Viral Microbiology and Baltimore Classification

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Questions and Answers

What are the key characteristics that differentiate viruses from other microorganisms like bacteria and archaea? (Select all that apply)

They lack the necessary machinery for replication, transcription, or translation.
They integrate with the host's metabolic network. (correct)
They do not always carry machinery for replication, transcription, or translation. (correct)
Their evolutionary rates are similar to bacteria and archaea.
Their evolutionary rates are very different from bacteria and archaea and vary from host to host. (correct)
They divide by binary fission.

Which of the following is NOT a component commonly found in the structure of a virus?

Cell Wall (correct)
RNA or DNA
Phospholipid envelope
Capsomeres
Virion

What is the basis for the Baltimore Classification of viruses?

The Baltimore Classification system categorizes viruses based on their method of producing mRNA, the messenger RNA that carries genetic information from DNA to ribosomes for protein synthesis.

Which Baltimore Class(es) include DNA viruses that require transcription to generate mRNA? (Select all that apply)

Class I (B) Signup and view all the answers

Which Baltimore Class includes RNA viruses that synthesize a complementary strand of RNA before transcribing it into mRNA?

Class IV (B) Signup and view all the answers

What is the main difference between the Baltimore Classification system and viral taxonomy?

The Baltimore Classification system is based on how viruses produce mRNA, while viral taxonomy relies on sequence-based relationships. Signup and view all the answers

Most viral classes primarily affect bacteria and archaea.

False (B) Signup and view all the answers

Describe the rolling circle replication process.

Rolling circle replication begins with a nick in the positive strand of the double-stranded replicative form (dsDNA). The negative strand is then used as a template to extend the positive strand. Once replication is complete, the original positive strand is cleaved and joined to the newly synthesized strand, resulting in the replication of the viral genome. Signup and view all the answers

Which of the following is a key characteristic of the lysogenic stage of a viral infection?

The viral genome integrates into the host genome. (A) Signup and view all the answers

ΦX174 is a (+) ssRNA virus that replicates through rolling circle replication.

False (B) Signup and view all the answers

How does λ phage integrate into the host genome?

Lambda phage integrates into the host genome by using a specific site on its DNA called an attachment site (att) that recognizes and binds to a corresponding site (att) on the bacterial chromosome. Signup and view all the answers

What is the primary role of RNA strands in Poliovirus infection?

They are transcribed into mRNA for protein synthesis. (E) Signup and view all the answers

Coronaviruses belong to Baltimore Class III, and their genome is dsDNA.

False (B) Signup and view all the answers

What is the unique characteristic of retroviruses, specifically exemplified by HIV, that distinguishes them from other viruses?

Retroviruses, such as HIV, are unique in their ability to convert their RNA genome into a double-stranded DNA copy using reverse transcriptase. This DNA copy can then integrate into the host genome, becoming a provirus and replicating with the host cell. Signup and view all the answers

Explain the concept of the viral shunt in marine ecosystems.

The viral shunt refers to the process by which viruses cause the lysis of microorganisms, releasing dissolved organic matter (DOM) and particulate organic matter (POM) into the environment. These organic materials are then taken up by other microorganisms, leading to a cycling of carbon and nutrients within the system. Signup and view all the answers

What are Auxillary Metabolic Genes (AMGs) and how can they benefit their host?

Auxillary Metabolic Genes (AMGs) refer to genes encoded by viruses that can enhance the metabolic functions of their host organism. For example, some cyanophages encode the psbA gene, which produces a subunit of photosystem II in the host cyanobacteria, increasing their photosynthetic efficiency. Signup and view all the answers

What are Gene Transfer Agents (GTAs) and how are they related to viruses?

Gene Transfer Agents (GTAs) are virus-like particles that play a role in the transfer of genetic material between different species. They are closely related to viruses as they involve incorporating their genome into a host, replicating it, and then producing and releasing progeny particles. Signup and view all the answers

What is microbial ecology?

Microbial ecology investigates the complex interactions between microorganisms and their environments, including both abiotic factors like temperature and nutrient availability and biotic factors, such as other microbial species. Signup and view all the answers

Why is studying microbial ecology important, considering the 'Great Plate Count Anomaly'?

Studying microbial ecology is crucial because the vast majority of microorganisms (estimated at 99%) cannot be cultured in the lab using conventional methods due to the Great Plate Count Anomaly. This means we are unable to fully understand microbial communities using solely lab cultures and need to utilize advanced techniques like molecular methods and environmental sampling to explore their diversity and interactions. Signup and view all the answers

Differentiate between microbial richness and microbial abundance.

Microbial richness refers to the number of different species present in a particular ecosystem, while microbial abundance refers to the proportion of each species within that community. Richness describes the diversity of species, while abundance reflects the relative dominance of each species. Signup and view all the answers

What are some key factors that influence microbial lifestyle?

Temperature (A), Interactions with other organisms (B), Nutrient availability (C), Energy availability (D), pH (E) Signup and view all the answers

Explain how microbial cooperation can benefit a community.

Microbial cooperation benefits a community when microorganisms share metabolic products or genetic information that allows them to thrive in situations where they would not succeed alone. For instance, one species may produce a nutrient that is essential for the growth of another, or they may share genes involved in breaking down complex compounds. Signup and view all the answers

How does microbial competition impact community composition?

Microbial competition impacts community composition by influencing the relative abundance of different species. When different species compete for the same limited resources, such as nutrients or space, one or more species may become dominant while others decline, leading to changes in the community's makeup. Signup and view all the answers

What are the main characteristics of microbial predation?

Microbial predation occurs when one microorganism hunts or disrupts another microorganism to obtain nutrients or resources. This can involve attacking, consuming, or releasing toxins to harm the prey organism. Signup and view all the answers

Which of the following are common tools used in microbial ecology research?

Chemical profiling (B), Microscopy (C), Mathematical modeling (D), Next Generation Sequencing (E) Signup and view all the answers

Describe the mutualistic relationship between the alga Chlamydomonas reinhardtii and the nitrogen-fixing bacterium Mesorhizobium sangaii.

This mutualistic relationship involves the alga Chlamydomonas reinhardtii providing carbon, a vital nutrient for the bacterium, while Mesorhizobium sangaii supplies fixed nitrogen, essential for the alga's growth and development. Signup and view all the answers

How does the human body provide a diverse range of microenvironments for microbial communities?

The human body provides various microenvironments each with distinct conditions for growth and development, These are all areas where conditions are altered to meet the needs of microbes. Signup and view all the answers

What are some key factors that influence the differences in microbial communities between different environments?

Microbial communities vary in their composition and diversity based on a number of key factors, including available nutrients, oxygen concentrations, pH levels, temperature, and competition between different species. Signup and view all the answers

Describe the oxygen and pH conditions in different regions of the human gut.

The human gut exhibits distinct oxygen and pH gradients. The lumen, the innermost part of the gut, is predominantly anaerobic with low oxygen concentration and pH levels of approximately 7. However, the epithelial layer closer to the intestinal wall can experience a higher oxygen concentration. Signup and view all the answers

What are the key characteristics of Bacteroides spp. that make them well-suited for inhabiting the human gut?

Bacteroides spp. are specialized for the gut with the ability to break down polysaccharides, both from the diet and the mucosal layer, producing beneficial short-chain fatty acids. They are also capable of respiring oxygen, allowing them to exist in the slightly more oxygen-rich environment near the epithelial layer. Signup and view all the answers

Provide examples of cooperation within the gut microbial community.

One example is the cross-feeding interaction between Bacteroides spp. and other gut bacteria like E. coli, S. enterica, and C. difficile. Bacteroides spp. provide simpler sugars and carboxylic acids to activate these other bacteria. Another example is the production of the C capsule by Bacteroides spp., which gets recognized by the host B cells and stimulates a positive immune response. Signup and view all the answers

Which of the following are the sequential steps that microorganisms undergo during infection?

Exposure-Adherence-Invasion-Multiplication (A) Signup and view all the answers

Virulence is synonymous with infection.

False (B) Signup and view all the answers

How is the virulence of an organism measured?

The virulence of a pathogen is commonly measured using the LD50 (Lethal Dose 50) assay. This involves determining the number of microbial cells necessary to kill 50% of a test population. Signup and view all the answers

Describe the concept of virulence factors and provide at least one example.

Virulence factors are molecules or mechanisms produced by bacteria or viruses that enhance their ability to cause disease. These factors can involve toxins, enzymes, capsules, or other specialized structures. An example of a virulence factor is the AB toxin produced by Vibrio cholerae, which causes severe diarrhea in infected individuals. Signup and view all the answers

What are some key characteristics of Pseudomonas aeruginosa that contribute to its pathogenicity?

Pseudomonas aeruginosa is a facultative anaerobe capable of utilizing oxygen or nitrate as an electron acceptor for energy production. It can use various sugars as carbon sources and is adept at colonizing the human respiratory system, often leading to chronic infections. It employs Type IV Pili and Type III Secretion Systems to attach to and invade host cells, respectively, and produces a variety of virulence factors, including toxins and enzymes, contributing to its pathogenic potential. Signup and view all the answers

Explain how Pseudomonas aeruginosa and Staphylococcus aureus interact in a biofilm in cystic fibrosis patients.

In cystic fibrosis patients, Pseudomonas aeruginosa and Staphylococcus aureus often coexist in biofilms. They have a complex interplay that prevents them from becoming spatially adjacent. Pseudomonas aeruginosa produces molecules like cyanide and pyocyanin, which inhibit Staphylococcus aureus, while Staphylococcus aureus produces acetoin, acetate, and peptides that are bactericidal to Pseudomonas aeruginosa. This antagonistic relationship shapes the structure and function of the biofilms in cystic fibrosis patients. Signup and view all the answers

What is symbiosis and how does it differ from parasitism?

Symbiosis refers to a cooperative interaction between two different organisms where both partners benefit. This partnership can be mutualistic, where both partners gain a clear advantage, or commensalistic, where one benefits while the other is neither harmed nor benefited. In contrast to parasitism, where one organism benefits at the expense of the other, in symbiosis, both partners ultimately thrive due to their collaborative relationship. Signup and view all the answers

Describe the symbiotic relationship that forms a lichen.

Lichens are fascinating symbioses between fungi and photosynthetic microorganisms, either algae or cyanobacteria. The algae or cyanobacteria provide fixed carbon via photosynthesis, which is essential for the fungus's growth. The fungus, in return, provides shelter, protection from desiccation and nutrient uptake capabilities, enabling the symbiotic partnership to flourish. Signup and view all the answers

Explain the symbiotic relationship between ANME (Anaerobic Methanotrophic Archaea) and SRB (Sulfate-Reducing Bacteria) in marine sediments.

ANME and SRB exhibit an obligate syntrophic relationship in marine sediments, particularly those rich in methane. ANME oxidizes methane, which under normal conditions is energetically unfavorable. However, they couple this reaction with SRB that performs sulfate reduction, a highly favorable reaction. This energy transfer fuels the ANME's metabolism while SRB receives electrons for their sulfate reduction process. Signup and view all the answers

What are some of the methods used to study syntrophic relationships in microbial communities?

Metagenomics (A), Fluorescence In Situ Hybridization (FISH) (B), Stable Isotope Probing (D), NanoSIMS (E) Signup and view all the answers

What is the role of nitrogen fixation in the symbiotic relationship between leguminous plants and nitrogen-fixing bacteria?

Leguminous plants form a close symbiotic relationship with nitrogen-fixing bacteria, primarily from the genera Rhizobium and Bradyrhizobium. The bacteria possess the enzyme nitrogenase, which can convert atmospheric nitrogen into a biologically usable form, ammonia. This newly fixed nitrogen is crucial for the plant's growth and development. In exchange for fixing nitrogen, the bacteria receive a safe and nutrient-rich environment within root nodules of the plant. Signup and view all the answers

Describe the key stages involved in the formation of root nodules in leguminous plants, highlighting the role of Nod and Myc factors.

The formation of root nodules in legumes is a complex process that begins with the recognition of the appropriate partner. Nod factors, oligosaccharide signaling molecules secreted by the bacteria, play a critical role in this early stage. These factors bind to receptors on the plant root hair and trigger a series of developmental changes. The bacteria then invade the root hair and form a specialized structure known as an infection thread. This thread acts as a pathway for the bacteria to move to the central root, where they eventually form the characteristic nodules. The nodules are specialized structures where the bacteria differentiate into bacteroids, which are adapted for nitrogen fixation. The Myc factors regulate these events, as well as the further development of the nodules. Signup and view all the answers

Explain the tripartite symbiotic relationship between the mealybug, Candidatus Trabutinella endobia, and Candidatus Trembalaya phenacola.

This tripartite symbiosis involves a host mealybug, an endosymbiont Candidatus Trembalaya phenacola, and a secondary symbiotic bacterium Candidatus Trabutinella endobia. Candidatus Trembalaya phenacola lacks genes for producing peptidoglycan, the structural component of bacterial cell walls, while Candidatus Trabutinella endobia lacks essential genes for amino acid synthesis. The mealybug contributes genes that enable the synthesis of peptidoglycan on the surface of Candidatus Trembalaya phenacola. The two endosymbionts then complement each other's metabolic functions, resulting in a cooperative relationship that benefits all three partners. Signup and view all the answers

What are the key genomic adaptations observed in the endosymbiont Sodalis compared to its free-living evolutionary relatives?

Endosymbiotic bacteria, such as Sodalis, experience notable genomic alterations compared to their free-living counterparts. These include a reduction in genome size, indicative of streamlining their metabolic capabilities to rely on their host for essential functions. They also exhibit a pronounced bias toward A+T bases, which is associated with increased genome stability, potentially due to reduced selection pressure for adaptive mutations within the stable endosymbiotic environment. Signup and view all the answers

What are the main components of soil composition?

Soil is a complex mixture of inorganic and organic components. It typically consists of about 40% inorganic mineral matter, such as silica and sand, 5% organic matter, including decomposed plant and animal material, 50% air and water, and 5% microorganisms, including bacteria, fungi, protozoa, and nematodes. Signup and view all the answers

Explain briefly how soil is classified based on particle size.

Soil is classified based on particle size into three main categories: sand, silt, and clay. Sand has the largest particle size (0.1-2 mm), silt is intermediate (0.002-0.1 mm), and clay has the smallest particle size (less than 0.002 mm). The proportions of sand, silt, and clay determine the soil's texture and properties, such as drainage, water retention, and nutrient availability. Signup and view all the answers

Flashcards

Viral Replication Difference

Viruses don't reproduce through binary fission; they sometimes lack their own replication/transcription/translation machinery, instead integrating into the host's metabolic network.

Viral Structure

Viruses have RNA or DNA, a capsid made of capsomeres, and sometimes an envelope.

Baltimore Classification

Classifies viruses based on how a virus gets mRNA, not on their taxonomic group.

Baltimore Class I, VII

DNA viruses whose transcripts are built off the minus strand (Class I) or by a reverse transcription step (Class VII).