18:Diversity of Microbial Eukaryotes

Acridine orange

a nonspecific fluorescent dye used to stain DNA in microbial cells in a natural sample

DAPI

a nonspecific fluorescent dye that stains DNA in microbial cells

Denaturing gradient gel electrophoresis (DGGE)

an electrophoretic technique capable of separating nucleic acid fragments of the same size that differ in base sequence

Enrichment bias

a problem with enrichment cultures in which “weed” species tend to dominate in the enrichment, often to the exclusion of the most abundant or ecologically significant organisms in the inoculum

Enrichment culture

highly selective laboratory culture methods for obtaining microorganisms from natural samples

Environmental genomics (metagenomics)

the use of genomic methods (sequencing and analyzing genomes) to characterize natural microbial communities

Flow cytometry

a technique for counting and examining microscopic particles by suspending them in a stream of fluid and passing them by an electronic detection device

Fluorescence in situ hybridization (FISH)

a method employing a fluorescent dye covalently bonded to a specific nucleic acid probe for identifying or tracking organisms in the environment

Fluorescent protein

any of a large group of proteins that fluoresce different colors, including the green fluorescent protein

Fundamental niche

the range of environments in which a species will be sustained when it is not resource-limited, such as may result from competition with other species

Isotopic fractionation

the discrimination by enzymes against the heavier isotope of the various isotopes of C or S, leading to enrichment of the lighter isotopes

Laser tweezers

a device for obtaining pure cultures by optically trapping a single cell with a laser beam and moving it away from surrounding cells into sterile growth medium

MAR-FISH

a technique that combines identification of microorganisms with measurement of metabolic activities

Metatranscriptomics

the measurement of whole-community gene expression using RNA sequencing

Metaproteomics

the measurement of whole-community protein expression using mass spectrometry to assign peptides to the amino acid sequences coded by unique genes

Microautoradiography (MAR)

the measurement of the uptake of radioactive substrates by visually observing the cells in an exposed photographic emulsion

Microbial ecology

the study of the interaction of microorganisms with each other and their environment

Microsensor

a small glass sensor or electrode for measuring pH or specific compounds such as O₂, H₂S, or NO₃⁻ that can be immersed into a microbial habitat at microscale intervals

Most-probable-number (MPN) technique

the serial dilution of a natural sample to determine the highest dilution yielding growth

Multiple displacement amplification (MDA)

a method to generate multiple copies of chromosomal DNA from a single organism

Nucleic acid probe

an oligonucleotide, usually 10–20 bases in length, complementary in base sequence to a nucleic acid sequence in a target gene or RNA

Phylotype

one or more organisms with the same or related sequences of a phylogenetic marker gene

Realized niche

the range of natural environments supporting a species when that organism is confronted with factors such as resource limitation, predation, and competition from other species

Stable isotope probing (SIP)

a method for characterizing an organism that incorporates a particular substrate by supplying the substrate in ¹³C or ¹⁵N form and then isolating heavy isotope–enriched DNA and analyzing the genes

Winogradsky column

a glass column packed with mud and overlaid with water to mimic an aquatic environment, in which various bacteria develop over a period of months