GBIO 60 (Systematics) Post-Lab Discussion - Aug 2024 PDF

8/13/2024...

8/13/2024 Timeline of Activities Face-to-face Activity Week Date Activity Parts to be completed during Asynchronous tasks Submission Due face-to-face session 1 None All parts 2 A and B C and D August 12, 2024 GBIO 60 (Systematics) August 5 (Monday) 3 B A and C 5PM 4 C A and B 3 POST-LABORATORY 5 All parts None August 6 (Tuesday) 6 All parts None August 14, 2024 DISCUSSION 5PM August 7 (Wednesday) 7 All parts None August 12 (Monday) 8 All parts None 9 All parts None August 27, 2024 5PM Laboratory Exercises 1-7 4 August 13 (Tuesday) 10 All parts None Post-laboratory discussion (Laboratory Exercises 1-7) August 14 (Wednesday) MIDTERM EXAMINATION 11 None All parts August 19 (Monday) 12 None All parts August 27, 2024 Alcona Mae P. Baltazar, MSc. 5 13 None All parts 5PM August 20 (Tuesday) Laboratory Instructor 14 None All parts August 21 (Wednesday) Holiday August 26 (Monday) Holiday 6 August 27 (Tuesday) Post-laboratory discussion (Laboratory Exercises 8-14) August 28 (Wednesday) FINAL EXAMINATION Even though deadlines are set about a week after the activity, the instructor will still check the completed laboratory tasks on a daily basis. Taxonomic Hierarchy in Biological Classification Superkingdom Kingdom Phylum Class Order Family Genus species Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. pone.0119248 Topic Outline Superkingdoms Laboratory Exercise 1 Superkingdom Prokaryota: Archaea and Bacteria Prokaryota. Eukaryota. Laboratory Exercise 2 The classification of prokaryotes is The superkingdom Eukaryota still unsettled. Woese and Fox includes all organisms with Superkingdom Eukaryota: Protozoa and Chromista treated Archaea and Bacteria as complex cells containing a separate kingdoms, while others Laboratory Exercise 3 grouped them under a single nucleus and membrane- Superkingdom Eukaryota: Fungi kingdom. bound organelles. Resources like LPSN and TOBA Within this superkingdom, the Laboratory Exercise 4 classify them as separate domains primary eukaryotic kingdoms Characterization of the Vegetative Plant Organs but do not address their kingdom are Laboratory Exercise 5 status. Protozoa Characterization of the Reproductive Plant Organs Since there is no official Chromista classification above the class rank, Laboratory Exercise 6 the authors use the Catalogue of Fungi Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Life's classification, treating Bacteria Plantae and Archaea as de facto kingdoms. Animalia Laboratory Exercise 7 Superkingdom Eukaryota, Kingdom Plantae: Angiosperms 1  8/13/2024 Kingdom Archaea Kingdom Archaea Morphology. Archaea, typically less than Habitat. one micron in size, appear as Archaeans can survive in tiny dots even under a high- extreme environments like hot power light microscope, but Hypersaline lake in Namibia where Halobacteria thrive, giving the water a reddish-pink color due to their purple membranes and the antioxidant sulfuric springs, hypersaline electron microscopes can bacterioruberin. Photo by Karsten Kotte, University of Heidelberg. waters, and thermal vents, reveal their diverse shapes. where other life forms can’t. However, new research shows exhibit a wide range of forms, they are also common in the including spherical (coccus), plankton of the open sea, not rod-shaped (bacillus), and just in extreme conditions. even unusual shapes like triangles or squares. Pyrococcus furiosus archaea, coloured scanning electron micrograph (SEM). Laboratory Exercise 1 Laboratory Exercise 1 Photo by: Eye Of Science / Science Photo Library Superkingdom Prokaryota: Archaea and Bacteria Superkingdom Prokaryota: Archaea and Bacteria Kingdom Archaea Kingdom Archaea Morphology. Phylogeny and Classification. Archaeans vary in structure, Initially, it was believed that primitive organisms were prokaryotic, with Woese including having one or more and Fox suggesting a simpler precursor flagella or none. led to Archaebacteria, Eubacteria, and Their tRNAs and ribosomes Eukaryotes. This view was later challenged by show features more like evidence showing that prokaryotic life is eukaryotes than bacteria. rooted in Gram-positive bacteria, with Archaeal cell walls do not Archaea evolving from Bacteria under antibiotic pressure. contain peptidoglycan, More recent research now suggests that cellulose, or chitin but instead Archaea might be the root of the have different chemical phylogenetic tree, but the exact relationships remain unresolved. compositions. These evolving theories reflect the ongoing refinement of our understanding of life's origins. Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Laboratory Exercise 1 Laboratory Exercise 1 Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. Superkingdom Prokaryota: Archaea and Bacteria Superkingdom Prokaryota: Archaea and Bacteria pone.0119248 Kingdom Bacteria Habitat. Bacteria are remarkably widespread, inhabiting environments as varied as mountain peaks, the depths of oceans, the intestines of animals, and even the frozen rocks and ice of Antarctica. Their ability to enter a dormant state for extended periods has greatly facilitated their extensive distribution and enduring presence. Laboratory Exercise 1 Superkingdom Prokaryota: Archaea and Bacteria 2  8/13/2024 Kingdom Bacteria Kingdom Bacteria Morphology. Morphology. Bacteria are diverse and Bacteria lack membrane-bound intricate microorganisms, nuclei and have DNA organized in typically classified into four loops within a nucleoid. Bacteria do not have organelles like primary shapes: spherical Escherichia coli. Photo by: www.cdc.gov mitochondria but may have folded (cocci), rod-shaped (bacilli), membranes to enhance curved (vibrio), and spiral photosynthesis. (spirochete). All but Mollicutes have a cell wall, with Gram-positive bacteria Bacteria typically range in size from retaining a purple stain due to a about 0.2 to 10 micrometers (µm) in thick peptidoglycan layer, while length. Most bacteria fall within the Gram-negative bacteria have a range of 1 to 5 µm. thinner peptidoglycan layer and an outer membrane. Vibrio cholerae. Photo by: news.ucsc.edu Laboratory Exercise 1 Laboratory Exercise 1 Superkingdom Prokaryota: Archaea and Bacteria Superkingdom Prokaryota: Archaea and Bacteria Kingdom Bacteria Phylogeny and Classification. Classifying bacteria by morphology is difficult due to their small size and simple shapes, though some have more complex forms. Traditionally, identification relied on shape, biochemistry, and growth conditions. Advances in molecular biology now use DNA sequence similarities for classification, revolutionizing bacterial systematics. Laboratory Exercise 1 Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. Superkingdom Prokaryota: Archaea and Bacteria pone.0119248 Kingdom Protozoa Kingdom Protozoa Habitat. Morphology. Protozoa are versatile and can The smallest forms range from 1 to 10 μm, while Balantidium coli can reach up to 150 μm. be found in a variety of Protozoa are unicellular eukaryotes, with a membrane- bound nucleus. environments. They thrive in A vesicular nucleus may contain a central body called an endosome or karyosome, which lacks DNA in freshwater and marine parasitic amoebas and trypanosomes. Protozoan organelles function similarly to organs in Various protozoans. Photo by: microbenotes.com/phylum-protozoa/ habitats, moist soil, and can higher animals.The plasma membrane covers the live as symbionts within other cytoplasm and locomotory pseudopodia, cilia, and flagella. structures like organisms or as parasites in Some protozoa have a rigid outer layer called a pellicle that maintains their shape, but they can still twist and host tissues and fluids. bend when moving. The cytoplasm is often differentiated into ectoplasm (outer transparent layer) and endoplasm (inner layer Their diverse habitats highlight with organelles). Some protozoa have a cytosome ("cell mouth") for their adaptability and ingesting fluids or particles, and contractile vacuoles for osmoregulation. ecological importance. Additional structures in parasitic protozoa include the Golgi apparatus, mitochondria, lysosomes, food vacuoles, and specialized organelles like conoids in Apicomplexa. (A) Strombidium sp, (B) Spirostrombidium sp, (C) Eutintinnus pectinis , (D) Favella ehrenbergii , (E) G. spirale , (F) P. divergens , (G) O. marina , (H) Protoceratium sp. Photo by: Almeda, Rodrigo & Hyatt, Cammie & Buskey, Edward. (2014). Toxicity of dispersant Corexit 9500A and crude oil to marine Laboratory Exercise 2 Laboratory Exercise 2 microzooplankton. Ecotoxicology and environmental safety. 106C. 76-85. 10.1016/j.ecoenv.2014.04.028. Superkingdom Eukaryota: Protozoa and Chromista Superkingdom Eukaryota: Protozoa and Chromista 3  8/13/2024 Kingdom Protozoa Phylogeny and Classification. Historically, protozoa were classified based on motility (amoebas, flagellates, ciliates, sporozoa), but this method was arbitrary and didn’t reflect true evolutionary relationships. The electron microscope and molecular techniques have led to more accurate classifications, identifying monophyletic groups like Apicomplexa and Alveolata. The classification of protists is still in flux, with debates about traditional schemes versus phylogenetic data, and the Linnaean system's limitations for microorganisms. Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Laboratory Exercise 2 Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. Superkingdom Eukaryota: Protozoa and Chromista pone.0119248 Kingdom Chromista Dinoflagellate. Photo by Murray, Shauna & Suggett, David Kingdom Chromista & Doblin, Martina & Kohli, Gurjeet & Seymour, Justin & Fabris, Michele & Ralph, Peter. (2016). Unravelling the functional genetics of dinoflagellates: a review of Habitat. approaches and opportunities. Perspectives in Phycology. 3. 10.1127/pip/2016/0039. Morphology. Chromista have turned out to include the vast majority of Most chromists have two flagella, marine algae and of one with tubular hairs heterotrophic protists, whether (mastigonemes), and the other marine or in soil or freshwater. without, attached to one side of the cell. Some chromists are one of the Many chromists are photosynthetic, most serious human disease containing chlorophyll c and agents such as malaria carotenoid pigments like parasites and agricultural fucoxanthin, giving them yellow, pathogens like potato blight orange, or brown colors. They store and sugar beet rhizomania energy in the form of leucosin or disease. laminarin, not starch. A typical chromistan structure. Photo by: ucmp.berkeley.edu/chromista Laboratory Exercise 2 Laboratory Exercise 2 (A) Dictyota dentata; (B) Padina australis; (C) Sargassum crassifolium; and (D) Turbinaria conoides. Photo by: Heriyanto, Heriyanto Juliadiningtyas, Ayu & Shioi, Yuzo & Limantara, Leenawaty & Brotosudarmo, Tatas. (2017). Analysis of Pigment Composition of Superkingdom Eukaryota: Protozoa and Chromista Seaweeds Collected from Panjang Island, Central Java, Indonesia. Philippine Journal of Science. 146. 323-330. Superkingdom Eukaryota: Protozoa and Chromista Kingdom Chromista Kingdom Chromista Phylogeny and Classification. Morphology. For many years, photosynthetic chromists were classified as Chromists often have chloroplasts plants, while non- with an eyespot and a common photosynthetic chromists were membrane with the nucleus. Some classified with the fungi or chromists form silica or calcium carbonate skeletons, while others animals. have cellulosic walls for structure The close relationship among and flexibility. chromists was not fully appreciated until the rise of Periplastid compartment is formed ultrastructural and molecular because of the enslavement of a studies. (presence of red algae by a chromistan chlorophyll "c" and a number of ancestor. The membrane of the other pigments, peculiarities of engulfed alga was retained the flagella, plastids, and thereafter. genetic arrangement) Laboratory Exercise 2 Laboratory Exercise 2 Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. Superkingdom Eukaryota: Protozoa and Chromista Superkingdom Eukaryota: Protozoa and Chromista pone.0119248 4  8/13/2024 Kingdom Fungi Habitat. Fungi are found all around the world, and grow in a wide range of habitats, including deserts. Most grow in terrestrial environments, but several species live only in aquatic habitats. Most fungi live in soil or dead Desert shaggy-mane. Photo by: Bryant Olsen/Flickr/Creative matter, and in symbiotic Commons License relationships with plants, animals, or other fungi. Laboratory Exercise 3 Superkingdom Eukaryota: Fungi Kingdom Fungi Kingdom Fungi Morphology. Virtually all fungi have chitin or chitosan as a component of the Phylogeny and Classification. skeletal framework for their cell walls. The best demarcation between Protozoa and Fungi lies They exist in various forms: immediately before the origin of Multicellular filamentous molds. the chitinous wall around Macroscopic filamentous fungi that form vegetative fungal cells and large fruiting bodies. Sometimes the group is referred to as ‘mushrooms’, but the associated loss of phagotrophy. mushroom is just the part of the fungus we see above ground which is also known as the fruiting body. Photo by: Science Photo Library Single celled microscopic yeasts. Laboratory Exercise 3 Laboratory Exercise 3 Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248. doi:10.1371/journal. Superkingdom Eukaryota: Fungi Superkingdom Eukaryota: Fungi pone.0119248 Complete Morphological Character List Laboratory Exercise 4 & 5 Characterization of the Vegetative and Reproductive Plant Organs 5  8/13/2024 Species Botanical Description Illustration Laboratory Exercise 4 & 5 Laboratory Exercise 4 & 5 Characterization of the Vegetative and Reproductive Plant Organs Characterization of the Vegetative and Reproductive Plant Organs Kingdom Plantae Kingdom Plantae Laboratory Exercise 6 Laboratory Exercise 6 Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Terrestrial Adaptations of Vascular Plants The Adaptive Strategies Succulence Transition from Desiccation Vascular Tissues aquatic to Wax covering Support (cuticle) terrestrial Lignified cells environment. Water for reproduction Multicellular bodies Algae – first plants – Asexual (spores) Why did they risk – Sexual (gametes) their lives on land? Laboratory Exercise 6 Laboratory Exercise 6 Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes 6  8/13/2024 Early vascular plants The Adaptive Strategy Desiccation Cooksonia Support Rhynia Water for reproduction Independence from water Horneophyton – Asexual (spores) Seed coat development Food source for embryo Trimerophyton. – Sexual (gametes) Can be dispersed in various ways Laboratory Exercise 6 Laboratory Exercise 6 Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Spores VS Seeds Laboratory Exercise 6 Laboratory Exercise 6 Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Early Seed Plants Gymnosperms – “gymno” – naked, “sperma” – seeds = naked seeds Phylogeny Posters for Plants https://drive.google.com/drive/folders/1stErCu5NX Angiosperms sMD1bo7ESsp-sREwOMk6Npz?usp=sharing – “angio” – vessel, “sperma” – seeds = enclosed seeds Laboratory Exercise 6 Laboratory Exercise 6 Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes Superkingdom Eukaryota, Kingdom Plantae: Bryophytes and Other Tracheophytes 7  8/13/2024 Laboratory Exercise 7 Superkingdom Eukaryota, Kingdom Plantae: Angiosperms 8