Marine and Freshwater environment

• Have varied surface areas and volumes: streams, lakes,

rivers, seas, oceans, water saturated zones in soils
• These environments can range from
– alkaline to extremely acidic,
– with temperatures from - 5 to -15°C at the lower range, to at
least 121°C in geothermal areas.
• Some of the most intriguing microbes have come from
the study of high-temperature environments, including
the Yellowstone National Park such as the discovery of
Thermus aquaticus, the source of the temperature-
stable DNA polymerase, which makes PCR possible.
 Water as a habitat
• The nature of water as a microbial habitat depends
on a number of physical factors such as
– temperature,
– pH,
– and light penetration,
– dissolved oxygen,
– CO2,
– other gases, (N2, H2, CH4)
– and nutrients
• These factors control microbial communities in water
 1. Dissolved oxygen
• The flux rate of oxygen through water is about 1/10,000 times less than
its rate through air.
– In some marine habitats the limits to oxygen diffusion can be offset by the
increased solubility of oxygen at colder temperatures and increasing atmospheric
pressures.
• Thus for the very deep ocean, the oxygen concentration actually increases
with depth, even though the air/water interface is literally miles away
• On the other hand, tropical lakes and summertime-temperate lakes may
become oxygen limited only meters below the surface
• In this case, aerobic microbes consume the surface-associated oxygen
faster than it can be replenished. This frequently leads to the formation of
hypoxic or anoxic zones in these aquatic environments.
• This enables specialized anaerobic microbes, both chemotrophic and
phototrophic, to grow in the lower regions of lakes where light can
penetrate.
 2. CO2
• CO2, plays many important roles in chemical and biological
processes.
• The pH of distilled water, which is not buffered, is
determined by the dissolved CO2 in equilibrium with the
air and is approximately 5.0 to 5.5.
• The pH of freshwater systems such as lakes and streams,
which are usually only weakly buffered, is therefore
controlled by the nature of terrestrial input (for instance,
minerals that may be either acidic or alkaline) and the rate
at which CO2 is removed by photosynthesis.
• When autotrophic organisms such as diatoms use CO2, the
pH of the water is often increased
• In contrast, seawater is strongly buffered by the
balance of CO2, bicarbonate (HCO3-), and
carbonate (CO32-).
• Atmospheric CO2 enters the oceans where it is
either converted to organic carbon by
photosynthesis or it reacts with seawater to form
carbonic acid (H2CO3), which quickly dissociates
to form bicarbonate and carbonate
• The oceans are effectively buffered between pH
7.6 and 8.2 by this carbonate equilibrium system.
 3. Other gases (N, CH4, H2)
• These gases vary in their water solubility
• N: used as a nitrogen source by nitrogen fixers
• H2: which is both a waste product and a vital substrate
• CH4: energy source and ideal waste product when
produced under anoxic conditions it leaves the
microorganism’s environment by diffusing up in the water
column where it can be oxidized by methanotrophs or
released to the atmosphere. This eliminates the problem of
toxic waste accumulation that occurs with many microbial
metabolic products, such as organic acids and ammonium
ion.
 4. Light
• critical for the health of marine and freshwater
ecosystems.
• Like all life on Earth, microbes in these environments
depend on primary producers—autotrophic organisms
—to provide organic carbon.
• In streams, lakes, and coastal systems, much of the
carbon is fixed by macroscopic algae and plants, and
organic carbon enters these systems in terrestrial runoff.
• The situation is very different in the open ocean where
all organic carbon is the product of microbial autotrophy
• about one-half of all the organic carbon on Earth is the result
of this microbial (eucaryotic and procaryotic) carbon fixation.
• Water from the surface to the depth to which light penetrates
with sufficient intensity to support these important autotrophs
is called the photic zone.
• There is a marked difference in the depth of the photic zone
when we compare nearshore waters with the open ocean.
• In lakes and estuaries where the water is turbid, the photic
zone may be only a meter or two in depth.
• This is in sharp contrast to nutrient-depleted areas such as the
open ocean and many tropical areas where the water seems
“crystal clear.”
– In these regions the photic zone ranges from 150 to 200 meters deep
 5. Temperature
• Solar radiation warms the water and this can lead to thermal
stratification.
• Warmer water is less dense than cool water, so as the sun warms the
surface in tropical and temperate waters, a thermocline develops.
• A thermocline can be thought of as a mass of warmer water “floating”
on top of cooler water.
• These two water masses remain separate until there is either a
substantial mixing event, such as a severe storm, or in temperate
climates, the onset of autumn.
• As the weather cools, the upper layer of warm water becomes cooled and
the two water masses mix.
• This is often associated with a pulse of nutrients from the lower, darker
waters to the surface.
• This can trigger a sudden and rapid increase in the population of some
microbes and a bloom may develop
 Nutrient Cycling in Aquatic Environments
• From a microbial point of view, lakes, estuaries, and other
coastal regions have relatively high rates of primary production.
• They therefore must have a higher influx and turnover (or re-
use) of essential nutrients.
• In these regions, nitrogen and phosphorus are most essential in
terms of limiting growth.
• Nearby agricultural and urban activity frequently generates
runoff that provides substantial nutrient inputs to these
environments.
• In contrast, nutrient levels are very low in the open ocean,
which is unaffected by rivers, streams, and terrestrial runoff.
• Here nitrogen, phosphorus, iron, and even silica which diatoms
need to construct frustules, can be limiting
• The major source of organic matter in illuminated surface
waters is photosynthetic activity, primarily from
phytoplankton [Greek phyto, plant and planktos,
wandering], autotrophic organisms that float in the photic
zone.
• Common planktonic cyanobacterial genera are
Prochlorococcus and Synechococcus, which can reach
densities of 104 to 105 cells per milliliter at the ocean
surface.
• These picoplankton (planktonic microbes between 0.2 and
2.0 um in size) can represent 20 to 80% of the total
phytoplankton biomass.
• Eucaryotic autotrophs, especially diatoms, also contribute a
significant fraction of fixed carbon to these ecosystems.
• As they grow and fix carbon dioxide to form organic
matter, phytoplankton acquire needed nitrogen and
phosphorus from the surrounding water.
• In marine systems, the nutrient composition of the water
affects the final carbon-nitrogen-phosphorus (C:N:P) ratio
of the phytoplankton, which is termed the Redfield ratio,
named for the oceanographer Alfred Redfield.
• A commonly used value for this ratio is 106 parts C, 16
parts N, and 1 part P.
• This ratio is important for following nutrient dynamics,
especially mineralization and immobilization processes,
and for studying the sensitivity of oceanic photosynthesis
to atmospheric additions of CO2 nitrogen, sulfur, and iron.
• In addition to their role as primary producers,
microbes play an essential role in cycling other
nutrients as well.
• Traditionally, the interaction of organisms at different
trophic levels has been depicted as a food chain in
which primary producers are most numerous.
• They must provide all the organic carbon consumed by
herbivores.
• Herbivores are then consumed by carnivores, which
may occupy several trophic levels.
• The microbial loop describes the many roles that microbes serve.
– For example, the metabolic flexibility of eucaryotic and procaryotic
microbes allows them to consume dissolved organic matter (DOM) that
larger organisms cannot degrade.
• Sources of DOM include the liquid waste of zooplankton and
material that leaks from the phytoplankton, sometimes called
photosynthate.
• Viruses are also a source of DOM. Marine viruses can be present
at concentrations up to 108 cells per milliliter; the lysis of their
host cells contributes significantly to the return of nutrients back
into the microbial loop.
• Protists, including flagellates and ciliates, consume these smaller
microbes, which can be thought of as particulate organic matter
(POM). Because these organisms are then consumed by
zooplankton, both DOM and POM are recycled back into the food
web for use at a number of trophic levels.
 Microbial adaptations to aquatic
environment
• Microbial diversity depends on available
nutrients, their varied concentrations (ranging
from extremely low to very high levels), the
transitions from oxic to anoxic zones, and the
mixing of electron donors and acceptors in this
dynamic environment.
• In addition, the penetration of light into many
anoxic zones creates environments for certain
types of photosynthetic microorganisms.
 1. Size
• One adaptation that has taken many marine microbiologists by surprise is just
how small most oceanic microbes are.
• In fact, they are so small it was not until the development of very fine filtration
systems (less than 0.2 um) and the application of direct counting methods such
as epifluorescence microscopy that the abundance of ultramicrobacteria was
discovered.
• Microbes assimilate their food through general body surface
• Cells with a large surface area relative to their total intracellular volume are
able to maximize nutrient uptake, and can therefore grow more quickly than
their larger neighbors.
• Thus the majority of microbes growing in nutrient-limited, or oligotrophic,
open oceans are between 0.3 um and 0.6 um.
• The ultramicrobacteria do not become larger when nutrients are added
suggests that, at least in these cases, the microbes have evolved to maximize
their surface area to volume ratio to oligotrophic conditions
• At the other extreme is an unusual marine microbe found off the coast of
Namibia in western Africa. Thiomargarita namibiensis, which means the
“sulfur pearl of Namibia,” is considered to be the world’s largest bacterium
• Individual cells are usually 100 to 300 um in diameter
• Sulfide and nitrate are used as the electron donor and acceptor, respectively.
• In this case nitrate, from the overlying seawater, penetrates the anoxic sulfide-
containing muds only during storms.
• When this short term mixing occurs, Thiomargarita takes up and stores the
nitrate in a huge internal vacuole, which may occupy 98% of the organism’s
volume.
• The vacuolar nitrate can approach a concentration of 800 mM. The elemental
sulfur granules appear near the cell edge in a thin layer of cytoplasm.
• Between storms, the organism lives using the stored nitrate as an electron
acceptor.
• These unique bacteria are important in sulfur and nitrogen cycling in these
environments.
Thiomargarita namibiensis
 2. Ability to link resources
• A critical adaptation of microorganisms in aquatic systems is the ability to
link and use resources that are in separate locations, or that are available
at the same location only for short intervals such as during storms.
• One of the most interesting bacteria linking widely separated resources is
Thioploca spp., which lives in bundles surrounded by a common sheath.
• These microbes are found in upwelling areas along the coast of Chile,
where oxygen-poor but nitrate-rich waters are in contact with sulfide-rich
bottom muds (much like the environment off the coast of western Africa).
• The individual cells are 15 to 40 um in diameter and many centimeters
long, making them, like T. namibiensis, one of the largest bacteria known.
• They form filamentous sheathed structures, and the individual cells can
glide 5 to 15 cm deep into the sulfide-rich sediments.
• These unique microorganisms are found in expanses off the coast of Chile.
 3. Taking advantage of surfaces
• In addition to living a planktonic existence, many microorganisms
take advantage of surfaces.
• These include sessile microorganisms of the genera Sphaerotilus
and Leucothrix and the prosthecate and budding bacteria of the
genera Caulobacter and Hyphomicrobium.
• There are also a wide range of aerobic gliding bacteria such as the
genera Flexithrix and Flexibacter, which move over surfaces
where organic matter is adsorbed.
• These organisms are characterized by their exploitation of
surfaces and nutrient gradients.
• They are obligate aerobes, although sometimes they can carry
out denitrification, as occurs in the genus Hyphomicrobium.
• In addition, bacteria may be primary colonizers of submerged
surfaces, allowing subsequent development of a complex biofilm.
 4. Motile fungal spores
• Microscopic fungi, which usually are thought to be
terrestrial organisms living in soils and on fruits and
other foods, also grow in freshwater and marine
environments.
• Zoosporic organisms adapted to life in the water
include the chytrids, which have motile asexual
reproductive spores with a single whiplash flagellum.
• Chytrids are important because of their role in
decomposing dead organic matter. In addition, many
chytrids attack algae
• Another important group includes filamentous fungi that can
sporulate under water. These hyphomycetes include the Ingoldian
fungi, named after C. T. Ingold. In 1942 Ingold discovered fungi
that produce unique tetraradiate forms
• The tetraradiate conidium forms on a vegetative mycelium, which
grows inside decomposing leaves.
• When the vegetative hyphae differentiate into an aerial mycelium,
conidia are released into the water.
• Released conidia are then transported and often are present in
surface foam.
• When they contact leaves, the conidia attach and establish new
centers of growth.
• These uniquely adapted fungi contribute significantly to the
processing of organic matter, especially leaves. Often aquatic
insects will feed only on leaves that contain fungi.
Microbes in Marine environments
 Estuaries
• An estuary is a semi-enclosed coastal region
where a river meets the sea.
• Estuaries are defined by tidal mixing between
freshwater and salt water.
• They feature a characteristic salinity profile
called a salt wedge.
• Salt wedges are formed because saltwater is
denser than freshwater, so seawater sinks below
overlying freshwater.
• Most estuaries undergo large-scale tidal flushing; this forces
organisms to adapt to changing salt concentrations on a daily
basis.
• Microbes that live under such conditions combat the resulting
osmotic stress by adjusting their intracellular osmolarity to limit
the difference with that of the surrounding water.
• Most protists and fungi produce osmotically active
carbohydrates for this purpose, whereas procaryotic microbes
regulate internal concentrations of potassium or special amino
acids such as ecoine and betaine.
• Thus most microbes that inhabit estuaries are halotolerant,
which is distinct from halophilic.
– Halotolerant microbes can withstand significant changes in salinity;
– halophilic microorganisms have an absolute requirement for high salt
concentrations.
• The calm, nutrient rich waters of estuaries serve
as nurseries for juvenile forms of many
commercially important fish and invertebrates
• But are also among most polluted environments
– Dumping of wastes in rivers – industrial sources
• If organic waste – chemoorganotrophic microbes
consumer available O2 forming dead anoxic zones devoid
of macroscopic life
• Organic pollution also results in dense algal growth – if
produce any toxin – harmful algal blooms (HABs) to
shellfish and other kinds of fish e.g. RED TIDES
– Dinoflagellate Alexandrium produces Brevitoxin causing paralytic
shellfish poisoning
– Pfiesteria piscicidia produces lethal lesions in fish
Microbes in freshwater environments
Microbes in glaciers and permanently frozen
lakes
• Extreme environment
• Surprisingly, microbes within glaciers are not dormant.
• Evidence that active microbial communities exist in
these environments has been growing over the last
decade.
• In fact, determining the diversity in these systems and
assessing the role of these microorganisms in
biogeochemical cycling can present their role in
building global carbon budget
• Antarctica’s McMurdo Dry Valley Lakes: the ice is 3 to 6 meters deep.
Life in these ecosystems depends on the photosynthetic activity of
microbial psychrophiles.
• In contrast, lakes that lie below glaciers are blocked from solar
radiation. These communities are driven by chemosynthesis.
• One of the most intriguing and well-studied Antarctic habitats is Lake
Vostok, one of 68 lakes located 3 to 4 kilometers below the East
Antarctic Ice Sheet.
• Geothermal heating, pressure, and the insulation of the overlying ice
keep these lakes in a liquid state.
• Lake Vostok was formed approximately 420,000 years ago and that its
water is about a million years old.
• This stable environment supports a number of microbes including
gram-negative proteobacteria and gram-positive actinomycetes. The
overlying ice also harbors similar microbes, although at lower
population densities.
 Microbes in lakes
• Oligotrophic lakes: Nutrient-poor lakes remain oxic
throughout the year, and seasonal temperature shifts
usually do not result in distinct oxygen stratification.
• Eutrophic lakes: usually have bottom sediments that are
rich in organic matter and present characteristic thermal
and oxygen stratification.
• In thermally stratified lakes the epilimnion (warmer, upper
layer) is oxic, while the hypolimnion (colder, bottom layer)
often is anoxic (particularly if the lake is nutrient- rich). The
epilimnion and hypolimnion are separated by a
thermocline.
• Because there is little mixing between the epilimnion and the
hypolimnion, the bottom waters may become deprived of oxygen
• This is a permanent situation in tropical eutrophic lakes and occurs in
the summer in temperate eutrophic lakes.
• If nutrient levels are high, this bottom, or benthic, zone becomes
dominated by anaerobic microbial activity.
• In very warm eutrophic lakes, anaerobic microbes release gases such as
H2S into the water.
• In addition, human activities (e.g., septic and agricultural runoff) may
add high levels of nitrogen and phosphorus to the lake waters.
• This can result in a bloom of algae, plants, and/or bacteria in the
epilimnion.
• During autumn cooling, temperate lakes lose their thermocline because
surface waters increase in density and storms mix the two layers.
• This sometimes happens within a 24- hour period; if bottom water has
become filled with anaerobic byproducts, the sudden upwelling causes
fish kills.
• In oligotrophic lakes, phosphorus is often the limiting
nutrient. If added to oligotrophic freshwater,
cyanobacteria capable of nitrogen fixation may bloom.
Several genera, notably Anabaena, Nostoc, and
Cylindrospermum, can fix nitrogen under oxic conditions.
• The genus Oscillatoria, using hydrogen sulfide as an
electron donor for photosynthesis, can fix nitrogen under
anoxic conditions. If both nitrogen and phosphorus are
present, cyanobacteria compete with algae.