Marine Microbes

This page describes a few of the general types of microbes we will be studying on the BioLINCS cruise. This is far from being a complete list of marine microbes at Station ALOHA, but it does include the most important groups known to be involved in the oceanic nitrogen cycles, as well as a few key primary producers (photosynthetic microbes).

A surprising number of these marine microbes have only recently been discovered, or are known only by their DNA. In some cases, we only know that they are really tiny and have certain types of genes, such as genes necessary for fixing nitrogen. This is one reason that there are no photographs of many of these organisms in the listings below.

At the broadest level, these microbes can be divided up between three main groups, which are three domains of living things on this planet:

The microbes listed below are grouped by these three domains. Within each domain, they are grouped according to their roles in nitrogen cycling. I have also included a few microbes that are key players in open-ocean photosynthesis and primary production. These microbes are important for nitrogen cycling in that they “assimilate” nitrogen and convert it into living tissue or “particulate nitrogen.”

Several terms are used to describe microbes that perform certain roles in nitrogen cycling, but which may or may not be related to one another. The bacteria and archaea that can convert nitrogen gas into more biologically useful forms such as ammonium are known as “nitrogen fixers” or “diazotrophs.” Microbes that convert ammonium to nitrate are called “nitrifying organisms.”


Marine bacteria are single-celled organisms that can be shaped like little spheres, rods, or (less commonly) spirals. The are often very small, with cell diameters of just a few microns (about 1/100th the width of a human hair). They perform all kinds of chemical processes in the open ocean, including most of the steps in nitrogen cycling.

Cyanobacteria are a large group of photosynthetic bacteria, some of which can “fix” nitrogen, converting nitrogen gas into more biologically useful compounds. Cyanobacteria live in all kinds of environments, but are especially important in open-ocean ecosystems. They were formerly known as “blue-green algae” but are now recognized as a type of bacteria, not a type of algae (algae are eukaryotes).


micrograph of Trichodesmium Trichodesmium

Microphotograph by Angel White, Oregon State University.

Trichodesimium is a genus of colonial cyanobacteria that is one of the most important and well-studied nitrogen-fixing organisms found in open-ocean areas such as Station ALOHA. It is one of the few organisms involved in the oceanic nitrogen cycle that is visible to the naked eye. Trichodesmium is a colonial organism that forms hair-like strands, which sometimes aggregate into tiny “puffballs” up to a millimeter or two across. When winds are light, Trichodesmium colonies may clump together and float right on the sea surface, where they are known as “sea sawdust.”

Trichodesmium uses an enzyme called “nitrogenase” to transform nitrogen gas into more biologically useful compounds (a process called “nitrogen fixation.”) However, nitrogenase is inactivated in the presence of oxygen (which is produced by many photosynthetic organisms as a byproduct of photosynthesis). Because of this, most nitrogen-fixing microbes separate the processes of nitrogen fixation and photosynthesis either spatially (using different types of cells for each process), or temporally, by performing photosynthesis in the daytime and fixing nitrogen at night.

Trichodesmium, however, uses neither of these strategies. It is able to fix nitrogen during the daytime, but does not have specialized cells to perform the job. Researchers are very interested in figuring out how Trichodesmium is able to fix nitrogen in the daytime.

During the BioLINCS cruise, Trichodesmium is being studied using microscopy, nitrogen-uptake experiments, and nucleic acid (DNA and RNA) analyses. These analyses will be carried both out on the ship and later on shore. Among other things, researchers will be using genetic “probes” that look for a gene called nifH, which is one of several genes that help microbes produce the nitrogenase enzyme. This will help them determine the abundance and nitrogen-fixing ability of Trichodesmium. The Environmental Sample Processor (ESP) will also be using the nifH gene to monitor the presence of Trichodesmium in real time.

Heterocystus cyanobacteria

Heterocystus cyanobacteria are multi-celled organisms that form microscopic filaments and perform nitrogen fixation in the open ocean. The most common genus of heterocystus cyanobacteria in open-ocean areas is Richelia, which is almost always found living inside of diatoms, a type of microscopic marine algae.

As part of this “symbiotic” living arrangement, the heterocystus cyanobacteria provide the diatoms with “fixed” nitrogen and other nutrients. It is not entirely clear what the bacteria get out of the arrangement.

Like all nitrogen fixing organisms, heterocystus cyanobacteria use an enzyme called “nitrogenase” to transform nitrogen gas into more useable forms of nitrogen. However, nitrogenase is inhibited in the oxygen-rich environment that exists inside most cells. As multi-cellular organisms, heterocystus cyanobacteria have evolved specialized cells called “heterocysts,” which provide an environment more conducive to nitrogen fixation.

During the BioLINCS cruise, heterocystus cyanobacteria are being studied using DNA analyses that are carried out manually on board the ship and performed automatically within the Environmental Sample Processor (ESP). Among other things, researchers will be looking for the nifH gene in Richelia diatoms. This is one of several genes that allow cyanobacteria to produce the nitrogenase enzyme. Researchers will also be combining DNA analyses with measurements using influx flow cytometer (IFC) to determine whether heterocystus cyanobacteria are associated with specific types of marine algae.


Crocosphaera is a genus of singled-celled cyanobacteria that lives through photosynthesis and can “fix” nitrogen. It grows in many tropical ocean areas where the water is about 24° Celsius (75° Fahrenheit). At about two to four microns across, Crocosphaera is much smaller than Trichodesmium. Like all nitrogen-fixing organisms, Crocosphaera uses an enzyme called “nitrogenase” to transform nitrogen gas into more biologically useful compounds. However, nitrogenase doesn’t work well in the presence of oxygen (a byproduct of photosynthesis). As a solution to this problem, Crocosphaera performs photosynthesis during the day and nitrogen fixation at night.

During the BioLINCS cruise, researchers will be studying Crocosphaera using the influx flow cytometer (IFC).

Uncultivated cyanobacteria group A (UCYN-A)

UCYN-A is a group of nitrogen-fixing cyanobacteria that were first discovered in the open ocean near Hawaii in 1998. Most of the time, they are not the most abundant nitrogen-fixing organism, but they can reproduce rapidly when conditions are right.

UCYN-A bacteria contain very few genes, compared with most other marine cyanobacteria. Although the entire UCYN-A genome has been sequenced, the organisms themselves have yet to be grown in the laboratory.

Surprisingly, sequencing of the UCYN-A genome revealed that that the bacteria lack genes that are necessary for “fixing” inorganic carbon and for key parts of the photosynthetic process. This allows UCYN-A to fix nitrogen during the daytime. However, because the bacteria cannot perform photosynthesis, they must have some other means of acquiring key organic compounds that are normally produced during photosynthesis. As with some heterocystus cyanobacteria, it is possible that UCYN-A form “partnerships” (symbioses) with other photosynthetic organisms to acquire these essential compounds.

During the BioLINCS cruise, UCYN-A are being studied using DNA and RNA analyses that are carried out manually on board the ship and performed automatically within the Environmental Sample Processor (ESP).

Alphaproteobacteria and gammaproteobacteria

Proteobacteria are an extremely diverse group of bacteria. Some alphaproteobacteria and gammaproteobacteria, two subgroups within the proteobaceria, carry the nifH gene, and may be able to fix nitrogen. The proteobacteria also include some key players in the process of “nitrification,” as described below.

During the BioLINCS cruise, the Environmental Sample Processor (ESP) will be looking for the nitrogenase (nifH) gene specific to gammaproteobacteria. This gene allows the bacteria to produce the enzyme nitrogenase, which they use to “fix” nitrogen. The ESP will also be looking for alphaproteobacteria using sandwich hybridization arrays.


Ammonium oxidizing bacteria (AOB)

The ammonium oxidizing bacteria (AOB) are bacteria that are all involved in a specific biochemical process (nitrification), but which may or may not be related to one another. They are involved in the first step of nitrification—the conversion of ammonium to nitrite (also known as “ammonium oxidation”).

Most of the known ammonium oxidizing bacteria are betaproteobacteria and gammaproteobacteria. These bacteria are believed to be involved in this process because they carry a gene that codes for the ammonia monooxygenase enzyme (amoA).

Nitrite oxidizing bacteria

Several different genera of marine bacteria are involved in in the second step in the nitrification process—converting nitrite to nitrate (also known as “nitrite oxidation”). These include Nitrobacter, Nitrospira, and Nitrospina. Of these, Nitrospira is believed to be the most important in the open ocean.


micrograph of Prochlorococcus Prochlorococcus

This scanning electron microscope image, taken by Claire Ting, shows several Prochlorococcus cells, including one in the process of dividing.

Prochlorococcus is a genus of cyanobacteria that is very common in open-ocean areas around the world. Although extremely tiny, with cells only 0.5 to 0.8 microns across, Prochlorococcus (along with another genus, Synechococcus) are so widespread and abundant that may produce a third of the oxygen in the Earth’s atmosphere. Prochlorococcus are “obligate photoautotrophs,” obtaining all of their energy through photosynthesis. However, they require nitrogen as a nutrient, and can use either nitrate or ammonium as a source of nitrogen. Thus, they are a key part of the “assimilation” process in oceanic nitrogen cycles.

During the BioLINCS cruise, researchers will be studying Prochlorococcus using the influx flow cytometer (IFC), and in some on-deck incubation experiments.


Synechococcus is another common type of marine cyanobacteria. It is arguably the second most common group of photosynthetic marine bacteria, after Prochlorococcus. It has a similar shape as Prochlorococcus, but is typically a little bit larger, at 0.8 to 1.5 microns across.

Like Prochlorococcus, Synechococcus are “obligate phototrophs,” which means that they can only obtain energy through photosynthesis, and require nitrate as a key nutrient. They can use nitrate or ammonium as sources of nitrogen, and are a key part of the “assimilation” process in oceanic nitrogen cycles.

During the BioLINCS cruise, researchers will be studying Synechococcus using the influx flow cytometer (IFC).


Archaea are single celled organisms that look similar to bacteria, but which are in an entirely separate biological domain. Historically, archaea were thought of as living mostly in extremely hot, acidic, or low oxygen environments. However, in the last decade, using DNA and RNA analysis, molecular biologists have found them to be very common in both freshwater and saltwater environments.

Ammonium oxidizing archaea (AOA)

Like ammonium oxidizing bacteria, ammonium oxidizing archaea are important in the nitrification process in open-ocean areas. They perform the first step of nitrification—the conversion of ammonium to nitrite, which is also known as “ammonium oxidation.” In the process of performing ammonium oxidation process, AOA may produce nitrous oxide, a greenhouse gas that is sometimes released from open-ocean waters into the atmosphere.

All of the known ammonium oxidizing archaea are in the group Thaumarchaea (formerly known as Crenarchaeota). These archaea are common in soils, in estuaries, and in the deeper parts of the open ocean, where there is little light and oxygen concentrations are relatively low.

Like ammonium oxidizing bacteria (AOB), AOA are able to make an enzyme called ammonia monooxygenase. Researchers often use DNA analysis to determine if a sample of seawater contains the gene (amoA) that allows AOA and AOB to produce ammonia monooxygenase. Once they identify organisms with this gene, the researchers can use genetic probes to tell if the organisms are bacteria or archaea

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