Question

describe molecular techniques used in microbial taxonomy and phylogeny

Answer 1

Microbes taxonomy: Taxonomy is an area of biological science which comprises three distinct, but highly interrelated disciplines that include classification, nomenclature and identification. Applied to all-living entities taxonomy provides a consistent means to classify name and identify organisms. This consistency allows biologists worldwide to use a common label for every organism they study within their particular disciplines. The common language that taxonomy provides minimizes the confusion about names and allows attention to center on more important scientific issues and phenomena. In diagnostic microbiology, classification, nomenclature and identification of microbes play a central role in providing accurate and timely diagnosis of infection. Classification is the organization of organisms that share similar morphologic, physiologic and genetic traits into specific groups or taxa. Nomenclature, the naming of microorganisms according to established rules and guidelines provide the accepted labels by which organisms are universally recognized. The classification of microbes is based on how they look and what they can do. The correct identification of micro organisms is of fundamental importance to microbial systematists as well as to scientists involved in many other areas of applied research and industry (e.g. agriculture, clinical microbiology and food production). Increased use of automation and user-friendly software makes these technologies more widely available. In all, the detection of infectious agents at the nucleic acid level represents a true synthesis of clinical chemistry and clinical microbiology techniques. Accurate identification requires a sound classification or system of ordering organisms into groups, as well as an unequivocal nomenclature for naming them. Molecular techniques for characterizing microbial genotypes provide a possible basis of defining a microbial species. Nucleic acid amplification technology has opened new avenues of microbial detection and characterization, such that growth is no longer required for microbial identification. Methods of microbial identification can be broadly delimited into genotypic techniques based on profiling an organism's genetic material (primarily its DNA) and phenotypic techniques based on profiling either an organism's metabolic attributes or some aspect of its chemical composition. Classification of microbes can be made on the basis of phenotypic characteristics and on genotypic characteristics.

PHENOTYPIC CHARACTERISTICS TO IDENTIFY MICROBES

Phenotypic characters of bacteria include morphology and biochemical reactions carrying out by bacteria whose results can be viewed. Morphological characteristics include colony morphology such as colour, size, shape, opacity, elevation, margin surface texture, consistency etc. These characters are observed after the incubation period on the cultures on the solid media. In liquid cultures, we can observe the pellicle formation and sediment formation. Biochemical characteristics include enzyme production, utilization of particular sugar, aerobic or anaerobic reactions etc.

Limited information exists on the phenotypic characteristics of bacteria found in biofilm. Both wet-mounted and properly stained bacterial cell suspensions can yield a great deal of information. These simple tests can indicate the Gram reaction of the organism; whether it is acid-fast; its motility; the arrangement of its flagella; the presence of spores, capsules, and inclusion bodies; and, of course, its shape. This information often can allow identification of an organism to the genus level, or can minimize the possibility that it belongs to one or another group. Colony characteristics and pigmentation are also quite helpful. For example, colonies of several Porphyromonas species autofluorescence under long-wavelength ultraviolet light, and Proteus species swarm on appropriate media. A primary distinguishing characteristic is whether an organism grows aerobically, anaerobically, facultatively (i.e., in either the presence or absence of oxygen), or

microaerobically (i.e., in the presence of a less than atmospheric partial pressure of oxygen). The proper atmospheric conditions are essential for isolating and identifying bacteria. Other important growth assessments include the incubation temperature, pH, nutrients required, and resistance to antibiotics. For example, one diarrheal disease agent, Campylobacter jejuni, grows well at 42° C in the presence of several antibiotics; another, Y. enterocolitica, grows better than most other bacteria at 4° C. Legionella, Haemophilus, and some other pathogens require specific growth factors, whereas E. coli and most other Enterobacteriaceae can grow on minimal media.

Most bacteria are identified and classified largely on the basis of their reactions in a series of biochemical tests. Some tests are used routinely for many groups of bacteria (oxidase, nitrate reduction, amino acid degrading enzymes, fermentation or utilization of carbohydrates); others are restricted to a single family, genus, or species.

USING GENOTYPIC CHARACTER TO IDENTIFY MICROBES

The classification of microbes is based on not only how they look but also what they can do.

These molecular techniques for characterizing microbial genotypes provide a possible basis of defining a bacterial species . Molecular microbial taxonomy relies upon the generation and inheritance of genetic mutations that is the replacement of a nucleotide building block of a gene by another nucleotide. Sometimes the mutation confers no advantage to the microorganism and so is not maintained in subsequent generations. Sometimes the mutation has an adverse effect, and so is actively suppressed or changed. But sometimes the mutation is advantageous for the microorganism. Such a mutation will be maintained in succeeding generations.

Because mutations occur randomly, the divergence of two initially genetically similar microorganisms will occur slowly over evolutionary time (millions of years). By sequencing a target region of genetic material, the relatedness or dissimilarity of microorganisms can be determined. When enough microorganisms have been sequenced, relationships can be established and a dendrogram constructed.

For a meaningful genetic categorization, the target of the comparative sequencing must be carefully chosen. Molecular microbial taxonomy of bacteria relies on the sequence of ribonucleic acid (RNA), dubbed 16S RNA, that is present in a subunit of prokaryotic ribosomes.

Ribosomes are complexes that are involved in the manufacture of proteins using messenger RNA as the blueprint. Given the vital function of the 16S RNA, any mutation tends to have a meaningful, often deleterious, effect on the functioning of the RNA. Hence, the evolution (or change) in the 16S RNA has been very slow, making it a good molecule to compare micro organisms thats are billions of a years old.

1. Nucleic acid proves to direct specific nucleotides sequence .

2. Amplifying specific DNA sequence using PCR.

This two are method for geno typic taxonomy.

Phylogeny : Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.

molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism’s evolutionary relationships.

Variation

Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as an individual being taller due to better nutrition rather than different genes.

Genetic diversity within a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in the DNA sequence, is the ultimate source of new alleles, or new genetic variation in any population.

Adaptations

A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fitness” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.

Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions. This two mainly depend on the phylogeny.

(NOTE:: Microbial Taxonomy is a means by which microorganisms can be grouped together. Organisms having similarities with respect to the criteria used are in the same group, and are separated from the other groups of microorganisms that have different characteristics. There are a number of taxonomic  criteria that can be used.)

Thank You.