archaeal diversity (ex 4 lec3)

traits only found to archaea

ether linked membrane lipids

these distinctive features are called archaeal signatures

ether linked membrane

most distinctive feature

have R-O-R ether instead of R-COO-R ester link

made from isoprenoid units branched at every fourth carbon

can contain cross linked lipids and cyclopentane rings 

unique genetic traits of archaea 

reverse gyrase enzyme of hyperthermophiles that contain positive supercoils at high temperature 

distinctive modified based in their tRNA such as archaesine which is a guanosine analog 

phylogeny of archaea

there are similarities between eukarya and asgard superphylum of archaea 

also have large portions derived from horizontal gene structure from bacteria

where to find hyperthermophiles

hot springs and undersea hydrothermal vents

important features of thermophiles

reduced minerals

low oxygen

steep temperature gradients

acidity

barophiles 

a type of microbe that grows undersea at high pressure 

what does tack superphylum include

the major phyla archaea that grow at temperature above 90 degrees C

marien hydrothermal vents and springs

what do tack superphylum metabloze

sulfur by anaerobic reduction or aerobic oxidation

other communities of some tack superphylum

mesophilic soil, marine and benthic (bottom of water) 

what do tack superphylum contribute to

the global carbon cycle and the nitrogen cycle

what do tack superphylum utilize during metabolism

variants of ED and EMP

distinguished in part by not phosphorylating glucose which is an important stel for essential ATP

what do desulfurococcales within the crenarcheaota have 

lack cell walls but posses elaborate S layer

have membranes that contain diethers and tetraethers 

many use higher temperatures that increase thermodynamic favorability of sulfur redox reactions 

desulfur. fermentans

isolated from hot springs

chemotrophs that use different sugars but not glucose

respires anaerobically by reducing sulfur to sulfide

ignicoccus islandicus

marine organism 

has a unique periplasmic space that contains membrane vesciles 

lithotroph that oxidizes hydrogen with sulfur as terminal electron acceptor 

what are the most extreme hyperthermophilies

barphiles which have adapted to grow in high pressures near hydrothermal vents at ocean floor

common feature of thermal vent

black smoker

the temp and pressure contribute to water temp over 400 degrees C

as water cools, FeS precipitates and supports growth

pyrodictium 

vent adapted member of desulfur. 

they use either hydrogen or organic compounds for energy 

grow as flat disk shaped cells that are thin asf 

the cells disks are interconnected by periplasmic extensions 

cannulae

periplasmic extensions that form during cell division

hollow tubules made of proteins

sulfolobales (within crenarchaeota)

grow at 80-90 degrees C within hot springs and volcanic vents that emit gas

genus sulfolbus 

has no cell walls only an S layer of glycoprotein 

membrane composed mainly of tetraethers with cyclopentane rings

possess archella 

what is archaella

structures for motility that consist of helical filaments driven by a motor embedded in the membrane

like flagella but not

thaumarchaeota

a phylum of mesophilic archaea

characteristics of thaumarchaeota 

have evolved from hyperthermophiles by gene acquisition from mesophilic bacteria 

the most significant ones discovered are the ammonia oxidizing archaea (AOA)

what are AOA

the dominant oxidizers of ammonia in marine, freshwater and wasteful communities

euryarchaeota

broad ranging archaea that are dominated by methoanogens

other eurarchaeota 

haloarchaea

supplement their metabolism with light driven bacteriorhodopsin ion pumps 

trait of all methanogens

they are poisoned by oxygen

they are strict anaerobes

require close association with bacterial partners to provide their substrates (syntrophy)

what is syntrophy

the removal or hydrogen and carbon dioxide

products of bacterial partners and enhances metabolism on those partners

structure of methanogens

rods (single or filamentous) cocci and spirals

pseudopeptidog

rigid cell walls that methanogens have which are sulfated polysaccharides or even proteins

what do filamentous methanogens form

chains of large cells similar to those in cyanobacteria 

environment of methanogens

can grow in soil, animal digestive tracts, marine floor sediment

anaerobic soil of wetlands especially rich in paddies

landfills

psychrophilic methanogens

are present in antarctica

near freezing water of ace lake is saturated with methane from methanogens present in high numbers

these methanogens have membrane lipids with double bonds

methanogens growing in cattle 

cattle support methanogensis within their rumen and reticulum 

where is the formation of methane from

CO2 and H2 anaerobic respiration

H2 is donor and Co2 is terminal electron acceptor

methanogenesis

fixing of CO2 onto the cofactor methanofuran (MFR)

carbon is then passed stepwise from one cofactor to the next each time losing an oxygen to form water or gaining a proton carried by another cofactor

important feature of methanogenesis 

the enzymes catalyzing each step require several transition metals

the hydrogenase that reduces F420 requires both nickel and iron

haloarchaea

the main inhabitants of high salt environments are members of euryachaeota class

most are phototrophs and colored red

require 1.5 M NaCl which is 10x the concentration of seawater

generally mesophilic but can be neutral or alklaino

how to haloarchaea adapt to high external NaCl

by maintaining a high intercellular KCl

this requires high GC content of DNA to prevent denaturation by high salt AND acidic proteins that interact with K+ to remain soluble

what can the recombinant cells of haloarchaea be used for 

vaccines 

a cheap and convenient delivery methods for developing countries where typhoid is widespread 

thermococcales

another order in euryarchaeota which grow at temp above 90 degrees C

most are anaerobes and use sulfur as terminal electron acceptor for anaerobic respiration

thermoplasmatales

another order within crenarchaeota which include acidiophiles and have no cell walls just S layer

what does deep branching asgard group indicate 

that marine thermophiles may be most closely related to the domain eukarya 

it was named for its inclusion of the lokiarchaeota 

have actin cytoskeleton and phagocytosis 

DPANN superphylum

the genome all show evolutionary loss of many genes which is typcal of obligate synbionts

contain small genomes that have lost metabolic pathways and require a partner

commonly found in freshwater and marine environments

nanoarchaeota

the best studied clade of the DPANN superphylum

obligate symbiont of the TACK hyperthermophile