At a Glance

Founded2007
Renewal dates2012
Members28
PartnersGordon and Betty Moore Foundation
Disciplines
Microbiology; evolutionary biology; bioinformatics; biochemistry and molecular biology; cell biology; marine and freshwater biology; oceanography; ecology; genetics; taxonomy; mycology; virology; zoology

How do microbes shape our world and ourselves?

For almost the entire history of life on Earth there were only microbes, and even today microbes are by far the most common forms of life. They live in the air, water and soil of every part of the planet, and form the foundation of every known ecosystem. Even our own bodies contain 10 times more microbes than human cells, and many are vital for good health.

Despite its importance, the microbial world remains largely an undiscovered country. Fewer than 1 per cent of all microbial species have been identified, leaving huge gaps in our overall understanding of life. But now the Integrated Microbial Biodiversity program is bringing diverse researchers together who are using cutting edge technologies in molecular and computational biology to understand the vast and largely unknown microbial world. Their work is throwing open new windows on our understanding of the environment, evolution, and human health.

Our unique approach

In 2007, CIFAR set up the Integrated Microbial Biodiversity program to explore the world of microbes with the aim to bridge gaps between related but disparate fields. The program brings together top scientists from around the world in bacteriology, virology, protistology and parasitology, focusing on ecology, statistics, genetics, immunology, and Earth science. This diversity of perspectives allows a more holistic view that identifies the interactions within an ecosystem which were previously unknown, as well as developing basic principles about microbial biology and interactions.

Ongoing collaborations have allowed program researchers to become leaders in new and powerful approaches like single cell genomics and metagenomics, where advanced genetic sequencing techniques can be used to create sequences of every kind of microbe in an environment. These genetic fingerprints are used to construct a big picture of the kinds of life in an ecosystem, and the often relationships among them.

Why this matters

Through its study of microbes, the CIFAR program team is exploring the complex evolutionary past, how these events shaped the biological present, and what may be in store for the future. The impact of its research is far-reaching, with implications for biology, industry, environmental policy, climate and medicine.

We are just beginning to appreciate the extent to which microbes are important for maintaining human health. We now know that they are responsible for basic functions such as synthesis of vitamins and amino acids, digestion of food, strengthening the immune system, and preventing pathogens from invading tissues and organs. Variations in the microbiome have also been linked to conditions as diverse as Crohn’s disease and depression.

Microbes play a vital role in maintaining the environment through processes including soil and cloud formation, the cycling of carbon dioxide, oxygen, and all other geochemical cycles that are central to life. Microbes in the oceans are responsible for half of the Earth’s net uptake of carbon dioxide, and understanding their biology can help predict their responses to external forces, including climate change, ocean acidification, alterations to the marine food web, and ultimately the future health of oceans.

Fossils tell us that massive extinctions in the past were linked to large-scale environmental changes. With the world experiencing another major change and the associated decline in diversity, and climate change threatening to speed the process, the work of the CIFAR team in understanding the nature and rate of this decline is essential.

MALLOMO2 - Keeling - cropped.2007
A photo taken with a scanning electron microscope the external scales of the chrysophyte Mallomonas sp. Photo by Brian S. Leander

In depth

The program aims to create a deeper understanding of the diversity of microbial life, and interactions among microbes and between microbes and macroscopic plant and animal life.

Exploring novel forms of life

Since its launch, exploration has been a key element of the program. CIFAR exploration has focused on promising diversity hotspots including:

  • extreme environments – low oxygen and high salt
  • high diversity environments – intertidal zones, open ocean, and coral reefs
  • environments rich in symbiotic interactions – arthropod tissues
  • parasites

Program researchers have also used phylogenetic information to untangle the evolutionary relationships among specific lineages for deep surveys, including alveolates, anaerobes, viruses, fungi, and marine unicellular green algae. Surveys like these promise insights into the evolution of important diseases ranging from malaria to the Irish potato famine, and relationships between lineages, such as the importance of opisthokonts in clarifying the relationship between animals and fungi, which diverged from a common ancestor a billion years ago.

CIFAR fellows are pioneers in novel uses of genomics, including metagenomic methods where whole environments are assessed at once, or single-cell methods where the genes expressed in an individual cell are extracted and characterized. They conducted the first comprehensive analysis of the metabolic processes occurring in microbial and viral communities in several major ecosystems. And they have revealed that viral communities serve as repositories for storing and sharing genes, and thereby influence global evolutionary and metabolic processes.

imb.curacao.field.trip
Collecting samples during a field trip to the CARMABI Research Institute on the island of Curacao

Identifying mechanisms of biological innovation

Program researchers are studying how cellular complexity changes over time, the rule of symbiotic and pathogenic interactions in generating biological innovation, and the genetic basis and mechanism of multicellularity.

A study led by Fellow Nicole King suggests that bacteria may have played a key role in our evolutionary history.  By studying choanoflagellates, single-celled organisms found in both fresh and marine waters around the world, she found that bacteria and the molecules they produce may have triggered single-celled organisms to form colonies, leading to the evolution of multi-celled animals, including humans.

 A team led by Program Director and Senior Fellow Patrick Keeling studies the genomics, evolution, and cell biology of protists and fungi  — microbial eukaryotes  of great complexity at the cellular and molecular levels. The team’s focus on cellular organelles such as mitochondria and plastids has improved understanding of how the process of endosymbiosis, or the merging of two cells, can lead to a new life form with characteristics different from either of the partners.

Keeling’s work on parasitism and how sophisticated intracellular parasites arise from free-living ancestors has shed light on how this process affects their cells, genomes, and metabolism. It also contradicts existing textbook theories about the origin of parasitism. Knowledge arising from the research could eventually be useful for fighting parasites that affect human health.

A recent collaboration between Senior Fellows Brian Leander, Keeling, and Curtis Suttle addressed how complexity is built in biological systems. Their study of the ocelloid, a complex sub cellular structure of dinoflagellate algae that resembles a larval eye, found that the eye is composed of normal parts of the cell that have been repurposed for a new function.

Connecting community structure, ecology and global change

CIFAR researchers have attempted to relate the structure of microbial communities to the physical properties of their environment, and understand how changes to that environment affect the ecological function of its inhabitants. Specifically, they’ve looked at how particular communities influence larger-scale ecosystem dynamics.

Program members have studied the importance of microbial biodiversity in the oceans. For example, Senior Fellow Alexandra Worden discovered genes that help the green algae Micromonas capture carbon dioxide from the atmosphere and transport it to the depths of the ocean. This activity influences the carbon cycle, a critical factor of climate change. And Senior Fellow Alastair Simpson  has studied organisms with the remarkable ability to grow and persist in a harsh world without oxygen.

Fellow Mike Grigg and his team have found the parasite Toxoplasma gondii, present in cat feces and kitty litter, infecting Arctic beluga whales for the first time, prompting new investigations to determine if climate change is contributing to the emergence of common food-borne pathogens in the North. This cat parasite, which is common in temperate climates, has found its way into waterways and into the bodies of about 14 per cent of western Arctic beluga whales, which are an important traditional staple of Inuit diet.

In 2014, Keeling, along with Fellow John McCutcheon and Advisor W. Ford Doolittle, curated a prestigious Arthur M. Sackler Colloquium of the U.S. National Academy of Sciences. The colloquium was called Symbiosis becoming permanent: The origins and evolutionary trajectories of organelles, and explored the origins of mitochondria and chloroplasts from symbiotic relationships between microorganisms. Results of the colloquium will be published as a special issue of the Proceedings of the National Academy of Sciences.

Senior Fellow John Archibald has written a book, One Plus One Equals One: Symbiosis and the evolution of complex life. It explores how single-celled organisms came together billions of years ago and laid the building blocks for the development of complex life.

Senior Fellow Forest Rohwer co-authored the book Coral Reefs in the Microbial Seas. It explored how coral reefs depend on a complex network of other living things, including microbes, and how these delicate relationships are threatened by human activity.

Selected papers

King et al, “The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity,” Nature 451, 7180 (2008): 783-8 doi:10.1038/nature06617.

Fischer et al, “Giant virus with a remarkable complement of genes infects marine zooplankton,” Proceedings of the National Academy of Sciences 107, (2010): 19508-19513 doi: 10.1073/pnas.1007615107.

Gray et al., “Irremediable Complexity?” Science 330, 6006 (2010): 920-921 doi: 10.1126/science.1198594.

P. Keeling et al, “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing,” PLOS Biology 12, 6 (June 24, 2014) doi:10.1371/journal.pbio.1001889.

Keeling PJ, McCutcheon J, Doolittle WF, “Symbiosis becoming permanent: survival of the luckiest,” Proceedings of the National Academy of Sciences, 112, 33 (2015): 10101-10103 doi: 10.1073/pnas.1513346112.

A.Z. Worden et al, “Rethinking the marine carbon cycle: factoring in mutifarious lifestyles of microbes,” Science 347, 6223 (2015) doi: 10.1126/science.1257594.

READ 2016’s ANNUAL UPDATE 

 

Fellows & Advisors

Photo of Patrick Keeling

Patrick Keeling

Program Director

Patrick Keeling’s research group studies the genomics, evolution and cell biology of protists and fungi, both microbial eukaryotes (cells that store their genetic material in a nucleus) of great complexity…

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Fellows

John Archibald

Senior Fellow

Dalhousie University

Canada

Yan Boucher

Fellow

University of Alberta

Canada

Nicolas Corradi

Fellow

University of Ottawa

Canada

Michael E. Grigg

Fellow

National Institutes of Health

United States

Steven Hallam

Fellow

University of British Columbia

Canada

Nicole King

Senior Fellow

University of California, Berkeley

United States

Brian S. Leander

Senior Fellow

University of British Columbia

Canada

Julius Lukeš

Senior Fellow

University of South Bohemia, Czech Academy of Sciences

Czech Republic

John McCutcheon

Fellow

University of Montana

United States

Steve J. Perlman

Fellow

University of Victoria

Canada

Adrián Reyes-Prieto

Fellow

University of New Brunswick

Canada

Thomas A Richards

Fellow

University of Exeter

United Kingdom

Andrew Roger

Senior Fellow

Dalhousie University

Canada

Forest Rohwer

Senior Fellow

San Diego State University

United States

Alyson Santoro

Associate Fellow

University of California

United States

Alastair Simpson

Senior Fellow

Dalhousie University

Canada

Claudio Slamovits

Fellow

Dalhousie University

Canada

Curtis A. Suttle

Senior Fellow

University of British Columbia

Canada

Laura Wegener Parfrey

Associate Fellow

University of British Columbia

Canada

Alexandra Zoe Worden

Senior Fellow

Monterey Bay Aquarium Research Institute (MBARI)

United States

Advisors

E. Virginia Armbrust

Advisor

University of Washington

United States

Thomas Cavalier-Smith

Advisor

University of Oxford

United Kingdom

W. Ford Doolittle

Advisor

Dalhousie University

Canada

Ursula Goodenough

Advisor

Washington University in St. Louis

United States

Michael W. Gray

Advisory Committee Chair

Dalhousie University

Canada

Joseph Heitman

Advisor

Duke University

United States

John W. Taylor

Advisor

University of California, Berkeley

United States

Ideas Related to Integrated Microbial Biodiversity