Chin J Plant Ecol ›› 2011, Vol. 35 ›› Issue (1): 45-55.DOI: 10.3724/SP.J.1258.2011.00045
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YAN Su-Li1, HUANGFU Chao-He1, LI Gang1, ZUO Zhao-Jiang2, MA Jie1,3, YANG Dian-Lin**()
Received:
2010-05-14
Accepted:
2010-10-20
Online:
2011-05-14
Published:
2011-01-24
Contact:
YANG Dian-Lin
About author:
First author contact:* Co-first author
YAN Su-Li, HUANGFU Chao-He, LI Gang, ZUO Zhao-Jiang, MA Jie, YANG Dian-Lin. Effects of replacement control with four forage species on bacterial diversity of soil invaded by Flaveria bidentis[J]. Chin J Plant Ecol, 2011, 35(1): 45-55.
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URL: https://www.plant-ecology.com/EN/10.3724/SP.J.1258.2011.00045
Fig. 1 The gel electrophoresis of total soil bacterial DNA in July. Fb CK, Flaveria bidentis CK; Ss CK, Sorghum bicolor × S. sudanense CK; Ss + Fb, Sorghum bicolor × S. sudanense mixed with Flaveria bidentis; Ha CK, Helianthus annuus CK; Ha + Fb, Helianthus annuus mixed with Flaveria bidentis; Ms CK, Medicago sativa CK; Ms + Fb, Medicago sativa mixed with Flaveria bidentis; Lp CK, Lolium perenne CK; Lp + Fb, Lolium perenne mixed with Flaveria bidentis.
Fig. 3 DGGE profiles of 16S rRNA V3 fragments in different stage soil bacteria. A, B, C, D, DGGE profiles of 16S rRNA V3 fragments in different soil bacteria in June, July, August and September, respectively. Abbreviations are the same as in Fig. 1. The number in the figure represents serial number for bands cut.
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Fb | 9 17 | FJ152853.1 FJ785824.1 | Uncultured bacterium clone TX5A_145 Uncultured bacterium clone EP9 | 100 94 |
7月 July | Fb | 23 | EF614061.1 | Uncultured bacterium clone NGD40 | 99 |
8月 August | Fb | 1 | GQ410521.1 | Uncultured Candidatus Amoebophilus sp. | 97 |
9月 September | Fb | 1 2 4 5 13 14 | GQ860246.1 EF651068.1 DQ828045.1 AM936427.1 DQ642734.1 DQ444104.1 | Uncultured bacterium clone AR141 Uncultured delta proteobacterium Uncultured proteobacterium Uncultured Rhodospirillaceae Uncultured soil bacterium Uncultured bacterium clone DS3-24 | 100 96 99 100 98 95 |
Table 1 Comparison results of cloned sequences of soil bacteria cultivated with Flaveria bidentis in different growth period and the most similar sequence in GenBank
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Fb | 9 17 | FJ152853.1 FJ785824.1 | Uncultured bacterium clone TX5A_145 Uncultured bacterium clone EP9 | 100 94 |
7月 July | Fb | 23 | EF614061.1 | Uncultured bacterium clone NGD40 | 99 |
8月 August | Fb | 1 | GQ410521.1 | Uncultured Candidatus Amoebophilus sp. | 97 |
9月 September | Fb | 1 2 4 5 13 14 | GQ860246.1 EF651068.1 DQ828045.1 AM936427.1 DQ642734.1 DQ444104.1 | Uncultured bacterium clone AR141 Uncultured delta proteobacterium Uncultured proteobacterium Uncultured Rhodospirillaceae Uncultured soil bacterium Uncultured bacterium clone DS3-24 | 100 96 99 100 98 95 |
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ss | 16 | GU118711.1 | Uncultured bacterium clone Mfra_M13 | 100 |
Ss + Fb | 11 | FJ870384.1 | Acidobacteria bacterium | 100 | |
7月 July | Ss | 14 17 18 | EU300452.1 EU834798.1 AY154495.1 | Uncultured actinobacterium Uncultured bacterium clone OTUc49 Uncultured earthworm intestine bacterium | 99 95 100 |
Ss + Fb | 3 4 8 | AB531400.1 GQ500847.1 EF651444.1 | Arthrobacter sp. Uncultured bacterium clone MACA- MR 18 Uncultured proteobacterium clone | 100 100 94 | |
8月 August | Ss | 10 13 | GU143709.1 AB451868.1 | Rhizobium sp. MerE-11 Uncultured Firmicutes bacterium | 100 100 |
Ss + Fb | 6 7 9 | GU056305.1 FJ966196.1 FJ930738.1 | Pseudoxanthomonas sp. Sphingobium sp. Uncultured bacterium clone W3-C09 | 98 98 98 | |
9月 September | Ss | - | - | - | - |
Ss + Fb | - | - | - | - |
Table 2 Comparison results of cloned sequences of soil bacteria cultivated with Sorghum bicolor × S. sudanense or mixed with Flaveria bidentis in different growth period and the most similar sequence in GenBank
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ss | 16 | GU118711.1 | Uncultured bacterium clone Mfra_M13 | 100 |
Ss + Fb | 11 | FJ870384.1 | Acidobacteria bacterium | 100 | |
7月 July | Ss | 14 17 18 | EU300452.1 EU834798.1 AY154495.1 | Uncultured actinobacterium Uncultured bacterium clone OTUc49 Uncultured earthworm intestine bacterium | 99 95 100 |
Ss + Fb | 3 4 8 | AB531400.1 GQ500847.1 EF651444.1 | Arthrobacter sp. Uncultured bacterium clone MACA- MR 18 Uncultured proteobacterium clone | 100 100 94 | |
8月 August | Ss | 10 13 | GU143709.1 AB451868.1 | Rhizobium sp. MerE-11 Uncultured Firmicutes bacterium | 100 100 |
Ss + Fb | 6 7 9 | GU056305.1 FJ966196.1 FJ930738.1 | Pseudoxanthomonas sp. Sphingobium sp. Uncultured bacterium clone W3-C09 | 98 98 98 | |
9月 September | Ss | - | - | - | - |
Ss + Fb | - | - | - | - |
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ha | 1 2 3 7 | GQ487891.1 GU117236.1 GQ500847.1 EU122663.1 | Uncultured bacterium clone T1-11 Uncultured bacterium clone Feb08_07C Uncultured bacterium clone MACA-MR18 Uncultured Acidobacteria bacterium | 100 100 99 100 |
Ha + Fb | - | - | - | - | |
7月 July | Ha | 5 6 9 10 13 20 | EF221451.1 FJ478699.1 EU849335.1 GQ495519.1 FJ946319.1 EU665105.1 | Uncultured Actinobacterium clone SI-1M_C07 Uncultured bacterium clone p9c21ok Uncultured actinobacterium Uncultured bacterium clone VR-12-13 Uncultured alpha proteobacterium Uncultured Gemmatimonadales | 100 99 98 99 100 98 |
Ha + Fb | 1 7 12 16 | AB196109.1 FJ184006.1 GQ468625.1 GQ067089.1 | Uncultured bacterium gene Uncultured alpha proteobacterium Uncultured Dactylosporangium sp. Uncultured bacterium clone nbw1121h01c1 | 95 100 100 98 | |
8月 August | Ha | 2 3 8 15 | AJ538059.1 FJ949425.1 GU201109.1 EU810962.1 | Uncultured Acidobacterium sp. Uncultured Chloroflexi bacterium Uncultured bacterium clone 6123Rh Uncultured actinobacterium | 94 95 100 100 |
Ha + Fb | 14 16 | GU122957.1 AY792291.1 | Agrobacterium sp. DBT2TW2 Uncultured alpha proteobacterium | 100 98 | |
9月 September | Ha | 10 11 16 | GQ859734.1 GU200785.1 GQ994692.1 | Uncultured bacterium clone AA145 Uncultured bacterium clone 1074Rh Uncultured organism clone anti_mic10 | 100 98 100 |
Ha + Fb | 6 7 | EU300503.1 EU300495.1 | Uncultured Firmicutes bacterium Uncultured Chloroflexi bacterium | 100 98 |
Table 3 Comparison results of cloned sequences of soil bacteria cultivated with Helianthus annuus or mixed with Flaveria bidentis in different growth period and the most similar sequence in GenBank
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ha | 1 2 3 7 | GQ487891.1 GU117236.1 GQ500847.1 EU122663.1 | Uncultured bacterium clone T1-11 Uncultured bacterium clone Feb08_07C Uncultured bacterium clone MACA-MR18 Uncultured Acidobacteria bacterium | 100 100 99 100 |
Ha + Fb | - | - | - | - | |
7月 July | Ha | 5 6 9 10 13 20 | EF221451.1 FJ478699.1 EU849335.1 GQ495519.1 FJ946319.1 EU665105.1 | Uncultured Actinobacterium clone SI-1M_C07 Uncultured bacterium clone p9c21ok Uncultured actinobacterium Uncultured bacterium clone VR-12-13 Uncultured alpha proteobacterium Uncultured Gemmatimonadales | 100 99 98 99 100 98 |
Ha + Fb | 1 7 12 16 | AB196109.1 FJ184006.1 GQ468625.1 GQ067089.1 | Uncultured bacterium gene Uncultured alpha proteobacterium Uncultured Dactylosporangium sp. Uncultured bacterium clone nbw1121h01c1 | 95 100 100 98 | |
8月 August | Ha | 2 3 8 15 | AJ538059.1 FJ949425.1 GU201109.1 EU810962.1 | Uncultured Acidobacterium sp. Uncultured Chloroflexi bacterium Uncultured bacterium clone 6123Rh Uncultured actinobacterium | 94 95 100 100 |
Ha + Fb | 14 16 | GU122957.1 AY792291.1 | Agrobacterium sp. DBT2TW2 Uncultured alpha proteobacterium | 100 98 | |
9月 September | Ha | 10 11 16 | GQ859734.1 GU200785.1 GQ994692.1 | Uncultured bacterium clone AA145 Uncultured bacterium clone 1074Rh Uncultured organism clone anti_mic10 | 100 98 100 |
Ha + Fb | 6 7 | EU300503.1 EU300495.1 | Uncultured Firmicutes bacterium Uncultured Chloroflexi bacterium | 100 98 |
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ms | 4 6 8 10 12 | EU300518.1 FJ898299.1 GQ302567.1 EU097123.1 EU300282.1 | Uncultured beta proteobacterium Lysobacter sp. Uncultured Acidobacterium bacterium Uncultured Acidobacteria bacterium Uncultured Firmicutes bacterium | 100 100 98 100 94 |
Ms + Fb | 15 | FJ439172.1 | Uncultured alpha proteobacterium | 98 | |
7月 July | Ms | 2 21 | GU171380.1 GU097375.1 | Arthrobacter aurescens Uncultured Nitrosospira sp. | 100 99 |
Ms + Fb | - | - | - | - | |
8月 August | Ms | - | - | - | - |
Ms + Fb | 4 | AM935033.1 | Uncultured Bacteroidetes bacterium | 100 | |
9月 September | Ms | 8 9 13 | GU143703.1 GQ397012.1 DQ642734.1 | Sinorhizobium medicae strain MerF-1 Uncultured bacterium clone AK1DE2_04C Uncultured soil bacterium | 100 95 98 |
Ms + Fb | - | - | - | - |
Table 4 Comparison results of cloned sequences of soil bacteria cultivated with Medicago sativa or mixed with Flaveria bidentis in different growth period and the most similar sequence in GenBank
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
---|---|---|---|---|---|
6月 June | Ms | 4 6 8 10 12 | EU300518.1 FJ898299.1 GQ302567.1 EU097123.1 EU300282.1 | Uncultured beta proteobacterium Lysobacter sp. Uncultured Acidobacterium bacterium Uncultured Acidobacteria bacterium Uncultured Firmicutes bacterium | 100 100 98 100 94 |
Ms + Fb | 15 | FJ439172.1 | Uncultured alpha proteobacterium | 98 | |
7月 July | Ms | 2 21 | GU171380.1 GU097375.1 | Arthrobacter aurescens Uncultured Nitrosospira sp. | 100 99 |
Ms + Fb | - | - | - | - | |
8月 August | Ms | - | - | - | - |
Ms + Fb | 4 | AM935033.1 | Uncultured Bacteroidetes bacterium | 100 | |
9月 September | Ms | 8 9 13 | GU143703.1 GQ397012.1 DQ642734.1 | Sinorhizobium medicae strain MerF-1 Uncultured bacterium clone AK1DE2_04C Uncultured soil bacterium | 100 95 98 |
Ms + Fb | - | - | - | - |
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
6月 June | Lp | - | - | - | - |
Lp + Fb | 14 15 | FM200957.1 FJ439172.1 | Uncultured bacterium partial Uncultured alpha proteobacterium | 100 98 | |
7月 July | Lp | 19 | EF651365.1 | Uncultured Actinobacterium clone | 97 |
Lp + Fb | 22 | EF614061.1 | Uncultured bacterium clone AR012 | 99 | |
8月 August | Lp | - | - | - | - |
Lp + Fb | 5 11 | EU305587.1 AJ519658.1 | Uncultured Mesorhizobium Uncultured gamma proteobacterium | 98 95 | |
9月 September | Lp | - | - | - | - |
Lp + Fb | 15 | EF018599.1 | Uncultured bacterium clone Amb_16S_871 | 100 |
Table 5 Comparison results of cloned sequences of soil bacteria cultivated with Lolium perenne or mixed with Flaveria bidentis in different growth period and the most similar sequence in GenBank
割取条带位置 Band cut site | 条带号 No. of the band | 登陆号 Accession No. in GenBank | 近缘菌群 Closest bacteria | 相似度 Similarity (%) | |
6月 June | Lp | - | - | - | - |
Lp + Fb | 14 15 | FM200957.1 FJ439172.1 | Uncultured bacterium partial Uncultured alpha proteobacterium | 100 98 | |
7月 July | Lp | 19 | EF651365.1 | Uncultured Actinobacterium clone | 97 |
Lp + Fb | 22 | EF614061.1 | Uncultured bacterium clone AR012 | 99 | |
8月 August | Lp | - | - | - | - |
Lp + Fb | 5 11 | EU305587.1 AJ519658.1 | Uncultured Mesorhizobium Uncultured gamma proteobacterium | 98 95 | |
9月 September | Lp | - | - | - | - |
Lp + Fb | 15 | EF018599.1 | Uncultured bacterium clone Amb_16S_871 | 100 |
Fig. 4 Changes of the Shannon diversity index of soil bacteria cultivated with replacement plants during the different growth periods (mean ± SE). A, B, C, D, showing the Shannon diversity index of soil bacteria cultivated with Sorghum bicolor × S. sudanense, Helianthus annuus, Medicago sativa and Lolium perenne in different growth periods, respectively. Abbreviations are the same as in Fig. 1.
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