Table 3.
Isolated microbes in this study and their related authentic species on the basis of 16S rRNA gene sequence
| Isolate- phylotype No.a | Isolate | Authentic species (Accession No.) | Identity (%) | Phylum (Class) | Length (bp) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
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| Reed | Japanese loosestrife | Pond water | ||||||||
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| Total no. of isolates | Name of representative strain | Total no. of isolates | Name of representative strain | Total no. of isolates | Name of representative strain | |||||
| 1 | 5 | YO-23 | Rubrivivax gelatinosus strain ATCC17011 (D16213) | 97 | Proteobacteria (Beta) | 709 | ||||
| 2 | 6 | YO-32 | 1 | MI-15 | Aquincola tertiaricarbonis strain L10T (DQ656489) | 97 | Proteobacteria (Beta) | 711 | ||
| 3 | 5 | YO-28 | Methylibium fulvum strain Gsoil 328 (AB245357) | 97 | Proteobacteria (Beta) | 653 | ||||
| 4 | 1 | YO-5 | Azoarcus buckelii strain U120 (AJ315676) | 94 | Proteobacteria (Beta) | 711 | ||||
| 5 | 3 | YO-6 | Curvibacter delicatus strain LMG 4328 (AF078756) | 97 | Proteobacteria (Beta) | 696 | ||||
| 6 | 1 | YO-8 | 1 | MI-36 | Chelatovorus multitrophus strain DSM 9103T (EF457243) | 91 | Proteobacteria (Alpha) | 709 | ||
| 7 | 1 | YO-9 | Herbaspirillum seropedicae strain ATCC 35892 (Y10146) | 91 | Proteobacteria (Beta) | 710 | ||||
| 8 | 1 | YO-13 | Bosea thiooxidans strain BI-42 (AF508803) | 93 | Proteobacteria (Alpha) | 710 | ||||
| 9 | 1 | YO-14 | Rhodobacter ovatus strain JA234T (AM690348) | 98 | Proteobacteria (Alpha) | 709 | ||||
| 10 | 1 | YO-16 | Limnobacter thiooxidans strain CS-K2 (AJ289885) | 91 | Proteobacteria (Beta) | 697 | ||||
| 11 | 1 | YO-17 | Sandaracinobacter sibiricus strain RB16-17 (Y10678) | 97 | Proteobacteria (Alpha) | 710 | ||||
| 12 | 1 | YO-18 | Rhodobacter blasticus strain ATCC 33485T (DQ342322) | 98 | Proteobacteria (Alpha) | 709 | ||||
| 13 | 3 | YO-19 | Ideonella dechloratans (X72724) | 98 | Proteobacteria (Beta) | 710 | ||||
| 14 | 1 | YO-26 | Leptothrix discophora strain SS-1 (L33975) | 95 | Proteobacteria (Beta) | 517 | ||||
| 15 | 1 | YO-27 | Pseudomonas pohangensis strain H3-R18T (DQ339144) | 98 | Proteobacteria (Gamma) | 711 | ||||
| 16 | 1 | YO-29 | Paracoccus marcusii (Y12703) | 95 | Proteobacteria (Alpha) | 709 | ||||
| 17 | 1 | YO-33 | Nitrosococcus oceani strain ATCC 19707 (AY690336) | 87 | Proteobacteria (Gamma) | 708 | ||||
| 18 | 1 | YO-34 | Pelomonas aquatica strain CCUG 52575T (AM501435) | 97 | Proteobacteria (Beta) | 695 | ||||
| 19 | 1 | YO-36 | Desulfotomaculum halophilum strain SEBR 3139 (U88891; Fir-micutes) | 80 | Candidate phylum OP10 | 709 | ||||
| 20 | 1 | YO-38 | Novosphingobium hassiacum strain W-51 (AJ416411) | 97 | Proteobacteria (Alpha) | 711 | ||||
| 21 | 1 | YO-40 | Sinorhizobium adhaerens strain 5D19 (AJ420773) | 98 | Proteobacteria (Alpha) | 709 | ||||
| 22 | 2 | YO-45 | Novosphingobium resinovorum strain NCIMB 8767 (EF029110) | 94 | Proteobacteria (Alpha) | 712 | ||||
| 23 | 8 | MI-1 | Azohydromonas lata strain IAM 12665 (AB201626) | 97 | Proteobacteria (Beta) | 690 | ||||
| 24 | 3 | MI-2 | Rubrivivax gelatinosus strain ATCC 17011 (D16213) | 96 | Proteobacteria (Beta) | 696 | ||||
| 25 | 1 | MI-5 | Sphingobium japonicum strain UT26 (AF039168) | 97 | Proteobacteria (Alpha) | 712 | ||||
| 26 | 1 | MI-6 | Rhodobacter blasticus strain ATCC 33485T (DQ342322) | 98 | Proteobacteria (Alpha) | 712 | ||||
| 27 | 1 | MI-8 | Steroidobacter denitrificans strain FS (EF605262) | 93 | Proteobacteria (Gamma) | 707 | ||||
| 28 | 2 | MI-9 | Rhodobacter capsulatus strain ATCC 11166T (DQ342320) | 96 | Proteobacteria (Alpha) | 695 | ||||
| 29 | 1 | MI-10 | Niastella jeongjuensis strain GR20-13 (DQ244076) | 94 | Bacteroidetes | 710 | ||||
| 30 | 1 | MI-11 | Asticcacaulis biprosthecium strain DSM 4723T (AJ247193) | 98 | Proteobacteria (Alpha) | 710 | ||||
| 31 | 1 | MI-12 | Phenylobacterium lituiforme strain FaiI3 (AY534887) | 97 | Proteobacteria (Alpha) | 711 | ||||
| 32 | 1 | MI-13 | Novosphingobium hassiacum strain W-51 (AJ416411) | 97 | Proteobacteria (Alpha) | 711 | ||||
| 33 | 3 | MI-14 | Rhodoferax antarcticus strain Fryx1 (AY609198) | 98 | Proteobacteria (Beta) | 696 | ||||
| 34 | 3 | MI-16 | Hyphomicrobium hollandicum strain IFAM KB-677 (Y14303) | 93 | Proteobacteria (Alpha) | 660 | ||||
| 35 | 1 | MI-20 | Sphingomonas suberifaciens strain IFO 15211 (D13737) | 95 | Proteobacteria (Alpha) | 709 | ||||
| 36 | 1 | MI-26 | Caulobacter henricii strain ATCC 15253T (AJ227758) | 98 | Proteobacteria (Alpha) | 708 | ||||
| 37 | 1 | MI-30 | Methylosinus trichosporium strain NCIMB 11131 (Y18947) | 91 | Proteobacteria (Alpha) | 709 | ||||
| 38 | 1 | MI-31 | Novosphingobium resinovorum strain NCIMB 8767T (EF029110) | 96 | Proteobacteria (Alpha) | 709 | ||||
| 39 | 1 | MI-32 | Pseudodevosia insulae strain DS- 56T (EF012357) | 96 | Proteobacteria (Alpha) | 711 | ||||
| 40 | 1 | MI-33 | Acidimicrobium ferrooxidans strain DSM 10331 (AFU75647) | 90 | Actinobacteria | 712 | ||||
| 41 | 1 | MI-34 | Rhodopseudomonas cryptolactis strain DSM 9987 (AB087718) | 95 | Proteobacteria (Alpha) | 712 | ||||
| 42 | 1 | MI-35 | Bradyrhizobium elkanii strain USDA 76 (U35000) | 99 | Proteobacteria (Alpha) | 711 | ||||
| 43 | 1 | MI-37 | Steroidobacter denitrificans strain FS (EF605262) | 93 | Proteobacteria (Gamma) | 709 | ||||
| 44 | 2 | MI-40 | Devosia insulae strain DS-56T (EF012357) | 92 | Proteobacteria (Alpha) | 712 | ||||
| 45 | 1 | MI-39 | Afipia massiliensis strain CCUG 45153T (AY029562) | 93 | Proteobacteria (Alpha) | 710 | ||||
| 46 | 9 | KW-15 | Rhodobacter massiliensis strain Framboise (AF452106) | 98 | Proteobacteria (Alpha) | 709 | ||||
| 47 | 3 | KW-13 | Flavobacterium terrae strain R2A1-13T (EF117329) | 94 | Bacteroidetes | 711 | ||||
| 48 | 9 | KW-16 | Limnohabitans curvus strain MWH-C5 (AJ938026) | 98 | Proteobacteria (Beta) | 710 | ||||
| 49 | 7 | KW-29 | Limnohabitans curvus strain MWH-C5 (AJ938026) | 97 | Proteobacteria (Beta) | 710 | ||||
| 50 | 5 | KW-28 | Herbaspirillum rubrisubalbicans strain M4 (AJ238356) | 97 | Proteobacteria (Beta) | 710 | ||||
| 51 | 1 | KW-22 | Novosphingobium aromati-civorans strain SMCC B0695 (U20755) | 98 | Proteobacteria (Alpha) | 711 | ||||
| 52 | 1 | KW-39 | Pedobacter caeni strain R-21937 | 86 | Bacteroidetes | 711 | ||||
| 53 | 1 | KW-40 | Methylotenera mobila strain JLW8T (DQ287786) | 94 | Proteobacteria (Beta) | 712 | ||||
| 54 | 2 | KW-45 | Tetrasphaera nostocoidensis strain Ben 70 (DQ007320) | 91 | Actinobacteria | 709 | ||||
| 55 | 1 | KW-42 | Polynucleobacter necessarius strain STIR1 (AJ811014) | 99 | Proteobacteria (Beta) | 682 | ||||
| 56 | 1 | KW-43 | Chitinophaga ginsengisegetis strain Gsoil 040T (AB264798) | 91 | Bacteroidetes | 680 | ||||
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| Total | 40 | 40 | ||||||||
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| Novel microbesb | 14 (11) | 8 (5) | ||||||||
a
The phylotypes were defined on the basis of the results of restriction fragment length polymorphism (RFLP) analysis. The isolate-phylotypes whose sequences indicated less than 95% identity with those from authentic species are underlined.
b
The number of phylotypes showing phylogenetic novelty is shown in parentheses.