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

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cocc

us s

p C

C93

11S

ynec

hoco

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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