The Term Autotroph Refers to an Organism That
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Prokaryotes (Domains Bacteria & Archaea)
2/4/15 Prokaryotes (Domains Bacteria & Archaea) KEY POINTS 1. Decomposers: recycle organic and inorganic molecules in environment; makes them available to other organisms. 2. Essential components of symbioses. 3. Encompasses the origins of metabolism and metabolic diversity. 4. Origin of photosynthesis and formation of atmospheric Oxygen Ceno- Meso- zoic zoic ANTIQUITY Humans Paleozoic Colonization of land Animals Origin of solar system and Earth • >3.5 BILLION years old. • Alone for 2 1 4 billion years Proterozoic Archaean Prokaryotes Billions of 2 years ago3 Multicellular eukaryotes Single-celled eukaryotes Atmospheric oxygen General characteristics 1. Small: compare to 10-100µm for 0.5-5µm eukaryotic cell; single-celled; may form colonies. 2. Lack membrane- enclosed organelles. 3. Cell wall present, but different from plant cell wall. 1 2/4/15 General characteristics 4. Occur everywhere, most numerous organisms. – More individuals in a handful of soil then there are people that have ever lived. – By far more individuals in our gut than eukaryotic cells that are actually us. General characteristics 5. Metabolic diversity established nutritional modes of eukaryotes. General characteristics 6. Important decomposers and recyclers 2 2/4/15 General characteristics 6. Important decomposers and recyclers • Form the basis of global nutrient cycles. General characteristics 7. Symbionts!!!!!!! • Parasites • Pathogenic organisms. • About 1/2 of all human diseases are caused by Bacteria General characteristics 7. Symbionts!!!!!!! • Parasites • Pathogenic organisms. • Extremely important in agriculture as well. Pierce’s disease is caused by Xylella fastidiosa, a Gamma Proteobacteria. It causes over $56 million in damage annually in California. That’s with $34 million spent to control it! = $90 million in California alone. -
Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). -
A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and Their Association with the Endangered, Endemic Snail Physella Johnsoni
A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and their Association with the Endangered, Endemic Snail Physella johnsoni By Michael Bilyj A thesis submitted to the Faculty of Graduate Studies in partial fulfillment of the requirements for the degree of Master of Science Department of Microbiology Faculty of Science University of Manitoba Winnipeg, Manitoba October 2011 © Copyright 2011, Michael A. Bilyj 1 Abstract The seasonal population fluctuation of anoxygenic phototrophs and the diversity of cyanobacteria at the Sulphur Mountain thermal springs of Banff, Canada were investigated and compared to the drastic population changes of the endangered snail Physella johnsoni. A new species and two strains of Rhodomicrobium were taxonomically characterized in addition to new species of Rhodobacter and Erythromicrobium. Major mat-forming organisms included Thiothrix-like species, oxygenic phototrophs of genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised upwards of 9.6 x 104 CFU/cm2 of mat or 18.9% of total aerobic heterotrophic bacterial isolates at certain sites, while maximal purple nonsulfur and purple sulfur bacteria were quantified at 3.2 x 105 and 2.0 x 106 CFU/cm2 of mat, respectively. Photosynthetic activity measurements revealed incredibly productive carbon fixation rates averaging 40.5 mg C/cm2/24 h. A temporal mismatch was observed for mat area and prokaryote-based organics to P. johnsoni population flux in a ―tracking inertia‖ manner. 2 Acknowledgements It is difficult to express sufficient gratitude to my supervisor Dr. Vladimir Yurkov for his unfaltering patience, generosity and motivation throughout this entire degree. -
Aerobic Respiration
Life is based on redox • All energy generation in biological systems is due to redox (reduction-oxidation) reactions Aerobic Respiration: + - C6H12O6 + 6 H2O ==> 6 CO2 + 24 H +24 e oxidation electron donor (aka energy source) + - (O2+ 4H + 4e ==> 2H2O) x6 reduction electron acceptor --------------------------------------- C6H12O6 + 6 O2 ==> 6 CO2 + 6 H2O overall reaction (24 electrons) Types of bacterial metabolisms • While eukaryotes only reduce O2 and oxidize organic compounds, prokaryotes can use a variety of electron donors and acceptors, organic and inorganic. - • Aerobic respiration: e acceptor is O2 - • Anaerobic respiration: e acceptor is not O2 • Fermentation: e- donor and acceptor are organic molecules • Chemolithotrophy: e- donor and acceptor are inorganic molecules • Phototrophy: e- donor is light and e- acceptor is either organic or inorganic all microorganisms energy source? chemical light chemotroph phototroph carbon source? carbon source? organic organic CO CO compound 2 compound 2 chemoheterotroph chemoautotroph photoheterotroph photoautotroph e- acceptor? Nitrifying and sulfur- use H O to reduce CO ? oxidizing bacteria 2 2 green non-sulfur and O Other than O 2 2 purple non-sulfur bacteria anoxygenic oxygenic photosynthesis: photosynthesis: green sulfur and most bacteria Organic Inorganic cyanobacteria compound compound purple sulfur bacteria fermentative organism anaerobic respiration: nitrate, sulfate, Fe(III) Aerobic or anaerobic respiration Chemolithotrophy Important molecules Redox Electron Carrier: for example the -
Nitrogen and Phosphorus Limitation of Oceanic Microbial Growth During Spring in the Gulf of Aqaba
Vol. 56: 227–239, 2009 AQUATIC MICROBIAL ECOLOGY Printed September 2009 doi: 10.3354/ame01357 Aquat Microb Ecol Published online August 27, 2009 Contribution to AME Special 2 ‘Progress and perspectives in aquatic primary productivity’ OPEN ACCESS Nitrogen and phosphorus limitation of oceanic microbial growth during spring in the Gulf of Aqaba David J. Suggett1,*, Noga Stambler2, Ondrej Prá$il3, Zbigniew Kolber4, Antonietta Quigg5, Evaristo Vázquez-Domínguez6, Tamar Zohary7, Tom Berman7, David Iluz8, Orly Levitan2, Tracy Lawson1, Efrat Meeder9,10, Boaz Lazar9,10, Edo Bar-Zeev2, Hana Medova3, Ilana Berman-Frank8 1Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK 2Department of Geography and Environment, Bar-Ilan University, Ramat-Gan 52900, Israel 3Photosynthesis Laboratory, Institute of Microbiology ASCR, Opatovicky mlyn, 379 81 Trˇ ebonˇ, Czech Republic 4Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA 5Department of Marine Biology and Oceanography, Texas A&M University, Galveston, Texas 77551, USA 6CSIC, Institut de Ciències del Mar, Passeig Marítim de la Barceloneta 39-43, 08003 Barcelona, Spain 7Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, PO Box 447, Migdal 14950, Israel 8The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel 9The Interuniversity Institute for Marine Sciences Coral Beach, PO Box 469, 88103 Eilat, Israel 10Institute of Earth Sciences, The Hebrew University Edmond J. Safra Campus, Jerusalem 91904, Israel ABSTRACT: Bioassay experiments were performed to identify how growth of key groups within the mi- crobial community was simultaneously limited by nutrient (nitrogen and phosphorus) availability during spring in the Gulf of Aqaba’s oceanic waters. -
IB HL Biology: Ecology Review Fall 2017 Populations 1. Define the Following Terms Associated with Population Ecology; Population and Carrying Capacity
IB HL Biology: Ecology Review Fall 2017 Populations 1. Define the following terms associated with population ecology; population and carrying capacity. 2. What processes contribute to changes in population size? 3. What are some factors which can increase the carrying capacity of a population? Decrease? 4. What is quadrat sampling? When would it be used? Communities 5. Define the following terms; community, autotroph, heterotroph, producer, primary consumer, secondary consumer, detritivore and saprotroph. 6. What is the initial energy source for all communities? 7. Be able to read food webs and determine the trophic level of different species. 8. Choose 2 regions below and determine the Simpson’s Diversity Index value for these regions. Which region is more diverse? A. An area of the Black Forest in Germany contains 134 pitch pines, 24 douglas firs, and 53 red pines. B. A meadow contains 1532 chestnut oaks, 342 black cherry trees, 12 white ash trees, and 1022 yellow birches. C. You school science classroom contains 12 beetles, 34 termites, 84 ants, 93 fleas, and 1 butterfly. D. An African park contains 15 lions, 94 giraffes, 1000 wildebeests, 50 elephants, and 5 hyenas. Choose more areas if you need more practice. 9. What is a keystone species? 10. Distinguish between primary and secondary succession. Ecosystems 11. What is an ecosystem? 12. Explain the 10% rule of energy transfer. How is the energy lost between trophic levels? 13. Review the Carbon Cycle. What are the main sources of carbon dioxide on earth? 14. Review the Nitrogen Cycle. 15. Distinguish between Gross Primary Productivity and Net Primary Productivity. -
Chapter 11 – PROKARYOTES: Survey of the Bacteria & Archaea
Chapter 11 – PROKARYOTES: Survey of the Bacteria & Archaea 1. The Bacteria 2. The Archaea Important Metabolic Terms Oxygen tolerance/usage: aerobic – requires or can use oxygen (O2) anaerobic – does not require or cannot tolerate O2 Energy usage: autotroph – uses CO2 as a carbon source • photoautotroph – uses light as an energy source • chemoautotroph – gets energy from inorganic mol. heterotroph – requires an organic carbon source • chemoheterotroph – gets energy & carbon from organic molecules …more Important Terms Facultative vs Obligate: facultative – “able to, but not requiring” e.g. • facultative anaerobes – can survive w/ or w/o O2 obligate – “absolutely requires” e.g. • obligate anaerobes – cannot tolerate O2 • obligate intracellular parasite – can only survive within a host cell The 2 Prokaryotic Domains Overview of the Bacterial Domain We will look at examples from several bacterial phyla grouped largely based on rRNA (ribotyping): Gram+ bacteria • Firmicutes (low G+C), Actinobacteria (high G+C) Proteobacteria (Gram- heterotrophs mainly) Gram- nonproteobacteria (photoautotrophs) Chlamydiae (no peptidoglycan in cell walls) Spirochaetes (coiled due to axial filaments) Bacteroides (mostly anaerobic) 1. The Gram+ Bacteria Gram+ Bacteria The Gram+ bacteria are found in 2 different phyla: Firmicutes • low G+C content (usually less than 50%) • many common pathogens Actinobacteria • high G+C content (greater than 50%) • characterized by branching filaments Firmicutes Characteristics associated with this phylum: • low G+C Gram+ bacteria -
Fermentation and Anaerobic Decomposition in a Hot Spring
Fermentation and anaerobic decomposition in a hot spring microbial mat by Karen Leigh Anderson A thesis submitted in partial fulfillment of requirements for the degree of Master of Science in Microbiology Montana State University © Copyright by Karen Leigh Anderson (1984) Abstract: Fermentation was investigated in a low sulfate hot spring microbial mat (Octopus Spring) according to current models on anaerobic decomposition. The mat was studied to determine what fermentation products accumulated, where in the mat they accumulated, and what factors affected their accumulation. Mat samples were incubated under dark anaerobic conditions to measure accumulation of fermentation products. Acetate and propionate (ca. 3:1) were the major products to accumulate in a 55°,C mat. Other products accumulated to a much lesser extent. Incubation of mat samples of varying thickness showed that fermentation occurred in the top 4mm of the mat. This has interesting implications for fermentative organisms in the mat due to the diurnal changes in mat oxygen concentrations. Fermentation measured in mat samples collected at various temperatures (50°,-70°C) showed acetate and propionate to be the major accumulation products. According to the interspecies hydrogen transfer model, the hydrogen concentration in a system affects the types of fermentation products produced. At a 65° C site, with natural high hydrogen levels, and at a 55°C site, with active methanogenesis, fermentation product accumulation was compared. There was a greater ratio of reduced fermentation products to acetate, with the exception of propionate, at 65°C. Ethanol accumulated at the 65°C site, as did lactate, though to a lesser extent. -
Principles of Ecology Section ●2 Flow of Energy in an Ecosystem
chapter 2 Principles of Ecology section ●2 Flow of Energy in an Ecosystem -!). )DEA Before You Read Autotrophs capture energy, making it available for all If a pet had to survive without your care, how would its diet members of a food web. change? Write your ideas on the lines below. Read about how What You’ll Learn organisms get food and energy in their environment. ■ the fl ow of energy through an ecosystem ■ food chains, food webs, and pyramid models 3TUDY#OACH Read to Learn Make Flash Cards Make a fl ash card for each question Energy in an Ecosystem heading in this section. On the One way to study the interactions within an ecosystem is to back of the fl ash card, write the trace how energy fl ows through the system. All organisms are answer to the question. Use the classifi ed by the way they obtain energy. fl ash cards to review what you have learned. How do autotrophs obtain energy? All green plants and other organisms that produce their own food are the primary producers of food in an ecosystem. They are called autotrophs. An autotroph (AW tuh trohf) is an organism that captures energy from sunlight or inorganic substances to produce food. Autotrophs make energy available for all other organisms in the ecosystem. How do heterotrophs differ from autotrophs? A heterotroph (HE tuh roh trohf), also called a consumer, is an organism that obtains energy by consuming other organisms. A heterotroph that consumes only plants is an herbivore (HUR buh vor). Cows, rabbits, and grasshoppers are herbivores. -
Bacterial Community Structure in a Sympagic Habitat Expanding with Global Warming: Brackish Ice Brine at 85€“90 °N
The ISME Journal (2019) 13:316–333 https://doi.org/10.1038/s41396-018-0268-9 ARTICLE Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N 1,11 1,2 3 4 5,8 Beatriz Fernández-Gómez ● Beatriz Díez ● Martin F. Polz ● José Ignacio Arroyo ● Fernando D. Alfaro ● 1 1 2,6 5 4,7 Germán Marchandon ● Cynthia Sanhueza ● Laura Farías ● Nicole Trefault ● Pablo A. Marquet ● 8,9 10 10 Marco A. Molina-Montenegro ● Peter Sylvander ● Pauline Snoeijs-Leijonmalm Received: 12 February 2018 / Revised: 11 June 2018 / Accepted: 24 July 2018 / Published online: 18 September 2018 © International Society for Microbial Ecology 2018 Abstract Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4–9.6) and immediate sub-ice seawater (SW; – 1234567890();,: 1234567890();,: salinity 33.3 34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. -
Determining the Contribution of Aquatic Autotrophs to the Carbon Budgets of Restored Wetlands in the Sacramento-San Joaquin River Delta
Determining the Contribution of Aquatic Autotrophs to the Carbon Budgets of Restored Wetlands in the Sacramento-San Joaquin River Delta A thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Environmental Sciences Ian J. UTZ College of Natural Resources, University of California, Berkeley August 6, 2016 Contents 1 Introduction 8 2 Background 11 2.1 Ecological Engineering . 12 2.2 Successional Community Ecology . 13 2.3 Food Web Interactions . 14 2.4 Plant Physiology . 15 2.5 Physical Habitat . 16 3 Methods 18 3.1 Locations . 18 3.2 Measurements . 22 3.2.1 Remotely sensing changes in aquatic primary produc- tivity using high resolution satellite imagery. 22 3.2.2 Remotely sensing changes in aquatic primary produc- tivity using continuous recording of changes in dis- solved oxygen and carbon dioxide. 23 3.2.3 Measuring physical habitat covariates to characterize environmental baselines. 24 3.2.4 Conducting field experiments and biomass estimation to attribute changes in dissolved oxygen to differences in the presence and intensity of aquatic primary pro- duction. 26 3.3 Treatments . 28 4 Results 32 4.1 Physical covariate measurements . 32 1 4.2 Remotely sensing changes in aquatic primary productivity us- ing high resolution satellite imagery. 34 4.3 Remotely sensing changes in aquatic primary productivity us- ing continuous recording of changes in dissolved oxygen, dis- solved carbon dioxide, and phenocam greenness data. 37 4.4 Conducting field experiments and biomass sampling to at- tribute changes in dissolved oxygen to differences in the pres- ence and intensity of aquatic primary production. -
Bioenergetics Module a Anchor 3
Bioenergetics Module A Anchor 3 Key Concepts: - ATP can easily release and store energy by breaking and re-forming the bonds between its phosphate groups. This characteristic of ATP makes it exceptionally useful as a basic energy source for all cells. - In the process of photosynthesis, plants convert the energy of sunlight into chemical energy stored in the bonds of carbohydrates. - Photosynthetic organisms capture energy from sunlight with pigments. - An electron carrier is a compound that can accept a pair of high-energy electrons and transfer them, along with most of their energy, to another molecule. - Photosynthesis uses the energy of sunlight to convert water and carbon dioxide into high- energy sugars and oxygen. - Among the most important factors that affect photosynthesis are temperature, light intensity, and the availability of water. - Organisms get the energy they need from food. - Cellular respiration is the process that releases energy from food in the presence of oxygen. - Photosynthesis removes carbon dioxide from the atmosphere and cellular respiration puts it back. Photosynthesis releases oxygen into the atmosphere, and cellular respiration uses that oxygen to release energy from food. - In the absence of oxygen, fermentation releases energy from food molecules by producing ATP. - For short, quick bursts of energy, the body uses ATP already in muscles as well as ATP made by lactic acid fermentation. - For exercise longer than about 90 seconds, cellular respiration is the only way to continue generating a supply of ATP. Vocabulary: ATP ADP autotroph heterotroph Photosynthesis pigment chlorophyll chloroplast Thylakoid stroma NADP+/NADPH calorie Cellular respiration aerobic anaerobic fermentation Glucose ATP and Energy Molecules: 1.