Marine microbes

Marine microbes are tiny, single-celled organisms that live in the ocean and account for more than 98 percent of ocean biomass. The term “marine microbe” covers a diversity of microorganisms, including microalgae, bacteria and archaea, protozoa fungi, and viruses. These organisms are exceedingly small—only 1/8000th the volume of a human cell and spanning about 1/100th the diameter of a human hair. Up to a million of them live in just one milliliter of seawater.

Microbes (which include Bacteria, Archaea, microbial eukaryotes and their associated viruses) are as varied as the marine environments they come from. From the ice-covered polar regions of the Arctic and Antarctic to the boiling hydrothermal vents in the depths of the sea and the calcareous oozes made up of the skeletons of single-celled eukaryotes called foraminifera that once recorded the temperature of the sea surrounding them—microbes are everywhere and they help to shape the features of our planet, past and present. When it comes to exploring marine microbial life, we are still very much in the age of discovery.

Major taxonomic groups of Marine Microbes

Prokaryotes

Most bacteria obtain energy by either absorbing marine dissolved organic matter through their cell membranes- osmotrophy . However, some rely on sunlight and photosynthesis (autotrophy or self-feeding). They are found in every environment, from sea ice at the poles to deep-sea hydrothermal vents. In seawater typical concentrations are about a million per ml or 5 million in a tablespoon.

Introducing Marine Viruses

In the late 1980s, oceanographers, led by Jed Fuhrman and others, began to appreciate the role of marine viruses in controlling the abundance and distribution of marine bacteria. Although their status as a true “life form” is debated, their importance in the ocean merits their introduction here. Marine viruses, like other viruses, consist of small amounts of genetic material encapsulated in protein. These viral particles (20-200 nm in length) exist solely at the expense of their host: viruses have no metabolic machinery of their own. Nearly all known viruses are specific to a single species or genus and all organisms appear to be susceptible to viral infection. They are very abundant in the sea; a tablespoon of seawater, 5 ml, commonly contains about 50 million viruses.

Viruses use their hosts to reproduce their genetic material, essentially hijacking the genome of the host cell to cause it to produce multiple copies of the viral particle. The infected host may continue to release viral “progeny” over several generations (chronic infection), the viral genome may become a “permanent” part of the host genome (lysogeny) or the virus may kill the host, causing the host to explode as a means for releasing copies of its viral progeny (lytic infection).

Viral lysis, the bursting of host cells by viral reproduction, may result in the mortality of 10-40% of marine bacteria. Thus, viruses may play a significant role in controlling populations of marine bacteria under certain conditions. One consequence of viral lysis is the release of dissolved organic matter which may stimulate the activity of surviving marine bacteria. Much remains to be learned about marine viruses but their importance in marine food webs has now been accepted.

Introduction to Marine Protists

Protists are eukaryotic, possessing a membrane-bound nucleus, but are single-celled or acellular organisms. The group includes all eukaryotic organisms which are not multi-cellular. Thus, it is a group of organisms united more by what they are not- multicellular- than by ancestry or common ecological characteristics. Marine protists typically range in size from 2 to 200 micrometers. Whereas viruses are parasites, and prokaryotes are osmotrophs or autotrophs, marine protist provide examples of these distinct life-styles as well as certain combinations of strategies.

  The different types are found in different concentrations. Protists which have chloroplasts, allowing them to perform photosynthesis thus act as autotrophs, are generally found in the highest concentrations. The larger forms (10 - 200 micrometers in size) include diatoms and many dinoflagellates. The most abundant are small (1 - 10 micrometers long) flagellates. Autotrophic protists are restricted to the upper sunlit portion of the seas and found in abundances of a thousand per ml for the small flagellates. While they have few morphological characteristics allowing us to distinguish species, recent genetic studies suggest that small marine flagellates may be a very diverse group of organisms. Larger autrophic protists such as diatoms and dinoflagellates typically occur in concentrations of about one cell per ml.

Protists which rely on aquiring pre-formed organic matter are heterotrophic. Usually in surface waters there are about a thousand per ml of small flagellates which feed on bacteria (both autotrophic and heterotrophic prokaryotes) and 1 or 2 ciliates, oligotrichs (Fig 2B) and tintinnids (Fig 2C) or heterotrophic dinoflagellates which feed on autotrophic protists. Besides these two large, common life-styles there are parasitic protists as well 'mixotrophic' protists. Mixotrophic protists use both photosynthesis from chloroplasts as well as feeding on pre-formed organic matter, often in the form of other protists. Some protist species retain and use the chloroplasts in the prey they eat while other protists harbor symbionts, entire autotrophic bacteria or protists.

Introducing Marine Bacteria

 For nearly 2 billion years, marine bacteria ruled the Earth. During the Age of Bacteria (from ~3.5– 1.8 bya), all of Earth’s biogeochemical cycles were established. But for bacteria, Earth’smaterial resources would have been bound into an irretrievable form a long time ago. Yet while the role of bacteria as “nature’s recyclers” is well-appreciated, less well known is their importance as a food source. Nourished by pools of dissolved organic carbon, marine bacteria play a central role in marine food webs providing nutrition to a host of small microorganisms. In doing so, they “recapture” energy in the form of carbon compounds that might otherwise be lost to the system. This microbial loop, the component of a marine food web that recycles minerals (e.g., regeneration of biologically important nutrients) and captures carbon and energy from dissolved organic matter, represents an integral component of marine food webs, especially in the open ocean. In recognition of their importance in the world ocean, oceanographers now often refer to water column bacteria as bacterioplankton (“bacteria drifters”). To this ever-growing list of accomplishments among marine bacteria, we must also emphasize their role as autotrophs, producers of organic matter (aka primary producers). Photosynthetic bacteria abound in the world ocean. In fact, oceanographers estimate that the contribution of photosynthetic bacteria to primary production exceeds that of all other primary producers in the ocean.

Much of what we know about marine bacteria has emerged since the 1980s. The application of molecular biology techniques to studies of marine bacteria has advanced considerably our knowledge of their diversity and distribution, but much remains to be learned regarding the types and scales of their metabolic activities. One of the major puzzles concerns the discrepancybetween marine bacteria that can be cultured and those that cannot. As far back as 1959, oceanographers recognized that the number of bacteria appearing under a microscope was far greater than the number that grew out on agar plates, a type of solid, nutrient-enriched sterile medium designed to study bacterial growth. This “great plate count anomaly”, as it came to be known, remained a puzzle until ocean genomics revealed a diverse suite of marine bacterioplankton. Intriguingly, the most abundant gene sequences (specifically, ribosomal DNA genes) found in the world ocean belong to groups that cannot be cultured in a laboratory.

On the basis of gene sequencing, eleven major groups of bacterioplankton are recognized in the world ocean, including the two groups of Archaea. Of these, only two groups contain species that have been cultured. Little is known about the most abundant group, discovered in 1990 and known simply by its gene cluster, SAR11. Its presence throughout the world ocean from shallow lagoons to the deep ocean suggests this “species” may be the most abundant marine bacteria in the world ocean. The Roseobacter group has been found throughout the world ocean and represents one of two culturable marine bacteria. While they exhibit diverse metabolic modes that change with environmental conditions, they all appear to utilize organic or inorganic sulfur compounds. Nevertheless, their ecological role remains uncertain. Perhaps the most well-known marine bacteria are the other culturable group, the cyanobacteria (literally, the blue-green bacteria), the dominant member of the picophytoplankton (see Table above). Unseen in the world ocean until the late 1970s, cyanobacteria are now believed to be the most abundant and possibly the most productive photosynthetic microorganisms on Earth. Two major groups of cyanobacteria can be found in the world ocean. The cyanobacterium Synechococcus (sin-eh-ko-KOK-us), discovered by John Waterbury in 1979, measures 1.5 – 2.5 μm in size. It seems to prefer high-light, tropical and subtropical waters, like the Sargasso Sea, although it may be found throughout the world ocean, including polar regions. Its cousin, Prochlorococcus (pro-chlor-oh-KOK-us) was found by Penny Chisholm in 1988 and measuresless than 0.7 μm in diameter (about 1/100th the width of a human hair), making it the smallest known photoautotroph on

Earth. Prochlorococcus has been found to inhabit waters between 40º N – 40º S (cold temperatures may be lethal) in at least two ecotypes (genetic variants): one that prefers high light and one that prefers low light. Both species appear to have very small genomes yet exhibit considerable plasticity in their ability to adapt to varying oceanic conditions. Both ecotypes may be capable of nitrogen fixation and heterotrophy (i.e., metabolizing organic substrates).

Though our knowledge of bacterioplankton species is limited, we do know that they inhabit different layers in the water column. We also know that bacteria associated with suspended particles are different from free-living types. As oceanographers are better able to attribute biochemical transformations and rate processes to specific groups of marine bacteria, our knowledge of their ecological roles will grow. We have much to learn and the future holds great promise for this exciting and rapidly growing field of oceanography.

Introducing Marine Archaea

There is a growing body of evidence that the first forms of life originated and evolved in extreme environments, like hydrothermal vents. The perfect candidate for such an existence is the Archaea, a group of “ancient” microbes commonly found in the most hostile environments on our planet. Archaea inhabit the hot acidic pools of Yellowstone, the salt flats of San Francisco and the deep-sea vents on the Juan de Fuca ridge. Oceanographers have even discovered subterranean forms of Archaea that live in the fluids and rocks beneath the sea floor. Though widely known as extremophiles, Archea have been discovered throughout the water column in the world ocean. The abundance of these pelagic Archaea rivals that of marine bacteria.

Some scientists prefer the term Archaea instead of Archaebacteria because these microbes differ substantially from bacteria. Their cellular and genetic makeup exhibit some similarities to eukaryotic cells, the type of cells that comprise all forms of life except bacteria, including humans.

 Two major groups of Archaea are commonly recognized: the Crenarchaeota and the Euryarchaeota. The Crenarchaeota include the thermoacidophiles, the hot- and acid loving microbes that thrive in warm-to-hot, acidic, sulfurous environments (e.g., Yellowstone Park).

This group, comprised of several species, may tolerate temperatures as high as 110 degrees C; most die at temperatures approaching the human body temperature (37 degrees C). These organisms may use elemental sulfur as an energy source to fix carbon dioxide, a form of metabolism called chemolithoautotrophy. They may also utilize simple organic molecules, a form of heterotrophy. Thus, these organisms are classified as facultative autotrophs (meaning they are capable of autotrophy but do not depend on it exclusively).

The Euryarchaeota include two groups of microbes living in quite different habitats, the methanogens, who live in anaerobic sediments, and the extreme halophiles, who live in extremely salty environments. The methanogens produce methane in the absence of oxygen, i.e., anaerobically, and are responsible for at least 90% of the world’s natural gas supply, as well as swamp gas and gas hydrates, the frozen deposits of methane found on the sea floor. Because of their intolerance of oxygen, methanogens are found in anaerobic sediments (in shallow or deep waters) and in the guts of animals, like cows. Methanogens are unable to use proteins, carbohydrates and sugars, like most organisms. Rather, they utilize hydrogen gas to reduce (“fix”) carbon dioxide. Their conversion of the organic breakdown products of other organisms serves one of the most important roles on Earth: the return of buried carbon to the atmosphere (as methane which quickly reacts or is converted by organisms to carbon dioxide). Without methanogens, there would be no carbon cycle, oxygen would build up in the atmosphere and

Earth would experience uncontrollable fires! The halophiles are salt-loving microbes, found in hypersaline springs and lagoons and salt flats, like those that border San Francisco Bay. They may be observed as a pinkish tinge in a salt flat, a color that results from pink pigments carotenoids) that allow them to tolerate intense sunlight. These microbes require sunlight to carry out a form of non-oxygenic photosynthesis (using bacteriorhodopsin, a bacterial photosynthetic pigment) that allows them to synthesize the energy-carrying molecule, ATP. Otherwise, halophiles respire oxygen and are considered heterotrophs.

Both groups also include pelagic Archaea of which little is known. The contrast between these free-living water column forms and the extreme forms tells us we have much more to learn about the physiology and ecology of these microbes. Clearly, these microbes extend their range beyond extreme habitats and make use of alternative energy sources and metabolic pathways. Pelagic non-thermophilic crenarchaeota may comprise up to 20% of all the world’s ocean picoplankton (organisms with a size range from 0.2 - 2 μm) (Karner et al., 2001).