Synecology and Traditional Autecology Flashcards
What is hypothesis
A proposed explanation for a phenomenon. Explanation based on previous observations when no scientific theory can explain the phenomenon. Must be testable
What is null hypothesis
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
What is the goal of experimental design
The goal is to falsify, or disprove the hypothesis
What the controls of experimental design
Differentiate between experimental effects and other effects
What are the factors to consider from experimental design
Heterogeneity and replication Needs to collect environmental 'metadata' Sample size Sampling method Storage and transport
What is the analysis of experimental design
Experimental effects
Variables
Statistical approaches
What are microscopic cell counts
Cells are stained with a dye, usually, fluorescent. Filter on to membrane (known area). Count selection of representative fields (also known area)
What is flow cytometry
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
What can flow cytometry detect
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
What is microbial biomass
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
What is photosynthesis/primary production
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
What are ‘potential’ activity measurements
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
What is Michaelis - Mentin Kinetics
- All members of the community respond in the same way to the substrate
- Uptake is functionally equivalent,
- Substrate utilized is representative of all substrates
What is thymidine uptake
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
What is the functional gene amplicon sequencing
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
What are transcriptomes
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.
What are proteomics
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
What are metabolomics
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!
What are the supervised assembly-based metagenomics
Sequence analysis (taxonomic) relative to databased to known sequences
What are the unsupervised metagenome-assembled gneome
Sequence usage patterns and frequency of sequences in sample
What are the single-amplified genome
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
What is the comprehensiveness of assembly-based analysis
Can construct multiple whole genomes, but only for organisms with enough coverage to be assembled and binned
What is the community complexity of assembly-based analysis
In complex communities, only a fraction of the genomes can be resolved by assembly.
What is the novelty of assembly-based analysis
Can resolve genomes of entirely novel organisms with no sequenced relatively.
What is the computational burden of assembly-based analysis
Requires computationally costly assembly, mapping, and binning.
What is genome-resolved metabolism on assembly-based analysis
Can link metabolism to phylogeny through completely assembled genomes, even for novel diversity
What is expert manual supervision of assembly-based analysis
Manual curation required for accurate binning and scaffolding and for missassembly detection
What is integration with microbial genomics in assembly-based analysis
Assemblies can be fed into microbial pipelines designed for analysis of genomes from pure cultured isolates
What is comprehensiveness of read-based analysis
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.
What is community complexity of read-based analysis
Can deal with communities of arbitrary complexity given sufficient sequencing depth and satisfactory reference database coverage
What is novelty of read-based analysis
Cannot resolved organisms for which genomes of close relatives are unknown
What is computational burden of read-based analysis
Can be performed efficiently, enabling large meta-analyses.
What is genome-resolved metabolism of read-based analysis
Can typically resolved only the aggregate metabolism of the community, and links with phylogeny are only possible in the contexts of known reference genomes.
What is expert manual supervision of read-based analysis
Usually does not require manual curation, but selection of reference genomes to use could involved human supervision
What is integration with microbial genomes in read-based analysis
Obtained profiles cannot be directly put into the contexts of genomes derived from pure cultured isolates
What are marine environments
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)
What is the zone and structure of the water in marine environments determined by
Depth, Light, Salinity, Temperature, Dissolved Oxygen, and Nutrients
What is pycnocline
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
How is the pH of water determined
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
What is anaerobic methane oxidation
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
