TABLE 2.
Distribution of 16S rRNA gene clones of endophytic bacteria from root samples of “Ca. Liberibacter asiaticus”-infected and uninfected citrus trees
| Group | Closest NCBI match (accession no.) | % Identity | Uninfected trees |
Infected trees |
||||
|---|---|---|---|---|---|---|---|---|
| No. of OTUs | No. of clonesa | % of total clonesa | No. of OTUs | No. of clonesa | % of total clonesa | |||
| Alphaproteobacteria | 14 | 85 | 30.68 | 9 | 174 | 72.19 | ||
| Mesorhizobium sp. Aci124 (AB480767) | 100 | 7 | 2.52 | |||||
| Mesorhizobium sp. S23423 (D84623) | 97 | 5 | 1.80 | |||||
| Rhizobium sp. HGR13 (GQ483459) | 99 | 2 | 0.72 | 3 | 1.24 | |||
| Ochrobactrum sp. 1605 (DQ989292) | 98 | 6 | 2.16 | |||||
| Caulobacter sp. DSV3 M (FJ948826) | 100 | 15 | 5.41 | |||||
| Paracoccus sp. GN-N06-15.1 (EU518706) | 100 | 8 | 2.88 | |||||
| Methylosinus sp. LW2 (AF150786) | 97 | 9 | 3.24 | |||||
| Methylobacterium sp. AR5.1/5 (EU789486) | 100 | 5 | 1.80 | 3 | 1.24 | |||
| Methylobacterium hispanicum GN05-11d (DQ872462) | 100 | 3 | 1.08 | 4 | 1.64 | |||
| Brevundimonas sp. DSV1M (FJ948824) | 100 | 11 | 4.03 | |||||
| Sphingopyxis sp. Geo 48 (EU816422) | 99 | 5 | 1.80 | |||||
| Bosea thioxidans BI-42 (AF508803) | 100 | 4 | 1.44 | |||||
| Ochrobactrum anthropi (EU119263) | 99 | 1 | 0.36 | |||||
| Mesorhizobium sp. REG321 (EU703136) | 97 | 4 | 1.44 | |||||
| Methylobacterium sp. PR3/11 (EU789499) | 98 | 10 | 4.41 | |||||
| Methylobacterium sp. PR1/3 (EU789497) | 98 | 18 | 7.46 | |||||
| Methylobacteriaceae bacterium KVD-1894-12 (DQ490353) | 98 | 9 | 3.73 | |||||
| Methylobacterium sp. Evap_S_01 (DQ132876) | 97 | 7 | 2.90 | |||||
| “Candidatus Liberibacter” sp. clone DS500 (FJ388873) | 99 | 117 | 48.54 | |||||
| Sphingomonas yunnanensis 215 (EU730917) | 100 | 3 | 1.24 | |||||
| Betaproteobacteria | 12 | 52 | 18.77 | |||||
| Burkholderia vietnamiensis WBP (EU563934) | 99 | 14 | 5.05 | |||||
| Ralstonia mannitolilytica Pap In Ba8 (EU839656) | 99 | 2 | 0.72 | |||||
| Janthinobacterium sp. IC161 (AB196254) | 98 | 2 | 0.72 | |||||
| Delftia sp. Hq4-10 (EU304256) | 99 | 6 | 2.16 | |||||
| Oxalobacter formigenes (U49749) | 96 | 6 | 2.16 | |||||
| Alcaligenes sp. adx-4 (FJ169469) | 99 | 3 | 1.08 | |||||
| Achromobacter sp. MT-E3 (EU727196) | 98 | 3 | 1.08 | |||||
| Burkholderia cepacia MSMB16 (F114403) | 100 | 4 | 1.44 | |||||
| Achromobacter xylosoxidans S18 (GQ889256) | 98 | 5 | 1.80 | |||||
| Comamonas aquatica 634 (EU841530) | 99 | 3 | 1.08 | |||||
| Herbaspirillum seropedicae (AJ238361) | 97 | 2 | 0.72 | |||||
| Diaphorobacter sp. GS-1 (FJ158841) | 97 | 2 | 0.72 | |||||
| Gammaproteobacteria | 13 | 46 | 16.60 | 4 | 7 | 2.90 | ||
| Stenotrophomonas sp. P1A (AJ495804) | 98 | 2 | 0.72 | |||||
| Pseudomonas putida AD-21 (EU258552) | 99 | 5 | 1.80 | 1 | 0.41 | |||
| Lysobacter antibioticus 156 (FN398326) | 100 | 9 | 3.24 | |||||
| Pantoea ananatis ESS29 (EF602556) | 100 | 7 | 2.52 | |||||
| Acinetobacter sp. 12524 (GQ475503) | 100 | 2 | 0.72 | |||||
| Acinetobacter lwoffii GN-M06-04.1 (EU518693) | 100 | 3 | 1.08 | |||||
| Enterobacter sp. xw 16S (EF592491) | 100 | 2 | 0.72 | |||||
| Xanthomonas perforans BC2923 (GQ461740) | 100 | 2 | 0.72 | |||||
| Erwinia tasmaniensis ET1/99 (AM292081.1) | 98 | 1 | 0.36 | 4 | 1.65 | |||
| Acinetobacter calcoaceticus TMPSB-D12 (EU513394.1) | 100 | 6 | 2.16 | |||||
| Pseudomonas sp. Zj5 (GQ859170) | 99 | 1 | 0.36 | |||||
| Pseudomonas stutzeri DQgbc15 (GQ470400) | 100 | 3 | 1.08 | |||||
| Stenotrophomonas maltophilia VUN 10 (AF068009) | 99 | 3 | 1.08 | |||||
| Pseudomonas sp. BSw10041N (FJ416144) | 99 | 2 | 0.82 | |||||
| Deltaproteobacteria | 1 | 4 | 1.44 | |||||
| Bdellovibrio bacteriovorus 100 (AF084850.1) | 95 | 4 | 1.44 | |||||
| Acidobacteria | 1 | 5 | 1.80 | |||||
| Acidobacteriaceae bacterium Gsoil 149 (AB245339) | 98 | 5 | 1.80 | |||||
| Actinobacteria | 7 | 28 | 10.10 | |||||
| Brachybacterium sp. GN0406-11.4.3 (DQ890505) | 99 | 4 | 1.44 | |||||
| Friedmanniella antarctica AA-1042 (NR_026536) | 99 | 1 | 0.36 | |||||
| Microbacterium paraoxydans (FN257489) | 100 | 2 | 0.72 | |||||
| Streptomyces alni D65 (DQ460470) | 98 | 3 | 1.08 | |||||
| Curtobacterium sp. C01 (EF411134) | 99 | 12 | 4.33 | |||||
| Microbacterium paraoxydans SS18 (FN257489) | 100 | 4 | 1.44 | |||||
| Kocuria kristinae GN-NO6-23.3 (EU518711) | 100 | 2 | 0.72 | |||||
| Firmicutes | 10 | 30 | 10.83 | 3 | 6 | 2.46 | ||
| Bacillus sp. B1(2007) (EU281627) | 99 | 2 | 0.72 | 2 | 0.82 | |||
| Bacillus pumilus JK-SX001 (GQ169785) | 98 | 8 | 2.88 | |||||
| Bacillus cereus S45 (GQ462533) | 98 | 3 | 1.08 | |||||
| Bacillus subtilis HJ5 (GQ249662) | 100 | 2 | 0.72 | 2 | 0.82 | |||
| Paenibacillus lentimorbus (AB110988) | 98 | 5 | 1.80 | |||||
| Cohnella soli strain 5GH36-9 (EF368009) | 97 | 1 | 0.36 | |||||
| Paenibacillus sp. GT-H3 (GQ355277) | 99 | 3 | 1.08 | |||||
| Brevibacterium sp. BN53-1 (AB066340) | 99 | 1 | 0.36 | |||||
| Bacillus firmus 26-18 (FJ607047) | 99 | 4 | 1.44 | |||||
| Aerococcus sp. 4103 (FJ405327) | 98 | 1 | 0.36 | |||||
| Bacillus oshimensis 1P09AA (EU977653) | 99 | 2 | 0.82 | |||||
| Deinococcus-Thermus | 1 | 4 | 1.44 | |||||
| Deinococcus sp. X-121sp (EU718060) | 99 | 4 | 1.44 | |||||
| Bacteroidetes | 1 | 22 | 9.12 | |||||
| Sphingobacterium daejeonense (AB249372) | 98 | 1 | 22 | 9.12 | ||||
| Uncultured | 6 | 23 | 8.30 | 5 | 32 | 13.27 | ||
| Uncultured bacterium clone SN27 (EU735655) | 97 | 7 | 2.52 | 6 | 2.48 | |||
| Uncultured soil bacterium clone M16_Pitesti (DQ378236) | 99 | 6 | 2.16 | 6 | 2.48 | |||
| Uncultured bacterium clone 1959a-21 (AY917654) | 96 | 1 | 0.36 | 6 | 2.48 | |||
| Uncultured Simkania sp. clone DA81 (FJ388266) | 97 | 1 | 0.36 | 7 | 2.90 | |||
| Uncultured Brevundimonas sp. clone DA155 (FJ388340) | 98 | 1 | 0.36 | 7 | 2.90 | |||
| Kordiimonas sp. clone DA162 (FJ388347) | 97 | 7 | 2.52 | |||||
a
Blank entries indicate that phylotypes were not detected.