Microbial Ecology Exam 2

Polymerase chain reaction (PCR)

This methods is required to do DGGE and T-RFLP

Single-cell genomics (MDA)

This method may use flow cytometry to isolate a cell and then sequence its genome

MAR-FISH

This method uses analytical chemistry to detect radioactive decay and can incorporate FISH probes

Raman microspectroscopy

This method uses analytical chemistry to focus light on cells and can combine FISH and SIP

Secondary ion mass spectrometry -> NanoSIMS FISH

This method uses analytical chemistry to bombard cells and read the molecules released

Stable isotope probing (SIP)

This is used to detect the transformation of a molecule such as carbon dioxide or glucose

Microsensors

These are used to measure gases, elements, and nutrients at a fine scale

Metaproteomics

This method recovers as many proteins as possible that were produced by a community

Metatranscriptomics

This method theoretically sequences all of the RNA from all organisms in a sample

Metagenomics

This method theoretically sequences all of the DNA from all organisms in a sample

Microarrays

These methods use hybridization of DNA to probes to identify species or gene functions

Next generation DNA sequencing

This includes ever-changing technology to determine the base sequences of chromosomes

DGGE

Can be used to estimate species richness and evenness based on PCR using a “GC clamp”

T-RFLP

Can be used to estimate species richness and evenness based on PCR and restriction enzyme digests

Fluorescence in situ hybridization (FISH)

Can be used to determine the total number of cells in a sample and identify them under microscopy

Direct counts

Can be used to determine the total number of cells in a sample

Most probable number (MPN)

Uses culturing to make counts of microbes performing the same function

Enrichment culturing

Uses culturing to assess microbes performing the same function

Which stable isotope would not be used to label DNA to determine the active species in a community of microorganisms?

34S

Which gene did we not sequence in lab when analyzing the communities in Dicks Creek?

23S rRNA

What is the major difference between DGGE and T-RFLP?

The primers used in PCR.

All of the following are biases in working with DNA from environmental samples, except which one?

Genome size differences in species within the sample.

Which method can detect the activity of thousands of genes being used at the same but not which species are producing the gene products?

Metatranscriptomics

Which eukaryotic taxonomic group has not incorporated a secondary endosymbiont?

Fungi

Which method(s) would you use to show that a particular species was present in an environmental sample AND was actively doing something like nitrogen fixation or photosynthesis?

MAR-FISH

Isotopes of chemical elements are used in all of the following methods but which?

Flow cytometry

Which method below does not use nucleic acids in some manner?

Metaproteomics

In a study examining microbial activity in a biofilm, an investigator wants to know if a particular gene is expressed by cells. Which method would best tell them this?

Metatranscriptomics

Which method below does not use fluorescence to detect cells or genes?

DGGE

Which method used in microbial ecology is free of any bias in detecting species from an environment?

None of the above

The “Great Plate Count Anomaly” is a good example of which aspect of microbial ecology?

Enrichment bias

Next generation sequencing

Which method shows most convincingly that we cannot culture the vast majority of prokaryotes?

Which form of nitrogen can only be metabolized by bacteria and archaea?

N2

Microsporidia/Chytridiomycota

Includes fungal parasites/opportunistic pathogens of humans; amphibian pathogens

Apicomplexans

Obligate animal parasites that contain chloroplasts that don’t photosynthesize

Brown algae/Golden algae

Can be single-celled or large, multicellular organisms like seaweed; colored by carotenoids

Green algae

Generally freshwater photosynthesizers closely related to plants

Diplomonads

Contain two nuclei and functionally reduced mitochondria; includes Giardia

Zygomycota/Mucoromycota

Fungi involved in food spoilage and can be found in soil and decomposing plant matter

Slime molds

Heterotrophic protists that have complex life cycles and make fruiting bodies and spores

Basidiomycota

May exist as mushrooms, yeasts, and pathogens of plants; can reproduce sexually

Dinoflagellates

Photosynthetic protists with two flagella; can cause red tides and fish kills

Foraminiferans

Heterotrophic protists that form tests made of calcium carbonate

Euglenids

Aquatic photosynthesizers that may contain five genomes (four from endosymbionts)

Oomycetes

Formerly classified as fungi, this group of protists is also known as the water molds

Ascomycota

Contain yeasts such as Saccharomyces and molds; can be symbionts in lichens

Diatoms

Most species rich group of protists; cell walls contain silica; photosynthesizers

Parabasalids

Anaerobic heterotrophic protists with hydrogenosomes and large genomes

Radiolarians

Marine heterotrophic protists that form silica tests and may form symbioses with algae

Chlorarachniophytes

Motile photosynthetic protists that can switch to heterotrophy in the dark; nonpathogenic

Red algae

Generally marine photosynthesizers with red pigmentation and small genomes

Kinetoplastids

Bacterial predators with one mitochondrion; can be human pathogens like Trypanosoma

Ciliates

Heterotrophic protists, including Paramecium, which eat or form symbioses with bacteria

Entamoebas/Gymnamoebas

Contain the true amoebas; some are free-living while others are pathogenic

Glomeromycota

Live obligately in plant roots as endomycorrhizae and probably helped plants colonize land

Haptophytes

Major unicellular photosynthesizers in the ocean; have calcium carbonate shells