LINKS TO ONLINE RESOURCES

AUTHOR’S BLOG

The marinemicro.org blog is maintained by the author Colin Munn, providing a dedicated resource to complement the textbook. It contains regular snippets of news items and longer “research focus” articles that provide updates and extended coverage to topics in the book. You can subscribe to receive alerts of new posts via RSS or email.

RECOMMENDED BLOGS

Here are links to the most relevant microbiology blogs.

• The Nature.com website provides an excellent update on the latest marine microbiology research and reviews.
• The American Society of Microbiology website contains a wealth of relevant resources and news links. The Small Things Considered blog and the This Week in Microbiology TWiM podcast are particularly useful.
• The Microbiology Society website features news items, a blog, podcast, and YouTube channel.

RECOMMENDED WEBSITES

Here are recommended links to the websites of some of the major research institutions and project consortia conducting research in marine microbiology, which contain regular news features, videos and articles.

• Australian Institute of Marine Science
• Bigelow Laboratory for Ocean Sciences
• Georgia Tech
• Gordon and Betty Moore Foundation Marine Microbiology Initiative 
• J. Craig Venter Institute
• Linnaeus University
• Marine Biological Association
• Max Planck Institute of Marine Microbiology
• Plymouth Marine Laboratory
• Royal Netherlands Institute for Sea Research
• Scripps Institution of Oceanography
• Simons Foundation Microbial Oceanography, Microbial Ecology and Evolution
• Tara Oceans
• University of Bergen
• University of Washington
• University of Vienna
• Woods Hole Oceanographic Institute (WHOI)

SELECTED VIDEOS AND ONLINE ARTICLES

DIVERSITY, EVOLUTION AND IMPORTANCE

• Milestones in Microbiology – an illustrated timeline from the Smithsonian Institution of major discoveries.
• TED talk(12:15) by Victoria Orphan (Caltech) — giving an overview of the importance of marine microbes. 
• Lecture (53:43) of a lecture by Dianne Newman (Caltech) — an overview of microbial life on Earth and metabolic diversity.
• Emergence of Life an online coursefrom the University of Illinois, Urbana including segments on the tree of life and early earth environments featuring the work of Carl Woese (videos can be viewed without enrolment).

DEEP SEA AND SUBSURFACE MICROBIOLOGY

• EV Nautilus YouTube channel, featuring live streams and archive videos of 40 years of exploration of hydrothermal vents and other deep-sea sites.
• Lecture (20:49) by Coleen Cavanaugh (Harvard) on the discovery of deep-sea chemosynthetic symbioses at hydrothermal vents.
• Lectures (16:17) by Julie Huber (WHOI) introducing the activities of deep-sea microbes and subsurface microbiology.
• Short talk (2:12) by Emil Ruff (MPI Marine Microbiology) describing research on the development of a methanotrophic microbiome in deep-sea sediments, including some excellent video footage.
• TED talk (12:52) by Karen Lloyd (University of Tennessee) on deep sub-surface microbiology.
• TED talk (7:40) by Victor Vescovo on development of human operated submersibles for deep sea exploration.
• Video collection of live footage of ROV exploration of Gulf of California (Schmidt Ocean Institute).
• Video presentation (4:50) from MARUM Institute showing footage of cold seep communities and explaining formation of methane hydrate.
• Video presentation (6:24) from MARUM showing how core samples from the sea floor are collected by using a drilling rig.
• Website from the International Ocean Discovery Program (IODP) containing a variety of educational resources, including information about the JOIDES Resolution ocean drilling vessel expeditions.

MICROBIAL OCEANOGRAPHY                          

• Darwin Project video (6:57) by MIT researchers, describing how ocean color may change.
• Lecture (50:09) by David Karl (University of Hawaii) providing a great overview of the development of microbial oceanography and the importance of ocean time series.
• NASA Earth Observatory website featuring a wide range of current and archived maps and satellite images of ocean, atmosphere and terrestrial phenomena, including ocean productivity and algal blooms.
• Polar microbiology and sea ice; conference talk (1:06:23) by Antje Boetius (AWI) on "The Poles and Deep Seas: Protecting the Unknown Realms of Earth."

METHODS

• DNA sequencing and genomics: Canadian Bioinformatics workshop talks  on the development of HTS technology (54:57) and metagenomics analysis (uses biomedical examples). Video animations of Nanopore sequencing (1:41), IonTorrent (3:20), Illumina (5:12), and PacBio SMRT (2:08) technology. Video animations of the principles of PCR, Q-PCR, and Sanger DNA sequencing. Single cell sequencing: video (6:46) introducing single cell sequencing (biomedical examples).
• Imaging and flow cytometry: website of Fluid Imaging Technologies containing videos and tutorials showing use of FlowCam® for plankton analysis, HAB monitoring and other aquatic applications. Video animations of the principles of epifluorescence microscopy (2:19), confocal microscopy (3:30), flow cytometry (4:35), and atomic force microscopy (2:28).
• Microfluidics: website of Roman Stocker lab, ETH Zurich; video presentation (2:18) by Justin Seymour (University of Technology Sydney). 

CELL STRUCTURE AND METABOLISM            

• Animations of key processes in oxygenic photosynthesis,  chemoorganotrophy and chemolithotrophy.
• JoVE animations from, explaining a range of cellular processes, including membranes and cellular transport, cell signalling, metabolism, respiration and photosynthesis.
• Virtual Cell Animation Collection, including various molecular and cellular processes, including photosynthesis, protein gradients and TCA cycle.

BACTERIAL AND ARCHAEAL DIVERSITY

• ANME Archaea: video with animations of syntrophic AOM by ANME-1 archaea and sulfate-reducing bacteria; video talk (2:41) by Victoria Orphan (Caltech) describing research on anaerobic oxidation of methane (AOM).
• Denitrifying bacteria: conference talk by Jim Prosser (University of Aberdeen).
• Thioploca: video (1:20) showing movement of cells within sheaths.
• Cable bacteria: TED talk (5:39) by Laurine Burdorf (Vrije Universiteit Brussel). 
• Prochlorococcus: TED talk (16:30) by Penny Chisholm (MIT).

PROTISTS

• Dinoflagellates: online article (Scientific American) featuring videos of newly discovered ballistic nematocyst-like organelles used in predation by dinoflagellates.
• Conference talk by Peter Franks (55:09) on instrumentation for studying phytoplankton.
• Diatoms: short video (2:54) illustrating microscopy of live diatoms and summarizing some of their key properties.
• Foraminifera: video presentation(6:06)from the American Museum of Natural History on the collection of fossil foraminifera and their importance in tracking changes in climate over time.
• Video (6:50) featuring Richard Lampitt, describing the importance of marine plankton.

MARINE VIRUSES                                              

• Virus ecology and evolution, adaptation, and phage therapy: lecture (33:03) by Paul Turner (Yale School of Medicine).
• Lab websites of Mya Breitbart, University of South Florida; Rebecca Vega Thurber, University of Oregon.
• Giant viruses: conference talk (1:00:14) by Jean-Michel Claverie (Aix-Marseille University).
• Viral diversity and importance: lecture  by Curtis Suttle (1:12:20), University of British Columbia; TED talk(14:04)by Karen Weynberg (AIMS); Video discussion  (26:30): Thomas Bosch (Christian-Albrechts-University of Kiel) talks to Forest Rohwer (San Diego State University) on the role of viruses, specifically phages, and their role in marine microbial ecosystems for example in coral reefs.
• Video presentation (3:56) (from Schmidt Ocean Institute) on deep ocean viruses, including discussion of high throughput filtration methods.

BIOGEOCHEMICAL CYCLES AND OCEAN PRODUCTIVITY  

• NASA Earth Observatory website featuring a wide range of current and archived maps and satellite images of ocean, atmosphere and terrestrial phenomena, including ocean productivity and algal blooms.
• ASLO e-lecture (Zip archive) on the biological carbon pump by Neuer et al .(2014).
• Nitrogen fixation: website of the Jonathan Zehr lab.
• Oxygen minimum zones: conference talk (29:16) by Bess Ward (Princeton) on microbial processes.
• Ocean fertilization: lecture (1:05) by Victor Smetacek (AWI) describing the effects of climate change of ocean processes and experiments on iron fertilization for mitigation of atmospheric CO2 accumulation; ABC TV video (8:10) about the importance of whales in natural fertilization of the Southern Ocean.
• Southern Ocean productivity: video presentation (7:13) by Philip Boyd (NIWA) explaining the role of phytoplankton species; conference talk video (32:23) by Laurence Clark on the krill microbiome.
• Lecture (20:24) by Steve Giovannoni on predicting effects of long-term impacts of ocean desertification on microbial plankton communities.

SYMBIOSIS, HEALTH, AND DISEASE

• Coral health: lecture (47:46); an inspirational talk (2017) by the late Ruth Gates (Hawaii Institute of Marine Biology) on the concept of assisted evolution for breeding corals with improved traits for resilience to environmental threats.
• Coral health: TED talk  (14:27) by Kirsten Marhaver (CARMABI Foundation) on the importance of corals, threats to their survival, and approaches to conservation and restoration; lectures (56:14) by Nancy Knowlton (Smithsonian) on the biology of coral reefs and threats to their survival; PBS TV video from 2012 on the investigations of coral disease in the Florida Keys; animation of coral bleaching(3:47)
• Coral microbiome: conference talk (28:04) by Jesse Zanefeld (Oregon State University) on coral microbiomes through space and time, with emphasis on nutrient inputs and algal competition; lecture by Forest Rohwer (San Diego) on coral microbiology and the discovery of the effects of overfishing, pollution and other human activities on the “microbialization” of coral reefs; conference talk (15:13) by Joseph Pollock on the Coral Microbiome Project.
• Harmful algal blooms: conference talk (49:49) by Clarissa Anderson (Scripps).
• Human health: Conference talk (37:52) by Rita Colwell on climate change, oceans and infectious disease & human health (especially cholera).
• Sea star wasting disease: video presentation; 2017 update (8:10).
• Symbiosis: lecture (20:49) by Coleen Cavanaugh (Harvard) on the discovery of deep-sea chemosynthetic symbioses; lectures (27:27) by Margaret McFall-Ngai (University of Hawaii) on the Euprymna scolopes–Aliivibrio fischeri symbiosis; conference talk (28:10) by Nicole Dubilier on chemosynthetic symbioses; website of Jillian Petersen (University of Vienna).