酸铝胁迫土壤中耐铝大豆根际不同部位细菌群落结构、功能及其对促生菌富集作用的研究

doi:10.16288/j.yczz.20-409

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Hereditas(Beijing) ›› 2021, Vol. 43 ›› Issue (5): 487-500.doi: 10.16288/j.yczz.20-409

• Research Article • Previous Articles Next Articles

Bacterial composition, function and the enrichment of plant growth promoting rhizobacteria (PGPR) in differential rhizosphere compartments of Al-tolerant soybean in acidic soil

Zhongling Wen, Minkai Yang, Xingyu Chen, Chenyu Hao, Ran Ren, Shujuan Chu, Hongwei Han, Hongyan Lin, Guihua Lu, Jinliang Qi, Yonghua Yang()

Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China

Received:2020-11-30 Revised:2020-12-29 Online:2021-05-20 Published:2021-01-27
Contact: Yang Yonghua E-mail:yangyh@nju.edu.cn
Supported by:
Supported by the National Key Research and Development Program of China No(2016YFD0101005);the National Natural Science Foundation of China Nos(31870495, 31372140);the Program for Changjiang Scholars and Innovative Research Team in University from the Ministry of Education of China No(IRT_14R27)

Abstract

Abstract:

Low pH with aluminum (Al) toxicity are the main limiting factors affecting crop production in acidic soil. Selection of legume crops with acid tolerance and nitrogen-fixation ability should be one of the effective measures to improve soil quality and promote agricultural production. The role of the rhizosphere microorganisms in this process has raised concerns among the research community. In this study, BX10 (Al-tolerant soybean) and BD2 (Al-sensitive soybean) were selected as plant materials. Acidic soil was used as growth medium. The soil layers from the outside to the inside of the root are bulk soil (BS), rhizosphere soil at two sides (SRH), rhizosphere soil after brushing (BRH) and rhizosphere soil after washing (WRH), respectively. High-throughput sequencing of 16S rDNA amplicons of the V4 region using the Illumina MiSeq platform was performed to compare the differences of structure, function and molecular genetic diversity of rhizosphere bacterial community of different genotypes of soybean. The results showed that there was no significant difference in alpha diversity and beta diversity in rhizosphere bacterial community among the treatments. PCA and PCoA analysis showed that BRH and WRH had similar species composition, while BS and SRH also had similar species composition, which indicated that plant mainly affected the rhizosphere bacterial community on sampling compartments BRH and WRH. The composition and abundance of rhizosphere bacterial community among the treatments were then compared at different taxonomic levels. The ternary diagram of phylum level showed that Cyanobacteria were enriched in WRH. Statistical analysis showed that the roots of Al-tolerant soybean BX10 had an enrichment effect on plant growth promoting rhizobacteria (PGPR), which included Cyanobacteria, Bacteroides, Proteobacteria and some genera and species related to the function of nitrogen fixation and aluminum tolerance. The rhizosphere bacterial community from different sampling compartments of the same genotype soybean also were selectively enriched in different PGPR. In addition, the functional prediction analysis showed that there was no significant difference in the classification and abundance of COG (clusters of orthologous groups of proteins) function among different treatments. Several COGs might be directly related to nitrogen fixation, including COG0347, COG1348, COG1433, COG2710, COG3870, COG4656, COG5420, COG5456 and COG5554. Al-sensitive soybean BD2 was more likely to be enriched in these COGs than BX10 in BRH and WRH, and the possible reason remains to be further investigated in the future.

Key words: acidic soil, aluminum-tolerant soybean, rhizosphere, bacterial community, PGPR

Zhongling Wen, Minkai Yang, Xingyu Chen, Chenyu Hao, Ran Ren, Shujuan Chu, Hongwei Han, Hongyan Lin, Guihua Lu, Jinliang Qi, Yonghua Yang. Bacterial composition, function and the enrichment of plant growth promoting rhizobacteria (PGPR) in differential rhizosphere compartments of Al-tolerant soybean in acidic soil[J]. Hereditas(Beijing), 2021, 43(5): 487-500.

Figures/Tables 13

Fig. 1

Fig. 2

Table 1

Fig. 3

Fig. 4

Table 2

Table 3

Fig. S1

Fig. S2

Fig. S3

Fig. S4

Supplementary Table 1

Relative abundance of species at genus level in each samples"

Genus	BX_16FWRH3	BX_16FWRH2	BX_16FWRH1	BD_16FBS1	BD_16FBS2	BD_16FBS3
Sphingomonas	0.040996	0.057843	0.041616	0.0483	0.043339	0.042133
Bryobacter	0.021704	0.02384	0.023668	0.01981	0.021049	0.022634
Mucilaginibacter	0.026389	0.026699	0.017329	0.02784	0.030248	0.007028
Burkholderia-Paraburkholderia	0.024563	0.055776	0.024839	0.01247	0.004961	0.007441
Massilia	0.004272	0.006373	0.00348	0.01316	0.033038	0.014917
Phenylobacterium	0.020843	0.024529	0.019051	0.00617	0.004547	0.003583
Acidibacter	0.015675	0.017088	0.020912	0.01612	0.00472	0.005857
Candidatus_Solibacter	0.010301	0.011128	0.009474	0.01027	0.009439	0.009887
Flavisolibacter	0.009302	0.008303	0.005994	0.00985	0.01602	0.006373
Gemmatimonas	0.00534	0.005064	0.004444	0.01495	0.014194	0.009577
Bradyrhizobium	0.009198	0.005788	0.009439	0.0052	0.004582	0.004926
Ralstonia	0.010749	0.010921	0.004823	0.00617	0.004237	0.002033
Granulicella	0.008061	0.00658	0.006132	0.00537	0.005684	0.006959
Dyella	0.008475	0.024081	0.010507	0.00348	0.001826	0.001585
Acinetobacter	0	3.45E-05	0	0.00896	0.043752	0.103559
Thermosporothrix	0.010439	0.012161	0.017811	0.00382	0.001344	0.001654
Niastella	0.009474	0.012196	0.010886	0.00555	0.001034	0.00062
Bacillus	0.000655	0.001964	0.003101	0.00513	0.011024	0.027767
Sorangium	0.005615	0.003824	0.004651	0.00961	0.005615	0.004858
Rhodanobacter	0.006718	0.006132	0.008165	0.00382	0.002377	0.00124
Terracidiphilus	0.01006	0.009646	0.006856	0.00365	0.004065	0.00248
Rhizobium	0.010818	0.007545	0.003893	0.00496	0.012678	0.030007
Acidothermus	0.003135	0.002894	0.003342	0.01977	0.007372	0.009784
Nitrospira	0.002274	0.003445	0.002825	0.003	0.001998	0.00155
Haliangium	0.005374	0.004479	0.004789	0.00431	0.002859	0.002239
Actinospica	0.00503	0.001068	0.005926	0.00872	0.000965	0.000861
Brevundimonas	0	0	0	0.00382	0.019844	0.051021
Lactococcus	0	0	0	0	0	0
Asticcacaulis	0.003617	0.008234	0.002687	0.00282	0.000379	0.000655
Pseudarthrobacter	0.000103	0.000103	6.89E-05	0.00744	0.004547	0.004134
Achromobacter	0	6.89E-05	3.45E-05	0.0032	0.015882	0.030868
Methylotenera	0.000827	0.000517	0.000103	0.00014	0.005684	6.89E-05
Aerococcus	0	0	0	0.00282	0.010783	0.027492
Heliimonas	0.00124	0.000241	0.003445	0.0000689	3.45E-05	0
Arthrobacter	6.89E-05	0	3.45E-05	0.00045	0.000517	0.000103
Pseudomonas	3.45E-05	0	0	0.00034	0.000551	0
Sphingomonas	0.037379	0.041926	0.054535	0.04499	0.030902	0.035725
Bryobacter	0.042684	0.050401	0.037517	0.02673	0.04706	0.050505
Mucilaginibacter	0.007751	0.010301	0.008647	0.00768	0.002584	0.004926
Burkholderia-Paraburkholderia	0.011644	0.009061	0.01223	0.01392	0.004823	0.00596
Massilia	0.000586	0.002446	0.00441	0.02205	0.000448	0.001171
Phenylobacterium	0.004031	0.007166	0.006615	0.01037	0.002239	0.004754
Acidibacter	0.023254	0.01192	0.011403	0.00985	0.009474	0.009991
Candidatus_Solibacter	0.018259	0.022014	0.01571	0.01223	0.024322	0.020291
Flavisolibacter	0.004031	0.005857	0.014745	0.01071	0.005478	0.006718
Gemmatimonas	0.008337	0.00975	0.016088	0.01192	0.006959	0.007924
Bradyrhizobium	0.004444	0.003583	0.004685	0.00565	0.003583	0.003032
Ralstonia	0.002067	0.001344	0.002584	0.00427	0.000792	0.001275
Granulicella	0.007476	0.007717	0.007614	0.0073	0.003514	0.004754
Dyella	0.001998	0.000861	0.003755	0.00541	0.001688	0.002653
Acinetobacter	0	0	0	0.00565	0	3.45E-05
Thermosporothrix	0.008406	0.001068	0.007235	0.00231	0.003307	0.003066
Niastella	0.00379	0.001447	0.009233	0.00551	0.003238	0.00565
Bacillus	0.012333	0.000965	0.001137	0.00462	0.001585	0.001791
Sorangium	0.004754	0.003548	0.004272	0.00758	0.003858	0.00472
Rhodanobacter	0.00155	0.002722	0.003101	0.00262	0.001137	0.001723
Terracidiphilus	0.0041	0.003101	0.004789	0.00372	0.002136	0.002859
Rhizobium	0.000207	0.000723	0.000896	0.0032	0.000207	0.000172
Acidothermus	0.004203	0.002928	0.003824	0.01051	0.00472	0.005926
Nitrospira	0.007545	0.006511	0.004513	0.00293	0.012264	0.010163
Haliangium	0.002963	0.002963	0.002687	0.00451	0.002859	0.003376
Actinospica	0.003066	0.000413	0.004926	0.00269	0.004444	0.003617
Brevundimonas	0	0	0	0.00303	0	0
Lactococcus	0	0	0	0	0	0
Asticcacaulis	0.000172	0.001412	0.000965	0.00072	0.000276	0.000345
Pseudarthrobacter	0.000172	0.000103	0.000138	0.00338	0.000138	6.89E-05
Achromobacter	0	0	0	0.00272	0	0
Methylotenera	0.000207	0.000345	0.002412	0.0000689	0	3.45E-05
Aerococcus	0	0	0	0.00231	0	0
Heliimonas	0	0.000138	0	0.0000345	3.45E-05	6.89E-05
Arthrobacter	3.45E-05	0.000103	0	0.00052	0	3.45E-05
Pseudomonas	0	0	0	0.00017	0	0
Sphingomonas	0.039825	0.045957	0.070452	0.06177	0.063079	0.049437
Bryobacter	0.026183	0.019396	0.01254	0.04572	0.033796	0.034864
Mucilaginibacter	0.039067	0.042202	0.020016	0.00469	0.021256	0.038275
Burkholderia-Paraburkholderia	0.04706	0.033796	0.013505	0.01003	0.009474	0.031591
Massilia	0.007855	0.010852	0.002205	0.00279	0.005133	0.002722
Phenylobacterium	0.029765	0.028904	0.052882	0.00217	0.005374	0.009991
Acidibacter	0.011679	0.016364	0.021291	0.01034	0.005857	0.025218
Candidatus_Solibacter	0.007269	0.007993	0.005857	0.01936	0.011644	0.011403
Flavisolibacter	0.010232	0.020843	0.005753	0.00641	0.018672	0.006925
Gemmatimonas	0.004547	0.0041	0.005891	0.01034	0.007958	0.006856
Bradyrhizobium	0.016984	0.015985	0.020912	0.00448	0.002549	0.006925
Ralstonia	0.009233	0.009198	0.004651	0.00227	0.001895	0.007097
Granulicella	0.009887	0.006993	0.008061	0.00637	0.004789	0.010266
Dyella	0.023151	0.010301	0.008854	0.00055	0.002067	0.002549
Acinetobacter	0	6.89E-05	0.00472	0	0	0
Thermosporothrix	0.007235	0.005168	0.003032	0.00152	0.001068	0.039343
Niastella	0.008199	0.017673	0.007028	0.00072	0.000758	0.007924
Bacillus	0.004203	0.009198	0.012264	0.00158	0.00124	0.002446
Sorangium	0.006304	0.009371	0.010163	0.00396	0.005237	0.003583
Rhodanobacter	0.00472	0.011472	0.012264	0.00251	0.005099	0.010266
Terracidiphilus	0.011782	0.008578	0.001998	0.00296	0.004306	0.005822
Rhizobium	0.008785	0.008957	0.004823	0.0000689	0.000103	0.000482
Acidothermus	0.003411	0.002825	0.00248	0.00338	0.002997	0.003617
Nitrospira	0.002722	0.003514	0.002308	0.00882	0.0041	0.004892
Haliangium	0.006546	0.007269	0.012919	0.00286	0.004203	0.00217
Actinospica	0.00503	0.007304	0.003652	0.00055	0.000551	0.012781
Brevundimonas	0	0	3.45E-05	0	0	0
Lactococcus	0	0	0.074999	0	0	0
Asticcacaulis	0.004789	0.005512	0.004961	0.00024	0.00031	0.014504
Pseudarthrobacter	0.000103	0.000103	0.000551	0.0001	0.000138	0.000276
Achromobacter	3.45E-05	0.001378	0.000138	0.0000345	0	3.45E-05
Methylotenera	3.45E-05	0.000965	0.000379	0.00303	0.000586	0.000345
Aerococcus	0	0	6.89E-05	0	0	0
Heliimonas	0.000689	0.002343	0.000758	0	0.000103	0
Arthrobacter	3.45E-05	0	0	0.0001	0	3.45E-05
Pseudomonas	0	0.000103	0.017122	0	0	6.89E-05
Sphingomonas	0.027871	0.045544	0.036483	0.07166	0.043029	0.068178
Bryobacter	0.014917	0.018776	0.017191	0.02746	0.033899	0.035553
Mucilaginibacter	0.046681	0.067179	0.038516	0.02849	0.014538	0.029834
Burkholderia-Paraburkholderia	0.040996	0.058738	0.032728	0.03745	0.01378	0.03135
Massilia	0.133462	0.02949	0.042684	0.00593	0.007304	0.006167
Phenylobacterium	0.011748	0.01974	0.015365	0.01619	0.016502	0.020257
Acidibacter	0.01068	0.01347	0.012161	0.01433	0.016054	0.009439
Candidatus_Solibacter	0.005684	0.006615	0.005512	0.01233	0.017914	0.011024
Flavisolibacter	0.004479	0.009405	0.010301	0.0165	0.012161	0.010645
Gemmatimonas	0.004031	0.005512	0.007751	0.00444	0.004995	0.007235
Bradyrhizobium	0.005994	0.009508	0.012988	0.00847	0.00627	0.012919
Ralstonia	0.05047	0.01726	0.018879	0.00682	0.002825	0.003376
Granulicella	0.00565	0.007614	0.007062	0.00906	0.008303	0.009646
Dyella	0.007441	0.021566	0.008061	0.00706	0.001929	0.008854
Acinetobacter	3.45E-05	0	0	0	0	0
Thermosporothrix	0.006787	0.004961	0.006167	0.00768	0.004582	0.004651
Niastella	0.004272	0.007889	0.005684	0.01003	0.010542	0.007372
Bacillus	0.002205	0.002894	0.006511	0.00975	0.001447	0.003583
Sorangium	0.003514	0.003927	0.005719	0.0051	0.005478	0.003342
Rhodanobacter	0.007614	0.007062	0.008268	0.00634	0.004616	0.006201
Terracidiphilus	0.002377	0.008888	0.005133	0.0072	0.004306	0.00472
Rhizobium	0.003204	0.006098	0.008475	0.00183	0.001585	0.0041
Acidothermus	0.002997	0.002343	0.003927	0.00537	0.003238	0.00472
Nitrospira	0.001654	0.002067	0.002067	0.00668	0.006546	0.006959
Haliangium	0.003893	0.003652	0.00596	0.00479	0.006787	0.002584
Actinospica	0.001412	0.000861	0.003342	0.00641	0.003652	0.005684
Brevundimonas	0	0	0	0	0	0
Lactococcus	0	0	0	0	0	0
Asticcacaulis	0.001688	0.002653	0.003686	0.00296	0.001344	0.003927
Pseudarthrobacter	0.017294	0.005409	0.011128	0.00045	0.000207	0.000172
Achromobacter	6.89E-05	0.000207	0.000138	0.0000689	0	0.000138
Methylotenera	0.004892	0.004341	0.019396	0.0000689	6.89E-05	3.45E-05
Aerococcus	0	0	0	0	0	0
Heliimonas	0.016433	0.005374	0.00093	0.00034	0.000172	0.000379
Arthrobacter	0.016709	0.002859	0.004375	0.0000689	6.89E-05	0
Pseudomonas	0	0	0.000103	0.0001	0	0

Supplementary Table 1

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对比样本信息	Adonis分析		ANOSIM分析
对比样本信息	R²	P-value	Statistic	P-value
BX_16FBS vs. BD_16FBS	0.487	0.1	1	0.098
BX_16FSRH vs. BD_16FSRH	0.291	0.2	0.2593	0.186
BX_16FBRH vs. BD_16FBRH	0.512	0.1	1	0.098
BX_16FWRH vs. BD_16FWRH	0.327	0.1	0.4815	0.098
BX_16FBS vs. BX_16FSRH	0.231	0.2	0.037	0.4
BX_16FBS vs. BX_16FBRH	0.580	0.1	1	0.098
BX_16FBS vs. BX_16FWRH	0.584	0.1	1	0.098
BX_16FSRH vs. BX_16FBRH	0.680	0.1	1	0.098
BX_16FSRH vs. BX_16FWRH	0.718	0.1	1	0.098
BX_16FBRH vs. BX_16FWRH	0.488	0.1	0.8148	0.098
BD_16FBS vs. BD_16FSRH	0.479	0.1	0.6296	0.098
BD_16FBS vs. BD_16FBRH	0.556	0.1	1	0.098
BD_16FBS vs. BD_16FWRH	0.603	0.1	1	0.098
BD_16FSRH vs. BD_16FBRH	0.447	0.1	0.9259	0.098
BD_16FSRH vs. BD_16FWRH	0.620	0.1	1	0.098
BD_16FBRH vs. BD_16FWRH	0.373	0.1	0.5926	0.098

COG #	BX_16FBS	BD_16FBS	BX_16FSRH	BD_16FSRH	BX_16FBRH	BD_16FBRH	BX_16FWRH	BD_16FWRH	描述
COG0347	25713	17226	24360	21215	18905	20106	22367	20821	氮调节蛋白P-II
	22495	19480	25742	24097	21382	22359	21680	20935
	21566	15366	24226	23440	19788	21784	21537	20783
COG1348	2601	2259	2034	2311	1925	2744	4363	3265	参与固氮过程中的关键酶反应
	4592	2250	2263	2079	2724	2609	3280	3692
	2323	2362	2828	2047	2841	2845	4484	3643
COG1433	2101	1652	2160	1511	1037	1977	1515	1704	二氮酶铁钼辅因子生物合成蛋白
	2290	1246	2080	2330	1211	2081	1301	1584
	1915	1048	1943	2114	1508	1864	1343	1970
COG2710	7747	6738	6558	6756	6622	8012	15425	10254	固氮酶
	12624	6483	7108	6558	8883	8205	11132	11770
	7342	7092	7938	6503	8734	8086	15733	10877
COG3870	2011	1483	1766	1322	547	1221	717	911	来自氮调节蛋白P-II的蛋白质
	1285	1245	1779	2107	675	1327	769	727
	1488	1421	1553	1967	726	1339	701	776
COG4656	2338	2037	2173	1998	1798	2088	1615	1589	固氮所需
	2161	1974	2105	1788	1831	2003	1919	1697
	2030	1701	2229	1797	1930	1996	1610	2008
COG5420	164	229	140	218	380	340	379	542	固氮
	221	170	159	128	426	273	289	500
	236	155	184	125	609	397	367	653
COG5456	253	534	305	508	738	909	1101	1418	固氮蛋白FixH
	283	658	430	273	934	758	1045	1416
	707	1229	362	280	1175	931	917	2132
COG5554	156	192	135	206	373	364	421	593	固氮蛋白
	211	158	162	129	440	273	340	557
	257	146	175	121	609	411	374	709

Bacterial composition, function and the enrichment of plant growth promoting rhizobacteria (PGPR) in differential rhizosphere compartments of Al-tolerant soybean in acidic soil

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门	种	BX_ 16FBS	BD_ 16FBS	BX_ 16FSRH	BD_ 16FSRH	BX_ 16FBRH	BD_ 16FBRH	BX_ 16FWRH	BD_ 16FWRH
Proteobacteria	Bradyrhizobium elkanii	0.004479	0.005202	0.004444	0.00565	0.005994	0.00844	0.009164	0.01695
		0.002549	0.004582	0.003583	0.003583	0.009508	0.00627	0.005788	0.015985
		0.006856	0.004926	0.004685	0.003032	0.012988	0.012919	0.009439	0.020912
Proteobacteria	Acinetobacter johnsonii	0	0.008957	0	0.00565	3.45E-05	0	0	0
		0	0.043752	0	0	0	0	0	0
		0	0.10349	0	0	0	0	0	0.002963
Proteobacteria	Brevundimonas diminuta	0	0.003824	0	0.003032	0	0	0	0
		0	0.019844	0	0	0	0	0	0
		0	0.051021	0	0	0	0	0	3.45E-05
Proteobacteria	Pseudomonas fragi	0	0.000276	0	0.000138	0	0	3.45E-05	0
		0	0.000551	0	0	0	0	0	6.89E-05
		0	0	0	0	0.000103	0	0	0.01006
Proteobacteria	Rhizobium radiobacter	0	0.004065	0	0.00248	0.000207	0.000172	0.000517	0.000241
		0	0.012333	0	3.45E-05	6.89E-05	0	6.89E-05	0.000965
		3.45E-05	0.028215	0	0	0.001034	0.000138	0.00062	0.000241
Actinobacteria	Pseudarthrobacter oxydans	0.000103	0.007441	0.000172	0.003376	0.017294	0.000448	0.000103	0.000103
		0.000138	0.004547	0.000103	0.000138	0.005409	0.000207	0.000103	0.000103
		0.000276	0.004134	0.000138	6.89E-05	0.011128	0.000172	6.89E-05	0.000551
Actinobacteria	Arthrobacter methylotrophus	0.000103	0.000448	3.45E-05	0.000517	0.01664	6.89E-05	6.89E-05	3.45E-05
		0	0.000517	0.000103	0	0.002859	6.89E-05	0	0
		3.45E-05	6.89E-05	0	3.45E-05	0.004341	0	3.45E-05	0
Firmicutes	Aerococcus viridans	0	0.002825	0	0.002308	0	0	0	0
		0	0.010783	0	0	0	0	0	0
		0	0.027492	0	0	0	0	0	6.89E-05