Cover bacteria/archaeota taxonomy

aigarchaeota.md

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+# Aigarchaeota
+

archaea.md

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+# Archaea
+
+- Different from [[bacteria]] in the generation of the cell membrane
+- All prokaryotic
+- More closely related to [[eukarya]] than [[bacteria]]
+- Newer findings imply that [[Lokiarchaeota]] are closer than the
+[[TACK Supergroup]] to [[eukarya]]
+- Vast majority are non-extremophile
+
+## Taxonomy
+
+- [[Archaea]]
+  - [[Euryarchaeota]]
+  - [[Proteoarchaeota]]
+    - [[TACK Supergroup]]
+      - [[Korarchaeota]]
+      - TC MRCA
+        - [[Thaumarchaeota]]
+        - [[Crenarchaeota]]
+    - [[Lokiarchaeota]]
+      - Loki1/Loki2
+      - Loki3/[[Eukarya]]
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[bacteria]: bacteria "Bacteria"
+[Lokiarchaeota]: lokiarchaeota "Lokiarchaeota"
+[TACK Supergroup]: tack-supergroup "TACK Supergroup"
+[Archaea]: archaea "Archaea"
+[Euryarchaeota]: euryarchaeota "Euryarchaeota"
+[Korarchaeota]: korarchaeota "Korarchaeota"
+[Thaumarchaeota]: thaumarchaeota "Thaumarchaeota"
+[Crenarchaeota]: crenarchaeota "Crenarchaeota"
+[//end]: # "Autogenerated link references"

bacteria.md

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+# Bacteria
+
+- Bacterial flagellum
+  - Most commonly, one flagellum creates a "run and twiddle" movement where
+  bacteria can achieve [[chemotaxis]]
+  - [[Spirochaeota]] have their flagellum throughout the inside of the cell,
+  which allows movement through viscous materials
+- By default, bacteria are Gram-negative, except for [[Fermicutes]]:
+Gram-negative bacteria form a [[symplesiomorphy]]
+
+## Taxonomy
+
+- [[Bacteria]]
+  - [[Terrabacteria]]
+    - [[Cyanobacteria]]
+    - [[Fermicutes]] (Gram-positive bacteria)
+  - [[Hydrobacteria]]
+    - [[Spirochaeota]]
+    - Proteo-Plancto MRCA
+      - [[Proteobacteria]]
+      - [[Planctobacteria]]
+        - [[Chlamydiae]]
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[chemotaxis]: chemotaxis "Chemotaxis"
+[Spirochaeota]: spirochaeota "Spirochaeota"
+[Fermicutes]: fermicutes "Fermicutes"
+[Bacteria]: bacteria "Bacteria"
+[Cyanobacteria]: cyanobacteria "Cyanobacteria"
+[Proteobacteria]: proteobacteria "Proteobacteria"
+[Chlamydiae]: chlamydiae "Chlamydiae"
+[//end]: # "Autogenerated link references"

chemotaxis.md

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+# Chemotaxis
+

chlamydiae.md

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+# Chlamydiae
+
+- No cell wall
+- No ATP synthesis
+- Extremely small

crenarchaeota.md

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+# Crenarchaeota
+
+- Extreme Thermo-acido-philes: Prefer hot and/or acidic habitats
+- Large cells, similar to eukaryotic amoebas

cyanobacteria.md

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+# Cyanobacteria
+
+- Responsible for The Great Oxygenation
+- [[Spirulina]]: Highly nutritious
+- [[Rivularia]]: Classifies as multi-cellular, as it can regrow its
+photosynthetic filament

euryarchaeota.md

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+# Euryarchaeota
+
+- [[Methanogens]]: Pick up waste molecules in anaerobic locations, such as H₂,
+CH₃CO₂H, HCO₂H, CH₄0
+- Extreme Halophiles: Prefer extremely salty habitats

fermicutes.md

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+# Fermicutes
+
+- Gram-positive: Lack an outer membrane, instead having a thick peptidoglycan
+cell wall
+- Include lactic acid bacteria

korarchaeota.md

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+# Korarchaeota
+

lokiarchaeota.md

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+# Lokiarchaeota
+
+- Proposed as a phylum in 2015
+- Closer than the [[TACK Supergroup]] to [[eukarya]]

proteobacteria.md

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+# Proteobacteria
+
+- Incredibly diverse in shape, physiology, and ecology
+
+## Taxonomy
+
+- [[Proteobacteria]]
+  - [[Acidobacteria]]
+  - αβγδεζ
+    - Deltaproteobacteria
+    - αβγεζ
+      - Epsilonproteobacteria
+      - αβγζ
+        - Mitochondrial Ancestor
+          - [[Alphaproteobacteria]]
+          - [[Mitochondrion]]
+        - βγζ
+          - Zetaproteobacteria
+          - βγ
+            - Betaproteobacteria
+            - Gammaproteobacteria
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Proteobacteria]: proteobacteria "Proteobacteria"
+[//end]: # "Autogenerated link references"

spirochaeota.md

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+# Spirochaeota
+
+- Free-living and parasitic
+- Includes agents of [[syphilis]] and [[Lyme disease]]
+- Periplasmic flagella, where the flagellum runs through the inside of the
+cell, allowing for movement through viscous materials

tack-supergroup.md

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+# TACK Supergroup
+
+- [[Thaumarchaeota]]
+- [[Aigarchaeota]]
+- [[Crenarchaeota]]
+- [[Korarchaeota]]
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Thaumarchaeota]: thaumarchaeota "Thaumarchaeota"
+[Aigarchaeota]: aigarchaeota "Aigarchaeota"
+[Crenarchaeota]: crenarchaeota "Crenarchaeota"
+[Korarchaeota]: korarchaeota "Korarchaeota"
+[//end]: # "Autogenerated link references"

thaumarchaeota.md

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+# Thaumarchaeota
+