1. science
2. physics
3. optics

THE MICROSCOPE
In this exercise you will learn about the principles of optical microscopy and become familiar with the use of the microscope. Microscopes are delicate and expensive instruments;
they should be handled with utmost care! Before you use the microscope, your instructor
will explain its proper use. Following are rules that will protect the microscope and insure
that you can make maximum use of it. Microscope safety rules are explained more thoroughly in the Biology Department's Lab Safety Rules which you signed at the beginning of
the semester.
TYPES OF MICROSCOPES
There are two different types of microscopes: light and electron. Light microscopes have glass lenses which magnify objects, and use light to illuminate the objects
being examined. You will be using two different kinds of light microscopes in this lab,
the compound microscope and the dissecting
microscope. Electron microscopes use
beams of electrons to examine incredibly
small objects (like the components of an individual cell) that have been specially prepared.
The different microscopes are explained in
more detail below.
The Compound Microscope
Compound microscopes are used to
examine objects in two dimensions. Very
small organisms or cross-sections of organisms are placed on clear glass slides; these
objects are viewed as light passes through
them. The parts of the compound microscope
are reviewed below.
The Dissecting Microscope
Dissecting microscopes are used to
observe material that is either too thick or too
large to be viewed with the compound light
microscope. With these microscopes, you
see the surface of things that reflect the light.
While the magnification and depth of field
Microscope
are smaller in the dissecting scope, the field
of view is much larger. As its name implies,
the dissecting scope is often used to look at
plants as you dissect them, since it allows
for manipulation of material. Since most of
the parts of the dissecting microscope are the
same as the compound microscope, they will
not be reviewed here.
Electron Microscopy
In these microscopes a beam of electrons (in place of light) and circular magnets
(in place of glass lenses) permit the resolution of structures in much finer detail than in
an optical microscope. There are two electron microscopes. The first is a "traditional"
transmission electron microscope (TEM)
in which an electron beam passes through
the specimen. The second is the scanning
electron microscope (SEM) in which a
beam of electrons scans the surface of an
opaque object and produces an image of that
surface. The images are viewed on a cathode tube, or in pictures taken with the microscope. Many of the photographs of cell
structure used in your text were taken with
an electron microscope. FIU hosts the Florida Center for Analytical Electron Microscopy, which has an SEM.
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RULES FOR USE OF THE MICROSCOPE -THE TEN COMMANDMENTS
1. Always carry the microscope in a straight upright position with one hand around the
arm and the other hand under the base. The eyepieces are not attached and will fall out
if the microscope is carried at an angle or upside down.
2. Check out the microscope to make sure all the lenses are clean and the mechanical
parts are in working order. Report any malfunction to the instructor so that it may be
remedied.
3. Keep the microscope clean. When anything is spilled or otherwise gets on the microscope, clean it up immediately.
4. When using the microscope start with the low power lens and work up to the desired
magnification. These microscopes are parfocal, which means that all powers should be
in focus when the turret is rotated.
5. Never move the stage upwards with the coarse adjustment while viewing through the
eyepieces. Get the lens close to the slide while viewing from the side to make sure that
they never touch. Then move the stage downward with the coarse adjustment while
viewing through the lense. This will prevent the possibility of ramming the lens into the
slide, thereby ruining a slide you have just made and, quite possibly, damaging the lens.
6. Moist, living or preserved materials must be observed through a coverslip. This protects the lens as well as tends to make the object under view optically flat. Be sure to
maintain a safe distance between the coverslip and the objective lenses.
7. Clean the lenses with lens paper only. DO NOT CLEAN THE LENSES WITH
HANDKERCHIEFS, FACIAL TISSUES, PAPER TOWELS, ETC.--they will scratch
the lenses. If your lenses are very dirty, obtain some lens cleaning solvent from the instructor.
8. If you cannot obtain clear focus or good lighting, or if your microscope seems not to
be working properly, IMMEDIATELY CALL YOUR INSTRUCTOR. He/she can either assist you or see that the microscope is repaired.
9. Return your scope to the cabinet with light cord wrapped around its base and with the
lowest power objective lens in position.
Microscope
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THE COMPOUND MICROSCOPE
Microscope
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THE PARTS OF A COMPOUND MICROSCOPE
1. The microscope has two magnifying lenses: the eyepiece or ocular lens and the objective
lenses on a turret which revolves above the stage. The eyepiece lenses are usually 10X and
are moveable so that they can be adjusted to the distance between the pupils of each viewer.
The objective lenses (there are four: 4X, 10X, 40X and 100X) rotate on the nosepiece. By
changing the objectives the effective power of magnification is changed. The total magnification observed is the product of the power of magnification of the eyepiece and the objective. Only the 100X objective is used immersed in a drop of special oil (between the lens
and the slide; all others are designed to be used with air between the object and lens surface.
The 100X objective will not be used in this course. The power of magnification is clearly
indicated on each lens along with the numerical aperture of each lens. Depending upon their
design and quality, different objectives have different resolving distances. The latter is the
smallest distance between two points that allows both points to be viewed as separate. This
resolving distance is dependent upon the wavelength of light used as well as the construction
of the lens.
2. Microscopes contain elements designed to project parallel beams of light through the
specimen and into the objective. These include the projection lens which focuses light onto
the condenser lens. The condenser lens focuses light onto the object. To get the condenser
lens in focus, place a slide containing a wax pencil mark on the stage. Focus on it with the
lowest power objective lens and turn the iris diaphragm to the smallest opening. Then focus
the condenser up and down until the edges of the iris diaphragm come into sharp focus without using the objective focusing adjustments. The condenser is now in focus.
3. The focusing knobs move the lens assembly up and down to bring the object in focus.
The coarse adjustment should only be used with the shortest, low power objective lens. The
fine adjustment (smaller knob) brings the object into critical focus. Notice that all objects
are projected upside down in the microscope field. It takes a little practice in using the mechanical stage to move the slide where you want it.
Microscope
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USING THE COMPOUND MICROSCOPE
1.Use both hands to carry the microscope to your seat. Place the microscope on the table in
front of you and position yourself so that you are comfortably seated while looking through
the microscope.
2.If necessary, clean the lenses with lens paper only. Do not use anything else, like KimWipes or your shirt to clean the lenses--this will damage the microscope.
3. Place a slide of the 'letter e' on the stage. If your microscope has a built in light, plug in
the scope and turn the light on. If not, bring a lamp to your table and position it so that the
light shines above the object being viewed.
4. Turn the nosepiece so that you are using the lowest power objective lens. You should always use the lowest power objective when you begin viewing an object. While looking
through the ocular lenses with both eyes, begin to focus on the object by turning the focus
adjustment on the side of the microscope arm. If you see two images of the object or the reflection of your own eye/eyelashes, you probably need to adjust the ocular lenses. These
lenses can be moved together or apart to better match the distance between your eyes.
5. Once the object is in focus, increase the magnification by rotating the nosepiece. Adjust
the focus by using the fine adjustment knob only. Make sure that the objective lens does
not come in contact with the slide.
6. Examine different parts of the object by moving it around the stage. Notice the direction
that the image moves when the object is moved from left to right. Change the light level and
observe differences in the way the image appears.
ADDITIONAL CONCEPTS
1. The field of view is the area visible when you look through the microscope. Knowing the
size of the field of view will enable you to determine the size of the object you are observing. Special rulers are used to determine the field of view and measure objects under the microscope. Accurate measuring can be very important when identifying plants or plant structures.
2.Drawing Objects To Scale: In drawing objects that you have seen with the microscope it
is important to describe how large they actually are. The actual magnification will depend
upon whether you have drawn "little" or "big" (you should draw "big"). The way to estimate
the actual size of the object is by knowing how wide the microscope's field of view is. This
can be estimated by using a scale that has been etched on a microscope slide. Using this
scale we have measured the width of each field for your microscopes:
44X = 4.6 mm, 4600 um
100X = 1.8 mm, 1800 um
440X = 0.46 mm, 460 um
Microscope
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THE PROKARYOTES
Prokaryotes are composed of
organisms with very simple cell structure: no nucleus or organelles. These
cells are usually very small, no more
than 2 microns in diameter. Their mode
of reproduction is almost always asexual, by simple binary fission. The Prokaryotes include the Archaebacteria, the
Eubacteria (or true bacteria) and the
Cyanobacteria (or blue-green algae).
Most of the prokaryotes don’t look very
different from each other, partly because they are so small. Most bacteria
can be split into groups based on their
cell shapes: as rods, spheres, spirals
and filaments.
They also can be distinguished because of differences in their cell walls, most notably as Gram + and Gram – bacteria. They can also be distinguished because of the dramatic
differences in their metabolism.
Prokaryotes are important to us in a variety of ways. Metabolically, bacteria perform
the work, and form the chemical links, that make different ecosystems operate. Many bacteria (but a tiny proportion of the total number of species) cause diseases in plants and animals,
including humans. These diseases include many of the great killers in history, like the
plague. Several sexually transmitted diseases, like syphilis, chlamydia and gonorrhea, are
caused by bacteria. Anthrax, of danger as a biological weapon, is a disease of animals that
can infect humans, but not be transmitted by us. Prokaryotes also perform many economically important tasks. They are used in food processing, and bio-engineered bacteria produce many valuable medicines and other substances.
Identify the bacteria on the plates that you prepared the first week of lab. The bacteria form shiny colonies, whereas fungi usually form fussy colonies. Are there differences in
among the cultures? These indicate different types of bacteria.
Prokaryotes
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SOME IMPORTANT PROKARYOTES
CYANOBACTERIA
These photosynthetic prokaryotes, formerly called blue-green algae, were the first
organisms to fix carbon dioxide and produce oxygen in photosynthesis. They transformed
the early atmosphere from reducing to oxygen-rich. They continue to be important today in
many ecosystems. Cyanobacteria, both filamentous and single to multiple cell organisms,
are an important portion of the periphyton communities in the Everglades.
CYANOBACTERIA
LACTOBACILLUS
These bacteria modify milk in the production of yogurt. Some people also take them
as a dietary supplement to improve their digestion, particularly after having received a dose
of antibiotics. They can easily be observed in yogurt that contains live cultures of this bacterium.
Prokaryotes
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ALGAE, SEAWEEDS, AND SEAGRASSES
THE ALGAE
The algae are organisms with eukaryotic cells (with organelles and a nucleus) that
are surrounded by a cell well. The cells are photosynthetic. Here we examine the major
groups of algae, using examples that you will see in South Florida, either in ponds or on the
coast. These groups vary in their photosynthetic pigments (although all have chlorophyll a),
in their cell walls, their storage of sugars, and other details.
CHRYSOPHYTA (Golden Algae)
These are the diatoms, single-cell photosynthetic organisms of both fresh and marine
waters. They are most closely related to the brown algae. These organisms cover rocks and
trunks, making them slippery. Diatoms have glass (silica) coverings. They divide repeatedly by cell fission, but in each generation the cells become smaller and smaller. Then they
produce gametes, reproduce sexually, and re-establish the original cell size. Their chloroplasts have both chlorophylls a and c. Here some typical diatoms are illustrated, and examples can also be seen in the periphyton exercise.
Algae
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PHAEOPHYTA (Brown Algae)
The brown algae are almost exclusively marine
and are very common in the coastal waters of Florida.
Many are very large in size, as the kelps of the Pacific
coast. Brown algae have walls containing cellulose and
chloroplasts with chlorophylls a and c. They often store
their sugars as laminarin. The most common brown
alga in South Florida is Sargasso (Sargassum sp.),
which is commonly left on our beaches after high tide.
Sargasso is very similar to the related Fucus, which is
common to New England coasts and is depicted in your
botany text. Here is a diagram of Sargasso, showing
the blades and flotation bladders. The life cycle of Fucus, very similar to ours in that the only haploid cells
are the sexual gametes, is almost identical to that of
Sargasso. It is diagrammed on p. 353 of your textbook.
Sargasso
(Sargassum filipendula)
Here are some other brown algae, quite commonly seen on rock reefs and mangrove
areas in south Florida.
Turbinaria
Stypopodium
Ectocarpus
Algae
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RHODOPHYTA (Red Algae)
The red algae are characterized by chlorophyll a and red pigments, called phycobilins, in their chloroplasts. These multicellular algae appear reddish in appearance and are
extremely common in marine waters in south Florida. Their walls contain cellulose and
quite often accumulate calcium carbonate. They store sugars as Floridean starch. Red algae
take on a variety of forms, often as flat blades or as highly branched “trees”. Here are some
examples of red algae often seen in south Florida.
Grateloupia
Dasya
Spyridia
Cryptarachne
Porphyra
Algae
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CHLOROPHYTA (Green Algae)
The green algae are the ancestors of terrestrial plants. They have chloroplasts with
chlorophylls a and b, the same as in land plants. They also have walls of cellulose, and they
store sugars as starch. They vary dramatically in size, from single and motile cells, to filaments, to much larger blades and branched structures. Some accumulate calcium carbonate
in their walls and are quite tough. Others, as Ulva – the sea lettuce, are very fragile. Single
celled and filamentous algae will be common in ponds and periphyton. The larger marine
algae will be encountered in coastal waters throughout south Florida. For examples of the
single-celled and filamentous algae look at the illustrations in the description of periphyton.
Here we give some examples of algae commonly seen in coastal marine waters.
Halimeda
Udotea
Ulva
Codium
Caulerpa
Algae
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PYRROPHYTA (Dinoflagellates)
These single celled algae are commonly known as the dinoflagellates. They are important in food webs in tropical marine waters. These algae are distinguished by their two
flagellae and the plates in their cell walls; also, they generally are motile. The toxic red tides
that occur on the Gulf Coast are blooms of dinoflagellates. Ciguatera, a toxin in some reef
fish, is due to the passage of a product of a dinoflagellate in the food web. Some dinoflagellates are illustrated below.
Algae
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SEA GRASSES
Sea grasses are specialized flowering plants that grow in shallow coastal areas, particularly in the tropics. They are
ecologically important because they provide habitats for fish and crustaceans, particularly during reproduction and early development. Thus, they are nurseries for
many economically important species.
You often see parts of sea grasses along
with various algae, after high tide at an
ocean beach or at locations around Biscayne and Florida Bay. Here we illustrate
two of the most common sea grasses in
South Florida.
Turtle Grass (Thalassia testudinum)
Halodule
Algae
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THE BIOLOGY OF PERIPHYTON
You may have noticed that the ponds in the Miami area are frequently covered with
clumps of light-colored slime, what some might call “pond scum”. It might look pretty disgusting to the average person, but to those of us who study the Everglades, it is very special
stuff. We call it periphyton. It is a community of micro and macro-organisms that lives under the water surface in the Everglades, or floats if it accumulates enough bubbles of oxygen.
Periphyton forms on the skeletons of flowering aquatic plants, particularly the bladderworts
(genus Utricularia). As a community, periphyton consists of a variety of organisms that live
in the matrix of dead organic matter: bacteria, protozoans, green algae, diatoms, rotifers,
insect larvae, and much more. We have added several pages of illustrations of organisms
that you can easily find when you observe preparations with a microscope. This exercise
also helps you learn how to use a microscope.
Periphyton is ecologically important in the Everglades because it photosynthesizes,
taking carbon dioxide from the air and transforming it into organic carbon, that can serve as
an energy source for other organisms. Much of this organic carbon is passed to other organisms, particularly apple snails and small fish, in food webs. The snails and fish are eaten directly by birds, or often by larger fish, that are then eaten by birds and alligators. So periphyton is the stuff on which the Everglades runs. A number of scientists at FIU are studying the effects of adding phosphorus (a key ingredient in the water from the sugar cane farms
to the north) on the function of the wetlands ecosystems. We are finding that even modest
additions of phosphorus cause the periphyton mat to break apart. This alters the Everglades
ecosystem.
Dead material
Alligators
Prawns
Crayfish
Periphyton
Gar
Rotifers
Copepods
Insect Larvae
Bass
Wading
Birds
Shellfish
Periphyton
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EXAMINING PERIPHYTON UNDER THE MICROSCOPE
In this laboratory exercise you will observe and identify organisms in the periphyton
community, taken from an Everglades pond, and supplied to the classroom. This is an enjoyable process, because you may see amazingly bizarre living organisms swimming around
in the water, or non-moving green and photosynthetic algae. Try to match what you see to
the organisms illustrated here. Make a list of the organisms you have seen. If it is unusually
interesting, share the view with your table partners.
EXAMINING MACRO-ORGANISMS
Take a piece of the periphyton mat without squeezing it and place it in a petri dish.
Place the dish on a dissecting microscope and examine the periphyton for macro-organisms.
Use the following diagrams to help you identify what you are observing. If possible, try to
isolate a few of the more interesting organisms by using tweezers.
Clam or Mussel
Leech
Adult Beetle
Mayfly larva
Rotifer
Copepod
Water Mite
Hemiptera
(Water Bug)
Gammarus (Scud)
Periphyton
Midge larva
Stonefly Larva
Snail
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EXAMINING MICRO-ORGANISMS
In order to see micro-organisms present in the periphyton, it needs to be homogenized
(ground up or pureed), diluted with water, and examined under a compound light microscope. This has already been done for you. Place one drop of homogenized periphyton
(“periphyton purée”) on a microscope slide. Gently add a cover slip, by placing one edge
against the slide and allowing it to fall over the tissue. This helps force out the air bubbles
that tend to be trapped under the coverslip. You can remove excess water by twisting an end
of a kleenex (or kimwipe) and placing it on the edge of the coverslip. It will absorb the excess water. Then place the slide on the microscope stage and begin your observations under
low power (10X). Look for a variety of micro-organisms, as illustrated in the following
pages, in the periphyton. You can boost the power by turning the nosepiece to a higher
power objective (watch your instructor demonstrate this). You can estimate the size of the
organism by comparing its length to the diameter of the field at any given magnification. If
you see absolutely nothing, then try preparing another slide of periphyton, then look again.
PROTOZOANS
Euglena
Volvox
Peridinium
GREEN ALGAE
Chlamydomonas
Mougeotia
Oedogonium
Spirogyra
Ulothrix
Bulbochaete
Periphyton
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DIATOMS
Gomphonema
Frustulia
Fragilaria
Navicula
Nitzchia
CYANOBACTERIA
DESMIDS
Nostoc
Desmidium
Oscillatoria
EXPERIMENTING ON PERIPHYTON
Using the techniques you have learned in the lab you could ask some interesting
questions about periphyton, and collect observations consistent or inconsistent with the hypotheses stemming from these questions. Here are some sample questions.
1. Light levels at the top should be much higher than at the bottom of a floating mat of periphyton. Organisms adapted to different light intensities should be found at different
levels in the mat. You could simply sample different levels of the mat and count the organisms you have observed.
2. Organisms adapted to specific light levels may move vertically up and down in the mat
during the day. You could count organisms at different levels and at different times of
the day.
3. Conditions, as water temperature and sunlight, change during the year. Periphyton organisms should change in abundance at different times of the year. Again, you could
count organisms in mats at different times of the year.
Periphyton
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FUNGI AND LICHENS
Traditionally, fungi had been lumped with plants and always studied in courses of
botany. They do have cell walls and often grow in soil or are associated with plants. However, their cell walls typically have quite a different chemical basis than do those of plants,
consisting primarily of chitin (the same compound as in insect exoskeletons) rather than cellulose. Furthermore, fungi are not photosynthetic. They obtain their carbon compounds
from other organisms, or from organic compounds in the soil. The distinctness of the fungi
from both plants and animals has led to their being classified as a separate kingdom among
all organisms, and they are now recognized as being more closely related to animals than to
plants.
The fundamental organization of all fungi is a tube consisting of a series of cells with
one or two nuclei (or sometimes with no cell walls partitioning the tube), which is called a
hypha (or plural, hyphae). They typically grow together as a mycelium, sometimes forming large, complex body like a mushroom, .
The fungi are typically classified into phyla based on the organization of their mycelia and their modes of reproduction. We will observe fungi in four of the more common
phyla. The classification of the fungi is based on the structures that are unique to each phylum and associated with sexual reproduction. However, many fungi do not reproduce sexually and are placed in a separate phylum, the Deuteromycota.
Fungi
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THE ZYGOMYCOTA
These are molding fungi, that primarily attack plants and food products. The most
common of these is the black bread mold, Rhizopus stolonifer. This phylum has a distinct
life cycle, that includes a brief diploid stage, the zygospore. This structure makes the bread
mold look black. This mold also attacks strawberries during their storage.
Look at the mold on the bread that you started the first week of class.
THE ASCOMYCOTA
These are the cup fungi, named for the fruiting structure that is characteristic of this
phylum. The fundamental reproductive structure of this group is a sac of 8 haploid spores,
called the ascus. The spores are called ascospores.
Although “yeasts” can be either ascomycetes or basidiomycetes, Baker’s yeast is an
ascomycete. It is unusual, however, in not producing an ascus, an it most often reproduces
asexually by budding. Look at the baker’s yeast that has been growing in the lab.
Fungi
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THE BASIDIOMYCOTA
These are the “club” fungi, named for the fruiting structure, the basidium, characteristic of this phylum. Each basidium produces four haploid basidiospores. The basidiomycetes vary dramatically in their appearances, from parasitic fungi like rusts to soil and wooddwelling fungi that produce large fruiting bodies, like mushrooms.
The basidiomycetes have fairly complex life cycles. These include (1) phases where
the hyphae contain a single nucleus, (2) then two nuclei per cell, (3) a mechanism for transferring nuclei to different hyphae, (4) then a fusion of nuclei, and (4) finally a meioitic division
that results in the formation of the basidiospores.
Such a life cycle produces the “fruiting” bodies of the most commercially important
mushroom species, Agaricus campestris, as well as the shitake mushroom, Lentinula
edodes. Both of these will be observed in the laboratory. The surfaces of the gills of these
mushrooms are covered with basidia and basidiospores. When these are ripe, tapping the
mushrooms releases the “smoke” of the mature spores. These will germinate to repeat the
life cycle.
Fungi
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THE DEUTEROMYCOTA
These fungi do not reproduce sexually. They also typically have an asexual sporeproducing stage called a conidium. The Conidia produce conidiospores. These are seen
very commonly in mold fungi. These fungi are often seen in moldy bread, Aspergillus in
whites and blacks and Penicillium in grays. You may particularly note the conidiospores of
these fungi, when viewed under a dissecting microscope. Penicillium is a particularly economically important member of this phylum. It and its relatives produce a variety of important antibiotics (penicillin, amoxocillin, etc.). It is the fungus that produces the distinct flavor of the blue cheeses and Camembert, the most famous being the French goat cheese,
Roquefort.
LICHENS
Fungi form important partnerships with other organisms. For example, fungi live on
or in the roots of many plants, as mycorrhizae. These fungi receive energy as carbohydrates
from the roots, and supply nutrients (particularly phosphorus) and water in return. However,
the most visible partnership is that with algae. Such lichenized fungi, or lichens, are found
throughout the world. They are among the toughest organisms, particularly abundant in extreme environments. They are common on high mountains and in the polar regions. Lichens
can be seen in Miami on old trees and palm trunks, and can be distinguished from the large
structures they develop. These include crusts (crustose) that hug the surface where they
grow, such as rocks or palm trunks, thalli (foliose), which are flat, leaf-like sheets, or
branches (fruticose), which stand erect. We mainly have crustose lichens in Miami.
Look at the examples of lichens on display.
Fungi
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