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Lecture 14: Microbiology of the built environment Microbial leaching of copper - Microbial leaching: low-grade ore(mixed metals?) is dumped in a large pile - Add weak(dilute) sulfuric acid (pH 2) is added - Want to solubilize copper - the liquid emerging from the bottom of the pile is enriched in di...

Lecture 14: Microbiology of the built environment Microbial leaching of copper - Microbial leaching: low-grade ore(mixed metals?) is dumped in a large pile - Add weak(dilute) sulfuric acid (pH 2) is added - Want to solubilize copper - the liquid emerging from the bottom of the pile is enriched in dissolved metals (Cu2+) and transported to a precipitation pond - Precipitation pond Cu0 - Bacterial oxidation of ferrous ion (Fe2+) to ferric ion (Fe3+) in the oxidation pond is critical as Fe3+ is used to oxidize other metals in the ores - quarter of all copper mined worldwide is obtained by microbial bleaching Microbial leaching of uranium and gold (GOAL IS TO SOLUBILIZE) - depends on the oxidation of U4+ to U6+ by Fe3+ with Acidithiobacillus ferrooxidans reoxidizing Fe2+ to Fe3+ - U6+ in the form of uranyl sulfate (UO2 SO4 ) is highly soluble and can be concentrated - Gold leaching: gold is deposited with minerals containing arsenic and FeS2 - some bacteria leach the arsenic and pyrite - Gold is then complexed with cyanide Acid mine drainage: an environmental problem in coal-mining regions - leaching is responsible for environmental damage - Coal or minerals are rich in sulfides - Oxidation of metal sulfide by bacteria can result in acidic conditions - Occurs when acidic mine waters are mixed with natural waters in rivers and lakes pH can drop <1 - Degrades water quality because both the acid and the dissolved metals (iron, aluminum, and heavy metals) are toxic to aquatic orgfc. anisms - Fe2+ to Fe3+ to FeS2 will result in extra H2 which acidifies Bioremediation (slow, not practical) Bioremediation of uranium-contaminated environments (from storage or processing) - groundwater contaminated with uranium - Some bacteria can convert U6+ to U4+ - U6+ is water soluble - U4+ is not water soluble - Uranium is contained, not removed - acetate is being infused into the open site, Acetate is an electron donor for reduction of U6+ to U4+, which immobilizes the uranium - Soluble to insoluble is goal Bioremediation of organic pollutants: hydrocarbon - With time, organic pollutants can be completely degraded to CO2 by microbes - Diverse bacteria, fungi, and some cyanobacteria and green algae can oxidize petroleum products aerobically - Hydrocarbon-degrading bacteria attach to oil droplets, decompose the oil, and disperse the slick - Oil-oxidizing activity is best if temperature and inorganic nutrient concentrations are optimal, so these nutrients are often added - Gasoline and crude oil storage tanks are potential habitats for hydrocarbon-oxidizing microbes - If sufficient sulfate is present in the oil, sulfate-reducing bacteria can grow and consume hydrocarbons while in the tank Bioremediation of chlorinated organics Xenobiotic compounds: synthetic chemicals that are not naturally occurring - Examples: pesticides, polychlorinated biphenyls (PCBs), munitions, dyes - Degrade extremely slowly because organisms lack enzymes to recognize these compounds - Microorganisms that degrade chlorinated compounds have a natural halogen cycle long before the introduction of manufactured chemicals - Aromatics breakdown needs to look like catechol or similar first THEN ring-cleaving dioxygenases break down rest of steps… Biodegradation of plastics - NOT readily degraded by microorganisms - Polyethylene terephthalate (PET) used to make drinking bottles is the only petroleum-based plastic that can be extensively degraded by microorganism Wastewater and drinking water treatment - Wastewater: domestic sewage or liquid industrial waste - Gray water: water resulting from washing, bathing, and cooking - Sewage: water contaminated with human and animal fecal material - Wastewater treatment: industrial-scale use of microorganisms for bioconversion - Main goals: - to reduce organic and inorganic materials to a level that no longer supports microbial growth - to eliminate potentially toxic materials - The efficiency of treatment is expressed in terms of a reduction in the biochemical oxygen demand (BOD) - BOD: The amount of dissolved oxygen consumed by microbes to completely oxidize all organic and inorganic matter in a water sample - Capacity of supporting microbial growth, how much oxygen left based on microbial consuption Multistep operation of wastewater treatment - both physical and biological processes - Primary, secondary, and sometimes advanced treatments are used - - - Primary treatment: Uses physical separation methods to separate solid and particulate organic and inorganic materials from wastewater Aerobic secondary treatment: digestive reactions carried out by microbes under aerobic conditions to treat wastewater with low levels of organic materials - Activated sludge: microorganisms in the aeration tank are responsible for oxidative degradation of the organic components of the wastewater - Aeration tank of an activated sludge installation(mirobe breakdown most of material) - Air will stir and pump to create current, heavy material will settle(clean stuff will go through the top to further treatments) - In the activated sludge process, wastewater is mixed and aerated in large tanks, and slime-forming bacteria - Wastewater flow through an activated sludge installation - Trickling filter: wastewater is distributed slowly by a rotating arm onto a bed of rocks (10-15 cm diameter) Anaerobic secondary treatment – anaerobic digester - A series of digestive and fermentative reactions carried out by various microbes under anoxic conditions in large enclosed tanks (sludge digesters or bioreactors) - Most treatment plants chlorinate the effluent after secondary treatment to reduce biological contamination Tertiary wastewater treatment: any physicochemical or biological treatment processes for further processing of secondary treatment effluent - Most complete method of treating sewage - Additional removal of organic matter and suspended solids Reduces the levels of inorganic nutrients (e.g., phosphate, nitrate, nitrite) Example: uses phosphorus-accumulating organisms to remove phosphorus - Not widely adopted owing to cost Emerging concerns - Wastewater treatment to date is designed for human and/or industrial wastes - New biologically active pollutants are being released in treated or untreated sewage - Pharmaceuticals, Personal care products, Household products, Sunscreens - New treatment systems are required to remove or degrade these chemicals Drinking water purification system - Sedimentation to remove particles - Coagulation and flocculation to form additional aggregates for sedimentation - Filtration - Disinfection – typically chlorine gas or UV irradiation Issues with water distribution systems - Water must travel through kilometers of municipal and domestic pipes to reach consumers - Lead to issues with: taste and odor; microbial growth - Elimination of microbial growth in water distribution system requires - Complete nutrient removal - Maintaining appropriate level of chlorine - Neither of the above is feasible - Opportunistic pathogens are found in water distribution systems including showerheads - opportunistic pathogens grow within protists The microbiology of homes - The microbiota of a home is very predictive of specific family, and can change within days of a change of occupancy - Flushing a toilet can release 100,000 bacteria into the air Microbially influenced corrosion of metals - Microorganisms can accelerate corrosion of metals by: - Changing pH - Changing redox - Production of corrosive metabolites - Production of corrosive microenvironments (biofilms) - Bacteria implicated in metals corrosion include: - sulfate-reducing bacteria, ferric iron-reducing bacteria, ferrous-iron oxidizing bacteria, and methanogens - Sulfate-reducing bacteria consume organic material in the anoxic wastewater, producing H2S. Then this is oxidized by sulfur-oxidizing chemolithotrophic bacteria that attach to the oxic upper (crown) pipe surface, accelerating corrosion from the production of H2SO4 (sulfuric acid). Biodeterioration:loss of structural integrity caused by microorganisms(colonize the surface of stone) Lec 15 Microbial Symbioses - - Symbiosis: close, prolonged association between two or more organisms from different species - Mutualism: relationship where both organisms interact to the benefit of both; most mutualistic organisms have coevolved over millions of years - Commensalism: relationship where one organism benefits and the other is indifferent - Parasitism: relationship where the parasite benefits while the host is harmed Between organisms - Lichens: mutualistic relationship between a fungus and an alga (or cyanobacterium) - Alga is photosynthetic and produces organic matter; many algae are nitrogen-fixing as well - The fungus provides a structure for the phototrophic partner to grow protected from erosion as well as providing dissolve inorganic nutrients - Lichens may contain bacterial and archaeal microbiota - Bacterial mutualism - “genus and species” names - Methanotrophic consortia - - - couple the activities of two anaerobes to effectively oxidizing methane to carbon dioxide in anoxic marine sediments - Use “nanowires” for direct interspecies electron transfer Plants as microbial habitats - The legume-root nodule symbiosis - The mutualistic relationship between legumes and nitrogen-fixing bacteria is one of the most important symbiosis known - Legume: plants with seeds in pods; e.g., soybeans, clover, alfalfa, beans, and peas - Rhizobia: the best known nitrogen-fixing bacteria engaged in legume-root nodule symbioses - Infection of legume roots by nitrogen-fixing bacteria leads to formation of root nodules that fix nitrogen - Features of the legume-root nodule symbiosis - leads to significant increases in combined nitrogen in soil - Nodulated legumes grow well in areas where other plants would not - different rhizobia infect different species of legumes, so the bacteria that infect peas are different than those that infect clover - Cross-inoculation group: group of related legumes that can be infected by a particular species of rhizobia - (unmodulated) = chlorosis: the result of nitrogen starvation. Leghemoglobin serves as “oxygen buffer” - Nitrogen-fixing bacteria need oxygen to generate energy for nitrogen fixation - Nitrogenase: the enzyme that fixes nitrogen are inactivated by high oxygen level - Leghemoglobin: oxygen-binding protein in the nodule binds the free oxygen and protect nitrogenase from free oxygen - The heme group of leghemoglobin cycles between the oxidized (Fe3+) and reduced (Fe2+) forms to supply enough oxygen for bacterial respiration while keeping free oxygen within the nodule low - Critical steps in root nodule formation - - - After infection, rhizobia rapidly divide in the root nodule These bacteria change shape and are called bacteroids that form a symbiosome within the nodule Attachment and infection - Roots of leguminous plants secrete organic compounds that stimulate the growth of diverse rhizosphere microbial community - If suitable rhizobia are present in the soil, they will form large populations and eventually attach to the root hairs - Cell surface proteins of rhizobia and plant, including the adhesion protein rhicadhesin of rhizobia, are involved in the attachment - After attachment, a rhizobial cell penetrates the root hair - Infection thread: a cellulosic tube formed by the plant, induced by the bacterium, that spreads down the root hair - Plant cells divide to form a tumour-like nodule consisting of plant cells filled with bacteroids - Note that some leguminous plants form nodules on their stems instead of roots Biochemistry of root nodules - Bacteroids depend on the plant to provide nutrients - Major organic compounds transported to the bacteroids are the C4 organic acids succinate, fumarate and malate - used as electron donors in two paths - TCA to ETC to get ATP - Pyruvate as electron donor - Nitrogenase converts nitrogen to ammonia, which is assimilated to glutamine and asparagine and transported throughout the plant - - Mycorrhizae: mutualisms between plant roots and fungi (grow larger) - The fungus transfers inorganic nutrients (N and P) - The plant transfer carbohydrates to the fungus - Two classes: ectomycorrhizae and endomycorrhizae - Ectomycorrhizae - Fungus remains outside the plant roots Fungal cells form an extensive sheath around the outside of the root with only a small penetration into the root tissue - Found primary in forest trees, particularly boreal and temperate forests – almost every root of every tree is mycorrhizal (ex. truffles) - Rarely found in nature except in association with roots - Some trees can form multiple mycorrhizal associations with multiple fungi - Allow exchange of nutrients and carbon between trees of the same and different species - Important for forest ecology and forest heal Endomycorrhizae - Fungal mycelium becomes deeply embed with the root tissues - Five classes, the most common is arbuscular mycorrhizae - More common than ectomycorrhizae - arbuscular mycorrhizae colonise >80% of terrestrial plants including many crop and grassland species - Cannot be cultured in pure culture - Arbuscular mycorrhizal root colonization - - - - - - - Plant roots release the hormone strigolactones, which stimulate growth of the root systems as well as germination of fungal spores and mycelial branching The fungi produce oligosaccharide signaling molecules to initiate formation of the mycorrhizal state The fungal mycelium forms an attachment structure called the hyphopodium (HP) and penetrates through the epidermal cells and cells of the outer cortex Mycelium can spread intercellularly or intracellularly in the outer cortex Heritable symbionts of insects - Microbial symbionts can be acquired from: - Environmental reservoirs (horizontal transmission) - Parent (heritable transmission) - Heritable symbionts of insects are obligate, lacking a free-living replicative stage - Divided into two classes based on host dependency - Primary symbionts – required for host reproduction - Secondary symbionts – not required for host reproduction Primary symbionts: found in several insect groups - Restricted to specialised region of the host called bacteriome - Within the bacteriome, bacterial cells reside in specialized cells called bacteriocytes Secondary symbionts: broadly distributed among insect groups - Can invade different cells or live extracellularly in insect hemolymph (body cavity fluid) - Can co-reside with primary symbionts in bacteriome or displace primary symbionts - Must confer benefits to the host; e.g., protection against pathogen Population control with secondary heritable symbionts - Wolbachia is a secondary endosymbiont of ~50% of insect species - When males of insects infected with Wolbachia mate with uninfected females, progeny are not viable - combat mosquito-borne viral diseases with promising results - In addition, transmission of viruses like dengue and yellow fever appears be reduced when mosquitoes are infected with Wolbachia - Defensive symbiosis - Production of toxic and antimicrobial chemicals: a widespread defensive strategy used by insects to deter pathogens and predators - The defensive chemical is most often the product of microorganisms symbiotically associated with the insect - Example: Rove beetle deters predators using the chemical pederin, which is synthesized by an endosymbiont Pseudomonas species - Pedrin is a cytotoxin inhibiting mitosis in eukaryotes that accumulates in the insect’s hemolymph and is deposited in its eggs, deterring insect predation on the eggs - Termites - Termites are classified as higher and lower based on phylogeny - Hind guts of termites are rich in diverse communities of anaerobes capable of digesting cellulose - Contain both acetate and organic acids producers Bioluminescent symbionts - Bioluminescence: several species of bacteria can emit light - Most bioluminescent bacteria inhabit marine environment - Some bioluminescent bacteria colonise specialised light organs of certain marine fishes and squids - The animals use light to communicate, avoid predators, and attract prey - The bacterial symbionts obtain nutrients from the host to expand populations Mammalian gut systems as microbial habitat Evolution of a herbivorous lifestyle - Phylogenetics suggests that different lineages evolved and herbivorous lifestyle - Microbial associations with certain animas led to their ability to catabolize plant fibres (cellulose, the most abundant biomass) Alternative mammalian gut systems - Herbivores have evolved twp digestive plans: - Foregut fermentation: fermentation chamber precedes the small intestine - Hindgut fermentation: uses caecum and/or large intestine - - Rumen - Ruminant animals: cows, sheep, goat, bison, muskoxen etc - Possess a special digestive organ, the rumen - Cellulose and other plant polysaccharides are digested with the help of microbes (bacteria, anaerobic fungi, protists) - Food travels from the oesophagus into the reticulo-rumen, consisting of the reticulum and rumen. The reticulum collects smaller digesta particles and moves them into the omasum. Larger particles remain in the rumen and are regurgitated as cud (partially digested fiber). Cud is chewed until food particles are small enough to pass from the reticulum into the omasum, abomasum, and intestines, in that order. The abomasum is an acidic vessel, analogous to the stomach of monogastric animals Rumen microbiota - Bacteria: 1010 – 1011/mL of rumen constituents; >300 species identified - Degradation of cellulose and starch - Archaea: 10^6 – 10^8 /mL; methanogens - Fills a functional niche of consuming the available hydrogen and carbon dioxide to methane - Major environmental impact - Ciliate protozoa: 10^4 – 10^6 /mL - Degradation of fibres and starch - Ingest bacteria for proteins - Fungi: 10^3 – 10^6 /mL; obligate anaerobes - Digestion of cellulose and other polysaccharides - Recent studies suggest they play an important role in degradation of large fibrous polysaccharides Polysaccharide-degrading enzymes and cellulosomes - Multiple enzyme activities are required for the complete digestion of polysaccharides; e.g., digestion of cellulose requires a minimum of endoglucanse, cellobiohydrolase, and beta-glucosidase activities - Cellulosomes: protein scaffold containing multiple polysaccharide-degrading enzymes found on the surface of polysaccharide-degrading, anaerobic bacteria and fungi - Efficient digestion of polysaccharides - Main fermentation products of ruminant microbes are volatile fatty acids (acetate, propionate, butyrate) and methane and carbon dioxide - Volatile fatty acids pass through the rumen wall into the bloodstream and used by the animal as its main energy source Dynamics of rumen microbial community - Microbial populations in the rumen change rapidly; e.g., population of anaerobic fungi increases rapidly and transiently following feeding with fibres - Digested microbes provide proteins for the animal - Microbial composition changes with changing diets - The bacterium Streptococcus bovis can increase from 107 /mL to 1010/mL when a fibre diet to a grain diet abruptly - Acidosis: inflammation of rumen epithelium caused by pH <5.5 (lower functional limit of rumen); severe cases can cause hemorrhaging and death - Caused by abrupt change from a fibre diet to a grain diet because S. bovis is a lactic acid producer - Prevention includes gradual transition of diets or mixture of fibre and grain diet Microbial Symbioses with Humans - Microbiome: functional collection of different microbes in a particular environmental system - all sites containing microorganisms - Different microhabitats support different microbes, skin vs mouth - Gastrointestinal Tract, Oral Cavity and Airways, Urogenital Tracts, The Skin - Cultivation independent studies have revealed microbiome diversity across body habitats - Gastrointestinal microbiota - most heavily colonised site(10^13 to 10^14 microbial cells) - Begins at birth - affect early development, health, and predisposition to disease - Consists of stomach, small intestine, and large intestine; comprises 400 m2 of surface area - Functions: - digestion of food - absorption of nutrients - production of nutrients by the indigenous microbiota - Stomach and Small Intestine - Low acidity(ph=2) prevents certain microbes from colonizing - Dif org in gastric fluid vs mucus layer - Large intestine and Colon - colon is essentially an in vivo fermentation vessel - microbiota use nutrients derived from the digestion of food - Some in lumen and some in mucosal layers - Couple hundred species found, few phyla but majority of all phylotypes are within the Bacteroidetes and Firmicutes - Gut enterotypes (classification of living organisms based on the bacteriological composition of their gut microbiota) - individuals may have mostly Firmicutes, mostly Bacteriodetes, or a mix of the two. - regulate metabolism and the host’s propensity for obesity - 3 basic enterotypes: functionally and phylogenetically distinct - #1 is enriched in Bacteroides - #2 is in Prevotella - #3 is enriched in Ruminococcus. - Many microbial metabolites or transformation products that can be generated in the gut have significant influence on host physiology. - vitamin production - modification of steroids - amino acid biosynthesis - Production of “symbiosis factors” by bacteria - such as oligosaccharides that signal to the immune system to promote tolerance of beneficial microbes Microbiota of the oral cavity - heterogeneous microbial habitat - Saliva contains antimicrobial enzymes - the tooth consists of a mineral matrix (enamel) surrounding living tissue, the dentin, and pulp - high concentrations of nutrients near surfaces in the mouth promote localized microbial growth. - bacteria is found in oral plaque and play a role in dental diseases Microbiota of the airway - thrive in the upper respiratory tract(throat up) - Enter from air while breathing - Most are trapped in the mucus of the nasal and oral passages and expelled with nasal secretions or swallowed and then killed in the stomach. - The lower respiratory tract has no normal microbiota in healthy adults (trachea down) - Ciliated mucosal cells move particles up and out of the lungs - Potential pathogens in the airway cause disease in ppl w compromised immune systems Microbiota of the urogenital tracts - In healthy individuals the kidney and bladder are sterile - The epithelial cells of the urethra are colonized by facultative aerobes. - Altered conditions can cause potential pathogens in the urethra to multiply and cause disease. - E. coli and P. mirabilis frequently cause urinary tract infections in women. - The vagina of the adult female is weakly acidic and contains significant amounts of glycogen - Lactobacillus acidophilus, a resident organism in the vagina, ferments the glycogen, producing lactic acid. - Lactic acid maintains a local acidic environment Microbiota of the skin - 10^10 skin microorganisms covering the average adult. - skin surface varies greatly in chemical composition and moisture content and can be categorized into three distinct microenvironments - Dry skin - Moist skin - Sebaceous skin - influenced by many factors including environmental factors, age, hygiene, level of activity How do we become colonized with microbes? - Community succession occurs over the first couple years, and an adult-like community develops by the age of three - Vaginal Delivery: First major step in microbial colonization - Massive fetal exposure to maternal vaginal, fecal (and skin) microbiota - Bifidobacterium species from the mother’s prenatal feces in the feces of infants born vaginally (but not by C- section) - A study of women at 35–37 weeks of gestation showed that many bacteria are shared between the rectum and the vagina - Changes in the gut microbiota during pregnancy - Vaginal microbiota + gut microbiota both change during pregnancy - Vaginal microbiota decrease diversity - Dominance of lactobacilli increase with gestational age - Adaptive changes – lactobacilli maintain low pH -> limit bacterial diversity -> prevent bacteria from ascending to the uterus - Gut microbiota decrease diversity - Dominance of high-energy-yielding fecal microbiota increase with gestational age - Adaptive changes - greater energy harvest during pregnancy to support the growth of mother and fetus Breastmilk - Lactose, fats, 200 human milk oligosaccharides(HMO) - HMOs can NOT be digested by babies - HMOs are metabolized by bacteria in the large intestine, esp. Bifidobacterium longum infantis - Promotes gut epithelia cell-to-cell adhesion - Produces sialic acid, necessary for brain development - Social primates have more oligosaccharides than solitary ones - Protects against pathogens as HMOs resembles gut glycans Mouse models for investigating the impact of the gut microbiome on health and development - Mice have a short life cycle and well-defined genetic lines and you can do experiments with them that can not be performed on humans - 1) The importance of host genetic background through selective gene knockout - 2) Effect of microbiota community composition using germ free mice colonized with different bacteria - 3) The influence of tightly controlled diets - 4) The consequences of antibiotic treatment - 5) Transfer of physiological traits through fecal transplants The Role of the Gut Microbiota in Obesity - Normal mice have 40 percent more fat than germ-free mice with the same diet - When germ-free mice were given normal mouse microbiota, they started gaining weight - Mice that are genetically obese have different microbiota than normal mice. - Obese mice have more Firmicutes and often more methanogens The Gut Microbiota and Human Obesity - Like the mouse model, obese humans have more Firmicutes than non-obese humans - Studies in obese/lean twins have shown that transfer of the gut microbiota to mice will influence the obese phenotype - The nature and transferability of gut microbiota is dependent on diet as well as genetics. Disorders Attributed to the Human Microbiome: Irritable bowel disease (IBD) and irritable bowel syndrome (IBS) - Microbiota in IBS - Heterogeneous clinical presentation (IBS-D, IBS-C) - Diarrhea predominant, constipation predominant - Low grade inflammation only in a subset of patients - Changes reported in diversity, temporal stability and metabolic activity of microbiota in IBS patients - NO consistent microbiotic signature in IBS - Transplant of IBS microbiota to germ-free rats = increase visceral hypersensitivity - Transplant of IBS microbiota to germ-free mice = increase GI transit + intestinal permeability - IBS : increased colonic VFAs produced by bacteria, correlates with increased symptom severity Maternal Immune Activation (mIA) and neuronal dysfunction - mIA involves elevated levels of inflammatory factors in the blood, placenta, and amniotic fluid during pregnancy - can be caused by viral or bacterial infection - Animal models have shown mIA to be a profound risk factor for neurochemical and behavioral abnormalities in the offspring - Human epidemiological studies have shown an association between maternal infection and neurodevelopmental disorders - For example, mIA is an environmental risk factor for a child developing autism - Influence of the gut microbiota on autistic-like behavior - poly I:C is an immunostimulant, used to simulate viral infections and mIA offspring in mice Modulation of the Human Microbiome: antibiotics - Oral antibiotics decrease ALL microbes in the human gut (both target and nontarget). - Use of antibiotics during the first few months of life increases the risk of developing IBD and other disorders related to dysbiosis - Dysbiosis: imbalance” in the gut microbial community that is associated with disease - Probiotics are live organisms that confer a health benefit to the host. - Prebiotics are typically carbohydrates that are indigestible by human hosts, but provide nutrition for fermentative gut bacteria.