Lecture 1 Plant Bio - • Plant Biology Lecture 1:

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Unformatted text preview: • Plant Biology Lecture 1: Introduction/Fungal Diversity and Reproduction 10.29.2010 Outline i) Introduction  ­ what are plants? ii) Fungi  ­ important characteristics  ­ major groups (begin) • From time of Aristotle until late 1960s, most biologists subscribed to two kingdom view of life: plants (botany) and animals (zoology) • Linnaeus (father of taxonomy) was a botanist, zoologists, and physician. o Came up with 3 kingdoms of existence (mineral, plants, animals) in the mid ­1700s. • Aristotle concerned himself with what animals were and basically defined what animals are. • Animals: Organisms that move about, have sense ­perceptive capacity (pleasure, pain, imagination, desire, voluntary motion) • Plants: Nutritive and reproductive capacity (just like in animals), but not sensory or perceptive abilities  ­ ­ ­ and don’t move about freely Old View of Animals vs. Plants • Animals: Can move about; have sensory and perceptive capability (literally means “soul”). • Zoology: Science focused on animals • Plants: Every other living thing; have bodies, nutritive and reproductive capabilities, but do not move about or have sensory abilities • Botany: Science focused on plants (huge scope of focus, organismally throughout history) 7th ed. Fig. 26.21 8th ed. Fig. 26.21 Saturday, October 30, 2010 Late 1960s, 5 ­Lateingdom view became ife became (mostly as before), plants (multicellular photosynthetic organisms), fungibecomes advances): k 1960s, 5-kingdom view of life of l widely accepted: Animals widely accepted (microscopy (non-photosynthetic, macroscopic), protista (microscopic eukaryotes), monera (all prokaryotes Animals (mostly as before), plants (multicellular photosynthetic organisms), fungi (non ­ photosynthetic, macroscopic), protista  unicellular (microscopic eukaryotes), monera unicellular (all prokaryotes, “bacteria” – some people include viruses here, but it is debatable)) Prokaryotes vs. Eukaryotes • Eukaryotes: Possess membrane ­bound nucleus and organelles (e.g., mitochondria, plastids) • Eukaryotes: include protists, animals, plants, and fungi in 5 ­kingdom system • Prokaryotes: Lack a nucleus and organelles • Prokaryotes: represent only 1 kingdom (monera) in the 5 ­kingdom system • Molecular biology went through a huge revolution and revealed that prokaryotes much more diverse than previously thought (most can’t be cultured) • Prokaryotes 1st evident from stromatolites ca. 3.5 billion years ago, well before the origin of eukaryotes (~2 billion years ago) • NI: Revolution: PCR method developed – Prokaryotes: ability to sequence DNA easily for a wide array of different organisms without isolating 2 of 3 major clades of life (archaea & them bacteria) Archaea may be more closely related to eukaryotes than to bacteria (controversial) Saturday, October 30, 2010 Molecular biology revealed that prokaryotes much more diverse than previously thought (most can’t be cultured) Prokaryotes 1st evident from stromatolites ca. 3.5 billion years ago, well before the origin of eukaryotes (~2 billion years ago) Extremophiles – included Archaea • Literally, “lovers of extreme conditions”; many archaea. These include: • Halophiles: In highly saline environments (e.g., inland seas or lakes); generally cant survive except under high salinity; fatal to eukaryotes; mostly aerobic  ­organisms that require oxygen. • Thermophiles: In very hot environments, 120 degree Celsius (e.g., hydrothermic or volcanic vents); primary producers at the bottom of the ocean, autotrophs that are able to produce their own energy from hydrogen sulfide ­ they make use of chemicals that are poisonous to us. • Methanogens: Live in anaerobic guts of ruminants (cattle, other ungulates) oxygen is deadly to them. They help cattle and other ruminants digest cellulose – important ecologically, produce methane as a waste product. • Highly valuable for molecular biology, including resolution of the tree of life; Extremophiles are responsible for PCR. • Archaea group was discovered because of Archaea Archaea “extremophiles” Saturday, October 30, 2010 Figure 26.23 Figure 26.23 Some Would Call It Hell; Archaea Call It Home. Masses of heat ­ and acid ­loving archaea form an orange mat inside a volcanic vent on the island of Kyushu, Japan. Sulfurous residue is visible at the edges of the archaean mat. Figure 26.24 Extreme Halophiles. Commercial seawater evaporating ponds, such as these in San Francisco Bay, are attractive homes for salt ­loving archaea. Some Would Call It Hell; Archaea Call It Home. Masses of heat- and acid-loving archaea form an orange mat inside a volcanic vent on the island of Kyushu, Japan. Sulfurous residue is visible at the edges of the archaean mat. Figure 26.24 Extreme Halophiles. Commercial seawater evaporating ponds, such as these in San Francisco Bay, are attractive homes for salt-loving archaea. Bacteria • Highly diverse group, representing every major mode of nutrition and metabolism  ­ (None of the archaea are capable of true photosynthesis, only cyanobacteria has figured out how to do this) • Some (cyanobacteria) capable of photosynthesis, unlike all known archaea; led to O2 ­rich atmosphere 1.8 billion years ago (also important for nitrogen fixation, along with other bacteria)  ­ Cyanobacteria are nitrogen fixers – they make nitrogen available – an essential nutrient for organisms, and it is easily lost from ecosystems. • Adaptations of bacteria were co ­opted in eukaryotes  ­ Cyanobacteria are essentially responsible for all of the photosynthetic eukaryotes. Diversity of Modes of Living 1) Autotrophs: Generate food from non organic sources (light or inorganic substances) a) Photo autotroph: capture energy from light; capture carbon from the atmosphere, as CO2. b) Chemo autotroph: capture energy from oxidizing inorganic substances, such as hydrogen sulfide, ammonia, and ferrous ions. 2) Heterotrophs: Feed on organic substances (other organisms or their products). o It is thought that the original organisms were Heterotrophs and they were feeding on organic compounds that were produced by non ­organic means – not my living organisms. Autotrophs really created the conditions for life to exist to a great extent. • The modern three domain system of classification (two prokaryotic & one eukaryotic) highlights the ancient divergence within prokaryotes, which pre ­dates the origin of eukaryotes • Recognition of only one eukaryotic domain is not because eukaryotes are less diverse than previously thought; their diversity is vast and much richer than earlier thought, with 5 supergroups that do not correspond with the four in the 5 ­kingdom system Saturday, October 30, 2010 Tree of Life: • The fungi, animals, and land plants are just minor twigs in the overall tree of life. o They are all major terrestrial multicellular groups. They are not closely related to one another. They have each been independent derived from unicellular organisms. So, multicellularity has arisen multiple times independently in these groups. • See tree ­of ­life website for more material on many of the prokaryotic and eukaryotic lineages that we won’t have time to cover (& on those we are covering) • Rooting the tree of life a challenge, and some lateral gene flow may have contributed archaeal and bacterial genetic material to eukaryotes Viruses: • Viruses left out of the classification and often treated as non ­living, because inert in isolation, relationships poorly known and difficult to include. • May have had origins with other mobile genetic elements (plasmids and transposons). Plasmids found in prokaryotes and yeasts; transposons are widespread. Relationships difficult to interpret based on small genome and probably extensive lateral transfer of genetic material. o Viruses evolve very quickly, but they are inert unless they are in the presence in the living cells of bacteria, archaea, or Eukarya. o They DNA but very much, RNA, nucleic acids o They inherit their DNA from horizontal transfer from their host. What is covered in the “Plants” section of Bio 1B: Fungi “Algae” Land Plants 7th ed. Fig. 27.12 8th ed. Fig. 26.21 Saturday, October 30, 2010 “Plants” (as originally conceived) grossly polyphyletic, as are the so-called “algae”, which are almost • “Plants” (as originally conceived) grossly polyphyletic, as all of thetphotosynthetic alled “algae”, which are are he so ­corganisms except for land plants, which are monophyletic. almost Fungi, of the photosynthetic organisms except for such as the slime molds,which are monophyletic. all on the other hand, constitute a clade, with some traditionally included groups removed, land plants, which are no more closely related to fungi ther hand, • Fungi, on the othan to animals. constitute a clade, with some traditionally included groups removed, such as the slime molds, which are no more closely related to fungi than to animals. • • • Fungi – used to be called plants. People who study fungi are now called mycologists instead of botanists. Algae: green, red, dinoflagellates, diatoma, euglena, cyanobacteria; o Typically marine or aquatic photosynthetic organisms. They are not a monophyletic group or a clade. The algae is much more scattered in the tree of life than anybody guessed prior to this molecular biology revolution back in the 1990s. But they all are more closely related to each other than they appear on this tree ­ that’s when we start talking about the origin of photosynthesis. Land Plants: occur on terrestrial habitats, a monophyletic group, closely related to some but not all the algae. Saturday, October 30, 2010 Animals Fungi distantly related Fungi Fungi to land plants (independently ~1 billion Fungi more closely related to evolved multicellularity) years ago animals than to any photosynthetic clades Fungi, although traditionally placed in the field of botany, they are in fact much more closely related Fungi and animals shared a common ancestor ~ 1 billion years ago; much more recently than either shared a common ancestor the animals nor the fungi show any evidence to animals. Fungi, although traditionally placed in the field of (Neither with land plants. • are in fact much more closely related Fungi and plants having ever plastids or photosynthetic apparatus of are each more closely related to unicellular groups than to each other. botany, they that they may have lost.) to animals than to plants. • Fungi and animals shared a common ancestor ~ 1 uch departments still existed, fungi o If s billion years ago; much more recently than either should be placed in the zoology shared a common ancestor with land plants. department rather than the botany o Based on fossil and molecular considerations department. • Fungi and plants are each more closely related to unicellular groups than to each other. Characteristics of Fungi: include a wide array of multicellular organisms and also some unicellular fungi (i.e. yeast). There are about 100,000 species of fungi that have been recognized and described, but there are probably vastly more fungi that remain not described and remain to be discovered – this especially true for the yeast ­ which may include more than 100,000 taxa (only 1,500 described). The yeasts may actually outnumber the multicellular fungi, but there is not a lot of morphology there to describe them. • Eukaryotes (have nuclei, mitochondria) o No plastids – no evidence of ever being photosynthetic • Bodies are non motile o One of the reasons they were considered plants at first; their main adult bodies are typically non ­motile – there are exceptions. • Filamentous (hyphae, making up mycelium) Saturday, October 30, 2010 • • • • • • • Made of discrete filamentous that are interwoven together – called hyphae. These make up together the body of the fungus that is called the mycelium. Absorptive mode of nutrition; heterotrophic o They need organic carbon that has been fixed by some other organism, but they cannot actually engulf or swallow big chunks of organic material – they are not capable of phagocytosis (like an ameba to surround something and digest it). They have to actually enzymatically degrade organic material outside their body. Cell walls present; contain chitin (not cellulose) – Similarities with some animals. o Animals don’t have cell walls, all the eukaryotes have cell membrane, but only certain eukaryotes have cell walls, which are outside the cell membrane – these impart rigidness to the cells. This is one of the reasons they were considered plants (plants have cell walls, unlike animals). But the cell walls in fungi contain chitin (substance that make up the skeletons of artherpods – insects and crustaceans) rather than cellulose (plants have cell walls made of cellulose) o Interesting similarity: fungi share a lot with artherpods – they both contain chitin in their cell walls o Both Chitin and Cellulose are complex carbohydrates, but they have different compositions – fundamental difference between plants and fungi Store carbon as glycogen (not starch)  Similarity with animals o In plants they store their carbon as starch, whereas in fungi they store their carbon as glycogen (just like humans do and animals do) Life cycle includes spores – Similarity with Plants o Plants also have spores in their life cycles – plant ­like feature of fungi, even though it is not diagnostic of a close relationship with plants. Unicellular & multicellular o Unicellular ­ yeast Decomposers derive nourishment from dead or decaying matter; often called saprophytes (“putrid plant”) 7th ed. Fig. 31.2 8th ed. Fig. 31.2 Hyphae: tubular filaments of high surface area/volume ratio (enhances absorption) Saturday, October 30, 2010 Figure: 29.6ab Caption: (a) Hyphae are often broken into cell-like compartments by partitions called septa. These electron micrographs show that septa are broken by pores. As a result, the cytoplasm of different compartments is continuous. (b) The hyphae from an individual make up a feeding body called a mycelium. During sexual reproduction, hyphae form fruiting bodies. Frequently, these fruiting bodies erupt from the ground or substrate, so spores can be dispersed by the wind. Question What sorts of environmental changes or cues might cause a feeding body to make a fruiting body? Can concentrate resources in production of fruiting body in just a few hours; common meadow mushroom can release a billion spores Hyphae compartmentalized by partially open partitions (septa) in most fungi (Ascomycota & Basiodiomycota) ay, October 30, 2010 Hyphae: tubular filaments of high surface area/volume ratio (enhances absorption by coming in contact with the environment to digest their food outside their body in part). They grow from their tips. • Hyphae are often broken into cell ­like compartments by partitions called septa. These electron micrographs show that septa are broken by pores. As a result, the cytoplasm of different compartments is continuous. • The hyphae from an individual make up a feeding body called a mycelium. During sexual reproduction, hyphae form fruiting bodies. Frequently, these fruiting bodies erupt from the ground or substrate, so spores can be dispersed by the wind. o The vast majority of the mycelium is underground Question What sorts of environmental changes or cues might cause a feeding body to make a fruiting body? Water, Rain. • Can concentrate resources and energy in production of fruiting body in just a few hours; common meadow mushroom can release a billion spores. o The fruiting bodies of the fungi can develop incredibly fast – an overnight phenomenon. 1. Septate Hypha – the septe do break of the hypha into partitions, but there a little whole inside of the septe that allow the cytoplasm to move freely through. Though, they do have some partitioning of the larger part of their cells, like the nuclei – but the cytoplasm can move freely through. So, the hypha is still capable of rapidly mobilizing resources to grow in places. For example, if they are going to produce a fruiting body, they can shunt resources quickly to different parts of the hypha. Each of the partitioned areas are “cell ­like.” 2. Coenocytic Hypha – filament is completely open inside, there are no partitions, or septe, that break up the hypha into cell ­like units. There is an open cytoplasm inside the hypha and we have the nuclei not separated from one another by cell membranes. • Specialized Hyphae (Fungi are not all decomposers; some are predatory fungi.) • Although many fungi are parasitic on other organisms, some ascomycetes (most diverse) can operate as predators (nematode trappers) in addition to being saprophytes (decomposers) or mutualists. • Mycorrhizal Associations: Mutualism between fungi and plants (symbiotic relationship that is positive to both partners). Positive interaction fundamental to our survival and most plants. o Most plants have mutualistic associations with fungi involving the plant roots. Such associations are called mycorrhizae. o Fungus obtains food (carbohydrates) from plant; the plant obtains enhanced uptake of inorganic nutrients (important ones like nitrogen and phosphorous that can be limiting in the environment – fungus is efficient at absorbing the minerals/nutrients and water) from fungus. o If you prevent this association from forming in plants, they do much more poorly in most cases – there are some plants that do not need this, but the vast majority of plants need this kind of association. Two Types of Mycorrhizal Associations: 1. Ectomycorrhizal fungi: These fungi associate with temperate & boreal trees (non ­tropical trees); fungal hyphae do not penetrate cell walls. Root cells • *Ectomycorrhizal fungi (EMF) form a dense network around the roots of plants. The combination of root and fungus is called a mycorrhiza. The drawing shows how the interaction works in EMF. Note that their hyphae penetrate the intercellular spaces of the root, but do not enter the cells themselves. • Associate with Conifers like pines and spruces and hardwoods like burches, oaks and flowering plant trees in temperate regions • Hyphae will penetrate between the cell walls, but they EMF wont go inside of a cell wall. 2. Arbuscular Mycorrhizal fungi: VAST MAJORITY OF PLANTS have this type of association. *Most plants These fungi associate with temperate & boreal trees; fungal hyphae do not associate with fungi that penetrate root cell wall (but penetrate cell walls not cell membrane), and have extensive contact with Saturday, October 30, 2010 Figure: 29.9a cell membrane. Caption: a. They penetrate the cell wall BUT they don’t Arbuscular mycorrhizalaround the roots of plants. The combination of root and fungus is called a mycorrhiza. The (a) Ectomycorrhizal fungi (EMF) form a dense network fungi drawing shows how the interaction works in EMF. Note that their hyphae penetrate the intercellular spaces of the root, but do not enter the cells penetrate or puncture the cell membrane – themselves. they just cover it so that they have a better contact area with the plant – a lot more Root surface in contact for transferring substances. cells • All the arbacious plants (plants that do not produce AMF wood), herbs, and a lot of tropical trees have this association. • *Interactions of arbuscular mycorrhizal fungi (AMF) with roots. The fungal hyphae penetrate the root cell walls and contact the plasma membrane, where they branch into bushy structures called arbuscules. The photograph shows a fossilized arbuscule, from an AMF, inside a plant cell. The fossil is over 390 million Root hair years old. • More common association – this association is seen in Most plants associate with fungi that penetrate root cell wall more than 80% of plant families– including in some of (but not cell membrane), and have extensive contact with cell membrane the earliest diverging plant families – these guys were Saturday, October 30, 2010 probably critical to the original colonization of land by Figure: 29.9b terrestrial plants. Caption: (b) Interactions of arbuscular mycorrhizal fungi (AMF) with roots. The fungal hyphae penetrate the root cell walls and contact the plasma structures called arbuscules. The photograph shows a fossilized arbuscule, from an AMF, inside a plant • In this particular group of fungi ­ There are only a membrane, where they branch into bushy cell. The fossil is over 390 million years old. couple hundred species of these type of fungi that we know of today, but they are really important Ectomycorrhizal fungi Five major clades of fungi Include most but not all organisms that have been called fungi 7th ed. Fig. 31.9 8th ed. Fig. 31.11 Saturday, October 30, 2010 Chytridiomycota Zygomycota • Fungi form a monophyletic group • Two major clades of the big macro fungi that produce the big fruiting bodies that are sister to each other, Ascomycota and Basiodiomycota Glomeromycota Ascomycota Basidiomycota Chytridiomycota: • Chytrids diverged early in history of fungi; only group of fungi that has motile spores and gametes with flagellae o (a single whip like flagellum – in that regard they are similar to some of the close relatives of animals in unicellular forms – they share this single whip ­like flagellum with a common ancestor with the animals) In the broad sense, they are this big fungal animal group called a uniconts (means having a single ­whip like flagellum). • Chytrids: Diverged early in evolution of fungi; once treated as protists • Only fungi with motile spores (bearing flagellae) • Some unicellular; some filamentous o Only about 1,000 species of these – small diversity – but very interesting, because they were one of the early diverging lineages here. It was questionable of whether they were really fungi in past, but the molecular data really nailed that down  ­ proved it to be fungi. Amphibian Decline Has Multiple Causes: • Chytrids are important ecologically – they are important decomposers. • Chytridiomycosis is a major factor in amphibian decline, we did not know about this phenomenon until fairly recently (over the last 10 ­20 years). • This Chytrid infection of particularly frogs and toads has led to the extinction and rapid demise of lots of amphibians worldwide – it is a really serious disease that has spread into California and other places familiar to us and it has been a huge problem to organisms that are already having plenty of trouble. These can be really aggressive pathogenic disease ­causing organisms. • Chytrids are important decomposers in soil and can be symbionts in guts of various animals  ­ ruminants, important in the digestive tract of ungulates important in aquatic situations, but also can be parasites of animals, including frogs and toads, many of which have been driven to extinction recently. • Chytridiomycosis is a leading contributor to this extinction and decline worldwide. ...
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