Micro 450 Exam 2
What is the definition of a generalist?
A specific species or set of closely related species is not required
What is the niche area of a generalist?
Broad
B. thetaiotaomicron is an example of what?
Generalist
What are the two degrees of specialization of mutualism?
Generalist and specialist
What are the two degrees of dependence of mutualism?
Obligate and facultative
Symbiosis is what?
Omnipresent and affects all organisms on the planet
What is a benefit of performing DGGE?
The analysis is not limited to only the 16s gene, rather you can analyze a separate gene
What is the definition of niche?
The environmental conditions that allow a species to grow and satisfy its minimum requirements so growth is greater than 0
What are the four ways to desires community composition and changes?
Culturing, 16S rRNA sequencing, fluorescent in situ hybridization, molecular fingerprinting (DGGE and t-RFLP)
Accumulation of hydrogen gas decreases the efficiency of what?
Fermentation
What are the steps of FISH?
Fixation of the sample, fixed cells are premeablized to be hybridized to flourescently labeled oligonucleotides and then washed, and cells are then quantified using epifluorescent microscopy
What kind of animals are are great models to study ecological principles?
Germ-free
What is niche not synonymous with?
Habitat
What is the ecological niche of a microbe primarily determined by?
The specific metabolic properties of that organism
What is ecology?
The study of interactions between organisms and their abiotic and biotic environment
What did the study in germ free mice fed either plant derived polysaccharide diet or the western diet (high fat/high sugar) find for E. rectale?
The western diet induced a down regulation of several glycoside hydrolases and sugar transporters
The realized niche can be regarded as what?
Competitive refuge
What is the definition for a fundamental niche?
Conditions where an organism can live without competition
What is the definition of realized niche?
Conditions which an organism actually lives
Disadvantages of culturing?
"Not yet culturable" microbes present and difficult to distinguish species and strains based only on morphological and chemical tests
What is the definition of pathogen?
A biological agent (typically a microbe) that causes disease
Despite the mouse gut being a selective environment, it is a what for many microbial species?
A fundamental niche
What is the definition of symbiosis?
A way to describe two species of organisms that live together in an intimate association, regardless of the outcome of the association
What are examples of abiotic components of an environment?
Climate, soil, altitude, latitude
What will two organisms that have the same habitat and similar niches do?
Compete with each other over the available resources
What are the two types of parasites?
Ectoparasites and endoparasites
What is critical to microbial ecology?
Integration of hypothesis testing
What are the mutualistic effects on individuals and populations?
Interactions have the ability to shift population dynamics by: increasing birth rates, decreasing death rates, and increase the carrying capacity for a population
Habitat is a ____, niche is a ____.
Place, pattern of living
What does mutualism promote?
Positive fitness through the exchange of benefits having a net positive effect on growth/reproduction
What are examples of biotic components of an environment?
Predators, parasites, hosts, competition
Pros of FISH?
Provides information about relative abundance and spatial organization and potential interactions among members of a community
What did the study in germ free mice fed either plant derived polysaccharide diet or the western diet (high fat/high sugar) find for B. thetaiotaomicron?
The western diet induced an up regulation of genes involved in degradation of host polysaccharides and a down regulation of genes involved in degradation of dietary plant polysaccharides
What are the purpose of antimicrobial peptides?
These are potent peptides that have the ability to kill Gram neg/pos bacteria, enveloped viruses, fungi and even cancerous cells
What is the definition of a specialist?
Associates with only 1 or a few species (species specific)
What does commensalism mean?
At table together
What does FISH aim to do?
Attempts to fix the limitations that are posed by culture independent sequencing
What are two examples of bacterial parasites?
Bacteriophages and Bdellovibrio
What is density dependence?
Benefits can decrease with increasing population due to costs associated with high density and benefits can also depend on higher density
What is required for analysis of Illumina sequences?
Bioinformatics to analyze the genom
What is mutualism?
Both partners benefit
What is a facultative degree of dependence?
Although organisms benefits, mutualism is not required for survival/reproduction
Limitations of Metagenomics?
DNA from dead cells, presence of a gene does not mean activity, and expensive due to need to sequence more than 16s rRNA
What are limitations to sequencing methods?
Dead cell counts, extra step to learn what species are represented by each band (must sequence), no insight about functions or interactions among organisms, and no insight on structural organization of the community
What is the definition for ecophysiology?
Deals with the function and performance of an organism in their environment
What are the two factors that affect context dependence?
Density dependence and abiotic conditions
How are E. rectale and B. thetaiotaomicron an example of commensalism?
E. rectale uses B. thetaiotaomicron derived acetate to generate more butyrate and grow better
What occurs after the gel is finished?
Each lane represents an individual sample containing a 16s fragment that can be excised and then sequenced
What are the two things that ecology is not?
Environmentalism and natural history
Why does evolutionary theory predict that mutualisms should be unstable?
Evolution does not select for organisms to be altruistic, evolution would select for organisms to cheat, and mutualisms should break down over evolutionary time due to the first two reasons
Limitations of Metatranscriptomics?
Expensive due to most RNA in cell is ribosomal, not good for microbes other than E. coli and bad for communities, and large dynamic range for mRNA in cell meaning you need to sequence deep to get information
What are the steps of DGGE (Denaturing Gradient Gel Electrophoresis)?
Extract DNA, PCR 16s rRNA genes with bacterial specific primers and the GC clamp, and electrophorese at constant temp to determine the critical denaturant concentration of DNA
What are the steps of Sanger sequencing?
Extract DNA, PCR amplification using 16s specific primers, clone 16s rRNA genes into plasmids, transform plasmid into E. coli, sequence the plasmids to create a phylogenetic tree
What are the steps of Terminal Restriction Fragment Length Polymorphism Analysis (TRFLP)?
Extract the DNA, PCR amplify 16s rRNA genes with a labeled primer, cut the DNA using restriction enzymes, and electrophorese the fragments on a gel
What do glycoside hydrolases do?
Hydrolyze/rearrange glycosidic bonds
What is the TnSeq strategy useful for?
Identifying genetic determinants of growth at a large scale using transposons
What is TnSeq used for?
Identifying genetic determinants of growth at large scales
What is problematic about Sanger sequencing?
If 16s rRNA gene is not isolated and pure sequencing is extremely error prone
What is the other sequencing method that is becoming more popular?
Illumina Next Generation sequencing
Advantages of culturing?
Inexpensive and you get isolated colonies to work with on future studies
What are three reasons that parasitism is important?
Influence different ecological levels (promote ecological fitness), they're a driving force shaping biological diversity (cause genetic and phenotypic polymorphism), and are a selection agent favoring sexual recombination
Antimicrobial peptides are a part of what?
Innate immune response
When you isolate a new species of bacteria and sequence it to determine its metabolic pathways, what do you discover?
Its fundamental niche
What are the 11 environmental constraints to microbes?
Limited nutrients (C, N, S), electron acceptors (anaerobic env), temperature, osmotic pressure, light (different intensities), pH, bile acids/antimicrobials, host produced antimicrobials, pressure, salinity, fluctuation of nutrients
What are endoparasites?
Live inside the body of the host
What are ectoparasites?
Live outside the body of the host
What are the results of Sanger sequencing?
Long read length, high accuracy, low sequence volume, and low-throughput
Cons of FISH?
Low throughput, laborious and time consuming, need equipment (fluorescent microscope), and dead cells are counted
Why are parasites important?
Majority of every taxonomic group includes members that are parasites and a large amount of organisms are hosts to parasites
What are the three things that are essential to hypothesis testing?
Making observations, experimentation, and mathematical models (analysis)
What occurs during experimentation when studying ecology?
Manipulation of a system to look for different responses
What are the two H2 consuming groups of microorganisms?
Methanogens and sulfate reducing bacteria
Three most common forms of symbiosis are what?
Mutualism, commensalism and parasitism
What is the niche area of a specialist?
Narrow
Realized niches are what compared to fundamental niches?
Narrower
What are the two types of questions that must be formulated when exploring microbes in a specific niche?
Natural history and ecological
What is commensalism?
Neither partner suffers, but one partner may obtain a benefit
What is the definition of context dependence?
Net benefits received may vary, depending on different factors
What is the competitive principle?
No two species can occupy the same ecological niche, however, if multiple different organisms have different niches they may coexist within the same ecological community
In a mutualistic relationship do both organisms need to have the same degree of specialization?
No, one could be a generalist while the other is a specialist
What do polysaccharide lyases do?
Non-hydrolytic cleavage of glycosidic bonds
Why can't two different organisms occupy the same niche?
One organism with out-compete the other (drive it locally extinct)
What is parasitism?
One partner benefits at the expensive of the other
What is an obligate degree of dependence?
Organism cannot survive and or reproduce without mutualism
What is the net benefits concept of mutualism?
Organisms provide "good" or "services" that are a cost to themselves equating to mutual exploitation for net gain
How do microbes alter sensitivity to cationic AMPs?
Remodeling Lipid A of Gram negative bacteria undergo derivitization or the removal of phosphate groups to render bacteria resistant to AMPs by decreasing the negative charge of the outer membrane
What are the two components of the term niche?
Requirements and impact to the ecosystem
What is an example of commensalism?
Shark and remora; gut microbes
What is an example of an abiotic condition that changes with context density?
Shelter
What are the results of Illumina?
Shorter read lengths, moderate accuracy, massive sequence volume, huge-throughput
E. rectale is an example of what?
Specialist
What does the GC clamp do?
The GC clamp is added to primers to anchor the DNA together once it is denatured
What are the types of "goods" and "services" exchanged in mutualism?
Typically is the giving on type of award to gain another in the form of food (energy/nutrients), protection from parasites/predators, shelter from physical environment, and dispersal (seeds)
What does ecophysiology attempt to do?
Understand the physiological mechanisms by which organisms confront constraints in the environment
What are the two goals of ecological research?
Understand the principles related to the operation of natural systems and predict their response to change
What are the five reasons that understanding microbial ecology is important?
Understanding how the world works, sustainability, human health, application, responsibility as earth guardians
Why use 16s rRNA sequencing for understanding microbial communities?
Universal to bacteria, conserved regions for primer design, variable regions for distinguishing, comparative databases
What does community fingerprinting aim to do?
Use methods that do not rely on sequencing to compare communities
What is an example of an ecological question?
When you feed cow X diet, the microbial community will ____?
What does metatranscriptomics use for sequencing to understand metabolism?
mRNA is sequenced and then is analyzed to compare abundance of expressed functions in the microbiota for different samples