Microbial Ecology and Microbiomes

Transcription

1 PowerPoint Lecture Presentations prepared by Mindy Miller-Kittrell, North Carolina State University Packet #16 Chapter #26 Microbial Ecology and Microbiomes

2 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

3 Environmental Microbiology Microbial Ecology Study of the interrelationships among microorganisms and the environment Biodiversity refers to the number of species living within a given ecosystem Biomass is the mass of all organisms in an ecosystem Microorganisms are the most abundant of all living things by either measure Levels of microbial associations exist in the environment

4 Figure 26.1 Terms to describe levels of microbial association in the environment.

5 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

6 Environmental Microbiology Microbial Ecology Role of adaptation in microbial survival Biodiversity held in balance by various checks Competition Best-adapted microbes have advantageous traits Antagonism One microbe actively inhibits the growth of another Microorganisms rarely outcompete all other rivals One microbe s metabolic activities sometimes make environment favorable for other microbes Biofilms are example of microbial cooperation

7 Environmental Microbiology Bioremediation Landfills Large pit where wastes are dumped, compacted, and buried Soil microbes break down biodegradable wastes Methanogens degrade organic molecules to methane Recalcitrant substances resist decay, degradation, or reclamation by natural means Bioremediation uses organisms to clean up toxic, hazardous, or recalcitrant compounds, degrading them to harmless compounds Well-known application is use of microbes to clean oil spills

8 Industrial Microbiology The Problem of Acid Mine Drainage Results from exposure of certain metal ores to oxygen and microbial action Resulting compounds carried into streams and rivers Causes decrease in ph Can kill fish, plants, and other organisms Acidic water unfit for human consumption Underground mining operations pose similar problems Some microbes flourish in these acidic conditions

9 Figure 26.2 The effects of acid mine drainage.

10 Figure 26.3 An acid-loving microbe.

11 Environmental Microbiology Role of Microorganisms in Biogeochemical Cycles Six elements make up most macromolecules Hydrogen, oxygen, carbon, nitrogen, sulfur, and phosphorus Many elements in chemical or physical forms are unavailable to organisms 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

12 Figure 26.4 Simplified carbon cycle.

13 Figure 26.5 Simplified nitrogen cycle.

14 Figure 26.6 Simplified sulfur cycle.

15 Environmental Microbiology Role of Microorganisms in Biogeochemical Cycle Phosphorus cycle Little change in oxidation state of environmental phosphorus 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 Phosphate-rich runoff can result in eutrophication Causes overgrowth of microorganisms called a bloom Resulting oxygen depletion allows anaerobes to flourish

16 Figure 26.7 Eutrophication

17 Environmental Microbiology Role of Microorganisms in Biogeochemical Cycle The cycling of metals Metal ions are important microbial nutrients Often involves transition from insoluble to soluble forms Allows trace metals to be used by organisms Biomining Microbes oxidize metals so the metals dissolve in water Extract mineral-rich water and reduce the ions Collect metals that come out of solution

18 Environmental Microbiology Soil Microbiology Examines the roles played by organisms living in soil The nature of soils Soil arises from the weathering of rocks Soil also produced through the actions of microorganisms

19 Figure 26.8 The soil layers and the distributions of nutrients and microorganisms within them.

20 Environmental Microbiology Soil Microbiology Factors affecting microbial abundance in soils Moisture content Moist soils support microbial growth and diversity better than dry soils Oxygen ph Oxygen dissolves poorly in water Moist soils are lower in oxygen than dry soils Anaerobes predominate in waterlogged soils Highly acidic and highly basic soils favor fungi

21 Environmental Microbiology Soil Microbiology Factors affecting microbial abundance in soils Temperature Most soil organisms are mesophiles Live well in areas without extreme summer or winter Nutrient availability Most soil microbes utilize organic matter Microbial community size determined by how much organic material is available

22 Environmental Microbiology Soil Microbiology Microbial populations in soils Microbial populations present in the soil Bacteria are numerous and found in all soil layers Archaea present but are difficult to culture and study Fungi are also populous group of microorganisms Many viruses (bacteriophage) are found in soils Algae live on or near the soil surface Most protozoa require oxygen and remain in the topsoil

23 Environmental Microbiology Soil Microbiology Microbial populations in soils Microbes perform a number of functions Cycle elements and convert them to usable form Degrade dead organisms and their wastes Produce compounds with potential human uses

24 Environmental Microbiology Soil Microbiology Soilborne diseases of humans and plants Some soil microorganisms cause disease Infections are acquired by direct contact, ingestion, or inhalation Microorganisms are deposited in soil via feces or urine Soil simply a vehicle for transmitting pathogen among hosts Majority of soilborne agents are fungal or bacterial

25 Table 26.1 Selected Soilborne Diseases of Humans and Plants

26 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 Many organisms exist in biofilms attached to surfaces Allow organisms to concentrate nutrients

27 Environmental Microbiology Aquatic Microbiology Types of aquatic habitats Divided primarily into freshwater and marine systems Freshwater systems Characterized by low salt content Groundwater, wells, springs, and surface waters Marine systems Characterized by a salt content of about 3.5% Open ocean and coastal waters Domestic water from sewage treatment and industrial waste can affect natural aquatic systems May alter water chemistry and microbial life present

28 Environmental Microbiology Aquatic Microbiology Types of aquatic habitats Freshwater ecosystems Microorganisms distributed vertically in lake systems Based on oxygen availability, light, and temperature Wave action in large lakes allows utilization of resources Stagnant waters become oxygen depleted Support anaerobic microorganisms

29 Environmental Microbiology Aquatic Microbiology Types of aquatic habitats Marine ecosystems Nutrient poor, dark, cold, and subject to great pressure Inhabited mainly by highly specialized microorganisms Must be salt tolerant and take up nutrients efficiently.

30 Figure 26.9 Vertical zonation in deep bodies of water.

31 Environmental Microbiology Aquatic Microbiology Types of aquatic habitats Specialized novel aquatic ecosystems Salt lakes, iron springs, and sulfur springs Inhabited by microorganisms adapted to the conditions Halobacterium salinarium survives the highly saline water of the Great Salt Lake

32 Environmental Microbiology Tell Me Why A blogger stated that germs (microorganisms) are dangerous and should be avoided in all cases. Why is this idea wrong?

33 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

34 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

35 Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Criteria for assessing biological threats to humans 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

36 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 Livestock in herds or flocks are most susceptible to infectious agents Many animal diseases are spread by contact or inhalation Make attack easier for terrorists

37 Biological Warfare and Bioterrorism Assessing Microorganisms as Potential Agents of Warfare or Terror Criteria for assessing biological threats to agriculture crops Plant diseases are often less contagious than animal or human diseases Threats assessed on predicted extent of crop loss, delivery and dissemination potential, and containment potential Greatest threats are pathogens that cause crop loss or produce toxins Such agents exist but are not easily mass-produced Plant pathogens could remain in the environment, causing continued crop loss

38 Biological Warfare and Bioterrorism Known Microbial Threats Various microorganisms are currently considered threats as agents of bioterrorism Three types Human pathogens Animal pathogens Plant pathogens

39 Table 26.2 National Institute of Allergy and Infectious Diseases (NIAID) Microbial Bioterrorist Threats to Humans

40 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 Spread by aerosols and direct or indirect contact Entire herd must be destroyed if detected on a farm

41 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

42 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 Category A diseases are reportable Must be reported to state health departments when they occur Active monitoring helps identify unusual outbreaks Forced quarantine, distribution of antimicrobial drugs, or mass vaccination may be implemented in response to an attack

43 Figure One aspect of the response to a bioterrorist attack.

44 Biological Warfare and Bioterrorism Defense Against Bioterrorism Agroterrorism Little security protecting nation s agricultural enterprises Livestock and poultry often moved around the country 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

45 Biological Warfare and Bioterrorism The Roles of Recombinant Genetic Technology in Bioterrorism Could be used to create new or to modify biological threats Could combine traits of various agents to create novel agents No immunity would exist in the population Terrorists theoretically could make their own microbes

46 Biological Warfare and Bioterrorism The Roles of Recombinant Genetic Technology in Bioterrorism Could be used to thwart bioterrorism Scientists can identify unique genetic sequences Aid in tracking and determining the source of biological agents Genetic techniques could help develop vaccines, treatments, and pathogen-resistant crops

47 Biological Warfare and Bioterrorism Tell Me Why Compare human, animal, and plant pathogens that could be used as biological agents in terms of environmental survivability. Why are animal and plant pathogens more common in environmental reservoirs than are human pathogens?