September 2018 (11:10)

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"If the last blue whale choked to death on the last panda, it would be disastrous but not the end of the world. But if we accidentally poisoned the last two species of ammonia-oxidizers, that would be another matter. It could be happening now and we wouldn't even know..."
Microbiologist Tom Curtis in Nature, 2006

Most marine microbes are marine organisms too small to be seen by the unaided human eye (that is, roughly less than 0.1 mm). They make up 98 percent of ocean biomass, are the foundation of all marine food webs, and are a major driver of most of Earth’s biogeochemical cycles, including those of carbon, nitrogen, oxygen, and phosphorus (not to mention those of sulfur, hydrogen, sodium, potassium, magnesium, calcium, and chlorine).

Microbes are found in all marine environments, from surface waters to abyssal depths, from coastal to offshore regions, and in specialized niches such as coral reefs and hydrothermal vents. Marine microbes are extraordinarily diverse – consisting of bacteria, archaea, protists, fungi, and algae, as well as the viruses associated with these taxa. A single liter of seawater can contain more than a billion microbes representing thousands of different types.

With this seemingly endless list of superlatives, you would think the ocean management and conservation communities would be talking about microbes all the time. But we don’t. In this issue of MEAM, we catch up with some of the latest news and research on marine microbes (specifically marine bacteria and viruses) and their influence on marine ecosystems. We also hear from microbial experts about what marine managers and conservationist practitioners should know about marine microbes in the systems in which they work.

The things we know we don’t know

  • Despite microbes’ ubiquity, there are many fundamental aspects of their ecology that we do not yet have a good handle on, including the full range of types of microbes in marine ecosystems and the full range of roles they play in those systems. There is not even general agreement on what would constitute a “species” of microbe.
  • One reason for this is that marine microbes are notoriously difficult to culture... They depend on complex, highly interactive communities that are difficult to replicate in a laboratory setting.
  • Our knowledge is growing rapidly, however, due to the recent development of metagenomics (the study of DNA recovered directly from environmental samples), as well as advances in remote sensing and sampling technologies (keep reading for more on this).

How we’re getting to know marine microbes

Remote operated vehicle (ROV) taking bacterial samples at the sediment surface using a 3-D-printed syringe sampler to map bacterial populations on the sea bottom in the Bay of Fundy. (Photo credit: S. Robinson, DFO)

Microbe-based monitoring of marine ecosystems

  • We asked a number of marine microbiologists what they thought marine managers and conservation practitioners should know (or do) about marine microbes in the marine ecosystems in which they work. The top response was that microbes can be tremendously useful for monitoring environmental impacts and marine ecosystem and organismal health.
  • Shawn Robinson, a research scientist with Fisheries and Oceans Canada, explains it this way: “If we assume the physical characteristics of an environment determine the mix of microbes present, then the microbe diversity in a sample will reflect environmental condition and allow us to infer ecosystem processes.”
  • He further explains that “we measure microbial diversity using environmental DNA (eDNA) and use these measurements to monitor changes in marine habitats and their relative rates of recovery. Impacts to habitats in the coastal zone can include nutrient loading from cities, aquatic and terrestrial farming, etc. and disturbances from industrial activities such as oil and gas development, dredging, and fishing. This approach can also be applied to measure indirect impacts to marine environments such as those from climate change. Spatially mapping bacterial populations allows us to evaluate the scale of impact and the timescale of ecosystem recovery.”
  • Robinson also added bacteria can be used as a metric for organism health: “Studies pioneered in the human health field have documented that the bacterial diversity in the human gut is reflective of the overall health of a person. This same relationship is likely true in other organisms and will become one of the tools used by managers to assess how other organisms are coping with environmental stress, either from human or natural causes.”

Probiotics for the ocean

  • Most people’s initial thoughts when they hear the terms ‘bacteria’ and ‘viruses’ are of the small subset of microbes that are pathogens (for coral, salmon, oysters, humans, etc.). This is slowly changing, however, as people get accustomed to the idea that healthy microbiomes are necessary for organismal health. And just as human microbiomes help determine people’s susceptibility and resistance to disease, new experiments are showing that coral microbiomes help determine coral susceptibility and resistance to warmer water temperatures and ocean acidification. (Not surprisingly, stressors such as overfishing and nutrient pollution disrupt coral microbiomes, leading to reduced coral recruitment, growth, and survivorship.)

Photo Credit:  The Ocean Agency / XL Catlin Seaview Survey / Richard Vevers

Bacteria to the rescue?

  • There are numerous other areas where understanding and working with microbes could lead to improved marine ecosystem and human health. An engineered bacterial enzyme that can digest polyethylene terephthalate (PET) – a common plastic used for food packing and soda bottles – is showing promise for being able to contribute to a circular plastics economy by reducing finished plastic products to raw ingredients that can be used again. (On the other hand, microbial breakdown of plastic in situ in the ocean may not be a good thing at all. The biodegradation of plastic into smaller pieces may be even more harmful to marine life than the larger pieces of plastic.)
  • Bacterial enzymes can also metabolize hydrocarbons, providing a way to decontaminate soil and water. This can help clean up oil spills in the marine environment, including sites difficult to access through other means. Microbes metabolized a great deal of the oil and natural gas from the Deepwater Horizon spill in the Gulf of Mexico.
  • Bacteria are also showing promise at being able to eat antibiotics in order to clean up antibiotic-contaminated soil and water – helping to reduce the development of additional antibiotic resistant microbes.

Some things that we didn’t know that we didn’t know

  • As with any big, complex phenomenon that is not well studied, surprises are always right around the corner. Many of the most consequential recent discoveries involve viruses and their potential influence on the earth’s climate.
  • Interestingly, in another set of experiments, a virus that infects marine phytoplankton actually made the infected hosts better at absorbing ammonium, a key source of the nitrogen needed for photosynthesis … for a while. And then the virus killed them. By initially helping its hosts be more competitive photosynthesizers, the virus promotes its own reproduction. It then enables the spread of its offspring by killing its hosts.

So what should marine managers and conservation practitioners DO about marine microbes?

  • Again, there was a consensus about this from the experts who MEAM interviewed, and that consensus was – research, research, research. Marine managers and conservation practitioners should learn as much as they can about what microbes are in the systems in which they work and what those microbes do.
  • Charles Cockell, a professor of astrobiology at the University of Edinburgh and lead author of the 2009 paper Advancing the case for microbial conservation published in Oryx-The International Journal of Conservation , framed the major research questions as:
  1. Which microbes perform crucial chemical transformations that we (and other organisms) depend on?
  2. Can functions carried out by specific microbes be replaced by other microbes or organisms?

Cockell added that “just as other aspects of environmental conservation are predicated on understanding which organisms are crucial to ecosystem functioning so we can prioritize their conservation, we need to know which microbes play the most decisive roles in microbial ecosystems and how sensitive they are to perturbations in environmental conditions. When we understand that we will better understand what impact human-induced change might have on microbial ecosystems. In short, we need to understand the dependent networks within microbial communities and their links to other organisms better.”

  • And, finally, should managers be doing this research themselves? Probably not yet. Marine researchers Anders Lanzén, Laura Alonso-Sáez, and Angel Borja of AZTI suggest that collaborations with microbial experts are still needed because the “toolbox for including microorganisms in biodiversity monitoring is still not standardized and depends on specialized expertise, though the impressive development of DNA sequencing technology should help change this in the near future.”

Photo credit: Argonne National Laboratory

Editor's note: Many thanks to Laura Alonso-Sáez, Linda Amaral-Zettler, Angel Borja, Charles Cockell, Anders Lanzén, Shawn Robinson, and Sufia Zaman for sharing their expertise on marine microbes and what marine managers and conservation practitioners should know (and do) about them with MEAM. They can be reached at:

  • Laura Alonso-Sáez, Angel Borja, and Anders Lanzén: aborja [at]
  • Linda Amaral-Zettler: linda.amaral-zettler [at]
  • Charles Cockell: c.s.cockell [at]
  • Shawn Robinson: shawn.robinson [at]
  • Sufia Zaman: zamansufia123 [at]

Editor's note: The goal of The EBM Toolbox is to promote awareness of tools and methods for facilitating EBM and MSP processes. It is brought to you by the EBM Tools Network (, a voluntary alliance of tool users, developers, and training providers.

In 2016, the EBM Tools Network compiled a list of hands-on activities for teaching about ecosystem services and ecosystem-based management (now updated with several more activities!). A university professor recently asked if we have any similar resources for teaching marine protected area (MPA) design and management. EBM Tools Network members pooled their collective knowledge again and came up with this fantastic list of resources for teaching about MPAs at all educational levels.

  • 50-minute teaching unit on MPAs for undergraduates. This unit is part of a two- to three-week module on ocean sustainability created for the InTeGrate project. In this unit, students review current pressures on ocean ecosystems, learn to define MPAs and marine reserves, and examine scientific evidence related to the presence of marine reserves. They also conduct a hands-on exercise to map ideal locations for the creation of a marine reserve, considering oceanographic, biological, and sociological factors in their decision-making process. Access the teaching unit.
  • Teaching module on MPAs for advanced undergraduates and graduate students (available in English and French). This module, hosted on the Network of Conservation Educators and Practitioners website, introduces MPAs, including costs and benefits, relationships to biodiversity and fisheries management, design and implementation, and governance and management issues. An accompanying role-playing exercise allows students to experience the challenges of developing an MPA plan that satisfies diverse users while meeting common objectives. A teaching presentation and evaluation tool and solutions are also available for educators. Access the module. (Note: Registration approval could take 1-2 days.)
  • Curricular materials for 6-week course for MPA professionals. This material was developed by WWF South Africa to train MPA staff. Originally developed for presentation in one-week-per-month intervals over the course of six months, the material has also been modified for use in a 5-day introductory course. For more information, contact Robin Adams at radams [at]
  • Curricular material for 10-day course for MPA professionals (available in EnglishSpanish and French). This material was developed by the UNEP Caribbean Environment Programme to train MPA managers and other senior personnel associated with MPAs in the region. It is typically presented in one ~10-day session. It consists of eight modules on Caribbean MPA planning, stakeholder participation, management, research, monitoring and regional policy, along with communication and teaching skills.
  • MPA management toolkit for MPA professionals. Developed by the IUCN/NORAD WIO Marine Biodiversity Conservation Project, this toolkit consists of a ring-binder of theme sheets, each of which addresses a key issue faced by an MPA manager, with a focus on the situation in the Western Indian Ocean. The toolkit is designed to address management issues relevant to all types of MPAs, from community-based, locally-managed areas to nationally-gazetted marine parks.

If you are looking for live training for MPA professionals, some programs that we know of (many scheduled on demand) include:

If you are interested in adding a resource to this list or getting the contact information for someone involved with a resource, please contact the EBM Tools Network coordinator at ebmtools [at]

The last two issues of MEAM featured two Skimmers chock full of cutting edge research and insights from some of our climate change researcher heroes. If you didn’t have a chance to check them out yet, we highly recommend doing so now!