Microbiology: Virology, Microbial Evolution, Diversity, Ecology, and Biogeochemistry

Comprehensive practice flashcards covering virus biology, replication, evolution, microbial systematics, metabolic diversity, fermentation pathways, ecological methods, biogeochemical cycling, and applied environmental microbiology.

What is the biological definition of a virus, and why is it not considered a living organism?

A virus is a genetic element that can only multiply inside a living host cell as an obligate intracellular parasite. It is not considered a living organism because, although it carries its own nucleic acid genome, it lacks metabolism and must borrow the host's energy supply, metabolic building blocks, and protein-synthesizing machinery.

What is the structural difference between a naked virus and an enveloped virus?

A naked virus consists only of a capsid surrounding its genome (typical of most plant and bacterial viruses). An enveloped virus possesses a nucleocapsid enclosed within a host-derived lipid bilayer studded with viral proteins (typical of many animal viruses).

What determines the length and width of a virus with helical capsid symmetry?

Its length is determined by the length of the viral nucleic acid, while its width is determined by the size and packaging arrangement of the individual capsomeres.

What are the structural features of an icosahedral viral capsid?

An icosahedral capsid has $20$ triangular faces and $12$ vertices, providing the most efficient geometric configuration to close a shell with the fewest capsomeres.

In the Baltimore classification scheme, what pathways do Class I, Class IV, and Class V viruses use to generate $\text{mRNA}(+)$?

Class I ($\text{dsDNA}$) transcribes the minus strand directly; Class IV ($\text{ssRNA}(+)$) uses its genomic RNA directly as mRNA; Class V ($\text{ssRNA}(-)$) transcribes the genomic minus strand into mRNA.

In viral quantification via a plaque assay, how does titer differ from plating efficiency?

Titer is the number of infectious virions per volume calculated from plaque counts. Plating efficiency is the ratio of plaque-forming units to total physical particles visible by electron microscopy, which is always below $100\%$ due to defective virions or suboptimal infection conditions.

What are the five steps of bacteriophage replication in a permissive host?

1. Attachment (adsorption) to a complementary host receptor; 2. Penetration (injection of the viral genome into the host); 3. Synthesis of viral nucleic acids and proteins; 4. Assembly and packaging of genomes into proheads; 5. Release via host lysis.

In a viral one-step growth curve, what defines the latent period and burst size?

The latent period consists of the eclipse phase (genome replication and protein synthesis where no infectious virions are detectable) plus maturation (packaging of genomes into capsids). The burst size is the number of infectious virions released per infected cell.

How do host restriction endonucleases protect prokaryotes from viral infection without damaging host DNA?

Restriction endonucleases cleave incoming foreign viral DNA at specific palindromic sequences of $4\text{--}8\,\text{bp}$, while the host cell's matching target sequences are protected from cleavage by methylation.

What are the four primary outcomes of an animal viral infection?

1. Virulent infection: Host cell lysis (most common outcome); 2. Latent infection: Viral DNA persists as a provirus without virion production until triggered; 3. Persistent infection: Slow release of virions by budding without killing the host cell; 4. Transformation: Conversion of a normal host cell into a tumor cell.

What sequential enzymatic activities allow HIV-1 to integrate its genetic material into the host genome?

HIV-1 uses reverse transcriptase to synthesize DNA from an RNA template, ribonuclease activity to degrade the RNA in the RNA:DNA hybrid, DNA polymerase activity to produce double-stranded DNA, and integrase to insert this viral DNA into the host chromosome.

What is antigenic shift in influenza viruses?

Antigenic shift occurs when two different influenza strains infect the same host cell and reassort their segmented RNA genomes (8 segments), producing a hybrid virion with novel surface antigens (hemagglutinin and neuraminidase) unrecognizable by the immune system.

What are the distinct evolutionary consequences of gene duplication and gene deletion in microbes?

Gene duplication allows one copy to retain ancestral function while the second is free to evolve a new function. Gene deletion is more frequent and eliminates non-essential or redundant genes, keeping genomes streamlined (most extreme in obligate intracellular symbionts and pathogens).

In Richard Lenski's Long-Term Evolution Experiment (LTEE), what notable gain-of-function mutation arose after approximately 31,500 generations?

One of the twelve populations evolved the ability to use citrate aerobically as a carbon and energy source, whereas previously citrate was present solely as a pH buffer.

What is the difference between orthologous and paralogous genes?

Orthologs are homologous genes in different species that diverged as a result of a speciation event. Paralogs are homologous genes that arose via gene duplication within a lineage.

How is the core genome differentiated from the pan genome of a bacterial species?

The core genome consists of the set of genes shared by every strain of that species, whereas the pan genome comprises the core genome plus all accessory genes found in only some strains.

What quantitative thresholds in SSU rRNA sequence identity and Average Nucleotide Identity (ANI) define a prokaryotic species?

An SSU rRNA gene sequence identity of $>97\%$ indicates the same species. In whole-genome comparisons, an Average Nucleotide Identity (ANI) of $>96\%$ denotes the same species, whereas $<93\%$ denotes different species.

How do aerobic respiration, anaerobic respiration, and fermentation differ in their terminal electron acceptors and ATP generation mechanisms?

Aerobic respiration uses external $\text{O}_2$ and yields the most ATP via oxidative phosphorylation. Anaerobic respiration uses an external acceptor other than $\text{O}_2$ (e.g., nitrate or sulfate) via oxidative phosphorylation with lower energy yield. Fermentation uses no external acceptor; internal metabolic intermediates are reduced to achieve redox balance, yielding the lowest ATP primarily via substrate-level phosphorylation.

What enzymatic and metabolic differences distinguish homofermentative from heterofermentative lactic acid bacteria?

Homofermenters possess aldolase and produce only lactic acid yielding $2\,\text{ATP}$ per glucose. Heterofermenters lack aldolase (cannot cleave fructose bisphosphate into triose phosphates) and produce lactic acid, ethanol, and $\text{CO}_2$, yielding only $1\,\text{ATP}$ per glucose.

How does the Stickland reaction function in proteolytic clostridia?

The Stickland reaction couples the fermentation of a pair of amino acids, where one amino acid acts as the electron donor and the other as the electron acceptor, producing $\text{NH}_3$, $\text{CO}_2$, and a carboxylic acid that is one carbon shorter than the oxidized donor amino acid.

How do hyperthermophilic archaea conserve energy during glucose fermentation without conventional substrate-level phosphorylation?

They convert pyruvate to acetate to yield reduced ferredoxin; an energy-converting hydrogenase then oxidizes ferredoxin to restore redox balance while pumping $\text{Na}^+$, generating a sodium motive force that drives ATP synthesis via a $\text{Na}^+$-linked ATP synthase, netting approximately $4\,\text{ATP}$.

What is syntrophy, and why does interspecies $\text{H}_2$ transfer permit ethanol fermentation?

Syntrophy is a cooperative interaction where two microbes together catalyze a reaction that neither can perform alone. Ethanol fermentation by the syntroph is endergonic ($\Delta G^{\circ\prime} > 0$) in pure culture, but consumption of $\text{H}_2$ by a partner methanogen keeps the partial pressure of $\text{H}_2$ extremely low, making the combined reaction exergonic ($\Delta G^{\circ\prime} < 0$).

What biochemical steps are involved in the aerobic breakdown of aliphatic hydrocarbons?

An oxygenase incorporates oxygen at a terminal carbon to form a fatty acid of equivalent length. This fatty acid then undergoes $\beta$-oxidation, removing two carbons per cycle to yield acetyl-CoA and NADH, leaving a fatty acid two carbons shorter.

What is enrichment bias, and why does it occur?

Enrichment bias is the phenomenon where lab-cultivated organisms represent only minor components of the real microbial community. It occurs because the high nutrient levels supplied in laboratory culture media heavily favor fast-growing organisms that are ecologically insignificant in nutrient-poor natural settings.

How do laser tweezers isolate specific single microbial cells from environmental samples?

A laser beam is focused through a microscope objective to physically trap a single bacterial cell using optical forces, allowing it to be steered away from other cells in a mixed culture.

How does fluorescence in situ hybridization (FISH) identify microbial taxa in mixed environmental samples?

FISH uses fluorescently labeled single-stranded oligonucleotide probes complementary to specific SSU rRNA sequences, hybridizing directly to intact cells within the sample to reveal their phylogenetic identity and spatial distribution under a fluorescence microscope.

What distinct community-level biological questions do metagenomics, metatranscriptomics, and metaproteomics answer?

Metagenomics identifies the total gene content to determine what metabolic processes the community has the genetic capacity to perform; metatranscriptomics assesses community mRNA to identify which genes are actively transcribed; metaproteomics measures the abundance and diversity of proteins to detect what is actually accumulated.

Why does biological carbon fixation lead to isotopic fractionation between $^{12}\text{C}$ and $^{13}\text{C}$?

Biological enzymes discriminate against heavier isotopes, favoring the lighter $^{12}\text{C}$ over $^{13}\text{C}$. Consequently, cellular organic matter becomes enriched in $^{12}\text{C}$ and depleted in $^{13}\text{C}$ relative to inorganic carbon sources.

How does stable isotope probing (SIP) identify which specific organisms execute a metabolic reaction?

The community is incubated with a substrate enriched in a heavy stable isotope (e.g., $^{13}\text{C}$-benzoate). Organisms consuming that substrate incorporate the heavy isotope into their DNA, which is separated from lighter $^{12}\text{C}$-DNA by cesium chloride density-gradient ultracentrifugation and sequenced.

In microbial ecology, how are a guild, a niche, and a community defined?

A guild consists of metabolically related populations exploiting the same resources. A niche is the specific habitat and set of conditions shared by a guild that supplies its nutrients. A community is the assemblage of multiple co-occurring guilds living in a shared environment.

What is the difference between an organism's fundamental niche and its realized (prime) niche?

The fundamental niche is the full range of physical and chemical conditions under which an organism can survive, whereas the realized (prime) niche is the specific range of conditions in which it is most ecologically successful and dominates competitors.

What are the defining characteristics of the four major soil horizons: O, A, B, and C?

Horizon O is the surface layer of undecomposed plant litter. Horizon A is the nutrient-rich topsoil where the highest level of microbial growth occurs. Horizon B is subsoil composed of minerals and organic matter leached from A with low microbial activity. Horizon C is the weathered base layer lying directly above bedrock.

What is biochemical oxygen demand (BOD)?

BOD is a measure of the capacity of water's aerobic microorganisms to consume dissolved oxygen while oxidizing the organic and inorganic matter present in a water sample.

What ecological significance does the cyanobacterium Prochlorococcus have in marine ecosystems?

Prochlorococcus is the dominant marine phototroph, accounting for $>40\%$ of total marine phototrophic biomass and approximately $50\%$ of open-ocean net primary production.

What is 'dark oxygen' in the abyssal ocean, and how is it hypothesized to form?

'Dark oxygen' is molecular oxygen ($\text{O}_2$) detected at the sunless abyssal seafloor around polymetallic nodules. It is hypothesized to be produced in situ via seawater electrolysis, where electric potentials generated by metals in the nodules split $\text{H}_2\text{O}$ into $\text{H}_2$ and $\text{O}_2$.

What is the overall reaction and enzyme requirement for biological nitrogen fixation?

The reaction is $\text{N}_2 + 8\,\text{H} \rightarrow 2\,\text{NH}_3 + \text{H}_2$, catalyzed by the nitrogenase enzyme complex in a limited group of free-living or symbiotic bacteria and archaea.

What is the biochemical distinction between canonical two-step nitrification and comammox?

Canonical nitrification requires two distinct functional groups: ammonia oxidizers oxidize ammonia to nitrite ($\text{NH}_3 \rightarrow \text{NO}_2^-$), and nitrite oxidizers oxidize nitrite to nitrate ($\text{NO}_2^- \rightarrow \text{NO}_3^-$). Comammox bacteria possess the complete enzymatic pathway to oxidize ammonia directly to nitrate ($\text{NH}_3 \rightarrow \text{NO}_3^-$) within a single organism.

What is anammox, and why is it valuable in municipal wastewater treatment?

Anammox (anaerobic ammonium oxidation) is the reaction $\text{NH}_3 + \text{NO}_2^- \rightarrow \text{N}_2$. It is valuable in wastewater treatment because it removes fixed nitrogen without requiring organic carbon donors or aeration, preventing downstream eutrophication.

How do the enzymes encoded by the bacterial mer operon sequentially detoxify methylmercury ($\text{CH}_3\text{Hg}^+$)?

MerB (organomercury lyase) cleaves $\text{CH}_3\text{Hg}^+$ into $\text{CH}_4$ and $\text{Hg}^{2+}$. Periplasmic MerP binds $\text{Hg}^{2+}$ and passes it to membrane transporter MerT, which delivers it to cytoplasmic MerA (mercuric reductase) to reduce $\text{Hg}^{2+}$ to volatile, non-toxic $\text{Hg}^0$, which diffuses out of the cell.

In microbial copper leaching, what is the exact role of iron-oxidizing chemolithotrophs?

Iron-oxidizing chemolithotrophs (such as Acidithiobacillus ferrooxidans) do not directly dissolve the metal; they re-oxidize $\text{Fe}^{2+}$ back to $\text{Fe}^{3+}$. The $\text{Fe}^{3+}$ then acts as the chemical oxidant that spontaneously oxidizes copper sulfide minerals to soluble copper sulfate.

How do the redox mechanisms differ between microbial uranium leaching and uranium bioremediation?

Uranium leaching uses microbial oxidation ($\text{U}^{4+} \rightarrow \text{U}^{6+}$) to convert insoluble uranium into soluble uranyl sulfate for collection. Bioremediation uses microbial reduction ($\text{U}^{6+} \rightarrow \text{U}^{4+}$, typically fueled by acetate) to precipitate soluble uranium into an insoluble, immobile form to contain groundwater contamination.

What distinct processes occur during primary, secondary, and tertiary wastewater treatment?

Primary treatment uses physical separation (screening and sedimentation) to remove solid debris. Secondary treatment uses aerobic or anaerobic microbial communities to biologically degrade dissolved organic matter and lower BOD. Tertiary treatment uses advanced physicochemical or specialized biological processes (e.g., phosphorus-accumulating organisms) to remove residual nutrients like phosphate and nitrate.

What microbiological reactions drive severe crown corrosion in municipal sewer pipes?

In anoxic sewage, sulfate-reducing bacteria reduce sulfate to volatile $\text{H}_2\text{S}$. In the oxic headspace of the pipe crown, attached sulfur-oxidizing chemolithotrophs oxidize the escaping $\text{H}_2\text{S}$ into sulfuric acid ($\text{H}_2\text{SO}_4$), which corrodes the concrete pipe.