Information

2.1: The Bacteria - An Introduction - Biology

2.1: The Bacteria - An Introduction - Biology


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

Bacteria evolved some 600 million years ago, and were probably responsible for the production of the earth's atmosphere (cyanobacteria). Bacteria were discovered in the 17th century after the development of the microscope.

  • Single cell organism
  • Widely dispersed in the environment
  • Invisible to naked eye, but discernible by their actions - milk sours, wounds become septic, meat putrefies, etc.
  • Prokaryotic type cells (other organisms are eukaryotic type cells)
Major differences between prokaryotic and eukaryotic cells
Prokaryotic cells
Eukaryotic cells
No nuclear membrane: chromosome(s) in direct contact with cytoplasmChromosomes are enclosed in a double layered nuclear membrane
Simple chromosome structureComplex chromosome structure; DNA associated with histone proteins
Cell division does not involve meiosisCell division involves mitosis and meiosis
If present, cell walls contain peptidoglycan, no cellulose or chitinIf present, cell walls contain cellulose or chitin, never peptidoglycan
No mitochondria or chloroplastsMitochondria usually present, chloroplasts in photosynthetic cells
Cells contain ribosomes of only one sizeCells contains two types of ribosomes, one in cytoplasm, and smaller type in mitochondria
Flagella, if present, have a simple structureFlagella, if present, have complex structure

Note: bacteria are microorganisms, but not all microorganisms are bacteria. Algae, fungi, lichens, protozoa, viruses and subviral agents are all microorganisms (with most of these being eukaryotic type cells

Bacterial activities

Pathogenic (disease causing) bacteria:

  • Cholera (vomiting, profuse diarrhea)
  • Botulism (muscle paralysis)
  • Tetanus (uncontrollable contractions of skeletal muscle)
  • Staphylococcal food poisoning (vomiting, diarrhea)
  • Shiga toxin (verotoxin) (classic dysentery)
  • Typhoid (septicemia: bacteria in blood, destruction of host tissue)
  • Oroya fever (Bartonella bacilliformis - destroys red blood cells)
  • Endotoxic shock (lipopolysaccharide cell wall component causes release of host inflammatory agents leading to shock and death)
  • Reactive arthritis (response in some people to Salmonella infection)

Most bacteria do no harm to humans, and can be quite useful:

  • Antibiotic production
  • Enzyme additives for detergents
  • Insecticides
  • Production of biodegradable plastics
  • "Biomining" - leaching of metals from low grade ores
  • Uses in food industry
    • Butter
    • Cheese
    • Yogurt
    • Vinegar
    • Cocoa
    • Coffee
  • Soil fertility

Classifying and Naming of bacteria

Differences between bacteria can include

  • shape
  • size
  • structure
  • chemical activities
  • required nutrients
  • form of energy required
  • required environment
  • reaction to certain dyes

Family, genus, species, strain

Bacteria in the same Family, in general would have:

  • similar structure
  • use the same form of energy
  • react similarly to certain dyes

Bacteria in the same Family may be divided into different Genera based on differences in

  • chemical activities
  • nutrient requirements
  • conditions for growth
  • shape and size (to some extent)

Strains of bacteria are bacteria of the same species, but with some subtle difference (maybe a single mutational difference)

Latin binomial name

  • Name of the genus, capitalized.
  • Followed by name of species, lower case
  • Italicized. Sometimes the genus name is abbreviated to a single letter (with a period)
Escherichia coli
E. coli
  • Strain name follows, usually in parentheses. In the vernacular, the strain name is commonly used to identify the bacteria
E. coli (JM101)
E. coli (CJ236)
"Can I borrow some JM101?"

Some Characteristics of Bacteria

Shape

  • Rounded or spherical cells - cocci (singular: coccus)
  • Elongated or rod-shaped cells - bacilli (singular: bacillus)
  • Rigid spirals - spirilla (singular: spirillum)
  • Flexible spirals - spirochetes (singular: spirochete)

Note

There is a genus of bacteria called Bacillus. Some bacillus shaped bacteria belong to the genus Bacillus, some do not.

Size

  • Bacteria are usually measured in micrometers (1x10-6 m)
  • The smallest bacteria are about 0.2 micrometers (Chlamydia)
  • The largest bacteria are about 600 micrometers (Epulopiscium fishelsoni. - inhabits the gut of a fish)
  • "Average" bacteria are 1-10 micrometers (note: limit of resolution of the light microscope is about 0.2 micrometers)

A "generalized" bacterium:

Figure 2.1.1: General bacterium diagram

  • The cell's DNA is extensively folded to form a body called the nucleoid
  • The cytoplasm fills the interior of the cells, and bathes the nucleoid
  • Storage granules contain a reserve of nutrients - typically polymeric forms of b-hydroxybutyrate and phosphate. Poly-b-hydroxybutyrate is the basis of a biodegradable plastic (Biopol)

Figure 2.1.2: Poly-b-hydroxybutyrate

  • The nucleoid, ribosomes, cytoplasm and storage granules are bounded by a membranous sac, the cytoplasmic membrane (cell membrane, or plasma membrane)
  • The outermost layer is a tough cell wall. Together, the plasma membrane and cell wall are called the cell envelope
  • The region between the plasma membrane and the cell wall is called the periplasmic space
  • The flagellum is used for motility

Cytoplasmic membrane

  • lipid bilayer, 7-8 nm thick, with protein molecules partly or completely embedded
  • The inner and outer layers are hydrophilic, while the interior of the bilayer is hydrophobic
  • In E. coli the main lipid is phosphatidylethanolamine; minor lipid components include phosphatidylglycerol and diphosphatidylglycerol

Figure 2.1.3: Phospholipid bilayer

The cytoplasmic membrane proteins include:

  • enzymes involved in the synthesis of the cell wall peptidoglycan
  • transport proteins (translocated ions and molecules across the cytoplasmic membrane
  • proteins of energy converting systems (ATPases and electron transport chains)
  • "sensory" proteins, which detect changes in cell's external environment

The cytoplasmic membrane is not freely permeable to most molecules

  • some small uncharged molecules (O2, CO2, NH3, H2O) can freely pass through
  • charged ions typically cannot pass across the membrane, and must be transported (with the expenditure of energy)

If the cell wall is removed, what remains of the cell is called the protoplast

  • can survive (in a test tube) and carry out most normal cell processes
  • quite sensitive to osmotic shock - if placed in pure water it will swell (as water enters the cell to balance the osmotic force) and rupture (osmotic lysis)
  • In an intact cell the cell wall prevents the protoplast from swelling and undergoing osmotic lysis
  • The cell wall also determines the shape of the bacteria - all protplasts are spherical, regardless of the shape of the intact bacteria

The Cell Wall

Among the Eubacteria (Kingdom of all bacteria excluding the archebacteria, which are typically halophiles and thermophiles) there are only two major types of cell wall

  • They can be identified by their reaction to certain dyes (characterized by Christian Gram in 1880's):

Figure 2.1.4: Gram positive and Gram negative bacteria

Gram positive type cell wall

  • relatively thick (30-100 nm)
  • 40-80% of the wall is made of a tough complex polymer called peptidoglycan (linear heteropolysaccharide chains cross-linked by short peptides)

Figure 2.1.5: Gram positive cell wall

  • The cell wall of a gram-positive cell is a multi-layed network which appears to be continually growing by the addition of new peptidoglycan at the inner face, with concommitant loss at the outer surface

Gram-negative type cell wall (e.g. E. coli)

  • thinner than gram-positive type cell wall (only 20-30 nm thick)
  • has distinctly layered appearance
  • inner region consists of a monolayer of peptidoglycan
  • outer layer of cell wall is essentially a protein containing lipid bilayer
    • inward facing lipids are phospholipids
    • outward facing lipids are macromolecules called lipopolysaccharides

Figure 2.1.6: Gram negative cell wall

  • half the mass of the outer membrane consists of proteins
    • the Braun protein, which is covalently linked to the peptidoglycan layer
    • transport proteins
    • porins - molecules which span the outer membrane to create a 'pore' through the membrane. These pores allow certain molecules and ions to pass through the outer membrane (e.g. ompC, ompF proteins)
  • adjacent outer lipopolysaccharides are held together by electrostatic interactions with divalent metal ions (Ca2+, Mg2+)
    • the addition of chelating agents (e.g. EDTA) can disrupt these interactions and weaken the outer membrane
  • lysozyme (produced by phage lambda, for example) can cleave the saccharide links in the inner peptidoglycan layer

How to lyse a gram-negative bacteria (e.g. E. coli):

  1. Add a chelating agent of divalent metals (e.g. EDTA) to disrupt outer membrane lipopolysaccharides
  2. Add lysozyme to break up peptidoglycan layer
  3. cell wall is now structurally weakened and cannot protect the protoplast from osmotic shock
  4. osmotically shock the cell to disrupt protoplast and release cytoplasmic contents (i.e. high osmotic shock using sucrose solution; low osmotic shock using pure water),
  5. or use mechanical shear/cavitation (French Press, Menton Gaulin press)
Human microflora: some of the bacteria commonly associated with the human body
Location
Genus
ColonBacteroides, Clostridium, Escherichia, Proteus
EarCorynebacterium, Mycobacterium, Staphylococcus
MouthActinomyces, Bacteriodes, Streptococcus
Nasal passagesCorynebacterium, Staphylococcus
NasopharynxStreptococcus, Haemophilus (e.g. H. influenzae)
SkinPropionibacterium, Staphylococcus, Others (personal hygiene, environment)
UrethraAcinetobacter, Escherichia, Staphylococcus
Vagina (adult, pre-menopausal)Acinetobacter, Corynebacterium, Lactobacillus, Staphylococcus

Introduction

All matter, including living things, is made up of various combinations of elements. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These elements form the major biological molecules—nucleic acids, proteins, carbohydrates, and lipids—that are the fundamental components of living matter. Biologists study these important molecules to understand their unique structures which determine their specialized functions.

All biological processes follow the laws of physics and chemistry. Therefore, in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics regulating the modes of fluid flow. Chemical laws dictate the breakdown of large, complex food molecules into smaller molecules as well as their conversion to energy stored in adenosine triphosphate (ATP). Polar molecules, the formation of hydrogen bonds, and the resulting properties of water are key to understanding living processes. Recognizing the properties of acids and bases is important to understand various biological processes such as digestion. Therefore, the fundamentals of physics and chemistry are the foundation for gaining insight into biological processes.

An example of how understanding of chemical processes can give insight to a biological process is recent research on seasonal affective disorder (SAD). This form of depression affects up to 10% of the population in the fall and winter. Symptoms include a tendency to overeat, oversleep, lack of energy, and difficulty concentrating on tasks. Now scientists have found out that not only may SAD be caused by a deficiency in vitamin D, but that it is more common in individuals with darker skin pigmentation. You can read more about it here.

Teacher Support

Before students begin this chapter, it is useful to review these concepts: Atoms consist of protons, neutrons, and electrons Atoms are most stable when their outermost or valence electron shells contain the maximum number of electrons Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds. Demonstrate how electrons can be transferred or shared to create bonds using a chemistry model kit or by drawing the atoms and electrons.


Biology Notes on Microbial Diversity | Microbiology

The below mentioned article provides notes on microbial diversity.

The term ‘microbial diversity’ or biodiversity has become so well known that a public servant is also aware about it. Microbial diversity is defined as the variability among living organisms. The main key of microbial diversity on earth is due to evolution. The structural and functional diversity of any cell represents its evolutionary event which occurred through Darwinian Theory of natural selection.

Natural selection and survival of fittest theory is involved on the microorganisms. This includes diversity within species, between species and of ecosystems. This was first used in the title of a scientific meeting in Washington, D.C. in 1986.

The current list of the world’s biodiversity is quite incomplete (Table 2.1) and that of viruses, microorganisms, and invertebrates is especially deficient. The fungal diversity indicates the total number of species in a particular taxonomic group. The estimates of 1.5 million fungal species is based principally on a ratio of vascular plants of fungi to about 1:6 (Fig. 2.1).

Fig. 2.1 : The number of known species of microorganisms in the world.

Attempts to estimate total numbers of bacteria, archaea, and viruses even more problematical because of difficulties such as detection and recovery from the environment, incomplete knowledge of obligate microbial associations e.g. incomplete knowledge of Symbiobacterium thermophilum, and the problem of species concept in these groups.

Take the case of mycoplasmas, which are prokaryotes having obligate associations with eukaryotic organisms, frequently have tradi­tional nutritional requirements or are mono-culturable and appear to have remarkable diversity. On the other hand, there is one group Spiro plasma, which was discovered in 1972, may be the largest genus on earth.

Spiro plasma species are prin­cipally associated with insects, and the overall rate of new species isolation from such sources of 6% annually indicates species richness. Similarly, marine ecosystems likely support a luxuriant microbial diversity. Further, microbial diversity can be seen on cell size, morphology, metabolism, motility, cell division, developmental biology, adaptation to extreme conditions, etc.

The microbial diversity, therefore, appears in large measure to reflect obligate or facultative associations with higher organisms and to be determined by the spatiotemporal diversity of their hosts or associates.

1. Revealing Microbial Diversity:

The perception of microbial diversity is being radically altered by DNA techniques such as DNA-DNA hy­bridization, nucleic acid fingerprinting and methods of assessing the outcome of DNA probing, and perhaps most important at present, is 16S rRNA sequencing.

The 16S rRNA has radically changed the classification of microbes into 3 domains, the Bacteria, Archaea and Eukarya. While DNA-based analysis (DNA fingerprinting by restriction fragment length polymor­phism i.e. RFLP analysis) is another accepted technique for evaluation of re­lationships between organisms, especially if they are closely related. Holben (1988) detected Brady-rhizobium japonicum selectively at densities as low as 4.3 х 10 3 organisms/gram dry soils.

2. The Concept of Microbial Species:

Biological diversity or biodiversity is actually evolved as part of the evolution of organisms, and the smallest unit of microbial diversity is a species. Bacteria, due to lack of sexuality, fossil records etc., are defined as a group of similar strains distinguished sufficiently from other similar groups of strains by genotypic, phenotypic, and ecological characteristics.

The adhoc committee on (he reconciliation of approach to international committee on systematic bacteriology (ICSB) recommended in 1987 that bacterial species would include strains with approximately 70% or more DNA-DNA relatedness and with 5% or less in thermal stability.

Hence, a bacterial species is a genomic species based on DNA-DNA relatedness and the modern concept of bacterial species differs from those of other organisms. To date, more than 69,000 species in 5100 genera of fungi and about 4,760 species of about 700 genera of bacteria have been described in the literature as given in Table 2.1.

3. Significance of Study of Microbial Diversity:

As quoted by American Society of Microbiology under Microbial Diversity Research Priority, “microbial diversity encompasses the spectrum of variability among all types of microorganisms in the natural world and as altered by human intervention”. The role of microorganisms both on land and water, including being the first colonizer, have ameliorating effects of naturally occurring and man-made disturbed environments.

Current evidence suggests there exist perhaps 3 lakh to 10 lakh species of prokaryotes on earth but only 3100 bacteria are described in Bergey’s Manual. More and more information’s are required and will be of value because microorganisms are important sources of knowledge about strategies and limits of life.

There are resources for new genes and organisms of value to biotechnology, there diversity patterns can be used for monitoring and predicting environmental change. Microorganisms play role in conservation and restoration biology of higher organisms. The microbial communities are excellent model for understanding biological interactions and evolutionary history.

Molecular microbiological methods involving DNA-DNA hybridization and 16S rRNA sequencing, etc. now more helpful in establishing microbial diversity. Data bases are becoming more widely available as a source of molecular and macromolecular information on microorganisms. New- technologies are being developed that are based on diverse organisms from diagnostics to biosensors and to biocatalysts.

In the year 1990s’ microbial diversity has burst forward in a new and exciting form due to efforts of environmental microbiologists, who kept the diversity flame alive during the paradigm organism years.

The molecular revolution that has been sweeping through environmental microbiol­ogy has shown how diverse microbes really are. It has also leashed new waves of creativity in the from of RNA sequence analysis to prove the metabolic activities and gene regulation of microbes in situ.

The gainful advantages may occur by enriching microbial diversity. Microbial genomes can be used for recombinant DNA technology and genetic engineering of organisms with environmental and energy related applications. Emergence of new human pathogen such as SARS is becoming quite important due to threat to public health can be solved by analyzing the genomes of such pathogen.

Culture collections can play a vital role in preserving the genetic diversity of microorganisms. Microbial information’s including molecular, phenotypic, chemical, taxonomic, metabolic, and ecological information can be deposited on databases. A large number of yet unexplored microorganisms may lead to beneficial information’s.

This can be further strengthened by multidisciplinary involvement of experts. There is a compelling need for discovery and identification of microbial bio-control agents, an assessment of their efficacy etc.

The mo­lecular nature of genomes of some important pathogens is necessary to understand the pathogenesis, bio-control, and bioremediation of pollution etc., besides helping in rapid de­tection and diagnosis and in identification of genes for transfer of desirable properties.

Microorganisms are sensitive indicators of envi­ronmental quality. Thus, microbial diversity may be helpful in determining the environmen­tal state of a given habitat of ecosystem. The diverse microorganisms can cause disease and could potentially be used as biological weap­ons. Knowing what is likely to be present can help in rapid diagnosis and treatment.

Biodegradation and bioremediation are potentially important to clean-up and destruction of unwanted materials. Microbial diversity of marine microorganisms is equally important. Sometimes, it is helpful to solve the contamination of sea­food by pathogenic microorganisms e.g. Vibrio vulnificus contaminated oysters. Blue green algae and cyanophages are another dangerous organisms to aquaculture industries.

4. Microbial Evolution:

The microbial evolution has entered a new era with the use of molecular phylogenies to determine relatedness. Certainly this type of phylogenetic analysis remains controversial, but it has opened up possibility of comparing very diverse microbes with a single yardstick and attempting to deduce their history.

Some scientists have opined that the ‘failure’ of molecular methods of find a single unambiguous evolutionary progression from a single ancestor to the present panoply of microorganisms.

The increasing appreciation of the ubiquity and frequency of gene transfer events open the possibility of learning quite essential prokaryotes is by establishing a central core of genes that has not participated in the general orgy of gene transfer. The increasing number of genome sequences may also contribute to a better understanding of the evolutionary history of microbe.


Biology

Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand.

To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom.

Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Features:
- Study progress
- Quiz progress
- 8 Study units
- 256 Lessons
- 47 Quizzes
- 676 Practice questions
- 440 Flashcards
- 2350 Glossaries

Unit 1: The Chemistry of Life. Our opening unit introduces students to the sciences, including the scientific method and the fundamental concepts of chemistry and physics that provide a framework within which learners comprehend biological processes.

Unit 2: The Cell. Students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.

Unit 3: Genetics. Our comprehensive genetics unit takes learners from the earliest experiments that revealed the basis of genetics through the intricacies of DNA to current applications in the emerging studies of biotechnology and genomics.

Unit 4: Evolutionary Processes. The core concepts of evolution are discussed in this unit with examples illustrating evolutionary processes. Additionally, the evolutionary basis of biology reappears throughout the textbook in general discussion and is reinforced through special call-out features highlighting specific evolution-based topics.

Unit 5: Biological Diversity. The diversity of life is explored with detailed study of various organisms and discussion of emerging phylogenetic relationships. This unit moves from viruses to living organisms like bacteria, discusses the organisms formerly grouped as protists, and devotes multiple chapters to plant and animal life.

Unit 6: Plant Structure and Function. Our plant unit thoroughly covers the fundamental knowledge of plant life essential to an introductory biology course.

Unit 7: Animal Structure and Function. An introduction to the form and function of the animal body is followed by chapters on specific body systems and processes. This unit touches on the biology of all organisms while maintaining an engaging focus on human anatomy and physiology that helps students connect to the topics.

Unit 8: Ecology. Ecological concepts are broadly covered in this unit, with features highlighting localized, real-world issues of conservation and biodiversity.


Watch the video: Ένζυμα - βιολογικοί καταλύτες (January 2023).