Agricultural Microbiology Lecture Notes PDF

MICR20010 Agricultural Microbiology Dr. Tadhg Ó Cróinín MICR20010 - remaining lectures • • • • • • • Lecture 10 – Microorganisms and Disease Lecture 11 – The Immune System Lecture 12 - Pathogenic Bacteria Lecture 13 – Pathogenic Fungi and Viruses Lecture 14 – Antibiotic Resistant Microorganisms...

MICR20010 Agricultural Microbiology Dr. Tadhg Ó Cróinín MICR20010 - remaining lectures • • • • • • • Lecture 10 – Microorganisms and Disease Lecture 11 – The Immune System Lecture 12 - Pathogenic Bacteria Lecture 13 – Pathogenic Fungi and Viruses Lecture 14 – Antibiotic Resistant Microorganisms Lecture 15 – Identification of Microorganisms Lecture 16 – Microbiology in the Food Industry – The Fungi • Lecture 17 – Microbiology in the Food Industry Fermentations • Lecture 18 – The Nitrogen Cycle Fermentations – Food and Drink.. • An ancient process which pre-dates the science of microbiology • Critical for the production of Beer, Wine and many Dairy products. Fermentation pathways Fermented Vegetables • Soya bean fermentation – Koji - Aerobic fermentation with Aspergillus – Moromi - Anaerobic Tetragenococcus halophila lowers pH as acid tolerant yeasts produce flavour • SaurKraut – Lactobacilli fermentation of shredded cabbage – Salt added to prevent Gram negative contaminants Fermented Meat and Fish • Various Dry Sausages – Salami, Pepperoni, Bologna etc. – Staphylococcus, Pediococcus, Micrococcus, Lactobacilli. • Fish Sauces – Variety of sauces and pastes used in Asian cooking. – Incubation of fish and shrimps and salt into sealed vessels to allow natural microflora work (mostly S. carnosus and Staphylococcus piscifermentans) Coffee and Cocoa • Coffee - Coffea arabica – Wet or dry process to obtain bean from berry – Wet process uses indigenous fungi and bacteria secreting proteolytic enzymes – Then an acidic fermentation by lactic acid bacteria • Cocoa - Theobrama cacao – To release the beans from the pods – A sequence of fermentations involving yeasts, lactic acid and acetic acid bacteria Saccharomyces cerevisiae Brewing • Ancient use of fermentation and most important economically. • Primarily S. cerevisiae but occasionally Zymomonas • Zymomonas – African palm wine or Mexican pulque. The Basics • Aerobic pathway is preferred by yeast so need to keep oxygen low to force fermentation and production of alcohol. • Carbon dioxide produced must be allowed to escape… • Glucose substrate is needed to provide the starting material. • Different approaches give different results. Wine making • Grapes used as the sugar source. • Fructose + Glucose and natural acidity • Soil, climate, grape variety, method of pressing, primary and secondary fermentations. • Red wine - made with skins - anthocyanins Making the “Must” • Grapes crushed mechanically or by hand (or foot). • Fermentation by indigenous yeasts or starter cultures. • Rate decided by temperature, pH, initial sugar content and yeast strain. The Fermentor • Typically wooden fermentors but now stainless steel mostly • Cooling required for fermentation as heat produced (1.3oC per 10g/L) • Reduce un-wanted yeasts using SO2. • Add starter culture of S. cerevesiae. • Secondary fermentation? • Clarifying agents, filtration and bottling. Wine Production Cider? • Cider production not unlike that of wine. • Often more sugar is added to help the reaction but apple juice does have high sugar levels. • But what about Beer? Where’s the sugar? The problem with Barley • Barley unsuitable as sugar source as 65% Starch • Starch must be accessed and converted to a usable sugar Malting Process - Partial Germination • Malting process used to generate enzymes (amylases) and carbon source useful for fermentation • Green malt, produced after five days of germination, is kiln dried and partly cooked in a forced flow of hot air (C). • Kilning used to preserve the malt Making Malt - The Steps • Soak or Steep for 2 days at 10-16oC. • Occasionally aerate • Germinate for 3-5 days at 16-19oC on malting floors. Aerated and turned mechanically • Kiln by drying at 50-60oC and then cure at 80110oC - arrests development, stops enzyme denaturation, adds flavour Making Wort • Malted grains provide both the enzymes and the substrate but adjuncts can be added. • Starch converted to simple sugars. • Wort prepared as the glucose source (mashing). • Then filtered Mashing - Making the Wort • Allowing the enzymes to work on the endogenous and added substrates • Various types of Mashing – Decoction mashing - First 35-40oC (protein rest), then remove some of mash and boil and reintroduce to raise temp… and repeat – Infusion mashing But what is happening? • Amylase and other enzymes breaking starch down to fermentable sugars. • Many proteases also present to break down cell walls to allow access to starch. • If enzymes limiting then commercial enzymes can be added • Finally boil the sweet wort with Hops Wort is boiled •Amylases inactivated •Starch breakdown now stopped •alpha acids and oils from hops Kills microbes in the wort •Sugars are caramelized 12 Hops are added; • • • • Bitter herb grown on a vine Have a preservative effect in the beer Stabilize flavor Hop oils have Alpha acids – bitter taste and preservative. Brewing • After preparation of Wort add yeast. • Allow to ferment for approx 3 days where large amounts of CO2 produced • Then a further 10 days Brewing: types of brewing yeasts Yeast strain type: 1. Top fermenting yeast Remain distributed in wort Carried to top by CO2 14-23C fermentation Ales S.cerevisiae Yeast strain type: 2.Bottom yeasts Settle to bottom 6-12C fermentation Saccharomyces carlsbergensis (budding yeast) Larger Differentiation of an ale yeast from a lager yeast 27oC S.carlsbergensis S. cervisiae S. Cervisiae and S. carlsbergensis will grow at 27oC 37oC S. cervisiae S.carlsbergensis S. cervisiae will grow at 37oC S. carlsbergensis will not Brewing • Allow yeast to settle to bottom • Siphon off beer into bottles and allow to age further. Distilled Beverages? Alcohol boils at 78 degrees Malt – Whiskey Wine - Brandy Molasses – Rum Grain/potatoes – Vodka Colour due to aging in barrels Economic importance? • We are one of the largest consumers of alcohol in Europe. • What is our history in brewing like? • A significant growth area.. Local breweries! Scaling up Ethanol production • 50 Billion litres from the fermentation of various feedstocks. • Industrial solvent • Biofuels Vinegar • Not only a condiment but an important preservative • A solution with greater than 4% Acetic acid • America - Cider • Europe - Wine • Britain - Malt • Key being Acetic acid bacteria Vinegar Production • Changing ethanol to Vinegar • Distilled vinegar • Acetic acid bacteria convert ethanol to acetic acid Vinegar Production Fermented Dairy products Milk • 87% water • Proteins: whey and casein • Fat- flavour • Carbohydrates- Lactose • Vitamines Cheese and Yoghurt Microorganisms involved in Dairy Fermentations • Lactococci, Lactobacilli and S. thermophilus are the main organisms. • Can be single or mixed cultures • Other organisms can be used to add flavour or texture Curdling Milk • Acidification of the milk leads to the coagulation of milk proteins - curd • This can be achieved by a pure starter culture or a mixed culture. • Rennet – enzyme mix that promotes curdling • Traditionally Calf Chymosin but now often using fungal proteases. Dairy Products A second inoculum • After curd salted a second microbial inoculum can be added and fermentation proceeds – Swiss Cheese - Propionibacterium freundenreichii flavour and gas bubbles – “Blue Cheeses” - Penecillium roqueforti inoculated into cheese – Camembert - Penicillium camemberti gives the characteristic rind and flavor • Different variations in the procedure lead to a huge variety in cheeses. Huge variation in Cheeses Dairy Products • Other Fermented milk products – Yoghurt – Buttermilk – Sour Cream • Streptococcus thermophilus Yoghurt • controlled fermentation of milk – Lactobacillus bulgaricus and Lactotococcus thermophilus (also known as Streptococcus thermophilus) • • • • Take pasteurised milk add Streptococcus thermophilus Lactobacillus bulgaricus incubate 42-45C..yoghurt • Symbiotic event: L.bulgaricus: proteases—peptides (stimulate) and lactic acid S. Thermophillus: acids (folic and formic) used by L bulgaricus for purine synthesis. The Probiotic World • The “Good Bacteria” theory • Begun by Elie Metchnikoff (1845-1916) • Later pasteur institute produces “la Ferment” • 1930s Minoru Shirota selects L. casei Shirota from Human feces… now produced by Yakult. The Probiotic World • Bifidobacteria and Lactic acid bacteria - Commensals found in gut (16 and 3% of normal flora) • Said to be useful in treating antibiotic induced diarrhea, IBS, IBD and even associated with Brain and behavior.. • Others suggest effects may be more placebo than effect • Still much research needed to find out how these organisms affect the host. In Summary • Fermentations key in Industrial Microbiology. • Critical for Dairy Industry – Cheese, Yoghurt, Probiotics • Beer and Wine – Fermentation by S. cerevesiae • Acetic acid bacteria and the production of vinegar. No lecture on Friday Final Lecture will be recorded and posted on brightspace The Nitrogen Cycle and Environmental Microbiology Dr. Tadhg Ó Cróinín