Post on 14-Feb-2020
BIOL 1010 Introduction to Biology: The
Evolution and Diversity of Life. Spring 2011
Sections A & BSteve Thompson: stthompson@valdosta.edu
http://www.bioinfo4u.net1
Wednesday, February 9, 2011
The major phyla: Bacteria and Archaea
Molecular techniques have reinforced just how amazing the
diversity is in the microbial world.
2Wednesday, February 9, 2011
And it all began with Carl . . .As unassuming as Carl Woese is, he started an incredible revolution in microbial taxonomy, though he would never admit it.One Nobel Prize winner, Salvador Luria, said to a colleague “you're going to ruin your career. You've got to disassociate yourself from this nonsense!” The hostility was shocking. Others soon followed, crossing boundaries of common courtesy by making fun of Woese. He was called a crank and a crackpot, being neither a microbiologist nor an evolutionist (Woese was a physicist). Many leading biologists thought Woese was "crazy" and that his RNA tools couldn't possibly answer the question he was asking.Check out http://home.planet.nl/~gkorthof/korthof88.htm for a really nice, concise story of this.
3Wednesday, February 9, 2011
Here’s one of the molecules that he used,
the 16S ribosomal RNA molecule from
Thermus thermophilus –
one of those Bacteria that really likes it
really hot, from 65º to
75º C! 4
Wednesday, February 9, 2011
Here’s what it really looks like:
http://molbio.info.nih.gov/cgi-bin/moldraw?2UU95
Wednesday, February 9, 2011
And so the story began.Now we KNOW, based on rRNA sequences, AND many full-length genomes, that . . .The microbial world is WAY more diverse than we ever imagined.It is split up into at least five Archaea phyla, and at least twenty-three Bacteria phyla. Though, as I said before, new organisms are being discovered all the time. Plus, since these are levels directly under domain, they are even considered kingdoms by some biologists!This is a contentious and constantly changing field!
6Wednesday, February 9, 2011
Around 100 complete Archaeal genomes have been completed, and over 1000
Bacterial genomes. They all confirm the rRNA story.
http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
7Wednesday, February 9, 2011
Adding an outgroup, yeast, shows that Archaea are more closely related to
Eukaryotes than are Bacteria.
8
Noticethe branch
lengths.
The numbers arecalled bootstrap
values and reflectconfidence levels.
Wednesday, February 9, 2011
Of course lateral gene transfer and primordial endosymbiosis confuses the picture some . . .
9
A graphicI’ve shownbefore, but
worthrepeating.
As portrayed by W. Ford Doolittle
(1999).
Wednesday, February 9, 2011
10
And most things have gone extinct. Nonetheless, the patterns are still there.
The story remains:Three domains.
Wednesday, February 9, 2011
Three of those Archaea phyla are well characterized.
11Wednesday, February 9, 2011
But many sources say there are five Archaea phyla (e.g. NCBI):
Crenarchaeota (eocytes)EuryarchaeotaKorarchaeotaNanoarchaeotaThaumarchaeota and see . . .http://www.tolweb.org/Archaea/ though they only discuss three of them.
12Wednesday, February 9, 2011
And the story pretty much comes out the same no matter what genes are used.
13
Euryarchaeota
Wednesday, February 9, 2011
CrenarchaeotaThe Crenarchaeota (Greek for "spring old quality") (also known as eocytes) were initially thought to all be extremophiles (e.g., thermophilic and psychrophilic organisms), but recent studies have identified them as the most abundant Archaea in the marine environment.Sulfolobus is a representative genera; it likes to grow in hot, acidic conditions, including in volcanoes!
14Wednesday, February 9, 2011
EuryarchaeotaThe Euryarchaeota (Greek for "broad old quality") is a diverse group including methanogens, which are often found in animal intestines; extreme halophiles, which like really, really salty conditions; extreme acidophiles, which need very acidic environments; and hyperthermophiles, which need it to be very, very hot.Representative genera include Methanobacterium, Halobacterium, Picrophilus, and Pyrococcus respectively.
15Wednesday, February 9, 2011
KorarchaeotaThe Korarchaeota are only found in high temperature hydrothermal environments. Analysis of their 16S rRNA gene sequences suggests that they are the most deeply-branching lineage of Archaea groups.A representative genus is Korarchaeum.
16Wednesday, February 9, 2011
So what’s the 23 Bacterial
phyla?
Actinobacteria
Aquificae
Bacteroidetes/Chlorobi group
Chlamydiae/Verrucomicrobia group
Chloroflexi (green nonsulfur bacteria)
Chrysiogenetes
Cyanobacteria (blue-green algae)
Deferribacteres
Deinococcus-Thermus
Dictyoglomi
Elusimicrobia
Fibrobacteres/Acidobacteria group
Firmicutes (Gram-positive bacteria)
Fusobacteria
Gemmatimonadetes
Nitrospirae
Planctomycetes
Proteobacteria (purple bacteria and relatives)
Spirochaetes
Synergistetes
Tenericutes
Thermodesulfobacteria
Thermotogae17
Wow, that’s way too many!
But, remember, I said that microbial
diversity is WAY huger than all of
Eukaryotic diversity combined. Don’t worry; you don’t
need to know them all.
Wednesday, February 9, 2011
The Bacterial story is more complicated.But the story remains the same — no
matter what you look at, here entire
genomes, and the diversity
is huge!18
Thermus thermophilus HB8
D einococcus geothermalis DSM 11300
Deinococcus radiodurans R1
Petrotoga mobilis SJ95
Thermotoga maritima MSB8
Thermotoga lettingae TMO
Thermosipho melanesiensis BI429
Fervidobacterium nodosum Rt17 B1
Aquifex aeolicus VF5
Rubrobacter xylanophilus DSM 9941
Tropheryma whipplei TW08 27
B ifidobacterium adolescentis ATCC 15703
Nocardioides sp JS614
Propionibacterium acnes KPA171202
Kineococcus radiotolerans SRS30216
Renibacterium salm
oninarum ATCC 33209
Arthrobacter aurescens TC1
Arthrobacter sp FB24
Clavibacter michiganensis
Leifsonia xyli subsp xyli str CTCB07
Streptomyces averm
itilis MA 4680
Acidothermus cellulolyticus 11B
Thermobifida fusca YX
Frankia sp EAN1pec
Frankia alni ACN14a
Frankia sp CcI3
Salinispora tropica CN
B 440
Salinispora arenicola CN
S 205
Saccharopolyspora erythraea NR
RL 2338
Rhodococcus sp R
HA
1
Nocardia farcinica IFM
10152
Mycobacterium
smegm
atis str MC
2 155
Mycobacterium
avium subsp paratuberculosis K
10
Corynebacterium
jeikeium K411
Corynebacterium
diphtheriae NC
TC 13129
Corynebacterium
efficiens YS 314H
erpetosiphon aurantiacus ATC
C 23779
Roseiflexus castenholzii D
SM
13941
Chloroflexus aurantiacus J 10 fl
Dehalococcoides sp C
BD
B1
Gloeobacter violaceus P
CC
7421
Synechococcus sp JA
2 3B a 2 13
Thermosynechococcus elongatus B
P 1
Acaryochloris m
arina MB
IC11017
Anabaena variabilis A
TCC
29413N
ostoc sp PC
C 7120
Trichodesmium
erythraeum IM
S101
Microcystis aeruginosa N
IES
843S
ynechocystis sp PC
C 6803
Synechococcus elongatus P
CC
6301P
rochlorococcus marinus str M
IT 9515
Prochlorococcus m
arinus subsp pastoris str CC
MP
1986
Pro
chlo
roco
ccus
mar
inus
str
MIT
921
1P
roch
loro
cocc
us m
arin
us s
ubsp
mar
inus
str
CC
MP
1375
Pro
chlo
roco
ccus
mar
inus
str
NA
TL1
A
Syn
echo
cocc
us s
p W
H 7
803
Syn
echo
cocc
us s
p C
C93
11S
ynec
hoco
ccus
sp
CC
9605
Syn
echo
cocc
us s
p W
H 8
102
Syn
echo
cocc
us s
p C
C99
02
Pro
chlo
roco
ccus
mar
inus
str
MIT
930
3P
roch
loro
cocc
us m
arin
us s
tr M
IT 9
313
Syn
echo
cocc
us s
p R
CC
307
Car
boxy
doth
erm
us h
ydro
geno
form
ans
Z 29
01
Pel
otom
acul
um th
erm
opro
pion
icum
SI
Des
ulfo
tom
acul
um re
duce
ns M
I 1
Moo
rella
ther
moa
cetic
a A
TCC
390
73
Des
ulfit
obac
teriu
m h
afni
ense
Y51
Sym
biob
acte
rium
ther
mop
hilu
m IA
M 1
4863
Syn
troph
omon
as w
olfe
i sub
sp w
olfe
i str
Goe
tting
en
Ther
moa
naer
obac
ter s
p X
514
Ther
moa
naer
obac
ter t
engc
onge
nsis
MB
4
Cal
dice
llulo
siru
ptor
sac
char
olyt
icus
DS
M 8
903
Clo
strid
ium
ther
moc
ellu
m A
TCC
274
05
Clo
strid
ium
per
fring
ens
SM10
1
Clo
strid
ium
bei
jerin
ckii
NC
IMB
8052
Clo
strid
ium
nov
yi N
T
Clos
tridi
um a
ceto
buty
licum
ATC
C 82
4
Clos
tridi
um te
tani
E88
Clost
ridiu
m b
otul
inum
A s
tr AT
CC 193
97
Clost
ridiu
m k
luyv
eri D
SM 5
55
Clo
strid
ium
diff
icile
630
Alka
liphi
lus
orem
land
ii O
hILA
s
Alka
liphi
lus
met
allir
edig
ens
QYM
F
Clo
strid
ium
phy
tofe
rmen
tans
ISD
g
Fuso
bact
eriu
m n
ucle
atum
sub
sp n
ucle
atum
ATC
C 255
86
Geobacillus k
austophilus H
TA426
Bacillus s
ubtilis su
bsp subtilis
str 168
Bacillus weihenstephanensis KBAB4
Bacillus halodurans C 125
Bacillus clausii KSM K16
O ceanobacillus iheyensis HTE831
Staphylococcus aureus subsp aureus USA300
Liste ria innocua Clip11262
Enterococcus faecalis V583
Streptococcus gordonii str Challis substr C
H1
Lactococcus lactis subsp lactis Il1403
Lactobacillus sakei subsp sakei 23K
Lactobacillus casei ATCC 334
Lactobacillus delbrueckii ATCC BAA 365
Lactobacillus helveticus DPC 4571
Lactobacillus johnsonii NCC 533
Lactobacillus salivarius subsp salivarius UCC118
Lactobacillus plantarum WCFS1
Lactobacillus brevis ATCC 367Pediococcus pentosaceus ATCC 25745
Lactobacillus reuteri F275Leuconostoc mesenteroides ATCC 8293
O enococcus oeni PSU 1
Achole
plasm
a lai
dlawii P
G 8A
Aster y
ellow
s witc
hes b
room
phy
topla
sma
AYWB
Mes
oplas
ma
floru
m L
1
Myc
oplas
ma ca
prico
lum su
bsp
capr
icolum
ATC
C 273
43
Mycop
lasma h
yopn
eumon
iae 74
48
Mycop
lasma m
obile
163K
Mycop
lasma p
ulmon
is UAB C
TIP
Myc
oplas
ma syn
oviae
53
Myc
oplas
ma aga
lactia
e PG2
Mycoplasm
a penetrans H
F 2
Ureaplasma parvu
m serova
r 3 st
r ATCC 700970
Mycoplasm
a galliseptic
um R
Mycoplasm
a pneumoniae M129
Mycoplasm
a genitalium G
37
Rhodopirellula baltica SH 1
Candidatus Protochlamydia amoebophila UWE25
Chlamydia trachomatis A HAR 13
Chlamydophila abortus S26 3
Chlamydophila pneumoniae J138
Leptospira borgpetersenii JB197Borrelia garinii PBiTreponema denticola ATCC 35405Treponema pallidum subsp pallidum str NicholsChlorobium tepidum TLSChlorobium phaeobacteroides DSM 266Pelodictyon luteolum DSM 273Prosthecochloris vibrioformis DSM 265
Chlorobium chlorochromatii CaD3Salinibacter ruber DSM 13855Cytophaga hutchinsonii ATCC 33406
Bacteroides fragilis NCTC 9343Parabacteroides distasonis ATCC 8503
Porphyromonas gingivalis W83Gramella forsetii KT0803
Flavobacterium johnsoniae UW101
Flavobacterium psychrophilum JIP02 86
C andidatus Sulcia muelleri GWSSAcidobacteria bacterium Ellin345
Solibacter usitatus Ellin6076Anaeromyxobacter dehalogenans 2CP C
Anaeromyxobacter sp Fw109 5
Myxococcus xanthus DK 1622
Sorangium cellulosum So ce 56
Bdellovibrio bacteriovorus HD100P elobacter carbinolicus DSM 2380
Geobacter uraniireducens Rf4
Geobacter metallireducens GS 15
G eobacter sulfurreducens PCA
Pelobacter propionicus DSM 2379
Syntrophus aciditrophicus SB
Syntrophobacter fumaroxidans MPOB
Desulfococcus oleovorans Hxd3
Desulfotalea psychrophila LSv54
Lawsonia intracellularis PHE MN1 00
Desulfovibrio vulgaris subsp vulgaris str Hildenborough
Desulfovibrio vulgaris subsp vulgaris DP4
Desulfovibrio desulfuricans G20
Nitratiruptor sp SB155 2
Campylobacter hom
inis ATCC BAA 381
Campylobacter jejuni RM
1221
Campylobacter jejuni subsp jejuni 81116
Campylobacter fetus subsp fetus 82 40
Campylobacter curvus 525 92
Campylobacter concisus 13826
Sulfurovum sp NBC37 1
Arcobacter butzleri RM4018
Sulfurim
onas denitrificans DSM 1251
Wolinella succinogenes DSM 1740
Helicobacter acinonychis str Sheeba
Magnetococcus sp M
C 1
Magnetospirillum
magneticum
AM
B 1
Rhodospirillum
rubrum A
TCC
11170
Acidiphilium
cryptum JF 5
Granulibacter bethesdensis C
GD
NIH
1
Gluconacetobacter diazotrophicus P
Al 5
Gluconobacter oxydans 621H
Sphingom
onas wittichii R
W1
Zymom
onas mobilis subsp m
obilis ZM4
Sphingopyxis alaskensis R
B2256
Novosphingobium
aromaticivorans D
SM
12444
Erythrobacter litoralis H
TCC
2594
Par
viba
culu
m la
vam
entiv
oran
s D
S 1
Azo
rhiz
obiu
m c
aulin
odan
s O
RS
571
Xan
thob
acte
r aut
otro
phic
us P
y2M
ethy
loba
cter
ium
ext
orqu
ens
PA
1
Rho
dops
eudo
mon
as p
alus
tris
CG
A00
9
Bra
dyrh
izob
ium
sp
BTA
i1
Bra
dyrh
izob
ium
sp
OR
S27
8N
itrob
acte
r ham
burg
ensi
s X
14
Sin
orhi
zobi
um m
edic
ae W
SM
419
Rhi
zobi
um le
gum
inos
arum
bv
vici
ae 3
841
Agr
obac
teriu
m tu
mef
acie
ns s
tr C
58
Mes
orhi
zobi
um s
p B
NC
1
Mes
orhi
zobi
um lo
ti M
AFF
3030
99
Och
roba
ctru
m a
nthr
opi A
TCC
491
88
Bru
cella
mel
itens
is b
iova
r Abo
rtus
2308
Bar
tone
lla b
acill
iform
is K
C58
3
Barto
nella
trib
ocor
um C
IP 1
0547
6
Barto
nella
hen
sela
e st
r Hou
ston
1
Barto
nella
qui
ntan
a st
r Tou
lous
e
Maricaulis m
aris MC
S10
Caulobacter crescentus C
B15
Hyphom
onas neptunium A
TCC
15444
Paracoccus denitrificans P
D1222
Rhodobacter sphaeroides 2 4 1
Dinoroseobacter shibae D
FL 12
Jannaschia sp CC
S1
Ros
eoba
cter
den
itrifi
cans
OC
h 11
4S
ilici
bact
er s
p T
M10
40
Sili
ciba
cter
pom
eroy
i DS
S 3
Candidatus Pelagibacter ubique HTCC1062
Rickettsia bellii O
SU 85 389
Rickettsia prow
azekii str Madrid E
Orientia tsutsugam
ushi Boryong
Wolbachia endosym
biont of Drosophila m
elanogaster
Wolbachia endosym
biont strain TRS of Brugia m
alayi
Ehrlichia rum
inantium str W
elgevonden
Ehrlichia canis str Jake
Ehrlichia chaffeensis str A
rkansas
Anaplasma m
arginale str St Maries
Anaplasma phagocytophilum
HZ
Neorickettsia sennetsu str M
iyayama
Chr
omob
acte
rium
vio
lace
um A
TCC
124
72
Nei
sser
ia g
onor
rhoe
ae F
A 10
90
Thio
baci
llus
deni
trific
ans
ATC
C 2
5259
Met
hylo
baci
llus
flage
llatu
s KT
Nitr
osos
pira
mul
tifor
mis
ATC
C 2
5196
Nitro
som
onas
eur
opae
a AT
CC 1
9718
Nitro
som
onas
eut
roph
a C9
1
Dech
loro
mon
as a
rom
atica
RCB
Azoa
rcus
sp
BH72
Azoa
rcus
sp
EbN1
Borde
tella
pet
rii
Jant
hinob
acte
rium
sp M
arse
ille
Herm
iniim
onas
ars
enico
xyda
ns
Bur
khold
eria
xeno
vora
ns L
B400
Rals
tonia
solan
acea
rum
GMI1
000
Polynu
cleob
acter
sp Q
LW P
1DMW
A 1
Methyli
bium pe
trolei
philu
m PM1
Rho
dofer
ax fe
rrired
ucen
s T11
8
P olarom
onas
sp JS
666
Polaromonas naphthalenivo
rans CJ2
Verminephrobacte
r eise
niae EF01 2
Acidovo
rax ave
nae subsp
citru
lli AAC00 1
Acidovo
rax sp JS
42
Delftia acid
ovorans S
PH 1
Methylococcu
s capsulatus s
tr Bath
Dichelobacte
r nodosus V
CS1703A
Nitrosococcus oceani A
TCC 19707
Alkalilimnicola ehrlic
hei MLHE 1
H alorhodospira halophila SL1
Xanthomonas campestris pv vesicatoria str 8
5 10
Xylella fastidiosa Temecula1
L egionella pneumophila str Corby
Coxiella burnetii RSA 493
Francisella tularensis subsp novicida U112
Thiomicrospira crunogena XCL 2
Candidatus Ruthia magnifica
Candidatus Vesicomyosocius okutanii HA
P seudomonas stutzeri A1501
Saccharophagus degradans 2 40
Marinobacter aquaeolei VT8
Hahella chejuensis KCTC 2396
Chromohalobacter salexigens DSM 3043M arinomonas sp MWYL1
Alcanivorax borkumensis SK2
Acinetobacter sp ADP1
Acinetobacter baumannii ATCC 17978
Psychrobacter sp PRwf 1
Psychrobacter arcticus 273 4
Pseudoalteromonas atlantica T6cIdiomarina loihiensis L2TRPseudoalteromonas haloplanktis TAC125Colwellia psychrerythraea 34HShewanella pealeana ATCC 700345Psychrom onas ingrahamii 37Aeromonas hydrophila ATCC 7966
Aeromonas salmonicida subsp A449Photobacterium profundum SS9
Vibrio fischeri ES114
Actinobacillus pleuropneumoniae L20
Haemophilus ducreyi 35000HP
Pasteurella multocida str Pm70
Haemophilus somnus 129PT
Haem ophilus influenzae PittEE
Mannheimia succiniciproducens MBEL55E
Actinobacillus succinogenes 130Z
Photorhabdus luminescens TTO1
Yersinia enterocolitica 8081
Serratia proteamaculans 568
Erwinia carotovora SCRI1043
Escherichia coli O157 H7 str Sakai
Sodalis glossinidius str morsitans
Baumannia cicadellinicola
Candidatus Blochmannia pennsylvanicus
Candidatus Blochmannia floridanus
Wigglesworthia glossinidia endosymbiont
Buchnera aphidicola str Sg Schizaphis graminum
Buchnera aphidicola str APS Acyrthosiphon pisum
Buchnera aphidicola str Bp Baizongia pistaciae
B uchnera aphidicola str Cc Cinara cedri
GammaproteobacteriaBetaproteobacteriaAlphaproteobacteriaEpsilonproteobacteriaDeltaproteobacteria
AcidobacteriaBacteroidetes/Chlorobi
Chlamydiae/PlanctomycetesSpirochaetes
Firmicutes
CyanobacteriaChloroflexiActinobacteriaAquificaeThermotogae
Deinococcus/Thermus
Wednesday, February 9, 2011
Let’s briefly survey some of those Bacterial phyla.
Actinobacteria are all Gram positive high G+C Bacteria and include some of the most common decomposers in the biosphere. Members include the usually harmless Streptomyces from which many antibiotics have been isolated; and Mycobacterium, of which two different species cause tuberculosis and leprosy.
19Wednesday, February 9, 2011
Aquificae like harsh environments and live chemolithoautotrophically. Many biologists believe they are one the most basal of the Bacterial lineages.Thermotogae also likes it hot and is also considered to be a quite basal Bacterial lineage. It’s got a bunch of Achaeal genes in it!The Deinococcus-Thermus group is another basal lineage of Bacteria. Deinococcus is unique in being able to withstand and even eat radioactive waste! Thermus aquaticus was the original source of Taq polymerase used in PCR. See http://tolweb.org/treehouses/?treehouse_id=4726.Many of the Chlamydiae/Verrucomicrobia group are obligate Eukaryotic pathogens causing nasty STDs.The Chloroflexi (green nonsulfur bacteria) make energy from light, but do not produce oxygen in the process.
20Wednesday, February 9, 2011
Cyanobacteria (blue-green ‘algae’) are incredibly important as they produced the original oxygen in the history of the earth and continue to be a major supplier of the oxygen we breathe. Their ancestors were also the cells that were engulfed and destined to become chloroplasts (endosymbiosis)!Firmicutes is a very diverse group and includes some of the most well known Bacteria such as Bacillus and Clostridium. It’s the largest Bacterial phylum with more than 250 genera.The second largest Bacterial phylum is the Proteobacteria. These are also very well studied and include a diverse assortment of organisms including E. coli, Salmonella, Rhizobium, Vibrio . . . . Mitochondrion were originally an aerobic Proteobacterium. They have all sorts of different metabolisms, both autotrophic and heterotrophic.Spirochaetes are largely anaerobic and include many human pathogens such as those that cause syphilis and Lyme disease.
21Wednesday, February 9, 2011
That’s enough for now!
Don’t get too hung up on all the scientific names. We’ll revisit the
ones I want you to know.We’ll go over the test results next time, including a review of those
questions that most people screwed up.
22Wednesday, February 9, 2011