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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.

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Presentation on theme: "©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microorganisms in the Environment and Microbial Biotechnology M J Larkin."— Presentation transcript:

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2 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microorganisms in the Environment and Microbial Biotechnology M J Larkin

3 ©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.

4 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Larkin Lab Research – Biological Sciences and QUESTOR 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: Overview from keynote lecture at: Web of Knowledge – name and address function

5 ©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.

6 ©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

7 ©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 % 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 tons - more than all flora and fauna - equivalent to 2 m layer over planet! see:

8 ©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

9 ©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

10 ©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

11 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbial genome sequencing links Sanger Institute UK Lists bacterial pathogens sequenced and ongoing Joint Genome Institute USA Many environmental microorganisms and metagenomic projects Belfast connection: Pathogen Bacteroides fragilis – unprecedented gene switching mechanisms see: Rhodococcus – analysis of largest bacterial genome at 9.7 mB Gene rearrangements and adaptation see:

12 ©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

13 ©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

14 ©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!

15 ©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

16 ©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 V SO 4 2- H2SH2S V Fe 3 + Fe V FAST GROWTH SLOW GROWTH

17 ©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

18 ©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

19 ©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

20 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Biological waste-water treatment: The activated sludge process.

21 ©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

22 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Cultivation of microorganisms for industrial use.

23 ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Cultivation of microorganisms for industrial use. Advanced laboratory fermenters in the Questor Centre

24 ©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 )

25 ©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


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