PEOPLE AND THE EARTH’S ECOSYSTEM
Chapter 3 - BIOGEOCHEMICAL
BIOGEOCHEMICAL
- “bio”, meaning biosphere, “geo” meaning
the geological components and “chemical”
meaning the element that move through a
form of atom
.
- Matter can neither be created nor
destroyed, it is recycled in the earth’s system
in various forms.
- Major elements:
Carbon, hydrogen, nitrogen, oxygen,
phosphorous, sulfur.
BIOGEOCHEMICAL CYCLES
 Gaseous cycle – carbon, oxygen,
nitrogen, and water cycle.
 Sedimentary cycle – includes
sulfur, phosphorous, rock style, etc.
WATER CYCLE
Water cycle – water is the most important
chemical of life for all living organisms on
earth. 93% of water is solid state mainly
comprising the ice caps and glaciers of polar
region.
CARBON CYCLE
Carbon cycle – carbon is one of the most
PEOPLE AND THE EARTH’S ECOSYSTEM
important elements sustain life on earth.
Carbon dioxide Chapter 4 – POPULATION
and methane gases AND COMMUNITIES
(compounds of carbon) in the earth’s
atmosphere has a substantial effect on earth’s
heat balance. It absorbs infrared and
hence may contribute to global warming
and climate change.
NITROGEN CYCLE
Nitrogen cycle – is by far the most
important nutrient cycle for plants life.
Processes of the nitrogen cycle.
Nitrogen gas - is the most abundant element
in the atmosphere and all the nitrogen in the
atmosphere and all the nitrogen found in
terrestrial ecosystems originate from
atmosphere. All organisms need nitrogen, an
important nutrient, to make proteins and
nucleic acids.
OXYGEN CYCLE
Oxygen cycle – the oxygen cycle escribes
the movement of oxygen within and between
its three main reservoirs: the atmosphere, the
biosphere, and the lithosphere.
SEDIMENTARY CYCLE
Sulfur in its natural form is solid and
restricted to the sedimentary cycle in this
form. It is transported by physical processes
like wind, erosion by water, and geological
events like volcanic eruptions. However, in
its compounds such as sulfur, sulfur can be
moved from the ocean to the atmosphere, to
land and then to the ocean through rainfall
and rivers.
Phosphorous is commonly found in water,
soil and sediments. Phosphorous cannot be
found in air in the gaseous state. This is
because phosphorous is usually a liquid at
standard temperatures and pressures.
LEVEL OF ORGANIZATION
SPECIES
 An organism similar to one another
that they can bread and produce
fertile offspring.
POPULATION
  Groups of individuals that belong to COMPETITION
the same species that live in the - Competition doesn’t always involve
same area. the same species, but it is more
COMMUNITIES severe among the same numbers of
 Assemblages of different specie because they have common
populations that live together in a needs.
defined area.
ECOSYSTEM SYMBIOTIC RELATIONSHIP
 The community of organism that
lives in a particular area, along with SYMBIOSIS
their nonliving (abiotic) - It means living together of two or
surroundings. more organisms of different species.
Example: parasitism, mutualism,
FEATURES OF POPULATION commensalism.
PARASITISM
SIZE - One organism benefit while the other
 Pertains to the number of individuals is harmed.
is a population. MUTUALISM
Example: the recorded population of - Both species benefits.
people in the Philippines in July COMMENSALISM
2000 is 72,000,000. - One species benefit while the other
DENSITY unaffected.
 Number of individuals or species
living in a particular area of that COMMUNITY ROLES
population.
Example: 100 cows/hectare. PRODUCERS
DISTRIBUTION - Organism that makes their own
 Describe the spacing of organism energy (food)
relative to each other.

VIEWPIONTS OF COMMUNITY CONSUMERS

- Organisms that can’t make their own
AUTECOLOGY – each organism is a food. Must eat producers or other
member of a community. consumers for energy.
DECOMPOSERS
- Organisms that feed on dead plants
SYNECOLOGY – group or organism in a
and animals.
particular area.

RELATIONSHIP AMONG ORGANISMS

PREDATION
o PREDATOR – consume that
captures and eats other consumers.
o PREY – the organism that is eaten
by a predator.
 MOCROBIOLOGY AND PARASITOLOGY
Chapter 1 - INTRODUCTION
MICROBES IN OUR LIVES
 Living things too small to be seen
with the unaided eye are called
microorganisms.
 Microorganisms are important in
maintaining Earth’s ecological
balance.
 Everyone has microorganisms in and
on the body; these make up the
normal microbiota or human
microbiome. The normal microbiota
is needed to maintain good health.
 Some microorganisms are used to
produce foods and chemicals.
 Some microorganisms cause disease
TYPES OF MICROORGANISM
BACTERIA
o Bacteria are unicellular organisms.
Because they have no nucleus, the
cells are described as prokaryotic.
o Most bacteria have a peptidoglycan
cell wall; they divide by binary
fission, and they may possess
flagella.
o Bacteria can use a wide range of
chemical substances for their
nutrition.
ARCHAEA
o Archaea consist of prokaryotic cells;
they lack peptidoglycan in their cell
walls.
o Archaea include methanogens,
extreme halophiles, and extreme
thermophiles.
HISTORY OF MICROBIOLOGY
FUNGI
o Fungi (mushrooms, molds, and
yeasts) have eukaryotic cells (cells
with a true nucleus). Most fungi are
multicellular.
o Fungi obtain nutrients by absorbing
organic material from their
environment.
PROTOZOA
o Protozoa are unicellular eukaryotes.
o Protozoa obtain nourishment by
absorption or ingestion through
specialized structures.
ALGAE
o Algae are unicellular or multicellular
eukaryotes that obtain nourishment
by photosynthesis.
o Algae produce oxygen and
carbohydrates that are used by other
organisms.
VIRUSES
o Viruses are noncellular entities that
are parasites of cells.
o Viruses consist of a nucleic acid core
(DNA or RNA) surrounded by a
protein coat. An envelope may
surround the coat.
 The principal groups of multicellular
animal parasites are flatworms and
roundworms, collectively called
helminths.
 The microscopic stages in the life
cycle of helminths are identified by
traditional microbiological
procedures.
 All organisms are classified into one
of three domains: Bacteria, Archaea,
and Eukarya. Eukarya includes
protists, fungi, plants, and animals.
THE FIRST OBSERVATIONS
o Hooke’s observations laid the
groundwork for development of the
 cell theory, the concept that all can oxidize the alcohol to acetic
living things are composed of cells. acid.
o Anton van Leeuwenhoek, using a o A heating process called
simple microscope, was the first to pasteurization is used to kill
observe microorganisms (1673). bacteria in some alcoholic beverages
and milk.
THE DEBATE OVER SPONTANEOUS o Agostino Bassi (1835) and Pasteur
GENERATION (1865) showed a causal relationship
o Until the mid-1880s, many people between microorganisms and
believed in spontaneous generation, disease.
the idea that living organisms could o Joseph Lister introduced the use of
arise from nonliving matter. a disinfectant to clean surgical
o Francesco Redi demonstrated that wounds in order to control infections
maggots appear on decaying meat in humans (1860s).
only when flies are able to lay eggs o Robert Koch proved that
on the meat (1668). microorganisms cause disease. He
o John Needham claimed that used a sequence of procedures, now
microorganisms could arise called Koch’s postulates (1876), that
spontaneously from heated nutrient are used today to prove that a
broth (1745). particular microorganism causes a
o Lazzaro Spallanzani repeated particular disease.
Needham’s experiments and o In 1798, Edward Jenner
suggested that Needham’s results demonstrated that inoculation with
were due to microorganisms in the cowpox material provides humans
air entering his broth (1765). with immunity to smallpox.
o Rudolf Virchow introduced the o About 1880, Pasteur discovered that
concept of biogenesis: living cells avirulent bacteria could be used as a
can arise only from preexisting cells vaccine for fowl cholera.
(1858). o Modern vaccines are prepared from
o Louis Pasteur demonstrated that living avirulent microorganisms or
microorganisms are in the air killed pathogens, from isolated
everywhere and offered proof of components of pathogens, and by
biogenesis (1861). recombinant DNA techniques.
o Pasteur’s discoveries led to the
development of aseptic techniques THE SECOND GOLDEN AGE OF
used in laboratory and medical MICROBIOLOGY
procedures to prevent contamination o The Second Golden Age began with
by microorganisms. the discovery of penicillin’s
effectiveness against infections.
THE FIRST GOLDEN AGE OF o Two types of chemotherapeutic
MICROBIOLOGY agents are synthetic drugs
o The science of microbiology (chemically prepared in the
advanced rapidly between 1857 and laboratory) and antibiotics
1914. (substances produced naturally by
o Pasteur found that yeasts ferment bacteria and fungi that inhibit the
sugars to alcohol and that bacteria growth of bacteria).
 o Paul Ehrlich introduced an arsenic-
containing chemical called
salvarsan to treat syphilis (1910).
o Alexander Fleming observed that
the Penicillium fungus inhibited the
growth of a bacterial culture. He
named the active ingredient
penicillin (1928).
o Researchers are tackling the problem
of drug-resistant microbes.
o Bacteriology is the study of bacteria,
mycology is the study of fungi, and
parasitology is the study of parasitic
protozoa and worms.
o The study of AIDS and analysis of
the action of interferons are among
the current research interests in
immunology.
o New techniques in molecular
biology and electron microscopy
have provided tools for advancing
our knowledge of virology.
o The development of recombinant
DNA technology has helped advance
all areas of microbiology.

THE THIRD GOLDEN AGE OF

MICROBIOLOGY
o Microbiologists are using genomics,
the study of all of an organism’s
genes, to study microbiomes in
different environments.
 MOCROBIOLOGY AND PARASITOLOGY
MICROSCOPY
UNIT OF MEASURE
 Microorganisms are measured in
micrometers, μm (10-6 m), and in
nanometers, nm (10-9 m).
MICROSCOPY
 A simple microscope consists of one
lens; a compound microscope has
multiple lenses.
LIGHT MICROSCOPY
o The most common microscope used
in microbiology is the compound
light microscope.
o The total magnification of an object
is calculated by multiplying the
magnification of the objective lens
by the magnification of the ocular
lens.
o The compound light microscope
uses visible light.
o The maximum resolution or
resolving power (the ability to
distinguish two points) of a
compound light microscope is 0.2
μm; maximum magnification is
1500*.
o Specimens are stained to increase
the difference between the refractive
indexes of the specimen and the
medium.
MOCROBIOLOGY AND PARASITOLOGY
o Immersion oil is used with the oil
immersion lens to reduce lightMICROSCOPY
loss
between the slide and the lens.
o Brightfield illumination is used for
stained smears.
o Unstained cells are more MICROSCOPY
productively observed using
darkfield, phase-contrast, or DIC
microscopy.
o The darkfield microscope shows a
light silhouette of an organism
against a dark background. It is most
useful for detecting the presence of
extremely small organisms.
o A phase-contrast microscope brings
direct and reflected or diffracted
light rays together (in phase) to form
an image of the specimen on the
ocular lens. It allows the detailed
observation of living organisms.
o The DIC microscope provides a
colored, three-dimensional image of
living cells.
o In fluorescence microscopy,
specimens are first stained with
fluorochromes and then viewed
through a compound microscope by
using an ultraviolet light source. The
microorganisms appear as bright
objects against a dark background.
o Fluorescence microscopy is used
primarily in a diagnostic procedure
called fluorescent-antibody (FA)
technique, or immunofluorescence.
o In confocal microscopy, a specimen
is stained with a fluorescent dye and
illuminated with short-wavelength
light.
TWO-PHOTON MICROSCOPY
 In TPM, a live specimen is stained
with a fluorescent dye and
illuminated with long-wavelength
light.
SUPER-RESOLUTION LIGHT
 Super-resolution light microscopy
uses two lasers to excite fluorescent
molecules.
 When a computer is used to process
the images, two-dimensional and
 three-dimensional images of cells
can be produced.
SCANNING ACOUSTIC MICROSCOPY
 Scanning acoustic microscopy
(SAM) is based on the interpretation
of sound waves through a specimen.
 It is used to study living cells
attached to surfaces such as biofilms.
ELECTRON MICROSCOPY
 Instead of light, a beam of electrons
is used with an electron microscope.
 Instead of glass lenses,
electromagnets control focus,
illumination, and magnification.
 Thin sections of organisms can be
seen in an electron micrograph
produced using a transmission
electron microscope. Magnification:
10,000–10,000,000*. Resolving
MOCROBIOLOGY AND PARASITOLOGY
power: 10 pm.
 Three-dimensional views of the
surfaces of whole microorganismsMICROSCOPY to the stains.
can be obtained with a scanning
electron microscope. Magnification:
1000–500,000*. Resolution: 10 nm.
SCANNED-PROBE MICROSCOPY
 Scanning tunneling microscopy
(STM) and atomic force microscopy
(AFM) produce three-dimensional
images of the surface of a molecule.
PREPARING SMEARS FOR STAINING
o Staining means coloring a
microorganism with a dye to make
some structures more visible.
o Fixing uses heat or alcohol to kill
and attach microorganisms to a slide.
o A smear is a thin film of material
used for microscopic examination.
o Bacteria are negatively charged, and
the colored positive ion of a basic
dye will stain bacterial cells.
o The colored negative ion of an acidic
dye will stain the background of a
bacterial smear; a negative stain is
produced.
SIMPLE STAINS
o A simple stain is an aqueous or
alcohol solution of a single basic
dye.
o A mordant may be used to improve
bonding between the stain and the
specimen.
DIFFERENTIAL STAINS
o Differential stains, such as the Gram
stain and acid-fast stain, differentiate
bacteria according to their reactions
o The Gram stain procedure uses a
purple stain, iodine as a mordant,
alcohol decolorizer, and a red
counterstain.
o Gram-positive bacteria remain
purple after decolorization; gram-
negative bacteria do not and appear
pink from the counterstain.
o Acid-fast microbes, such as
members of the genera
Mycobacterium and Nocardia, retain
carbolfuchsin after acid-alcohol
PREPARATION OF and
decolorization SPECIMENS
appear red;FOR
non–
LIGHT MICROSCOPY
acid-fast microbes take up the
methylene blue counterstain and
appear blue.
SPECIAL STAINS
o Negative staining is used to make
microbial capsules visible.
o The endospore stain and flagella
stain are special stains that are used
to visualize specific structures in
bacterial cells.