Supporting information Supplementary Table S1

Supporting information Supplementary Table S1. Phylogenetic affiliations of 16S rRNA gene clones Clonephylotype a No.

Reed

1

Total no. of clone 6

Name of representative clone CYO-1

2

1

CYO-2

3

1

CYO-3

4

2

CYO-4

5

2

CYO-5

6

1

CYO-6

7

2

CYO-7

8

1

CYO-8

9

1

CYO-9

10

4

CYO-10

11

1

CYO-11

12

1

CYO-12

13

1

CYO-13

14

1

CYO-14

Japanese loosestrife Total no. of clone

Name of representative clone

Pond water Total no. of clone

13

2


CKW-13

CKW-28

Authentic species (Accession No.) Cellvibrio mixtus subsp. mixtus strain ACM 2601 (AF448515) Flavobacterium segetis strain AT1048T (AY581115) Leptothrix discophora strain SP-6 (L33974) Limnohabitans curvus strain MWH-C5 (AJ938026) Roseateles aquatilis strain CCUG48205T (AM501446) Aquaspirillum delicatum strain LMG 4328 (AF078756) Leptothrix cholodnii strain CCM 1827 (X97070) Aquaspirillum delicatum strain LMG 4328 (AF078756) Rhodoferax ferrireducens strain T118T (CP000267) Azohydromonas lata strain IAM 12665 (AB201626) Rhodoferax antarcticus strain Fryx1 (AY609198) Aquaspirillum delicatum strain LMG 4328 (AF078756) Prosthecobacter debontii strain DSM 14044 (AJ966882) Spirochaeta aurantia strain J1 (M57740)

Identity (%)

Phylum (Class)

Length (bp)

94

Proteobacteria (Gamma) Bacteroidetes

553

646

82

Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Verrucomicrobia

97

Spirochaetes

591

96 97 97 97 97 97 98 98 97 98 98

591

514 568 523 620 607 579 581 567 604 536

Supplementary Table S1. Clonephylotype a No.

Reed

15



16

1

CYO-17

17

1

CYO-18

18

1

CYO-19

19

1

CYO-20

20

3

CYO-22

21

1

CYO-23

22

1

CYO-25

23

1

CYO-26

24

1

CYO-27

25

1

CYO-28

26

1

CYO-29

27

1

CYO-30

28

1

CYO-31

29

1

CYO-32

30

1

CYO-36


2


CMI-5

(continued)



1

CKW-12

1

CKW-25

Authentic species (Accession No.)

Identity (%)

Phylum (Class)

Length (bp)

Ideonella dechloratans (X72724)

98

569

Owenweeksia hongkongensis strain UST20020801 (AB125062) Pedobacter terricola strain DS-45 (EF446147) Lewinella agarilytica strain SST-19 (AM286229) Methylobacter tundripaludum strain SV96T (AJ414655) Rhodobacter blasticus strain ATCC 33485T (DQ342322) Sediminibacterium salmoneum strain NJ-44 (EF407879) Labrys miyagiensis strain G24116 (AB236171) Blastochloris sulfoviridis strain DSM729 (D86514) Asticcacaulis biprosthecium strain DSM 4723T Azonexus fungiphilus strain BS5-8 (AF011350) Ehrlichia muris strain AS145 (U15527; Proteobacteria) Emticicia oligotropha strain GPTSA100-15 (AY904352) Emticicia oligotropha strain GPTSA100-15 (AY904352) Ochrobactrum anthropi strain ATCC 49188 (CP000759) Azospirillum amazonense strain DSM 2787 (Z29616)

88

Proteobacteria (Beta) Bacteroidetes

82

Bacteroidetes

571

86

Bacteroidetes

566

91

Proteobacteria (Gamma) Proteobacteria (Alpha) Bacteroidetes

525

556

75

Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Beta) Unclassified

94

Bacteroidetes

649

94

Bacteroidetes

519

90

Proteobacteria (Alpha) Proteobacteria (Alpha)

598

98 97 92 87 95 97

92

530

585 598

357 306 539 611

640


Reed

31



32

1

CYO-38

33

1

CYO-40

34

1

CYO-41

35

1

CYO-42

36

4

CYO-43

37

1

CYO-44

38

3

CYO-45

39

1

CYO-48

40

2

CYO-49

41

1

CYO-50

42 43

1 1

CYO-51 CYO-52

44

1

CYO-53

45

1

CYO-54

46

1

CYO-55

47

1

CYO-56



(continued)




Identity (%)

Phylum (Class)

Length (bp)

Rubrivivax gelatinosus strain ATCC17011 (D16213) Pseudodevosia insulae strain DS-56 (EF012357) Sphingomonas xenophaga strain BN6 (X94098) Dechloromonas hortensis strain MA-1 (AY277621) Persephonella guaymasensis strain H2 (AF385630; Aquificales) Fluviicola taffensis strain RW262 (AF493694) Phenylobacterium koreense strain Slu-01 (AB166881) Denitratisoma oestradiolicum strain AcBE2-1 (AY879297) Undibacterium pigrum strain CCUG 49009 (AM397630) Rubrivivax gelatinosus strain ATCC17011 (D16213) Methylobacter tundripaludum strain SV96T (AJ414655) Nitrospira moscoviensis (X82558) Rhodobium orientis strain MB312 (D30792) Flexibacter ruber strain IFO 16675 (AB078064) Bdellovibrio bacteriovorus strain DSM 50705 (AJ278145) Terrimonas lutea strain 14990Y (AB192292) Opitutus terrae strain ACB90 (AJ229246)

98

528

76

Proteobacteria (Beta) Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Beta) Unclassified

94

Bacteroidetes

812

89

Proteobacteria (Alpha) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Gamma) Nitrospirae Proteobacteria (Alpha) Bacteroidetes

573

463

93

Proteobacteria (Delta) Bacteroidetes

91

Verrucomicrobia

642

98 96 98

95 98 98 93 98 87 85 92

556 574 574 568

565 532 533 596 571 603 620

646


Reed

48



49

1

CYO-58

50

1

CYO-59

51

1

CYO-60

52

1

CYO-62

53

1

CYO-63

54

1

CYO-64

55

1

CYO-65

56

1

CYO-66

57

1

CYO-68

58

1

CYO-69

59

1

CYO-71

60

1

CYO-73

61

1

CYO-74

62

1

CYO-76


1


CMI-18

(continued)




Identity (%)

Phylum (Class)

Length (bp)

Byssophaga cruenta strain DSM 14553T (AJ833647) Opitutus terrae strain ACB90 (AJ229246) Thermosulfidibacter takaii strain ABI70S6 (AB282756; Aquificales) Acidithiobacillus ferrooxidans strain DSM 2392 (AJ459800) Haliscomenobacter hydrossis strain DSM 1100 (EF554367) Cystobacter violaceus strain Cb vi29 (AJ233905) Opitutus terrae strain ACB90 (AJ229246) Chondromyces lanuginosus strain Sy t2 (AJ233939) Paracoccus aminovorans strain JCM 7685 (D32240) Polyangium thaxteri strain Pl t3 (AJ233943) Chondromyces apiculatus strain Cm a14 (AJ233938) Dechloromonas hortensis strain MA-1 (AY277621) Trojanella thessalonices strain L13 (AF069496) Gemmata obscuriglobus strain ACM 2246 Curtobacterium ammoniigenes strain NBRC 101789 (AB266600; Actinobacteria)

95

Proteobacteria (Delta) Verrucomicrobia

646

78

Candidate phylum GN1

619

86


647

Proteobacteria (Delta) Verrucomicrobia

523

Proteobacteria (Delta) Proteobacteria (Alpha) Proteobacteria (Delta) Proteobacteria (Delta) Proteobacteria (Beta) Proteobacteria (Alpha) Planctomycetes

645

Candidate phylum OP10

807

92

86 99 92 91 97 91 92 98 89 85 79

596

620

640

610 814 694 804 799 780


Reed

63



64

1

CYO-78

65

1

CYO-79

66

1

CYO-80



67

1

CMI-1

68

1

CMI-2

69

1

CMI-3

70

2

CMI-4

71

2

CMI-6

72

1

CMI-7

73

1

CMI-8

74

1

CMI-9

75

1

CMI-10

76

1

CMI-11

77

1

CMI-12

78

2

CMI-13

(continued)

Pond water Total no. of clone 8

9

Name of representative clone CKW-22

CKW-3


Identity (%)

Phylum (Class)

Length (bp)

Flavobacterium terrae strain R2A1-13T (EF117329) Polyangium thaxteri strain Pl t3 (AJ233943) Fluviicola taffensis strain RW262 (AF493694) Dechloromonas hortensis strain MA-1 (AY277621) Methylophilus methylotrophus strain NCIMB 10515 (AB193724) Methylophilus methylotrophus strain NCIMB 10515 (AB193724) Beijerinckia mobilis strain DSM 2326 (AJ563932) Bacteroides capillosus strain ATCC 29799 (AY136666; Bacteroidetes) Steroidobacter denitrificans strain FS (EF605262) Steroidobacter denitrificans strain FS (EF605262) Clostridium putrefaciens strain DSM 1291 (AF127024; Firmicutes) Flavisolibacter ginsengisoli strain Gsoil 643 (AB267477) Haematobacter massiliensis strain CCUG 47968 (DQ342309) Steroidobacter denitrificans strain FS (EF605262) Lachnobacterium bovis strain LRC 5436 (AF298665; Firmicutes) Bacteroides capillosus strain ATCC 29799 (AY136666; Bacteroidetes)

94

Bacteroidetes

640

91

Proteobacteria (Delta) Proteobacteria (Delta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Alpha) Unclassified

735

539

83

Proteobacteria (Gamma) Proteobacteria (Gamma) Acidobacteria

94

Bacteroidetes

651

98

557

80

Proteobacteria (Alpha) Proteobacteria (Gamma) Acidobacteria

84

Unclassified

640

94 95 95 97 93 84 93 94

93

803 817 619 656 659 625

582 640

600 625


Reed Total no. of clone


Japanese loosestrife

79


Name of representative clone CMI-14

80

2

CMI-15

81

1

CMI-16

82

2

CMI-19

83

1

CMI-20

84

1

CMI-21

85

1

CMI-22

86

1

CMI-23

87

2

CMI-24

88

1

CMI-25

89

1

CMI-29

90

1

CMI-30

91

1

CMI-31

92

1

CMI-32

(continued)




Identity (%)

Phylum (Class)

Length (bp)

Haliscomenobacter hydrossis strain DSM 1100 (AJ784892; Bacteroidetes) Steroidobacter denitrificans strain FS (EF605262) Clostridium aminophilum strain F (L04165; Firmicutes) Azohydromonas lata strain IAM 12665 (AB201626) Rhodoferax ferrireducens strain T118 (AF435948) Clostridium aminophilum strain F (L04165; Firmicutes) Clostridium aminophilum strain F (L04165; Firmicutes) Prosthecobacter debontii strain DSM 14044 (AJ966882) Aquincola tertiaricarbonis strain L10 (DQ656489) Aquaspirillum itersonii subsp. nipponicum strain LMG 7370 (EF612766) Hyphomicrobium sulfonivorans strain ATCC BAA-113 (AF235089) Pelobacter propionicus strain DSM 2379 (CP000482) Steroidobacter denitrificans strain FS (EF605262) Novosphingobium nitrogenifigens strain Y88 (DQ448852)

85

Bacteroidetes

590

92

Proteobacteria (Gamma) Acidobacteria

556

578

82

Proteobacteria (Beta) Proteobacteria (Beta) Acidobacteria

83

Acidobacteria

640

84

Verrucomicrobia

633

95

Proteobacteria (Beta) Proteobacteria (Alpha)

653

96

Proteobacteria (Alpha)

571

83

Proteobacteria (Delta) Proteobacteria (Gamma) Proteobacteria (Alpha)

549

82 98 98

88

93 97

630

591 520

558

646 520





93



94

1

CMI-34

95

2

CMI-35

96

1

CMI-37

97

1

CMI-38

98

1

CMI-39

99

1

CMI-40

100

1

CMI-41

101

1

CMI-42

102

1

CMI-43

103

1

CMI-44

104

1

CMI-45

105

1

CMI-47

106

1

CMI-48

107

1

CMI-49

(continued)




Identity (%)

Phylum (Class)

Length (bp)

Steroidobacter denitrificans strain FS (EF605262) Planctomyces limnophilus strain IFAM 1008 (X62911) Novosphingobium pentaromativorans strain US6-1 (AF502400) Novosphingobium aromaticivorans strain DSM 12444 (CP000248) Lewinella agarilytica strain SST-19 (AM286229) Methylophilus leisingeri strain DSM 6813 (AB193725) Methylophilus leisingeri strain DSM 6813 (AB193725) Sporichthya polymorpha strain DSM 46113 (X72377) Pseudomonas fluorescens strain ATCC13525 (DQ207731) Steroidobacter denitrificans strain FS (EF605262) Methylocella silvestris strain BL2 (AJ491847) Devosia subaequoris strain HST3-14T (AM293857) Streptomyces hiroshimensis strain NBRC 14693 (AB249979; Actinobacteria) Ralstonia insidiosa strain CCUG 46388 (AJ539233) Owenweeksia hongkongensis strain UST20020801 (AB125062)

93

Proteobacteria (Gamma) Planctomycetes

519

98

Proteobacteria (Alpha)

580

96

Proteobacteria (Alpha) Bacteroidetes

626

Proteobacteria (Beta) Proteobacteria (Beta) Actinobacteria

652

Proteobacteria (Gamma) Proteobacteria (Gamma) Proteobacteria (Alpha) Proteobacteria (Alpha) Acidobacteria

657


522

92

85 95 96 87 88 88 96 92 84 93 86

600

649

653 656

660 514 610 608

399





108



109

1

CMI-51

110

1

CMI-53

111

1

CMI-54

112

2

CMI-55

113

1

CMI-56

114

2

CMI-57

115

2

CMI-59

116

1

CMI-60

117

1

CMI-61

118

1

CMI-62

119

1

CMI-63

120

1

CMI-64

121

1

CMI-66

122

1

CMI-67

123

1

CMI-68

(continued)




Identity (%)

Phylum (Class)

Length (bp)

Niastella jeongjuensis strain GR20-13 (DQ244076) Persephonella guaymasensis strain H2 (AF385630; Aquificales) Desulfomonile limimaris (AF230531; Proteobacteria) Polyangium vitellinum strain Pl vt1 (AJ233944) Planctomyces maris strain DSM 8797T (AJ231184) Devosia subaequoris strain HST3-14T (AM293857) Devosia subaequoris strain HST3-14T (AM293857) Hyphomicrobium zavarzinii strain ZV-622 (Y14305) Hyphomicrobium vulgare strain ATCC 27500 (Y14302) Methylocapsa acidiphila strain B2T (AJ278726) Haliscomenobacter hydrossis strain DSM 1100 (AJ784892) Bradyrhizobium elkanii strain strain USDA 76 (U35000) Porphyrobacter neustonensis strain DSM 9434T (AF465838) Solirubrobacter soli strain Gsoil 355 (AB245334) Sphingopyxis flavimaris strain SW-151 (AY554010) Clostridium putrefaciens strain DSM 1291 (AF127024; Firmicutes)

93

Bacteroidetes

565

78

Planctomycetes

647

79

Acidobacteria

532

89

Proteobacteria (Delta) Planctomycetes

630

Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Alpha) Proteobacteria (Alpha) Bacteroidetes

640

Proteobacteria (Alpha) Proteobacteria (Alpha) Actinobacteria

567

Proteobacteria (Alpha) Acidobacteria

632

85 93 93 93 94 97 85 100 98 88 96 83

653

599 598 547 650 542

429 548

624





124



125

1

CMI-70

126

1

CMI-71

127

1

CMI-72

128

1

CMI-73

129

1

CMI-74

130

1

CMI-75

131

1

CMI-77

132

1

CMI-78

133

1

CMI-79

134

1

CMI-80

135

1

CMI-81

136

1

CMI-82

137

1

CMI-83

138

1

CMI-85

(continued)




Identity (%)

Phylum (Class)

Length (bp)

Steroidobacter denitrificans strain FS (EF605262) Phenylobacterium koreense strain Slu-01 (AB166881) Rhodobacter sphaeroides strain ATCC 17023T (DQ342321) Hespellia porcina strain PPC80 (AF445239; Firmicutes) Desulfonatronum cooperativum strain Z-7999 (AY725424; Proteobacteria) Planctomyces brasiliensis strain DSM 5305T (AJ231190) Flavobacterium ferrugineum strain DSM 30193T (AM230484) Desulfovibrio intestinalis strain KMS2 (Y12254; Proteobacteria) Spirulina laxissima strain SAG B256.80 (Y18798; Cyanobacteria) Pirellula staleyi strain ATCC 35122 (AF399914) Geopsychrobacter electrodiphilus strain A2 (AY187304; Proteobacteria) Flavisolibacter ginsengisoli strain Gsoil 643 (AB267477) Hyphomicrobium zavarzinii strain ZV-622 (Y14305) Nitrincola lacisaponensis strain 4CA (AY567473) Sorangium cellulosum strain DSM14627 (EU240497)

94

540

82

Proteobacteria (Gamma) Proteobacteria (Alpha) Proteobacteria (Alpha) Candidate phylum OP10 Acidobacteria

85

Planctomycetes

558

94

Bacteroidetes

609

78

Unclassified

524

74

Planctomycetes

604

87

Planctomycetes

638

82

Unclassified

545

94

Bacteroidetes

631

88

Proteobacteria (Alpha) Proteobacteria (Gamma) Proteobacteria (Delta)

666

98 97 82

86 85

648 576 572 592

649 797






(continued)

Pond water

139



140

1

CKW-2

141

2

CKW-3

142

1

CKW-4

143

1

CKW-5

144

3

CKW-6

145

1

CKW-7

146

1

CKW-8

147

2

CKW-16

148

3

CKW-17

149

2

CKW-18

150

6

CKW-19

151

3

CKW-20

152

6

CKW-29

153

3

CKW-30

154

1

CKW-31


Identity (%)

Phylum (Class)

Length (bp)

Polynucleobacter necessarius strain STIR1 (CP001010) Aquaspirillum delicatum strain LMG 4328 (AF078756) Streptacidiphilus jiangxiensis strain 22202 (AY389139) Leifsonia poae strain DSM 15202 (AM410682) Leifsonia aquatica strain JCM 1368 (D45057) Aquaspirillum delicatum strain LMG 4328 (AF078756) Aquaspirillum delicatum strain LMG 4328 (AF078756) Acidovorax facilis strain LMG 2193 (EU024133) Acidovorax facilis strain LMG 2193 (EU024133) Acidovorax facilis strain LMG 2193 (EU024133) Aquaspirillum delicatum strain LMG 4328 (AF078756) Tetrasphaera vanveenii strain Ben 70 (DQ007320) Cetobacterium somerae strain WAL 14325 (AJ438155) Arcocella aquatica strain NO-502T (AJ535729) Emticicia oligotropha strain GPTSA100-15 (AY904352) Emticicia oligotropha strain GPTSA100-15 (AY904352)

99

462

91

Proteobacteria (Beta) Proteobacteria (Beta) Actinobacteria

95

Actinobacteria

438

95

Actinobacteria

567

97

534

91

Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Proteobacteria (Beta) Actinobacteria

99

Fusobacteria

593

90

Bacteroidetes

501

97

Bacteroidetes

583

98

Bacteroidetes

602

96

96 96 96 98 98

580 580

574 583 583 582 550 570


a b

Reed

155


156

1

CKW-38

157

1

CKW-46

158

1

CKW-47

159

1

CKW-59

160

1

CKW-60

161

1

CKW-62

162

1

CKW-71

163

1

CKW-72

164

1

CKW-75

165

1

CKW-76

166

1

CKW-77

167

1

CKW-82

168

1

CKW-83

85 50 (40)


Total no. of clone

85 65 (57)


Pond water Total no. of clone 1

Total Novel b microbes

Total no. of clone


(continued)

85 34 (16)


Identity (%)

Phylum (Class)

Length (bp)

Aquaspirillum delicatum strain LMG 4328 (AF078756) Owenweeksia hongkongensis strain UST20020801 (AB125062) Flexibacter canadensis strain IFO 15130 (AB078046) Legionella taurinensis strain ATCC 700508 (DQ667196) Emticicia oligotropha strain GPTSA100-15 (AY904352) Limnobacter thiooxidans strain CS-K2 (AJ289885) Methylophilus methylotrophus strain NCIMB 10515 (AB193724) Niastella jeongjuensis strain GR20-13 (DQ244076) Acidovorax konjaci strain ICMP 7733 (AF137507) Fluviicola taffensis strain RW262 (AF493694) Fluviicola taffensis strain RW262 (AF493694) Rhodoferax ferrireducens strain T118T (CP000267) Aquaspirillum delicatum strain LMG 4328 (AF078756) Cytophaga fermentans strain ATCC 19072 (M58766)

98

602

89


86

Bacteroidetes

456

93


480

Proteobacteria (Beta) Proteobacteria (Beta) Bacteroidetes

521

562

92


93

Bacteroidetes

558

98

Proteobacteria (Beta) Proteobacteria (Beta) Bacteroidetes

538

97 94 95 93 98

96 87

The clonal phylotypes whose sequences indicated less than 95% identity with those from authentic species are underlined. The number of phylotypes showing phylogenetic novelty was provided in parentheses.

590

580

627 572

572

522 602