FINAL EXAM STUDYGUIDE (MICR 401)

Microbes associated with sea-ice are likely to be...

psychrophilic

In a sympagic environment, water exists mainly as a...

solid - ice

Sympagic

ice-associated

The two major types of sea-ice are...

fast and pack

You can collect a sediment sample with...

a piston corer

Deep in sediments you may find...

methanogenic Archaea

A microbiological consideration in sediment sampling is...

A. not contaminating the sample
B. maintaining sediment structure
C. not exposing cells and chemistry to the air
D. processing samples in a controlled atmosphere
E. All of the above

Sediments in the deep sea are usually anoxic below...

5 mm

You see curved-rod shape cells. Which term describes this shape?

Vibrio

Bacterial Cell Shapes

spheres (cocci), rods (bacilli), spirals (spirilla), curved rods (vibrio)
unusual: star, box, poly/pleomorphic

Where would you expect to see peritrichous flagella?

All over a bacterial cell's surface

types of bacterial flagella

monotrichous
amphitrichous
lophotrichous
peritrichous

All marine bacteria contain...

16S ribosomes

You Gram stain a pure culture of Bacteria cells. All cells appear blue. The cells are...

Gram positive

The Archaea cytoplasmic membrane contains...

isoprenoids linked to L-glycerol via ether linkages

A biomarker for members of the domain Bacteria is...

peptidoglycan

A biomarker for Gram negative Bacteria is...

LPS

Where are proteins made in bacterial cells?

In ribosomes

Which of these has been used to define oligotrophy?

A. Presence or absence of xenobiotics
B. Concentration of phosphorus
C. Presence or absence of viruses
D. Amount of ultraviolet radiation
E. Concentration of radioactive elements

Redfield defined the ratio of X:X:X in seawater. What is X:X:X

C:N:P (usually 106:16:1)

"A physiological state resulting from an insufficient amount of nutrients, especially energy, to permit growth (i.e., increase in cell size) and/or reproduction" describes...

starvation-survival

A response to insufficient nutrients may be...

spore formation
bacteria cells divide
little or no competition between species
a decrease in levels of DNA, RNA and some proteins

Bacteria that need organic carbon for growth are...

heterotrophic

The surface area to volume ratio of small cells is ________ that of large cells.

Greater than...

Using different conditions to grow different microbes from the same sample was developed by...

the Delft School

The enrichment technique...

uses a specific medium or condition to favor the growth of particular microbes

What are peptones?

water-soluble derivatives of proteins partly hydrolyzed by an acid or enzyme

Marine photoautotrophic bacteria require...

DIC
light
water
inorganic nutrients

Agar shake tubes may not be appropriate for cultivating marine bacteria because...

the temperature may be too high

In genes such as 5S, 16S, 18S, 23S, who is the 'S' named after?

Svedberg

A restriction site is...

a nucleotide sequence in DNA which may be targeted and 'cut' by a specific enzyme

Which procedure calculates species richness for a given number of sampled individuals?

Rarefaction

A disadvantage of terminal restriction fragment length polymorphism (T-RFLP) is...

short fragments are not reliable in assigning a sequence to a species

Which gene do we usually sequence to assign an Archaea or Bacteria to a taxonomic group?

16S rRNA

Who coined the terms 'Archaea, Bacteria, Eucarya" in the 20th century?

Woese and colleagues

Approximately how many bacteria species have been formally described?

19,000

Name a phylum in the Archaea

Euryarchaeota (7150 spp, diverse)
Korarchaeota (Thermophiles, vents/springs)
Crenarchaeota (marine vents, terrestrial springs)
Nanoarchaeota (1 spp, marine vents)
Geoarchaeota (Yellowstone, 2013)
Lokiarchaeota (arctic marine sediment near vent)

many known only by DNA

many known only by DNA

Oligonucleotides are...

short chains of nucleotides (up to 20 nucleotides)

Fluorescence in situ hybridization (FISH) enables...

detection of single microbial cells through use of specific probes

Fluorescence in situ hybridization (FISH) procedures...

do not require cultivation of cells
require permeable cells
do not require PCR (polymerase chain reactions)
do not require that DNA be extracted from cells

Organisms that convert inorganic nutrients to organic compounds in the absence of light are...

chemoautotrophic

Photosynthetically available radiation (PAR) is...

energy in solar radiation between 400 and 700 nm

Albedo is...

the proportion of the incident light or radiation that is reflected by a surface

Liebig's law refers to...

growth is dictated not by total resources available, but by the scarcest resource

Rates of primary production are generally considered lowest in/on...

gyres

A unit used to describe the amount of PAR is...

microE/sq. m/second

Bottom up control is...

how nutrient availability may control primary production

New production is...

that based on N in NO3 from upwelling, and from N2-fixation

A Profiling Natural Fluorometer System measures...

chlorophyll fluorescence emitted under ambient light conditions

Substrates used in tracer methods to measure primary production are...

radioactively labeled

Regenerated production is that based on...

N in ammonium or urea

The attenuation of light in seawater refers to...

absorption or scattering of light by water and materials in water

The term 'diel' refers to

a period of 24 hours

What has been used to stain nucleic acids in bacteria?

acridine orange

Which nucleotide is not found in DNA?

Uracil

Bacterial cell structure

slime layer, capsule, or extracellular polysaccharide (EPS)

As depth and pressure increase, the boiling point of seawater...

increases

Water temperature in the deep sea, away from hydrothermal vents, is typically...

2-4ºC

CFCs are [......] tracers of water masses. [Which word is missing?]

xenobiotic

The most abundant dissolved elements in seawater are

Na, Cl

Dissolved oxygen (O2) in the deep sea comes from...

the euphotic zone

A micronutrient that may limit phytoplankton growth in the open ocean is...

iron

Halophilic bacteria require...

sodium chloride

The mean depth of the ocean is said to be...

3711 m

This ocean is not described as a gyre...

Southern Ocean

The term 'high latitudes' refers to...

polar regions above 60°S and 60°N

The amount of an element in the ocean divided by its rate of removal or addition refers to...

the element's residence time in the ocean

In marine microbiology, what is DIC?

Dissolved inorganic carbon

The solubility pump moves...

inorganic carbon from the euphotic zone

The surface layer of water at almost uniform temperature and salinity is...

the mixed layer

The three major layers of an open ocean water column are...

surface, intermediate, deep

Which two factors affect the density of seawater?

Temperature and salinity

The Coriolis effect describes...

how Earth's rotation causes winds and moving objects to curve over the surface

Who proposed the azoic theory in 1843?

Edward Forbes

The term describing the role of microbes in nutrient cycling in the ocean is...

the Microbial Loop

The three domains of life found in the ocean are...

Archaea, Bacteria, Eucarya

Which set of terms is in the correct order of size, from smallest (left) to largest (right)?

Femtoplankton, Picoplankton, Nanoplankton, Microplankton

The term 'neuston' refers to what?

The upper 1000 microns of the ocean's surface

By which mechanism(s) does carbon leave the euphotic zone?

A. The biological pump
B. Passive export
C. The solubility pump
D. Active export
E. All of the above

Bacteria in this genus are considered the most abundant cells on Earth...

Prochlorococcus

In which marine habitat would you expect to find thermophilic bacteria?

Hydrothermal vents

Individuals of this group dominate microbial biomass in the deep sea

Archaea

Which of these is produced by Archaea in marine sediments?

Methane

Which organisms in the ocean characteristically contain calcium carbonate?

Coccolithophores

The deepest sediments are found...

on continental shelves near the mouths of major rivers

This device can collect seawater from a depth of 1000 m...

A Go-Flo

Which of these collects a water sample?

A. ATE sampler
B. Nansen bottle
C. Van Dorn bottle
D. Niskin bottle
E. All of the above

Cells in a biofilm may produce EPS. What is EPS?

Extracellular polymeric substance

'Fluvial' refers to processes related to...

rivers

Which of these terms can be used when referring to sediments?

A. Terrigenous
B. Lithogenous
C. Pelagic
D. Biogenic
E. All of the above

Which of these may be used to sample the neuston?

A. Rotating drum
B. Screen sampler
C. Paper sheet
D. Glass plate
E. All of the above

The Neutrally Buoyant Sediment Trap (NBST) is designed to catch...

particles

Microbes consistently exposed to high levels of UV radiation might...

have a high GC content in their DNA

Which of these defines the plankton

Weakly motile or non-motile organisms in the water column whose movement largely depends on currents

Mycoplankton refers to...

fungi and yeasts in the water column

What would characterize a point 100 m below the surface of sediments in the open ocean?

No dissolved oxygen

Hydrothermal vents are found...

A. on mid-ocean ridges, hot-spots, subduction zones
B. off the coast of Hawai'i
C. on the Juan de Fuca Ridge
D. on the mid-Atlantic Ridge
E. All of the above

Cold seeps are characterized by...

high methane and sulfide concentrations

The maximum known growth temperature for life is...

>100ºC (thermophilic archaea)