Environmental Microbiology Lecture Notes PDF

ENVIRONMENTAL MICROBIOLOGY by DR. MOHAMMAD KAFEEL A. ANSARI MSc, PhD, FCRF, ERF (Australia) DEPARTMENT OF BIOLOGY FACULTY OF NATURAL SCIENCES UNIVERSITY OF GUYANA GEORGETOWN, SOUTH AMERICA Email: [email protected]  OFFICE HOURS...

ENVIRONMENTAL MICROBIOLOGY by DR. MOHAMMAD KAFEEL A. ANSARI MSc, PhD, FCRF, ERF (Australia) DEPARTMENT OF BIOLOGY FACULTY OF NATURAL SCIENCES UNIVERSITY OF GUYANA GEORGETOWN, SOUTH AMERICA Email: [email protected]  OFFICE HOURS Dr. Mohammad Kafeel A. Ansari Reader (Associate Professor) Department of Biology Faculty of Natural Sciences E-mail: [email protected] (Primary) E-mail: [email protected] (Secondary) Contact: +592-6155-509 IN-PERSON OFFICE VIRTUAL OFFICE HOURS: HOURS: Monday 11:00 hrs. – 01:00 hrs. Tuesday, 10:30 hrs. – 12:30 OFFICE: Room No. C-8, C-Block-East, hrs. Natural Sciences Building Zoom Link: https://zoom.us/j/97647353971?pwd=NERuvWw1nDT6uXZva3uWQuBuHVSbjE.1  COURSE DESCRIPTION This course is designed to expose students to the fundamental features and importance of microorganisms and their roles in the ecosystem. The course will also focus on the applications of microorganisms to solve environmental problems and public health aspects of microbiology. It covers the history, diversity and importance of microorganisms, microbial transmission, microbes from wastewater, air and food, bioremediation, and microbial assessment. Readings, lectures, discussions, research, presentations will be used to deliver the course. Case studies and laboratory exercises will enable students to gain practical knowledge and experience on the techniques used in microbial assessment. This course offers a foundation for students seeking careers as environmental managers, microbiologists, environmental scientists, educators, etc.  COURSE ASSESSMENT S. No. Mode of Total percentage assessment 1. Tests 3@10 30% 2. Labs 10@1 10% 3. Assignment + 10% Presentations 1@10 4. Final Written Exam 50 %  ENVIRONMENTAL MICROBIOLOGY-BOOKS  ENVIRONMENTAL MICROBIOLOGY It consists by the two components as following: ENVIRONMENT + MICROBIOLOGY Environment The term “environment” was coined by the Thomas Carlyle (1795–1881) in the Lowlands of Scotland in 1828. It comes from the French word ‘Environ’ which means things that “surrounding”. The surrounding area in which animal, human, microbes and plants lives together. The study of environment or rather environmental studies is a multi- disciplinary subject which needs knowledge interest from physical sciences (physics, chemistry, mathematics), biological sciences (botany, zoology, microbiology, biochemistry), social sciences (economics, sociology, education, geography) etc.  MICROBIOLOGY Microbiology (Greek; Micro=Small, Bios=Life, Logia=Study) The term “Microbiology” was coined by French chemist Louis Pasteur (1822- 95). Microbiology can be define as the study of living organisms of microscopic size. Antonie Van Leeuwenhoek (1632-1723) is considered as “Father of Microbiology”. Leeuwenhoek also known as “Father of Bacteriology”. In 1625, the Italian Francesco Stelluti used the term “microscope”. In the 17th century Antoni van Leeuwenhoek was observed “animalcules” as microorganisms in rainwater, which later became known as bacteria, fungi and protozoa. What are Microbes? The term microbe was first used by Sedillot (1878). Microbes are microscopic organisms that are found all around us. Example: Algae, bacteria, fungi, viruses etc. Microorganisms had been on the Earth for some 4000 million years, when Dutch scientist Antoni van Leeuwenhoek started out on his pioneering microscope work in 1673.  MICROBES Microbiology (Greek; Micro=Small, Bios=Life, Logia=Study) The term “Microbiology” was coined by French chemist Louis Pasteur (1822- 95). Microbiology can be define as the study of living organisms of microscopic size. Antonie Van Leeuwenhoek (1632-1723) is considered as “Father of Microbiology”. Leeuwenhoek also known as “Father of Bacteriology”. In 1625, the Italian Francesco Stelluti used the term “microscope”. In the 17th century Antoni van Leeuwenhoek was observed “animalcules” as microorganisms in rainwater, which later became known as bacteria, fungi and protozoa. What are Microbes? The term microbe was first used by Sedillot (1878). Microbes are microscopic organisms that are found all around us. Example: Algae, bacteria, fungi, viruses etc. Microorganisms had been on the Earth for some 4000 million years, when Dutch scientist Antoni van Leeuwenhoek started out on his pioneering microscope work in 1673.  INTRODUCTION ENVIRONMENTAL MICROBIOLOGY is the study of microbial interactions, microbial processes and microbial communities in the environment (air, soil & water). It includes study of structure and activities of microbial communities. It allow microbial interactions or interactions with microorganisms. It admit the study of population biology of microorganisms. It includes analysis of microbial communities genetic and evolutionary processes. It includes microbial life in extreme and unusual environment. The root of environmental microbiology is most closely to the microbial ecology, which comprises the study of the interaction of microorganism within the environment (air, soil or water). Environmental Microbiology is the study of effect of microbes on the environment. Environmental microbiology is also related to many other disciplines. ENVIRONMENTAL MICROBIOLOGY INTERFACES WITH THE VARIOUS FIELDS OF MICROBIOLOGY  MICROBIAL ECOLOGY Microbial ecology is the relationship of microorganisms with one another and with their environment. It concerns the four major domains of life–Archaea, Bacteria, Eukaryota, and Viruses. Microorganisms, by their omnipresence, impact the entire biosphere. They are present in almost all of our planet's environments, including some of the most extreme, from acidic lakes to the deepest ocean, and from frozen environments to hydrothermal vents. Environmental microbiology vs microbial ecology Environmental microbiology is the science of interactions between microorganisms and the environments in which they occur (air, soil & water). Microbial ecology is the study of interactions between microorganisms that share a particular environment.  WHY DO WE NEED TO UNDERSTAND ENVIRONMENTAL MICROBIOLOGY? The emergence of a series of new waterborne and food-borne pathogens that posed a threat to human and animal health. The past waste disposal practices contaminate the surface and groundwater with organic and inorganic chemicals. The discovery of the structural DNA engaged the development of new technologies (like PCR) for measuring and analyzing microbes. These together caused the scientists to question the notion that our food and water supplies are safe and also allowed the development of tools to increase the ability to detect and identify microbes and their activities in the environment. Goal of environmental microbiologist To pursue the goal of environmental sustainability, which defined as “ the utilization of environmental resources for the benefit of human health and welfare without deterioration of the physical environment or the biological communities contained therein”. Critical components of these biological communities are the microbial communities housed within the environment. The challenge for the environmental microbiologists is to enhance the understanding of these communities in order to achieve environmental sustainability. HISTORY OF ENVIRONMENTAL MICROBIOLOGY The initial scientific focus of the field of environmental microbiology was on water quality and the fate of pathogens in the environment in the context of protection of public health. The roots for water quality go back to the turn of the 20th century, when the treatment of water supplies by filtration and disinfection resulted in a dramatic decrease in the incidence of typhoid fever and cholera. Until the 1960s, it could suppose that threats from waterborne disease had been eliminated. However, it could be found that some other agents, such as viruses and protozoa, were more resistant to disinfection than enteric bacteria. This concern became a reality with the discovery of waterborne outbreaks caused by the protozoan parasite Giardia and by Norovirus , both of which were found in disinfected drinking water.  HISTORY CONT’D… Water quality continues to be a major focus in environmental microbiology because new waterborne pathogens continue to emerge. One of the best documented and largest outbreaks occurred in 1993 when more than 400,000 people became ill and over 100 died in Milwaukee, Wisconsin, during a waterborne outbreak caused by the protozoan parasite Cryptosporidium. As concern about chemicals in the environment emerged in the 1960s, perhaps best highlighted by Rachel Carson’s landmark book “Silent Spring”, it became clear that this was a natural extension for the field of environmental microbiology. We now know that chemical pollutants in soil and groundwater have profound effects on human health and welfare, in terms of both potential disease that the intake of these chemicals can cause, and the economic impact of cleaning up contaminated environments.  MICROBIAL DIVERSITY Microbial diversity refers to the various types of archaea, bacteria, fungi, protists, and unicellular creatures. The biosphere is populated by a wide variety of bacteria that define the parameters of life, and establish the conditions required for the evolution and survival of other organisms. The various types of microorganisms can be divided into groups according to their diverse genomic structure, evolution, expression, their diverse physiology, cellular metabolism, and morphological characteristics.  MICROBIAL WORLD AT A GLANCE MICROBIOLOGY Applied Microbiology Pure Microbiology  APPLIED MICROBIOLOGY Food microbiology The study of microorganism causing food spoilage and food borne illness. It is all the use of microbes to produce food. Microbial biotechnology It is manipulation of microorganisms at genetics and molecular level to generate useful products, for example, generation of insulin from E. coli. Pharmaceutical microbiology The study of microorganisms which are related to the production of antibiotics, enzymes, vitamins, biologics and other pharmaceutical products and those microbes which cause pharmaceutical contamination and spoilage. Veterinary microbiology The study of microbes of veterinary importance such as probiotics and pathogens which are related to veterinary medicine.  PURE MICROBIOLOGY Bacteriology The study of bacteria. Mycology The study of fungi. Phycology The study of algae. Protozoology The study of protozoa. Virology The study of virus. Parasitology The study of parasite.  BACTERIA Bacteria Bacteria are unicellular, microscopic, prokaryotic microorganisms that contain no true nucleus. Their cell wall is made up of peptidoglycan. They have a flagellum that facilitates locomotion. Bacteria are of different types depending on their shapes and sizes. E.g., spherical-shaped bacteria are known as cocci; rod-shaped bacteria are known as bacilli; spiral-shaped, spirilla, etc. They reproduce through binary fission, transfer of genetic material occurs through transformation, transduction and conjugation, and through sporulation. Bacteria play an important role in human survival. They break down nutrients in the digestive system into simpler forms. Few bacteria such as Rhizobium are involved in nitrogen fixation. They are also used for making antibiotics and can also be used in agriculture as biopesticides. WHAT DO THEY LOOK LIKE?  SALIENT FEATURES OF BACTERIA Unicellular prokaryotic cell. Present in different shape, size and arrangement. The cell lack nucleus and membrane-bound cell organelles. Bacterial DNA is found in the cytoplasm and not packaged to form chromatin as in eukaryotic cell. Bacteria cell is 10 times smaller than the human cell. The diameter of a bacteria cell is ~1µm (10-6 m). The outer covering of a bacteria cell is the cell wall, which is rigid and provides structural integrity. The bacteria cell wall is made up of peptidoglycan or murein. Different shapes of bacteria cell are the characteristic feature of a bacteria species. Bacteria cells may contain external appendages like cilia, flagella, etc. Bacteria can be photoautotrophs, chemoautotrophs or parasites.  USEFUL BACTERIA Not all bacteria are harmful to humans. There are some bacteria which are beneficial in different ways. Listed below are few benefits of bacteria: Convert milk into curd – Lactobacillus or lactic acid bacteria Ferment food products – Streptococcus and Bacillus Help in digestion and improving the body’s immunity system – Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria Production of antibiotics, which is used in the treatment and prevention of bacterial infections – Soil bacteria HARMFUL BACTERIA There are bacteria that can cause a multitude of illnesses. They are responsible for many of the infectious diseases like pneumonia, cholera, tuberculosis, diphtheria, typhoid are some of the infectious diseases caused by bacteria.  FUNGI Fungi are eukaryotic organisms that include microorganisms such as yeasts, moulds and mushrooms. These organisms are classified under kingdom fungi. The organisms found in Kingdom fungi contain a cell wall and are omnipresent. They are classified as heterotrophs among the living organisms. These can be unicellular or multicellular with the cell wall made of chitin. These are heterotrophic and cannot synthesise their own food. They comprise membrane-bound organelles. Yeasts, moulds, mushrooms are some of the important fungi. They decompose dead plants and animals, extracting nutrients from them. Few fungi are harmful and cause fungal infections like ringworm. The others are used in making antibiotics like penicillin. Fungi such as yeast are used in the baking industries and also in the beer and wine industries.  FUNGI Fungi are eukaryotic organisms that include microorganisms such as yeasts, moulds and mushrooms. These organisms are classified under kingdom fungi. The organisms found in Kingdom fungi contain a cell wall and are omnipresent. They are classified as heterotrophs among the living organisms. These can be unicellular or multicellular with the cell wall made of chitin. These are heterotrophic and cannot synthesise their own food. They comprise membrane-bound organelles. Yeasts, moulds, mushrooms are some of the important fungi. They decompose dead plants and animals, extracting nutrients from them. Few fungi are harmful and cause fungal infections like ringworm. The others are used in making antibiotics like penicillin. Fungi such as yeast are used in the baking industries and also in the beer and wine industries. SALIENT FEATURES OF FUNGI Almost all the fungi have a filamentous structure except the yeast cells. They can be either single-celled or multicellular organisms. Fungi consist of long thread-like structures known as hyphae. These hyphae together form a mesh-like structure called mycelium. Fungi possess a cell wall which is made up of chitin and polysaccharides. The cell wall comprises a protoplast, which is differentiated into other cell parts such as cell membrane, cytoplasm, cell organelles and nuclei. The nucleus is dense, clear, with chromatin threads. The nucleus is surrounded by a nuclear membrane.  VIRUSES The term Virus was coined by the Dutch microbiologist, Martinus Willem Beijerinck in the year 1897. He called as the “Father of Virology”. Viruses are non-cellular, microscopic infectious infectious agents, made up of genetic material and protein that can only replicate inside a host cell. Schelsinger (1933) was first to determine the composition of a Virus. In 1887, the Russian botanist Dmitry Ivanovsky began his work on the Tobacco Mosaic Disease (Tobacco Mosaic virus) which could lead to the first discovery of the Virus. Viruses are still biologists’ puzzle because they show both living and nonliving characters. Hence viruses are regarded as a separate entity. It is not taken into account in Whittaker’s five kingdom classification. Viruses are tiny, smaller in its size, ranging between 20-250 nm than the smaller bacteria and change rapidly. A virus can be now defined as ultramicroscopic particle that gets inside the cell and often cause disease called cellular obligate parasites. CHARACTERISTICS OF VIRUSE Viruses are a connecting link between living and non- living. They are non-cellular microorganisms, composed of protein, nucleic acids, and lipids. They are measured in nanometers with sizes ranging from 20 nanometers to 250 nanometers and could only be seen with an electron microscope. They contain the core of nucleotides surrounded by a protein coat which could invade living cells. They are active inside host cells and reproduce inside them by infecting living cells.  ARE VIRUSES LIVING? Like living things, viruses contain genetic material and protein. But Viruses don’t act like living things. They can only reproduce inside a living cell that serve as a host. They can’t eat, can’t grow or break down food. Can’t use oxygen. Can’t function on its own. Living characteristics of virus Ability to multiply inside a host plant or animal cell. Ability to cause diseases Possession of nucleic acid, protein, enzyme, etc. Ability to undergo mutation Non-living characteristics of virus Inability to multiply extra cellularly. Absence of any metabolic activity. Absence of protoplasm, Can be crystallized.  PROTISTS The term ‘Protista’ is derived from the Greek word “protistos”, meaning “the very first”. These are simple, eukaryotic, unicellular, microscopic organisms that are neither plants nor animals. They may be autotrophic or heterotrophic. They reproduce mainly through binary fission or budding. This group includes plant-like protists such as diatoms, dinoflagellates, animal-like protists such as amoeba, and fungus-like such as slime moulds. Protists supply us with oxygen and recycle crucial nutrients to make it available to other life forms. Most protists live in water, damp terrestrial environments or even as parasites.  EUGLENA IS AN EXAMPLE OF PROTISTS The term ‘Protista’ is derived from the Greek word “protistos”, meaning “the very first”. These are simple, eukaryotic, unicellular, microscopic organisms that are neither plants nor animals. They may be autotrophic or heterotrophic. They reproduce mainly through binary fission or budding. This group includes plant-like protists such as diatoms, dinoflagellates, animal-like protists such as amoeba, and fungus-like such as slime moulds. Protists supply us with oxygen and recycle crucial nutrients to make it available to other life forms. Most protists live in water, damp terrestrial environments or even as parasites.  SALIENT FEATURES OF PROTISTS These are usually aquatic, present in the soil or in areas with moisture. Most protist species are unicellular organisms, however, there are a few multicellular protists such as kelp. Some species of kelp grow so large that they exceed over 100 feet in height. (Giant Kelp). Just like any other eukaryote, the cells of these species have a nucleus and membrane-bound organelles. They may be autotrophic or heterotrophic in nature. An autotrophic organism can create its own food and survive. A heterotrophic organism, on the other hand, has to derive nutrition from other organisms such as plants or animals to survive. Symbiosis is observed in the members of this class. For instance, kelp (seaweed) is a multicellular protist that provides otters, protection from predators amidst its thick kelp. In turn, the otters eat sea urchins that tend to feed on kelp. Parasitism is also observed in protists. Species such as Trypanosoma protozoa can cause sleeping sickness in humans. Protists exhibit locomotion through cilia and flagella. A few organisms belonging to the kingdom Protista have pseudopodia that help them to move. Protista reproduces by asexual means. The sexual method of reproduction is extremely rare and occurs only during times of stress.  ARCHAEA Archaea means “ancient”. These are unicellular, prokaryotic organisms and have a structure similar to bacteria. Their cell wall is different from bacteria and contains unique lipids that enable them to survive in extreme conditions. Archaea do not possess a peptidoglycan layer in their cell wall, unlike bacteria. They are found in extreme environmental conditions such as hot springs, marshy areas and extreme salty areas. They are also found in human gut, mouth and skin.  SALIENT FEATURES OF ARCHAEA Archaea are found in various shapes and sizes. The size ranges from 0.1 μm to over 15 μm. They occur in various forms such as spiral, sphere, and rod. Even flat square cells have been found in Haloquadratum walsbyi. Most archaea possess a cell wall. The cell walls of archaea do not contain peptidoglycan. They have pseudopeptidoglycan. They do not have a membrane-bound nucleus or cell organelles. They have a single circular chromosome and also have plasmids like bacteria. Archaea reproduce by binary fission or multiple fission. IMPORTANCE OF MICROBES  IMPORTANCE OF MICROBES Penicillium is a fungus that produces antibiotics like penicillin. Rhizobium helps in nitrogen fixation in soil, thus, increasing the fertility of the soil. Yeast is used in bakeries for making bread and cake. Blue-green algae perform nitrogen fixation. Lactobacillus is employed in dairy industries for the setting of curd and in cheese making. Many microorganisms carry out the decomposition of dead remains of plants and animals. Spirulina and yeast are used as single-cell proteins (superfood). Yeast is used on a commercial basis for the production of alcohol through fermentation. Microorganisms carry out the processing and aging of cheese. Some microbes are used as a probiotic (maintain a healthy gut of the host).  ACKNOWLEDGMENT I would like to acknowledged all sources of study materials used in this lecture. QUESTIONS PLEASE? Thank you!