Exam 3

• Mutualism


  Associating pairs get benefit
• Parasitism 


  Only one associating pair gets the benefit
• Pathogenicity


  One associating pair may consume the host until its demise
• Commensalism


  The microbial symbiont has no negative or positive effect on the host
• Describe a lichen


  a mutualists relationship between two organisms, usually a fungus and an alga or cyanobacterium
• What benefits do the associating pairs in the lychen symbiont offer to each other?

  The algae or cyanobacteria produces organic matter which feeds the fungus. The fungus is an anchor where the partner can grow, away from erosion.
• What is the common characteristic among the bacteria collectively called "rhizobia"?

  nitrogen-fixing bacterial symbionts
• What is the purpose for the production of leghemoglobin?

  Leghemoglobin is an oxygen buffer. It keeps unbound O2 low by cycling between Fe3+ and Fe2+
• bacteroid


  modified, swollen, misshapen, and branched bacterial cells that occur when rhizobia multiply rapidly in plants
• What are nod genes?

  Nod genes direct the steps for nodulation in a legume
• True or false: Ectomycorrizhae can associate with more than one plant species

  true
• Can non-Rhizobia bacteria form associations with plants? If so, provide examples

  Yes, other bacteria such as Chryseobacterium, which promotes and regulates plant growth through cycling of nutrients and hormone production
• Describe the main characteristics of endomycorrhizal fungi

  Endomycorrhizal fungi penetrate into the plant. Most are arbuscular mycorrhizae and most species are obligate plant symbionts
• Rhizobacteria produce Nod factors to initiate the process of nodule formation. What are the factors produced by mycorrhizal fungi to initiate the mycorrhizal state?

  Myc factors are lipochitin oligosaccharides signaling factors in AM fungi that initiate the formation of the mycorrhizal state.
• What are the main microbial groups in the adult human microbiome?

   Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, along with other unclassified or minor bacterial groups
• How does the increase in methanogenic archaea and the reduction of Bacteroidetes affects the biochemical balance in obese mice?

  Methanogenic archaea and low levels of Bacteroidetes results in low levels of H2. Low levels of H2 promote fermentation and produces CH4
• During this process of microbial transformation, two microbes connect through a pilus and exchange genetic material such as a transposon or plasmid:

  conjuagtion
• During this process of microbial transformation, a virus carries a gene from a former host and introduces it to a new microbe:

  transduction
• What is a competent cell?

  A competent cell is the cells ability to take in foreign DNA from the environment. 
• True or False: Some microbes are naturally competent and may kill other microbes to get new genes or genetic material for DNA synthesis

  True
• How are chemically competent cells prepared for transformation?

  Chemically competent cells are made competent through a salt treatment and heat shock.
• What does treatment with CaCl2 or MgCl2 do to the bacterial membrane that facilitates DNA intake?

  CaCl2 is positive and interacts with the negative membrane to allow for a neutral membrane and lets DNA pass through.
• What does the application of electrical pulse do to the bacterial membrane during the transformation?

  The electrical pulse allows for the rearrangement in orientation of the bilayer to form a gap.
• These are the basic components of a cloning vector:

  A selection marker, an origin of replication, a cloning site, and a promoter
• During cloning, a gene of interest is first ligated into a vector; then, the vector is introduced into a bacterium using chemical transformation or electroporation. Describe the process of transformation of your choice: chemical transformation or electroporation.

  During electroporation the plasmid DNA is mixed with the electrocompetent cell and put on ice. The sample is the exposed to electric shock at 15kV/cm in an electroporator. This allows the cells membrane to become permeable. They cells are then put in recovery in the form of an ice bath. 
• How is yeast mating performed?

  Haploid yeasts are put together to create a diploid
• What does the term "community composition" refer to?

  the abundance of all taxa in a community
• Mechanisms of community assembly can be classified as:

  Deterministic and stochastic
• List and describe the main mechanisms of community assembly:

  Diversification is where some organisms get abilities to thrive in an environment due to genetic changes.

  Dispersal  is due to a accessibility or lack of accessibility to a new environment.

  Drift includes birth, death and reproduction as well as other mechanism but is random.

  Selection is based on factors such as the environment, competition, or predation.
• Mutations are considered random processes and as such they are classified as

  Stochastic process
• Is dispersal limitation a mechanism that can affect community assembly of bacteria? Why?

  Yes, dispersal can affect community assembly of bacteria. Environmental changes can affect what organisms can live in certain areas. If a nutrient becomes lacking in a certain area, bacteria that rely on that nutrient will cease to live there. 
• This mechanism of community assembly has elements of stochastic and deterministic processes

  Dispersal
• What does the presence or absence of species depend on if only selection operates?

  Selection can only occur in the presence of genetic variation, the capacity of the organisms to thrive in the environment, their genes and physiology
• What are the two categories in which controllers of community assembly can be classified?

  Bottom-up controllers or top-down controllers
• List potential bottom-up controllers of community assembly

  pH, water, salinity, carbon and nitrogen sources, temperature
• Diversification

  some organisms get abilities to thrive in an environment due to genetic changes
• Dispersal

  an accessibility or lack of accessibility to a new environment
• Drift

  includes birth, death and reproduction as well as other mechanism but is random
• Selection

  factors such as the environment, competition, or predation
• Bottom-down controllers

  environmental properties