Prokaryotic Growth and Nutrition
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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. -
The First Cells Were Most Likely Very Simple Prokaryotic Forms. Ra- Spirochetes
T HE O RIGIN OF E UKARYOTIC C ELLS The first cells were most likely very simple prokaryotic forms. Ra- spirochetes. Ingestion of prokaryotes that resembled present-day diometric dating indicates that the earth is 4 to 5 billion years old cyanobacteria could have led to the endosymbiotic development of and that prokaryotes may have arisen more than 3.5 billion years chloroplasts in plants. ago. Eukaryotes are thought to have first appeared about 1.5 billion Another hypothesis for the evolution of eukaryotic cells proposes years ago. that the prokaryotic cell membrane invaginated (folded inward) to en- The eukaryotic cell might have evolved when a large anaerobic close copies of its genetic material (figure 1b). This invagination re- (living without oxygen) amoeboid prokaryote ingested small aerobic (liv- sulted in the formation of several double-membrane-bound entities ing with oxygen) bacteria and stabilized them instead of digesting them. (organelles) in a single cell. These entities could then have evolved This idea is known as the endosymbiont hypothesis (figure 1a) and into the eukaryotic mitochondrion, nucleus, and chloroplasts. was first proposed by Lynn Margulis, a biologist at Boston Univer- Although the exact mechanism for the evolution of the eu- sity. (Symbiosis is an intimate association between two organisms karyotic cell will never be known with certainty, the emergence of of different species.) According to this hypothesis, the aerobic bac- the eukaryotic cell led to a dramatic increase in the complexity and teria developed into mitochondria, which are the sites of aerobic diversity of life-forms on the earth. At first, these newly formed eu- respiration and most energy conversion in eukaryotic cells. -
Criticalreading #Wickedproblem
#CRITICALREADING #WICKEDPROBLEM We have a “wicked problem” . and that is a fantastic, engaging, exciting place to start. Carolyn V. Williams1 I. INTRODUCTION I became interested in the idea of critical reading—“learning to evaluate, draw inferences, and arrive at conclusions based on evidence” in the text2—when I assumed that my students would show up to law school with this skill . and then, through little fault of their own, they did not. I have not been the only legal scholar noticing this fact. During the 1980s and 90s a few legal scholars conducted research and wrote about law students’ reading skills.3 During the 2000s, a few more scholars wrote about how professors can help develop critical reading skills in law students.4 But it has not been until the past few years or so that legal scholars have begun to shine a light on just how deep the problem of law students’ critical reading skills 1 Professor Williams is an Associate Professor of Legal Writing & Assistant Clinical Professor of Law at the University of Arizona, James E. Rogers College of Law. Thank you to Dean Marc Miller for supporting this Article with a summer research grant. Many thanks to the Legal Writing Institute for hosting the 2018 We Write Retreat and the 2018 Writers’ Workshop and to the participants at each for their comments and support of this project. A heartfelt thank you to Mary Beth Beazley, Kenneth Dean Chestek, and Melissa Henke for graciously providing comments on prior drafts of this Article. Thank you to my oldest Generation Z child for demonstrating independence and the desire to fix broken systems so that I know my solution is possible. -
Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean Off the Iberian Peninsula
Microbial Ecology https://doi.org/10.1007/s00248-019-01320-y MICROBIOLOGY OF AQUATIC SYSTEMS Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula Elisabeth L. Clifford1 & Marta M. Varela2 & Daniele De Corte3 & Antonio Bode2 & Victor Ortiz1 & Gerhard J. Herndl1,4 & Eva Sintes1,5 Received: 28 June 2018 /Accepted: 3 January 2019 # The Author(s) 2019 Abstract Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids. -
Specificity Re-Evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fl
fmicb-08-00854 May 24, 2017 Time: 20:18 # 1 ORIGINAL RESEARCH published: 29 May 2017 doi: 10.3389/fmicb.2017.00854 Specificity Re-evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fluorescent In Situ Hybridization Virginie Riou, Marine Périot and Isabelle C. Biegala* Centre National de la Recherche Scientifique, Mediterranean Institute of Oceanography – Institut de Recherche pour le Développement, Aix Marseille Université – Université de Toulon, Marseille, France Edited by: Sophie Rabouille, Oligonucleotide probes are increasingly being used to characterize natural microbial Centre National de la Recherche Scientifique (CNRS), France assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA- Reviewed by: FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA Fernanda De Avila Abreu, databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic Federal University of Rio de Janeiro, Brazil probes and competitor frequently used for the quantification of marine picoplankton. Tom Bibby, We performed tests on cell cultures to decrease the risk for non-specific hybridization, University of Southampton, before they are used on environmental samples. The probes were confronted to recent United Kingdom databases and hybridization conditions were tested against target strains matching *Correspondence: Isabelle C. Biegala perfectly with the probes, and against the closest non-target strains presenting one [email protected] -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
Potential Probiotic Bacillus Subtilis Isolated from a Novel Niche
microorganisms Article Potential Probiotic Bacillus subtilis Isolated from a Novel Niche Exhibits Broad Range Antibacterial Activity and Causes Virulence and Metabolic Dysregulation in Enterotoxic E. coli Sudhanshu Sudan 1, Robert Flick 2, Linda Nong 3 and Julang Li 1,* 1 Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] 2 Biozone, Mass Spectrometry and Metabolomics, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; robert.fl[email protected] 3 Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] * Correspondence: [email protected] Abstract: Microbial life in extreme environments, such as deserts and deep oceans, is thought to have evolved to overcome constraints of nutrient availability, temperature, and suboptimal hygiene environments. Isolation of probiotic bacteria from such niche may provide a competitive edge over traditional probiotics. Here, we tested the survival, safety, and antimicrobial effect of a recently isolated and potential novel strain of Bacillus subtilis (CP9) from desert camel in vitro. Antimicrobial assays were performed via radial diffusion, agar spot, and co-culture assays. Cytotoxic analysis was Citation: Sudan, S.; Flick, R.; Nong, performed using pig intestinal epithelial cells (IPEC-J2). Real time-PCR was performed for studying L.; Li, J. Potential Probiotic Bacillus the effect on ETEC virulence genes and metabolomic analysis was performed using LC-MS. The subtilis Isolated from a Novel Niche results showed that CP9 cells were viable in varied bile salts and in low pH environments. CP9 Exhibits Broad Range Antibacterial showed no apparent cytotoxicity in IPEC-J2 cells. -
Arxiv.Org | Cornell University Library, July, 2019. 1
arXiv.org | Cornell University Library, July, 2019. Extremophiles: a special or general case in the search for extra-terrestrial life? Ian von Hegner Aarhus University Abstract Since time immemorial life has been viewed as fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles. Knowledge of their emergence, adaptability, and limitations seems to provide a guideline for the search of extra-terrestrial life, since some extremophiles presumably can survive in extreme environments such as Mars, Europa, and Enceladus. Due to physico-chemical constraints, the first life necessarily came into existence at the lower limit of it‟s conceivable complexity. Thus, the first life could not have been an extremophile, furthermore, since biological evolution occurs over time, then the dual knowledge regarding what specific extremophiles are capable of, and to the analogue environment on extreme worlds, will not be sufficient as a search criterion. This is because, even though an extremophile can live in an extreme environment here-and-now, its ancestor however could not live in that very same environment in the past, which means that no contemporary extremophiles exist in that environment. Furthermore, a theoretical framework should be able to predict whether extremophiles can be considered a special or general case in the galaxy. Thus, a question is raised: does Earth‟s continuous habitability represent an extreme or average value for planets? Thus, dependent on whether it is difficult or easy for worlds to maintain the habitability, the search for extra- terrestrial life with a focus on extremophiles will either represent a search for dying worlds, or a search for special life on living worlds, focusing too narrowly on extreme values. -
Archaeal Distribution and Abundance in Water Masses of the Arctic Ocean, Pacific Sector
Vol. 69: 101–112, 2013 AQUATIC MICROBIAL ECOLOGY Published online April 30 doi: 10.3354/ame01624 Aquat Microb Ecol FREEREE ACCESSCCESS Archaeal distribution and abundance in water masses of the Arctic Ocean, Pacific sector Chie Amano-Sato1, Shohei Akiyama1, Masao Uchida2, Koji Shimada3, Motoo Utsumi1,* 1University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305-8572, Japan 2National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki 305-8506, Japan 3Tokyo University of Marine Science and Technology, Konan, Minato-ku, Tokyo 108-8477, Japan ABSTRACT: Marine planktonic Archaea have been recently recognized as an ecologically impor- tant component of marine prokaryotic biomass in the world’s oceans. Their abundance and meta- bolism are closely connected with marine geochemical cycling. We evaluated the distribution of planktonic Archaea in the Pacific sector of the Arctic Ocean using fluorescence in situ hybridiza- tion (FISH) with catalyzed reporter deposition (CARD-FISH) and performed statistical analyses using data for archaeal abundance and geochemical variables. The relative abundance of Thaum - archaeota generally increased with depth, and euryarchaeal abundance was the lowest of all planktonic prokaryotes. Multiple regression analysis showed that the thaumarchaeal relative abundance was negatively correlated with ammonium and dissolved oxygen concentrations and chlorophyll fluorescence. Canonical correspondence analysis showed that archaeal distributions differed with oceanographic water masses; in particular, Thaumarchaeota were abundant from the halocline layer to deep water, where salinity was higher and most nutrients were depleted. However, at several stations on the East Siberian Sea side of the study area and along the North- wind Ridge, Thaumarchaeota and Bacteria were proportionally very abundant at the bottom in association with higher nutrient conditions. -
Oceans of Archaea Abundant Oceanic Crenarchaeota Appear to Derive from Thermophilic Ancestors That Invaded Low-Temperature Marine Environments
Oceans of Archaea Abundant oceanic Crenarchaeota appear to derive from thermophilic ancestors that invaded low-temperature marine environments Edward F. DeLong arth’s microbiota is remarkably per- karyotes), Archaea, and Bacteria. Although al- vasive, thriving at extremely high ternative taxonomic schemes have been recently temperature, low and high pH, high proposed, whole-genome and other analyses E salinity, and low water availability. tend to support Woese’s three-domain concept. One lineage of microbial life in par- Well-known and cultivated archaea generally ticular, the Archaea, is especially adept at ex- fall into several major phenotypic groupings: ploiting environmental extremes. Despite their these include extreme halophiles, methanogens, success in these challenging habitats, the Ar- and extreme thermophiles and thermoacido- chaea may now also be viewed as a philes. Early on, extremely halo- cosmopolitan lot. These microbes philic archaea (haloarchaea) were exist in a wide variety of terres- first noticed as bright-red colonies trial, freshwater, and marine habi- Archaea exist in growing on salted fish or hides. tats, sometimes in very high abun- a wide variety For many years, halophilic isolates dance. The oceanic Marine Group of terrestrial, from salterns, salt deposits, and I Crenarchaeota, for example, ri- freshwater, and landlocked seas provided excellent val total bacterial biomass in wa- marine habitats, model systems for studying adap- ters below 100 m. These wide- tations to high salinity. It was only spread Archaea appear to derive sometimes in much later, however, that it was from thermophilic ancestors that very high realized that these salt-loving invaded diverse low-temperature abundance “bacteria” are actually members environments. -
Arsenite Efflux Limits Microbial Arsenic Volatilization
Arsenite eux limits microbial arsenic volatilization Changdong Ke Huaqiao University Qingyue Kuang Huaqiao University Chungui Zhao ( [email protected] ) Jiafu Luo Huaqiao University Wenzhang Wei Huaqiao University Hend A. Alwathnani King Suad University Quaiser Saquib King Saud University Yanshuang Yu King Suad University Christopher Rensing Fujian Agriculture and Forestry University Suping Yang Huaqiao University Research article Keywords: Arsenic, As eux transporter, As methylation, Rhodopseudomonas palustris Posted Date: July 4th, 2019 DOI: https://doi.org/10.21203/rs.2.10508/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: Arsenic (As) methylation is regarded as a potential way to volatize and thereby remove As from the environment. However, most microorganisms conducting As methylation display low As volatilization eciency as As methylation is limited by As eux transporters as both processes compete for arsenite [As(III)]. In the study, we deleted arsB and acr3 from Rhodopseudomonas palustris CGA009, a good model organism for studying As detoxication, and further investigated the effect of As(III) eux transporters on As methylation. Results: Two mutants were obtained by gene deletion. Compared to the growth inhibition rate (IC50) [1.57±0.11 mmol/L As(III) and 2.67±0.04 mmol/L arsenate [As(V)] of wildtype R. palustris CGA009, the As(III) and As(V) resistance of the mutants decreased, and IC50 value of the R. palustris CGA009 ∆arsB mutant was 1.47±0.02 mmol/L As(III) and 2.12±0.03 mmol/L As(V), respectively, and that of the R. -
Prokaryotes, Protists, Reconstructing the Photosynthesis, Evolution of Living Things
Prokaryotes, Protists, Reconstructing the Photosynthesis, evolution of living things Endosymbiosis • Systematists study evolutionary relationships Ch 28 & 29 •Look for shared derived (=different from ancestor) traits to group organisms • Evidence used: morphology, 26 February 2009 development, and molecular data (especially DNA sequences) ECOL 182R UofA K. E. Bonine 1 2 Why can’t we figure it out perfectly? • More distant history is obscured by more changes trypanosomes • Among oldest lineages of Bacteria and Archaea in particular, lots of “lateral gene transfer.” Makes it difficult to infer relationships from phylogeny of red blood cells single genes. 3 4 Early prokaryote fossil Diversity of Prokaryotes Bacteria & Archaea 5 6 1 What are microbes? Life can be divided into 3 domains • Only a minority make us sick •Robert Koch, Germ Theory of Disease • In ordinary English, might be anything small 3.8bya –bacteria 1.5bya –yeast –protists – viruses •Prokaryotes = bacteria + archaea • In science, classify by evolutionary • Prokaryote was ancestral and only form for relationships… 7 billions of years 8 Eukarya Scheme has been revised before: Haeckel (1894) Whittaker (1959) Woese (1977) Woese (1990) Three kingdoms Five kingdoms Six kingdoms Three domains Eubacteria Bacteria Monera (prokaryotes) Protista Archaebacteria Archaea Protista Protista Fungi Fungi Plantae Eukarya are Prokaryotes monophyletic, Plantae Plantae Animalia Animalia Animalia paraphyleticparaphyletic, polyphyletic? 9 modified from Wikipedia 10 Shared by all 3 domains Unique to