Applied and Environmental Microbiology Chapter 25 Applied and Environmental Microbiology

Microorganisms are involved in producing many foods and beverages Food Microbiology Microorganisms are involved in producing many foods and beverages Fermentation produces desirable characteristics of various foods Microbial metabolism has other functions Acts as a preservative Destroys many pathogenic microbes and toxins Can add nutritional value in form of vitamins or other nutrients Microbes are used in food production Microbes can help control food spoilage © 2012 Pearson Education Inc. 2

The Roles of Microorganisms in Food Production Food Microbiology The Roles of Microorganisms in Food Production Fermentation Any desirable change to a food or beverage that occurs as a result of microbial growth Spoilage is unwanted change to a food due to various reasons Undesirable metabolic reactions Growth of pathogens Presence of unwanted microorganisms in the food © 2012 Pearson Education Inc. 3

The Roles of Microorganisms in Food Production Food Microbiology The Roles of Microorganisms in Food Production Use starter cultures in commercial food and beverage production Composed of known microorganisms Consistently perform specific fermentations Many common products result from fermentation of vegetables, meats, and dairy products © 2012 Pearson Education Inc. 4

Figure 25.1 The cheese-making process Pasteurization kills unwanted microorganisms Addition of starter bacterial culture Coagulation of milk proteins (curd formation) Disposal of liquid whey as waste product Production of unprocessed cheeses Cutting of curds Production of processed cheeses through pressing, addition of secondary microbial cultures, and aging (ripening)

The Roles of Microorganisms in Food Production Food Microbiology The Roles of Microorganisms in Food Production Products of alcoholic fermentation Alcoholic fermentation Microorganisms convert simple sugars into alcohol and carbon dioxide Specific starter cultures used in commercial applications of alcohol fermentation Various alcoholic products made through fermentation © 2012 Pearson Education Inc. 6

Figure 25.2 The wine-making process Preparation of must by stemming and crushing of grapes (or other fruit) Addition of starter culture of yeast and bacteria Fermentation of must (crushed fruit) or of juice alone into wine Clarification of wine Aging of wine Bottling of wine

Figure 25.3 The beer-brewing process Barley is moistened and germinated, producing enzymes that convert starch into sugars. Barley is then dried to halt germination, and crushed to produce malt. Mashing malt and adjuncts with warm water allows enzymatic activity to generate more sugars. Solids are removed to produce wort. Mashing kettle Addition of hops for flavoring Cooking of wort halts enzymatic activity, extracts flavor from hops, and kills the microorganisms present. Removal of hops Addition of yeast culture Wort ferments into beer. Aging, filtering or pasteurization, and bottling finish the process.

The Causes of Food Spoilage Food Microbiology The Causes of Food Spoilage Food spoilage results from intrinsic or extrinsic factors Intrinsic factors are inherent properties of the food itself Extrinsic factors involved with processing or handling of food © 2012 Pearson Education Inc. 9

Table 25.2 Factors Affecting Food Spoilage

The Causes of Food Spoilage Food Microbiology The Causes of Food Spoilage Classifying foods in terms of potential for spoilage Three categories based on likelihood of spoilage Perishable Nutrient rich, moist, and unprotected by coverings Semi-perishable Can store sealed for months without spoiling Many fermented foods are semi-perishable Nonperishable Dry or canned foods that can be stored indefinitely Often nutrient poor, dried, fermented, or preserved © 2012 Pearson Education Inc. 11

The Causes of Food Spoilage Food Microbiology The Causes of Food Spoilage The prevention of food spoilage Food-processing methods Industrial canning Eliminates mesophilic bacteria and endospores Pasteurization Lowers microbe numbers, but some microbes survive Lyophilization A vacuum draws off ice crystals from frozen foods Gamma radiation Can achieve complete sterilization © 2012 Pearson Education Inc. 12

Figure 25.4 Industrial canning

The Causes of Food Spoilage Food Microbiology The Causes of Food Spoilage The prevention of food spoilage Use of preservatives Salt and sugar remove water from the food Garlic contains allicin, which inhibits enzyme function Benzoic acid interferes with enzymatic function Certain spices and herbs interfere with the functions of membranes of microorganisms Chemical preservatives can be purposely added to foods © 2012 Pearson Education Inc. 14

The Causes of Food Spoilage Food Microbiology The Causes of Food Spoilage The prevention of food spoilage Attention to temperature during processing and storage High temperatures desirable to prevent food spoilage Proteins and enzymes become denatured Low temperatures are desirable for food storage Cold slows metabolism and retards microbial growth Listeria monocytogenes can grow in cold storage Found in certain dairy products © 2012 Pearson Education Inc. 15

Food Microbiology Foodborne Illnesses Consumption of spoiled foods or foods containing harmful microbes or their products Two categories of food poisoning Food infections Consumption of living microorganisms Food intoxications Consumption of microbial toxins rather than the microbe Symptoms include nausea, vomiting, diarrhea, fever, fatigue, and muscle cramps © 2012 Pearson Education Inc. 16

Industrial Microbiology Important field within the microbiological sciences Industrial microbiology used in various applications Microbes in fermentation Microbes in the production of several industrial products Treatment of water and wastewaters Disposal and cleanup of biological wastes Treatment of mine drainage © 2012 Pearson Education Inc. 17

Industrial Microbiology The Roles of Microbes in Industrial Fermentations Industrial fermentations Large-scale growth of particular microbes for producing beneficial compounds Examples include amino acids and vitamins © 2012 Pearson Education Inc. 18

Industrial Microbiology The Roles of Microbes in Industrial Fermentations Primary metabolites Produced during active growth and metabolism Required for reproduction or are by-products of metabolism Secondary metabolites Produced after the culture has entered stationary growth Substances are not immediately needed for growth © 2012 Pearson Education Inc. 19

Figure 25.5 Fermentation vats

Industrial Microbiology Industrial Products of Microorganisms Microorganisms produce array of industrially useful chemicals Recombinant organisms add to this diversity Produce substances not normally made by microbial cells © 2012 Pearson Education Inc. 21

Industrial Microbiology Industrial Products of Microorganisms Enzymes and other industrial products Microbial products used as food additives and supplements Include vitamins, amino acids, organic acids, dyes Alternative fuels Some microbes produce carbohydrates used as fuels Other microbes convert biomass into renewable fuels Pharmaceuticals Includes antimicrobials, recombinant hormones, and other cell regulators © 2012 Pearson Education Inc. 22

Figure 25.6 Burning methane gas released from a landfill

Industrial Microbiology Industrial Products of Microorganisms Pesticides and agricultural products Microbes used to help crop management Biosensors and bioreporters Use of microorganisms to solve environmental problems Biosensors Bacteria or microbial products combined with electronic measuring devices Bioreporters Composed of microbes with innate signaling capabilities © 2012 Pearson Education Inc. 24

Industrial Microbiology Water Treatment Water pollution Water pollution can occur three ways Physically Chemically Biologically Polluted waters support a greater than normal microbial load © 2012 Pearson Education Inc. 25

Industrial Microbiology Water Treatment Waterborne illnesses Consuming contaminated water can cause various diseases Diarrheal diseases occur worldwide Waterborne diseases rare in the United States Outbreaks are point-source infections Water treatment removes most waterborne pathogens © 2012 Pearson Education Inc. 26

Industrial Microbiology Water Treatment Treatment of drinking water Potable water is water considered safe to drink Water is not devoid of microorganisms and chemicals Levels are low enough that they are not a health concern Presence of coliforms in water indicates fecal contamination Increased likelihood that disease-causing microbes are present Treatment of drinking water involves four stages © 2012 Pearson Education Inc. 27

Figure 25.7 The treatment of drinking water-overview

Industrial Microbiology Water Treatment Water quality testing Majority of waterborne illnesses caused by fecally contaminated water Indicator organisms signal possible presence of pathogens E. coli or other coliforms used as indicator organisms E. coli is a good indicator organism Consistently found in human waste Survives in water as long as most pathogens Easily detected by simple tests © 2012 Pearson Education Inc. 29

Figure 25.8 Two water quality tests-overview

Industrial Microbiology Water Treatment Treatment of wastewater Wastewater Water that leaves homes or businesses after use Wastewater contains a variety of contaminants Treatment intended to remove or reduce contaminants Processed to reduce the biochemical oxygen demand (BOD) Oxygen needed by aerobic bacteria to metabolize wastes Levels reduced so unable to support microbial growth © 2012 Pearson Education Inc. 31

Figure 25.9 Traditional sewage treatment-overview

Figure 25.10 A home septic system Sedimentation in septic tank Filtration in leach field House Sludge (must be pumped out eventually) Pipes beneath ground distribute water through leach field

Figure 25.11 Wastewater treatment in an artificial wetland Houses and businesses of planned community release sewage Pond 1: Aeration Marsh Pond 2: Still water Meadow Aerobic digestion of wastes in water column • Soil microbes digest organics • Algae continue digestion of organics • Grasses filter out pollutants • Water Water Water Anaerobic digestion of wastes in sludge • Water release into third pond or waterway

Environmental Microbiology Studies the microorganisms as they occur in their natural habitats Microbes flourish in every habitat on Earth Microbes are important to the cycling of chemical elements © 2012 Pearson Education Inc. 35

Environmental Microbiology Microbial Ecology Study of the interrelationships among microorganisms and the environment Two aspects to consider Levels of microbial associations in the environment Role of adaptation in microbial survival © 2012 Pearson Education Inc. 36

Soil particle microhabitats Figure 25.12 The basic relationships among microorganisms and between microorganisms and the environment Biosphere Heterogeneous microbial communities (all guilds together) Soil ecosystem Guilds of related populations (e.g., photosynthetic microorganisms at surface) Soil habitats Populations of microbes inhabit microhabitats (e.g., cyanobacteria, algae) Soil particle microhabitats

Environmental Microbiology Microbial Ecology Role of adaptation in microbial survival Most microorganisms live in harsh environments Microbes must be specially adapted to survive Microbes must adapt to constantly varying conditions Extremophiles Adapted to extremely harsh conditions Can survive only in these habitats © 2012 Pearson Education Inc. 38

Environmental Microbiology Microbial Ecology Role of adaptation in microbial survival Biodiversity held in balance by various checks Competition Antagonism Cooperation © 2012 Pearson Education Inc. 39

Environmental Microbiology Bioremediation Uses organisms to clean up toxic, hazardous, or recalcitrant compounds by degrading them to harmless compounds Most known application is use of bacteria to clean oil spills © 2012 Pearson Education Inc. 40

Industrial Microbiology Two Types of Bioremediation Natural bioremediation Microbes “encouraged” to degrade toxic substances in soil or water Addition of nutrients stimulate microbe growth Artificial bioremediation Genetically modified microbes degrade specific pollutants © 2012 Pearson Education Inc. 41

Industrial Microbiology The Problem of Acid Mine Drainage Drainage results from exposure of certain metal ores to oxygen and microbial action Resulting compounds are carried into streams and rivers Causes decrease in pH Can kill fish, plants, and other organisms Acidic water unfit for human consumption Some microbes flourish in these acidic conditions © 2012 Pearson Education Inc. 42

Figure 25.13 The effects of acid mine drainage

Figure 25.14 An acid-loving microbe

Environmental Microbiology Role of Microorganisms in Biogeochemical Cycles Biogeochemical cycles Processes by which organisms convert elements from one form to another Elements often converted between oxidized and reduced forms Involve the recycling of elements by organisms © 2012 Pearson Education Inc. 45

Environmental Microbiology Role of Microorganisms in Biogeochemical Cycles Biogeochemical cycling entails three processes Production Inorganic compounds converted into organic compounds Consumption Organisms feed on producers and other consumers Decomposition Organic compounds in dead organisms converted into inorganic compounds © 2012 Pearson Education Inc. 46

Figure 25.15 Simplified carbon cycle Atmospheric CO2 and CO2 dissolved in water Decomposition Fixation (into organic carbon) Respiration Combustion Autotrophs (plants, algae, photosynthetic bacteria, protozoa, chemoautotrophic bacteria) Methane Consumption Fungi, bacteria Animals Dead organisms Fossil fuels Plastics and other artificial products

Figure 25.16 Simplified nitrogen cycle Nitrogen fixation N2 in atmosphere Denitrification Organisms (proteins, nucleic acids, etc.) NH3 NO2 Ammonification Anammox reactions Wastes, dead cells Deamination Nitrification NO3 NO2 NH4

Figure 25.17 Simplified sulfur cycle Amino acids Proteins from dead organisms Animal proteins Dissimilation Plant, algal, and prokaryotic proteins Reduction Oxidation SO42 H2S S0 Oxidation

Environmental Microbiology Role of Microorganisms in Biogeochemical Cycle Phosphorus cycle Environmental phosphorus undergoes little change in oxidation state Phosphorus converted from insoluble to soluble forms Becomes available for uptake by organisms Conversion of phosphorus from organic to inorganic forms Occurs by pH–dependent processes © 2012 Pearson Education Inc. 50

Environmental Microbiology Role of Microorganisms in Biogeochemical Cycle The cycling of metals Metal ions are important microbial nutrients Primarily involves transition from insoluble to soluble forms Allows trace metals to be be used by organisms © 2012 Pearson Education Inc. 51

Environmental Microbiology Soil Microbiology Examines the roles played by organisms living in soil Nature of soils Soil arises from the weathering of rocks Soil also produced through the actions of microorganisms © 2012 Pearson Education Inc. 52

Numbers of microorganisms Figure 25.18 The soil layers and the distributions of nutrients and microorganisms within them Organics, nutrients Numbers of microorganisms Topsoil Decrease with depth Decrease with depth but still present in bedrock Subsoil Bedrock

Environmental Microbiology Soil Microbiology Environmental factors affecting microbial abundance in soils Moisture content Moist soils support microbial growth better than dry soils Oxygen Moist soils are lower in oxygen than dry soils Oxygen dissolves poorly in water pH Highly acidic and highly basic soils favor fungi © 2012 Pearson Education Inc. 54

Environmental Microbiology Soil Microbiology Environmental factors affecting microbial abundance in soils Temperature Most soil organisms are mesophiles Nutrient availability Microbial community size determined by how much organic material is available © 2012 Pearson Education Inc. 55

Environmental Microbiology Soil Microbiology Microbial populations in soils Microbial populations present in the soil Bacteria Archaea Fungi Algae and protozoa Microbes perform a number of functions Cycle elements and convert them to usable form Degrade dead organisms Produce compounds with potential human uses © 2012 Pearson Education Inc. 56

Table 25.7 Selected Soilborne Diseases of Humans and Plants

Environmental Microbiology Aquatic Microbiology Study of microbes living in freshwater and marine environments Water ecosystems support fewer microbes than soil Due to dilution of nutrients Types of aquatic habitats Freshwater systems – characterized by low salt content Marine systems – characterized by a salt content of ~3.5% Specialized aquatic systems – salt lakes, iron springs, and sulfur springs © 2012 Pearson Education Inc. 58

Environmental Microbiology Aquatic Microbiology Types of aquatic habitats Freshwater systems Characterized by low salt content Marine systems Characterized by a salt content of ~3.5% Specialized aquatic systems Salt lakes, iron springs, and sulfur springs © 2012 Pearson Education Inc. 59

Figure 25.19 Vertical zonation in deep bodies of water-overview

Biological Warfare and Bioterrorism Microbes can be fashioned into biological weapons Bioterrorism Uses microbes or their toxins to terrorize human populations Agroterrorism Uses microbes to terrorize human populations by destroying the food supply © 2012 Pearson Education Inc. 61

Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Not all organisms have potential as biological weapons Governments have criteria to assess biological threats to humans Evaluate the potential of microorganisms to be “weaponized” Help focus research and defense efforts where needed © 2012 Pearson Education Inc. 62

Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Criteria for biological threats to humans based on: Public health impact Ability of hospitals and clinics to handle the casualties Delivery potential How easily agent can be introduced into the population Public perception Effect of public fear on ability to control an outbreak Public health preparedness Existing response measures © 2012 Pearson Education Inc. 63

Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Criteria for assessing biological threats to livestock and poultry Criteria similar to those used to evaluate potential human threats Include agricultural impact, delivery potential, and plausible deniability © 2012 Pearson Education Inc. 64

Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Criteria for assessing biological threats to agriculture crops Plant diseases generally not as contagious as animal or human diseases Criteria based on several factors Predicted extent of crop loss Delivery and dissemination potential Containment potential © 2012 Pearson Education Inc. 65

Biological Warfare and Bioterrorism Known Microbial Threats Various microorganisms considered threats as agents of bioterrorism Three types Human pathogens Animal pathogens Plant pathogens © 2012 Pearson Education Inc. 66

Table 25.8 Bioterrorist Threats to Humans in Order of Concern

Biological Warfare and Bioterrorism Known Microbial Threats Animal pathogens Divided into categories based on level of danger Some agents could potentially amplify an outbreak Infect wild animal populations in addition to livestock Foot-and-mouth disease is most dangerous of the agents It affects all wild and domestic cloven-hoofed animals © 2012 Pearson Education Inc. 68

Biological Warfare and Bioterrorism Known Microbial Threats Plant pathogens Most potential agents are fungi Dissemination could easily result in contamination of soils All agents are naturally present Detecting difference between a natural outbreak and an intentional attack would be difficult © 2012 Pearson Education Inc. 69

Biological Warfare and Bioterrorism Defense Against Bioterrorism Much can be done to limit impact of an attack Key is coupling surveillance with effective response protocols © 2012 Pearson Education Inc. 70

Figure 25.20 One aspect of the response to a bioterrorist attack

Biological Warfare and Bioterrorism Defense Against Bioterrorism Agroterrorism Little security protecting nation’s agricultural enterprises Livestock and poultry often moved without being tested for disease Many agricultural facilities are open to the public Methods to help defend against agroterrorism Screening of animals Restricting public access to agricultural facilities © 2012 Pearson Education Inc. 72

Biological Warfare and Bioterrorism The Roles of Recombinant Genetic Technology in Bioterrorism Could use to create new or modify biological threats Traits of various agents could be combined to create novel agents No immunity would exist in the population Terrorists theoretically could make their own microbes © 2012 Pearson Education Inc. 73

Biological Warfare and Bioterrorism The Roles of Recombinant Genetic Technology in Bioterrorism Could be used to thwart bioterrorism Scientists can identify unique genetic sequences May aid in tracking biological agents and determining their source Genetic techniques could help develop vaccines, treatments, and pathogen-resistant crops © 2012 Pearson Education Inc. 74