tsypin, Lev ; Wandro, Stephen ; Zhou, Lei
    "Searching for PCA Reducers and Oxidizers" by Yinon Bar-On
  • Article
    Microbial Diversity: Marine Biological Laboratory 2018 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Alexiev, Alexandra ; Arrington, Eleanor ; Bertolet, Brittni ; Campbell, Danielle ; Chappell, Callie ; Chong, Grace ; Gajigan, Andrian ; Graham, Elaina ; Hai, Yang ; Lai, Peggy ; Lanpher, Kaycie ; Lynch, Shannon ; McCallum, Monica ; Plata, Germán ; Rizk, Sandra ; Schwenck, Sarah ; Tucker, Sarah ; Urtecho, Guillaume ; Vargas-Muñiz , José M. ; Weissman, Jake
    "A Tale of Two Coral Microbes: How motility and quorum sensing may play a role in competition between Vibrio species" by Alexandra Alexiev
  • Article
    Microbial Diversity: Marine Biological Laboratory 2010 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Campbell, Kate ; Hall, Edward K. ; Henriksen, James R. ; Irizarry, Ivelisse ; Jaekel, Ulrike ; Kelly, Libusha ; Li, Meng ; Ling, Alison ; Melton, Emily D. ; Meredith, Laura ; Singer, Esther ; Sharon, Gil ; Wang, Harris H. ; Wilbanks, Elizabeth G. ; Humphrey, Parris T. ; Moraru, Cristina ; Ward, Rebekah ; Orphan, Victoria J. ; Williams, David ; Xu, Yan
    "A bioelectrical system (BES) for enriching Fe(III)-reducing bacteria" by Kate Campbell
  • Article
    Microbial Diversity: Marine Biological Laboratory 2019 Final Reports
    (Marine Biological Laboratory, 2023-07-25) Archie, Elizabeth ; Ascensao, Joao ; Baubin, Capucine ; Bennett, Anna ; Bonitatibus, Sheila ; Brown, Malory O. ; Depetris, Anna ; Díaz-Díaz, Lymarie M. ; Eshel, Adi ; Fogarty, Emily ; Junger, Pedro ; Osopale, Babasola Adewunmi ; Quiñones-Olvera, Natalia ; Saladi, Shyam ; Sandfeld, Tobias ; Schroer, William F. ; Starcevich, Hannah ; van der Graaf, Lot ; Villarreal, Alex
    "Same Game, Different Players: Tannin-degrading Bacterial Consorita Differ Across Microhabitats" in Cedar Swamp by Elizabeth Archie