BIO 163 Microbial Communities PDF

BIO 163 Prof. Jay-ann Tallad | Microbial Communities Topic Outline: • Microbes in air • Microbes in soil • Microbes in water MICROBES IN AIR Aerobiology - a study of living microbes which are suspended in the air Bioaerosols - microbes suspended in the air - they can be attach to a particle that ca...

BIO 163 Prof. Jay-ann Tallad | Microbial Communities Topic Outline: • Microbes in air • Microbes in soil • Microbes in water MICROBES IN AIR Aerobiology - a study of living microbes which are suspended in the air Bioaerosols - microbes suspended in the air - they can be attach to a particle that can be solid (dust) or liquid (droplets) CATEGORIES OF BIOAEROSOLS Classification Category Size Fine particles Nuclei mode 0.01µm to 0.1 µm (viruses) Accumulation 0.1µm to 1.0µm mode (AC) Coarse Coarse mode 1.0µm to 100µm particles (protozoa, fungi, and bacteria but can be found in AC) AIR - transport medium microorganisms can be dispersed through wind or precipitation microorganisms found in the air are usually from soil or aquatic ecosystem or from human increases occurrence of widespread diseases Relative humidity, temperature, and radiation can affect survival of microbes - Low humidity → desiccation - High temp → desiccation and protein denaturation - Low temp → freezing and ice formation in cell - Radiation → DNA mutation and ROS AEROMICROBIOLOGICAL PATHWAY (LIFE CYLCE IN ATMOSPHERE) A. launching into the air • falls/ droplets (aqutic) • cough (human) • disturbed soil (soil) B. transportation/ suspension in the air • the bigger the bioaerosols → the less time it is suspended in the air → the less distance it can cover • the small bioaerosols have more advantage in being transported category based of transportation microscale travel time is only in hours and the distance it covers is only in meters to 1km mesoscale travel time is in days macroscale travel time is in months and the distance it covers is in miles/hectares → e.g., viruses C. deposition • gravitational pull • downward molecular diffusion • surface impaction → collision with other surface • through rain/ precipitation ATMOSPHERE - ecosystem → contains water droplets, dust particles, other matter, and microorganism Atmosphere is not conducive environment for the microbes - if the bioaerosols are spore formers → they can tolerate different kind of stresses - The organism can go back to soil/aquatic sources; they are usually NOT permanent resident of atmosphere → Only use atmosphere for dispersal 1 |AGAS o Fungi • Virus • Figure 1. Life cycle of Microbes in the atmosphere Toxin exposure can cause death after 12 hrs Aspergillus fumigatus o Major airborne pathogen → opportunistic pathogen o Adapts to changing environmental conditions o Spore is small thus is capable of mass infection o Infection is through inhalation of spores Avian Influenza virus o Viral airborne pathogen o Infects broad range of animal species CLOUDS Cloud Water - mixture of organic and inorganic compounds suspended within moisture - if the microorganism is included in the water cloud, depending on the concentration, they can experience osmotic pressure Agents of dispersal of microbes Not conducive to life - freezing temperature - desiccation - extreme radiation - acidic (pH 3-7) Rain-making Bacteria • microorganism that participate in Bioprecipitation • rain or snow is produced by microorganism • Pseudomonas synringae → plant pathogen • Ice nucleation protein Z EXAMPLES OF AIRBORNE PATHOGENS Bacteria • Bacillus anthracis o Anthrax o Can resist environmental stresses because they are spore-formers ▪ Extreme temperatures ▪ Chemical contamination ▪ Low nutrient o They are used as biological weapon • Clostridium botulinum o Botulism AIR MONITORING 1. Passive monitoring • Settle plates • Inexpensive and easy to use • Rely on the gravity for deposition • Qualitative analysis of airborne microorganism o Not used in quantitative analysis because you cannot quantify the amount of air • To detect airborne contamination o Trends of contamination → consistent presence of the contaminants o Contamination of specific surfaces • Monitor air quality • Disadvantage of using passive monitoring 2 |AGAS o Viability of the biological particles → if the microbes do not form spores there’s a possibility that they cannot grow in a specific area o Does not detect smaller particle or droplet → gravity is not enough for them to settle o No specific volume of air → no quantitative analysis o Vulnerable to inference and contamination o Overgrowth in heavily contaminated conditions making the data interpretation difficult 2. Active monitoring • Sucking in of air; do not rely on gravitational pull only • Use microbiological air sampler 2. 3. 4. 5. 6. 7. • Quantitative monitoring MICROBES IN SOIL Soil - More microbes in soil than people Bacteria, actinomycetes, and protozoa dominate tilled soils - Fungal and nematode populations dominate untilled or no-till soils - “microbes eat; thus we eat” • They provide plants nutrients to assimilate SOIL STRESSES Biotic Stresses • Competition → nitrogen sources • Predation Abiotic Stresses 1. Light → yung light narereach nya lang ay surface; phototrophic organism is only found in top soil. • Without the presence of light, they are switching their metabolism in heterotrophy → They are called as switch hitter. Moisture→ (clay have finer pore, sand has big pores) if the soil has large pores therefore the water can flow easily. If the soil has finer pores the moisture is higher because it will retain the water easily Soil temperature • soil has buffering system • Soil microorganisms are mesophiles pH • acidic pH allows the leaching of nutrients • Optimal pH is neutral so that the nutrients are maintained in the area where microorganisms live Soil Texture • Sand • Silt • Clay • Mixed Nutrients Redox potential → potential of the soil to be oxidized or reduced • The chemotrophs have different types of electron terminal acceptors, which are needed for respiration or growth • Aerobic microorganisms’ electron terminal acceptor is oxygen; as long as there is oxygen they can respire or grow • As you go down the layers of the soil, there is a depletion of oxygen which leads to the competition for oxygen among microorganism → other organism uses other compounds as their electron terminal acceptor • If the redox potential of the soil is low (oxidation is high and little reduced material), growth is limited Bacteria highest population: fungi have lower population, but they have high biomass per meter square. 3 |AGAS MICROORGANISMS IN SURFACE SOILS Surface soil has higher nutrients compared to the subsurface soil; oxygen Bacteria - K-selected/ oligrotrophs → Live in areas that are not rich in nutrients → Slow metabolizers • Not all surface soils have rich vegetation; nutrients in surface soil is not evenly distributeed - R-selected/ copiotrophs → Found in rich nutrients like rhizospheres → Fast metabolism - Before, microorganisms are discovered through cultur-dependent techniques; Now, we have molecular studies to identify unidentified microorganisms - Operational taxonomic units (OTUs) → Equal to one microbial population that has not been unidentified before - Bacteriophage control the population of bacteria - Viable but nonculturabe (VBNC) microbes • They are live organism but cannot be culture - Viable but difficult to culture (VBDC) microbes • They are live organism that can be culture but difficult • Most organisms in subsurface soils are oligotrophs → Therefore, you need to dilute the media → lessen the nutrients present in order to replicate the low nutrient environment of subsurface soil Diversity is heavily affected by low nutrient content Aggregation of Soil by Microorganism Actinomycetes - Novel secondary metabolites - They produce antibiotics, anti-cancer/tumor compounds Fungi - Higher soil microbial mass Since they are saprophytes, they are crucial in nutrient cycling and decomposisition Algae - Colonize soild decoid of preformed organic matter - Important in soil formation because they can produce carbonic acid (important in weathering of rocks) through photosynthesis - Population affected by seasons → Rainy season and light are favorable to algae growth Protozoa - Amoeba as the most numerous - Population depends on bacterial population because they prey on them MICROORGANISMS IN SUBSURFACE SOILS Distribution is similar with surface soil - In patches; they are found where the nutrients are found Less cultureable microbes because of lesser amount of nutrients found in the subsurfcae soil Some organisms are important in the formation of pores; aggregation of soils happens because of the exopolysaccharides that are excreted by the bacteria; in fungi, the thread-like hyphae allow physical entrapment of the soil. ROLE OF SOIL MICROORGANISMS 1. Break down organic matter • Soil organic matter (SOM) o Composed of the living microorganisms, the dead (fresh residues), and the “very dead” (humus) o Decomposition provides energy for growth and carbon for new cells 2. Nutrient Cycling • Minerilzation of nutrients • CO2, nitrogen, phosphorus, iron, etc. 3. Creates Humus • Dark-brown jelly-like substance part of soil that remains unchanged for a long time 4 |AGAS • 4. 5. 6. 7. Helps retain soil moisture, affects soil’s cation exchange capacity o For example, sodium has low cation sorption. In the presence of potassium, sodium is displaced • Negatively charged → More cations are adsorb • Suppresses plant diseases o Humus is a good fertilizers because it is rich with nutrients o It increases the immunity or resistance of plant Creation of soil structure • Porous soil is essential for good plant growth • Binds soil o Secretes polysaccharide, gums, and glycoproteins o Fungal hyphae Fixes nitrogen • Biological nitrogen fixation (BNF)- 60% of all fixed nitrogen • Free-living and rhizobia can perform nitrogen fixation Promote plant growth • Produce substances like auxins, gibberellins, and antibiotics Control pests and diseases • Bacillus thuringiensis (Bt) o Control caterpillar, pests, beetles, and flies • Trichoderma sp. o For fungal root diseases • MBCA → Microbiological Control Agents are microorganisms that control pests and diseases MICROBES IN WATER Water microbiology Study of microorganisms living in water or can be transported by water Water - Supports growth of diverse microorgnisms - Dispersal of disease-causing microbes • Fecal cauliforms like E. Coli • Bacteria form intestinal tracts of humans ▪ Contamination of municipal water • Viruses from GIT of warm blooded animals - Differences from other habitats • Low concentration of nutrients (similar to air) • Relative homogeneity of water properties ▪ Metabolic products released are diluted • Water movement/flow ▪ Microorganisms are attached to a surface for support • Stalked bacteria • Fomation of filaments • Gelatinous balls • Freedom of movement → no iterference like in the soil ▪ Most possess flagella or cilia ROLE OF WATER MICROORGANISMS 1. Participates in nutrient cycling 2. Promote decomposition 3. Serves as food for animals 4. Produce oxygen FUNCTIONAL GROUPS OF MARINE MICROBES 1. Cyanobacteria • Photosynthesis • N2 fication • Produce blooms in eutrophic environments → Detrimental to other microorganisms 2. Other bacteria • Ubiquitous but no the most abundant • Can colonize any habitat becase they are metabolically diverse • Crucial in biogeochemical fluxes • Some are pathogens to aquatic plants and animals • Contribute to dissolve organic assimilation 3. Viruses • Most abundant group of microorganism in marine environment • 10^7 er mL of seawater and more per g of sediment • Viral biomass → 200 Mt of carbon (largest) • Phages may lyse 2-24% of bacterial population per hours o Impacts carbon and nutrient flow 4. Archaea • Mostly found in deep-sea vents and deep water 5 |AGAS 5. Fungi • As single cells or filaments • Hypomycetes • Heterotrophic o Exoenzyme to decompose plant matter and get the nutrients like Cellulose and lignin 6. Protozoa • Single celled or in colonies • Heterotrophic • Make up biofilm coating on sediments and hard surfaces together with bacteria and algae → Heterotrophic protozoans are secondary residents of the biofilm and algae is the primary Some are parasites • 7. Periphyton and Biofilm • Periphyton o Layer of algae in the biofilm o Usually found in the river • Food source of larger organisms • Important in absorbing or breaking down chemical contaminants o Exopolysaccharides are ionic therefore some of the contaminants like chemicals and metals are broken downs and used as food source 6 |AGAS