1.
Microorganism &
Environmental
Microbiology
Program Studi Teknik Lingkungan
Semester Ganjil 2021/2022
Learning Plan
Pekan 1. Mikroorganisme dan mikrobiologi lingkungan
Pekan 2-3. Jenis dan karakteristik sel mikroorganisme
Pekan 4. Teknik pengambilan sampel di berbagai media, mikroskopi, metode aseptik
Pekan 5-6. Metabolisme sel
Pekan 7. Blueprint of life
Pekan 9. Siklus biogeokimia
Pekan 10. Lingkungan dan ekologi mikroorganisme
Pekan 11-12. Pertumbuhan mikroorganisme
Pekan 13. Mikroorganisme indikator
Pekan 14. Microbial source tracking
Pekan 15. Identifikasi pendekatan-pendekatan yang dipakai untuk menyelesaikan
masalah di bidang teknik lingkungan
Sub-CPMK 1
Capaian
Mahasiswa mampu menjelaskan peran
Pembelajaran
mikroorganisme di bidang teknik
Sesi lingkungan [C2, A3]
Pepper, I. L., Gerba, C. P., & Gentry, T. J. (2014).
Environmental Microbiology.
Elsevier Science.
References Madigan, M. T., Martinko, J. M., Bender, K. S.,
Buckley, D. H., & Stahl, D. A.
(2015). Brock Biology of
Microorganisms. 14th Edition.
Pearson Education.
Topics
1. Microbiology
2. Environmental Microbiology
3. Microorganisms
4. Structure and Activities of Microbial Cells
5. Evolution and Diversity of Microbial Cell
6. Microorganisms and Their Environment
7. The Impact of Microorganisms on Humans
1. Microbiology
o Study about microorganisms.
o A microorganism, or microbe, is
a microscopic organism,
which may exist in its single-
celled form or a colony of
cells.
http://ofbacteriaandmen.blogspot.com/2013/02/bacteria-in-wastewater-treatment-plant.html, 5/10/21
1. Microbiology
o Microbiology revolves around two themes:
1. Understanding basic life processes
❑ Microbes are excellent models for understanding cellular
processes in unicellular and multicellular organisms
2. Applying that knowledge to the benefit of humans
❑ Microbes play important roles in medicine, agriculture, and
industry
1. Microbiology
o The importance of microorganisms
• Oldest form of life
• Largest mass of living material on Earth
• Carry out major processes for biogeochemical cycles
• Can live in places unsuitable for other organisms
• Other life forms require microbes to survive
1. Microbiology
o Microorganisms occur everywhere on Earth.
o An adult human body contains 10 times as many microbial cells as
mammalian cells, consisting of approximately 1.25 kg of microbial biomass.
o The beginning of environmental microbiology starts with the discovery of:
▪ environmental pathogenic microorganisms that invaded human
body.
▪ waterborne human pathogens.
o Louis Pasteur and Robert Koch developed the Germ Theory of Disease in
the 1870s.
o This became the initial focus of environmental microbiology.
2. Environmental Microbiology
o A study of microbes within all habitats (lithosphere, hydrosphere, and
atmosphere), and their beneficial and detrimental impacts on human
health and welfare.
o Beneficial in term of environmental engineering is associated with
environmental quality improvement.
o Used for the biotreatment of water, wastewater, solid wastes, soil, and gas.
o Environmental microbiology is related to many other disciplines.
The efficacy of bioremediation was
demonstrated in 1989, when the Exxon
Valdez oil tanker spilled approximately
11 million gallons of crude oil into Prince
William Sound.
Optimization of bioremediation was a
2. Environmental major factor in cleaning up and restoring
Prince William Sound.
Microbiology
Bioremediation has also been shown to
be critically important in cleaning up the
more recent 2010 Gulf of Mexico oil
spill.
12
2. Environmental Microbiology
o Why Microbes Are Used in Environmental Engineering?
1. Microorganisms have the highest cell surface to cell volume ratio (Table
1.2).
2. Microorganisms can perform diverse biochemical reactions, so they are
useful in biotransformation and the degradation of environmental
pollutants (Table 1.3).
The role of
How to apply
microorganisms Microorganism
those
in environmental characteristics
characteristics
engineering field
Remember This?
https://medium.com/english-fluente/5-dicas-para-come%C3%A7ar-a-pensar-em-ingl%C3%AAs-38960eeb8bbd, 21/8/19
The role of
How to apply
microorganisms Microorganism
those
in environmental characteristics
characteristics
engineering field
3. Microorganisms
o Microorganisms include all unicellular organisms and so are extremely
diverse.
o They live in almost every habitat: from the poles to the equator, deserts, geysers,
rocks, and the deep sea.
o Some are adapted to extremes such as very hot or very cold conditions, others to
high pressure, and a few, such as Deinococcus radiodurans, to high radiation
environments.
o Microorganisms also make up the microbiota found in and on all multicellular
organisms.
✓ There is evidence that 3.45-billion-year-old Australian rocks once contained microorganisms,
the earliest direct evidence of life on Earth.
4. Structure and Activities of Microbial Cells
o The cell
• A dynamic entity that forms the fundamental unit of life (Figure 1.2)
o Elements of microbial structure
• All cells have the following in common:
❑ Cytoplasmic (cell) membrane
Barrier that separates the inside of the cell from the outside environment
❑ Cytoplasm
Aqueous mixture of macromolecules, ions, and ribosome
❑ Ribosomes
Protein-synthesizing structures
❑ Cell wall
Present in most microbes; confers structural strength
Cell wall
Cytoplasmic
membrane
Nucleoid
Cytoplasm
Bacteria
Plasmid
Ribosomes
Prokaryote
Archaea
Cell wall
Cytoplasmic
membrane
Mitochondrion
Nuclear
membrane
Nucleus
Ribosomes
Endoplasmic
reticulum
Cytoplasm
Golgi
complex
Eukarya
Eukaryote
Figure 1.2
4. Structure and Activities of Microbial Cells
o Prokaryotic versus eukaryotic cells
• Prokaryotes (Figure 1.2a)
❑ No membrane-enclosed organelles, no nucleus
❑ Generally smaller than eukaryotic cells
• Eukaryotes (Figure 1.2b)
❑ DNA enclosed in a membrane-bound nucleus
❑ Cells are generally larger and more complex
❑ Contain organelles
4. Structure and Activities of Microbial Cells
o Genes, genomes, nucleus, and nucleoid
• Genome
❑ A cell's full complement of genes
• Eukaryotic DNA is linear and found within the nucleus
❑ Associated with proteins that help in folding of the DNA
❑ Usually more than one chromosome
❑ Typically, two copies of each chromosome
❑ During cell division, nucleus divides by mitosis
❑ During sexual reproduction, the genome is halved by meiosis
4. Structure and Activities of Microbial Cells
o Genes, genomes, nucleus, and nucleoid
• Prokaryotic cells generally have a single, circular DNA molecule called a
chromosome
❑ DNA aggregates to form the nucleoid region (Figure 1.2a)
❑ Prokaryotes also may have small amounts of extrachromosomal DNA called
plasmids that confer special properties (e.g., antibiotic resistance)
4. Structure and Activities of Microbial Cells
o Genes, genomes, nucleus, and nucleoid
• Escherichia coli genome
❑ 4.64 million base pairs
❑ 4,300 genes
• Human cell
❑ 1,000✕ more DNA per cell than E. coli
❑ 7✕ more genes than E. coli
4. Structure and Activities of Microbial Cells
o Characteristics of living cells (Figure 1.3)
• Metabolism: chemical transformation of nutrients
• Reproduction: generation of two cells from one
• Differentiation: synthesis of new substances or structures that modify the cell
(only in some microbes)
• Communication: generation of, and response to, chemical signals (only in
some microbes)
• Movement: via self-propulsion, many forms in microbes
• Evolution: genetic changes in cells that are transferred to offspring
Properties of all cells: Properties of some cells:
Metabolism Differentiation
Cells take up nutrients, Some cells can form new cell
transform them, and expel structures such as a spore.
wastes.
1. Genetic (replication,
transcription, translation)
2. Catalytic (energy, Spore
biosyntheses)
Communication
Cell
Cells interact with each other
Environment by ehemical messengers.
Growth
Nutrients from the
environment are converted
into new cell materials to Genetic exchange
form new cells.
Cells can exchange genes by
several mechanisms.
DNA
Evolution
Cells evolve to display new
Donor cell Recipient cell
properties. Phylogenetic
trees capture evolutionary Motility
relationships.
Some cells are capable of
Distinct self-propulsion.
species
Flagellum
Ancestral Distinct
cell species
4. Structure and Activities of Microbial Cells
o Metabolism and genetics
1. Cells carry out chemical reactions
❑ Enzymes: protein catalysts of the cell that accelerate chemical reactions
❑ Cells store and process information that is eventually passed on to offspring
during reproduction through DNA (deoxyribonucleic acid) and evolution
❑ Transcription: DNA produces RNA
❑ Translation: RNA makes protein
4. Structure and Activities of Microbial Cells
o Growth
• The link between
cells as machines and
cells as coding
devices
Binary fission in a prokaryote
https://en.wikipedia.org/wiki/Fission_(biology), 5/10/21
5. Evolution and Diversity of Microbial Cells
o The first cells
• First self-replicating entities may not have been cells
• Last universal common ancestor (LUCA): common ancestral cell from
which all cells descended
5. Evolution and Diversity of Microbial Cells
o Life on Earth through the ages (Figure 1.4)
• Earth is 4.6 billion years old
• First cells appeared between 3.8 and 3.9 billion years ago
• The atmosphere was anoxic until ~2 billion years ago
❑ Metabolisms were exclusively anaerobic until evolution of oxygen-producing
phototrophs
• Life was exclusively microbial until ~1 billion years ago
Mammals Humans
Vascular
plants
Shelly Origin of Earth
invertebrates (4.6 bya)
Present
~20% O2
1 Origin of
bya 4
bya cellular life
O2
Anoxygenic
Algal phototrophic
diversity bacteria
2 3 Anoxic
bya bya Earth
Earth
Modern is slowly
eukaryotes oxygenated Origin of
cyanobacteria
Bacteria
LUCA
Archaea
Eukarya
4 3 2 1 0
bya
billion years ago
Figure 1.4
5. Evolution and Diversity of Microbial Cells
o Evolution
• The process of change over time that results in new varieties and species of
organisms
o Phylogeny
• Evolutionary relationships between organisms
• Relationships can be deduced by comparing genetic information in the different
specimens (Figure 1.6a)
• Ribosomal RNA (rRNA) is excellent for determining phylogeny
• Relationships visualized on a phylogenetic tree
DNA
Gene encoding 3. Sequence DNA. Aligned rRNaA
ribosomal RNA gene sequences
3
A G T GGG T A G 1
Cells A T T CCG TA G 2 1
1. Isolate DNA 2. Make copies 4. Analyze A G C GGT T A G 3 5. Generate
from each of rRNA gene sequence. phylogenetic
organism. by PCR. A G C T A A G tree. 2
Figure 1.6a
5. Evolution and Diversity of Microbial Cells
o Comparative rRNA sequencing has defined three distinct lineages of
cells called domains:
• Bacteria (prokaryotic)
• Archaea (prokaryotic)
• Eukarya (eukaryotic)
o Archaea and Bacteria are NOT closely related (Figure 1.6b)
o Archaea are more closely related to Eukarya than Bacteria (Figure 1.6b)
5. Evolution and Diversity of Microbial Cells
o Eukaryotic microorganisms were the ancestors of multicellular organisms
(Figure 1.6b)
o From the last universal common ancestor (LUCA), evolution proceeded to
form two domains (Figure 1.6b)
• Bacteria
• Archaea
o Archaea later diverged to form two domains (Figure 1.6b)
• Archaea
• Eukarya
BACTERIA ARCHAEA EUKARYA
Macroorganisms
Animals
Entamoebae Slime
Green nonsulfur molds
bacteria Euryarchaeota
Fungi
Methanosarcina
Mitochondrion Methano- Plants
Extreme
Gram- Crenarchaeota bacterium
halophiles
Proteobacteria positive Thermoproteus Ciliates
bacteria
Chloroplast Pyrodictium Thermoplasma
Cyanobacteria Thermococcus
Flagellates
Nitrosopumilus Pyrolobus
Green sulfur Methanopyrus
Trichomonads
bacteria
Thermotoga
Thermodesulfobacterium Microsporidia
Aquifex Diplomonads
Figure 1.6b
6. Microorganisms and Their Environment
o Microorganisms exist in nature in populations of interacting assemblages
called microbial communities (Figure 1.7)
o The environment in which a microbial population lives is its habitat
o Ecosystem refers to all living organisms plus physical and chemical
constituents of their environment
o Microbial ecology is the study of microbes in their natural environment
Figure 1.7
6. Microorganisms and Their Environments
o The diversity in microbial cells is the product of almost 4 billion years of
evolution
o Microorganisms differ in size, shape, motility, physiology, pathogenicity,
etc.
o Microorganisms have exploited every conceivable means of obtaining
energy from the environment
6. Microorganisms and Their Environments
o Diversity and abundances of microbes are controlled by resources
(nutrients) and environmental conditions (e.g., temp, pH, O2)
o The activities of microbial communities can affect the chemical and
physical properties of their habitats
6. Microorganisms and Their Environments
o Microbes also interact with their physical and chemical environment
• Ecosystems are greatly influenced (if not controlled)
by microbial activities
• Microorganisms change the chemical and physical properties of their
habitats through their activities
❑ For example, removal of nutrients from the environment and the excretion of
waste products
6. Microorganisms and Their Environments
o The extent of microbial life
• Microbes are found in almost every environment imaginable
❑ Extremophiles are Bacteria and Archaea that can grow in extremely harsh
environments
▪ Very hot or very cold
▪ Very acidic or very caustic
▪ Very salty or very osmotically stressing
▪ Very high pressure
6. Microorganisms and Their Environments
o The extent of microbial life
• Global estimate is 5 ✕ 1030 cells
❑ Most microbial cells are found in oceanic and terrestrial subsurfaces
• Microbial biomass is significant, and cells are key reservoirs of essential
nutrients (e.g., C, P, N)
7. The Impact of Microorganisms on Humans
o Microorganisms can be both beneficial and harmful to
humans
o Emphasis is typically on harmful microorganisms
(infectious disease agents, or pathogens)
o Many more microorganisms are beneficial than are
harmful
o Microorganisms as disease agents
• Control of infectious disease during last century
(Figure 1.8)
Figure 1.8
7. The Impact of Microorganisms on Humans
o Microorganisms and agriculture
• Many aspects of agriculture depend on microbial activities (Figure 1.9)
❑ Positive impacts
▪ Nitrogen-fixing bacteria
▪ Cellulose-degrading microbes in the rumen
▪ Regeneration of nutrients in soil and water
❑ Negative impacts
▪ Diseases in plants and animals
Soybean
plant
Rumen
Grass Cellulose Glucose Microbial fermentation
Fatty acids CO2 + CH4
(Nutrition for animal) (Waste products)
Figure 1.9
7. The Impact of Microorganisms on Humans
o Microorganisms and the human gastrointestinal (GI) tract
• High numbers of microorganisms occur in colon and oral cavity (Figure
1.10)
❑ Positive impacts
▪ Synthesize vitamins and other nutrients
▪ Compete with pathogens for space and resources
Stomach
(pH 2, 104
cells/g)
Small intestine
(pH 4–5, up to
108 cells/g)
Large intestine
(pH 7, about
1011 cells/g)
Figure 1.10
7. The Impact of Microorganisms on Humans
o Microorganisms and food
• Negative impacts
❑ Microorganisms can cause food spoilage; for many foods, methods of
preservation are needed
• Positive impacts (Figure 1.11)
❑ Microbial transformations (typically fermentations) yield
▪ Dairy products (e.g., cheeses, yogurt, buttermilk)
▪ Other food products (e.g., sauerkraut, pickles, leavened breads, beer)
Propionic acid + Acetic
acid + CO2
2 Lactic acid
GLUCOSE
2 Ethanol + 2 CO2
2 Acetic acid
Fermentations Fermented foods
Figure 1.11
7. The Impact of Microorganisms on Humans
o Microorganisms, energy, and the environment (Figure 1.12)
• The role of microbes in production of biofuels
❑ For example, methane, ethanol, hydrogen
• The role of microbes in cleaning up pollutants (bioremediation)
Figure 1.12
That’s All for Now
