Magnified bacteria.

Milestones In Marine Microbiology

Microbes Timeline


Marine microbes are abundant and diverse. But their tiny size means they are not easy to study. First observed in 1675, marine microbes were not cultured in the lab for over 100 years allowing for further observation. Molecular advances and large DNA libraries allowed for many advances since the 1970s and there is still much to learn!

Thanks to David Karl and Jody Deming for review of this timeline.

This work was supported by the National Academies Keck Futures Initiative of the National Academy of Sciences under award number NAKFI DBS17. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Academies Keck Futures Initiative or the National Academy of Sciences.

A portrait of Leeuwenhoek
A portrait of Leeuwenhoek

Early Discoveries


First observations of aquatic microbes

The Dutch lensmaker Antonie van Leeuwenhoek devises a simple, yet powerful single lens microscope that allows him to observe microbes for the first time. He calls the small creatures "wee animalcules."

An assortment of microbe illustrations seen by Leeuwenhoek under the microscope.
Colored engravings of the "animalcules" Leeuwenhoek saw under his microscope. Credit: Anton van Leeuwenhoek, U.S. Public Domain
Illustration of Leeuwenhoek's microscope
An illustration of one of Leeuwenhoek's microscopes. Credit: Dobell and van Leeuwenhoek, 1960
Microscope image of bacteria from microbial mat in Mexico.
Microscope image of bacteria from microbial mat in Mexico.

'Golden Age' of Microbiology


First attempts at cultivating microbes from the ocean

Adolph-Adrien Certes, a student of Louis Pasteur (the French microbiologist known for his breakthrough work on vaccinations and, of course, pasteurization), reports on his deep-sea microbial cultivation experiments from the French Travailleur and Talisman expeditions.

Illustration of Talisman ship
An illustration of the Talisman ship. Credit: Sous les mers; campagnes d'explorations du "Travailleur" et du "Talisman" (BHL)

Publishing of the earliest known book specifically dedicated to marine microbes

The German microbiologist Bernhard Fischer publishes his treatise Die Bakterien des Meeres (Bacteria of the Sea).

A diagram showing marine carbon cycle.
An early diagram showing how carbon gets moved around in the sea. Credit: Die Bakterien des Meeres via Biodiversity Heritage Library
Cover page of book.

The cover page of Die Bakterien des Meeres. Credit: Marine Microbiology: A Monograph on Hydrobacteriology


van Niel begins his summer course in microbiology at Stanford University's Hopkins Marine Station

Running until 1962, Cornelis Bernardus van Niel influences generations of microbiologists with his Hopkins Marine Station summer microbiology course, bringing the Dutch techniques of enrichment culture (a method that allows for the growth of a specific microorganism) to the U.S. and highlighting the tremendous metabolic diversity of microbes in the environment.

Black and white image of brick building.
The Stanford Hopkins Marine Laboratory as it appeared in 1918. Credit: Photograph courtesy of Harold A. Miller Library and Hopkins Marine Station, Stanford University

ZoBell publishes seminal marine microbe text

Claude ZoBell, often known as the "father of marine microbiology," publishes the foundational text Marine Microbiology: A Monograph on Hydrobacteriology.

Black and white photo of a man holding up an instrument while on a boat.
Claude Zobell prepares a water sampling bottle on the Scripps Institution of Oceanography pier, November 1952. Photograph courtesy of Scripps Institution of Oceanography, UC San Diego.

Radiotracers first applied to study the activity of marine microbes

The discovery, by Martin Kamen and Sam Ruben, of a radioactive isotope of carbon (14C) allows oceanographer Einer Steeman-Nielsen to follow the uptake of carbon into microbial cells. Scientists begin to quantify the activity of microbes at the base of the food web without having to first culture them in the lab.

A yellow background with three black shapes in a circle.
Credit: Wikimedia Commons

Establishment of the Microbial Ecology course at the Marine Biological Laboratory

Holger Jannasch begins the summer Microbial Ecology course (now the Microbial Diversity course) at the Marine Biological Laboratory in Woods Hole, Massachusetts.

Postcard image of a dock with boats and buildings in the background.

The Marine Biological Laboratory in Woods Hole, MA as it appeared sometime between 1930 and 1945. Photo Courtesy of Boston Public Library.


Importance of marine microbes in marine food webs and dissolved material cycling first recognized

Lawrence Pomeroy publishes his work on the role of microbes in the ocean's food web, later dubbed "The Microbial Loop."

An zoomed-in, purple microbe illustration.
A microbe absorbs dissolved molecules in the water column. Credit: Smithsonian Institution
A green phytoplankton is coming apart where a yellow virus attacks it.
A virus kills a phytoplankton. Credit: Smithsonian Institution
Black and white magnified image of SAR11.
Black and white magnified image of SAR11.

Molecular Era


Analysis of small subunit ribosomal RNA gene (rRNA) sequences are used to describe the relatedness of organisms leading to the first description of the archaea

Carl Woese and George Fox first propose using rRNA gene sequences as molecular markers for determining the relatedness and organization of life, including marine microorganisms. Ribosomal RNA gene cloning and sequencing from the environment would later be applied to uncultivated microbes in hydrothermal vent symbionts (in 1984) and lead to the discovery of some of the most abundant microbes in the ocean.

The molecular structure of a section of bacterial rRNA
A section of bacterial rRNA, the RNA that serves as the building blocks for the cell's protein-making factories. Credit: Molecular and Cellular Biology WikiProject

Cultivation of the first barophilic (or pressure-adapted) microorganisms from the deep sea

Pressure makes it difficult to study specimens collected from the deep sea—at a depth of 6,500 feet, the pressure is almost 200 times what we feel on land. A concerted effort across three laboratories, those of Holger Jannasch, Aristides Yayanos, and Rita Colwell, is undertaken to recover uniquely pressure-adapted ('barophilic') microorganisms from the deep sea. The work eventually leads to the discovery of the first barophile in 1979 and an obligate barophile in 1981 by Yayanos. Colwell and her then-graduate student, Jody Deming, demonstrate that entire communities of microorganisms can be barophilic using the microbes found in the guts of deep-sea animals.
A yellow, transparent sea creature on a sandy ocean bottom.
Some sea cucumbers found in the deep-sea are home to barophilic, or "pressure-loving," bacteria in their guts. Credit: NOAA Ocean Explorer, DeepCCZ expedition

Nuclepore filters and fluorescent staining are used to count marine microbes

A technique is developed for creating a plastic filter with uniform holes so tiny that bacteria can be filtered from seawater. Prior to the invention of these Nuclepore filters, most estimates of microbial abundance in the ocean were based on the number of microbes that could be cultured in rich liquid media or on solid medium in Petri dishes. The development of staining techniques, first used by ecologist John Hobbie, confirms that microbes are hundreds of times more abundant in the environment than estimated using culture-based methods.
Black background with bright blue clusters of dots.
A modern fluorescent stain, called DAPI, shows magnified bacterial marine cells. Credit: Anthony D'Onofrio,, Flickr

Discovery of hydrothermal vents in the deep sea, along with bacteria that thrive only in these high-pressure, high-temperature environments

An expedition to the Galapagos Rift—where tectonic plates slowly spread apart—provides the first visual confirmation of hydrothermal vents, pouring out heated water full of minerals, and a surprise discovery that dense ecosystems of previously unknown organisms are supported by the vent fluid chemistry. Many of these animals depend on symbiotic relationships with bacteria that harvest energy from chemicals like hydrogen sulfide released from the vents. In a follow-on expedition to the East Pacific Rise—the fastest seafloor spreading zone—black smokers are discovered, releasing fluids at an extraordinary temperature of 250°C/482°F (kept liquid by the high pressure of the deep sea). This leads to the discovery of deep-sea hyperthermophiles—organisms that thrive in extremely hot environments—living in a subseafloor biosphere.

Red and white worms on the sea floor.
Riftia tube worms living near a hydrothermal vent. Credit: NOAA
Dark smoke coming out of two vertical vents on the seafloor.
A black smoker hydrothermal vent. Credit: NOAA

Discovery of the abundant marine cyanobacterium Synechococcus

Tiny fluorescent cells observed by John Waterbury on an expedition to the Arabian Sea introduces researchers to Synechococcus. Since then, they have been found in large quantities in almost all ocean water, serving as an important base of the food web for fish and larger mammals.

Magnified bright green cells with a black background.
The green fluorescence shows chemical reactions in living Synechococcus cells. Credit: Pacific Northwest National Laboratory

Discovery of the abundant marine cyanobacterium Prochlorococcus

Sallie (Penny) Chisholm discovers this tiny but super abundant photosynthesizer— estimated to be more abundant than any other on the planet, and responsible for producing 20 percent of the oxygen released to the atmosphere every year.

neon green closeup of prochlorococcus
A colored image of Prochlorococcus. Credit: Anne Thompson, Chisholm Lab, MIT

Establishment of the Hawai'i Ocean Time-series and the Bermuda Atlantic Time-series Study

Two long-term ocean monitoring programs are established—the Hawai'i Ocean Time-series at Station ALOHA by David Karl and Roger Lukas and the Bermuda Atlantic Time-series Study by Anthony Knap. Both programs capture regular physical and biological measurements in order to better understand nutrient cycling, where microbes play a huge role. The information is also important for tracking the impact of climate change and ocean acidification on marine microbes.

Researchers work with an instrument on a ship while wearing hard hats and life vests.
Scientists conducting research for the BATS project. Photo Courtesy of Craig Carlson.

Abundance of viruses in aquatic environments first described

While previous researchers had known viruses existed in the ocean, Øivind Bergh and colleagues first report their abundance in marine waters. Later developments in fluorescent staining show that even these high abundances vastly underestimated the actual number of viruses in seawater, now thought to be close to one billion per milliliter. Viruses play important roles in aquatic ecosystems by transferring genes among microbes and by lysing, or killing, microbes.
Black and white image of a magnified cyanophage.
A virus called a cyanophage that attacks cyanobacteria. The bar indicates a scale of 100 nm. Credit: Bin Ni, Chisholm Lab, MIT
Black background with hundreds of green dots that indicate a cyanophage.
A sampling of cyanophages that glow from a stain in this magnified image. Credit: Matthew Sullivan, Chisholm Lab, MIT

Molecular cloning and DNA sequencing is first applied to planktonic marine microbes and leads to discovery of SAR11, one of the most abundant bacteria in the ocean

Microbes in the SAR11 clade (SAR stands for the Sargasso Sea where they were first discovered by Stephen Giovannoni and colleagues) are the most abundant organic carbon-eating bacteria in the ocean and can make up to 25 percent or more of microbial cells at any given time. DNA sequencing and the ability to clone molecular structures was necessary for the discovery of SAR11 as no cultures of the organism existed at that time.

an orange kidney bean shape filled will yellow orbs and with a blue outline
A 3D model of a SAR 11 microbe, also called Pelagibacter. Image courtesy of Xiaowei Zhao.
Black and white magnified image of SAR11.
A magnified look at SAR11. Credit: Kehau Manoi courtesy of Michael Rappe

Mesophilic archaea discovered in the marine water column

Prior to 1992, archaea were thought to exist as one of three types—either an extremist that lives in very salty environments (a halophile), an extremist that lives in scalding hot water (a thermophile), or as a methane producer (a methanogen). In separate reports, marine microbiologists Edward Delong and Jed Fuhrman show that archaea also inhabit coastal and deep-water habitats as drifting plankton. And what's more, they are abundant in these locations.
A scanning electron micrograph of hyperthermophilic archaea.
Archaea are one of the many microbes that exist throughout the ocean. This particular microbe is found in hydrothermal vents. Image Courtesy of Gerhard Wanner, University of Munich, Germany.
Many colored lines make up a circle representing the Prochlorococcus genome.
Many colored lines make up a circle representing the Prochlorococcus genome.

Genomic Era


Large-insert DNA libraries are first applied to study metabolic function of uncultivated microbes in the ocean, leading to the discovery of a new type of energy harvest (or phototrophy) in the sea

Discovering microbes by trying to culture them is not easy. Instead, scientists use DNA sequencing to identify just the presence of the microbes' genes without first having to culture them. An early method for doing this involves cloning large pieces of environmental DNA into easily grown E. coli bacteria. Eventually, these techniques lead to the discovery of proteorhodopsin, a protein related to one found in the human eye, which harvests light energy and had not previously been found in bacteria.

Purple, blue and gray curly objects that are linked together by tiny thread-like structures.
A model of the proteorhodopsin protein structure. Courtesy of UniProt

Publication of first complete genomes of marine microbes

The full genomes of several marine microbes including Prochlorococcus, Synechococcus, Pirellula, Silicibacter pomeroyii, the cold-adapted bacterium Colwellia psychrerythraea, and the diatom Thalassiosira pseudonana are published ushering in the genomic era of marine microbiology.

Many colored lines make up a circle representing the Prochlorococcus genome.
A visual representation of prochlorococcus' genome. Credit: Katherine Huang, Chisholm Lab, MIT

A fuller picture of the microbes in a marine environment are seen using metagenomics

The first full genetic snapshot of a marine environment—the Sargasso Sea—is completed in 2004 by J. Craig Venter, using shotgun metagenome methodology identifying over one million previously unknown genes.
An illustration that depicts genomes coming from the environment.
DNA taken from the ocean is used to determine the types of species that live there.

Global Ocean Sampling, Tara Oceans, and Malaspina Expeditions

As it becomes more apparent that marine microbes play critical roles in the marine environment, extensive expeditions that cross multiple ocean basins prioritize studying the microbial world. In 2003, the Global Ocean Sampling Expedition samples 41 locations spanning a distance of 8,000 km (almost 5,000 miles) from the Atlantic to the Pacific, collecting an unprecedented amount of information on marine microbial diversity and abundance. Then in 2010, the Malaspina Expedition circumnavigates the globe, researching the metabolic diversity of microbes in the deep-sea. The Tara Oceans Expeditions spans 2009 to 2013. Crossing the globe, they make monumental strides in understanding the diversity of microbial life in the ocean.

Tara ship at sail amidst icy waters.
The Tara Oceans Expedition makes its way through Arctic waters. Credit: ©Joseph Ppevek / Tara Expéditions

Discovery of Lokiarchaeota; believed to be most recent common ancestor of eukaryotes

Lokiarchaeota found in a deep-sea hydrothermal vent show an evolutionary link between archaea and the more complex eukaryotes. After examining the archaeal DNA, researchers discover that these microbes share about 100 genes for complex cellular functions with eukaryotes, suggesting they are the closest living prokaryotic relatives of eukaryotes.

A gray deep-sea vent sticks up from the sea floor.
The hydrothermal vent, Loki's Castle, where Lokiarchaea were found. Credit: Centre for Geobiology (University of Bergen, Norway)
A black and white illustration of the Norse god Loki tied to a rock with a serpent.
Lokiarchaea are named after the vent where they were found, Loki's Castle, referencing Loki, the trickster Norse god. Credit: "The Punishment of Loki", by Louis Huard, U.S. Public Domain
Image of microscopic phytoplankton swirl.
Image of microscopic phytoplankton swirl.


Present - ?

Connecting the dots

The last thirty years have seen rapid discoveries around the diversity of microbial life enabled by new technologies. In the future, we will need to make sense of this vast diversity and better understand how all these organisms interact with one another and with animals of all sizes.
Photo of small multi-colored bobtail squid sitting on ocean floor.
Within hours of birth, the Hawaiian bobtail squid attracts bioluminescent bacteria, which colonize a special light organ above its eyes. Credit: Nick Hobgood