Article(id=1241357435911328309, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241357427292033288, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20230557, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1693324800000, receivedDateStr=2023-08-30, revisedDate=null, revisedDateStr=null, acceptedDate=1698249600000, acceptedDateStr=2023-10-26, onlineDate=1773892276027, onlineDateStr=2026-03-19, pubDate=1709481600000, pubDateStr=2024-03-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1773892276027, onlineIssueDateStr=2026-03-19, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1773892276027, creator=13701087609, updateTime=1773892276027, updator=13701087609, issue=Issue{id=1241357427292033288, tenantId=1146029695717560320, journalId=1192105938417971205, year='2024', volume='64', issue='3', pageStart='651', pageEnd='967', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=0, createTime=1773892273972, creator=13701087609, updateTime=1773892616576, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1241358864344478487, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241357427292033288, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1241358864344478488, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241357427292033288, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=854, endPage=868, ext={EN=ArticleExt(id=1241357436301398615, articleId=1241357435911328309, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Neorhizobium petrolearium OS53 combined with alfalfa (Medicago sativa L.) for remediation of petroleum-contaminated soil, columnId=1241045257748533520, journalTitle=Acta Microbiologica Sinica, columnName=Research Articles, runingTitle=null, highlight=null, articleAbstract=

[Objective] To explore the mechanism ofNeorhizobium petrolearium OS53 combined with alfalfa (Medicago sativa L.) in the remediation of petroleum-contaminated soil. [Methods] Illumina and Nanopore were employed to sequence the whole genome ofN.petrolearium OS53, and the complete genome map of the strain was constructed. Gene prediction and functional annotation were carried out to analyze the genes involved in nodulation and oil degradation. The abilities of strain OS53 to produce indole acetic acid (IAA), secrete siderophore, and solubilize phosphorus and potassium were tested. The activities of urease, dehydrogenase, polyphenol oxidase, and lipase in soil and the levels of chlorophyll, malondialdehyde, proline, soluble protein, soluble sugar, and superoxide dismutase in alfalfa were measured by kits. [Results] The genome of strain OS53 consisted of a circular chromosome of 5.56 Mb and two plasmids of 0.92 Mb and 0.38 Mb, respectively, with the G+C content of 60.2%. The genome encoded a total of 6 968 genes. The strain OS53 andN.petrolearium DSM 26482T showed the 16S rRNA gene sequence similarity of 99.86%, and formed stable branches on the phylogenetic tree, indicating that strain OS53 andN.petrolearium were the same species. Therefore, OS53 was named asN.petrolearium OS53. The strain OS53 had the ability to produce IAA, and the related genes were identified in the genome. After 120 days of remediation of the soil with the initial oil content of (4 403.30±222.10) mg/kg, OS53 and alfalfa showed the remediation efficiency up to 57.53%, which was 44.26%, 41.69%, and 8.84% higher than that of no inoculation of strain OS53, inoculation of OS53 only, and planting alfalfa only, respectively. In the combined remediation system, alfalfa showed elevated the levels of chlorophyll, soluble protein, and soluble sugar and lowered levels of malondialdehyde, proline, and superoxide dismutase, and the soil showed increased activities of polyphenol oxidase, dehydrogenase, lipase, and urease. [Conclusion] The strain OS53 had the ability to produce IAA to promote the growth of alfalfa in the petroleum-contaminated soil, which increased the activity of enzymes involved in oil degradation in the soil. Finally, the combined system improved the remediation efficiency of the soil.

, correspAuthors=Yingying JIANG, authorNote=null, correspAuthorsNote=
*JIANG Yingying, E-mail:
, copyrightStatement=Copyright ©2024 Acta Microbiologica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Xiaodong LIU, Tianfei YU, Zhenshan DENG, Xiaohong FAN, Wei ZHANG, Yu YANG, Ying HE, Jiamin AI, Yingying JIANG), CN=ArticleExt(id=1241357439111582402, articleId=1241357435911328309, tenantId=1146029695717560320, journalId=1192105938417971205, language=CN, title=Neorhizobium petrolearium OS53联合紫花苜蓿协同修复石油污染土壤研究, columnId=1192149544164012138, journalTitle=微生物学报, columnName=研究报告, runingTitle=null, highlight=null, articleAbstract=

【目的】探究Neorhizobium petrolearium OS53与紫花苜蓿协同修复石油污染土壤的机制。【方法】使用Illumina和Nanopore平台对菌株OS53进行全基因组测序,构建菌株基因组完成图,并进行基因预测及功能注释,分析其中与结瘤促生及石油降解相关基因,并通过实验测定菌株OS53产吲哚乙酸(indole acetic acid, IAA)、铁载体、溶磷和解钾等与促生相关的能力。使用试剂盒对联合修复前后土壤中土壤脲酶、脱氢酶、多酚氧化酶和脂肪酶活性及紫花苜蓿的叶绿素、丙二醛、脯氨酸、可溶性蛋白、可溶性糖和超氧化物歧化酶等生理指标进行测定。【结果】菌株OS53的基因组由一个5.56 Mb的环形染色体和2个大小分别为0.92 Mb和0.38 Mb的质粒组成,基因组G+C含量为60.2%,共编码6 968个基因。菌株OS53与N.petrolearium DSM 26482T的16S rRNA基因序列相似性最高,为99.86%,且在系统发育树上形成稳定分支,表明菌株OS53与N.petrolearium为同一种,因此将OS53命名为N.petrolearium OS53。试验结果表明,菌株OS53具有产IAA能力,并在其基因组中也发现相关基因。在初始石油含量为(4 403.30±222.10) mg/kg时,经过120 d修复,OS53与紫花苜蓿协同修复效率能够达到57.53%,比不接种OS53、仅接种OS53和仅种植苜蓿分别提高了44.26%、41.69%和8.84%。在联合修复体系中,紫花苜蓿叶绿素、可溶性蛋白和可溶性糖的含量有所提高,丙二醛和脯氨酸的含量以及超氧化物歧化酶的活性有所降低,同时土壤中多酚氧化酶、脱氢酶、脂肪酶和脲酶的活性都有所提高。【结论】菌株OS53具有产IAA的能力,并且能够促进紫花苜蓿在石油污染土壤中的生长,进而提高土壤中与石油降解相关部分酶活,最终提高联合修复体系对石油污染土壤的修复效果。

, correspAuthors=姜影影, authorNote=null, correspAuthorsNote=null, copyrightStatement=版权所有©《微生物学报》编辑部2024, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=Eb5a2a4LnzVLrE6JSM20LQ==, magXml=0BRiVyKh41QZ++o6jTPQJQ==, pdfUrl=null, pdf=6o0nWpwC9ydGi8JoJ3MKnA==, pdfFileSize=926017, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=iNWDp35Ev5vrJaS48Pl27w==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=c71+FvCOJHlgeGaW7/qKbA==, mapNumber=null, authorCompany=null, fund=null, authors=

#These authors contributed equally to this work.

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Mechanism and bacterial community analysis of petroleum hydrocarbon degradation by microorganism-halophyte model[D]. 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SP: Soil+Alfalfa treatment; S: Soil; OP: Soil+Petroleum+Alfalfa treatment; OPB: Soil+Alfalfa+OS53 treatment; O: Soil+Petroleum treatment; OB: Soil+OS53 treatment. I: The initial samples; E: The sample after 120 days of treatment., figureFileSmall=jSzbmWHxJYmA+fZnW6Ursg==, figureFileBig=+gPT/viOow56ZP0bPm2Z5A==, tableContent=null), ArticleFig(id=1241784845509132425, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=图1, caption=菌株OS53联合紫花苜蓿模拟修复石油污染土壤示意, figureFileSmall=jSzbmWHxJYmA+fZnW6Ursg==, figureFileBig=+gPT/viOow56ZP0bPm2Z5A==, tableContent=null), ArticleFig(id=1241784845861453962, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=EN, label=Figure 2, caption=Petroleum content in samples with different treatment methods. "I" stands for the initial sample number, and "E" stands for the sample after 120 days of treatment; The "*" in the plot represent the oil content in sample I and sample E in different treatment methods were significant differences at the levels ofP < 0.05 byt-test; The "ns" represents no significant difference between the oil content in sample I and sample E; The red lowercase letters in the diagram represent the enzyme activity of different treatment methods in the I samples was significant different atP < 0.05 level after one-way analysis of variance (one-way ANOVA); The blue uppercase letters in the diagram represent the enzyme activity of different treatment methods in the E samples was significant different atP < 0.05 level after one-way ANOVA., figureFileSmall=MZzVRIf44nrjcXeOOelkeQ==, figureFileBig=vwD9IyJ5TreK96P/nHMoHg==, tableContent=null), ArticleFig(id=1241784846092140683, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=图2, caption=不同处理方式样品中的石油含量, figureFileSmall=MZzVRIf44nrjcXeOOelkeQ==, figureFileBig=vwD9IyJ5TreK96P/nHMoHg==, tableContent=null), ArticleFig(id=1241784846436073612, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=EN, label=Figure 3, caption=The contents of chlorophyll, soluble protein, soluble sugar, MDA, proline (A–E) and the activities of SOD (F) of alfalfa in ESP, EOP and EOPB groups. The "*, **, and ***" in the figure represent the significant differences at the levels ofP < 0.05,P < 0.01, andP < 0.001 usingt-test under different treatment methods, respectively., figureFileSmall=7D2+6b8HfgVm/I4r8zT1Sw==, figureFileBig=SEUv4dqF6HjW88AjTzeiJA==, tableContent=null), ArticleFig(id=1241784846704509069, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=图3, caption=ESP、EOP和EOPB组中紫花苜蓿生理指标, figureFileSmall=7D2+6b8HfgVm/I4r8zT1Sw==, figureFileBig=SEUv4dqF6HjW88AjTzeiJA==, tableContent=null), ArticleFig(id=1241784846977138830, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=EN, label=Figure 4, caption=The polyphenol oxidase (A), lipase (B), dehydrogenase (C) and urease activities (D) in samples treated by different methods. "I" is the initial sample number; "E" is the sample after 120 days of treatment; "*" in the plot indicated that the enzyme activity in samples I and E in different treatment methods was significantly different at the levels ofP < 0.05 aftert-test; "ns" represents no significant difference between samples I and E. The red lowercase letters in the diagram represent the enzyme activity of different treatment methods in the I samples was significant different atP < 0.05 level after one-way ANOVA; The blue uppercase letters in the diagram represent the enzyme activity of different treatment methods in the E samples was significant different atP < 0.05 level after one-way ANOVA., figureFileSmall=AuF+MBE6OgnHaI2hKlfuew==, figureFileBig=GDMuU/pOp1N6WuX8lrEnSw==, tableContent=null), ArticleFig(id=1241784847262351503, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=图4, caption=不同处理方式样品中的酶活性, figureFileSmall=AuF+MBE6OgnHaI2hKlfuew==, figureFileBig=GDMuU/pOp1N6WuX8lrEnSw==, tableContent=null), ArticleFig(id=1241784847568535696, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=EN, label=Figure 5, caption=The mechanism of strain OS53 promoting the repair efficiency of the combined repair system., figureFileSmall=lDA6CtaKcRIZFMOmYTfJug==, figureFileBig=Q29VRURF0S5e35/NDF8V5w==, tableContent=null), ArticleFig(id=1241784849225285777, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=图5, caption=菌株OS53促进联合修复体系修复效率的机制, figureFileSmall=lDA6CtaKcRIZFMOmYTfJug==, figureFileBig=Q29VRURF0S5e35/NDF8V5w==, tableContent=null), ArticleFig(id=1241784849552441490, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=EN, label=Table 1, caption=

Statistics of genome components of strain OS53

, figureFileSmall=null, figureFileBig=null, tableContent=
Genome featuresValue
Genome size (bp)6 855 582
Gene number6 968
Gene total length (bp)6 100 863
Gene length/Genome (%)88.99
Gene density (per kb)1.02
23S rRNA3
5S rRNA3
16S rRNA3
tRNA52
), ArticleFig(id=1241784849967677587, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241357435911328309, language=CN, label=表1, caption=

菌株OS53基因组组分统计

, figureFileSmall=null, figureFileBig=null, tableContent=
Genome featuresValue
Genome size (bp)6 855 582
Gene number6 968
Gene total length (bp)6 100 863
Gene length/Genome (%)88.99
Gene density (per kb)1.02
23S rRNA3
5S rRNA3
16S rRNA3
tRNA52
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Neorhizobium petrolearium OS53联合紫花苜蓿协同修复石油污染土壤研究
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柳晓东 # , 余天飞 # , 邓振山 , 范晓虹 , 张薇 , 杨昱 , 何颖 , 艾加敏 , 姜影影 *
微生物学报 | 研究报告 2024,64(3): 854-868
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微生物学报 | 研究报告 2024, 64(3): 854-868
Neorhizobium petrolearium OS53联合紫花苜蓿协同修复石油污染土壤研究
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柳晓东#, 余天飞#, 邓振山, 范晓虹, 张薇, 杨昱, 何颖, 艾加敏, 姜影影*
作者信息
  • 延安大学生命科学学院, 陕西 延安 716000
Neorhizobium petrolearium OS53 combined with alfalfa (Medicago sativa L.) for remediation of petroleum-contaminated soil
Xiaodong LIU, Tianfei YU, Zhenshan DENG, Xiaohong FAN, Wei ZHANG, Yu YANG, Ying HE, Jiamin AI, Yingying JIANG*
Affiliations
  • College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
出版时间: 2024-03-04 doi: 10.13343/j.cnki.wsxb.20230557
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【目的】探究Neorhizobium petrolearium OS53与紫花苜蓿协同修复石油污染土壤的机制。【方法】使用Illumina和Nanopore平台对菌株OS53进行全基因组测序,构建菌株基因组完成图,并进行基因预测及功能注释,分析其中与结瘤促生及石油降解相关基因,并通过实验测定菌株OS53产吲哚乙酸(indole acetic acid, IAA)、铁载体、溶磷和解钾等与促生相关的能力。使用试剂盒对联合修复前后土壤中土壤脲酶、脱氢酶、多酚氧化酶和脂肪酶活性及紫花苜蓿的叶绿素、丙二醛、脯氨酸、可溶性蛋白、可溶性糖和超氧化物歧化酶等生理指标进行测定。【结果】菌株OS53的基因组由一个5.56 Mb的环形染色体和2个大小分别为0.92 Mb和0.38 Mb的质粒组成,基因组G+C含量为60.2%,共编码6 968个基因。菌株OS53与N.petrolearium DSM 26482T的16S rRNA基因序列相似性最高,为99.86%,且在系统发育树上形成稳定分支,表明菌株OS53与N.petrolearium为同一种,因此将OS53命名为N.petrolearium OS53。试验结果表明,菌株OS53具有产IAA能力,并在其基因组中也发现相关基因。在初始石油含量为(4 403.30±222.10) mg/kg时,经过120 d修复,OS53与紫花苜蓿协同修复效率能够达到57.53%,比不接种OS53、仅接种OS53和仅种植苜蓿分别提高了44.26%、41.69%和8.84%。在联合修复体系中,紫花苜蓿叶绿素、可溶性蛋白和可溶性糖的含量有所提高,丙二醛和脯氨酸的含量以及超氧化物歧化酶的活性有所降低,同时土壤中多酚氧化酶、脱氢酶、脂肪酶和脲酶的活性都有所提高。【结论】菌株OS53具有产IAA的能力,并且能够促进紫花苜蓿在石油污染土壤中的生长,进而提高土壤中与石油降解相关部分酶活,最终提高联合修复体系对石油污染土壤的修复效果。

Neorhizobium petrolearium  /  全基因组测序  /  紫花苜蓿  /  石油  /  联合修复

[Objective] To explore the mechanism ofNeorhizobium petrolearium OS53 combined with alfalfa (Medicago sativa L.) in the remediation of petroleum-contaminated soil. [Methods] Illumina and Nanopore were employed to sequence the whole genome ofN.petrolearium OS53, and the complete genome map of the strain was constructed. Gene prediction and functional annotation were carried out to analyze the genes involved in nodulation and oil degradation. The abilities of strain OS53 to produce indole acetic acid (IAA), secrete siderophore, and solubilize phosphorus and potassium were tested. The activities of urease, dehydrogenase, polyphenol oxidase, and lipase in soil and the levels of chlorophyll, malondialdehyde, proline, soluble protein, soluble sugar, and superoxide dismutase in alfalfa were measured by kits. [Results] The genome of strain OS53 consisted of a circular chromosome of 5.56 Mb and two plasmids of 0.92 Mb and 0.38 Mb, respectively, with the G+C content of 60.2%. The genome encoded a total of 6 968 genes. The strain OS53 andN.petrolearium DSM 26482T showed the 16S rRNA gene sequence similarity of 99.86%, and formed stable branches on the phylogenetic tree, indicating that strain OS53 andN.petrolearium were the same species. Therefore, OS53 was named asN.petrolearium OS53. The strain OS53 had the ability to produce IAA, and the related genes were identified in the genome. After 120 days of remediation of the soil with the initial oil content of (4 403.30±222.10) mg/kg, OS53 and alfalfa showed the remediation efficiency up to 57.53%, which was 44.26%, 41.69%, and 8.84% higher than that of no inoculation of strain OS53, inoculation of OS53 only, and planting alfalfa only, respectively. In the combined remediation system, alfalfa showed elevated the levels of chlorophyll, soluble protein, and soluble sugar and lowered levels of malondialdehyde, proline, and superoxide dismutase, and the soil showed increased activities of polyphenol oxidase, dehydrogenase, lipase, and urease. [Conclusion] The strain OS53 had the ability to produce IAA to promote the growth of alfalfa in the petroleum-contaminated soil, which increased the activity of enzymes involved in oil degradation in the soil. Finally, the combined system improved the remediation efficiency of the soil.

Neorhizobium petrolearium  /  whole genome sequencing  /  Medicago sativa L.  /  petroleum  /  combined system for remediation
柳晓东, 余天飞, 邓振山, 范晓虹, 张薇, 杨昱, 何颖, 艾加敏, 姜影影. Neorhizobium petrolearium OS53联合紫花苜蓿协同修复石油污染土壤研究. 微生物学报, 2024 , 64 (3) : 854 -868 . DOI: 10.13343/j.cnki.wsxb.20230557
Xiaodong LIU, Tianfei YU, Zhenshan DENG, Xiaohong FAN, Wei ZHANG, Yu YANG, Ying HE, Jiamin AI, Yingying JIANG. Neorhizobium petrolearium OS53 combined with alfalfa (Medicago sativa L.) for remediation of petroleum-contaminated soil[J]. Acta Microbiologica Sinica, 2024 , 64 (3) : 854 -868 . DOI: 10.13343/j.cnki.wsxb.20230557
石油污染是全球范围内面临的主要环境问题之一。石油污染土壤后会对土壤的化学性质(例如pH、电导率和有机质含量)和肥力特性(例如氮、磷等)造成巨大影响,对植物产生毒害作用,并且石油中的部分组分也可以在农作物中积累,从而转移到陆地食物链中,最终对人类的健康造成严重威胁[1-3]。虽然传统的物理和化学修复方法,例如燃烧、土壤洗涤和淋洗、热解吸以及化学氧化法等,可以高效去除土壤中石油,但是在修复过程中土壤的景观和结构极易遭受破坏,造成二次污染,此外,还需要投入大量的人力和物力。上述缺陷极大地限制了物理、化学修复技术的应用情景[2-4]。因此具有经济环保、操作简便、适用范围广等特点的生物修复技术近年来受到广泛关注。
生物修复主要包括植物修复、微生物修复及联合修复,此外一些原生动物、藻类等也在某些生境中发挥重要作用。许多研究表明,植物修复是降低土壤中有害污染物含量和毒性最为有效且经济的方法[5-7]。植物根系与土壤的巨大接触面积能够有效增加功能菌与土壤污染物接触面积,同时根系分泌物也能够促进功能菌的代谢活动,加快污染物降解,此外许多植物也能够通过植物积累、植物稳定、植物降解等来修复石油污染[8-9]。大多数石油碳氢化合物的疏水性可能会降低植物养分的可利用度,因此养分缺乏已被认为是限制石油污染土壤植物修复技术发展的主要因素之一[10-11]。豆科植物不仅可以与根瘤菌通过共生固氮以促进自身在氮素贫瘠土壤中的生长,而且共生体系也能够有效改良土壤生态,为功能微生物的代谢提供良好的环境条件。此外,也有许多根瘤菌由于共生基因的丢失,丧失了共生固氮能力,但是其可以通过产生吲哚乙酸(indole acetic acid, IAA)等生长激素,促进植物生长。研究表明,根际促生菌(rhizosphere growth-promoting bacteria, PGPR)可以通过溶磷解钾、产生铁载体和植物激素等来改善植物营养状态[12],促进植物生长,增强植物对生物和非生物胁迫的耐受性[13-14],为植物在高浓度污染物环境中的生长提供支持。因此,基于植物-促生微生物联合修复策略修复体系要比单一体系更具优势[15-16]
紫花苜蓿(Medicago sativa L.)为多年生草本豆科植物,具有适应性强、耐贫瘠干旱等特点,并且根系发达,在黄土高原地区广泛分布,是修复有机污染物和重金属污染土壤常用植物[17-18]。同时,课题组在前期研究中,从陕北石油污染土壤中分离得到一株细菌,经16S rRNA基因序列比对分析,其与Neorhizobium petrolearium DSM 26482T的相似性最高为99.86%。N.petrolearium DSM 26482T为从石油污染土壤中分离得到的一株具有多环芳烃降解能力的菌株,并且其可以与紫花苜蓿共生结瘤[19]。通过石油降解试验及共生结瘤试验发现,菌株OS53不能够降解石油,并且也不能够与紫花苜蓿形成共生根瘤。但是菌株OS53与紫花苜蓿在联合修复石油污染土壤中表现出较高的修复效率,因此为了探究联合修复机制,对菌株OS53进行全基因组测序,构建菌株OS53基因组完成图,对可编码的基因进行功能注释,探究该菌株基因组中与石油降解及结瘤相关基因分布。同时也对联合修复体系修复前后土壤中多酚氧化酶(soil polyphenol oxidase, S-PPO)、脱氢酶(soil dehydrogenase, S-DHA)、脂肪酶(soil lipase, S-LPS)和脲酶(soil urease, S-UE)活性以及石油含量进行测定,并对紫花苜蓿的叶绿素、可溶性蛋白、可溶性糖、丙二醛(malondialdehyde, MDA)和脯氨酸(proline, Pro)的含量以及超氧化物歧化酶(superoxide dismutase, SOD)的活性进行测定,以期揭示非石油降解促生菌OS53提高联合修复体系修复效率的机制。
菌株OS53为课题组前期从石油污染土壤中分离得到,悬浮于20% (体积分数)甘油中在−80 ℃下保藏。
PYG培养基(g/L):蛋白胨5.0,酵母粉0.2,葡萄糖5.0,牛肉膏3.0,NaCl 0.5,MgSO4·7H2O 1.5,pH为7.5,配制固体培养基时需要加入15.0 g/L琼脂粉,121 ℃灭菌15 min后使用。
基础盐培养基(minimal salt medium, MSM) (g/L):葡萄糖10.0,NH4Cl 5.0,KH2PO4 0.5,K2HPO4 1.0,MgSO4·7H2O 0.5,CaCl2 0.02,KCl 0.1,pH为7.5,121 ℃灭菌15 min后使用。
紫花苜蓿(Medicago sativa L.)草种由延安大学生命科学学院植物生态学实验室提供。
菌株的细胞形态使用场发射扫描电镜(JEOL公司)进行观察。使用PYG液体培养基对菌株pH和NaCl耐受性进行测定。测定pH耐受范围时,培养基的NaCl浓度为0.5%,使用1 mol/L的HCl和NaOH调节培养基的pH依次为3.0、4.0、5.0、6.0、7.0、8.0、9.0、10.0、11.0和12.0;测定NaCl耐受范围时,培养基的pH为7.0,使用NaCl配制盐度依次为0、0.5%、1.0%、2.0%、3.0%、4.0%、5.0%和6.0%的PYG培养基。
使用MSM培养基对菌株的碳氮源利用情况进行测试。测定碳源时,培养基中的氮源为KNO3,在培养基中按1% (质量体积分数)的比例添加碳源,所测试的碳源包括葡萄糖、淀粉、α-酮戊二酸、柠檬酸、D-海藻糖、D-棉子糖、肌苷、D-纤维素、蜜二糖、水苏糖、D-苹果酸和D-甘露醇;测定氮源时,培养基中的碳源为葡萄糖,在培养基中按1% (质量体积分数)的比例添加氮源,所测试的氮源为天冬氨酸、丙氨酸、l-精氨酸、l-丝氨酸、组胺二盐酸盐、D-丝氨酸、l-脯氨酸、l-色氨酸、硫酸铵、硝酸钾、亚硝酸钠和硝酸铵。
最后按照0.1% (体积分数)的比例在培养基中接种OD600为1.0的菌株OS53种子液,在28 ℃、160 r/min的条件下培养48 h,测定OD600的吸光度。
将菌株OS53接种在PYG液体培养基中,在28 ℃、160 r/min的条件下培养48 h。然后,取10 mL的培养液,在4 ℃、10 000 r/min条件下离心20 min,收集菌体。将收集的菌体使用干冰运送至广东美格生物科技公司进行细菌基因组的提取和测序。
将原始测序数据过滤后得到clean data,使用Unicycler软件[20]进行组装,并使用BUSCO v5.4.7软件[21]对所组装的基因组完整性进行评估,将组装后的基因组序列上传至GenBank数据库。基于组装得到的基因组,分析基因组的编码基因和非编码的RNA等组分,将编码的基因上传至京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)数据库进行功能注释。提取基因组中16S rRNA基因完整序列并在EzBioCloud中进行BLAST比对[22],选择与菌株OS53相似性最高的18株模式菌,在MEGA 5.1软件中使用邻接法(neighbor-joining method, NJ)构建系统发育进化树[23]
菌株OS53植物促生特性选择产IAA、铁载体、溶磷、解钾为指标进行测定,具体测定方法参考文献[24]。
于2022年10月−2023年4月在室内开展了OS53联合紫花苜蓿修复石油污染土壤研究。具体试验设计见图1。首先,从野外采集未受石油污染的土壤,去除岩石和树枝等杂物后,按照400 mg/kg的氮素含量添加KNO3补充土壤中的氮素。然后,按照5 000 mg/kg的浓度称取石油,将其溶于石油醚中,均匀地添加至土壤中,并在通风橱中将石油醚完全挥发干净。最后,按照图1的方式对石油污染土壤进行为期120 d的修复处理。其中编号S为土壤;SP为土壤+紫花苜蓿处理;OP为土壤+石油+紫花苜蓿处理;OPB为土壤+紫花苜蓿+OS53处理;O为土壤+石油处理;OB为土壤+OS53处理。采集修复前后的土壤样品,测定其石油含量和酶活性(S-PPO、S-DHA、S-LPS和S-UE),并收集植物叶片,测定叶绿素、可溶性蛋白、可溶性糖、MDA和Pro的含量以及SOD的活性,以上每个试验设置5重复。
土壤中石油含量测定参考国家标准《土壤石油类的测定红外分光光度法(HJ 1051——2019)》[25],具体步骤如下:称取10.0 g土壤样品,向其中添加3.0 g无水硫酸钠,在研钵中研磨,充分混匀以去除土壤样品中的水分,然后将样品转移至锥形瓶中,向其中添加10.0 mL四氯乙烯,160 r/min振荡30 min萃取石油,使用玻璃纤维素滤膜过滤,收集萃取液,再使用20.0 mL四氯乙烯重复萃取1次,最后使用10.0 mL四氯乙烯清洗上述中所使用的玻璃仪器,合并3次滤液,过硅酸镁吸附柱,收集流出液,待测。
使用北京索莱宝科技有限公司生产的土壤脲酶(BC0120)、脱氢酶(BC0390)、多酚氧化酶(BC0110)和脂肪酶(BC3980)试剂盒,对样本中的4种酶活性进行测定,具体方法按照试剂盒所提供的说明书进行。植物叶片的叶绿素(BC0990)、MDA (BC0020)、Pro (BC0290)、可溶性蛋白(BC3720和PC0020)、可溶性糖(BC0030)和SOD (BC0170)活性使用北京索莱宝科技有限公司生产的试剂盒进行测定,具体方法按照试剂盒所提供的说明书进行。
以上试验均设置5个平行对照,结果为平均值±标准差(standard deviation, SD),使用Origin 2022和R 4.1.3软件对数据进行统计分析。
菌株OS53的菌落颜色为乳白色,表面光滑,能够产生胞外多糖,革兰氏染色为阴性,细胞形态为卵状,大小为(1.8−2.8) μm×(2.7−3.5) μm。菌株OS53生长的pH范围为5.0−11.0,最适生长pH为7.0,NaCl的浓度耐受范围为0−3.0%,最适生长NaCl浓度为0.5%。菌株OS53可利用葡萄糖、淀粉、蜜二糖、水苏糖和D-甘露醇作为碳源,可利用硝酸铵、硝酸钾、硫酸铵、亚硝酸钠、丙氨酸、D-丝氨酸和D-色氨酸作为氮源。
基于菌株OS53的全基因组测序结果,构建基因组完成图,菌株OS53基因组包括1个环形染色体和2个质粒,其中环形染色体的大小为5 559 109 bp,质粒的大小分别为916 660 bp和379 813 bp,共编码6 968个基因,编码基因的碱基数为6 100 863 bp,占整个基因组全长的88.99%,基因组的其他统计信息如表1所示。将OS53的基因组序列提交到GenBank数据库,登录号为GCA_029854435.1。
菌株OS53基因组在KEGG数据库注释结果表明,代谢通路在level-2层级中被注释具有膜转运(membrane transport)功能的基因数目最多,其次为细胞群落-原核生物(cellular community- prokaryotes)和氨基酸代谢(amino acid metabolism)。在level-3分类层级中,被注释具有ABC转运蛋白(ABC transporters)功能的基因数目最多,为355个,参与群体感应(quorum sensing)的基因数量次之,为315个,参与氨基酸生物合成(biosynthesis of amino acids)和碳代谢(carbon metabolism)的基因数量分别为163个和149个。
由于菌株N.petrolearium DSM 26482T具有多环芳烃降解能力,并且能够与紫花苜蓿共生结瘤,但是这与前期结果完全相反,因此对OS53全基因组KEGG注释结果进行分析,寻找与石油和多环芳烃降解以及与结瘤相关的基因。然而经过筛选分析,没有在基因组中发现常见的与石油降解相关基因及结瘤相关基因,这与石油降解相关试验结果及结瘤试验结果相符合。表明菌株OS53与N.petrolearium DSM 26482T虽然分类地位相同,但是存在较大的功能差异。
从基因组测序结果中提取菌株OS53的16S rRNA基因序列,BLAST比对分析结果表明,菌株OS53与N.petrolearium DSM 26482T的16S rRNA基因序列的相似性为99.86%,并且通过NJ法构建的系统发育树也显示菌株OS53与标准菌株N.petrolearium DSM 26482T聚在一起,形成稳定的分支,因此,确定菌株OS53与N.petrolearium为同一物种不同菌株,并将菌株OS53命名为N.petrolearium OS53。
全基因组测序结果分析表明,菌株OS53基因组中具有吲哚-3-乙酰胺(indole-3-acetamide, IAM)途径中色氨酸-2-单加氧酶基因(iaaM)和吲哚-3-乙酰水解酶基因(iaaH),为菌株OS53生成IAA提供了分子基础。同时试验结果也表明,菌株OS53具有产IAA的能力,IAA产量可达到37.5 g/L,但是无产铁载体、溶磷和解钾的能力。
在初始石油浓度为(4 402.30±222.10) mg/kg时,经过120 d处理后,菌株OS53处理组(EOB)的石油浓度降低至(3 705.21±149.87) mg/kg,与自然衰减组(EO)相比[(3 818.41±130.12) mg/kg]无显著差异(P > 0.05),表明单独接种菌株OS53并不能提高石油降解率(图2)。经过紫花苜蓿处理后(EOP),土壤中的石油浓度与自然衰减组(EO)相比显著降低(P < 0.05),降低至(2 259.31±222.47) mg/kg;紫花苜蓿和菌株OS53联合处理后(EOPB)石油浓度与紫花苜蓿处理组(EOP)相比显著下降(P < 0.05),降低至(1 870.00±81.88) mg/kg。以上结果说明,相较于单独接菌或单独种植植物,联合修复体系具有更好的石油污染修复效果。
经过120 d不同修复方式处理后,对ESP、EOP和EOPB组中的紫花苜蓿叶绿素、可溶性蛋白、可溶性糖、MDA、Pro和SOD活性的含量进行测定,结果如图3所示。栽种在未受石油污染土壤(ESP)中的植物叶绿素、可溶性蛋白和可溶性糖的含量分别为(5.12±0.18) mg/g、(5.46±0.30) mg/g和(99.25±3.52) mg/g,石油污染土壤(EOP)中植株的叶绿素、可溶性蛋白和可溶性糖含量降低至(2.94±0.13) mg/g、(3.46±0.39) mg/g和(91.76±6.98) mg/g,显著低于未受石油污染土壤(ESP)中的植株(P < 0.05)。经过与OS53协同处理(EOPB)后,植株的叶绿素、可溶性蛋白和可溶性糖的含量分别为(3.42±0.19) mg/g、(6.47±0.63) mg/g和(107.91±7.82) mg/g,均显著高于EOP组(P < 0.05),其中可溶性蛋白和可溶性糖的含量恢复至未受污染的水平。在EOP组中植株的MDA和Pro含量以及SOD活性分别为(6.09±0.86) nmol/g、(31.53±2.04) mg/g和(380.40±12.20) U/g,均显著高于(P < 0.05) ESP组中植株[(3.46 ±0.69) nmol/g、(17.29±1.74) mg/g和(321.16±21.01) U/g]。在EOPB组中,MDA和Pro含量以及SOD活性相比于EOP组含量均显著降低(P < 0.05),含量分别为(5.30±0.86) nmol/g、(24.98±2.11) mg/g和(347.91±22.88) U/g。以上结果说明,石油污染使紫花苜蓿的生长受到胁迫,导致紫花苜蓿的叶绿素、可溶性蛋白和可溶性糖的含量降低,MDA、Pro和SOD活性升高,而接种菌株OS53,植株受石油胁迫得到缓解。
对处理前后土壤S-PPO、S-LPS、S-DHA和S-UE的活性进行了测定,结果如图4所示。经过6种方式处理后,土壤中的4种酶活性均出现了升高,并且第120天的样本(E)酶活性显著高于(P < 0.05)起始的样本(I)。在EOPB、EOP、EOB、EO、ES和ESP组中,S-PPO活性分别为(25.31±0.83)、(19.69±1.35)、(14.86±1.27)、(16.27±1.17)、(13.60±0.85)和(14.81±0.0.90) U/g;S-LPS活性分别为(39.73±1.01)、(34.19±1.40)、(25.87±1.10)、(23.83±2.14)、(16.90±1.33)和(25.92±1.35) U/g;S-DHA活性分别为(53.31±3.46)、(44.35±2.47)、(38.19±2.23)、(36.66±2.24)、(21.36±2.30)和(35.11±1.08) U/g;S-UE活性分别为(24.52±1.97)、(22.52±0.75)、(14.49±0.69)、(15.01±162)、(15.99±0.41)和(19.83±1.55) U/g。所测定的4种酶活性均在EOPB组中最高,其次为EOP组,并且EOPB组中的酶活性显著高于EOP组(P < 0.05),EOP组显著高于EOB组(P < 0.05),EOB组与EO组无显著差异(P > 0.05)。
本研究使用Illumina和Nanopore平台对菌株OS53进行了全基因测序,其基因组由1个大小为5 559 109 bp的环形染色体和2个大小分别为916 660 bp和379 813 bp的质粒组成,G+C含量为60.2%,共编码6 968个基因,与模式菌株N.petrolearium DSM 26482T基因组的16S rRNA基因序列相似性高达99.86%,结合系统发育分析结果,确定菌株OS53属于N.petrolearium的一个新菌株。Neorhizobium属在2015年建立,目前隶属于该属的微生物共有8种[26],但是N.petrolearium在Genome数据库中仅有1个基因组草图,因此本研究对N.petrolearium OS53进行基因组完成图测序分析,将有助于更进一步揭示该种遗传信息,挖掘该种的相关功能。
根瘤菌因其能与豆科植物共生固氮而被广泛研究,根瘤菌结瘤基因(nodnolnoe)是绝大部分根瘤菌与豆科植物形成共生体系所必需的基因[27],但是也有研究表明部分根瘤菌可以在缺少结瘤基因的情况下与豆科植物共生结瘤[28-29]。通过对OS53全基因组预测基因分析,菌株OS53缺少完整的结瘤相关基因,表明菌株OS53极难与豆科植物形成根瘤;而随后本研究结瘤试验结果也证明,该菌株既不能与紫花苜蓿结瘤,也不能与大豆、刺槐、三叶草等其他豆科植物结瘤。根瘤菌共生固氮作用由固氮酶基因(nif)调控,发挥固氮功能至少需要9个nif基因参与:nifH、nifE、nifN、nifS、nifU、nifV、nifB和nifQ[30]。通过对全基因组基因分析发现,该菌基因组中无完整固氮酶基因簇,仅有nifU和nifS这2个基因,可能是在进化过程中发生了固氮基因丢失。基因组分析结果与结瘤试验结果都表明,菌株OS53不能够与紫花苜蓿形成共生固氮体系,这与菌株N.petrolearium DSM 26482T的结瘤表型完全相反[19]。因此,在不同生境下分离的根瘤菌同种不同菌株,其表型可能存在巨大差异。
固氮根瘤菌作为根际促生菌体系中的一类,除了生物固氮以外,还具有产生植物激素、铁载体、溶解磷酸盐和1-氨基环丙烷-1-羧酸(1-aminocyclopropane-1-carboxylic acid, ACC)脱氨酶的促生作用[31]。目前微生物依赖色氨酸产IAA的途径有吲哚-3-乙酰胺(IAM)、吲哚-3-丙酮酸、色胺、吲哚-3-乙腈和色氨酸侧链氧化等途径[32]。虽然菌株OS53不能够进行共生固氮,但是在菌株OS53基因组中发现完整的IAM途径所编码的2个关键酶基因——色氨酸-2-单加氧酶基因(iaaM)和吲哚乙酰胺水解酶基因(iaaH),表明该菌株可能具有产IAA的能力。菌株OS53的IAA产量能够达到37.5 g/L,因此,菌株OS53具有促进植物生长的潜力。
石油污染会对植物生长造成胁迫作用,影响植物正常生长。植物细胞叶绿素、可溶性蛋白、可溶性糖、Pro、MDA和SOD等含量能够在一定程度上反映植物受胁迫的大小。为了抵御胁迫,植物胞内的Pro、MDA和SOD等物质会明显上升,同时当胁迫较为严重时,叶绿素、可溶性蛋白及可溶性糖的含量则会降低[33-36]。在本研究中石油污染土壤(EOP)紫花苜蓿的叶绿素、可溶性蛋白、可溶性糖含量相比于未污染土壤(ESP)均显著下降(P < 0.05),Pro、MDA和SOD的含量相比于ESP组显著升高(P < 0.05),这与先前的研究结果发现石油会对植物的生长产生负面影响的结果一致[37]。当紫花苜蓿联合菌株OS53处理石油污染土壤(EOPB)之后,紫花苜蓿叶绿素、可溶性蛋白、可溶性糖含量相比单独种植植物都有显著上升;而MDA、Pro的含量及SOD的活性则有显著降低(图3)。上述结果表明,接种OS53能够在一定程度上帮助紫花苜蓿抵御来自石油污染的胁迫,进而提高石油降解效率。但是菌株OS53与紫花苜蓿的具体作用机制、协同修复过程土壤中石油降解微生物群落变化、土壤养分情况是否有所改善等,仍需进一步地研究。
土壤酶活是土壤生态重要指标之一,能够反映环境压力变化,并且在维持土壤健康和肥力方面发挥着重要作用[38]。土壤酶主要来自土壤微生物的生长代谢,因此土壤酶活性强弱能够在一定程度上反映土壤微生物活力。多酚氧化酶(S-PPO)能够催化石油降解过程中产生的一些酚类物质的转化,因此S-PPO活性能间接反映土壤中石油降解程度。本研究中,经过120 d后,所有组别的S-PPO活性都有不同程度的升高,表明各处理中都有一定的微生物活动;其中OPB组的S-PPO活性要显著高于其他组别,表明该组的微生物活动要多于其他组。在脂肪酶(S-LPS)的作用下,土壤中的脂类物质分解成脂肪酸和甘油,为微生物生长提供能源,已成为评价土壤质量一个很重要的指标[39-40]。与S-PPO结果类似,所有处理组在经过120 d后,S-LPS活性都有一定程度的升高,同时OPB组的S-LPS活性显著高于其他组别。在石油污染的土壤里,土壤脱氢酶(S-DHA)的活性与石油代谢强度相关;而脲酶(S-UE)对土壤的稳定起着重要的作用,催化尿素水解成NH4+和CO32−,进而为植物提供氮素营养[41]。S-DHA与S-UE的测定结果与S-PPO也十分相似,即所有处理组在经过120 d后,S-DHA与S-UE活性都有一定程度的升高,同时OPB组的S-DHA与S-UE活性显著高于其他组别。较高的酶活表明OPB组的微生物活动最多,这也与该组最高的石油降解效率相一致(图2)。然而在李炜的研究中发现,使用微生物菌剂+营养液进行为期18周的修复试验后,石油污染土壤中过氧化氢酶活及S-LPS酶活具有明显的上升趋势,但是S-DHA和S-PPO的酶活却不断下降[39]。而王傲的研究结果则表明,使用微生物+碱蓬进行为期32 d的石油污染土壤修复,S-DHA、S-LPS和S-UE的酶活具有增加趋势,而土壤过氧化氢酶活则先升高后降低[42]。综上所述,利用微生物-植物联合修复石污染土壤具有较高的修复效率,但是修复过程中土壤酶活变化则受到土壤质地、植物和微生物种类、营养情况等影响,不同酶活具有不同的变化趋势。并且土壤酶活的主要来源——土壤微生物的群落结构及代谢如何响应联合修复体系仍需进一步了解。
根据上述结果及讨论,推测菌株OS53促进其与紫花苜蓿协同修复机制如图5所示。OS53具有产IAA能力,能够促进紫花苜蓿在污染土壤中的生长,改善在石油污染胁迫下的部分生理指标,从而改变紫花苜蓿根际微环境,为石油降解微生物提供有利的条件;联合修复体系通过自己本身及土壤微生物的作用,改善石油污染土壤酶活,进而提高石油污染修复效率。
  • 陕西省教育厅专项科研计划(21JK0992)
  • 延安大学2022年校级大学生创新创业训练计划(D2022013)
  • 国家自然科学基金(42207037)
  • 延安市科技专项经费(2019-27)
  • 延安市科技专项经费(203010105)
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2024年第64卷第3期
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doi: 10.13343/j.cnki.wsxb.20230557
  • 接收时间:2023-08-30
  • 首发时间:2026-03-19
  • 出版时间:2024-03-04
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  • 收稿日期:2023-08-30
  • 录用日期:2023-10-26
基金
Special Scientific Research Project of Shaanxi Education Department(21JK0992)
陕西省教育厅专项科研计划(21JK0992)
Innovation and Entrepreneurship Training Plan for 2022 College Students of Yan'an University(D2022013)
延安大学2022年校级大学生创新创业训练计划(D2022013)
National Natural Science Foundation of China(42207037)
国家自然科学基金(42207037)
Special Fund for Science and Technology of Yan'an City(2019-27)
延安市科技专项经费(2019-27)
Special Fund for Science and Technology of Yan'an City(203010105)
延安市科技专项经费(203010105)
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    延安大学生命科学学院, 陕西 延安 716000

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2种不同金属材料的力学参数

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genus
种数
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占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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