MICR20010I (1).pptx

MICR20010 Agricultural Microbiology Dr. Tadhg Ó Cróinín Final Announcements • All practical reports for practical 2 should be submitted by 29th Nov but if anyone who attended the lab is intending to submit a late report (with grade penalty) this needs to be submitted by 5pm Wednesday December 6th...

MICR20010 Agricultural Microbiology Dr. Tadhg Ó Cróinín Final Announcements • All practical reports for practical 2 should be submitted by 29th Nov but if anyone who attended the lab is intending to submit a late report (with grade penalty) this needs to be submitted by 5pm Wednesday December 6th as submission link will then disappear. • MCQ practical exam results are on brightspace under the Quiz tab and will be converted to grades using the standard UCD conversion scale. • Final exam is scheduled in RDS for Friday 15th December at 16.30. Worth 70% of grade. Some tips at end of lecture. 2 MICR20010 - remaining lectures • Lecture 11 – Microorganisms and Disease • Lecture 12 – The Immune System • Lecture 13 - Pathogenic Bacteria • Lecture 14 – Pathogenic Fungi and Viruses • Lecture 15 – Antibiotic Resistant Microorganisms • Lecture 16 – Identification of Microorganisms • Lecture 17 – Microbiology in the Food Industry – The Fungi • Lecture 18 – Microbiology in the Food Industry Fermentations • Lecture 19 – The Nitrogen Cycle Important Cycles for life on earth • Carbon cycle • Oxygen Cycle • Nitrogen Cycle • Others are “minor” but still critical • Microorganisms play key roles in all 4 Carbon Cycle 5 Oxygen Cycle 6 Importance of Microorganisms • Microorganisms such as Prochlorococcus account for a huge percentage (20% by some estimates) of photosynthetic oxygen production on the planet • This is more than all the tropical rain forests combined. • Other organisms such as marine Algae play a critical role • Need to also remember the historical context and endsymbiosis. 7 The arrival of Oxygen based metabolism • Iron oxide bands from cyanobacterial photosynthesis • Makes a huge difference to energy production and evolution of life Time Line • Oxygen available as an electron carrier • Much greater potential for energy than in the anoxic environment • Ozone layer protects from UV allowing for more stable DNA From Prokaryote to Eukaryote So what about Nitrogen? 11 Micro-organisms and the Nitrogen cycle. Healthy/normal Phosphate-deficient Potassium-deficient Nitrogen-deficient Nitrogen: • Basic element for life- proteins, nucleic acids • An element that is plentiful in the atmosphere (78%) • However, we and most other life forms cannot use this form of Nitrogen. • Micro-organisms play a key role in providing us access to usable nitrogen sources. Brock 10th ed, Fig 19.29 Nitrogen: Brock 10th ed, Fig 17.36 Nitrogen: Brock 10th ed, Fig 17.36 Nitrogen: Brock 10th ed, Fig 17.36 Nitrogen: Brock 10th ed, Fig 17.36 Nitrogen: Brock 10th ed, Fig 17.36 Nitrogen: 3 major processes of m/o transformation 1. Nitrogen fixation 2. Denitrification 3. Nitrification 1. Nitrogen fixation: reduction • N2= major reservoir, very stable • NH3 is more usable nitrogen form • Only certain prokaryotes can fix N2 • Free living • Symbiotic • The key enzyme in Nitrogenase Heterocysts • Anabaena a Cyanobacteria • Nitrogenase sensitive to oxygen • Heterocyst evolves to solve problem • Also gas vesicles for buoyancy 1. Nitrogen fixation: Free living:Aerobic: Azotobacter Anaerobic: purple and blue green bacteria Symbiotic: Rhizobium Symbiotic Nitrogen fixation: • Interaction between leguminous plants + certain Gram neg. N fixing m/os • Legumes=plants that bear seeds in pods • Agriculturally- these plants can grow well in low N levels Brock 10th ed, Fig19.62 Brock 10th ed, Fig 19.63 Stages of Root Nodule formation: 1. Recognition 2. Excretion 3. Bacterial Invasion of root hair 4. Travel to main root 5. Formation of modified bacterial cells, bacteroids 6. Continued plant + bacterial division Brock 10th ed, Fig 19.65 Brock 10th ed, Fig 19.65 CAC e_ Bacteroid: needs 1. 2. Nitrogenase Energy source from plant. 1. CAC intermediates given to m/o 2. Succinate, malate, fumarate act as edonors 3. NH3 is 1st stable product—assimilation into organic nitrogen is carried out by pant. 4. Oxygen levels maintained low by leghemoglobin Returning Nitrogen to the atmosphere 1. Denitrification 2. Ammonification 3. Nitrification 4. Anammox 1. Denitrification NO3- Brock 10th ed, Fig 19.29 Denitrification 1. 2. Main biological means of forming N2 Can be detrimental  Nitrate fertilised fields once waterlogged anoxicdenitrificationfix Nitrogen removed 3. Beneficial for removing nitrate from water  Reduces algal growth on discharge of water Fertiliser: Anhydrous ammonia– used as nitrogen fertiliser Nitrapyrin-can be added to inhibit nitrification N2 in fertilisers +: High performance agriculture -: nitrate accumulation in ground water (consumption is associated with disease) NO3- presence- problems • Get increase in algae + cyanobacteria due to nutrients • These develop in response to pollution Returning Nitrogen to the atmosphere 1. Denitrification 2. Ammonification 3. Nitrification 4. Anammox Ammonification: Organic-N  NH4+ amino acids, nucleotides Ammonia • release by aerobic decomposition…rapidly recycled amino acids in plants and m/os • 15% of the nitrogen released to Atmos. Returning Nitrogen to the atmosphere 1. Denitrification 2. Ammonification 3. Nitrification 4. Anammox nitrification NH4+NO3• Oxidation –in well drained soil at neutral pH • Produces nitrate • Readily assimilated by plants- but easily leached from soil • NH4+ much easier held by soil NH4+NO2- nitrosomonas NO2- NO3- nitrobacter Nitrifying Bacteria • Chemolithotrophs • Nitrosifyers and Nitrofyers • Phylum Nitrospira • High Ammonia conc. Nitrification • Nitrosococcus oceani • Nitrosifying • Nitrobacter winogradskyi • Nitrifying • Membranes play an important role Returning Nitrogen to the atmosphere 1. Denitrification 2. Ammonification 3. Nitrification 4. Anammox Anammox Anaerobic catabolism by Brocadia NO2- + NH3 2N2 oxidised Brock 10th ed, Fig 19.29 Brock 10th ed, Fig 19.29 And now for the exams……. MICR20010 – Final Exam • Final Exam – 16.30 Friday 15th December • 60 MCQ Questions over 2 hours • On Lecture Material • Worth 70% of grade • Sample questions on brightspace • https://www.ucd.ie/students/exams/examinationsinformation/ howtocompleteamultiplechoiceexam/ Final Exam Tips • Do the sample questions and familiarize yourself with the format. • Use your time wisely. • Answer all questions, there is no negative marking • If you don’t know the answer can you identify some answers as being definitely wrong? Shorten your odds!! Finally! Please get in contact if you have any questions – [email protected] Best of Luck in the Exams and the Future!