Microbiology for

Environmental Engineering
AN INTRODUCTION TO
MICROBIOLOGY

Aussie Amalia ST., M.Sc

aussieamalia.tl@upnjatim.ac.id

Jurusan Teknik Lingkungan

Fakultas Teknik
Universitas Pembangunan Nasional Veteran , Jawa Timur
 Topics Covered
◦ Scope of Microbiology
◦ Importance of Microorganisms
◦ Characteristics of Microorganisms
◦ History of Microbiology
◦ Taxonomy
 References
Betty ,Laksmi, Jenie, 1993,Pernanganan Limbah industri pangan, Penerbit Kanisius,
Yogjakarta.hal 27-35
Dwijo S, 1998, Dasar-dasar mikrobiologi, penerbit Jambatan, Jakarta ,hal. 146-154
 Ratna Siri Hadioetomo, 1993, mikrobiologi dasar dalam praktek, PT Gramedia,
Jakarta hal 21, 24, 27, 28. 53
 Raina M. Maier, LanPepper and Charles P. Gerba., 2009, Environmental
Microbiology, Academic press and Elsevier, ISBN: 978-0-12-370519-8
The Scope of Microbiology
 Microbiology: The study of living things
too small to be seen without magnification

◦ Microorganisms or microbes- these

microscopic organisms
◦ Commonly called “germs, viruses,
agents…”
◦ Include bacteria, viruses, fungi, algae,
protozoa and helminths
◦ But not all cause disease and many more
are useful or essential for human life
 The Scope of Microbiology
Microorganism Microbiology

 Living things which individually are too small to be Study of microorganism

seen with the naked eyes Fondation of modern biotechnology

 All of the following may be considered Among the many specialized fields of
microorganism:
microbiology
 Bacteria (Eubacteria, archaebacteria)  Virology, Mycology, Bacteriology, Immunology,
 Fungi (yeasts, molds) Microbial Ecology, Biotechnological
 Protozoa Microbiology, Environmental Microbiology, Food
 Microscopic algae Microbiology, Forensic Microbiology, Molecular
 Viruses Biology
 Various parasitic worms
Why study Microbiology
Microbes are related to all life.
◦ In all environments
◦ Many beneficial aspects
◦ Related to life processes (food web, nutrient cycling)
◦ Only a minority are pathogenic.
◦ Most of our problems are caused by microbes
Why study Microbiology
Microbiology as a BASIC Science
Bacteria and yeast are useful in studying molecular biology, biochemistry and genetics
--reproduce rapidly
--are genetically (DNA) and biochemically more simple than higher order organisms
--working with bacteria and yeast for understanding life processes has no ethical
ramifications
Microbiology as an APPLIED Science
Medicine—Vaccine development, production of antibiotics, production of
important biological enzymes (insulin)
Industry—Production of beer, wine, cheeses and yogurt
Agriculture—maintenance of soil fertility/digestion in cattle
Ecology—Bioremediation—microorganisms that degrade toxic waste materials
Themes in Microbiology and
its field
Specializations in Microbiology
 Epidemiology and Public Health Microbiology
distribution and spread of diseases and their control and
prevention
 Food Microbiology
use of microbes in the production of food products and drinks
 Agricultural and Veterinary Microbiology
use of microbes to increase crop and livestock yield and control of
plant pests and animal diseases
 Environmental Microbiology
study of the beneficial and harmful effects of microbes on the
environment
Microbes in our lives
o Some are pathogenic (disease-causing)
o Decompose organic waste
o Produces through photosynthesis (e.g. Purple Sulphur
bacteria must fix CO2 to live)
o Play role in industry ( e.g. fermentation to produce ethanol
and acetone)
o Produce fermented food (vinegar, cheese & bread)
Photosynthetic Microbes

 Microbes are involved in photosynthesis and accounts for

>50% of earth’s oxygen.
 Also involved in decomposition and nutrient recycling.
Beneficial Uses of Microbes

Extraction of copper from ore

Beneficial Uses of Microbes

Synthesis of drugs, hormones and enzymes

Beneficial Uses of Microbes

Bioremediation is the use of microbes to degrade organic matter in sewage and detoxify
pollutants such as oil spills.
Modern Uses of Microbes

 Biotechnology, the use of microbes as miniature biochemical

factories to produce food and chemicals is centuries old.
 Genetic engineering makes use of molecular biology and
recombinant DNA techniques as new tools for biotechnology.
 Gene therapy replaces missing or defective genes in human cells
through genetic engineering.
 Genetically modified bacteria are used to protect crops from pests
and freezing.
Brief History of Microbiology
 The Microscope

 Spontaneous Generation
The First Microscope
ANTONY VAN LEEUWENHOEK (1632-1723)

First to observe living microbes

His single-lens magnified 50-300X
magnification
Between 1674-1723 he wrote series
of papers describing his observations
of bacteria, algae, protozoa, and fungi
(Animalcules)
The First Microscope Cont.
Abiogenesis vs. Biogenesis
 “Spontaneous Generation” was an early belief that living things can
arise from vital forces present in nonliving and decaying matter.
(Ex: maggots from meat or mushrooms from rotting wood

 The alternative hypothesis that living organisms can arise only from
preexisting life forms is called “Biogenesis”.
The Pros and Cons

Francisco Redi (ca. 1668)

The Pros and Cons
 1745 -John Needham boiled nutrient broth into covered
flasks
Conditions Results
Nutrient broth All showed
heated then growth
placed in sealed
flasks

From where did the microbes come?

Spontaneous generation or biogenesis?
The Pros and Cons
The Pros and Cons
The Pros and Cons
LOUIS PASTEUR (1822 - 1895)

• Disproved spontaneous generation of

microbes by preventing “dust particles” from
reaching the sterile broth
• In 1861 completes experiments that lays to
rest spontaneous generation.
• Showed microbes caused fermentation
• Studied spoilage and introduced
“Pasteurization” to prevent it
PASTEUR’S
EXPERIMENT

Trapped airborne organisms in cotton; he also heated the necks of flasks, drawing them out into
long curves, sterilized the media, and left the flasks open to the air.
In this way Pasteur disproved the theory of spontaneous generation
Phylogenetic classification of
micro-organisms
Eukaryotic
Algae
Prokaryotic Fungi
Eubacteria Archaeabacteria Protozoa

Universal Ancestor
Phylogenetic classification
of micro-organisms
EUBACTERIA most abundant of the bacteria
found in soil, water and animal digestive tracts
ARCHAEACTERIA live in extreme conditions (temperature, pH
etc) mostly anaerobic (unable to live in the
presence of oxygen)
EUKARYOTES algae: live in soil and water, contains chlorophyll
for photosynthesis, has a cell wall
fungi: yeast, molds. Lack chlorophyll and
obtains energy from organic compounds in soil
and water, has a cell wall
protozoa: colorless, lacks a cell wall, ingests
other organisms or organic particles
The General
Characteristics of
Microorganism
• Cellular Organization
- “Prokaryotic” vs “eukaryotics” cells
 Prokaryotic (bacterial and archaeal) cells are about 10 times smaller than
eukaryotic cells
 Prokaryotic cells lack many cell structures such as double membrane-bound
organelles
 All prokaryotes are microorganism, but only some eukaryotes are
Major Differences between
prokaryotic and eukaryotic
micro-organisms
Cell Types

Comparative cellular structures of microbes

The Microbes
viruses protozoa

bacteria

bacteriophage

algae
cyanobacteria
spirochaetes

fungi
Size of Microbes

Microbes vary in size ranging from

10 nm (nanometers) to 100 mu
(micrometers) to the macroscopic.

Viruses in nm = 10-9 m (meter)

Bacteria in um = 10-6 m

Helminths in mm = 10-3 m
Diversity of Microbes
 Bacteria-single celled prokaryotes
 Protozoa-eukaryotic, single celled, colonial, many
ways of nutrition
 Fungi- absorb nutrients, single celled filamentous
 Viruses-acellular entities
 Others- worms, insects
 Bacteria & Archaea
◦ Unicellular and lack nuclei
◦ Much smaller than eukaryotes
◦ Found everywhere there is sufficient moisture;
some found in extreme environments
◦ Reproduce asexually
◦ Two kinds
◦ Bacteria – cell walls contain peptidoglycan;
some lack cell walls; most do not cause
disease and some are beneficial
◦ Archaea – cell walls composed of polymers
other than peptidoglycan
Archaea
Prokaryotes
Lack peptidoglycan
Live in extreme environments
(extremophiles)
Include:
 Methanogens
 Extreme halophiles
 Extreme thermophiles
Fungi
◦ Eukaryotic (have membrane-bound
nucleus)
◦ Obtain food from other organisms
◦ Possess cell walls
◦ Composed of
◦ Molds – multicellular; have
hyphae; reproduce by sexual and
asexual spores
◦ Yeasts – unicellular; reproduce
asexually by budding; some
produce sexual spores
 Protozoa
◦ Single-celled eukaryotes
◦ Similar to animals in nutrient needs and
cellular structure
◦ Live freely in water; some live in animal hosts
◦ Asexual (most) and sexual reproduction
◦ Most are capable of locomotion by
◦ Pseudopodia – cell extensions that flow in
direction of travel
◦ Cilia – numerous, short, hairlike protrusions
that propel organisms through environment
◦ Flagella – extensions of a cell that are fewer,
longer, and more whiplike than cilia
 Algae

◦ Unicellular or multicellular
◦ Photosynthetic
◦ Simple reproductive structures QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
◦ Categorized on the basis of
pigmentation, storage products,
and composition of cell wall
Helminths
Eukaryotes
Multicellular animals
Parasitic flatworms and
roundworms called
helminths
Microscopic stages in life
cycles
Viruses
 Not independently living cellular organisms

 Much simpler than cells- basically a small

amount of DNA or RNA wrapped in protein
and sometimes by a lipid membrane

 Individuals are called a virus particle or

virion

 Depend on the infected cell’s machinery to

multiply and disperse