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MICRB 320 > Synecology and Traditional Autecology > Flashcards

Synecology and Traditional Autecology Flashcards

1
Q

What is hypothesis

A

A proposed explanation for a phenomenon. Explanation based on previous observations when no scientific theory can explain the phenomenon. Must be testable

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2
Q

What is null hypothesis

A

A statement that there is no relationship between two conditions. Called H0 (null) until it is given statistical significance. Aim to disprove rather than prove within the scientific method

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3
Q

What is the goal of experimental design

A

The goal is to falsify, or disprove the hypothesis

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4
Q

What the controls of experimental design

A

Differentiate between experimental effects and other effects

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5
Q

What are the factors to consider from experimental design

A 
Heterogeneity and replication
Needs to collect environmental 'metadata'
Sample size
Sampling method
Storage and transport
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6
Q

What is the analysis of experimental design

A

Experimental effects
Variables
Statistical approaches

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7
Q

What are microscopic cell counts

A

Cells are stained with a dye, usually, fluorescent. Filter on to membrane (known area). Count selection of representative fields (also known area)

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8
Q

What is flow cytometry

A

Objects can be detected by a flow cytometer because they scatter light. More often absorption and emission of light is used (fluorescence). Some organisms are fluorescent (auto-fluorescent), and others we stain with fluorescent dyes or proteins

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9
Q

What can flow cytometry detect

A

Flow cytometry can identify organisms using: Shape, Pigments (chlorophyll, phycoerythrin), DNA stains (heterotrophs, diving, and sexual cells), Respiration stains (live dead for bacteria, caspase for apoptosis in eukaryotes), and Cell structure stains (actin). Can be used to sort cells-cultivation, single-cell genomics

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10
Q

What is microbial biomass

A

Conversion factor from cell size and volume. Biochemical assays. Measure specific biomolecules. All microbial biomass has same amount of biochemical assayed. ATP + ADP + AMP (can tell growth state). Cell wall components: Muramic acid, Limulus assay (gram negative only), and Chitin (fungi only). DNA, protein, or lipid concentration

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11
Q

What is photosynthesis/primary production

A

Primary productivity: Uptake of radiolabeled 14CO2, Chlorophyll A content. Short time spans measure gross primary productivity. Long time spans measures net primary productivity (PP – Respiration

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12
Q

What are ‘potential’ activity measurements

A

Remove “bottom up” constraints by adding nutrients and/or substrate. Note – can be used to determine limiting nutrient. Measure and compare maximum possible rate of that activity for that system

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13
Q

What is Michaelis - Mentin Kinetics

A
  1. All members of the community respond in the same way to the substrate
  2. Uptake is functionally equivalent,
  3. Substrate utilized is representative of all substrates
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14
Q

What is thymidine uptake

A

DNA synthesized by growing cells at rate proportional to biomass. Use radiolabeled thymidine uptake rates to determine community growth rate. Assumes all bacteria take up thymidine and incorporate into DNA at the same rate

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15
Q

What is the functional gene amplicon sequencing

A

Do a bunch of sequence. Get a bunch of sequences. PCR amplification and amplify the sequence that is variable to differentiate between different organisms. Functional genes would be like the core genes

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16
Q

What are transcriptomes

A

All of the genes that are expressed under specific conditions. Must compare to control to understand regulation. Need genome sequence to understand context. Use reverse transcriptase to copy extracted RNA (usually enriched for mRNA) into cDNA. Sequence cDNA.

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17
Q

What are proteomics

A

All of the proteins synthesized under specific conditions. Same concerns as transcriptomes. Fragment isolated proteins, mass spec to determine fragment sequence, assemble using genome scaffold and/or overlapping fragments. Mostly developed over the last decade

18
Q

What are metabolomics

A

All metabolites present (either inside or outside a cell) under specific conditions. End products of metabolic pathways, can be used to determine specific functions. Mass spec to characterize – very complex!

19
Q

What are the supervised assembly-based metagenomics

A

Sequence analysis (taxonomic) relative to databased to known sequences

20
Q

What are the unsupervised metagenome-assembled gneome

A

Sequence usage patterns and frequency of sequences in sample

21
Q

What are the single-amplified genome

A

Cells sorted by flow cytometry or microfluids. DNA extracted from individual cells. Amplified by whole-genome amplification (introduces errors and contamination). Quality assessed as for MAGs

22
Q

What is the comprehensiveness of assembly-based analysis

A

Can construct multiple whole genomes, but only for organisms with enough coverage to be assembled and binned

23
Q

What is the community complexity of assembly-based analysis

A

In complex communities, only a fraction of the genomes can be resolved by assembly.

24
Q

What is the novelty of assembly-based analysis

A

Can resolve genomes of entirely novel organisms with no sequenced relatively.

25
Q

What is the computational burden of assembly-based analysis

A

Requires computationally costly assembly, mapping, and binning.

26
Q

What is genome-resolved metabolism on assembly-based analysis

A

Can link metabolism to phylogeny through completely assembled genomes, even for novel diversity

27
Q

What is expert manual supervision of assembly-based analysis

A

Manual curation required for accurate binning and scaffolding and for missassembly detection

28
Q

What is integration with microbial genomics in assembly-based analysis

A

Assemblies can be fed into microbial pipelines designed for analysis of genomes from pure cultured isolates

29
Q

What is comprehensiveness of read-based analysis

A

Can provide an aggregate picture of community function or structure, but it is based only on the fraction of reads that map effectively to reference databases.

30
Q

What is community complexity of read-based analysis

A

Can deal with communities of arbitrary complexity given sufficient sequencing depth and satisfactory reference database coverage

31
Q

What is novelty of read-based analysis

A

Cannot resolved organisms for which genomes of close relatives are unknown

32
Q

What is computational burden of read-based analysis

A

Can be performed efficiently, enabling large meta-analyses.

33
Q

What is genome-resolved metabolism of read-based analysis

A

Can typically resolved only the aggregate metabolism of the community, and links with phylogeny are only possible in the contexts of known reference genomes.

34
Q

What is expert manual supervision of read-based analysis

A

Usually does not require manual curation, but selection of reference genomes to use could involved human supervision

35
Q

What is integration with microbial genomes in read-based analysis

A

Obtained profiles cannot be directly put into the contexts of genomes derived from pure cultured isolates

36
Q

What are marine environments

A

Marine environments cover ~71% of the Earth’s surface and contain ~97% of the Earth’s water. 85% of the salt in the ocean is NaCl. Seawater has an AVERAGE salinity of 3.5%, but it varies significantly between systems (35 parts per thousand)

37
Q

What is the zone and structure of the water in marine environments determined by

A

Depth, Light, Salinity, Temperature, Dissolved Oxygen, and Nutrients

38
Q

What is pycnocline

A

The water should be mixable. There is a density difference throughout the ocean. The warmer water floats on top of the colder water and they don’t mix. The reason there is higher salinity in that bump is due to evaporation because when water is evaporated it doesn’t take its water with it. Only can a very strong wind cause the waters to mix between each other

39
Q

How is the pH of water determined

A

Balance between Carbonate and Bicarbonate determine the pH of the ocean. As Calcium Carbonate sinks it will dissolve again because the deep ocean is undersaturated from carbonate, but there is a region of accumulation. Starts to dissolve in the lysocline. You don’t see CaCO3 past the CCD barrier due to rapid dissolution. Coccolithophores: Organisms that make the carbonate tests. If we acidify the ocean the lysocline and makes the job of the coccolithophores job difficult

40
Q

What is anaerobic methane oxidation

A

There was a split in the field on this topic. Archaea will run in reverse to allow for the anaerobic methane oxidation. It’s hard to prove who did this exactly. They then measured the isotopic signatures to verify that these were the same organisms. They were able to prove this was happening. Originally it was sulfate reducing methanotrophs however we are discovering many new ways that this is occurring such as nitrate, iron, and manganese

MICRB 320 (6 decks)

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