28
Microorganisms in Marine and Freshwater
Ecosystems
CHAPTER OVERVIEW
This chapter discusses the general characteristics of marine and freshwater environments and describes some
of the microorganisms that live there. Life in aquatic environments is most impacted by the levels of light,
oxygen, and nutrients present. These are determined by physical properties and by the activities of
microorganisms. The chapter discusses life in estuaries and salt marshes, the photic zone of the open ocean,
and the benthic zone at the seafloor. Freshwater environments discussed include ices, rivers, and lakes.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
•
•
•
•
•
•
•
•
list the gases of major importance to aquatic microbial communities
discuss the nutrient levels observed in various types of bodies of water
describe the vertical stratification of microbial populations, nutrients, and oxygen that are observed in a
Winogradsky column
discuss the cycling of carbon, nitrogen, phosphorus, and sulfur in aquatic environments
describe the microbial loop and its role in the cycling of nutrients in aquatic environments
compare and contrast marine and freshwater environments
compare and contrast lake environments and stream and river environments
discuss frozen aquatic environments
CHAPTER OUTLINE
I.

Water as a Microbial Habitat
A. Gases in aquatic environments
1. Oxygen
a. Aquatic environments are low-oxygen diffusion environments; this can lead to the
formation of hypoxic or anoxic zones, which are inhabited by anaerobic microbes
b. At higher temperatures and with lower pressure the solubility of oxygen in water is
further decreased
2. Carbon dioxide
a. Important in many chemical and biological processes
b. The carbonate equilibrium system buffers the pH of water, with seawater highly buffered
by the interplay of carbon dioxide, bicarbonate, and carbonate
c. This equilibrium is impacted by the activity of aquatic microorganisms
3. Other gases such as nitrogen, hydrogen, and methane are important; they vary in terms of their
solubility in water, with methane being the least soluble
B. Light is critical for primary production by autotrophs in marine and freshwater ecosystems; the zone
where light penetrates is the photoic zone; solar radiation can warm surface waters and create a
thermocline where warm waters float on cooler waters
C. Nutrient cycling in marine and freshwater environments
1. Major source of organic matter in illuminated water is phytoplankton (including tiny
picoplankton), consisting of photoautotrophic organisms that acquire needed nitrogen and
phosphorous from surrounding water; microplankton include diatoms and dinoflagellates
253 
2.
II.

Redfield ratio—ratio of carbon-nitrogen-phosphorus (C:N:P) in phytoplankton; is important
for following nutrient dynamics and for studying factors that limit microbial growth
3. The microbial loop recycles much of the organic matter produced by phytoplankton
(photosynthate in the form of dissolved organic matter); the chemoheterotrophic bacteria that
function in the microbial loop (thought of as particulate organic matter) are consumed by a
series of larger predators (protists)
Microorganisms in Marine Ecosystems
A. Marine environments represent the major portion of biosphere; contain 96% of the Earth’s water;
vital to global biogeochemical cycles
B. Microorganisms in estuaries and salt marshes
1. In estuaries, tidal mixing of freshwater and saltwater creates a salinity profile characterized by
salt wedges, where heavier saltwater forms a layer below freshwater
2. The salinity varies in the estuary in time and space; microbial inhabitants need to be
halotolerant (withstands salinity changes)
3. These nutrient-rich waters are often polluted and this can create dead zones or greatly increase
microbial growth; harmful algal blooms (HABs), including red tides caused by dinoflagellates,
occur when algae grow to high numbers and then release toxic compounds
C. Winogradsky columns can be used to model salt marshes and illustrate the interactions and
gradients that occur in aquatic environments
1. Made by mixing together mud, water, and sources of nutrients (e.g., cellulose and other
materials), then incubating the column in light
2. In the bottom, anaerobic conditions foster the activity of fermentative microorganisms, which
leads to the accumulation of fermentation products
3. Other anaerobic microorganisms use the fermentation products to carry out anaerobic
respiration using sulfate as the electron acceptor and producing sulfide
4. Sulfide diffuses upward, creating an anaerobic, sulfide-rich zone where anoxygenic
photosynthetic bacteria reside
5. Further up in the column, chemolithotrophic and mixotrophic organisms may use hydrogen
sulfide as an energy source and oxygen as the electron acceptor
6. At the top are oxygenic photosynthetic organisms such as diatoms and cyanobacteria
D. Microorganisms in the open ocean
1. The open ocean regions (pelagic) account for half of the world's photosynthesis; it is an
oligotrophic environment (very low nutrient levels) that supports a diverse microbial
community
2. Organic matter found in the photic zone (upper 200–300 meters) where light penetrates falls as
marine snow into lower depths; much of the marine snow is not easily degraded; it is colonized
by microbes that consume it, such that only about 1% reaches the seafloor; the collection of
organic matter on the seafloor is important in moderating the effects of global warming; the
addition of iron may increase draw down of carbon dioxide in high-nutrient low-chlorophyll
(HNLC) ocean areas
3. Cyanobacteria (including Trichodesmium) are important in fixing nitrogen in the pelagic zone;
some bacteria can perform the anammox reaction wherein ammonia is oxidized to nitrogen gas
anaerobically below the photic zone, and lost from the seas
4. The most abundant monophyletic group of organisms is an -proteobacterial lineage called
SAR11; these small bacteria have recently been isolated and have small, efficient genomes;
they are responsible for about 50% of bacterial biomass production and DOM flux in some
marine environments
5. Proteorhodopsin may supplement ATP production for a variety of microorganisms in nutrientpoor waters; aerobic anoxygenic phototrophs do not fix carbon, but use light energy to
generate ATP; lithoheterotrophs also do not fix carbon, but use inorganic chemicals as a
source of energy
E. Aquatic viruses
1. Virioplankton are the most numerous members of marine ecosystems; counting viruslike
particles (VLPs) can be challenging
254 
2.
Virioplankton are major agents of mortality in the sea, influence microbial loop, are involved
in horizontal gene transfer, and influence microbial community diversity
F. Microorganisms in benthic marine environments
1. Benthos—oceanic sediments and the seafloor including hydrothermal vents; mainly high
pressure, low light, and cold (1 to 4 °C) environments
2. Microbes found not only on seafloor but to a depth of at least 0.6 km where pressures are high
and the organisms must be piezophilic (barophilic)
3. Hydrocarbon metabolism fuels microbial communities on continental margins; massive
deposits of methane hydrates are found at the ocean floor below 500 meters
III. Microorganisms in Freshwater Ecosystems
A. Microorganisms in glaciers and permanently frozen lakes
1. These ancient deposits hold microorganisms that may provide information about the
biogeographic distribution of microorganisms and life on icy, extraterrestrial worlds (e.g.,
Europa)
2. Metabolically active environments that support a variety of microbes; frozen lakes may have
thick ice caps that block solar radiation, leading to chemosynthetic communities
B. Microorganisms in streams and rivers
1. Differ from lakes in that horizontal movement minimizes vertical stratification and most of the
functional biomass is attached to surfaces (not planktonic); can be lotic (free running) or lentic
(free standing)
2. Support benthic communities including biofilms of diverse microorganisms including
photosynthetic primary producers; phytoplankton also are supported by dissolved and
particulate organic carbon
3. Nutrients available in streams and rivers can be from in-stream production (autochthonous) or
from out-stream sources (allochthonous) such as leaves, and runoff from riparian areas; under
most conditions, such added organic material does not exceed the oxidative capacity of the
stream and it remains productive and aesthetically pleasing
4. Ability to process organic matter is limited
a. If the amount of organic material is excessive (eutrophic), oxygen is used faster than it
can be replenished, which causes the water to become anaerobic
1) Point sources of pollution include inadequately treated municipal wastes and other
materials from specific locations
2) Nonpoint sources of pollution include field and feedlot runoffs
b. If the amount of organic material is not excessive, algae will grow, which leads to oxygen
production in the daytime and respiration at night (diurnal oxygen shifts)
C. Microorganisms in lakes
1. Lakes vary in nutrient status
a. Oligotrophic lakes are nutrient-poor; typically oxic throughout
b. Eutrophic lakes are nutrient-rich; typically anoxic at the bottom
2. Deep lakes have a littoral zone where light penetrates and a lower pelagic zone, each with
distinct nutrient cycles
3. Lakes can be thermally stratified; stratified waters undergo seasonal turnovers because of
temperature and specific gravity changes
a. Epilimnion—warm, aerobic, upper layer
b. Thermocline—region of rapid temperature decrease that spans the metalimnion; acts as a
barrier to mixing
c. Hypolimnion—cold, often anaerobic (particularly in nutrient-rich lakes) lower layer
d. Oligotrophic lakes remain oxic and do not exhibit oxygen stratification; eutrophic lakes
usually have bottoms rich in organic matter; cyanobacterial and heterotrophic bacterial
blooms can degrade eutrophic waters

255 
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____
____
____
____
1.
2.
3.
4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
____ 15.
____ 16.
____ 17.
A nutrient-enriched environment
A nutrient-poor environment
Environments with high flux rates for oxygen
A columnar set-up designed to resemble a naturally
occurring aquatic ecosystem
Ratio of C:N:P; it is impacted by nutrient dynamics
and is used to monitor these processes
Planktonic photosynthetic microorganisms and small
aquatic plants
Planktonic viruses
Depleted in oxygen
The zone where light penetrates an aquatic system
Clumps of organic matter that escapes the photic zone
and falls to the seafloor
Nutrients that enter from outside of streams
Nutrients produced by in-stream processes
The upper warmer layer in thermally stratified lakes
The colder bottom layer of thermally stratified lakes
The process primarily responsible for buffering the pH
of oceans
The photic zone of deep lakes
Organisms adapted to high physical pressure
environments
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
n.
o.
p.
q.
allochthonous
autochthonous
carbonate
equilibrium system
epilimnion
eutrophic
high-oxygen
diffusion environments
hypolimnion
hypoxic
littoral
marine snow
oligotrophic
photic
phytoplankton
piezophilic
Redfield ratio
virioplankton
Winogradsky column
FILL IN THE BLANK
1.
2.
3.
4.
5.
6.
7.
8.

Partially enclosed coastal regions where a river meets the sea called __________ have a characteristic
salinity profile called a _____________ ___________ where freshwater floats on denser __________.
When nutrients are added to a lake, it can become ____________ (nutrient rich) and this can degrade the
quality of the lake.
Lakes can be thermally stratified. The warm upper layer is called the _________, and the deeper colder
layer is called the
. These two are separated by a zone of rapid temperature decrease called the
_________.
If the amount of organic material added to a river or stream is not excessive, algae grow and produce
oxygen during the day. At night, the oxygen is consumed, resulting in
.
Aquatic environments are termed
environments because oxygen diffuses
slowly through water. Furthermore, the solubility of oxygen in water is limited. This can lead to the
formation of
(low oxygen levels) and
(oxygen-free) zones, which allow
specialized microorganisms to grow.
Photosynthetic microbes and small plants suspended in water are called
. They create
organic matter that enters the
, a complex process that cycles organic matter from
dissolved forms to particulate forms and then back to carbon dioxide and other materials.
To supplement ATP production some microbes in the oligotrophic ocean areas use
in the
same way that archaea use bacteriorhodopsin. Other bacteria will use
, although it is not true photosynthesis since carbon is not fixed. Others acquire energy from
inorganic compounds while using organic carbon sources in the process of
.
Lakes vary in nutrient status. Some are
(nutrient poor) and some are
(nutrient rich).
256 
9.
The release of inadequately treated wastes and other materials at a single location on a river or stream is a
type of
pollution. Runoff from fields and feedlots is a type of
pollution.
MULTIPLE CHOICE
For each of the questions below select the one best answer.
1.
2.
3.
Which of the following is a mechanism by
which microbes can be added to aquatic
environments?
a. from the atmosphere
b. within animal carcasses and plant
detritus
c. within dust
d. All of the above are mechanisms by
which microbes are added to aquatic
environments.
In which of the following types of waters do
seasonal climatic temperature changes result
in distinct chemical and microbial
stratification?
a. oceans
b. eutrophic lakes
c. oligotrophic lakes
d. fast-flowing rivers
If phosphorus is added to an oligotrophic
lake, what organisms will play a major role in
nutrient accumulation?
a. cyanobacteria
b. nonphotosynthetic bacteria
c. archaea
d. eukaryotic algae
4.
5.
6.
7.
Which of the following describes when
microbes interact at several trophic levels to
recycle nutrients?
a. microbial loop
b. nutrient cycle
c. organic dissolution
d. benthic precipitation
Which of the following often cause harmful
algal blooms?
a. Thiothrix spp.
b. pan algae
c. chlorobia
d. dinoflagellates
Which of the following is a term used for
open ocean regions?
a. pelagic
b. benthic
c. photic
d. anoxic
Microbial growth in the open ocean is
typically limited by which nutrient?
a. iron
b. phosphorus
c. nitrogen
d. calcium
TRUE/FALSE
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.

Water covered by ice year-round does not support the growth of microorganisms.
The Winogradsky column is a microcosm of an aquatic environment that is used to demonstrate the
microbial stratification that can occur in nonagitated waters.
Microbial grazing, or the use of microbes as a food source by protozoans, plays a role in nutrient
cycling in aquatic environments.
The horizontal water flow in rivers and streams minimizes vertical stratification.
The largest portion of the Earth’s waters is freshwater.
Despite their small size, microorganisms in the ocean can have a significant impact on the
atmosphere on a global scale.
The Redfield ratio is impacted by the addition of minerals to the ocean and is important for
monitoring nutrient cycling.
Because marine viruses are obligate parasites, they are not important to nutrient cycling in the
ocean.
Mixing and diffusion of materials in aquatic environments are critical processes in creating unique
environments for different microorganisms.
257 
CRITICAL THINKING
1.
Ocean microbiota are critical for global nutrient cycling. Given that the oceans are closely connected to
the atmosphere, how might global climate change be expected to affect microbial communities in the
oceans? How might ocean chemistry be affected? Will the influx of nutrients cause changes to ocean
communities, and how might this affect global nutrient cycles?
2.
There are enormous accumulations of methane hydrates on the ocean floor. What kind of microbial
communities do you think would form around these deposits? What types of metabolisms would you
expect to find? What do you think would be the consequences of harvesting these deposits for our energy
needs?
ANSWER KEY
Terms and Definitions
1. e, 2. k, 3. f, 4. q, 5. o, 6. m, 7. p, 8. h, 9. l, 10. j, 11. a, 12. b, 13. d, 14. g, 15. c, 16. i, 17. n
Fill in the Blank
1. estuaries; salt wedge; seawater 2. eutrophic 3. epilimnion; hypolimnion; thermocline 4. diurnal oxygen shifts
5. low-oxygen diffusion; hypoxic; anoxic 6. phytoplankton; microbial loop 7. proteorhodopsin; aerobic
anoxygenic phototrophy; lithoheterotrophy 8. oligotrophic; eutrophic 9. point source; nonpoint source
Multiple Choice
1. d, 2. b, 3. a, 4. a, 5. d, 6. a, 7. c
True/False
1. F, 2. T, 3. T, 4. T, 5. F, 6. T, 7. T, 8. F, 9. T

258 