Chapter 6 – Aquatic Environments - Objectives
1. Be able to describe the four types of aquatic habitats for microbes 2. Be able to describe the microbial loop3. Understand why activity in the benthos is high and have a basic
understanding of the biogeochemical cycling of carbon and nitrogen in the benthos.
4. Be able to describe the makeup of a microbial mat including examples of microorganisms found in a mat.
5. Understand how biofilms develop and the reasons why microbes form biofilms
6. Be able to define the different regions of a water body: neuston, limnetic, littoral, and profundal zones
7. Be able to define the thermocline, epilimnion, and hypolimnion8. Understand the ranges of numbers of microbes in oligotrophic and
eutrophic water bodies9. Understand the driving force behind the vertical stratification of primary
producers in the water column10. Understand how microbes adapt to extreme temperatures11. Be able to describe geothermal vents and their associated community
Aquatic environments
• Cover 70% of the earth’s surface
• Important zone of primary production
• Provides potable water
• Provides water for agriculture and industry
• Provides unique and extreme habitats
• Includes:Freshwater (rivers, lakes, streams, aquifersMarine (oceans, estuaries)
Primary producers zooplankton filter feeders/fish
Habitats
1. Planktonic – microbes suspended in the water column2. Benthic3. Mats4. Biofilms
Grazing food chain:
In coastal zones it take 1.5 to 3.5 steps to produce fish because plants are responsible for some primary production
In the open ocean it takes approximately 5 steps to produce exploitable fish.
Responsible for most of the primary production in aquatic environments.
Major food supply in aquatic environments.
Support a complex food web.
Phytoplankton are photosynthetic microbes (primarily cyanobacteria and algae).
1. Planktonic – Microbes suspended in the water column
Grazing
GrazingMineralization
Gra
zin
g
Upt
ake
Exc
retio
n
and
lysi
s
Up
take
Excretion
and lysis
Excretion
and lysis
Excre
tion
and
lysi
s
Phytoplankton Zooplankton
BactivorouszooplanktonBacteria
Dissolved organiccompounds
CO 2
primary production
Microbial Loopsecondary production
50% of fixed carbon is released as DOM
The benthos is a transition zone between the water column and the mineral subsurface.
This interface is a diffuse and noncompacted mix of organic matter that has settled from the surface/mineral particles/water.
Microbial numbers are up to 5 orders of magnitude higher than in the planktonic environment.
Since activity is high, oxygen is utilized quickly and as a result, biogeochemical gradients develop that control the types of microbes and microbial activities found in this region.
2. Benthic habitat
NH /NH3 4+
NO -
3
NO assim ilation-3
NH /NH assim ilation3 4 +
Nitrification
Denitrification
SO assim ilation- 4 2
SO reduction2
-4
Aerobic respiration (m ineralization)
Anaerobic respiration (m ineralization)
CH oxidation4
CH 4
CO 2
Fermentation andmethanogenesis
NO -2
O 2
O 2SO 4
-2
H S2
S 0
S oxidation-2
S assimilation-2
O 2
Surface
Inner (core region)
Inner (core region)
Inner (core region)
Surface
Surface
Biogeochemicaltransformations
Nitr
oge
nS
ulfu
rC
arb
on
M Icrobialtransformations
Biogeochemicaltransformations
Microbialtransformations
Carbon
Aerobic respiration (mineralization)
Anaerobic respiration (mineralization)
CH oxidation4
CH 4
CO2
Fermentation andmethanogenesis
O2
Inner (core region)
Surface
Car
bon
NH /NH3 4+
NO -3
NO assim ilation-3
NH /NH assim ilation3 4 +
Nitrification
DenitrificationNO -2
O 2
Surface
Inner (core region)
Biogeochemicaltransformations
Nitr
oge
n
M icrobialtransformations
Nitrogen
A microbial mat
Sand layer
Cyanobacteria
Oxidized iron
Purple sulfur bacteria
Precipitated iron sulfide
Microbial mats are also an interface in the aquatic environment in which many microbial groups are laterally compressed into a thin mat.
The width of the mat ranges from several mm to cm
Mats are vertically stratified with an aerobic zone on the top which is separated from the bottom anaerobic zone by a layer of oxidized iron.
3. Mats
Stromatolites are fossilized mats that are 3.5 billion years old and are among the first indications of life on earth.
Stromatolites were thought to be extinct but were discovered 40 years ago in Shark Bay, Australia in a hypersaline area. The hypersalinity prevents marine animals from thriving and grazing on the mat material.
Mats form in extreme environments.
Biofilms are a layer of organic matter with attached microbes.
Biofilms form on submerged rock surfaces, plants, skin, ship hulls, pipes, teeth, catheters and implants, and basically any submerged surface.
Biofilms can be beneficial (wastewater treatment, skin barrier) and can be harmful (pipeline corrosion, medical implants, tartar).
Benefits (to the microbe) of biofilm growth: Microbes growing in a biofilm are more resistant to: antibiotics, predation, dessication, changes in environmental factors (pH, temperature). They also have better access to solution nutrients because the solution is constantly flowing over the biofilm.
4. Biofilms
Organic molecule
M icroorganism
1) the surface is modified by attachment of organic molecules
Biofilm development proceeds in three phases:
2) reversible attachment of microbes to the organic layer and colonization
3) irreversible attachment and biofilm formation. In a mature biofilm, the cells are organized into columns surrounded by large void spaces that form channels to carry nutrients (O2) deep into the biofilm
Freshwater • Lentic (standing) vs. lotic (running)• Springs• Lakes
oligotrophic – deep, low biomasseutrophic – shallow, high biomass
• Groundwater
Marine • Estuaries• Oceans
Aquatic environments
Littoralzone
Limneticzone
Neuston layer
Profundalzone
Benthiczone
Freshwater - A typical lake has several regions of interest.
Neuston layer
Water lipid layer
Air
Protein-polysaccharide layer
Bacterioneuston layer
0
10 nm
0.1 um
1.0 um
Lower neuston
Up to 10 um
The neuston layer occurs at the air-water interface.
Nutrients and microbes aggregate at the neuston.
Littoralzone
Limneticzone
Neuston layer
Profundalzone
Benthiczone
The limnetic zone which is the surface layer of open water where light can penetrate
0 5 10 15 20 25 Temp Co
0 2 4 6 8 10 O mg/l2
Dep
th (
m)
Sediment zone
Water surface
Temperature
Dissolved oxygenThermocline
The thermocline is a zone defined by a rapid change in temperature. The zone above the thermocline is the epilimnion and the zone below is the hypolimnion. The thermocline prevents mixing of lake water through much of the year. Mixing can only occur in the fall and spring as the water either cools (fall) or warms (spring) so that the thermocline disappears.
Epilimnion > 4oC
Hypolimnion < 4oC
Summer
0 2 4 6 8 10 O2 mg/l
Sediment zone
0 5 10 15 20 25 Temp oC
Water surface
Thermocline
Tem
peratu
re
Winter
Epilimnion 0 – 4oC
Hypolimnion > 4oC
Dep
th (
m)
0
-4
-8
-12
-16
Estuaries are transition areas between freshwater and ocean environments. Salinities range from 1 to 3.2%. Estuaries harbor unique ecosystems such as the mangrove swamps and are subject to high levels of pollution from freshwaters carrying surface runoff that enter the estuary. Estuaries also serve as environments that can be used to treat polluted waters before they reach the open ocean.
Oceans have a salinity of 3.5% compared to a salinity of 0.05% in freshwater environments. Oceans can reach depths of 11,000 m and are generally divided into two zones, the photic zone (where light penetrates) which ranges from 1 to 200 meters, and the aphotic zone.
Marine water
Numbers vary so much with different water bodies that it is difficult to provide generalities. However, there are ranges and patterns of microbes in an oligotrophic and a eutrophic lake environment.
Planktonic numbers are up to 5 orders of magnitude lower than benthic numbers.
Heterotrophic numbers increase dramatically at the neuston, the thermocline, and the benthos.
Primary producers arrange themselves in zones according to the wavelength of light that their chlorophyll-like molecules absorb and according to availability of H2S.
Microbes in the aquatic environment
Cyanobacteria
Chlorobacteria
Colorless sulfur bacteria andsulfate reducing organism s
Heterotrophic bacteria
Hypolim nion
Epilim nion
Neuston
Benthos
0
4
8R
ela
tiv
e d
ep
th (
m)
3 4 5 6 7 8Log CFU/l
Therm ocline
O 2
H S2
Cyanobacteria
Chlorobacteria
Colorless sulfur bacteria and sulfate reducing organisms
Heterotrophic bacteria
Hypolim nion
Epilim nion
Neuston
Benthos
0
10
20
Re
lati
ve d
ep
th (
m)
1 2 3 4 5 6 7Log CFU/l
Therm ocline
O 2
H S2
Oligotrophic Lake Eutrophic Lake
Heterotrophic counts
Chlorophyll a concentration
400 600 800 1000
Wavelength (nm)
( )Chlorophycophyta
Porphyridium(Rhodophycophyta)
Synechococcus(Cyanobacteria)
Rhodopseudomonas (nonsulfur purple bacteria)
Re
lativ
e ab
sorp
tion
Stratification of primary producers
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