Transcript Freshwater microbiology 2013 (1)

Aquatic Microbiology
H.A.Foster
revised November 2013
Water
• 71% of the Earth’s
surface is covered
with water.
• 97% of this is marine
and much of the
freshwater is frozen.
• ¾ of the oceanic water
is at a depth of
>1000m
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Physiological conditions
• Temperature below 300m
relatively constant at
approximately 3ºC.
(remember ocean currents
e.g Gulf stream)
• Pressure increases with
depth (1 atm per 10m)
• Deepest parts are 11,000m
(1100atm).
• Organism can be
barotolerant or barophilic.
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Freshwater habitats
LENTIC
(Lakes, ponds, reservoirs)
LOTIC
Rivers and streams
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Biological Zones in a Lake
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Microbiological habitats
• Planktonic - the water
column, floating free in
the water.
• Neustonic – the surface
film.
• Benthic – in and on
permanently submerged
sediments.
• Epibiotic – On living
surfaces.
• Sestonic – On floating
organic matter e.g.faeces.
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Food web
in pelagic
zone
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Colonisable surfaces within water
Epiphyton
Episammon
Hyposammon
Epipelon
Endopelon
Epilithon
Endolithon
Epizoon
Fouling
Surface of plants
Surface of sand or silt
Interstitial water
Surface of sediment (mud)
Inside the sediment
Surface of stones
Cavities in rocks/stones
Surface of animals
Surface of artificial objects
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• Temperature
Temperature is an important variable in
aquatic ecosystems:
- changes the reaction rates (kinetics) of
chemical and biochemical reactions
- influences species distributions
- controls dissolved O2 and CO2
- changes density of water
Greatest density of water occurs at 4°C
below this temperature, water adopts a crystalline
structure on its way to form ice. Ice has a much more
open structure.
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The changes in density with temperature cause
stratification in lakes and physical turnovers.
Stratified lakes separate into 3 zones known as
the:
EPILIMNION
HYPOLIMNION
THERMOCLINE (METALIMNION, or
CHEMOCLINE)
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Leonard W. Casson, Ph.D., P.E., DEE
Lake Stratification in
Summer and Winter
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Holomictic lakes
• Show two cycles of mixing in spring and
autumn (fall).
– In winter a thermocline develops with water at
<4°C on top of water at 4°C.
– In spring, the surface layer warms and the
thermocline disappears. This leads to mixing of
the upper and lower layers and can lead to
eutrophication and an algal bloom.
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Holomictic lakes
– The upper layers then warm and during the
summer the thermocline is re-established with
warm surface water on top of colder waters.
– During autumn, the combination of cooling
surface waters and mixing due to autumnal
gales removes the thermocline and mixing and
algal blooms can occur again.
– The thermocline leads to spatial distribution of
organisms.
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Lake types
a)
Holomictic (dimictic), two periods of
circulation as described.
b)
Amictic - sealed permanently by ice.
c)
Cold monomictic - lake temp < 4°C (one
period of circulation in summer).
d)
Warm monomictic - lake temp > 4°C circulates in winter; stratifies in summer; sub
tropical regions, e.g. Florida.
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Lake types
e)
Oligomictic - rare circulation (tropics).
f)
Polymictic - frequent circulation.
g)
Meromictic - does not undergo complete
circulation due to stratification by
something other than temperature, e.g.
salinity; can be caused by humans
connecting sea and freshwater systems.
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Food
web for
fast
flowing
waters
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Bdellovibrio
bacteriovorans
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Hyphomicrobium sp.
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Lakes and Rivers
• Water Pollution has different effects on lakes and
rivers.
• Pollution of lakes and rivers can cause
eutrophication.
• Because lake water is not quickly replaced the
effects can accumulate gradually, in rivers
pollution is eventually washed away to the sea.
• Waste, especially wastewater, from human or
animal origin can contain pathogens.
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Eutrophication
Eutrophication is a natural process that occurs to all lakes over
time as the weathering of rocks and soils from the surrounding
catchment area leads to an accumulation of nutrients in the water
and associated sediments.
Young lakes (and man made reservoirs) usually have low levels
of nutrients and correspondingly low levels of biological activity.
Such lakes are referred to a being oligotropic from the Greek
work oligos meaning little or few. Literally oligotrophic means
little-nourished.
Old lakes usually have high levels of nutrients and
correspondingly high levels of biological activity. Such lakes are
referred to as being eutrophic from the Greek word eu meaning
well. Literally eutrophic means well-nourished.
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The main causes of eutrophication are:
• natural run-off of nutrients from the soil and the
weathering of rocks.
• run-off of inorganic fertiliser (containing nitrates and
phosphates).
• run-off of manure from farms (containing nitrates,
phosphates and ammonia).
• run-off from erosion (following mining, construction work
or poor land use).
• discharge of detergents (containing phosphates).
• discharge of partially treated or untreated sewage
(containing nitrates and phosphates).
• In most freshwater lakes the limiting nutrient is
phosphorus, so an input of phosphorus in the form of
phosphate ions (PO43-) results in an increase in biological
activity.
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Development of eutrophy
in lakes
The natural time scale for the aging of a lake from being
oligotrophic to eutrophic is of the order of thousands of years.
However, a high rate of input of nutrients (from human
activities) can increase the rate of aging significantly resulting in
eutrophic conditions developing after only a few decades. This
artificial eutrophication has already happened in many parts of
the world including the Norfolk Broads and parts of Holland,
Denmark and Norway.
To renew all the water in a lake may take up to a hundred years
compared to a few days for the renewal of the water in a river.
Consequently, lakes are particularly susceptible to pollution such
as artificial eutrophication.
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Oligotrophic Lake
Artificial input of nutrients
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Effects of Eutrophication
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•
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•
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An increase in plant and animal biomass
An increase in growth of rooted plants, e.g. reeds
An Increase in turbidity (cloudiness) of water
An increase in rate of sedimentation
The development of anoxic (anaerobic) conditions (low
oxygen levels)
• A decrease in species diversity
• A change in dominant biota (e.g. carp replace trout and
blue-green algae replace normal algae) and an increase in
the frequency of algal blooms.
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Eutrophic lake with high concentrations of
plant nutrients, especially PO4
Rapid growth of algae/cyanobacteria
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Heavy algal growth, increased turbidity and
increased sedimentation
Increased growth of plants e.g. reeds
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Consequences of Eutrophication
Some of the main consequences of eutrophication
are:
• increased vegetation may impede water flow and the
movement of boats
• the water may become unsuitable for drinking even after
treatment
• decrease in the amenity value of the water (e.g. it may
become unsuitable for water sports such as sailing)
• disappearance of commercially important species (such as
trout)
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Algal blooms followed by lysis
Development of anaerobic conditions
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Sources of Phosphorus in Lakes
• Weathering of Rocks
• Wastewaters
– Industrial
– Municipal
• Seepage from Septic Tanks
• Agricultural Runoff (Fertilizers)
Leonard W. Casson, Ph.D., P.E., DEE
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Reducing Eutrophication
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•
•
•
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Treating effluent before it reaches the lake.
reducing the use of phosphates as builders in detergents.
reducing the use of nitrate containing fertilisers.
using tertiary sewage treatment methods to remove
phosphate and nitrate before discharge of the effluent into
rivers and lakes.
directing treated waste water away from lakes to rivers and
the sea.
aerating lakes and reservoirs to prevent oxygen depletion
particularly during algal blooms.
removing phosphate-rich plant material from affected
lakes.
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removing phosphate-rich sediments by dredging..
Effects of Oxygen
• Concentration of oxygen affects microbial
growth.
• Redox potential decreases from +600mv
(aerated) to –350mv (anaerobic).
• Redox potential depends on pH (above
results at neutral pH.
• Effects more severe at acid pH e.g acid
mine drainage.
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Effects of reduction of [O2]
• +600mv Normal redox potential for well aerated
water. Large number of aerobic species e.g.
Pseudomonas. Alkaligenes, Achromobacter,
appendaged bacteria, Aquatic phycomycetes,
diatoms (Pinnularia, Navicula), algae e.g.
Ankistrodesmus (Chlorophycae).
• +600 to +200mv Facultatively anaerobic Gramnegative rods predominate. NO3-, Mn, Fe
reduced. Pseudomonas, diatoms (Nitzschia,
Synedra), filamentous chlorophycae e.g.
Stigeoclonium, cyanobacteria e.g.Calothrix.
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Effects of reduction of [O2]
• +200mv to 0mv
Dominance of
cyanobacteria, microaerophiles and
flagellates.
– Pseudomonas, Oscillatoria,
Phormidium, Spirillum, Chlamydomonas,
Euglena.
– “Sewage fungus” complex(see later).
– Nitrification begins to be inhibited.
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Effects of reduction of [O2]
• 0mv to –150mv Nitrification inhibited, build-up
of H2 and fermentation products (acids, alcohols),
SO42- reduced to H2S, Blooms of green and purple
sulphur bacteria, population switches to
anaerobes.
– Desulphovibrio, Clostridium, Chromatium,
– Beggiatoa (microaerophilic sulphur oxidisers )
in upper layers.
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Effects of reduction of [O2]
• -150mv to –350mv terminal stage with
CH4, H2, H2S production.
– Devoid of eukaryotes except anaerobic
protozoa, Tubifex etc.
– Anaerobes only.
– Very few species.
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Consequences of anaerobiosis
• When plants and algae die their remains gradually sink and
are consumed by aerobic bacteria. Microbial predators
such as Lysobacter spp. can bloom and kill the algae
rapidly. This results in a reduction of the level of dissolved
oxygen. Eventually, often near the bottom of a lake,
virtually no oxygen remains and the water is said to be
anoxic. Under these conditions anaerobic bacteria
flourish. Anaerobic bacteria often produce foul-smelling
compounds such as:
– hydrogen sulphide (H2S) thioalcohols (RSH) and methyl
mercaptan (CH3SH)
– ammonia (NH3) and polyamines such as cadaverine.
resulting in the water becoming extremely unpleasant.
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Low oxygen
concentrations result in
fish kills
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“Sewage fungus”
• Bacteria:
– Sphaerotilus natans, zoogleal bacteria, Beggiatoa,
Flavobacterium.
• Filamentous fungi:
– Geotrichium, Leptomitus lacteus (Apodya lactea),
Fusarium.
• Algae:
– Stigoclonium tenue, Navicula sp., Fragilaria, Synedra,
Cladophora.
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“Sewage fungus”
• Protozoa:
–
–
–
–
–
–
–
–
–
Colpidium
Childonella
Cinetochilum
Trachellophylum
Paramecium
Uronema
Hemiophrys
Glaucoma
Carchesium
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Synedra
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Sewage fungus organisms
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Marine Microbiology
Oceans
• Primary producers are algae and cyanobacteria =
phytoplankton.
• Responsible for 40% total photosynthesis.
• In open ocean cyanobacteria, particularly
Prochlorococcus and Synechococcus are
dominant (>105 ml-1).
• Large numbers of viruses (107 ml-1) 1030 in total.
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Viruses may control phytoplankton levels
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OCEANS
• 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, 50%
in the euphotic zone . (Morris et al., 2002, Nature
Dec 420:806-810). Globally 2.4 x1028 cells.
• Prochlorococcus and Synechoccus species
dominate the microbial ecology of the ocean. They53
account for 25% of global photosynthesis.
Oceans
• Phytoplankton fed upon by zooplankton etc.
• Productivity in oceans limited (?by
micronutrients e.g. Fe2+).
• Open seas have 90% of surface area but
only produce 0.7% of fish cf. coastal zones
with 54% (remaining 46% in so-called
“upwelling” regions where currents bring
nutrient rich sediments to the surface.
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Marine
“snow”
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Mid ocean ridges (spreading tectonic plates)
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Black Smokers
• Organisms
Korarchaeota
– Archaea:
– Extremophiles
– Pompeii worms:
A. pompejana
– Gastropod:
Cypraea chinensis
• Crustacea feed on these
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organisms
Symbiosis
• Mussels
– Microbes live in the gills, using the chemicals
from the hydrothermal vent fluids to produce
sugars
– Mussels utilize those sugars
• Clams
– Also have bacteria that live in their gills that
perform the same process as the microbes that live
symbiotically with the mussels.
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Tubeworms e.g. Giant tubeworm
Riftia pachyptila
• Do not have a mouth or a stomach, so they use billions
of symbiotic bacteria to produce sugars from carbon
dioxide, hydrogen sulfide and oxygen in an organ
termed a symbiosome.
• Use some of the sugars as food and provide the bacteria
with the hydrogen sulfide and oxygen that the worms
take up from the water
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Vent crab
• The hydrothermal vent crab, Bythograea thermydron,
is a top predator at vent sites in the Pacific Ocean. This
crab is present in such high densities that scientists actually
use it as an indicator that they are approaching an active
vent field.
• The vent crab is typically found among dense clusters of
tubeworms at an average depth of 1.7 miles and can
tolerate a temperature gradient that ranges from 77°F in the
tubeworm clumps, to 36°F, which is the temperature of the
water surrounding the vent sites.
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Vent crab
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Pompei worm
• The Pompeii worm (Alvinella pompejana)
can survive an environment as hot as 80° C
• Covering the Pompeii worm’s back is a
“fleece” of thermophilic bacteria.
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Pompei worm
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Common copepod
Common limpet
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Glob snail
Gyre snail
gastropod
Maia snail
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Rattail fish
Fathead sculpin
Vent fish
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Anemone
Nematodes
Ciliate
Palm worm
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OTHER ANIMALS
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Some web sites
• www.ocean.udel.edu/expeditions/index.html
• www.pmel.noaa.gov/vents/geology/video.html
• http://www.shef.ac.uk/aps/level2modules/aps2
01/aps201.html
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Books
• Biology of freshwater pollution , C.F. Mason. - 3rd ed.. Harlow : Longman, 1996. - 0582247322
• Microbial ecology : fundamentals and applications,
Ronald M. Atlas, Richard. - 4th ed. - Menlo Park, Calif.;
Harlow : Benjamin/Cummings, 1998. - 0805306552
• Manual of environmental microbiology / editor-in-chief
Christon J. Hurst. - Washington, D.C. : ASM Press,
1997. - 155581087x
• VARNUM, A.H.. - Environmental microbiology. Manson, 1997. - q5356919
• Freshwater microbiology David Sigee, John Wiley, 2002
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