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Microbiology
Table of Contents
Unit 1 Overview: An Invisible World
1.1 What Our Ancestors Knew
1.2 A Systematic Approach
1.3 Types of Microorganisms

🦠microbiology review

1.2 A Systematic Approach

Citation:

Microbial taxonomy organizes microbes into groups based on shared traits. From cell shape to genetic makeup, various characteristics help scientists classify these tiny organisms. This system allows for standardized naming and understanding of microbial relationships.

Modern approaches to microbial classification blend traditional methods with cutting-edge genetic techniques. By combining morphological, biochemical, and genetic data, scientists can create more accurate and comprehensive taxonomies, revealing the complex evolutionary relationships among microorganisms.

Microbial Taxonomy and Classification

Classification of microorganisms

  • Taxonomic hierarchy organizes microorganisms into increasingly specific groups based on shared characteristics (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)
  • Shared characteristics used for classification include morphology such as cell shape (cocci, bacilli, spirilla), cell arrangement (pairs, chains, clusters), and presence or absence of structures (flagella, capsules, endospores)
  • Staining properties like Gram stain reaction (positive or negative) and acid-fast stain reaction also aid in classification
  • Biochemical and metabolic properties including oxygen requirements (aerobic, anaerobic, facultative), nutrient requirements and utilization, enzyme production, and fermentation products further differentiate microorganisms
  • Genetic composition characteristics such as DNA base composition (G+C content), DNA-DNA hybridization, and 16S rRNA gene sequencing provide high-resolution classification
  • The two-part naming system for species (binomial nomenclature) provides a standardized way to refer to organisms

Approaches to microbial taxonomy

  • Historical approaches relied on morphological characteristics from microscopic observations and colony appearance, as well as biochemical and metabolic properties like nutrient utilization, enzyme production, and fermentation products
  • Modern approaches incorporate genetic methods such as DNA base composition (G+C content), DNA-DNA hybridization which measures the degree of genetic similarity between two organisms with species defined as having ≥70% DNA-DNA hybridization, and 16S rRNA gene sequencing of a highly conserved gene present in all bacteria and archaea used to determine phylogenetic relationships with species defined as having ≥97% 16S rRNA gene sequence similarity
  • Polyphasic taxonomy integrates multiple types of data (morphological, biochemical, genetic) to provide a more comprehensive and accurate classification

Interpretation of phylogenetic trees

  • Phylogenetic tree components include nodes representing taxonomic units (species, genera), branches representing evolutionary relationships, and branch length indicating the degree of genetic divergence
  • Types of phylogenetic trees include rooted trees which indicate the common ancestor and direction of evolution determined by an outgroup (a distantly related organism), and unrooted trees which show relationships without specifying the common ancestor but can be rooted later with additional information
  • Interpreting phylogenetic trees reveals that closely related organisms cluster together, longer branches indicate greater genetic divergence, and the common ancestor is located at the node where branches diverge
  • Applications of phylogenetic trees include understanding evolutionary history, identifying novel or uncultured microorganisms, designing targeted primers for PCR amplification, and developing molecular diagnostic tests

Modern Classification Methods

  • Phenotype refers to the observable characteristics of an organism, which can be influenced by both genetic and environmental factors
  • Genotype represents the genetic makeup of an organism, which determines its potential traits
  • Phylogeny studies the evolutionary relationships among organisms, often represented through phylogenetic trees
  • Cladistics is a method of classification that groups organisms based on shared derived characteristics
  • Molecular systematics uses genetic and molecular data to determine evolutionary relationships and classify organisms

Key Terms to Review (39)

Archaea: Archaea are a domain of single-celled microorganisms that are genetically distinct from bacteria and eukaryotes. They often inhabit extreme environments but can also be found in more common habitats.
Bacteria: Bacteria are single-celled, prokaryotic microorganisms that lack a nucleus and membrane-bound organelles. They can be found in nearly every habitat on Earth and have diverse metabolic capabilities.
Bergey’s Manual: Bergey’s Manual is an essential reference work for the classification and identification of bacteria and archaea. It provides detailed descriptions of bacterial species based on their morphological, physiological, and genetic characteristics.
Binomial nomenclature: Binomial nomenclature is a formal system of naming species using two Latinized names: the genus name and the species identifier. This system standardizes names across different languages and regions, aiding in clear communication among scientists.
Eukaryote: Eukaryotes are organisms whose cells contain a nucleus enclosed within a membrane, along with various specialized organelles. They include animals, plants, fungi, and protists.
Fox: A fox is a small to medium-sized omnivorous mammal belonging to the family Canidae. Known for their cunning and adaptability, foxes are found across various habitats worldwide.
Haeckel: Ernst Haeckel was a German biologist, naturalist, and philosopher who contributed significantly to the field of evolutionary biology. He is known for his work in phylogeny and for coining terms such as 'ecology' and 'phylogeny'.
Linnaean taxonomy: Linnaean taxonomy is a hierarchical system for classifying and naming organisms developed by Carl Linnaeus. It organizes biological diversity into categories like kingdom, phylum, class, order, family, genus, and species.
Linnaeus: Carl Linnaeus was a Swedish botanist, physician, and zoologist who created the binomial nomenclature system. This system is the foundation for modern taxonomy and classification of organisms.
Phylogenies: Phylogenies are the evolutionary histories and relationships among species or groups of organisms. They are often depicted as tree-like diagrams showing common ancestors and divergence points.
Prokaryote: Prokaryotes are unicellular organisms that lack a membrane-bound nucleus and other organelles. They include bacteria and archaea.
Taxonomy: Taxonomy is the scientific classification system used to organize and categorize organisms based on shared characteristics. It helps in understanding the relationships and evolutionary history among different species.
Whittaker: Whittaker refers to Robert H. Whittaker, an American ecologist who proposed the five-kingdom system of classifying organisms. His system was a significant development in biological taxonomy and is still influential today.
Woese: Carl Woese was an American microbiologist who revolutionized the understanding of life's diversity by discovering the domain Archaea. His work on ribosomal RNA led to a new phylogenetic tree that includes Bacteria, Archaea, and Eukarya.
Domain: In the context of biology and microbiology, a domain is the highest level of classification in the three-domain system of life, which divides all living organisms into three fundamental groups based on their genetic and biochemical characteristics.
Phylum: A phylum is a taxonomic rank used in the biological classification of organisms, representing a major division of life. It is the second-highest level of classification, below the domain and above the class. Phylums are used to group together organisms that share fundamental structural and developmental similarities, indicating a common evolutionary origin.
Kingdom: In the context of biological classification, the kingdom is the highest and broadest level of taxonomic hierarchy, representing the most fundamental division of living organisms. Kingdoms are used to group together organisms that share fundamental characteristics and evolutionary relationships.
Family: In the context of a systematic approach, the term 'Family' refers to a taxonomic rank used to classify and organize living organisms based on their evolutionary relationships and shared characteristics. Families are one of the fundamental units in the hierarchical classification system that biologists use to understand the diversity of life on Earth.
Order: Order refers to the systematic and structured manner in which organisms are classified and organized within the biological hierarchy. It is a crucial component of the taxonomic system, which aims to establish clear relationships and distinctions between different life forms.
Genus: A genus is a taxonomic rank used in the biological classification of organisms, which groups closely related species that share many common characteristics. It is a fundamental unit in the hierarchical system of classification, situated between the family and the species level.
Class: In the context of a systematic approach, the term 'Class' refers to a fundamental unit of classification that groups together organisms with similar characteristics and evolutionary relationships. This hierarchical system of classification helps organize the vast diversity of life on Earth.
Species: A species is the fundamental unit of biological classification, defined as a group of living organisms that can interbreed and produce fertile offspring. It is the basic category used in the taxonomic classification of organisms, reflecting their evolutionary and genetic relationships.
Cocci: Cocci are a group of spherical-shaped prokaryotic cells that are commonly found in the domain Bacteria. They are one of the four main morphological groups of bacteria, along with bacilli (rod-shaped), spirilla (spiral-shaped), and vibrios (curved rods).
Spirilla: Spirilla are a type of spiral-shaped bacteria that belong to the domain Bacteria. They are characterized by their distinctive helical or corkscrew-like morphology, which is a unique feature among prokaryotic cells.
Endospores: Endospores are specialized, dormant structures formed by certain Gram-positive bacteria, such as Bacillus and Clostridium species, in response to environmental stressors. These resilient structures allow the bacteria to survive harsh conditions and remain viable for extended periods, even in the absence of nutrients or water.
Capsules: Capsules are protective structures formed by some microorganisms, particularly bacteria, that surround the cell wall. They are composed of polysaccharides, proteins, or other macromolecules and provide an additional layer of defense and structural support for the cell.
DNA-DNA Hybridization: DNA-DNA hybridization is a technique used to detect and quantify the degree of genetic similarity between two DNA sequences by measuring the strength of the hydrogen bonds formed between complementary base pairs when the two DNA strands are brought together. It is a fundamental tool in the field of molecular biology and genetics.
Gram Stain: The Gram stain is a differential staining technique used to classify bacteria based on their cell wall composition. It divides bacteria into two main groups - Gram-positive and Gram-negative - which have distinct structural and functional differences.
Acid-Fast Stain: The acid-fast stain is a specialized staining technique used in microbiology to identify certain types of bacteria, particularly those with a waxy cell wall that makes them resistant to decolorization by acidic solutions. This staining method is crucial for the detection and identification of acid-fast bacteria, which include the causative agents of tuberculosis and leprosy.
G+C Content: G+C content, also known as guanine-cytosine content, refers to the proportion of guanine and cytosine nucleotides present in the DNA sequence of an organism. This measure provides insights into the overall genomic composition and can be used to differentiate and classify various bacterial species.
16S rRNA: 16S rRNA is a type of ribosomal RNA molecule that is essential for the structure and function of the small subunit of prokaryotic ribosomes. It plays a crucial role in the systematic identification and classification of bacteria and archaea, as well as in the study of prokaryotic habitats, relationships, and microbiomes.
Polyphasic Taxonomy: Polyphasic taxonomy is an approach to the classification and identification of organisms that utilizes multiple, complementary methods and data sources to establish taxonomic relationships. It combines various techniques, such as morphological, biochemical, genetic, and phylogenetic analyses, to provide a comprehensive understanding of an organism's taxonomic position and evolutionary relationships.
Phylogenetic Tree: A phylogenetic tree is a diagram that depicts the evolutionary relationships and ancestry of different species or organisms. It is a visual representation of the hypothesized evolutionary history and the degree of relatedness between various life forms based on their shared characteristics and genetic similarities.
Binomial Nomenclature: Binomial nomenclature is the formal system of naming species of living organisms by giving each a name composed of two parts, both of which are Latin or Greek words. This system provides a standardized way to identify and classify different organisms.
Phenotype: Phenotype refers to the observable physical and biochemical characteristics of an organism, which are the result of the interaction between its genotype and the environment. It represents the expression of an organism's genetic makeup and is the foundation for understanding the relationship between genes and their observable effects.
Genotype: Genotype refers to the specific genetic makeup or genetic constitution of an individual, which is determined by the combination of alleles inherited from their parents. It represents the complete set of genes present in a cell or organism and is the fundamental determinant of an organism's physical and functional characteristics.
Phylogeny: Phylogeny is the evolutionary history and relationships of a species or group of organisms. It is the study of the evolutionary development and diversification of a species or higher taxonomic grouping over time.
Molecular Systematics: Molecular systematics is the study of evolutionary relationships between organisms using molecular data, such as DNA or protein sequences. It is a field that combines molecular biology and evolutionary biology to understand the phylogenetic relationships and classification of living organisms.
Cladistics: Cladistics is a method of biological classification that groups organisms based on shared derived characteristics, known as synapomorphies. It aims to reconstruct the evolutionary relationships between different species by analyzing their similarities and differences in a hierarchical manner.