一株耐镉促生菌的筛选、鉴定及全基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-1193

摘要/Abstract

摘要：

目的从重金属污染土壤中筛选耐镉促生菌，评估其镉（Cd）耐受性与促生功能，为镉污染农田的微生物修复及植物促生菌肥开发提供菌种资源。方法以河南省新乡市卫辉市污染土壤为样本，通过含镉培养基分离获得菌株，分别采用火焰光度法、铬天青S（CAS）法和Salkowski比色法测定其解钾、产铁载体和产吲哚乙酸（IAA）能力。对优势菌株进行形态学、生理生化及16S rDNA鉴定，并结合全基因组测序，通过生物信息学方法进行基因组装、功能注释以及耐镉与促生相关基因的挖掘。通过小麦和玉米籽粒发芽实验，分析镉胁迫下菌株对发芽率、芽长和根长的影响。结果共分离到8株耐镉菌，其中菌株F2镉耐受性最强，经鉴定为高地芽胞杆菌（Bacillus altitudinis）。该菌株在Cd²⁺浓度为50 mg/L的LB培养基中培养72 h后，镉去除率为27.59%，产IAA量为31.72 μg/mL，解钾量为23.10 mg/L，铁载体相对产量为65.30%。全基因组测序显示，其染色体大小为3 718 742 bp，GC含量为41.34%，共预测到3 726个编码基因，并含有79个tRNA和24个rRNA。功能注释表明，该菌株携带多个与重金属耐受和植物促生相关的基因。在镉胁迫条件下，菌株F2可显著提高小麦和玉米籽粒的发芽率、芽长和根长。结论高地芽胞杆菌F2是一株具有多重促生功能的耐镉菌，全基因组分析揭示其耐镉与促生的遗传基础，该菌株在镉胁迫下对作物种子萌发和生长有显著促进作用，展现出作为微生物肥料的良好应用潜力。

关键词: 耐镉细菌, 镉去除率, 促生, 全基因组分析, 高地芽胞杆菌, 环境微生物

Abstract:

Objective This study aimed to isolate cadmium-tolerant plant growth-promoting bacteria from heavy metal-contaminated soil, evaluate their cadmium resistance and growth-promoting functions, and provide microbial resources for the bioremediation of cadmium-polluted farmland and the development of plant growth-promoting biofertilizers. Method Soil samples from Weihui county, Xinxiang city, Henan province were used to isolate strains using a cadmium-containing medium. Potassium solubilization, siderophore production, and indole-3-acetic acid (IAA) production were determined by flame photometry, chrome azurol S (CAS) assay, and the Salkowski colorimetric method, respectively. Dominant strains were further identified through morphological, physiological, biochemical, and 16S rDNA sequencing analyses, and whole-genome sequencing was performed. Bioinformatics tools were used for genome assembly, functional annotation, and mining of genes related to cadmium resistance and plant growth promotion. Wheat and maize seed germination experiments were conducted to analyze the effects of bacterial strains on germination rate, shoot length, and root length under cadmium stress. Result Eight cadmium-tolerant strains were isolated. Strain F2 showed the strongest tolerance to cadmium and was identified as Bacillus altitudinis. After 72 h of culture in LB medium with 50 mg/L Cd²⁺, strain F2 demonstrated a cadmium removal rate of 27.59%, produced 31.72 μg/mL IAA, released 23.10 mg/L soluble potassium, and showed siderophore production with a relative activity of 65.30%. Whole-genome sequencing revealed a chromosome size of 3 718 742 bp, a GC content of 41.34%, and 3 726 predicted genes, along with 79 tRNA and 24 rRNA genes. Functional annotation indicated that the strain carried multiple genes associated with heavy metal tolerance and plant growth promotion. Under cadmium stress, strain F2 significantly increased the germination rate, shoot length, and root length of wheat and maize seeds. Conclusion Bacillus altitudinis F2 is a cadmium-tolerant strain with multiple plant growth-promoting traits. Whole-genome analysis reveals the genetic basis for its cadmium resistance and growth-promoting capabilities. The strain significantly enhances seed germination and seedling growth under cadmium stress, demonstrating its potential for use as a microbial fertilizer.

Key words: cadmium-tolerant bacteria, cadmium removal rate, growth promotion, whole-genome analysis, Bacillus altitudinis, environmental microorganisms

郭家鑫, 王梦霞, 马耀武, 张麒宇, 张振宇, 柳海涛, 裴久渤, 姜瑛. 一株耐镉促生菌的筛选、鉴定及全基因组分析[J]. 生物技术通报, 2026, 42(7): 257-268.

GUO Jia-xin, WANG Meng-xia, MA Yao-wu, ZHANG Qi-yu, ZHANG Zhen-yu, LIU Hai-tao, PEI Jiu-bo, JIANG Ying. Screening， Identification， and Whole-genome Analysis of a Cadmium-tolerant Plant Growth-promoting Bacterium[J]. Biotechnology Bulletin, 2026, 42(7): 257-268.

图/表 11

参考文献 35

[1]	Xia F, Zhao ZF, Niu X, et al. Integrated pollution analysis, pollution area identification and source apportionment of heavy metal contamination in agricultural soil [J]. J Hazard Mater, 2024, 465: 133215.
[2]	Chen RH, Zhang QR, Chen HY, et al. Source apportionment of heavy metals in sediments and soils in an interconnected river-soil system based on a composite fingerprint screening approach [J]. J Hazard Mater, 2021, 411: 125125.
[3]	中华人民共和国农业部. 关于印发《到2020年化肥使用量零增长行动方案》和《到2020年农药使用量零增长行动方案》的通知 [Z]. 北京: 中华人民共和国农业部. (2015-02-17)[2025-12-27].
	Ministry of agriculture of the People’s Republic of China. Notice on issuing the action plan for zero growth in chemical fertilizer use by 2020 and the action plan for zero growth in pesticide Use by 2020 [Z]. Beijing: ministry of agriculture of the People’s Republic of China. (2015-02-17)[2025-12-27].
[4]	Satarug S, Garrett SH, Sens MA, et al. Cadmium, environmental exposure, and health outcomes [J]. Environ Health Perspect, 2010, 118(2): 182-190.
[5]	Nordberg GF. Historical perspectives on cadmium toxicology [J]. Toxicol Appl Pharmacol, 2009, 238(3): 192-200.
[6]	环境保护部, 国土资源部. 全国土壤污染状况调查公报 [R]. 北京: 环境保护部, 国土资源部. (2014-04-17)[2026-01-05].
	Ministry of environmental protection, Ministry of land and resources. Report on the national general survey of soil contamination [R]. Beijing: Ministry of environmental protection, Ministry of land and resources. (2014-04-17)[2026-01-05].
[7]	Yuan XH, Xue ND, Han ZG. A meta-analysis of heavy metals pollution in farmland and urban soils in China over the past 20 years [J]. J Environ Sci, 2021, 101: 217-226.
[8]	Huang FY, Chen L, Yang X, et al. Unveiling the impacts of microplastics on cadmium transfer in the soil-plant-human system: a review [J]. J Hazard Mater, 2024, 477: 135221.
[9]	Lewis AE. Review of metal sulphide precipitation [J]. Hydrometallurgy, 2010, 104(2): 222-234.
[10]	王泓博, 苟文贤, 吴玉清, 等. 重金属污染土壤修复研究进展: 原理与技术 [J]. 生态学杂志, 2021, 40(8): 2277-2288.
	Wang HB, Gou WX, Wu YQ, et al. Progress in remediation technologies of heavy metals contaminated soil: Principles and technologies [J]. Chin J Ecol, 2021, 40(8): 2277-2288.
[11]	徐文婷, 陈国梁, 屈志慧, 等. 微生物在镉污染土壤修复中的应用及其作用机理 [J]. 生物工程学报, 2023, 39(7): 2612-2623.
	Xu WT, Chen GL, Qu ZH, et al. Microbial remediation of cadmium-contaminated soils and its mechanisms: a review [J]. Chin J Biotechnol, 2023, 39(7): 2612-2623.
[12]	Priyadarshanee M, Das S. Biosorption and removal of toxic heavy metals by metal tolerating bacteria for bioremediation of metal contamination: a comprehensive review [J]. J Environ Chem Eng, 2021, 9(1): 104686.
[13]	Bravo D, Braissant O. Cadmium-tolerant bacteria: current trends and applications in agriculture [J]. Lett Appl Microbiol, 2022, 74(3): 311-333.
[14]	Hou J, Liu MQ, Li Y, et al. Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice [J]. Environ Int, 2025, 204: 109840.
[15]	Guzmán-Moreno J, García-Ortega LF, Torres-Saucedo L, et al. Bacillus megaterium HgT21: a promising metal multiresistant plant growth-promoting bacteria for soil biorestoration [J]. Microbiol Spectr, 2022, 10(5)
[16]	Ankati S, Podile AR. Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner [J]. J Plant Physiol, 2019, 243: 153057.
[17]	王亚, 冯发运, 葛静, 等. 植物根系分泌物对土壤污染修复的作用及影响机理 [J]. 生态学报, 2022, 42(3): 829-842.
	Wang Y, Feng FY, Ge J, et al. Effects and mechanisms of plant root exudates on soil remediation [J]. Acta Ecol Sin, 2022, 42(3): 829-842.
[18]	Guo JK, Muhammad H, Lv X, et al. Prospects and applications of plant growth promoting rhizobacteria to mitigate soil metal contamination: a review [J]. Chemosphere, 2020, 246: 125823.
[19]	唐飞, 陈亚刚, 龙新宪. 金属抗性促生菌对玉米的生长和累积镉的影响 [J]. 农业环境科学学报, 2013, 32(10): 1941-1949.
	Tang F, Chen YG, Long XX. Effects of metal-resistant plant growth promoting bacteria on growth and cadmium accumulation of corn [J]. J Agro Environ Sci, 2013, 32(10): 1941-1949.
[20]	Vazquez A, Zawoznik M, Benavides MP, et al. Azospirillum brasilense Az39 restricts cadmium entrance into wheat plants and mitigates cadmium stress [J]. Plant Sci, 2021, 312: 111056.
[21]	Wang YJ, Zheng XY, He XS, et al. Effects of Pseudomonas TCd-1 on rice (Oryza sativa) cadmium uptake, rhizosphere soils enzyme activities and cadmium bioavailability under cadmium contamination [J]. Ecotoxicol Environ Saf, 2021, 218: 112249.
[22]	Guo JK, Chi J. Effect of Cd-tolerant plant growth-promoting Rhizobium on plant growth and Cd uptake by Lolium multiflorum Lam. and Glycine max (L.) Merr. in Cd-contaminated soil [J]. Plant Soil, 2014, 375(1): 205-214.
[23]	陈素素. 产脲酶菌修复典型矿冶园区周边农田土壤镉、铅污染研究 [D]. 北京: 北京有色金属研究总院, 2022.
	Chen SS. Study on the remediation of Cd-Pb contaminated farmland soil by urease-producing bacteria in typical mining and metallurgy parks [D]. Beijing: General Research Institute for Nonferrous Metals, 2022.
[24]	王鑫. 产碱菌Bacillus XT-4的筛选、鉴定及阻控蔬菜镉积累效应的研究 [D]. 南京: 南京农业大学, 2019.
	Wang X. Study on isolation and identification of an alkaline-producing Bacillus XT-4 and its effect on cadmium accumulation by vegetables [D]. Nanjing: Nanjing Agricultural University, 2019.
[25]	布坎南. 伯杰细菌鉴定手册第八版 [M]. 8版. 北京: 科学出版社, 1984.
	Buchanan RE. Bergey’s manual of determinative bacteriology [M]. 8th ed. Beijing: Science Press, 1984.
[26]	Yin DX, Niu LL, Liu J, et al. Cadmium-resistant bacterium Ralstonia sp. YDR alleviated Cd toxicity in rice seedlings by enhancing antioxidant defense and inhibiting Cd²⁺ influx and H⁺ efflux [J]. Environ Technol Innov, 2024, 34: 103614.
[27]	Schober I, Koblitz J, Sardà Carbasse J, et al. BacDive in 2025: the core database for prokaryotic strain data [J]. Nucleic Acids Res, 2025, 53(D1): D748-D756.
[28]	李卓阳, 曹苗苗, 周登博, 等. 高耐镉细菌Burkholderia sp. DF3-1对镉的吸附特性及机理 [J]. 热带作物学报, 2022, 43(3): 589-596.
	Li ZY, Cao MM, Zhou DB, et al. Adsorption characteristics and mechanism of high cadmium-tolerant bacteria Burkholderia sp. DF3-1 to cadmium [J]. Chin J Trop Crops, 2022, 43(3): 589-596.
[29]	Abdollahi S, Golchin A, Shahryari F. Lead and cadmium-resistant bacterial species isolated from heavy metal-contaminated soils show plant growth-promoting traits [J]. Int Microbiol, 2020, 23(4): 625-640.
[30]	Cho I, Lee SY, Cho KS. Enhancement of the germination and growth of Panicum miliaceum and Brassica juncea in Cd- and Zn-contaminated soil inoculated with heavy-metal-tolerant Leifsonia sp. ZP3 [J]. World J Microbiol Biotechnol, 2024, 40(8): 245.
[31]	谢伟霞, 朱梦可, 范瑞娟, 等. 抗镉菌株的吸附特性及抗镉机制 [J]. 农业环境科学学报, 2024, 43(12): 2889-2900.
	Xie WX, Zhu MK, Fan RJ, et al. Cadmium adsorption characteristics and mechanisms of cadmium-resistant strains [J]. J Agro Environ Sci, 2024, 43(12): 2889-2900.
[32]	唐敏, 李荣萍, 梅娟, 等. 高地芽孢杆菌的分离鉴定及对稻瘟病的防控机制 [J]. 微生物学通报, 2026, 53(2): 1024-1039.
	Tang M, Li RP, Mei J, et al. Screening and identification of Bacillus altitudinis and revealing of its biocontrol mechanism against rice blast (Magnaporthe oryzae) [J]. Microbiol China, 2026, 53(2): 1024-1039.
[33]	高强, 王丽丽, 张渐隆, 等. 高地芽孢杆菌CY1的分离鉴定及其对烟草黑胫病的防治作用 [J]. 浙江农业学报, 2025, 37(2): 405-416.
	Gao Q, Wang LL, Zhang JL, et al. Screening and identification of Bacillus altitudinis strain CY1 and its control effects against tobacco black shank [J]. Acta Agric Zhejiangensis, 2025, 37(2): 405-416.
[34]	Shan YJ, Wang D, Zhao FH, et al. Insights into the biocontrol and plant growth promotion functions of Bacillus altitudinis strain KRS010 against Verticillium dahliae [J]. BMC Biol, 2024, 22(1): 116.
[35]	Khan M, Kamran M, Kadi RH, et al. Harnessing the potential of Bacillus altitudinis MT422188 for copper bioremediation [J]. Front Microbiol, 2022, 13: 878000.

菌株 Strains	Cd²⁺浓度 Cd²⁺ concentration （mg/L）
菌株 Strains	10	25	50	100	150	200
B2	+++	+++	++	+	-	-
D1	+++	++	+	-	-	-
D2	+++	++	++	+	-	-
D3	+++	++	+	-	-	-
F1	+++	++	++	+	-	-
F2	+++	+++	+++	++	+	-
F3	+++	+++	++	+	-	-
F31	+++	++	+	-	-	-

菌株 Strains	Cd²⁺浓度 Cd²⁺ concentration （mg/L）
菌株 Strains	10	25	50	100	150	200
B2	+++	+++	++	+	-	-
D1	+++	++	+	-	-	-
D2	+++	++	++	+	-	-
D3	+++	++	+	-	-	-
F1	+++	++	++	+	-	-
F2	+++	+++	+++	++	+	-
F3	+++	+++	++	+	-	-
F31	+++	++	+	-	-	-

项目 Item	F2	参比菌株B. altitudinis 41KF2B^［27］ Reference strain B. altitudinis 41KF2B
过氧化氢酶 Catalase	+	+
甲基红 Methyl red（MR）	-	-
VP实验 Voges-Proskauer test（VP test）	+	-
革兰氏染色 Gram staining	+	+
淀粉水解 Starch hydrolysis	-	+
明胶水解 Gelatin hydrolysis	+	+
硝酸盐还原 Nitrate reduction	+	-
ONPG试验 ONPG assay	+	+

项目 Item	F2	参比菌株B. altitudinis 41KF2B^［27］ Reference strain B. altitudinis 41KF2B
过氧化氢酶 Catalase	+	+
甲基红 Methyl red（MR）	-	-
VP实验 Voges-Proskauer test（VP test）	+	-
革兰氏染色 Gram staining	+	+
淀粉水解 Starch hydrolysis	-	+
明胶水解 Gelatin hydrolysis	+	+
硝酸盐还原 Nitrate reduction	+	-
ONPG试验 ONPG assay	+	+

特征 Features	染色体 Chromosome
Size （bp）	3 718 742
G+C content （%）	41.34
tRNA	79
rRNA	24
Total number of CDSs	3 726
CDSs with NR number assignments	3 722
CDSs with COG number assignments	3 026
CDSs with GO assignments	1 754
CDSs with KEGG pathway	2 781
CDSs with TCDB assignments	1 754