Exam 2: In class questions, hw, and quiz

HW ch 4 pt 1

Which statement is most strongly supported by these data?

Cultivation-independent methods reveal higher diversity and help us detect abundant groups that are underrepresented by cultivation.

describe the species evenness and richness b/w community 1 and 2.

community 1 has greater species evenness compared to community 2 but both have the same species richness

The ___________ gene is present in all bacteria and archaea. Even eukaryotes have it in the genomes within mitochondria and chloroplasts. The sequences of this gene helped build the tree of life as shown in Figure 1.11 and described in depth in the part of Ch 1 describing the molecular work of Woese’s group.

16S ribosomal RNA gene

ch 4 pt 1

one way to “examine” new microbes is to subject to microscopy alone or a biochemical test followed by microscopy (gram stain). Which groups are examined using Gram staining?

bacteria and archaea

ch 4 pt 1

when we do amplicon library sequencing, what method is used regardless if the subsequent sequencing method is done?

PCR

ch 4 pt 1

what is an amplicon

DNA produced in vitro by PCR

ch 4 pt 1

which gene is the phylogenetic marker gene that is the target of PCR for determining community structure of all prokaryotes (all bacteria + all archaea)?

16S (SSU) rRNA gene

ch 4 pt 1

which gene is a protein encoding gene, whereas the others in the list are simply part of the tRNA, rRNA operon?

mtCO1 (mitochondrial cytochrome c oxidase subunit I)

ch 4 pt 1

what is the proper cutoff for DNA sequence similarity to group two organisms sequences into the same species or better OTU (operational taxonomic unit)?

used to be 97%, now its 100%

ch 4 pt 1

why is species a bad word to use when describing different taxonomic groups of bacteria or archaea?

the classical definition of species is a collection of individuals that can mate and reproduce, so this word doesn’t mean anything w/ asexually reproducing organisms (most microbes)

Quiz 3

Bacteria in the SAR11 clade are both ubiquitous and abundant in the global oceans. These heterotrophs can make up as much as 40% of the heterotrophic bacteria community in surface waters. They are capable of growing aerobically on very low concentrations of organic material because of their small cell size and hence are categorized as __________________.

oligotrophs

Quiz 3

define amplicon

a segment of DNA produced by PCR

Quiz 3

what does the sequencing of PCR amplicons yields

yields a list of different sequences, each from a different organism that was in the mitochondrial community

Quiz 3

define OTU

aka operational taxonomic unit, refers to highly similar-sequence taxa, especially when referring to the DNA sequence of a phylogenetic marker gene

Quiz 3

for bacteria, what would make these microbes belong to the same OTU

the OTU of these microbe must have >97% similar 16S rRNA genes

Quiz 3

Below is a stacked-bar graph showing diversity in 6 different bacterial communities. The Y-axis label, "Abundance," refers to Relative abundance of each particular taxonomic group (% of total individuals). Which community's biodiversity is more even (greater evenness)?

community 2

Quiz 3

define rare biosphere

the community of microbes w/ very low abundances w/in the entire microbial community

Quiz 3

describe the abundant and rare OTUs in bacterial communities

bacterial communities have few very abundant OTUs and many rare ones

Quiz 3

See below Figure 4.8, relative abundances of major groups of bacteria in aquatic systems. As was shown in a different way of graphing similar data in the Ch 4 part 1 HW question, it is clear that data obtained from culturing is different from the data obtained with molecular techniques, as described in Chapter 4 (Figures 4.8 & 4.9). Given the data shown below, which statement is true?

Alpha proteobacteria are the most abundant group in marine waters, based on the most reliable method of estimating abundances.

HW ch 4 pt 2

Baas Becking’s hypothesis (“Everything is everywhere, but the environment selects”) is described in the text. Before and after a major marine oil spill, local scientists collected seawater bacterioplankton by filtering and subsequently extracted DNA from both sets of samples. To assess basic microbial community structure shifts potentially influenced by the oil spill, the microbial ecologists performed 16S rRNA gene sequencing of both DNA samples. Which observation best supports Baas Beckings Hypothesis in the scenario above?

Hydrocarbon-degrading bacteria were present at very low abundance before the spill but increased dramatically after hydrocarbons became available.

HW ch 4 pt 2

In surveys of microbial communities using 16S rRNA gene sequencing, we often observe that Proteobacteria are lower in relative abundance in deep ocean waters compared to surface waters. This is shown in Chapter 4 (Figure 4.11, page 64). In contrast, many archaea dominate deeper waters since they function as chemolithoautotrophs (e.g., oxidizing ammonia or other reduced compounds). Refer back to Chapter 1 (Figure 1.13) for a reminder of what chemolithoautotrophs use for carbon, energy, and electrons. Similar to the data shown in Figure 4.11, additional datasets from other studies representative of this phenomenon are as in this stacked bar graph:

describe how Archaea differ b/w surfance and deep water

Archaea make up 10% of prokaryotes in surface waters, while in the deep, they comprise ~70% of prokaryotes.

HW ch 4 pt 2

both deterministic and stochasitc (random) processes control community structures. Which ecological and evolutionary factor(s) are random?

diversification and drift

ch 4 pt 2

define the “kill the winner” hypothesis

viruses that infect bacteria directs the “kill” part of this scenario

ch 4 pt 2

who would have an advantage in the deep ocean where sunlight is limiting/absent?

Chemolithoautotrophs who can oxidize ammonia for energy

ch 4 pt 2

if limited to clone library studies for marine prokaryote diversity, would you rather do it in Lewes, DE or PCOLA, FL?

PCOLA

ch 5 pt 1

define functional gene

a stretch of DNA encoding an enzyme

ch 5 pt 1

when an omic approach is applied to a mixture of the molecules from the entire community the prefic “meta” is added. This means that when we examine and sequence all RNA from a sample of seawater, we are doing ____ .

metatranscriptomics (RNA looks at expression of ALL bacteria)

ch 5 pt 1

what can a metatranscriptomics study tell us?

a metatranscriptomics study can tell us about the expression patterns of the consortium of bacteria in the ocean w/out having to culture any of those bacteria

ch 5 pt 1

define metabolomics

the study of metabolites or the low molecular weight compounds in cells

ch 5 pt 1

what is a factor that correlates w/ prokaryote genome sizes and also correlates well w/ maximum growth rates?

number of copies of rRNA operon

ch 5 pt 2

what does the streamlining hypothesis state?

states that cells in some ecosystems are subject to powerful selection to minimize the material costs of cellular replication. selection acts to reduce genome size bc of the metabolic burden of replicating DNA w/ no adaptive value

ch 5 pt 2

what is the streamlining hypothesis used for?

the streamlining hypothesis was used to explain genome reduction in Prochlorococcus

ch 5 pt 2

which types of environments do oligotrophic bacteria live in?

what is the genome like in oligotrophic bacteria

OM limiting, w/ rare passing patch of material

smaller genomes and less functional genes, plus smaller cells w/ greater S/V will thrive in places the open ocean

ch 5 pt 2

what factor correlates w/ prokaryote genome sizes and also correlates well with maximum growth rates?

number of copies of rRNA operon

ch 5 pt 2

what clues can codon usage bias provide?

codon usage bias can provide clues about possible trophic strategies of the bacteria from which the genomes were derived

ch 5 pt 2

codon use bias can lead to lower Nitrogen content in the DNA because A:T pairs require one less N per base pair than a G:C pair. Lower G+C % therefore means ________, and hence higher A+T% is more common in oligotrophs.

.less N is required for DNA synthesis and chromosome replication

ch 5 pt 2

In Fig 2 from Laiolo et al. (2024), what gene(s) was/were sequenced to determine the relative abundances of each of the microbial groups present in each of the ocean depths?

• A. The 16S rRNA gene

• B. The 18S rRNA gene

• C. The rbcL gene (the gene encoding Rubisco, the enzyme needed by photolithoautotrophs to fix Carbon)

• D. All genes

all genes

ch 5 ot 2

define phylogenomics studies

compare sequences of all genes in whole genomes to determine phylogeny and relationships among organisms

ch 5 pt 2

In Table 2 from Laiolo et al. (2024), why do alphaproteobacterial genes make up pretty much the same percentage of all genes from all groups, regardless of depth, but cyanobacterial genes are only in reasonable amounts (>5%) in the euphotic zone?

A. Cyanobacteria need access to light

B. Alphaproteobacteria are heterotrophs

C. Heterotrophic bacteria outnumber cyanobacteria by about 100X (Fig. 1.8)

D. All of the above

all of the above

If metatranscriptomic data shows which genes are active, how can researchers distinguish between genes that are truly responding to environmental change versus genes that are just part of normal cellular maintenance under stress?

A. By focusing only on the absolute number of transcripts detected for each gene.

B. By sequencing the DNA instead of RNA to see which genes are encoded in the genome.

C. By comparing gene expression levels before and after the environmental change to identify differential expression.

D. By assuming all highly expressed genes are part of the stress response.

C. By comparing gene expression levels before and after the environmental change to identify differential expression.