From c417512ece12a123f9286d8168e4c2bec7caba64 Mon Sep 17 00:00:00 2001 From: Aly Cerruti Date: Tue, 12 Oct 2021 23:08:07 -0700 Subject: [PATCH] Cover bacteria/archaeota taxonomy --- aigarchaeota.md | 2 ++ archaea.md | 33 +++++++++++++++++++++++++++++++++ bacteria.md | 32 ++++++++++++++++++++++++++++++++ chemotaxis.md | 2 ++ chlamydiae.md | 5 +++++ crenarchaeota.md | 4 ++++ cyanobacteria.md | 6 ++++++ euryarchaeota.md | 5 +++++ fermicutes.md | 5 +++++ korarchaeota.md | 2 ++ lokiarchaeota.md | 4 ++++ proteobacteria.md | 25 +++++++++++++++++++++++++ spirochaeota.md | 6 ++++++ tack-supergroup.md | 13 +++++++++++++ thaumarchaeota.md | 2 ++ 15 files changed, 146 insertions(+) create mode 100644 aigarchaeota.md create mode 100644 archaea.md create mode 100644 bacteria.md create mode 100644 chemotaxis.md create mode 100644 chlamydiae.md create mode 100644 crenarchaeota.md create mode 100644 cyanobacteria.md create mode 100644 euryarchaeota.md create mode 100644 fermicutes.md create mode 100644 korarchaeota.md create mode 100644 lokiarchaeota.md create mode 100644 proteobacteria.md create mode 100644 spirochaeota.md create mode 100644 tack-supergroup.md create mode 100644 thaumarchaeota.md diff --git a/aigarchaeota.md b/aigarchaeota.md new file mode 100644 index 0000000..800d73c --- /dev/null +++ b/aigarchaeota.md @@ -0,0 +1,2 @@ +# Aigarchaeota + diff --git a/archaea.md b/archaea.md new file mode 100644 index 0000000..2e3fc3b --- /dev/null +++ b/archaea.md @@ -0,0 +1,33 @@ +# 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" diff --git a/bacteria.md b/bacteria.md new file mode 100644 index 0000000..9b10027 --- /dev/null +++ b/bacteria.md @@ -0,0 +1,32 @@ +# 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" diff --git a/chemotaxis.md b/chemotaxis.md new file mode 100644 index 0000000..3d4e3f5 --- /dev/null +++ b/chemotaxis.md @@ -0,0 +1,2 @@ +# Chemotaxis + diff --git a/chlamydiae.md b/chlamydiae.md new file mode 100644 index 0000000..2ab11b4 --- /dev/null +++ b/chlamydiae.md @@ -0,0 +1,5 @@ +# Chlamydiae + +- No cell wall +- No ATP synthesis +- Extremely small diff --git a/crenarchaeota.md b/crenarchaeota.md new file mode 100644 index 0000000..711b8d1 --- /dev/null +++ b/crenarchaeota.md @@ -0,0 +1,4 @@ +# Crenarchaeota + +- Extreme Thermo-acido-philes: Prefer hot and/or acidic habitats +- Large cells, similar to eukaryotic amoebas diff --git a/cyanobacteria.md b/cyanobacteria.md new file mode 100644 index 0000000..bedca38 --- /dev/null +++ b/cyanobacteria.md @@ -0,0 +1,6 @@ +# Cyanobacteria + +- Responsible for The Great Oxygenation +- [[Spirulina]]: Highly nutritious +- [[Rivularia]]: Classifies as multi-cellular, as it can regrow its +photosynthetic filament diff --git a/euryarchaeota.md b/euryarchaeota.md new file mode 100644 index 0000000..67893b2 --- /dev/null +++ b/euryarchaeota.md @@ -0,0 +1,5 @@ +# Euryarchaeota + +- [[Methanogens]]: Pick up waste molecules in anaerobic locations, such as H₂, +CH₃CO₂H, HCO₂H, CH₄0 +- Extreme Halophiles: Prefer extremely salty habitats diff --git a/fermicutes.md b/fermicutes.md new file mode 100644 index 0000000..93bbe0d --- /dev/null +++ b/fermicutes.md @@ -0,0 +1,5 @@ +# Fermicutes + +- Gram-positive: Lack an outer membrane, instead having a thick peptidoglycan +cell wall +- Include lactic acid bacteria diff --git a/korarchaeota.md b/korarchaeota.md new file mode 100644 index 0000000..f128eca --- /dev/null +++ b/korarchaeota.md @@ -0,0 +1,2 @@ +# Korarchaeota + diff --git a/lokiarchaeota.md b/lokiarchaeota.md new file mode 100644 index 0000000..cebd34d --- /dev/null +++ b/lokiarchaeota.md @@ -0,0 +1,4 @@ +# Lokiarchaeota + +- Proposed as a phylum in 2015 +- Closer than the [[TACK Supergroup]] to [[eukarya]] diff --git a/proteobacteria.md b/proteobacteria.md new file mode 100644 index 0000000..6556e8c --- /dev/null +++ b/proteobacteria.md @@ -0,0 +1,25 @@ +# 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" diff --git a/spirochaeota.md b/spirochaeota.md new file mode 100644 index 0000000..f5ae958 --- /dev/null +++ b/spirochaeota.md @@ -0,0 +1,6 @@ +# 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 diff --git a/tack-supergroup.md b/tack-supergroup.md new file mode 100644 index 0000000..76a48d5 --- /dev/null +++ b/tack-supergroup.md @@ -0,0 +1,13 @@ +# 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" diff --git a/thaumarchaeota.md b/thaumarchaeota.md new file mode 100644 index 0000000..8fb6589 --- /dev/null +++ b/thaumarchaeota.md @@ -0,0 +1,2 @@ +# Thaumarchaeota +