Week 11 Flashcards by Tami Ojewole

microbiome (def.)

collection of microorganisms in environment

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the ocean microbiome contains all the microbes that are _____ & the primary producers of _____

-responsible for nearly all the energy flux that occurs in oceans
-fuel (photosynthesis and chemosynthesis)

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concentration of microbes in ocean microbiome

billions per little of sea water (both free living and complex communities)

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the ocean microbiome is not a homogenous soup – it depend on _______

location, depth, season, temp, pH

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____ has a massive impact on ocean microbiome

pollution (oil spills, microplastics)

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Microbial biomass in soil is greatest where? smallest where?

-equator & rainforest
-desert

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soil microbiome is dominated by _____ and less by ______

-bacteria & fungi
-protists & viruses

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Bacteria plays a major role in recycling ______-> breakdown of dead ______

-organic matter
-plants and animals

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Bacteria also play a major role in _______ and ____

-nutrient cycling (control nutrient availability in the environment)
-pH

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Nutrients cycled by bacteria (4)

Phosphorus
Nitrogen
Sulfur
Iron

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Bacteria produce large quantities of greenhouse gases (4)

methane (CH4)
carbon dioxide (CO2)
nitric oxide (NO)
nitrous oxide (N2O)

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Rice fields account for _____ of global methane emissions
* Produced by ______ growing in flooded fields

-5-10%
-methanogens

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Cable bacteria summary

-filmanetous, electrically conductive bacteria from family Desulfobulbaceae
-filaments transport e- over centimeter distances

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Cable bacteria & rice fields

cable bacteria deep in soil oxidize H2S to SO42- deep in soil
transport e- to surface
reduce O2 to water
-this increase conc of SO42- in the soil
-sulfate reducing bacteria outcompete other organisms for organic carbon (no food for methanogens)
-bacteria reduce SO42- to H2S and cycle continues

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Adding cable bacteria to plant pots growing rice reduces ________

methane emissions by >90%

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___ animals have microbiomes. generally a complex mixture of __________. animal microbiome generally forms a _____ & varies widely between _______

-all
- archaea, bacteria, fungi, and viruses
-stable environment (resistant to disturbances)
-organisms and environment

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Euprymna scolopes (bobtail squid) lives in a symbiotic relationship with _____

-Aliivibrio fischeri

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Bobtail squid has a light organ which contains a _______

-network of unique reflector and lens tissues that help reflect and focus the light ventrally through the mantle

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Quorum sensing in Aliivibrio fischeri

Bioluminescent Gram-negative, rod-shaped bacterium found globally in marine environments
Stimulated by AHL when cell density is high = produces light

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enzymes that makes light + substrate for enzyme

-luciferase
-aldehydes

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luxCDABE operon

luxCDE - produce aldehydes from fatty acids
lux
luxAB - luciferase

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A. fischeri and the bobtail squid

The squid provides the bacteria with a sugar and amino acids
A. fischeri grows and uses quorum sensing to stimulate bioluminescence
The squid uses this bioluminescence to hide its silhouette when viewed from below by matching the amount of light hitting the top of the mantle (counter-illumination)
Bioluminescence demands a substantial amount of energy from a bacterial cell

Colonization is specific for A. fischeri

-hatchlings of bobtail squid lack bacteria; need to carefully select for bacteria
-A. fischeri has flagella to move through ducts to the light organ (squid flushes ducts to eliminate non-motile bacteria)
-Squid halide peroxidase (uses H2O2 to oxidize halides) in ducts is antimicrobial -> A. fischeri possesses a periplasmic catalase → eliminates H2O2
- Squid produces nitric oxide (NO) (antimicrobial) in the light organ but A. fischeri produce NO inactivating enzymes

Cellulose (def.)

linear polymer of β-1,4-linked glucose

few organisms use cellulose as an energy source due to the ________

limited expression of cellulose-degrading enzymes (cellulases)

_______ consume cellulose as plant fibre; depends on presence of ________

-Termites -Trichonympha, a symbiotic protozoa

Trichonympha internalize wood particles by _____ and partially digest them

phagocytosis

Trichonympha contain both ___ and _____

-endo -ectosymbionts

Endo + Ectosymbionts of Trichonympha

* Bacteria which help with nitrogen fixation (contain nitrogenase) * Conversion of sugar to energy by Trichonympha produces CO2 and H2, which contributes to making environment anoxic * Bacteria use H2 and CO2 to make acetate → AcCoA

mutualism (def.)

organism A: benefit organism B: benefit obligatory interaction

cooperation (def.)

organism A: benefit organism B: benefit non-obligatory interaction

Commensalism (def.)

organism A: no effect organism B: benefit

Predation (def.)

organism A: dies organism B: benefit B eats A

Parasitism (def.)

organism A: negative organism B: benefit Host/parasite co-exist

amensalism (def.)

organism A: negative organism B: no effect release of toxic molecules

competition (def.)

organism A: negative/small negative organism B: benefit/small negative competition for resources

The human microbiome (def.)

-Combined microbes that live in and on humans (gut, skin, mouth)

Microbes in human microbiome frequently identified by _______

gene encoding 16S rRNA

Human microbiome is ____ to the individual and is formed within _____. more or less _____. different in different _________. necessary for ______

-unqiue -the first 3 years -stable -areas of the body -health

Human microbiome responds to ______ but returns to normal when ______ is removed

-disturbances -disturbance

skin, saliva, urogenital tract are dominated by ________

gram + bacteria

GI tract dominated by _____

gram - bacteria

Despite this enormous inter-individual variety in microbiome, the symbiosis between microbes and humans results in a stable and common ______ and a well-balanced _______-> resistant to ______

-metabolic pattern -physiological homeostasis -exogenous microbes like pathogens

Human microbiome depends on your _______

* parents * diet * environment * genetics * health conditions

Birth mode dictates _____

initial gut microbiome - C section = microbes from skin - Vaginal = microbes from vagina

Infant microbiome changes after ____

birth regardless of mode of delivery (becomes more stables, generally end up similar between different delivery modes)

When studying bacteria in microbiome, classification of bacteria by phylum does not provide enough information?

-phylum classification does not show if species are good, bad, or both

Functional genomics (def.)

field of molecular biology that attempts to describe gene functions and interactions

Metagenome (def.)

all the genes in an environmental sample; genes more common=activity needed/required for life

KEGG (_____) + does what?

-Kyoto Encyclopedia of Genes and Genomes -puts enzymes into categories based on metabolic pathway

heat map tells us _____

which genes are enriched/depleted in different environments/microbiome

CHILD Cohort Study

-3600 children in Manitoba -study lots of variables & gut health/makeup -mostly small correlations

Caveats to microbiome research

* Taxonomic information tells you nothing about function * Enzyme class information tells you nothing about outcomes * Soooooooooooooooooo many variables * Diving into metagenomic datasets to look for correlations is a computational nightmare * Mice are not humans * Correlation does not equal causation

_____ change your diet/lifestyle or provide advice to others based on a single study

DO NOT