Freshwater microbiology 2013 (1)

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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

2

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.

3

4

5

Freshwater habitats

LENTIC LOTIC

(Lakes, ponds, reservoirs)

Rivers and streams

6

Biological Zones in a Lake

7

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.

8

Food web in pelagic zone

9

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

10

11

12

Temperature

Temperature is an important variable in aquatic ecosystems:

- changes the reaction rates (kinetics) of chemical and biochemical reactions

-

influences species distributions

-

controls dissolved O

2 and CO

- changes density of water

2

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.

13

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)

14

Lake Stratification in

Summer and Winter

15

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.

16

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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18

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a) b) c) d)

Lake types

Holomictic (dimictic), two periods of circulation as described.

Amictic - sealed permanently by ice.

Cold monomictic - lake temp < 4

°

C (one period of circulation in summer).

Warm monomictic - lake temp > 4

°

C circulates in winter; stratifies in summer; sub tropical regions, e.g. Florida.

20

Lake types

e) f) g)

Oligomictic - rare circulation (tropics).

Polymictic - frequent circulation.

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.

21

22

23

Food web for fast flowing waters

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Bdellovibrio bacteriovorans

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Hyphomicrobium

sp.

26

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

.

27

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.

28

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 (PO

4

3-

) results in an increase in biological activity.

29

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

• 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 PO

4

Rapid growth of algae/cyanobacteria

33

Heavy algal growth, increased turbidity and increased sedimentation

Increased growth of plants e.g. reeds

34

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

36

Sources of Phosphorus in Lakes

• Weathering of Rocks

• Wastewaters

– Industrial

– Municipal

• Seepage from Septic Tanks

• Agricultural Runoff (Fertilizers)

37

Leonard W. Casson, Ph.D., P.E., DEE

Reducing Eutrophication

• 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.

• removing phosphate-rich sediments by dredging

..

38

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.

39

Effects of reduction of [O

2

]

• +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. NO

3

-

, Mn, Fe reduced.

Pseudomonas

, diatoms (

Nitzschia,

Synedra

), filamentous chlorophycae e.g.

Stigeoclonium

, cyanobacteria e.g.

Calothrix.

40

Effects of reduction of [O

2

]

• +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.

41

Effects of reduction of [O

2

]

• 0mv to –150mv Nitrification inhibited, build-up of H

2

SO

4

2and fermentation products (acids, alcohols), reduced to H

2

S, Blooms of green and purple sulphur bacteria, population switches to anaerobes.

Desulphovibrio, Clostridium, Chromatium

,

Beggiatoa

(microaerophilic sulphur oxidisers ) in upper layers.

42

Effects of reduction of [O

2

]

• -150mv to –350mv terminal stage with

CH

4

, H

2

, H

2

S production.

– Devoid of eukaryotes except anaerobic protozoa,

Tubifex

etc.

– Anaerobes only.

– Very few species.

43

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 (H

2 mercaptan (CH

3

SH)

S) thioalcohols (RSH) and methyl

– ammonia (NH

3

) and polyamines such as cadaverine.

resulting in the water becoming extremely unpleasant.

44

Low oxygen concentrations result in fish kills

45

“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.

46

“Sewage fungus”

• Protozoa:

Colpidium

Childonella

Cinetochilum

Trachellophylum

Paramecium

Uronema

Hemiophrys

Glaucoma

Carchesium

47

Synedra

48

Sewage fungus organisms

49

Marine Microbiology

Oceans

• Primary producers are algae and cyanobacteria = phytoplankton.

• Responsible for 40% total photosynthesis.

• In open ocean cyanobacteria, particularly

Prochlorococcus

and

Synechococcus

dominant (>10

5 ml

-1

).

are

• Large numbers of viruses (10

7 ml

-1

) 10

30 in total.

51

Viruses may control phytoplankton levels

52

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 x10

28 cells.

Prochlorococcus

and

Synechoccus

species dominate the microbial ecology of the ocean. They

53 account for 25% of global photosynthesis.

Oceans

• Phytoplankton fed upon by zooplankton etc.

• Productivity in oceans limited (?by micronutrients e.g. Fe

2+

).

• 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.

54

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56

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Marine

“snow”

58

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Mid ocean ridges (spreading tectonic plates)

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64

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68

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Black Smokers

• Organisms

Korarchaeota

– Archaea:

– Extremophiles

– Pompeii worms:

A. pompejana

– Gastropod:

Cypraea chinensis

• Crustacea feed on these organisms

70

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 gastropod

Gyre snail

Maia snail

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Rattail fish

Fathead sculpin

Vent fish

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Nematodes

Anemone

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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