practical lab 1: bacteria, protists, & fungi

What are the 3 main domains?

1. Archaea

2. Bacteria

3. Eukarya

What is the order of organisms

1. Domain

2. Kingdom

3. Phylum

4. Class

5. Order

6. Family

7. Genus

8. Species

what organism(s) are the Domain Archaea and Bacteria consist of?

prokaryotic

how do Archaea and Bacteria differ?

Archara and Bacteria differ in structual, biochemical, and physiological characteristics

• the most obvious though is that Archaea tend to live in extreme environments, like salty lakes and boiling hot springs.

what organisms does domain eukarya consist of?

eukaryotes

• e.g. single-celled organisms, multicellular plants, fungi, and animals

what do prokaryotes consist of?

1. nucleoid region

2. ribosomes

3. plasmids

4. cell walls with peptidoglycan that is covered by a capsule (a sticky layer of polysaccharide)

what is peptidoglycan?

a network of sugar polymers cross linked by short polypeptides

how do bacteria reproduce?

binary fission

what is binary fission?

a form of asexual reproduction where the cell duplicates it's components and divides into two new cells

• in other words the cell pinches into two with the complex movement of chromosomes seen in mitosis

  • newly produced cells become independent, but may remain attached in linear chains or grapelike clusters

what is an example of simple sexual reproduction?

conjugation

• where two cells forma cytoplasmic bridge through which they pass at least a portion of a chromosome

how do most bacteria live?

they live as heterotrophs

• they derive their energy from organic molecules made by other organisms

why are bacteria important?

many of these bacterias are important in the ecosystem as decomposers

• they feed on dead organic matter and release nutrients locked in dead tissues

  • they secrete enzymes that cause the breakdown of organic matter in dead organisms and their wastes.

what does decomposition do?

the process releases key ions, such as nitrates, phosphates, and sulphates, which then become available to other organisms

what are other heterotrophs?

parasites and symbionts

parasites

also known as pathogens

• these cause many of the diseases of plants and animals (including humans)

symbionts

these are heterotrophic bacteria that form partnerships with other organisms in which both benefit.

what are the three basic bacteria shapes?

1. Bacilli

2. Cocci

3. spirilla

what shape are bacilli?

rods

what shape are cocci?

spheres

what shape are spirilla?

spirals or corkscrews

what is a gram stain

a technique used to classify bacteria into two groups based on differences in cell wall composition.

• the two groups are: Gram Positive and gram negative

Gram positive bacteria

these bacteria have walls with a relatively large amount of peptidoglycan

• the protein will trap crystal violet in the cytoplasm

  • therefore the cells will appear violet under the microscope

Gram negative bacteria

these bacteria's walls have less peptidoglycan

• which means the crystal violet is easily rinsed from the cytoplasm

  • these cells will appear either pink or red under the microscope

Cyanobacteria

commonly known as blue-green algae that are prokaryotic

• these are autotrophic, which mean that they derive their energy from photosynthesis or the oxidation of inorganic molecules

  • along with chlorophyll a, they contain phycocyanin (blue) and phycoerythin (red)

    • their chlorophyll is in their thykaloids, extensions of the cell membrane (contains chlorophyll a & beta-carotene)

what specialized cells are produced cyanobacteria?

heterocysts

• these cells take part in nitrogen-fixing

what are the roles of heterocysts?

to incorporate atmospheric nitrogen into a form useful for producing amino acids and other nitrogen containing molecules

what is the gtelatinous sheath in cyanobacteria?

seen in Gloeocapsa sp.

• these are colonies which produce a thick gelatinous sheath

  • provides protection

    • when colonies bundle up together it creates a giant sheet

what else do cyanobacteria produce?

they can also produce spores

• known as akinetes that are resistent to drying

  • these allow cyanobacteria to surviv unfavourable environmental conditions

what 3 kingdoms are in the domain eukarya?

1. Plantae

2. Fungi

3. Animalia

what other kingdoms are included in the domain eukarya?

several kingdoms of protists

• used to be a singular kingdom Protista

  • however upon furtehr research they realized there are multicellular forms which resulted in the split into 7 kingdoms.

are protists eukaryotic or prokaryotic?

eukaryotic

• meaning they consist of membrane-bound nucleus and other membrane bound organelles

how do protists show incredible variety?

some protists resemble animals, others resembles plants, and others still resemble fungi.

what are the general characteristics of protists?

• Most are single-celled organisms however some exist as colonies of cells and others are multicellular

• majority of the species are aquatic, freshwater or marine environments

  • terrestial protists are found in damp soil or leaf litter

• protists are represented by both autotrophic and heterotrophic

• reproduction can vary, but all of them can reproduce asexually while many species can reproduce sexually

what are the 3 large groups of protists?

1. the algae (plant-like protists)

2. the protozoa (animal-like protists)

3. the fungal-like protists

what are the 4 groups of algae (plant-like protists)

1. Dinoflagellates

2. Euglenozoans

3. Diatoms

4. Chlorophytes

dinoflagellates (phylum dinoflagellata)

they are unicelluar protists found in both fresh and marine water

• reproducion is primarily asexual

• the cell wall is composed of plate-like cellulose segments

  • called Theca

• motile dinoflagellates possess two flagella located in perpendicular grooves

  • this allows the algae to move through the water in a spinning motion

what happens when there is a rapid increase in algae?

this can result in an ‘algal bloom' which colours the water red or brown.

• these are referred to ‘red tides’ and can cause the shellfish that eat these algae to accumulate a deadly toxin, making them toxic to eat

Euglenozoans (Phylum Euglenozoa)

these are unicellular flagellates which contain a spiral or crystalline rod inside their flagella

• they inhabit freshwater pools and possess either one or two flagella

• Reproduction is asexual by longitudinal cell division

What is the pellicle in euglenozoans?

a flexible layer of protein bands called a pellicle (found beneath the plasma membrane)

• this allows them to change their body shape as they swim

Euglenozoans are mixtrophs. What does it mean?

this means in sunlight they are autotrophic but when sunlight isn’t available they can become heterotrophic

Diatoms (Phylum Bacillariophyta)

unicellular algae that have a unique glass-like wall perforated by a delicate lacework of holes and grooves.

• diatoms are major component of plankton in oceans and lakes

  • they tend to bloom when ample nutrients are available

• hug accumulations of fossilized diatom walls are major components to sediment known as diatomaceous earth

• they mainly reproduce asexually by mitosis

What is the major characteristic of diatoms?

Their walls

• the wall is made of silica (silicon dioxide) embedded in an organic matrix

  • they consist of two parts that overlap like a shoebox and it's lid

    • this provides effective protection from the crushing jaws of predators

What is it called when diatoms population rapidly increase?

They bloom

• this is when there are ample nutrients available in their environment

What is Diatomaceous earth?

huge accumulations of fossilized diatom walls that are major components to sediment

Chlorophytes (Phylum chlorophyta)

this group is known as the green algae

• they share many common features with true plants such as:

  • they are photosynthetic, contains chlorophylls a & b and carotenoids, primary engery sources are stored as starch and both have cell walls composed of cellulose

  • there are 3 morphological types

1. unicellular

2. colonial

3. filamentous

Unicellular Chlorophytes (green algae)

the simplest algae

• mainly live in aquatic environments that supply nutrients, water, means of dispersal and a degree of support

  • there are a few that live in damp terrestrial habitats

• they consist of a single cell

  • they have an adaptation for floatation (or predation avoidance)

Why do Unicellular cholorphytes need to stay close to the surface of the water?

they need to remain near to the surface to obtain sufficient light for photosynthesis

Why do larger/irregularly shaped unicellular chlorophytes ahve an advantage over small ones?

Larger and/or irregularly shaped cells have the advantage of being avoided by herbivores

• this is because most animals that eat algae are tiny, so larger/irregular shaped algae is harder to ingest

Colonial Chlorophytes

found primarily in the aquatic environment

• Colonial chlorophytes divide to form colonies

  • division in consistent planes = regular colony

  • division in random planes = irregular colony

    • usually made up of, 16, 32, or 48 cells

Why do colonial chlorophytes inhabit shallow water?

to prevent sinking from being a colony

• this ensures they stay in the photosynthetic zone

What do some colonies possess?

flagella for motility

• each cell has 2 flagella

Why does each cell in the colony secrete mucilage?

The mucilage is less dense which aids in the colonies buoyancy

What is different about this colonial chlorophyte (Scenedesmus)

It has spikes, which helps it protect itself from predators

Filamentous Chlorophyta

these algae can vary in how many planes they divide in

• can be one, two, or three planes

What are some cellular differences between filamentous chlorophyta. What does it lead to?

1. thin portions for penetrating the substrate

2. thicker portions lie on the surface

3. erect portions project the mass and bear reproductive structures

• this leads to division of labour among the three areas

  • these are algae that evolved on the substrate or lived on damp soil

Division in one plane

creates a single chain of cells

• can only divide ← or →

division in 2 planes

branching algae

• can divide in two ways, up & down, and, left & right

division in 3 planes

creates large algae

• can divide in 3 ways, up & down, left & right, both ways diagonally

Protozoa (animal-like protists)

these are protists that are heterotrophic and motile

• they are found in freshwater or marine

• they have no special organelles for respiration

  • cell membrane is the site for gas exchange

• reproduction is mainly asexual

What do protozoa, that live in hypotonic environments, have?

one or more contractile vacuoles for osmoregulation

• pumps out excess water

flagellated protozoans

these cause diseases in humans & domestic animals

• in other words they are parasitic protozoans

  • e.g. Trypanosoma - lives in the blood or tissue fluids of the host

    • spread by insect bites (mosquitoes, sand flies, and tsetse flies)

• has an elongate body and a whip-like flagellum used for loco motion

• has an organized mass of dna called a kinetoplast

Pseudopodia-using protozoans

an amoeboid protozoa that posses flowing extensions of the body called pseudopodia (pseudopodium)

• these are temporary projections of the cytoplasm that are used to engulf food and serve as locomotory structures

Ciliated protozoans

these have large numbers of cilia (the most specialized and complicated of the animal-like protists

• the cilia is used for movement and/or feeding

  • they may completely cover the body or may be clustered in rows or tufts

• e.g. Paramecium are free-living, unicellular, freshwater organism

  • reprouces asexually by binay or transverse fission

    • this is a division of an organism into two that are genetically similar

Fungal-like protists

consists of slime molds and water molds

• used to be associated with the kingdom fungi but later found evidence that showed there is little to no relation between them

  • so they are grouped with the protists

Plasmodial Slime molds

these protist stream along the damp forest floor in a mass of plasmodium.

• brightly coloured cytoplasm

  • they are thin streaming masses of protoplam that creep alon in an amoebid fashion

  • resembles a moving mass of slime

    • as they travel that engluf (via phagocytosis) and digest bacteria, yeast cells, fungal spores, and small particles of decayed plant and animal matter

Plasmodium are coenocytic. What does it mean?

Also known as multinucleate

• this means that they have many diploid nuclei that are not divided by cell walls

Oomycetes

these protists are water molds and downy mildews

• they have cell walls that are composed of cellulose or cellulose-like polymers

• they range from unicellular, highly branched, and coenocytic filamentous ones

• they can also reproduce sexually and asexually

Sexual reproduction in Oomycetes

heterogamy (oogamous)

• the egg is large and non-motile, and the sperm is smaller and biflagellate

  • the union results in the production of a thick-walled zygote, called oospore

ASexual reproduction in Oomycetes

by the means of zoospores that have two flagella

The water molds

these molds are principally aquatic, inhabiting freshwaters

• they are decomposers that grow as a cottony mass on dead algae and animals

  • while some are weak parasites

• they have profusely branched multinucleate hyphae

• They can reproduce sexually and asexually

what are hyphae and what do they form?

hyphae are slender filaments of cytoplasm and nuclei

• these forms colonies around decaying organic material in the water

Sexual reproduction in water molds

Sexual reproduction is by the means of gametangial contact

• gametangia are gamete producing structures

Asexual reproduction in water molds

• Asexual reproduction is by the means of sporangia, which produce biflagellate zoospores

Saprolegnia

a kind of water mold

• members of this genus decompose dead fish, inseacts and other organic matter in freshwater

• For sexual reproduction, compatible oogonia and antheridia develop on the same diploid mycelium

  • meiosis occurs within these gametangia

how does saprolegnia reproduce sexually? - oogonium

oogonia (plural_ are enlarged cells where a number of spherical eggs, called oospheres, are produced

• this is found on vegetative hyphae that will be fertlized from the antheridium

how does saprolegnia reproduce sexually? - antheridium

• the antheridia develop from the tips of other filaments of thesame individual and produce numerous male nuclei

  • they will grow toward the oogonia and develop tubular processes called “fertilization tubes"

how do sparolegnia reproduce sexually? - fertilization + oospore

• Male nuclei will travel down the fertilization tubes to the female nuclei and fuse with them

  • this will create the oospore (zygote)

    • this will then develop into hyphae, then into produces into sporangium, beginning the cycle anew

how do saprolegnia reproduce asexually?

Sporangia found on the vegetative hyphae will produce spores

• these spores will exit and grow via mitosis into zoospores

  • The zoospores contain two flagella that will swim elsewhere, where they can grow into vegetative hyphae

the downy mildews (peronosporales)

these molds generally live on land and are parasites of plants.

• these cause big impacts on plants and tremendous losses of crops each year

how do you know if a plant is infected by downy mildews?

• the infected plants are distinguished by their swollen and distorted stems bearing a white layer of powdery (flower-like) sporangiophores (sporangia bearers)

  • these cover the surface of leaves and stems, this gives them a downy appearance

how do downy mildews infect other plants?

The sporangia produced are released and fall onto the ground to be picked up by the emerging seedlings or carried by the wind to land on the leaves of more mature plants

how do downy mildews affect other plants if water is present?

the sporangia germinate and release flagellated zoospores

• the zoospores will swim and enter the plant tissue through open stomata or any break in the cuticle

  • the zoospores will then develop into hyphae, which invades the plants tissue

    • this forms a network called mycelium

how do downy mildews infect other plants inf water is present? - mycelia

the mycelia will feed on living cells by the use of haustoria (means the one who drinks)

• the haustoria will penetrate the living host’s cells, absorb nutrients, and pass the, to the growing hyphae

Kingdom fungi

the kingdom fungi are the decomposers of the biosphere

• they are responsible for recycling essential chemical elements back to the environment

  • they help plant roots absorb water and minerals from the soil,

    • while the ddecomposition releases CO2 into the atmosphere and returns nitrogenous compounds and other minerals to the soil where they can be used again by green plants and eventually animals.

What is the bad side to the Kingdom Fungi?

as decomposers, they often come into direct conflict with human interests

• e.g. a fungus that feeds on wood makes no distinction between a fallen tree in the forest or a railway tie

• in other words fungi are equipped with a powerful arsenal of enzymes that breakdown organic products, fungi are often nuisances and are sometimes highly destructive due to having so many enzymes.

What else do fungi do that isn't decomposing things?

• they reduce the palateable-ness of food and make it essentially unsafe to eat.

• a number of fungi also produce extremely poisonous toxins

• there are many of them that are pathogenic and attack living organisms rather than dead ones.

What is the good side to the Kingdom Fungi?

• Organisms like yeast are useful for their abilities to produce substances such as ethanol and CO2 (which plays a central role in baking)

  • Others are of interest as sources of antibiotics, including penicillin, which was the first antibiotic to be widely used

    • as well as they are food potential sources of proteins

What associations are formed with the Kingdom Fungi?

They are usually between the Kingdom Plantae

• fungi and plants will form associations between the plants roots, which is called mycorrhizae

  • this increases the absorptive surfaces of the plant roots and aid in mineral exchange between the soil and the plant.

Basic Structure of Kingdom Fungi

The basic structure of a fungus is the hypha

• a slender filament of cytoplasm and nuclei enclosed by a cell wall

  • a mass of hyphae make up an individual organism and is collectively called a mycelium

    • this fungi can (seemingly) grow everywhere

• The cell walls of fungi are made of chitin, the same polysaccharide that comprises the exoskeleton of insects and crustaciens

Nutrition of Kingdom Fungi - Saprophytes

Most fungi obtain food from dead organic matter and are called saprophytes

• the hyphae will secrete enzymes for extracellular digestion of the organic substrate, and it will, along with the mycelium, absorb the digested nutrients

  • this is why fungi are called absorptive heterotrophs

Nutrition of Kingdom Fungi - Parasites

Other fungi feed on living organisms and are parasites

• these parasitic fungi have modfied hyphae called haustoria

  • haustoria are thin extensions of the hyphae that penetrate living cells and absorb nutrients

saprophytes

fungi that feed on decomposing dead or decaying organic matter

parasites

fungi that feed on living organisms

• causes bad side effects for the living organism

what do hyphae have in some species? What about other species?

they have cross walls called septa

• this separates cytoplasm and nuclei into cells

Other species have incomplete or no septa (aseptate) and therefore are coenocytic (multinucleate)

Reproduction in Kingdom Fungi

Fungi can reproduce sexually or asexually.

Asexual Reproduction in Kingdom Fungi

This is the common way that fungi reproduce

• This is done by production of haploid vegetative cells called spores in sporangia, and conidia on condiophores.

  • Spores are microscopic and surrounded by a covering well suited for whatever the distribution lies ahead.

• Budding and fragmentation is two other ways that fungi reproduce.

Asexual reproduction in Kingdom fungi - Budding

Budding is mitosis with uneven distribution of cytoplasm that will eventually detaches and matures into a new organism

Asexual reproduction in the Kingdom Fungi - Fragmentation

Fragmentation is the breaking of an organism into one or more pieces, each of which can develop into a new individual

Sexual Reproduction in Kingdom Fungi

Fungi reproduce sexually when hyphae of two genetically different individuals of the same species encounter each other.

• But the timing of vegetative growth, meiosis, and fertilization, is unique

What are the four important features of the sexual cycle on fungi? #1

1. Nuclei of a (monokaryotic) fungal mycelium are haploid during much of the life cycle