玫瑰红球菌NB1对玉米的耐盐促生效应及其全基因组研究

doi:10.13560/j.cnki.biotech.bull.1985.2024-0503

摘要/Abstract

摘要：

【目的】对玫瑰红球菌NB1菌株进行耐盐、促生特性研究，分析其全基因组信息，并挖掘NB1菌株的耐盐促生基因。【方法】利用形态学观察和16S rRNA基因序列分析对NB1菌株进行鉴定。利用固氮菌改良阿须贝氏培养基、Pikovaskaia's培养基、DF液体培养基和ADF液体培养基对NB1菌株的固氮、溶磷以及产ACC脱氨酶能力进行鉴定。将NB1菌株分别接种至盐浓度为0%、5%、10%、15%的NB固体培养基上，培养48 h后确定菌株的可耐受浓度。将经NB1菌株处理和未处理的玉米种子分别接种至1/2 MS培养基上，连续培养15 d后测定其株高、根长、鲜重与根重。以盆栽试验的形式，在同一盐浓度胁迫下，分别测量施加NB1菌液和未处理的玉米幼苗的生长指标。利用Illumina二代测序和PacBio三代测序对NB1菌株进行全基因分析。【结果】NB1菌株鉴定为玫瑰红球菌Rhodococcus rhodochrous，能产生ACC脱氨酶，具有固氮、溶磷等能力，可耐受5%的盐浓度，无土培养条件下，经NB1菌株处理后的玉米幼苗其株高、根长、鲜重和根重均显著增加，盆栽种植后，施加NB1菌液的玉米幼苗株高、鲜重显著高于CK。NB1菌株共编码基因5 259个，编码基因总长度5 230 674 bp，平均GC含量为68.30%。在NR、Pfam、COG、Swiss-Prot、GO、KEGG数据库分别注释到基因5 235、4 379、4 195、3 758、3 263个、2 449个。NB1菌株中有178个基因编码的蛋白质结构属于CAZy家族，内含几丁质酶、蔗糖酶等酶的基因。同时，预测NB1菌株中有14个次级代谢产物基因簇、457个毒力因子、324个耐药基因，且从NB1基因组内发现具有耐盐、促生特性的四氢嘧啶、四环素类抗生素等相关基因。【结论】玫瑰红球菌NB1具有耐盐促生特性，对玉米有一定的促生效果，为植物耐盐促生菌剂提供了新的菌种资源。

关键词: Rhodococcus rhodochrous, 全基因组, 玉米, 耐盐碱, 促生作用

Abstract:

【Objective】To study the salt tolerance and growth-promoting characteristics of Rhodococcus rhodochrous NB1, analyze its whole genome information, and explore the salt tolerance promoting genes of NB1 strains.【Method】NB1 strain were identified using morphological observations and 16S rRNA gene sequence analysis. The nitrogen fixation, phosphorus lysis and ACC deaminase production were identified by modified medium, Pikovaskaia's medium, DF liquid medium and ADF liquid medium. The NB1 strain was inoculated to NB solid concentrations of 0, 5%, 10% and 15% on the trophic base, the tolerable concentration of the strain was determined after 48 h of incubation. Maize seeds treated with and without the NB1 strain were inoculated onto 1/2 MS medium, and the plant height, root length, fresh weight and root weight were determined after 15 d of continuous culture. Growth indicators of maize seedlings watered and untreated with NB 1 broth were measured in the form of pot experiments under the same salt concentration stress. Whole gene analysis of NB1 strain was conducted using Illumina second generation sequencing and PacBio third generation sequencing. 【Result】The NB1 strain belongs to Rhodococcus rhodochrous, it may produce ACC deaminase, has the ability of fixing nitrogen and dissolving phosphorus, and may tolerate the salt concentration of 5%. Under soil-free culture conditions, the plant height, root length, fresh weight and root weight of maize seedlings treated with NB1 strain increased significantly. After pot planting, the plant height and fresh weight were significantly higher than that of CK. The NB1 strain has 5 259 coding genes, the total length of coding genes is 5 230 674 bp, and the average GC content is 68.30%. They are annotated to 5 235, 4 379, 4 195, 3 758, 3 263, and 2 449 genes in NR, Pfam, COG, Swiss-Prot, GO, and KEGG databases, respectively. The protein structures encoded from 178 genes in NB1 strain belongs to the CAZy family and containing genes of chitinase,sucrase and other enzymes.Meanwhile, it is predicted that there are 14 secondary metabolite gene clusters, 457 virulence factors and 324 resistance genes in NB 1 strains, and related genes such as tetrahydropyrimidine and tetracycline antibiotics with salt resistance and promoting properties were found from the NB1 genome. 【Conclusion】Rhodococcus rhodochrous NB1 has salt resistance and growth promoting effect on maize, which provides new strain resources for plant salt resistance.

Key words: Rhodococcus rhodochrous, whole genome, maize, growth-promoting effect, salt-alkali tolerance

殷子薇, 红雨. 玫瑰红球菌NB1对玉米的耐盐促生效应及其全基因组研究[J]. 生物技术通报, 2024, 40(12): 193-207.

YIN Zi-wei, HONG Yu. Study on the Effect of Rhodococcus rhodochrous NB1 on the Tolerance to Salt and Growth-promoting of Maize and Its Whole Genome[J]. Biotechnology Bulletin, 2024, 40(12): 193-207.

图/表 13

图1 NB1菌株基于16S rRNA基因的系统发育树

Fig. 1 A phylogenetic tree based on the 16S rRNA gene of the strain NB 1

图2 NB1菌株耐盐碱能力

Fig. 2 Tolerance of NB 1 strains to salinity

表1 NB1菌液对玉米幼苗生长的影响

Table 1 Effect of NB1 broth on the growth of maize seedlings

处理Treatment		株高Plant height/cm	根长Root length/cm	鲜重Fresh weight/g	根重Root weight/g
无土培养Soil-free culture	CK	7.21±1.33	6.21±1.25	1.50±0.13	0.40±0.07
无土培养Soil-free culture	NB1	10.45±1.12^**	11.76±1.13^**	1.72±0.16^*	0.52±0.07^*
盆栽实验Pot experiment	CK	24.97±0.96	15.98±2.38	4.33±0.59	2.14±0.32
盆栽实验Pot experiment	NB1	34.38±2.38^**	19.13±3.38	5.29±0.70^*	2.27±0.26

图3 NB1菌株对玉米幼苗生长的影响

Fig. 3 Effect of strain NB1 on the growth of maize seedlings

图4 基于NB1菌株基因组序列的系统发育树

Fig. 4 Phylogenetic tree based on the genome sequence of the strain NB1

图5 NB1菌株基因组图圈图的最外面一圈为基因组大小的标识；第二圈和第三圈为正链、负链上的CDS，不同的颜色表示CDS不同的COG的功能分类；第四圈为rRNA和tRNA；第五圈为GC含量，向外的红色部分表示该区域GC含量高于全基因组平均GC含量，峰值越高表示与平均GC含量差值越大，向内的蓝色部分表示该区域GC含量低于全基因组平均GC含量，峰值越高表示与平均GC含量差值越大；最内一圈为GC-Skew值，具体算法为G-C/G+C，可以辅助判断前导链和后滞链，一般前导链GC skew>0，后滞链GC skew<0，也可以辅助判断复制起点（累计偏移最小值）和终点（累计偏移最大值），尤其对环状基因组最为重要

Fig. 5 Genome map of strain NB1 The outermost circle of the circle diagram is the genome size logo. The second and third turns are the CDS on the positive and negative strand. Different colors indicate the functional classification of different COG in CDS. The fourth circle is for the rRNA and the tRNA. The fifth circle shows the GC content. The red portion outward indicates a higher GC content in this region than the genome-wide average GC content. A higher peak indicates a larger difference from the mean GC content. The inward blue part indicates that the GC content in this region is lower than the genome-wide average GC content. A higher peak indicates a greater difference from the mean GC content. The innermost lap is the GC-Skew value, the specific algorithm is G-C/G + C, may assist in the judgment of the leading and lagging strand. The general leading strand, GC skew> 0, the lagging strand GC skew <0, you may also help in judging the replication origin（cumulative offset minimum）and the endpoint（cumulative offset maximum）, especially most important for the circular genome

图6 NB1菌株基因功能注释数据库分布情况

Fig. 6 Distribution of gene functional annotation database in strain NB1 genome

图7 NB1菌株基因组COG数据库比对分析结果横坐标代表不同COG类型，纵坐标代表基因个数。具体每种COG类型的功能描述请见右侧图例

Fig. 7 Results of COG database alignment analysis of strain NB1 genome The abscissa indicates the different COG types, and the ordinate indicates the number of genes. Specific functional description of each COG type is provided in the legend on the right

图8 NB1菌株基因组GO数据库比对分析结果

Fig. 8 Results of GO database alignment analysis of strain NB1 genome

图9 NB1菌株基因组KEGG数据库比对分析结果

Fig. 9 Results of KEGG database alignment analysis of the strain NB1 genome

表2 NB1菌株次级代谢产物合成基因簇

Table 2 Secondary metabolite synthesis gene cluster of strain NB1

基因编号Cluster ID	位置Location	类型Type	登录号MIBiG accession	相似基因簇Similar gene cluster	相似度Similarity/%	基因数量Gene No.
Cluster1	Plasmid B	Butyrolactone	-	-	-	8
Cluster1	Chromosome	Terpene	BGC0001456	Isorenieratene	25	17
Cluster2		T1PKS	-	-	-	29
Cluster3		Betalactone	-	-	-	30
Cluster4		NAPAA	-	-	-	30
Cluster5		NRPS	BGC0000371	Heterobactin A / Heterobactin S2	36	40
Cluster6		NRPS	-	-	-	37
Cluster7		Ectoine	BGC0000853	Ectoine	75	8
Cluster8		Terpene	BGC0000269	SF2575	6	16
Cluster9		NRPS	BGC0000368	Streptobactin	11	43
Cluster10		NRPS	BGC0000893	Chloramphenicol	17	41
Cluster11		Terpene	BGC0000664	Isorenieratene	42	19
Cluster12		NRPS	-	-	-	39
Cluster13		NRPS	-	-	-	29

图10 NB1菌株毒力因子预测分析

Fig. 10 Prediction analysis of virulence factors in strain NB1

表3 NB1菌株耐药基因预测分析统计

Table 3 Statistics on prediction analysis of resistance genes in strain NB1

药物类别Drug class	基因数量Gene No.	药物类别Drug class	基因数量Gene No.
Disinfecting agents and antiseptics	57	Polyamine antibiotic	6
Tetracycline antibiotic	51	Elfamycin antibiotic	5
Macrolide antibiotic	42	Pleuromutilin antibiotic	4
Fluoroquinolone antibiotic	31	Streptogramin antibiotic	4
Peptide antibiotic	30	Fusidane antibiotic	3
Penam	24	Sulfonamide antibiotic	3
Cephalosporin	22	Thioamide antibiotic	3
Rifamycin antibiotic	22	Diaminopyrimidine antibiotic	3
Phenicol antibiotic	21	Penem	3
Aminoglycoside antibiotic	20	Salicylic acid antibiotic	3
Phosphonic acid antibiotic	18	Nitroimidazole antibiotic	3
Glycopeptide antibiotic	16	Mupirocin-like antibiotic	3
Aminocoumarin antibiotic	15	Nucleoside antibiotic	2
Isoniazid-like antibiotic	13	Sulfone antibiotic	2
Carbapenem	13	Pyrazine antibiotic	2
Oxazolidinone antibiotic	13	Antibacterial free fatty acids	2
Cephamycin	10	Nitrofuran antibiotic	1
Glycylcycline	9	Streptogramin B antibiotic	1
Monobactam	7	Streptogramin A antibiotic	1
Lincosamide antibiotic	7	Nybomycin-like antibiotic	1

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