BMT307: LECTURE 1

Introduction to Environmental Microbiology

Dr. Kamarul Zaman Zarkasi | Ext: 6152 | Room: G08-225| Email: kamarul.zarkasi@usm.my
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Week 1:www.usm.my
14.2.2017
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 ENVIRONMENTAL MICROBIOLOGY
•The study of the composition and physiology of microbial
communities in the environment.

• The environment in this case means the soil, water, air and
sediments covering the planet and can also include the
animals and plants that inhabit these areas.

• Environmental microbiology also includes the study of

microorganisms that exist in artificial environments such as
bioreactors.

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 MICROBIAL ECOLOGY
What is microbial ecology?

• Study of microbes and their interactions with the environment.

• Some examples of microbial ecology:

– Quantifying sulfur oxidizers in a deep sea hydrothermal vent.

– Determining biodiversity of prokaryotes in the human GI tract.
– Monitoring the distribution of ctx gene in marine estuaries.

• The subject of investigation can be application based or fundamental.

– Application based science (or applied science) is usually driven by

problems effecting society in some way.
– Fundamental science aims to advance the understanding of a
particular process in nature.
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 Microbial Ecology

• ECOLOGY = "law of the household" (Haeckel 1866)

• Study of the factors regulating the abundance and

distribution of microorganisms and their interactions
with the physical or chemical and biological environment.

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 Microbial Ecology

• The study of interrelationships between microorganisms and their

living and nonliving environments.

• Microbial populations are able to tolerate and to grow under varying

environmental conditions, including habitats with extreme
environmental conditions such as hot springs and salt lakes.

• the environmental factors controlling microbial growth and survival

offers insight into the distribution of microorganisms in nature, and
many studies in microbial ecology are concerned with examining the
adaptive features that permit particular microbial species to function
in particular habitats.
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 Microbial Ecology
• Within habitats some microorganisms are autochthonous
(indigenous), filling the functional niches of the ecosystem, and
others are allochthonous (foreign), surviving in the habitat for a period
of time but not filling the ecological niches.

• Because of their diversity and wide distribution, microorganisms are

extremely important in ecological processes. The dynamic interactions
between microbial populations and their surroundings and the
metabolic activities of microorganisms are essential for supporting
productivity and maintaining environmental quality of ecosystems.

• Microorganisms are crucial for the environmental degradation of

liquid and solid wastes and various pollutants and for maintaining the
ecological balance of ecosystems—essential for preventing
environmental problems such as acid mine drainage and
eutrophication.
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 Microbial Ecology
• The various interactions among microbial populations and between
microbes, plants, and animals provide stability within the biological
community of a given habitat and ensure conservation of the
available resources and ecological balance.

• Interactions between microbial populations can have positive or

negative effects, either enhancing the ability of populations to survive
or limiting population densities.

• Sometimes they result in the elimination of a population from a

habitat.

• Only a few bacterial species are capable of biological nitrogen

fixation.
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 Microbial Ecology
• In terrestrial habitats, the microbial fixation of atmospheric nitrogen is carried out
by free-living , such as Azotobacter, and by bacteria living in symbiotic association
with plants, such as Rhizobium or Bradyrhizobium living in mutualistic association
within nodules on the roots of leguminous plants. In aquatic habitats,
cyanobacteria, such as Anabaena and Nostoc, fix atmospheric nitrogen.

• The incorporation of the bacterial genes controlling nitrogen fixation into

agricultural crops through genetic engineering may help improve yields.
Microorganisms also carry out other processes essential for the biogeochemical
cycling of nitrogen.

• The biodegradation (microbial decomposition) of waste is a practical application

of microbial metabolism for solving ecological problems. Solid wastes are
decomposed by microorganisms in landfills and by composting.

• Liquid waste (sewage) treatment uses microbes to degrade organic matter,

thereby reducing the biochemical oxygen demand (BOD)
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 Microbial Ecology
1. Interactions of microorganisms with their abiotic
environment (including biogeochemical cycles)., where
microbes play a far more important role in natural
environments than their small size would suggest.

2. Interactions among various microorganisms,

consortia, assemblages, communities (competition,
symbiosis and predation).

3. Interactions of microorganisms with plants and animals

(e.g. rhizosphere, gut flora, microbes that “jump”
organisms).
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 Microbial Ecology
1. Understanding what types of microbes are there

2. How many there are

3. What they are doing

4. How they survive

5. What controls their activity and numbers

6. What role they play in the large cycles of C, trace

gases and nutrients

7. How microbes chemically and physically change their

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 MICROBES
Introduction to microbes

• enormous diversity of organisms which are

“microscopic” and found in virtually all habitats (air,
water, soil, ice)

• enormous metabolic diversity: bacteria in particular

can utilize virtually any substrate available (from various
types of organic matter to high-tech. plastics…)

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 Classification of Ecology
i. Based on function (e.g. energy source)

• autotrophy, heterotrophy and mixotrophy

– among the autotrophs: lithotrophs(chemoautotrophes),

photoautotrophs (both anoxygenic and oxygenic)

– among heterotrophs: organotrophs use a wide variety of

organic chemicals in decomposition processes
(anaerobic and aerobic) using carbohydrates, proteins,
lipids, hydrocarbonsetc..

– mixotrophs can switch from autotrophy to heterotrophy

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 Classification of Ecology
ii. Based on habitat

• suspended in water = plankton (e.g. phytoplankton,

bacterioplankton)

• attached communities or biofilms: periphyton,

epiphyton, epilithon, epipelon, endolithon

• extreme environments: thermophiles vs psychrophiles,

barophiles, halophiles, acidophiles vs alkalophiles
(e.g. hyperthermophile from deep-sea vents that
tolerate boiling water - archaebacteria
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 Classification of Ecology
iii. Based on size used for planktonic microbes:

• femptoplankton (< 0.2 m) = "colloids", viruses

• picoplankton (0.2 - 2 m) = bacteria, cyanobacteria,

prochlorophytes, eukaryotes

• nanoplankton ( 2.0 - 20 m) = "algae", cyanobacteria,

protozoa, fungi, "marine snow"

• microplankton (20 - 200 m) = "algae" especially colonial

forms, protozoa (ciliates), rotifers

• (macroplankton (200 - 2000 m) = large colonial algae,

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ciliates, rotifers, crustaceans) 14
 Taxonomic classifications

- viruses acellular
- bacteria prokaryotic
- fungi eukaryotic
- Algae "
- Protozoa "

• using Whittacker’s (1969) 5 kingdom

classification, microorganisms occur in 4 of the
5 kingdoms

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 Organisms divided into 5 Kingdoms:

1. Monera – all procaryotes

2. Protista – unicellular or colonial eucaryotic cells

lacking true tissues; includes algae, protozoa & simpler
fungi

3. Fungi – eucaryotic; includes molds, yeasts and

mushrooms

4. Plantae – multicellular

5. Animalia – multicellular

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 Composition of the Microbial World:

Procaryotes: relative simple morphology and lack true membrane

delimited nucleus

Eucaryotes: morphologically complex with a

true membrane enclosed nucleus
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 Bacteria

* Prokaryotic cell
* Cell wall contains peptidoglycan
* Asexual reproduction via binary fission
* Energy supply from photosynthesis, organic
or non-organic materials.

Archaea

* Prokaryotic cell
* Cell wall lacks of peptidoglycan
* Living in extreme environments
* Groups: Methanogen, extreme halophilic
and extreme thermophilic microorganisms. 18
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Shape and
Arrangement
of Bacteria
• Spherical/cocci
• Rod
• Spring
• Vibrio (coma)

Spherical shape Rod shape/ bacillus Spring/spirochaete

Cocci Diplobacillus (2 bacillus)

Diplococci (2 cocci)
Streptococci (in chain)
Staphylococci (in cluster)
Coma/vibrio shape
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 Fungal hyphae

Various type of fungal spores/conidia

Fungal mycellium
Fungi
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 Penicillium Aspergillus Mucor
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 Yeasts

Unicellular and buddings

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 Virus

• Acell (Non-cell)
• Contain DNA or RNA as cores
• Cores may be enveloped by a protein
• Then sourounded by an envelop
• Multiplying in a living host

Bacteriophage
Virion Virus Influenza Hepatitis C
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 Microflora of the soil
The soil is the major environment for a habitation of
microorganisms. The first bacteria, as well as all alive ones, have
appeared in water. However in more later geological periods,
when on a surface of globe the soil was derived, it became main
habitation of microorganisms and main arena of their vital activity.
The amount of bacteria in one gram of soil can be very great -
from 200 millions up to 10 billions. Manured and ploughing ground
are stocked with microorganisms most densely. The soil of
woods, moor, the sands of desert contain few microbes. The most
surface sphere of soil (crust by width of 2-3 mm) is very poor by
microorganisms. A desiccation and the solar rays perniciously
influence them. The ground mass of bacteria is on depth 10-20
cm. On depth of 1,5-2 m of untouched ground the microbes do not
meet almost.
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 Microflora of the soil
The microflora of soil includes hundreds of species of bacteria, viruses,
protozoa, actinomyces and fungi. It is various species of putrefactiving,
nitrifying, denitrifying, nitrogen-fixing bacteria. The most often inhabitants
of soil are the representatives of genus Azotobacter, Nocardia, and
Clostridium. Many bacteria of genus Rhisobium, Nitrosomonas,
Nitrosospira, Nitrobacter, Pseudomonas are very often found. Almost
always there are denitrifying bacteria (B.denitrificans), ammonifying
microbes (Urobacillus pasteurii, Urobacillus leybii), numerous iron
bacteria and sulphur-bacteria. All of them play the great role in a
turnover of materials in a nature, improve productivity of our fields,
provide life on the Earth. The microorganisms of soil take an active part
in all processes of transformation of materials and energy: synthesis of a
biomass, biological nitrogen fixation, fermentation, corruption,
denitrification of the cycle sulfur, iron lactas, phosphorum, carboneum
and other elements. 25
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 Microflora of the water
Water is a natural medium of a habitation of various
microorganisms. In sweet and salty waters representatives
of all groups of bacteria are found Protozoa, Fungi, Viruses,
Water - plant. The collection of all aqueous microorganisms
is named as a microbial plankton. The microflora of
reservoirs consists of two groups of microbes: autochtonal
(or aqueous) microorganisms and allochtonal (brought from
the outside). The autochtonal microflora are presented by
microorganisms, which permanently live and are multiplied
in water. It is more often such species: Micrococcus
candicans, M. roseus, Sarcina lutea, Bacterium aquatilis
communis, Pseudomonas fluorescens. The anaerobes
represent by species Clostridium, Bacillus cereus, B.
mycoides.
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 Microflora of the water
The microbial composition of water is in the large degree
mirrors a soil microflora. A major factor, which determines
quantity of microbes in water is presence in it of necessary
nutritious materials, that are various biological matters. Main
path of microbial contamination of water is penetration of
unpurified waste from sewage of the populated area.
Therefore, the more water is polluted with similar organic
matters, there are more in it of microorganisms. It is
distinguished polisaprogenic, mesosaprogenic and
oligosarpogenic zones of water.

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 Microflora of the water
Zones of water clearness

1. Polisaprogenic zone is the zone of strong contamination. It

contains many organic matters and almost there is no oxygen. The
quantity of bacteria in 1 ml of water reaches one million and more.

2. Mesosaprogenic zone is the zone of moderate

contamination(pollution)). In it the nitrifying and aerobic bacteria
prevails. The total number of microorganisms compounds
hundreds of thousand in one ml.

3. Oligosaprogenic a zone (zone of pure water). The quantity of

bacteria
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changes from 10 up to 1000 in one ml. 28
 Common microbial number of water is examined by inoculation of 1 ml of
water in melted and refrigerated up to 50 C in agar in Petri dishes. Coli-
index is determined by a method of membrane filters or fermentation
tests.

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 Microflora of the air
Air for microorganisms is less favorable environment, than
soil and water. There are almost no the nutritious materials
necessary for reproduction of bacteria. Desiccation and the
ultraviolet rays operate perniciously on microorganisms.
Nevertheless, many microbes in air can be saved more or
less long time. The composition of a microflora of air is very
various. It depends on cleanness of air, deposits,
temperature, humidity, climate and geographical conditions.
Than it is more in air of a dust, smoke, soot, the more
microorganisms. Vice-versa, above mountains, seas, oceans
and woods, where air is pure, it is not enough of microbes.
Main sources of microbial air pollution is the soil, water and
man. 30
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 Microflora of foodstuff
In foodstuff there is a specific microflora, which adds them
the defined gustatory qualities and consistence (curdled milk,
yogurt).
The microflora can penetrate into many products from the
outside - nonspecific microflora. The intensive
reproduction of separate species of bacteria makes products
unsuitable for the use. Often foodstuff contaminate with
bacteria of such genus as Salmonella, Shigella,
Staphylococcus, Escherichia, Clostridium botulinum,
C.perfringens, C. difficile. They can cause typhoid,
dysentery, cholera, gastroenteritis, botulism and other
illnesses.
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 Microflora of foodstuff
Milk contaminate with such microbial genus as Staphylococcus,
Streptococcus, Mycobacterium, Salmonella, Brucella, Enterovirus. It
happens at milking, transportation and processing of milk and lactic
products.
Meat is contaminated during disease of animals and poultry, during
their killing, cutting, incorrect storage and transportation. Often in meat
it is found the representatives of genus Salmonella, Proteus,
Staphylococcus, Streptococcus, Clostridium.
The fish is contaminated by many species of microorganisms. They get
in it from water, flakes, intestine, hands of staff, which handles fish
production. The most dangerous bacteria are C.botulinum,
V.parahaemolyticus. There may be also causative agents of a typhoid,
dysentery, cholera, hepatites.
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 Microflora of foodstuff
Vegetables and fruit are contaminated by species of Salmonella,
Shigella, Vibrio, Enterovirus. They get from hands of the people,
which gather, transport and sell these products. The incorrect
preservation of vegetables (tomatoes, mushrooms and others) can
cause botulism.
Eggs often are infected by Salmonella, Fungi, Actinomycetes, and
egg powder by Staphylococcus. Especially dangerous are the eggs
of gooses and ducks.
Bread product are poorly favourable environment for reproduction
of the pathogenic microorganism. Only products from the
overwintered grain cause sometimes toxic agranulocytosis. It is
caused by the representatives of species of Fusarium.
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 Normal microflora of humans
The microflora of the human is a complex of microbiocenoses,
which meet in an organism of the healthy people. They were
generated during evolution, and are characterized by surprising
persistence. The quantity and species composition of a normal
microflora are influenced age, sex, climate, feeding habits,
bacteria of an environment, individual sanitary and hygienic
habits etc. Special role in change of a microflora play
antibiotics, chemotherapeutic and immunological drugs. They
render the large selective influence on a population of some
bacteria. These medicines delay sensitive individuals and
promote development of resistance species. The struggle with
these resistant bacteria is one of difficult and urgent problems
of practical medicine
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 Microflora of a skin
The quantity of microorganisms on a skin can vary in the large
limits: from 100 microbial bodies on 1 см2 in the field of a forearm
up to 2,5 million/см2 in axillary fosses. From a surface of a skin of
the man is washed off about 1,5 billion of bacteria. Density of
microbial populations on a skin is subjected daily, monthly and
seasonal fluctuations. It also depends on a status of health, trade,
age, sex etc.
Most typical the representatives of the inhabitants of a skin are
Propionibacteria, Corynebacterium species (C.acnes, C.xerosis,
C.pseudodiphtheriticum, C.minutissimum, C.lipоphylicum) and
species Staphylococcus (S. epidermidis, S.saprophyticus,
S.hominis, S.haemolyticus, S.capitis – total 29 species) are.
Approximately for 10 % of the people on a skin as found S.aureus.
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 Skin bacteria

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 Microflora of an oral cavity
In an oral cavity there is a plenty of microorganisms. More than
100 species of aerobic and anaerobic bacteria are described.
In 1 ml of a spit can be found about 100 million of microbial
cells. Constant (stationary) temperature (37 0С), humidity, the
oddments of food, alkaline reaction of a spit and wide aeration
promote reproduction of microbes.
The basic group of bacteria of an oral cavity is compounded by
streptococci (S.salivarius, S.mitis, S.mutans, S.haemolyticus,
S.viridans). Here permanently dwell Lactobacterium,
Veilonella, Neisseria, Corynebacterium, Bacteroides. Besides
in an oral cavity we meet H.influenzae, T.oralis, T.denticola,
T.pseudopallida, C.albicans, Leptospira, Actinimycetes,
Mycoplasma, Protozoa. 39
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 The opportunistic pathogenic bacteria of an oral cavity can cause an
endogenic infection. This is promoted by traumas, change of pH spit,
application of antibiotics. The large value there is also sensibilization of an
organism to microbial allergens. Main causative agents of a caries are
S.mutans and S.sanguis.

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 DEEP BIOSPHERE
Strong evidence now supports the presence of a biosphere living up to 1 km below
the earth’s surface. Bacteria in this deep biosphere have been found in even
crystalline basalt rocks below marine sediments, and their biomass is on the order
of that above the surface. This biosphere is driven by geogasses, and is similar to
deep ocean vent ecosystems. Could also exist on other planets, e.g., Mars.

Hydrothermal Vent Tubeworms and

bacterial symbionts

Chemistry of the Deep Biosphere

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 STRESS RESPONSE
• The bacterial stress response ensures that bacteria can survive
adverse and fluctuating conditions in their immediate surroundings.

• Various mechanisms recognise different environmental changes

and mount an appropriate response.

• A bacterial cell can react simultaneously to a wide variety of

stresses.

•The stress response in bacteria involves a number of systems that

act against the external stimulus.

• A complex network of global regulatory systems in bacteria

ensures that the various stress response systems interact with each
other and leads to a coordinated and effective response. 42
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 METAGENOMICS
• Metagenomics is the cultivation-independent analysis of the
collective genomes of microbes within a given environment,
using sequence- and function-based approaches.

• Metagenomic studies have revealed the vast size and

richness of the microbial and viral world and demonstrated
the phylogenetic diversity of various environments.

• to huge volume genomic sequence data from uncultured

organisms has opened up many new avenues of research.
Advances in the throughput of sequencing and screening
technologies have greatly facilitated metagenomics research.
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 Thank You

Question?
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