MMG 301 - Module 26: Ecology Concepts and Methods

The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature. T/F

False

Metagenomics involves the analysis of a microbial community by __________.

sampling and sequencing all genes in an environment

The phylogenetic diversity analysis of complex microbial communities often targets small subunit (SSU) ribosomal RNA genes. This is because rRNA is found in all organisms and __________.

is highly conserved over evolutionary time

Organisms in natural environments can be detected by assaying for the presence of their genes. T/F

True

A microbial population can contain several microbial communities. T/F

False

Functional differences can be observed by using 16S rRNA gene phylogenetics of a microbial community. T/F

False

Staining methods are suitable for obtaining

quantitative information from natural samples

Fluorescent in situ hybridization (FISH) can be used to determine __________.

the phylogenetic diversity of an environmental sample; whether a specific piece of mRNA is being produced; how many Salmonella typhimurium cells are present in a sample of unpasteurized apple juice (all of the above)

Phylogenetic stains, such as those used in phylogenetic FISH, hybridize with

ribosomal RNA

How do viability stains usually distinguish between living cells and dead cells?

The dye specifically targets intact cytoplasmic membranes.

Fluorogenic dyes, autofluorescence, and genetically engineered autofluorescence can be used to identify cells. T/F

True

In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter without special dyes. T/F

True

One way to study a microbial ecosystem is to isolate microorganisms from it and study their properties in laboratory culture. T/F

True

The goal of environmental genomics is to detect as many genes as possible and then, if possible, to determine to the phylogeny of the organisms to which the genes belong. T/F

True

The purpose of the enrichment culture technique is to enrich for organisms with specific physiological properties from a microbial community. T/F

True

Which of the following represents increasing microbial diversity?

population-guild-community

Genes encoding ________ are widely used as target genes in molecular biodiversity studies.

16s rRNA

A population of metabolically related microorganisms is called a(n)

guild

An ecosystem includes both the living organisms and abiotic materials that function together. T/F

True

For microbial biodiversity studies, it is common to identify the ________ rather than the ________ as a measure of biodiversity.

genes / organisms themselves

Culture-independent approaches avoid issues associated with

growing organisms in the lab.

By isolating total community RNA, using reverse transcriptase to make cDNA copies of it, and then sequencing the cDNA, ecologists can __________.

determine the community genome expression at the moment of sampling

Phylogenetic analysis of microbial communities in nature using various PCR techniques has revealed that only a minority of phylotypes have been cultured from the environment and the most common phylotypes have not been grown in in the laboratory. This is due in part to __________.

enrichment bias

Which molecular method allows for the detection of a specific organism within a diverse microbial community?

fluorescent in situ hybridization (FISH)

In microbial ecology studies, the FISH technique identifies organisms based on

hybridization of a fluorescent probe to specific ribosomal RNA sequences.

Ecological theory states that for every organism there is at LEAST one ________, and the microenvironment where the organism is most successful is called the ________.

niche / prime niche

Microarrays that have been designed to screen samples for specific groups of bacteria are called __________.

phylochips

Genes that retain their function yet change over evolutionary time as organisms diverge are called orthologs. Organisms with identical or very similar orthologous genes belong to the same __________.

phylotype

Thirty organisms containing the same phylogenetic marker, with identical or similar orthologous genes, are all considered to be within the same

phylotype

In the soil, oxygen concentrations are highly variable even within a soil particle. The center of the particle may be anoxic even if the outer portions are oxygen rich. In this context, facultative anaerobes could be found

throughout the particle.