Diversity and Composition of Bacterioplankton along a Trophic

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1
Supplementary Material
2
3
Table S1. Results from reverse line blot hybridization with 18 probes specific for freshwater bacteria.
Probe a
Targeted Group
Affiliation
Wuli Bay b
Meiliang Bay b
Mouth of
Meiliang Bay b
Aug.
Sep.
X
X
O
O
X
O
O
O
Lake
Center b
Aug. Sep.
X
X
O
O
X
O
O
O
Aug. Sep.
Aug.
Sep.
LD12
Alphaproteobacteria
X
X
X
X
CRFL11
Alphaproteobacteria
X
X#
O
X
LD28
Betaproteobacteria
X
X#
X
O
Polynucleobacter sp.
Betaproteobacteria
O
O
O
O
(subcluster PnecC)
Polynuc123d
Polynucleobacter spp.
Betaproteobacteria
X
X
O
X
X
X
O
X
(subcluster PnecB and PnecC)
PolynucD123-144e
Polynucleobacter sp.
Betaproteobacteria
O
O
O
O
O
O
O
O
(subcluster PnecD)
GKS98-442
GKS98
Betaproteobacteria
O
O
O
X
O
X
O
O
Sta230-187
Sta2-30 (acI-B)
Actinobacteria
X
X
O
X
X#
X
X
X
Sta230-208
Sta2-30 (acI-B)
Actinobacteria
O
X
O
X
X#
X
X
X
Urk014-126
Urk-014
Actinobacteria
X
X
X
X
X
X
X
X
ACK-M1-193
ACK-M1 (acI-A)
Actinobacteria
X
X
O
X
X
X
X
X
CL0-14-464
CL0-14
Verrucomicrobia
O
O
O
O
O
O
O
O
Sta235-83
Sta2-35
Verrucomicrobia
O
O
O
O
O
O
O
O
FukuN18-209
FukuN18
Verrucomicrobia
X
X
X
X
X
X#
O
X
CL500-6-64
CL500-6
Bacteroidetes
O
O
O
O
O
X
O
X
FukuN47-208
FukuN47
Bacteroidetes
O
O
O
O
O
O
O
O
LD2-457
LD2 (SOL cluster)
Bacteroidetes
O
O
O
O
O
O
O
O
PRD01a001b-134
PRD01a001b
Bacteroidetes
O
O
O
O
O
O
O
O
a
All probe sequences and working conditions except for CRFL11-135 have been shown in reference 53 (Wu et al., 2006).
b
X donates positive detection by the respective probes in all samples of an area (if not stated differently), whereas O refers to no detection.
c
The probe sequence is 5’-GTTGTTCCGTACCCCTAGG-3’. This probe was not included in TableS2 of the reference 53 (Wu et al., 2006) due to negligence.
d
Targeting a subgroup of subcluster PnecB and all members of subcluster PnecC except of three endosymbiotic strains.
e
Four strains belonging to subcluster PnecD are not targeted by the probe. The probe has one mismatch to sequences of all four strains.
$
Two samples tested for East Bay.
#Probe was only positive for two or one sample taken in the area.
LD12-143
CRFL11-135 c
LD28-451
Polynuc451
4
5
6
7
8
9
10
Littoral zone
of Wuli Bay b
Sep.
O
X
O
O
1
East Bay b,$
Aug.
O
O
O
O
Sep.
O
O
O
O
O
O
X
O
O
X
O
X
X
X#
X
O
O
O
O
O
O
O
O
X
X
O
X
O
O
O
X
O
O
X
O
X
X
O
X
O
O
O
X
O
O
X
1
Table S2. Phylogenetic affiliations of cloned 16S rRNA gene sequences obtained from the East Bay library
2
representing the bacterioplankton community composition in the macrophyte-dominated environment.
Groups
Clones
Actinobacteria
TH3-91, 101
TH3-102
TH3-4
TH3-103
TH3-14, 37
TH3-15, 22
TH3-28
TH3-30
TH3-33, 94
TH3-40
TH3-60
TH3-61, 93
TH3-51, 68, 88
TH3-70
TH3-71
TH3-73, 85
TH3-80
TH3-84
TH3-2, 24, 29, 39,41, 49,
50, 72, 82, 99, 104
TH3-1, 6, 38, 52, 54
TH3-7, 25, 48, 63, 67, 76
TH3-5, 100
TH3-8, 53, 79
TH3-3
TH3-16, 20, 105
Gammaproteobacteria
TH3-56, 92
Betaproteobacteria
TH3-59, 78
TH3-97
TH3-45
TH3-87
TH3-62
TH3-34
TH3-64, 66
TH3-17
TH3-18
TH3-9
TH3-27, 55
Verrucomicrobia
TH3-106
TH3-89
TH3-32, 75, 107
TH3-44
TH3-36
TH3-11
TH3-13
Alphaproteobacteria
TH3-65
TH3-74
TH3-12
Planctomycetes
TH3-86
TH3-90
Bacteroidetes
TH3-47
TH3-69
TH3-81
Fibrobacteres
TH3-98
Cyanobacteria
TH3-10, 42, 46, 96
TH3-43
3
4
5
closest relatives
ACC number
Similarity
(%)
Freshwater clusters
Sources
Clone HTDD3
Isolate MWH-Dar
Clone ML-3-48.2
Isolate Tsukamurella sp.
Clone ST11-16
Isolate Actinomycetales GP5
Clone S9
Clone SV1-11
Clone ML-9-97.2
Clone sponge 8
Clone STH11-14
Clone P38.31
Clone PRD01a002B
Clone NM3
Clone AKYG965
Clone S9D-06
Clone SV1-12
Clone S9F-09
Clone ML-9-87.2
AF418956
AJ565416
DQ520161
AY741505
DQ316361
AY145533
AJ575510
AJ575520
DQ520197
AY948357
DQ316359
AY752098
AF289150
AJ575536
AY922081
AB154303
AJ575521
AB154305
DQ520196
98
99
95
93
99
97
98
97
97-99
97
99
97-100
98-99
93
93
96-99
99
97
98
acTH-2**
¶
Luna1
$
Sta2-30 (acI-B)
acII
acII
Sta2-30 (acI-B)
Soil II+III##
acTH-1**
¶
Luna1
acI-C
acIV
acIV-B
acII
Sta2-30 (acI-B)
acTH-1**
Particles
FW*
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
FW
Clone N4
Clone S4
Clone PRD18H10
Clone NO3
Isolate MWH-VicMua1
Clone R5
AJ575531
AJ575506
AY948072
AJ575556
AJ565417
AJ575501
99
97
98
99
96
97-99
Sta2-30 (acI-B)
acIV-B##
$
ACK-M1 (acI-A)
ACK-M1 (acI-A)
acII-A
ACK-M1 (acI-A)
Clone MRT-87
EF371492
99-100
-
Isolate MWH-IPGL7W22
Isolate Ralstonia strain TA
Isolate Ralstonia CH34
Isolate Acidovorox GPTSA100-27
Clone C1-A6
Clone DR-29
Clone 220ds20
Clone 17 up
Clone EV818EB5CPSAJJ33
Clone P38.4
Clone 173ds20
AJ876403
DQ908951
CP000353
DQ854967
DQ676998
AY945920
AY212668
AY212631
DQ337037
AY752086
AY2126324
99
100
99
99
99
96
99
99
99
99
99
PnecB#
-
Clone aab56b01
Clone SLB624
Clone P38.38
Clone aab52e08
Clone LD29
Clone W4-B59
Clone ST11-29
DQ814962
DQ787718
AY752101
DQ815271
AF009975
AY345492
DQ501335
98
93
99
99
91
93
96
-
Fish gut
Sediment
FW
Fish gut
FW
FW
FW
Clone ML-7-85
Isolate Sphingmonas MTR-71
Isolate Sphingmonas P1S1
DQ520197
DQ898300
AJ620198
98
98
99
-
FW
Sediment
FW
Clone Liuu-5-192
Clone Dpcom243
AY509489
AY453254
97
96
-
FW
Sediment
Clone CR99-2-72
Clone 207ds20
Clone SF33
AF429258
AY212653
AJ697700
96
99
98
PRD01a001b$
PRD01a001b$
FW
FW
FW
Clone Green sulfur OPB56
AJ630296
95
-
FW
Isolate Cyanobium LBG2
Isolate Synechococcus OBB26S03
AF330249
AJ639899
98
99
-
FW
FW
$
FW
FW
FW
FW
FW
FW
Estuary
FW
Soil
Soil
FW
Soil
FW
FW
FW
FW
FW
FW
¶
* FW refers to freshwater. #Subcluster B of Polynucleobacter cluster (Hahn, 2003; Wu & Hahn, 2006). Zwart et al., 2002; Warnecke et al., 2004. Hahn et
al., 2003. ##Allgaier and Grossart, 2006. ** Newly proposed cluster in this study.
2
1
Table S3. Phylogenetic affiliations of cloned 16S rRNA gene sequences obtained from the Meiliang Bay library
2
representing the bacterioplankton community composition in a phytoplankton-dominated environment.
Groups
Clone name
Actinobacteria
TH1-11
TH1-24
TH1-25
TH1-29
TH1-41
TH1-43
TH1-44, 49
TH1-65, 77
TH1-84
TH1-93
TH1-90, 95
TH1-86, 94
TH1-96
TH1-97
TH1-9, 13, 15, 16, 18, 34,
40, 42, 57, 66, 70
TH1-22, 61, 63, 89,91, 98
TH1-2, 7, 36, 51
Gammaproteobacteria
TH1-32
TH1-3,64
TH1-17
TH1-21
TH1-35
TH1-39
TH1-87
TH1-73
TH1-88
TH1-46
Betaproteobacteria
TH1-69
TH1-83
TH1-5, 59
TH1-38, 74
Verrucomicrobia
TH1-67, 100
TH1-55
Alphaproteobacteria
TH1-53
TH1-60
TH1-62
TH1-30, 76
TH1-19
Deltaproteobacteria
TH1-8, 14
Planctomycetes
TH1-12, 20, 56
TH1-10
TH1-27
Bacteroidetes
TH1-82
TH1-50
Fibrobacteres
TH1-4
Cyanobacteria
TH1-45, 54, 80
TH1-1, 52, 71, 92
TH1-58, 85
Others
TH1-31
TH1-99
TH1-23
3
# The
closest relative
Accession
number
Similarity
%
Freshwater
Clusters#
Isolate Mycobacterium sp.
Clone S5
Clone P38.54
Clone ARFS-33
Clone Elev_16S_1332
Isolate Bacterium rJ7
Clone LT11OP1A8
Clone STH5-13
Clone ST5-1
Clone Elev_16S_634
Clone Sponge 8
Clone ST5-26
Clone Ihad10
Clone ML-9-97.2
Clone S4
AJ002094
AJ575507
AY752108
AJ277699
EF019953
AB021325
DQ444430
DQ316383
DQ316368
EF019399
AY948357
DQ316371
DQ648909
DQ520197
AJ575506
98
99
92
93
94
97
97
94
94
92
96-97
93-98
97
99
93-98
acTH-2**
acIV-A
acIV-B##
acIV-D##
acIV-D##
Sta2-30 (acI-B)
acIV-B##
Clone ML-9-55.2
Clone ML-9-87.2
DQ520190
DQ520196
98-99
98-99
acIV
acTH-1**
Isolate Acinetobacter sp.
Clone 88_17
Clone 91_11
Clone WD2124
Isolate Stenotrophomonas sp.
Clone 91_18
Clone 86
Clone AH72
Isolate Acinetobacter WW21
Clone F5S6
DQ842493
AF467302
AF467306
AJ292676
AM402950
AF467295
DQ165130
AY963365
EF433555
DQ068810
96-99
99
99
99
99
99
96
95
99
98
-
Soil
Soil
Soil
Soil
Sediment
Soil
Sediment
Soil
Soil
Soil
MWH-UniP4
Isolate Ralstonia sp.
Isolate Leptothrix mobilis
Clone C1-A6
AJ565422.1
AF280433
X97071
DQ676998
97
99
96-98
99
-
FW
Soil
Soil
Sediment
Clone P38.38
Clone P38.12
AY752101
AY752089
96
97
FukuN18
FukuN18
Clone GKS2-215
Clone 53
Isolate Rhodobacter sp.
Clone ML-3-64.2
Clone HTH6
AJ290032
DQ413112
AB251408
DQ520162
AF418965
95
99
98
92-96
99
LD12
Clone FAC87
DQ451526
91
-
Soil
Isolate Pirellula sp.
Clone LT110P1D4
Clone ST11-26
X81940
DQ444439
DQ501334
98
96
98
-
Particles
FW
FW
Clone S1-4-CL9
Clone S9A-31
AY728066
AB154301
93
95
-
Soil
FW
Clone ML-7-70.2
DQ520175
99
-
FW
Isolate Cyanobium LB03
Isolate Synechococcus PCC9005
Isolate Merismopedia sp.
AY183115
AF216950
AJ639891
99
99
98-99
-
FW
FW
FW
Plastid
Clone 655952
Clone LGD10
AY221720
DQ404824
AF047567
99
86
98
-
FW
Sediment
Sediment
name of freshwater bacterial clusters were the same as in Table S1. $ FW refers to freshwater.
3
Sources
Sediment
FW$
FW
Rice paddy
Soil
Activated sludge
FW
FW
FW
Soil
FW
FW
Soil
FW
FW
FW
FW
FW
FW
FW
SBR reactor
Ditch
FW
FW
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