Eukarya

Phylogenetic overview
diplomonads and microsporidia are probably the most ancient of the eukaryotes. They are obligate parasites.
Next are the flagellates, slime molds, brown algae, diatoms and oomycetes and then a evolutionary radiation encompassing the ciliates, dinoflagellates, fungi, plants, red algae, green algae and animals.

Algae -
diverse group of organisms that contain chlorophyll and carry out oxygenic photosynthesis. These do not include cyanobacteria.
May be either unicellular or colonial or filamentous with or without branching. Most are green though some are red or brown due to other pigments masking the green color due to chlorophylls.
Pigments - All contain chlorophyll a and other types of chlorophyll molecules. These differences are important characteristics in the taxonomic status of different algaes.
Characteristics - are carry out oxygenic photosynthesis using water as the source of electrons. Some use H2 as a source of electrons and do not evolve oxygen.
Most are obligate phototrophs though some can grow as chemoorganotrophs in the dark. These may use acetate as a sole carbon and energy source. Some can grow photoheterotrophically assimilating simple carbon sources in the presence of light.

Cell walls -
frequently composed of cellulose fibrils - What is cellulose? which is modified by the addition of other polysaccharides such as pectin, xylans, alginic acids or fucinic acids. Sometimes chitin is present. What is chitin? a polymer of N-acetyl-glucosamine. In euglenoids the cell wall is absent, in diatoms the cell wall is composed of silica with proteins and polysaccharides.

Motility and ecology of algae
Some are flagellated and motile. single or two or four polar flagellas are common. In some cases the vegetative state is non-motile and the gametes are motile.
Algaes are found in both fresh and marine bodies, soils, fish tanks and pools.

Fungi
nutrition via absorption from the environment - therefore they are what? heterotrophs. Do not have chlorophyll but contain a nucleus, mitochondria, vacuoles typical of eukaryotic cells.

Habitats are diverse and include fresh water and terrestrial habitats. They are the decomposers and play an important role in the carbon cycle. Some are parasitic on animals and plants and can cause major damage to both.

Characterisitics contain rigid cell wall composed primarily of chitin. All fungi are chemoorganotrophs. They are phylogenetically homogeneous but morphologically and sexually they are very different - which is the basis of their taxonomy.
Ascomycetes form ascospores
Basidiomycetes form basidiospores
Zygomycetes form zygospores
Oomycetes form oospores
Deuteromycetes form no spores.
Major groups of fungi
Molds, yeasts and mushrooms

Molds - filamentous, called hyphae, fungi found everywhere including molding bread, cheese and fruits. Hyphae form mycelium which are visible. Remember the hyphae is composed of cells end on to make the filament. Aerial branches are where the spores called conidia are formed. These are asexual spores and frequently pigmented. There function is to disperse the fungus to new habitats. These are frequently responsible for allergies.

Sexual spores occur in some molds. Spores formed in sacs are referred to as ascospores. Spores formed at the ends of club-shaped structures are called basidiospores. These spores are resistant to drying, freezing, heating and some chemical agents.

Ecological niche - degradation of wood, paper, cloth and other products derived from natural products. Basidiomycetes are especially good at this. They can utilize cellulose or lignin as a source of carbon and energy. The basidiomycete wood-rotting fungi are responsible for most of the lignin degradation. Brown rot degrades cellulose and leaves lignin alone and white rot degrades both cellulose and lignin. The degradation of wood by the white rot fungi is ecologically important in woody habitats.

Yeasts - round, oval, or cylindrical, unicellular, fungi and most are Ascomycetes. They are much larger than bacteria. Reproduce by budding where the offspring is an outgrowth that enlarges before it separates. Usually not filamentous though some pathogenic yeasts have a filamentous phase that is essential for pathogenecity, e.g., Candida albicans which causes vaginal infections, thrush, lung infections. Sexual reproduction occurs in some yeasts - where two cells fuse to form a zygote where the ascospores are formed.

Ecology - they flourish where simple sugars are present, e.g., fruits, flowers, and bark of trees. Some are symbionts with insects and some are pathogens of animals including humans.

Commercial - bakers and brewers yeast - Saccharomyces are very important to the food industry. They are genetically modified through selection for improved activities.

Mushrooms - filamentous fungi that typically form an aerial fruiting body - the mushroom that you see. Many are mycorrhizae - that are symbiotic with plant roots and others live off of dead organic matter in soils or trees.

Sexual spores called basidiospores are produced. These are dispersed and germinate to initiate mycelial growth on suitable surfaces. The mycelium is haploid (What do we mean by haploid?) and only forms a fruiting body when two haploid mycelia fuse to form two cells that are dikaryotic - with two nuclei. These grow together to form a button which is the start of the mushroom. Under appropriate conditions, e.g., a rainshower, the buttons grow and emerge as mushrooms.

Commercial - edible mushrooms are grown commercially. Others are found in the wild and picked and sold.

Slime molds
- non-photosynthetic microorganisms that are phenotypically similar to fungi and protozoa but phylogenetically distinct. Divided into cellular, composed of single amebalike cells and acellular slime molds are naked masses of protoplasmof indefinite sizes and shapes called plasmodia.
Live on decaying plant material. Their food consists primarily of bacteria which they engulf by phagocytosis.

Cellular slime molds - interesting life cycle in which vegetative cells aggregate, migrate as a cell mass, and form a fruiting body composed of stalk cells and spores.

Dictyostelium discoideum - is an example of a slime mold. As the cells become starved, they aggregate and form a pseudoplasmodium, a structure in which the cells lose their identity but do not fuse.
A chemical signal including cyclic AMP attracts cells of D. discoideum which leads to the attraction of additional cells to form a slug. A fruiting body forms when the slug no longer moves. The cells of the forward end of the slug become the stalk cells and the cells of the posterior end become the spores. This is an asexual process of reproduction. There is a sexual process as well.

Acellular slime molds - a mass of protoplasm much like a giant ameba. Motile by ameboid motion due to cytoplasmic streaming. They are often brightly colored in nature. They are diploid and produce sporangia and sclerotia. Sporangia are part of their sexual lifecycle where an aerial structure is made and haploid spores develop. These germinate under appropriate conditions, conjugate, and produce diploid ameboid cell which divide to produce new diploid plasmodium.

Sclerotia are resting structures that are resistant to environmental stresses and allow the organism to survive these stresses before recovering to form a new plasmodium.

Protozoa -
unicellular eukaryotes that lack a cell wall. Nutrition by ingestion or phagocytosis of other microorganisms or of organic particles or pinocytosis of dissolved organic compounds- they are heterotrophs. What is pinocytosis? Found in fresh and marine habitats, many are parasitic to animals, and many are found in soils. Many are motile which is an important taxonomic characteristic. The group of Mastigophora are flagellated, Sarcodina are amebas, Ciliophora are ciliates, and Sporozoa are generally non motile. All of them have genera that are parasitic to man and causing such diseases as amebic dysentery, malaria, or African sleeping sickness.

Mastigophora
Flagellated, many are free living and many parasitic. Trypanosomes are very important pathogen. Trypanosoma gambiense causes African sleeping sickness which is chronic and usually fatal. Parasite lives in the blood and is well equipped with a flagella that allows it to move in blood which is rather viscous.

Sarcodina
Includes Amoeba which are naked in the vegetative stage and foraminifera, which form carbonate shells in the vegetative state. Many of the sarcodina are parasitic for example Entamoeba histolytica which may cause no symptoms in some people or produce ulcers which leads to diarrheal condition called amebic dysentery. Foraminiferas are exclusively marine organisms that produce carbonate shells called tests. Their shells are relatively resistant to decay and become fossilized easily. They compose the White Cliffs of Dover, England and have an excellent fossil record.

Ciliphora
Ciliates, contain two types of nuclei - a micronucleus which is concerned with inheritance and sexual reproduction and a macronucleus which is concerned with making mRNA for various aspects of growth and development. Best studied is the genus Paramecium. Most ciliates ingest their food through a mouth like opening, down the gullet to a vacuole for digestion.

Micronucleus is diploid but the macronucleus is polyploid and contains from 40 to 500 times as much DNA as the micronucleus. Micronucleus plays no role the vegetative state since it may be deleted and the cell still grows. Remove the macronucleus and the cell dies. Many ciliates harbor bacterial symbionts that may play a role in the nutrition of the ciliate. There are obligate anaerobic ciliates in the forestomach of ruminant animals and their role is thought to be in the fermentative and digestive processes that occur here.

Sporozoa
All are parasitic, lack motility, and absorb soluble nutrients through the outer wall. They do not form spores!!! but instead form sporozoites which are involved in their transmission to a new host. Usually have alternative hosts during specific stages of their life. Important sporozoa causes malaria.