University of Guyana Bio 2107 Lecture 6 Environmental Microbiology PDF

UNIVERSITY OF GUYANA FACULTY OF NATURAL SCIENCES DEPARTMENT OF BIOLOGY BIO 2107 THE BIOLOGY OF MICROORGANISMS LECTURE 6 ENVIRONMENTAL MICROBIOLOGY (MICROBIAL ECOLOGY) Dr. Sabrina Dookie 18th October, 2024 ...

UNIVERSITY OF GUYANA FACULTY OF NATURAL SCIENCES DEPARTMENT OF BIOLOGY BIO 2107 THE BIOLOGY OF MICROORGANISMS LECTURE 6 ENVIRONMENTAL MICROBIOLOGY (MICROBIAL ECOLOGY) Dr. Sabrina Dookie 18th October, 2024  Environmental Microbiology Environmental microbiology is the study of microbial interactions, microbial processes and microbial communities in the environment. It includes the study of: ▪The structure and activities of microbial communities. ▪Microbial interactions among themselves, and with macroorganisms. ▪Population biology of microorganisms. ▪Microbial community genetics and evolutionary processes. ▪Element cycles and biogeochemical processes. ▪Microbial life in extreme and unusual environments.  Microbial Ecosystems and Habitats ▪An ecosystem is a dynamic complex of plant, animal, and microbial communities and their abiotic surroundings, all of which interact as a functional unit. ▪An ecosystem contains many different habitats, parts of the ecosystem best suited to one or a few populations. ▪ Microorganisms are ubiquitous on Earth’s surface and even deep within it; they inhabit boiling hot springs and solid ice, acidic environments near pH 0, saturated brines, environments contaminated with radionuclides and heavy metals, and the interior of porous rocks that contain only traces of water. ▪Therefore, some ecosystems are mostly or even exclusively microbial.  Microbial Ecosystems and Habitats ▪Collectively, microorganisms show great metabolic diversity and are the primary catalysts of nutrient cycles in nature. ▪The types of microbial activities possible in an ecosystem are a function of the species present, their population sizes, and the physiological state of the microorganisms in each habitat. ▪By contrast, the rates of microbial activities in an ecosystem are controlled by the nutrients and growth conditions that prevail. ▪Depending on several factors, microbial activities in an ecosystem can have minimal or profound impacts and can diminish or enhance the activities of both the microorganisms themselves and the macroorganisms that may coexist with them.  Species Diversity in Microbial Habitats ▪A group of microorganisms of the same species that reside in the same place at the Microbial Diversity same time constitutes a microbial population and may be descendants of a single cell. ▪A microbial population differs from a Species abundance (is the microbial community which consists of Species richness proportion of each species in the populations of one species living in community) association with populations of one or more other species. ▪The microbial species richness and (the total number of different species present). abundance of a community are functions of Species richness may also be expressed through the conditions that prevail and the kinds and cell identification and molecular terms by the amounts of nutrients available in the habitat. diversity of phylotypes (for example ribosomal RNA genes) observed in a given community.  Species Diversity in Microbial Habitats In some microbial habitats, such as undisturbed organic-rich soils, high species richness is common with most species present at only moderate abundance. Nutrients in such a habitat are of many different types, and this helps select for high species richness. In other habitats, such as some extreme environments, species richness is often very low and abundance of one or a few species very high. This is because the physical and chemical attributes in the environment exclude all but a handful of species, and key nutrients are present at such high levels that the highly adapted species can grow to high cell densities.  The Microbial Environment ▪Besides living in the common habitats of soil and water, microorganisms thrive in extreme environments and also reside on and within the cells of other organisms. ▪The habitat in which a microbial community resides is governed by physicochemical conditions that are determined in part by the metabolic activities of the community. For example, the organic material used by one species may have been a metabolic by-product of a second species. ▪Because microbes are very small, they directly experience only a tiny local environment; this small space is called their microenvironment. ▪Numerous microenvironments can exist in one habitat, however, the conditions within microenvironments themselves can change rapidly!  The Microbial Environment Nutrient levels and growth rates: ▪Resources typically enter an ecosystem intermittently. Microorganisms in nature often face a “feast-or-famine” existence. It is thus common for them to produce storage polymers as reserve materials when resources are abundant or scarce. ▪Extended periods of exponential microbial growth in nature are probably rare. Microorganisms typically grow in spurts, linked closely to the availability and types of resources. ▪Because all relevant physicochemical conditions in nature are rarely optimal for microbial growth at the same time, growth rates of microorganisms in nature are usually well below the maximum growth rates recorded in the laboratory.  Microbial Competition and Cooperation ▪Competition among microorganisms for resources in a habitat may be intense, with the outcome dependent on several factors, including rates of nutrient uptake, inherent metabolic rates, and ultimately, growth rates. ▪Some microbes work together to carry out transformations that neither can accomplish alone—a process called syntrophy—and these microbial partnerships are particularly important for anoxic carbon cycling. ▪Metabolic cooperation can also be seen in the activities of organisms that carry out complementary metabolisms. For example, metabolic transformations that are carried out by two distinct groups of organisms, such as those of the nitrifying Bacteria and Archaea.  Microbial Surfaces ▪Surfaces are important microbial habitats, typically offering greater access to nutrients, protection from predation and physicochemical disturbances, and a means for cells to remain in a favorable habitat, modify the habitat from their own activities, and not be washed away. ▪Flow across a colonized surface increases transport of nutrients to the surface, providing more resources than are available to planktonic cells (cells that live a floating existence) in the same environment. ▪A surface may also be provided by another organism or by a nutrient such as a particle of organic matter. For example, plant roots become heavily colonized by soil bacteria living on organic exudates from the plant.  Microbial Surfaces ▪Surface colonization may be sparse, consisting only of microcolonies not visible to the naked eye, or may consist of so many cells that microbial accumulation becomes visible. ▪In a few extreme environments that lack small animal grazers (for example, hot springs), microbial accumulation on a surface can be many centimeters in thickness. ▪Called microbial mats, such accumulations often contain highly complex yet very stable assemblages of phototrophic, chemolithotrophic, autotrophic, and heterotrophic microbes.  Microbial Biofilms ▪As bacterial cells grow on surfaces they commonly form biofilms— assemblages of bacterial cells attached to a surface and enclosed in an adhesive matrix that is the product of excretion by cells and cell death. ▪Biofilms trap nutrients for microbial growth and help prevent the detachment of cells on dynamic surfaces, such as in flowing systems. ▪Biofilms may contain one or two species or, more commonly, many species of bacteria. Biofilms are thus functional and growing microbial communities and not just cells trapped in a sticky matrix.  Microbial Biofilms ▪Biofilms are a means of microbial self-defense that increase survival. Biofilms resist physical forces that could otherwise remove cells only weakly attached to a surface. Biofilms also resist phagocytosis by protozoa and cells of the immune system, and retard the penetration of toxic molecules such as antibiotics. ▪Biofilm formation allows cells to remain in a favorable niche. Biofilms attached to nutrient-rich surfaces, such as animal tissues, or to surfaces in flowing systems fix bacterial cells in locations where nutrients may be more abundant or are constantly being replenished. ▪Third, biofilms form because they allow bacterial cells to live in close association with each other. This facilitates cell-to-cell communication, offers more opportunities for nutrient and genetic exchange, and in general increases chances for survival.  Microbial Habitats ▪Microbes are found in a wide variety of habitats. ▪They are incredibly diverse, thriving in environments that are very cold to those that are very hot. ▪They are also tolerant to conditions such as limited water availability, high salt content, and low oxygen levels. ▪However, not all microbes can survive in all habitats.  Terrestrial Microbial Habitats ▪Only one percent of microbes that live in the soil have been identified. ▪These organisms take part in the formation of soil and are essential components of the ecosystem. ▪Bacteria and fungi that live in the soil feed on organic matter such as plants and animals. ▪These microbes are very sensitive to the environment. ▪Factors such as carbon dioxide levels, oxygen levels, pH, temperature, and moisture all affect the growth of microbes in the soil.  Aquatic Microbial Habitats ▪Microbes have the ability to live in both salt and fresh water. ▪These organisms include microscopic plants and animals as well as bacteria, fungi, and viruses. ▪As with other microbes, the ones that dwell in water are adapted to specific conditions present within the environment. ▪Habitats can range from ocean water with extremely high salt content to freshwater, lakes and rivers.  Microbial Habitats on Other Organisms ▪Microbes can also live on other organisms. ▪Similar to the species found on humans, these microbes can either be beneficial or harmful to the host. ▪For example, bacteria grow in the nodules of the roots of peas and bean plants. These microbes convert nitrogen in the air to a form that the plants can use (nitrogen fixation). ▪In many ways, plants and animals have evolved as habitats for millions of microbes to call home.  Extreme Microbial Environments ▪Microbes that live in extreme environments are called extremophiles. ▪Extremophiles have become adapted to their own habitats and can tolerate high temperatures and pressures. ▪Extremophiles have been found at depths of 6.7 km inside the Earth’s crust, more than 10 km deep inside the ocean—at pressures of up to 110 MPa; from extreme acid (pH 0) to extreme basic conditions (pH 12.8); and from hydrothermal vents at 122 °C to frozen sea water, at −20 °C. ▪Extremophiles include members of all three domains of life, i.e., bacteria, archaea, and eukarya. ▪Most extremophiles are microorganisms (and a high proportion of these are archaea), but this group also includes eukaryotes such as protists (e.g., algae, fungi and protozoa) and multicellular organisms.  Microbial Symbiosis ▪Symbiosis (“living together”) is a term used to describe when organisms develop prolonged and intimate relationships with each other. ▪Microorganism + microorganism or microorganism + macroorganism. ▪Symbiosis can be divided into two categories: 1. Negative interactions 2. Positive interactions.  Microbial ‘Symbiotic’ Interactions Positive Interactions Negative Interactions Mutualism Amensalism (antagonism) Commensalism Competition Proto – cooperation Predation Syntrophism Parasitism  Mutualism (Positive Interaction) ▪It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which the mutualist and host are metabolically dependent on each other. ▪Mutualistic relationship is very specific where one member of association cannot be replaced by another species. ▪Mutualism requires close physical contact between interacting organisms. ▪Relationship of mutualism allows organisms to exist in a habitat that could not occupied by either species alone. ▪Mutualistic relationship between organisms allows them to act as a single organism.  Mutualism (Positive Interaction) Examples: ▪Rhizobium – legume association. ▪Mycorrhizae – represents a mutualistic relationship between the root system of higher plants and fungal hyphae. Examples include Ectomycorrhizae, Endoomycorrhizae, and Ectendomycorrhizae. ▪Lichens- symbiotic partnership between a fungus and an alga. The dominant partner is the fungus (mycobiont) which gives the lichen the majority of its characteristics while the alga (phycobiont) may be cyanobacteria. ▪Herbivore – microbial interactions (intestinal bacteria of ruminants, Ruminococcus flavefaciens, Ruminococcus albus, and Fibrobacter succinogenes).  Mycorrhizae symbiosis Rhizobium – legume association Herbivore - microbial Lichen symbiosis symbiosis  Commensalism (Positive Interaction) ▪Commensalism represents a relationship between two microbial populations in which one benefits and the other remains unaffected (neither harmed nor benefitted). It is a unidirectional relationship between species. ▪Example – a disease-causing microbial population opens a lesion on a host and creates an entry passage for other microbial populations. Mycobacterium leprae (which causes leprosy) opens lesions on the body surface and allows other organisms to establish secondary infections. ▪Staphylococcus: is a bacteria with numerous pathogenic species that cause infections and illnesses in humans. However, some of them are metabolic commensals that reside as a part of skin flora. S. aureus is found living in ambient conditions in nasal and oral cavities. ▪Aspergillus: is one of the few microbial species that can survive in the highly changing (alkaline and acidic) environment of the gastrointestinal tract. This fungal species does not produce any illness in normal conditions; however, if the person is immunocompromised or suffering from conditions such as tuberculosis, it can cause aspergillosis.  Proto-cooperation (Synergism) (Positive Interaction) ▪This is an association between two microbial populations in which both populations benefit from each other. It allows populations to perform metabolic activities (involving the exchange of nutrients between two species). ▪This association is different from mutualism since the association formed is NOT OBLIGATORY. ▪Example 1: the Desulfovibrio bacteria supplies hydrogen sulphide and carbon dioxide to Chromatium bacteria and in turn the Chromatium makes sulphates and organic material available to Desulfovibrio. The mixture of the two populations produce more cellular material than either alone. ▪Example 2: the interaction between N2-fixing bacteria Azotobacter (uses glucose provided by Cellulomonas) and cellulolytic bacteria such as Cellulomonas (uses nitrogen provided by azotobacter)  Syntrophism (Positive Interaction) Special kind of symbiosis between two metabolically different types of microorganisms which cooperate by short-distance metabolite transfer. Thus, both organisms together can carry out a metabolic function that neither one can do alone. It is an association in which the growth of one organism either depends on or is improved by the substrate provided by another organism. In syntrophism both organism in association gets benefits. Compound A Utilized by population 1 Compound B Utilized by population 2 Compound C utilized by both Population 1+2 Products  Syntrophism (Positive Interaction) Examples include: ▪ Methanogenic ecosystem in sludge digester Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria. Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane. ▪Lactobacillus arobinosus and Enterococcus faecalis: In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone. The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid which is produced by L. arobinosus and in turn lactobacillus require phenylalanine which is produced by Enterococcus faecalis.  Amensalism (antagonism) (Negative Interaction) ▪When one microbial population produces substances that is inhibitory to other microbial population then this inter population relationship is known as Ammensalism or Antagonism. ▪The first population which produces inhibitory substances are unaffected or may gain a competition and survive in the habitat while other population gets inhibited. ▪This chemical inhibition is known as antibiosis.  Amensalism (antagonism) (Negative Interaction) ▪Penicillin – The bread mould penicillium secretes penicillin which kills bacteria. ▪Skin (normal flora) - Fatty acid produced by skin flora inhibits many pathogenic bacteria in the skin. ▪Lactic acid produced by lactic acid bacteria in the vaginal tract: Lactic acid produced by many normal floras in the vaginal tract is inhibitory to many pathogenic organisms such as Candida albicans. ▪Thiobacillus thiooxidant: Thiobacillus thiooxidant produces sulfuric acid by oxidation of sulfur which is responsible for lowering of pH in the culture media which inhibits the growth of most other bacteria.  Competition (Negative Interaction) ▪The competition represents a negative relationship between two microbial populations in which both populations are adversely affected with respect to their survival and growth. ▪Competition occurs when both population uses the same resources such as the same space or the same nutrition, so, the microbial population achieve a lower maximum density or growth rate. ▪Microbial populations compete for any growth-limiting resources such as carbon source, nitrogen source, phosphorus, vitamins, growth factors etc. ▪Competition inhibits both populations from occupying exactly the same ecological niche because one will win the competition and the other one is eliminated.  Competition (Negative Interaction) Examples: ▪Competition between Paramecium caudatum and Paramecium aurelia: ▪ Both species of Paramecium feed on the same bacteria population when these protozoa are placed together. ▪However, P. aurelia grows at a better rate than P. caudatum due to competition.  Parasitism (Negative Interaction) ▪It is a relationship in which one population (parasite) get benefits and derive its nutrition from another population (host) in the association which is harmed. ▪The host-parasite relationship is characterized by a relatively long period of contact which may be physical or metabolic. ▪Some parasite lives outside the host cell, known as ectoparasite while other parasite lives inside the host cell, known as endoparasite.  Parasitism (Negative Interaction) Examples: Fungi: When a fungus parasites another, it is known as mycoparasitism. Necrotrophic mycoparasitism – parasite makes contact with the host, excretes a toxic substance which kills host cells and utilises the nutrients from the host. Biotrophic mycoparasitism – parasite obtains nutrients from living host cells. Viruses: Viruses are obligate intracellular parasite that exhibit great host specificity. There are many viruses that are parasites to bacteria (bacteriophage), fungi, algae, protozoa etc. Bdellovibrio: Bdellavibrio is ectoparasite to many gram-negative bacteria. The parasite Bdellovibrio penetrates the outer membrane of its host and enters periplasmic space but not inside the host cytoplasm.  Predation (Negative Interaction) It is a wide spread phenomenon when one organism (predator) engulfs or attacks another organism (prey). The prey can be larger or smaller than predator and this normally results in death of prey. Normally predator-prey interaction is of short duration. Examples of Predation: i. Protozoan-bacteria in soil: Many protozoans can feed on various bacterial population which helps to maintain count of soil bacteria at optimum level ii. Bdellovibrio, Vampirococcus, Daptobacter etc are examples of predator bacteria that can feed on wide range of bacterial population. END OF LECTURE 6