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©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microorganisms in the Environment and Microbial Biotechnology M J Larkin
©M J Larkin Biological Sciences. The Queen’s University of Belfast. INTRODUCTION Microorganisms in the environment Where are they found? How diverse are they? Role in geochemical nutrient cycles. How do they grow and what are their requirements for growth and biodegradation? Microorganisms in waste treatment: Biodegradation and environmental clean up. Microbial production and products in industry The genomic – metagenomic future DIRECTED READING: Prescot. Ch40 microorganisms as components of the environment Ch 44 Industrial microbiology and Biotechnology.
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Larkin Lab Research – Biological Sciences and QUESTOR http://questor.qub.ac.ukhttp://questor.qub.ac.uk Basic theme is molecular biology and biochemistry of microorganisms that mediate global processes and remediation of the environment. Currently: Function of dioxygenases – structure and biochemistry Bioproducts – chiral chemicals for pharmaceutical use Diversity of biodegradative genes in environment – evolution from Archaea Metagenomic approaches Funded by UK government – BBSRC, EC and Industry Perception: http://www.qub.ac.uk/mlpage/researchoverview/space.ppt Overview from keynote lecture at: http://www.qub.ac.uk/mlpage/researchoverview/overview.ppt Web of Knowledge – name and address function
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microorganisms in the environment; Challenging conventional views of life. Sagan and Margulis (1998) “Garden of Microbial Delights”. –“ALL of the elements crucial to global life- oxygen, nitrogen,phosphorus, sulfur, carbon- return to a usable form through the intervention of microbes… Ecology is based on the restorative decomposition of microbes and molds, acting on plants and animals after they have died to return their valuable chemical nutrients to the total living system of life on earth” Gould (1996) “Life’s Grandeur” The Power of the Modal Bacter. –The first multicellular organisms do not enter the fossil record until about 580 million years ago - this is after about five sixths of life’s history have passed. Bacteria have been the stayers and keepers of life’s history.
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Where are they found? Diverse environments Virtually every environmental niche Extremes of pH and salinity Extremes of temperature and pressure Without air (Anaerobic) Growth on many chemical substrates Attached to surfaces in biofilms Geothermal vents and subterranean deposits
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Where are they found? Biomass on the planet. Most culturing analysis misses over 99% of the microbial population. Molecular techniques now reveal hidden diversity Heterotrophs - 5-20% biomass in sea waters - up to 80% of the primary production Rich bacterial communities in sub-surface strata (600 m deep) - up to 2 x 10 14 tons - more than all flora and fauna - equivalent to 2 m layer over planet! see: http://www.stephenjaygould.org/library/gould_bacteria.html http://www.stephenjaygould.org/library/gould_bacteria.html
©M J Larkin Biological Sciences. The Queen’s University of Belfast. How diverse are they? Diverse range of species Earliest life on the planet Anaerobic then aerobic Three Kingdoms Eukaryote Plants & Animals Eubacteria Archaebacteria Exteme living bacteria 3 billion years Eubacteria Plants & Animals Archaea
©M J Larkin Biological Sciences. The Queen’s University of Belfast. How diverse are they? Diversity of bacteria in soil 16s rRNA sequences reveal true diversity in soil DNA
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Genomics and Metagenomics Chain termination sequencing used for genomes to date – 800 bps per read Pyrosequencing “454” direct sequencing of single strands – 300 bps per read – but rapid. Use in analysis of RNA transcipts Use for rapid analysis of ALL DNA in environment – metagenomics Screening environment for useful genes. Expression requires suitable host E.Coli not always suitable Other hosts more useful – e.g Rhodococcus – used in many industrial processes
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbial genome sequencing links Sanger Institute UK http://www.sanger.ac.uk/Projects/ Lists bacterial pathogens sequenced and ongoing Joint Genome Institute USA http://www.jgi.doe.gov/ Many environmental microorganisms and metagenomic projects Belfast connection: Pathogen Bacteroides fragilis – unprecedented gene switching mechanisms see: http://www.sanger.ac.uk/Projects/B_fragilis/http://www.sanger.ac.uk/Projects/B_fragilis/ Rhodococcus – analysis of largest bacterial genome at 9.7 mB Gene rearrangements and adaptation see: http://www.rhodococcus.ca/
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Role in geochemical nutrient cycles. Microorganisms play a role as: PRIMARY PRODUCERS BIODEGRADERS AND CONSUMERS Critical role in cycles of many elements; Carbon and Oxygen cycle – oxygenases and oxygen fixation Nitrogen cycle – nitrogenase - denitrification Sulfur cycle – sulphate reduction Phosphorus cycle
©M J Larkin Biological Sciences. The Queen’s University of Belfast. How do they grow: requirements for biodegradation? Nutrients Carbon, Nitrogen, Phosphorus, Sulfur Many chemicals supply these Micronutrients/ trace metals/ vitamins Electron acceptors - usually O 2 Converts / burns carbon substrate to CO 2 Energy and biomass ie GROWTH
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Biodegradation SINGLE BACTERIUM BACTERIUM 2.0 m ORGANIC POLLUTANT AND NUTRIENTS (C,P,N,O,Fe,S……) GROWTH - CELL DIVISION INCREASE IN BIOMASS CO 2 evolved O 2 consumption Controlled release of energy Slow Burning!
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Oxygen and Electron Acceptors: crucial for Biodegradation reactions in the environment. SUBSTRATE METABOLISM CARBON ADP Pi ATP H 2 /2e - 2H + O2O2 ENERGY GROWTH/Biomass H2OH2O CO 2 Electron acceptor
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Role of electron acceptors; rate of biodegradation O2O2 H2OH2O 0.814V NO 3 - NO 2 - N 2 0.741V SO 4 2- H2SH2S -0.214V Fe 3 + Fe 2 + -0.185V FAST GROWTH SLOW GROWTH
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Anaerobic growth and biodegradation Organic matter Fermented Acetic Acid H 2 CO 2 + CH 4 CO 2 H 2 O Methanogenesis
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Further degradation Cell membrane Cell Biomass CO 2 Fixation of oxygen as a first step in biodegradation – the key step – biodegradion – complex biochemistry
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Biological waste treatment; Managing microorganisms for environmental cleanup Municipal waste-water treatment Biodegradation of industrial wastes petrochemicals, bulk chemical processes textiles, leathers metals Remediation of contaminated land in situ 10 x 10 6 Chemicals –8 x 10 6 Xenobiotic –1 x 10 6 Recalcitrant 0.4 x 10 6 traded at over 50 tonnes per year Toxicological/ biodegradative data on only around 5000- 6000
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Biological waste-water treatment: The activated sludge process.
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Biological waste treatment; Advanced industrial membrane reactor. WASTE -WATER CONTAINING POLLUTANTS EFFLUENT FREE OF POLLUTANT
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Cultivation of microorganisms for industrial use.
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Cultivation of microorganisms for industrial use. Advanced laboratory fermenters in the Questor Centre
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Products from Microorganisms: Overview of range of examples. Various foods and drinks Enzymes for varied uses (GM enzymes); biocatalysts Engineered proteins ( antibodies ) Vaccines and antibiotics (secondary metabolites) Primary metabolites and bulk chemicals (amino acids (glutamic acid) and organic acids (acetic acid) Pharmaceuticals and novel chiral chemicals Recovery of metals in bioleaching Biosensors (use of enzymes to specifically detect chemicals in medical and )
©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbes are everywhere ! “where the bee sucks, there suck I ----- “where the bee sucks, there suck I in a cowslip’s bell I lie” in a cowslip’s bell I lie” ------ Ariel in “The Tempest” proclaiming his ubiquity in all manifestations of life
Why are microbes important? Ecological Importance of Microbes (Applied and Environmental Microbiology Chapter 25)
Microbial Ecology Ecology: interactions among living things and their environments –Think globally act locally: microbes metabolize in microenvironments,
Chapter 27 Environmental Microbiology. Microbes live in the most widely varied habitats on Earth –due to metabolic diversity –dynamic associations occur.
Chapter 22 Lecture Outline Microbes and the Global Environment.
Ch 27 Environmental Microbiology What do Microbes do? How can we use this to our advantage?
METHANOGENS AND BIOGAS. Methanogen An anaerobic microorganism that grows in the presence of carbon dioxide and produces methane gas. Methanogens are found.
DIVERSITY!!! Bacteria and Archaea. eukaryotes prokaryotes bacteria archaea.
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Sudan Raj Panthi Advanced Remediation and Treatment (ART), Lab Biological Phosphorus Removal.
Introduction to Environmental Engineering Dr. Kagan ERYURUK.
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Circulation of Nutrients Environmental Biology Unit 2 Advanced Higher Biology.
The Biosphere Vocabulary Ecology Biosphere Species Population Community Ecosystem Biome Producer Consumer Autotroph Heterotroph Decomposer Food Chain.
Microbial Growth Chapter 4. Objectives What are the factors that influence bacteria growth? Oxygen requirements Nutrient requirements –Carbon, Nitrogen,
Phosphorus Cycle Phosphorus is essential to the energetics, genetics and structure of living systems. Phosphorus forms part of the ATP, RNA, DNA and phospholipid.
Microbial Biotechnology Commercial Production of Microorganism LECTURE 11: Biotechnology; 3 Credit hours Atta-ur-Rahman School of Applied Biosciences (ASAB)
The Biosphere Vocabulary Ecology Biosphere Species Population Community Ecosystem Biome Producer Consumer Autotroph Heterotroph Decomposer Habitat Niche.
BIOGEOCHEMICAL CYCLES 3-4
Science Standard 1a: Biogeochemical Cycles/ Nutrient Cycles Ch. 5 Sec. 2.
Ecosystems Chapters 55 & 56. Ecosystems All abiotic factors & species.
Intro to Ecosystems Chapter 55. Ecosystems All abiotic factors & species.
Microbiology of Waste Treatment/ Biodegradation of Pollutants Biology 422, Fall 2012 Michael D. Aitken Department of Environmental Sciences & Engineering.
BIO-CHEMICAL ENGINEERING. What is Chemical Engineering ?
Growth requirements. Growth Requirements Most common nutrients contain necessary elements (carbon, oxygen, nitrogen, and hydrogen) Microbes obtain nutrients.
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BioGeoChemical Cycles. ENERGY & MATTER Energy is not the only thing that moves through the ecosystem. Atoms are never destroyed... only transformed. Take.
Principles of Ecology Chapter 13. Ecologists Study Relationships Interactions and Interdependence Interactions and Interdependence Ecology – the scientific.
Section Food Chains: sequence of organisms related to one another as food and consumer Food Webs: interconnecting food chains in an ecological.
Ecosystems and Livig Organisms Chapter 4. The Gaia Theory Dynamic Equilibrium Negative Feedback Positive Feedback The Gaia Theory: The organic and inorganic.
BIOREMEDIATION Jiří Mikeš. "use of living organisms (e.g., bacteria) to clean up oil spills or remove other pollutants from soil, water, and wastewater.“
BIOGEOCHEMICAL CYCLES 3-3
Lesson Overview Lesson Overview Studying Life Lesson Overview 1.3 Studying Life.
Chapter 21 Lecture Outline Microbial Ecology. Microbiology: An Evolving Science © 2009 W. W. Norton & Company, Inc. 2 Microbes in Ecosystems Microbes.
BIOREMEDIATION Bioremediation is the use of biological systems (mainly microoganisms) for the removal of pollutants from aquatic or terrestrial systems.
The Biosphere. Chapter 3 Outline 3-1: What is Ecology? –Interactions and Interdependence –Levels of Organization –Ecological Methods 3-2: Energy Flow.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint ® Lecture Slide Presentation prepared by Christine L. Case Microbiology.
Ecology Unit Learning Goal #2: Explain relationships between matter cycles and organisms.
Microbial growth Microbial growth indicates “an increase in a population (number) of microbes, and not the size of a microbe”. Eukaryotes growth Eukaryotes.
Geochemical Cycles Science Biological Processes Involved 1.Photosynthesis –Plants convert CO 2 and H 2 O into O 2 and sugar 6CO 2 + 6H 2 O + energy.
Chapter 3. What Is Ecology? Ecology – the study of interactions among organisms and between organisms and their environment – From Greek: oikos (house)
The biogeochemical cycle is the processes by which inorganic materials move from the atmosphere or soil into living organisms and back again. Some.
Nitrogen Cycle The nitrogen cycle is the movement of nitrogen through different environmental segments.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings PowerPoint ® Lecture Slide Presentation prepared by Christine L. Case M I C R.
Nitrogen Cycle Sources Lightning Inorganic fertilizers Nitrogen Fixation Animal Residues Crop residues Organic fertilizers.
Biogeochemical Cycles. What is ecology? The scientific study of interactions among organisms and between organisms and their environment is ecology.
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The Biosphere Ch 3; Essential Standards: 2.1.1,
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