Microbial Ecology Methods

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

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

Next generation sequencing

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

N2