intro to ecology, 26, & 27 Flashcards
what is dissimilatory sulfate reduction?
-anaerobic respiration
- Sulfate is terminal electron acceptor
- preformed by some bacteria, few archaea
- Sulfate to H2S
where is the hotspot for HGT on plants?
rhizosphere (roots)
high conc of acetic acid causes more plasmid transfer as well as the large amount of nutrients and water.
what are different types of culture dependent approaches?
enrichments, conventional media, dilutions, “next generation” culturing- cell sorting
what are types of nonculture dependent approaches?
microscopy, spectroscopy, microscoms measuring activity- Next Generation Sequencing
axenic culture
pure culture
great plate count anomaly
Discrepancy between the number of microbial cells observed by microscopic examination and the number of colonies cultivated from the same natural sample.
why cant some microbes be cultured?
- slow growing
- low abundance
- inhibition by other microbes in a mixed culture
- lack triggers for growth or exit from a dormant state
- etc.
How do people discriminate between live and dead cells?
- viability PCR (Polymerase Chain Reaction)
dye enters dead cells with damaged membranes
enrichment culture
- promotes growth of a microorganism that was restricted
- inhibits growth of other microbes
- must understand the specific niche the microbes inhabit
- know feature that set the microbe apart
what are the different types of identifying microbes that cant be cultured?
genetic sequencing, whole-genome comparison, molecular approaches, and metagenomic analysis
Oligonucleotide signature sequences (genetic sequencing)
short conserved nucleotide sequences specific for phylogenetically defined
groups
Phylotype
uncultivated microorganisms identified solely on sequence
what are the types of whole-genome comparison
average nucleotide identity-
- Standard for species identification.
- ANI values for 2 genome in the same species should be at least 95%
G-C content-
- Percentage of DNA that is made of G and C
comparative genomics-
- identify common genes between two organisms
what are the types of molecular approaches?
metagenomics-
- sequencing all DNA from an environment
- infer biogeochemical conditions of a habitat
Metatranscriptomics-
- mRNA in the environment is reverse transcribed and sequenced (using lab enzymes)
- presence of mRNA demonstrates gene product is alive
Metaproteomics-
-identifies proteins present at the time of sampling (pulls out proteins to see their purpose) (easy in water, hard in soil)
what is metagenomic analysis?
computer programs analyze abundance of sequences.
High frequency genes- core-genome
Moderate frequency genes- encode secreted products
Low frequency genes- species specific
how do we quantify gene abundance?
Digital Droplet PCR- new method, replacement of quantitative PCR
Population
group of microorganisms within a single species or other taxon in an ecosystem
Guild
group of microbes defined by physiological activity
Microbial community
microorganisms that share a common
habitat.
how do we measure microbial activity?
stable isotope analysis- using probing and the compounds enriched in naturally rare isotopes
Microscoms- examine nutrient cycling (measure respiration w/ CO2 release)
Quantitative stable isotope probing
Spins microbes really fast to centrifuge and then the microbes are sorted by density and weight
what are the types of microbial interactions?
symbiosis- stable association of 2 or more organisms
Facultative- alternative lifestyle probable
Obligatory- Host is absolutely required
what are the types of symbiosis?
Mutualism- both partners benefit from each other (often obligatory)
Cooperation- nonobligatory
Antagonism- one organism negatively impacts another
syntrophy
when one species benefits from the metabolic products of another
(interspecies Hydrogen/ electron transfer)
