DNA/RNAtargeted molecular analysis of bacterial communities Lysis, - - PowerPoint PPT Presentation

▶
dna rna targeted molecular analysis of bacterial
SMART_READER_LITE
LIVE PREVIEW

DNA/RNAtargeted molecular analysis of bacterial communities Lysis, - - PowerPoint PPT Presentation

Feb 28, 2023 465 likes •642 views

DNA/RNAtargeted molecular analysis of bacterial communities Lysis, DNA/RNA DNA/RNA extraction purification PCR/RTPCR amplification of 16S rRNA or functional genes

slide-1
SLIDE 1
  • Lysis, DNA/RNA

extraction DNA/RNA purification PCR/RTPCR amplification of 16S rRNA or functional genes

DNA/RNAtargeted molecular analysis of bacterial communities

DGGE, TGGE, RFLP, tRFLP, SSCP Cloning Sequencing Identification Phylogenetic analysis Fingerprinting:

slide-2
SLIDE 2
  • The universal SSU rRNA tree

Hugenholtz . 1998

  • 180, 4765–

4774.

Bacteria, 1998

slide-3
SLIDE 3
  • Nitrification
  • !"

#" "# # $

  • "
  • #
  • #
  • %

% &!

  • "
  • ##

$

  • $
  • TEM Image credit: W.J. Hickey, University of

WisconsinMadison, 2006.

N flux 1.5 x 1015 g soil N y1 6 x 1015 g marine N y1

slide-4
SLIDE 4
  • Ammonia oxidiser taxonomy
slide-5
SLIDE 5
  • !
  • !

" # ! !

  • $

%

  • &

& & '

  • "

! $ ! ! & !

  • &

$ $

  • !

&!

  • %(

)*+,,-%& & '

  • & !

./0- ./0- ! $

  • !

$$ )*+,,& 12 1) 3& 3 3$ 3$ 3$ 3 3 3! 3! 3 3 )*+,,!& )*+415% 3 3 3 )*+415-!

  • 3

12 3! 3 3 3 6) ! 12 *71,* *71,* *71,*%" *71,*%"

  • *71,*%"

*71,*%"& 3 3 1) 6) ) 1) 6).. 6). 1) 1) 62 62 12 3 )& ) 62 )*+,,! )*+,,8 )*+,, )*+,,&$ )*+,, 2" )!)9 9 2"

  • '()

Cluster 2 Cluster 3 Cluster 1 Cluster 4 Cluster 5 Cluster 6 Cluster 7 Reference βproteobacteria

* *

+ & +" ,

)*+,,! )*+,,8 2" )*+,, )*+,,&$ )*+,,

  • !

Stephen ., 1996 AEM 62, 414754.

slide-6
SLIDE 6
  • !

##$

'("

'#

  • '#""'

'("

'# ! !

  • .
  • .
  • .+%
  • ##/

Webster ., 2005 7, 676684.

slide-7
SLIDE 7
  • (

(( %(( 0(( 1(( '((( '(( '%(( '0(( '1(( ( ( %( 0( 1( '((

2#34 "536"#'4

  • %

%7 7

  • %

%7 7

  • 7

7

  • Webster

., 2005 7, 676684.

slide-8
SLIDE 8
  • (

(( %(( 0(( 1(( '((( '(( '%(( ( ( %( 0( 1( '((

2#34 "536"#'4 7 7

  • %

%7 7

  • %

%7 7

Webster ., 2005 7, 676684.

slide-9
SLIDE 9
  • /###5

"!

58 '58 (58 (58 '58 58 58 ( 8( '(( '8( ((

2#34

"3

596"#'4 '# '(# '((# '(((#

  • 34

34

  • :

: 34 34

'5( (58 (5( (58 '5( '58 ( 8 8( ;8 '(( '8 '8( ';8 ((

2#34

"3

596"#'4 '# '(# '((# '(((#

Webster ., 2004 7, 676684.

slide-10
SLIDE 10
  • /###5

"!!#

'5( (58 (5( (58 '5( '58 ( 8 8( ;8 '(( '8 '8( ';8 ((

2#34

"3

596"#'4 '# '(# '((# '(((#

:;1 4:*6 /1% /1% 34 34

'5( (58 (5( (58 '5( '58 5( ( 8( '(( '8( ((

2#34

"3

596"#'4 '# '(# '((# '(((#

Webster ., 2005 7, 676684.

slide-11
SLIDE 11
  • Stable isotope probing

DNASIP

  • "

"

' '

&

  • Radajewski

. 2000 403, 646649

'

  • /$
  • Boschker

1998

  • 392, 801

804.

'

  • /$
  • ,
  • Stable isotope probing

13CPLFA analysis

'

#! ,< #= '0+< "

'

#!

slide-12
SLIDE 12
  • Stable isotope probing

DNASIP

'

  • /$
  • "

"

  • '

'

&

  • Stable isotope probing

RNASIP

'

  • /$

<

  • "

"

  • '<

'<

&

  • &
  • Manefield

2002

  • 58 5367–

5373 Lueders . 2003 6, 6072 6, 7378

> < , *"

slide-13
SLIDE 13
  • Stable isotope probing in the field:

RNASIP

'

  • /$

<

  • "

"

  • '<

'<

&

  • '

!# </

  • '0+?'1+

<"

slide-14
SLIDE 14
  • The Crenarchaeota
  • !

" #$ %$ ! $ &$ '()! $ '(%

  • *%(
  • "<:

"<:

  • +!
slide-15
SLIDE 15
  • Isolation of

Kınnneke . 2005, 437, 543546.

' '= => > ' '= => > (5' (5'= => > (5' (5'= => >

slide-16
SLIDE 16
  • Relative abundance of bacterial ammonia
  • xidiser clusters in soils of different pH
  • &

!

  • &

& && ! !! + <3)4

  • !1

Stephen 1998,

  • 64,

29582965