Microbial

Ecology
MICR3213/BC31M:
Applied and
Environmental
Microbiology

Dr. Stacy Stephenson-

Clarke
stacy.stephenson02
@uwimona.edu.jm
 Learning Objectives of
Course

❑Understand the ecology of microorganisms at

population, community and ecosystem levels

❑Describe the approaches used to study microorganisms

in their natural environments and the limitations
associated with each

❑Describe community function and dynamics at both the

molecular and the organismal level
 Learning Objectives of
Course

❑Appreciate the (vast) genetic and physiological diversity

of microbes, and classify them based on their metabolic
fuelling reactions

❑Understand how the specific environmental properties

of soils, oceans and biofilms affect microbial
communities therein

❑Discuss how microbes are useful in biotechnological and

environmental applications such as sewage treatment,
bioremediation, etc. and to relate the physiology of
microbes to their role in these processes
 Microbial Ecology:
Further Reading

❑ See Madigan, M., Martinko, J., Bender, K.,

Buckley, D. and Stahl, D. (2015). Brock Biology of
Microorganisms (14th Ed). Person Education
Limited

❑Chapters 18 and 19
 Microbial Ecology
❑ Studyof inter-relationships between microorganisms
and their environments

ECOSYSTEM

COMMUNITY

GUILD

POPULATION

INDIVIDUAL
 Microbial Ecology

❑ Microbes and Ecosystem Niches

❑ Organization of Ecosystems
❑ Role of Microbes in Biogeochemical Cycling
❑ Microbial Environments and Microenvironments
 History of Microbial Ecology
❑The term “microbial ecology” really wasn’t in common use until
the late 1960s

❑Why?

❑Microbial ecology has its roots in microbiology, rather than

ecology

❑The history of the field is largely a transition from laboratory

pure cultures to studying organisms in nature…
 Louis Pasteur
(1822-1895)

❑ “basic” vs. “applied” science

❑ fermentation = biological process
carried out by microorganisms.
❑ Germ theory = foundation of
brewing of beer, wine-making, and
pasteurization.
❑ Nature of contagious diseases: potato
blight, silkworm diseases, and
anthrax.
❑ Immunization (anthrax, rabies)
❑ Public experiments!

"Imagination should give wings to our thoughts but we always

need decisive experimental proof, and when the moment comes
to draw conclusions and to interpret the gathered observations,
imagination must be checked and documented by the factual
results of the experiment."
 Robert Koch
(1843-1910)

❑ Discovered the Bacillus

strains that cause
cholera and anthrax

❑ Agar media for pure

cultures (earlier had tried
sliced boiled potatoes!)

❑ Pure culture
paradigm: isolate an
❑ Disease and medical organism and see what it
microbiology does
❑ Pure culture paradigm
 Pure Culture Paradigm
❑Extremely important conceptual development in microbiology (and
in microbial ecology, too)
❑Remove organisms from complex communities
❑Isolate key processes
❑Obtain reproducible results
❑This method is still used today

❑Attitude of Koch’s time:

❑“Work with impure cultures yields nothing but nonsense and
Penicillium glaucum“ (Oscar Brefield 1881)
Sir Alexander Fleming (1929), examining exactly such
an impure culture (Staphylococcus culture contaminated
by Penicillium), led to the discovery of penicillin.

Agar petri dish zone of no

bacterial growth,
Staphylococcus due to penicillin
colonies produced
by fungus
Penicillium
contaminant

Interference competition!
classic ecological process
 Sergei Winogradsky
(1856-1953)

❑ Isolated nitrifying bacteria

❑ Winogradsky column:
microbial communities develop
along a gradient of oxygen
tension; method still used
today
❑ Described oxidation of
hydrogen sulfide, sulfur,
ferrous iron
❑ …all leading to the concept of
chemoautotrophy – deriving
❑ Bacteria: central in element energy from chemical oxidation
of inorganic compounds and
transformations
carbon from CO2
❑ Founder of soil
microbiology
 Martinus Beijerinck
(1851-1931)

“The way I approach

microbiology...can be
concisely stated as the
study of microbial
ecology, i.e., of the
relation between
environmental conditions
and the special forms of
life corresponding to
them”
Founder of the Dutch Delft
School of Microbiology
 Martinus Beijerinck (1851-1931)
❑ “a man of science does not marry”
❑ Isolated N fixers and S reducers
❑ ‘Microbial ubiquity’: all microorganisms are
everywhere; conditions and resources determine who
flourishes
❑ Enrichment culture: growth medium tailored to suit
particular metabolic function
❑ With Winogradsky, recognized that microbes are the
major players in element transformations
❑ Led to field of global biogeochemistry
Albert Jan Kluyver
(1888-1956)

❑ Student of Beijerinck

❑ Microbial
physiology

❑ Comparative
approach

❑ Unifying metabolic
features among
microbes

❑ Leader of the Dutch

school after Beijerinck
 Cornelius Bernardus
van Niel (1897-1985)
❑ Student of Kluyver, third in the
Dutch Delft School
❑ Isolated purple sulfur
bacteria
❑ Major contribution, chemistry of
photosynthesis:
❑ H2A + CO2 → CH2O + 2A + H2O
where A can be S or O
❑ Extended model green plants;
oxygen from water, not from CO2
❑ Also, chemistry of denitrification,
definition of prokaryote in 1961
(with R. Stanier)
❑ Taught lab course focusing on studying microbes from nature
(first course in microbial ecology?)
❑ Philosophy of hypothesis testing, falsification “moving from
clearly erroneous to more ‘correct’, but never immutable
conclusions”
 Robert E. Hungate
(1908-2004)

❑ Student of van Niel

❑ Developed methods for

isolating anaerobes

❑ Devised culture methods that

select using natural substrates,
rather than guesses about what
organisms eat

❑ Microbiology of guts of rumen,

termites

❑ ASM president when

❑ AKA “Grampa Bob”
“Environmental Microbiology” and
“Microbial Ecology” formally
recognized
 Other contributions

❑1960s: Ronald Atlas, Richard Bartha

❑ Studies of petroleum degradation
❑ Led to new field of bioremediation,
❑ Extended to many other pollutants: DDT, PCBs, mercury, selenium,
industrial solvents

❑1970s fuel-shortage:
❑ Shortage in N fertilizer
❑ Sparked interest in the biology of nitrogen fixers
 Paul D Brown
(1960s - )

❑ Environmental regulation of
bacterial virulence

❑ Genetic determinants of
antimicrobial resistance

❑ If it can be perceived and

believed, it can be achieved!
Microbial Ecology
Energetics and
heterotroph
carbon flow in
microbial
metabolism

(e.g., NH4+, S, H2S, Fe2+)

autotroph
 Objectives in microbial
ecology
❑ Understanding the biodiversity of microorganisms in nature, and
interactions in communities
❑ Measurement of microbial activities in nature, and monitoring of effects
on ecosystems
❑ Activities commonly measured when studying microorganisms within an
ecosystem:
❑ Primary production of organic matter (phototrophic,
chemolithotrophic activity)
❑ CO2 + H2O + energy → new biomass
❑ Decomposition of organic matter
(chemoorganotrophic/heterotrophic activity)
dead biomass → CO2 + H2O + energy
❑ Biogeochemical cycling of elements (C, O, N, P, S, Fe)
 Microorganisms in nature
❑Live in habitats suited to higher organisms, also in “extreme”
environments
❑ extremes in temperature, pH, pressure, salinity; anoxic habitats
❑ inanimate (soil, sediment, water, food) & animate habitats (on/in
animals, plants, insects)
❑ necessities for growth include available resources, suitable
physiochemical conditions
 Psychrophiles,
thermophiles,
hyperthermophiles:
“extremophiles” that live
in habitats of extreme
temperature, including
cold (e.g., deep sea,
Antarctica, the Arctic), or
hot habitats (e.g.,
compost piles, deep sea
hydrothermal vents)
Seawater evaporating
ponds near San Francisco
Bay, used to harvest
“solar” salt. The red
colour is due to pigments
of the extreme
halophile
Halobacterium, an
Archaeal species that
inhabits the ponds. (Fig. 13.2(b), p. 423, Madigan & Martinko)
 Microorganisms in nature
❑ Niche: the functional role of an
organism within an ecosystem;
combined description of the
physical habitat, functional role,
and interactions of the
microorganism occurring at a
given location

❑ Microenvironment: where a
microorganism lives, metabolizes
within its habitat
❑ physicochemical gradients
❑ spatial, temporal variability

Figure illustrates O2 contours within a soil

particle, measured by microelectrode. Each
zone could be considered a different
microenvironment
❑ Microcolonies in soil particles

❑ Very few microbes are free; most reside in microcolonies

attached to soil particles

❑ Soil aggregates can contain many different microenvironments

supporting the growth of several types of microbes
 Nutrient levels and growth rates

❑ Microbial life in nature does not necessarily resemble microbial

life in lab culture
❑ Entry of nutrients into an ecosystem is often intermittent
❑ Feast-or-famine existence
❑ Adaptations
❑ Accumulate reserves in times of plenty
❑ High growth rate when growth possible; quiescence when growth is not
possible
❑ Periods of extended exponential growth rare in nature
❑ Distribution of resources in nature is often non-uniform
❑ Competition for resources is likely
 Surfaces and biofilms
Biofilm: a community of microorganisms embedded
in an organic polymer matrix (extracellular polymeric
substances, EPS), adhering to a surface

❑ physicochemical gradients
Time within mature biofilm result
in a number of potential
microenvironments within a
small area
❑ Recall image of soil particle?
 Biofilm formation
Rendueles & Ghigo, 2012, FEMS Microbiol Rev
Bacterial microcolonies Natural biofilm on a leaf surface
developing on a microscope ❑ cell colour indicates depth in biofilm:
slide immersed in a river red (surface) → blue (18 μm deep)
(phase contrast microscopy) ❑ (confocal laser scanning microscopy)
Biofilm developed on a stainless steel pipe
❑ stained with DAPI (fluorescent; interacts with nucleic acids)
❑ note water channels through biofilm
Viability staining – Fig 18.7 Brock Biology of Microorganisms 14th ed, 2015
❑ stained with LIVE/DEAD BacLight bacterial viability stain
❑ Live (green) and dead (red) cells of M. luteus and B. cereus
Biofilm of iron-oxidizing
prokaryotes on rocks
Rio Tinto Spain

Evidence of a dental biofilm:

❑ left front tooth exposed to sucrose solution for 5 min while right served as a
control
❑ both then stained with iodine solution
❑ brown colouration results from reaction of iodine with extracellular glucans
(EPS) produced by the sucrose-supplied biofilm
 Surfaces and Biofilms

❑ Pseudomonas aeruginosa
❑ Biofilm producer
❑ Intracellular communication (quorum sensing) is critical
in the development and maintenance of a biofilm
❑ The major intracellular signaling molecules are acylated
homoserine lactones
❑ Both intraspecies signaling and interspecies signaling
likely occur in biofilms
 Surfaces and Biofilms

❑ Bacteria form biofilms for several reasons:

❑ Self-defense
❑ Biofilms resist physical forces that sweep away unattached cells,
phagocytosis by immune system cells, and penetration of toxins (e.g.,
antibiotics)
❑ Allows cells to remain in a favorable niche
❑ Allows bacterial cells to live in close association with one
another
 Biofilms
❑ Advantages of biofilm mode: attachment to surface;
nutrient trapping; cooperative interactions possible;
protection from toxic substances, predators
❑ Disadvantages: highly competitive; localized biomass
can be efficiently preyed upon, infected by viruses
❑ Problems resulting from biofilm formation: periodontal
disease; pipe clogging; high microbial numbers in potable
water distribution systems; accelerated corrosion of
pipelines and structural steelwork; increased drag on
ship’s hull
❑ Exploitation of biofilms: slow sand filtration (water
purification); microbial leaching of low-grade ores;
vinegar production
 Microbial Mats
❑Microbial mats: are very
thick biofilms
❑Built by phototrophic and/or
chemolithotrophic bacteria
❑Photosynthetic mats contain
filamentous cyanobacteria
❑Cyanobacterial mats are complete
ecosystem
❑ Have existed for over 3.5 billion years

❑Chemolithotrophic mats contain

filamentous sulfur-oxidizing
bacteria (Fig. 12.5, p. 334, Madigan & Martinko)

❑ Often found associated with hot

springs, shallow marine basins
 green:
cyanobacterial layers
(aerobic phototrophs)

~3 cm thick
orange:
layers of anoxygenic
phototrophic bacteria

A coring taken through a

microbial mat from a hot spring

Could you guess the microbes occupying the

other layers?
Thioploca mat: Filaments/sheaths of large sulfur-oxidizing
chemolithotroph off Chilean coast
Fossing et al. 1995; Jørgensen and Gallardo 1999
 General Ecological Concepts:
Symbiotic Relationship

❑Many microbes establish relationships with other organisms

(symbioses)
❑Parasitism
❑ One member in the relationship is harmed, and the other benefits

❑Mutualism
❑ Both species benefit

❑Commensalism
❑ One species benefits, and the other is neither harmed nor helped
 General
Ecological
Concepts

❑ Diversity of microbial species in an ecosystem is expressed in

two ways:
Species richness: total number of different species present
Species abundance: proportion of each species in an ecosystem

❑ Microbial species richness and abundance are functions of the

kinds and amounts of nutrients available in a given habitat
 Examples of interactions between microbial populations

(i) Negative effect for (one or both) interacting populations:

* Competition – outcome depends on innate capabilities of nutrient
uptake, metabolic rates
• “competitive exclusion” is one possible outcome

* Antagonism – specific inhibitor or metabolic product may impede

growth/metabolism of others
• antibiotic or bacteriocin release, lactic acid production

(ii) Positive effect for (one or both) interacting populations:

* Cooperative interactions - interacting microbes must share
same/nearby microenvironment

* Syntrophy – microorganisms together carry out transformation

neither can conduct alone

(iii) Complementary metabolic interactions

• e.g., in nitrification: NH3 → NO2- (nitrosifying bacteria); NO2- → NO3-
(nitrifiers)
• e.g., in S cycling: anaerobic sulfate reducing bacteria (SO42- → H2S)
provide substrate for microaerophilic sulfide-oxidizing bacteria (H2S → S0)
 Current trends in microbial
ecology

❑ Space exploration – microbes in extreme environments (hot

springs, thermal vents, lithosphere)

❑ Molecular techniques – diversity of microorganisms (Carl

Woese), new methods to assess presence or abundance of
individual species in situ

❑ Realization that with pure culture/enrichment techniques, we

know somewhere between 1-10% of existing microbial species
– lots to learn!

❑ Biology of climate change, global biogeochemistry

 Recent Discovery

❑In 2008, Prof. Gary Strobel ,Montana State University and students
explored the Patagonia rainforest they found an endophytic fungus
inside the tissues of the Ulmo tree. The fungus Gliocladium roseum
liberates a number of volatile compounds in the air, the mixture is
similar to diesel fuel and can be produced when grown in the lab
with good yields on cellulose - dubbed mycodiesel

❑Also, Prof. Scott Strobel and a group of Yale students in 2012 found
in the Amazon rainforest a fungus Pestialotiopsis microspora that
degrades polyurethane (plastic). The fungus is able to survive
on polyurethane alone under anaerobic conditions