Exam 1

• Which of the following taxonomic levels describes Proteobacteria in the domain Bacteria?

  Phylum
• Which of the following bacteria are the most prevalent in the human gut?

  Bacteroides
• The term “deeply branching” refers to which of the following?

  The position in the evolutionary tree of deeply branching bacteria.
• This genus from the order Rickettsiales is known to be prevalent in around 70% of insects species and induce parthenogenesis:

  Wolbachia
• What is the structural differences between gram-positive and gram-negative bacteria?

  Gram-positive have a thick peptidoglycan cell wall that retains crystal violet, while gram position have a thin peptidoglycan cell wall.
• What order of Beta-proteobacteria includes organisms able to oxidize ammonia?

  Nitrosomonadales
• Communion wafers are on the the first know examples of culture media. What was the microbe that was confused with blood on the wafer?

  Serratia marcescens
• This characteristic is shared among most Alphaproteobacteria:

  Most are oligotrophs
• This order of alpha-proteobacteria includes many bacteria genera able to fix nitrogen

  Rhizobiales
• Among the Proteobacteria, this class is characterized by members requiring large amounts of organic nutrients

  Betaproteobacteria
• Describe some of the main characteristics of the Burkholderiales (Betaproteobacteria).

  chemoorganotrophs, free-living nitrogen fixers
• This is the largest class of Proteobacteria with at least 1500 characterized members

  Gammaproteobacteria
• The order Bdellovibrionales includes

  Predatory bacteria
• The following bacterial classes include gram-positive bacteria

  Actinobacteria and Firmicutes
• This genus from the Planctomycetes is known for containing a nuclear envelope:

  Gemmata
• This genus of gram-positive bacteria is known for its capacity to produce antibiotics

  Streptomyces
• These are the bacterial groups able to produce spores and endospores

  Clostridiales, Bacillales, Actinobacteria (Streptomyces)
• This group of betaproteobacteria includes bacteria once thought to be the main drivers of ammonia oxidation in soil until the discovery of the Thaumarchaeota

  Nitrosomonadales
• What are the categories in which we can classified the methods to study microbial communities?

  Culture-dependent and culture-independent methods.
• Why do you think that we are unable to culture more than 1% of environmental microbes?

  Specific growth requirements
• What ribosomal marker is used to characterize bacteria and archaea using sequencing?

  16S rRNA
• Who developed the Petri dishes and the use of agar as a solidifying agent?

  Julius Petri & Fannie Hesse
• How long do you think DNA can stay in the environment?

  ~500 years
• What is the mechanism of action of the nucleic acid dye known as DAPI?

  DAPI binds to the minor groove of DNA and emits fluorescence when excited by ultraviolet light.
• Microbes are found in all domains of life and include:

  Bacteria, archaea, viruses, fungi, and protists
• The smaller the organism, the more numerous it is. With this in mind, these are most abundant biological entities in the environment:

  Viruses
• Why is it important to use culture independent methods ( more than one answer may be selected)?

  Only 1% of microbes in the environment are able to be cultured
• Why is it important to study microbial environments (more than one answer apply)?

  To learn about microbial communities in their natural habitat
• Can bacteria be useful symbionts (organisms that benefit their host) for humans?

  Yes, most microbes help prevent diseases
• What is the assumption behind the plate count method?

  All microbes in a sample will grow in culture media, for example a Petri dish with agar
• One solution to the problem of identifying microbes that can't be cultured is:

  Sequencing
• Uncultured microbes can be characterized using: 

  Sequencing
• What is metagenomics?

  Sampling all microbes and all genes.
• What is a genetic marker?

  a known location (gene or DNA sequence) on a chromosome. It is used to identify species
• What are the components of ribosomes?

  2/3 RNA and 1/3 proteins
• What is the function of the ribosomes?

  Protein synthesis
• List different genetic markers proposed as useful markers to identify bacteria.

  16S rRNA gene, 23S rRNA gene and 16S-23S rDNA ISR, rpoB gene
• The following approach relies in the sequencing of a single gene

  Amplicon sequencing
• This gene encodes the beta subunit of a DNA gyrase, which is a type II topoisomerase

  gyrB
• Match the microbial with the recommended gene for their analysis using amplicon sequencing

  Fungi (ITS1 or ITS2), Bacteria & Archaea (16S rRNA), Protists (18S rRNA)