Microbial Food Webs
Life in the ocean is microbe based. Most of the biomass
and biological activity in the ocean is microscopic, and microbes dominate
earth's carbon, oxygen, sulphur, and nitrogen
cycles. There are 100 million times more bacteria in the ocean than stars
in the known universe, and there are a thousand times more viruses than
bacteria. Yet we know little about the relationships between microbes
and their environment because only one tenth of one percent of the bacteria
have ever been cultured. The traditional
marine food web exists in a sea of microbes and dissolved carbon-based
The pelagic food web is microbe-centric...The ‘diatom-copepod-fish’ food
web is a relatively minor component.
Barber & Hilting
The entire microbial food web, including
protozoan micro-zooplankton, is typically some five to ten times
the mass of all multi-cellular marine organisms. The potential metabolic
dominance of microorganisms is even greater than their biomass suggests
... Put in more understandable terms, a mass of B. natrigens [a bacteria]
equal to 100 humans would have an energy throughput of about a gigawatt,
much the same as a nuclear power station. This metabolic potential
under optimal circumstances would be rarely, if ever, achieved in
nature for a number of reasons, notably the low concentrations of
organic nutrients ...
Pomeroy et al (2007).
The microbial food web...has been a major
theme of biological oceanography over the past two decades…
One approach to understanding the relationships between micro-organisms
and their ocean environment is to examine their RNA and DNA using, for
example, the shotgun
technique whereby DNA is removed from cell samples and forced through
a tiny nozzle to break the DNA into millions of fragments. In 2003, Craig
Venter and colleagues used the technique to analyze the DNA sequences
of micro-organisms in water collected from the Sargasso Sea near Bermuda
1800 genomic species based on sequence relatedness,
including 148 previously unknown bacterial phylotypes. We have identified
over 1.2 million previously unknown genes represented in these samples,
including more than 782 new rhodopsin-like photoreceptors. – Venter
et al (2004).
Read more about Venter's ocean work in the Wired Magazine article Craig
Venter's Epic Voyage to Redefine the Origin of the Species and
Carleton University's web pages on marine
Another approach has been to measure the number of microbes, their productivity,
and the amount of particulate matter in the water to calculate how much
the microbes contribute to various parts of the oceanic food web. This
approach shows that microbes, especially the picoplankton, microbial
plankton with sizes ranging from 0.2 to 2.0 microns, are as important
as the traditional marine food web.
The microbial food web (loop on the left) is an important part of the
marine food web. Picoplankton feed larger zooplankton directly (path
6) and indirectly (paths 3, 4, and 6), and they contribute to particulate
and dissolved carbon in the ocean. Click on image for a zoom.
The Microbial Food Web Is Mostly Unknown
The staggering variety of microbes discovered through shotgun DNA analysis
shows how little we know about the microbial web. Craig Venter, in a
second voyage of discovery from New England to the southwest Pacific,
returned with billions of bases of DNA sequences.
Venter’s team has found evidence of
so many new microbial species that the researchers want to redraw
the tree of microbial life... [They] identified more than 400 microbial
species new to science... The vast majority of the microbes that
found themselves snared in Venter’s filters were genetically
unique... Based on their best guess as to the beginning and end of
each gene teased out from the DNA sequences, Venter Institute computational
biologist Shibu Yooseph and his colleagues have concluded that the
DNA encodes 6.12 million hypothetical proteins. That finding almost
doubles the number of known proteins in a single stroke... Most of
the predicted proteins are of unknown function, and a quarter of
them have no similarity to any known proteins... By comparing predicted
amino acid sequences with those of known proteins, they found a surprising
abundance of signaling proteins thought to be used only by multicellular
organisms. Among the hypothetical proteins from their marine samples,
the researchers found 28,000 of the so-called eukaryotic protein
kinases, as well as another 19,000 of a group that are highly similar
to these kinases—
triple the number previously known...
From Ocean Study Yields a Tidal Wave of Microbial DNA by Bohannon (2007).
Read that quote again. One 10-month expedition that sampled the ocean
at just 41 locations returned with hundreds of new species able to make
millions of proteins that were previously unknown, including tens of
thousands that were thought to occur only in higher, multi-celled organisms.
And this is from only a tiny part of the ocean. Clearly, the microbial
web is almost unknown. A vast new frontier of life awaits discovery.
With this in mind, here is a brief outline of what we have learned so
Organisms Comprising the Microbial Food Web
The microbial web includes bacteria and archaea (prokaryotes without
a cell nucleus) and very small eukaryotes (organisms having cells with
a nucleus), ranging in size from 0.01 micrometers for viruses to 20 micrometers
for ciliates, living in a dilute broth of carbon-based matter ranging
from individual molecules to tangled polymers to colloids to clumps of
dead matter called marine snow.
Here is an impressionistic view of microbial life in the sunlit waters
of the ocean.
The microbial loop: impressionist
version. A bacteria-eye view of the ocean's sunlit layer.
Seawater is a carbon-based matter continuum [a
scientific way to say "soup"],
a gel of tangled polymers with embedded strings, sheets, and bundles
of fibrils and particles, including living organisms, as "hotspots." Bacteria
(red) acting on marine snow (black) or algae (green) can control
sedimentation and primary productivity; diverse micro-niches (hotspots)
can support high bacterial diversity.
- Viruses, including bacteriophages Most
of the biomass in the ocean is made up of viruses–Zimmer
They attack and kill bacteria, archaea and other micro-organisms,
which releases the dead's cell contents, adding to the carbon-based
material in the water, and they are able to manipulate the evolution
of other microbial life in the ocean in remarkable ways. There
are more than 5,000 different types of viruses in 100 ml of seawater,
and more than 1,000,000 in a kilogram
of sediment (Rowher 2009).
Patrick Forterre, an evolutionary biologist
at the University of Paris-Sud in Orsay, France, believes that
viruses are at the very heart of evolution. Viruses, Forterre argues,
bequeathed DNA to all living things. Trace the ancestry of your
genes back far enough, in other words, and you bump into a virus. – Zimmer
Viruses can be considered to be on the
threshold between living and non-living. In a sense, they can cause
themselves to be reproduced, so they could be considered as being "alive".
But they can only do this by using the machinery of a host cell.
Without a host they exist only as inert, almost crystal-like, "non
living" particles in the environment. They range generally
from 17 to 1000 nm in size (a nanometer = 10-9m). Viruses
are generally host specific, that is a given virus will generally
affect only a certain species or group of related species, or even
only certain kinds of cells within a species.
From Background information on Viruses, Bacteria and Prions at Marine
Science Online Magazine (no longer in production).
...ocean waters contain about ∼ 4 × 1030 viruses.
Because a marine virus contains about 0.2 fg [1
fg = 1 femto-gram = 10-15 gram] of
carbon and is about 100 nm long, this translates into 200 Megatons
of carbon in marine viruses. If the viruses were stretched end to end
they would span ∼ 10
million light years. In context, this is equivalent to the carbon in ∼ 75
million blue whales (∼ 10% carbon, by weight), and is ∼ 100
times the distance across our own galaxy. – Suttle, C.
Marine viruses and viral-like entities, including
eukaryotic viruses, phage and generalized transducing agents (GTAs),
can have various effects on host cells. When a phage infects its bacterial
host cell, it can either kill the cell (lysis), or transfer genetic
material obtained from a previous host (horizontal gene transfer) or
from its own genome (accessory genes expression). The transferred genes
can allow a cell to expand into different niches (for example, through
the activation of photosynthetic genes, changing the life cycle of
important phytoplankton such as cyanobacteria and coccolithophorids).
Similarly, small viral-like particles known as GTAs can transfer genes
between marine organisms. Two possible scenarios have been proposed
for viral effects on cells. In the 'Red Queen' effect, the virus and
cell are locked in an evolutionary 'arms race', such that they continue
to evolve mechanisms of resistance to each other until eventually the
virus causes the host cell (illustrated here by a coccolithophorid)
to die. In the 'Cheshire Cat' hypothesis, however, the coccolithophorid
simply moves from its diploid, non-mobile stage to a motile, haploid
stage, thereby evading the virus.
From Rohwer 2009.
Left: A T4 bacteriophage infecting a
bacterium. From An
Introduction to the Bacteriophage T4 Virus at dFORM.
Right: A cartoon of a typical bacteriophage.
From Molecular nanomachines at the Department of Biochemistry, University
To learn more about how a phage can inject DNA into a cell read The
Physics of Phages (Gelbart and Knobler, 2008)
- Bacteria The ocean is filled with
a countless mob of bacteria with a staggering variety of genes according
to Bohannon (2007). The bacteria are a critical part of the marine
food web, processing more than half of all the flow of carbon-based
matter. Some use sunlight for energy to synthesize hydrocarbons, the
photosynthetic bacteria, some use both sunlight and carbon-based material
for energy, the mixotrophs, and some attack other organisms, the heterotrophs
(see the vocabulary section below). The photosynthetic bacteria produced
the oxygen and reduced carbon (carbohydrates) starting billions
of years ago. As carbon was buried in sediments, oxygen accumulated
in the atmosphere (see Role of Ocean
The total mass of bacteria in the ocean
exceeds the combined mass of zooplankton and fishes.– Pomeroy
et al (2007).
It [was] generally thought that pelagic
bacteria passively receive dissolved carbon-based matter leaking
from the grazing food chain and diffused homogeneously. However,
recent studies on the complex nature of the carbon-based matter
field and behavioral strategies of bacteria have suggested that
bacteria do not use only preformed dissolved carbon-based matter;
they also attack all carbon-based matter, even live organisms,
thus liberating dissolved carbon-based matter. Hence, bacterial
attack can profoundly modify the biogeochemical behavior of carbon-based
matter in ways not inferred from measuring cumulative carbon-based
matter fluxes into bacteria.
- Cyanobacteria are the most common type of
bacteria in the ocean, and SAR11 (Pelagibacter clade
[group of closely related organisms] of the Synechoccus types of bacteria)
is the most common organism on earth, accounting for roughly 25% of all the
bacteria in the ocean. Prochlorococcus and Synechoccus species
dominate the microbial ecology of the ocean. They account for 25%
of global photosynthesis. Yet, they were mostly
unknown until Sallie W. Chisholm, a professor at the Massachusetts
Institute of Technology, first discovered Prochloroccus in
The marine bacterium SAR11, the most common organism on earth. It was
discovered by Stephen Giovannoni of Oregon State University in 2002.
Giovannoni, Oregon State University, Department of Microbiology.
- Vibrio bacteria
Although bacteria are very common in the ocean, very few cause disease
in people. But some are deadly.
- The marine bacteria found in most coastal waters, Vibrio
cholerae, causes cholera.
- Vibrio vulnificus, which is
also found in coastal waters, including Texas lagoons, causes
a flesh-eating disease (necrotizing
fasciitis) that can kill in a few days without prompt treatment.
If you have a cut that becomes infected after you were in warm
lagoon water, go directly to an emergency room, especially if
the infection spreads. Some infections can increase from the
size of a nickel to the size of a quarter in a few hours. The
bacteria causes roughly 500 infections and 40 deaths each year
in the USA.
V. vulnificus bacterial
infection that developed one day after a fish bone injury
on the fourth finger of the left hand (arrow) in a 45-year-old
patient with uremia.
at UW- Madison. A Danish web site on Vibrio
vulnificus has more images.
- Archaea They look very much like bacteria,
but they are no more closely related to bacteria than we are to bacteria.
The Archaea dominate some oceanic areas, especially below the sunlit
zones, where "they make up typically
40% of deep-sea organisms–and the deep sea is by far the largest
habitat on earth." –
Jed Fuhrman, University of Southern California, quoted in Copley (2002).
Overall, "20% of all the picoplankton
cells in the world ocean appear to be represented by one specific clade,
the pelagic [open-ocean] crenarchaeota". – Karner,
Archaea are important for earth's nitrogen and methane cycles. They
are important chemotrophes. As far as is known, however, archaea do
not photosynthesize and produce oxygen. But they can use sunlight as
a source of energy.
They also dominate subsea sediments:
The deep biosphere is large, and, at least in aggregate, it is 'alive'.
The data almost defy imagination — on the order of a million
cells in every cubic centimetre of sediment buried half a kilometre
below the sea floor, or more than 50% of all microbial cells on Earth.
The overall order of magnitude is the same as the biomass of all
surface plant life. In investigating what kind of cells they are,
Lipp et al. (2008) conclude that, deeper than 1 metre below the sea
floor, it is Archaea, not Bacteria, that contribute the bulk of sedimentary
microbial biomass. If true, Archaea would be the most abundant cell
type in the marine system, rivalling Bacteria in total numbers globally.
From Pearson (2008).
Transmission electron micrograph of Nitrosopumilus
maritimus, (also known as SCM-1), an archae of the kingdom crenarchaeota.
Very similar, open-ocean crenarchaeota are thought to have an important
influence on the nitrogen cycle. Scale bar represents 0.1 micrometer.
From Nature Article: Isolation
of an autotrophic ammonia-oxidizing marine archaeon by Könneke
et al (2005).
- Chromalveolata This very large group
of single-celled eukaryotes (organisms with a cell nucleus), includes
dinoflagellates, coccolithophores, and diatoms which are important
organisms at the base of the marine-fisheries
food webs, and other
organisms, such as ciliates, described below.
- Dinoflagellates are a large group
of organisms with two, hair-like flagella
which they use to swim through the water. About half of the species
are photosynthetic. Some species occur in dense blooms of more
than 109 cells
per liter called
blooms, producing potent neurotoxins that accumulate
in marine animals and that kill fish. People become ill or die
when they eat fish or shell fish that have accumulated the toxins. Some
species are the zooxanthellae that live in
the cells of corals and anemones. Others, such as Noctiluca,
produce light when disturbed. Dinoflagellates tend to dominate
in regions of low turbulence and nutrients, such as oceanic areas
in late summer. Sizes range from 30 micrometers for some marine
species up to 2,000 micrometers (2 mm) for Noctiluca. Heterotrophic dinoflagellates such as Gyrodinium sp. and Protodinium sp. are major grazers of diatoms (Sherr and Sherr, 2007).
Protoperidinium crassipes, a marine dinoflagellate species found in many regions of the ocean.
From: Smithsonian National Museum of Natural History, Dinoflagellates.
- Coccolithophores are small organisms
with two smooth flagella and covered by calcareous plates
called coccoliths.They dominate in regions of moderate turbulence
and nutrients such as mid-latitudes in late spring in sub-polar
regions and in equatorial regions. Typical size is 5–10 micrometers
in diameter. They are one of the world’s major primary producers,
contributing about 15 per cent of the average oceanic phytoplankton
biomass to the oceans (Berger, 1976). The white cliffs of
Dover, England are made up mostly of coccoliths.
Emiliania huxleyi, a very common marine coccolithophore.
- Diatoms are described in the chapter on Marine
Fisheries Food Webs.
- Ciliates They
are filter feeders with many hairlike cilia. Some are no larger
than a large bacteria, others can be seen by the naked eye. A paramecium
is a common example of a cilate.
A marine ciliate of the genus strombidium.
From Gulf of Alaska Plankton Photos.
All organisms need energy, electrons, and carbon (plus associated nitrogen,
phosphorus, and sulphur) to grow and thrive. Organisms can be classified
by how they obtain energy and nutrients. Note -troph means to nourish.
From Greek trophos = "nourishment."
- Autotrophs synthesize their own complex carbon
- Phototrophs such as phytoplankton use energy from sunlight plus
carbon dioxide and water to synthesize complex carbon
- Chemotrophs use energy from inorganic chemical compounds, such
as methane, hydogen sulphide, or reduced iron plus carbon dioxide
or some organic carbon to synthesize complex carbon compounds.
- Mixotrophs are organisms that can use energy
from both sunlight and chemical compounds.
- Heterotrophs are organisms that must eat other organisms
to obtain complex carbon compounds. Some are able to use sunlight or
inorganic compounds for energy, others must use organic carbon compounds
for energy. People are heterotrophs that get complex carbon compounds
and energy from other organisms.
- Bacteriovores eat bacteria.
- Herbivores eat plants.
- Carnivores eat animals.
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20 September, 2010