Complex Intracellular Structures in Prokaryotes: 2 (Microbiology Monographs)

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When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase , a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. The log phase is marked by rapid exponential growth.

The rate at which cells grow during this phase is known as the growth rate k , and the time it takes the cells to double is known as the generation time g. During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth.

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The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair , antioxidant metabolism and nutrient transport. Most bacteria have a single circular chromosome that can range in size from only , base pairs in the endosymbiotic bacteria Carsonella ruddii , [] to 12,, base pairs Bacteria genomes usually encode a few hundred to a few thousand genes.

The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes. Bacteria, as asexual organisms, inherit an identical copy of the parent's genomes and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations.

Mutations come from errors made during the replication of DNA or from exposure to mutagens.

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Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome.

In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance. Many bacteria are motile and can move using a variety of mechanisms. The best studied of these are flagella , long filaments that are turned by a motor at the base to generate propeller-like movement.

Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria such as E.


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The tumbling allows them to reorient and makes their movement a three-dimensional random walk. The flagella of a unique group of bacteria, the spirochaetes , are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves. Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus , [] and gliding motility , that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward.

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes : these include chemotaxis , phototaxis , energy taxis , and magnetotaxis. Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton , which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.

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A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals. Bacteria often function as multicellular aggregates known as biofilms , exchanging a variety of molecular signals for inter-cell communication , and engaging in coordinated multicellular behaviour.

The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. One type of inter-cellular communication by a molecular signal is called quorum sensing , which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light.

Quorum sensing allows bacteria to coordinate gene expression , and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population. Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA , fatty acids , pigments, antigens and quinones.

Chapter 4 The Prokaryotes

This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics , using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes.

However, molecular systematics showed prokaryotic life to consist of two separate domains , originally called Eubacteria and Archaebacteria , but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. These two domains, along with Eukarya, are the basis of the three-domain system , which is currently the most widely used classification system in microbiology.

The identification of bacteria in the laboratory is particularly relevant in medicine , where the correct treatment is determined by the bacterial species causing an infection.

Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. The Gram stain , developed in by Hans Christian Gram , characterises bacteria based on the structural characteristics of their cell walls. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups gram-positive cocci, gram-positive bacilli, gram-negative cocci and gram-negative bacilli. Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia , which show acid-fastness on Ziehl—Neelsen or similar stains.

Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia , while stool specimens are cultured on selective media to identify organisms that cause diarrhoea , while preventing growth of non-pathogenic bacteria.

Specimens that are normally sterile, such as blood , urine or spinal fluid , are cultured under conditions designed to grow all possible organisms.

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction , are increasingly popular due to their specificity and speed, compared to culture-based methods. Following present classification, there are a little less than 9, known species of prokaryotes, which includes bacteria and archaea; [] but attempts to estimate the true number of bacterial diversity have ranged from 10 7 to 10 9 total species—and even these diverse estimates may be off by many orders of magnitude.

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism , mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat , and large populations of these organisms in humans are the cause of body odour.

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria. Certain bacteria form close spatial associations that are essential for their survival.

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One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids , such as butyric acid or propionic acid , and produce hydrogen , and methanogenic Archaea that consume hydrogen. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow. In soil, microorganisms that reside in the rhizosphere a zone that includes the root surface and the soil that adheres to the root after gentle shaking carry out nitrogen fixation , converting nitrogen gas to nitrogenous compounds.

Many other bacteria are found as symbionts in humans and other organisms.

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For example, the presence of over 1, bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins , such as folic acid , vitamin K and biotin , convert sugars to lactic acid see Lactobacillus , as well as fermenting complex undigestible carbohydrates. If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus Caused by Clostridium tetani , typhoid fever , diphtheria , syphilis , cholera , foodborne illness , leprosy caused by Micobacterium leprae and tuberculosis Caused by Mycobacterium tubeculosis.

A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture , with bacteria causing leaf spot , fire blight and wilts in plants, as well as Johne's disease , mastitis , salmonella and anthrax in farm animals. Each species of pathogen has a characteristic spectrum of interactions with its human hosts.

Some organisms, such as Staphylococcus or Streptococcus , can cause skin infections, pneumonia , meningitis and even overwhelming sepsis , a systemic inflammatory response producing shock , massive vasodilation and death. Other organisms invariably cause disease in humans, such as the Rickettsia , which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus , while another causes Rocky Mountain spotted fever. Chlamydia , another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease.

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