Interactions among Rhizosphere Microorganisms, Mechanisms and Potential Application in Phytoremediation

Yuming Feng

doi:10.1051/shsconf/202214401003

All issues

Volume 144 (2022)

SHS Web Conf., 144 (2022) 01003

References

Open Access

Issue		SHS Web Conf. Volume 144, 2022 2022 International Conference on Science and Technology Ethics and Human Future (STEHF 2022)


Article Number		01003
Number of page(s)		5
Section		Research on Bioethics and Medical Science and Technology Ethics
DOI		https://doi.org/10.1051/shsconf/202214401003
Published online		26 August 2022

O. Tyc, M. van den Berg, S. Gerards, J.A. van Veen, J.M. Raaijmakers, W. de Boer, et al. Impact of interspecific interactions on antimicrobial activity among soil bacteria. Frontiers in Microbiology. 2014:5. [Google Scholar]
A. Zelezniak, S. Andrejev, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(20):6449-54. [CrossRef] [Google Scholar]
J. Kramer, Oezkaya O, Kuemmerli R. Bacterial siderophores in community and host interactions. Nature Reviews Microbiology. 2020;18(3):152-63. [CrossRef] [Google Scholar]
K. Velmourougane, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. Journal of Basic Microbiology. 2017;57(7):548-73. [CrossRef] [Google Scholar]
J.E. Berleman, Kirby J.R. Deciphering the hunting strategy of a bacterial wolfpack. Fems Microbiology Reviews. 2009;33(5):942-57. [CrossRef] [Google Scholar]
J. Moran, McGrath C. Comparison of methods for mapping rhizosphere processes in the context of their surrounding root and soil environments. Biotechniques. 2021;71(6). [Google Scholar]
S.J. Shi, Nuccio E.E. , Shi Z.J. , He Z.L. , Zhou J.Z. , Firestone M.K. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecology Letters. 2016;19(8):926-36. [CrossRef] [Google Scholar]
H.Z. Kang, Gao HH, Yu WJ, Yi Y, Wang Y, Ning ML. Changes in soil microbial community structure and function after afforestation depend on species and age: Case study in a subtropical alluvial island. Science of the Total Environment. 2018;625:1423-32. [CrossRef] [Google Scholar]
M. Altaf-Ul-Amin, Afendi FM, Kiboi SK, Kanaya S. Systems Biology in the Context of Big Data and Networks. Biomed Research International. 2014;2014. [Google Scholar]
D.S. Lundberg, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488(7409):86-+. [CrossRef] [Google Scholar]
J.Y. Zhang, Zhang N, Liu YX, Zhang XN, Hu B, Qin Y, et al. Root microbiota shift in rice correlates with resident time in the field and developmental stage. Science China-Life Sciences. 2018;61(6):613-21. [CrossRef] [Google Scholar]
H. Toju, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS. Network modules and hubs in plant-root fungal biomes. Journal of the Royal Society Interface. 2016;13(116). [Google Scholar]
M.A. Hassani, Duran P, Hacquard S. Microbial interactions within the plant holobiont. Microbiome. 2018;6. [CrossRef] [Google Scholar]
C.E. Lawson, Wu S, Bhattacharjee AS, Hamilton JJ, McMahon KD, Goel R, et al. Metabolic network analysis reveals microbial community interactions in anammox granules. Nature Communications. 2017;8. [CrossRef] [Google Scholar]
G. D’Souza, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Natural Product Reports. 2018;35(5):455-88. [CrossRef] [Google Scholar]
K. Wang, Li X, Yang CX, Song SA, Cui CY, Zhou XF, et al. A LysR Family Transcriptional Regulator Modulates Burkholderia cenocepacia Biofilm Formation and Protease Production. Applied and Environmental Microbiology. 2021;87(12). [Google Scholar]
Schmidt R., Etalo D.W., de Jager V., Gerards S., Zweers H., de Boer W., et al. Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions. Frontiers in Microbiology, 2016. [Google Scholar]
Nadell C.D., Drescher K., Foster K.R. Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 2016, 14(9):589-600. [CrossRef] [Google Scholar]
Madsen J.S., Burmolle M., Hansen L.H. , Sorensen SJ. The interconnection between biofilm formation and horizontal gene transfer. Fems Immunology and Medical Microbiology. 2012;65(2):183-95. [CrossRef] [Google Scholar]
Viollet A., Pivato B., Mougel C., Cleyet-Marel J.C., Gubry-Rangin C., Lemanceau P., et al. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza. 2017;27(1):23-33. [CrossRef] [Google Scholar]
Duran D., Bernal P., Vazquez-Arias D., BlancoRomero E., Garrido-Sanz D., Redondo-Nieto M., et al. Pseudomonas fluorescens F113 type VI secretion systems mediate bacterial killing and adaption to the rhizosphere microbiome. Scientific Reports. 2021;11(1). [CrossRef] [Google Scholar]
Mei K., Wu G.R., Liu J.C, Wu J.J. , Hong H.L. , Lu H.L. , et al. Dynamics of low-molecular-weight organic acids for the extraction and sequestration of arsenic species and heavy metals using mangrove sediments. Chemosphere. 2022;286. [Google Scholar]
Nascimento SVd, Costa PHdO, Herrera H., Caldeira C.F., Gastauer M., Ramos S.J. , et al. Proteomic Profiling and Rhizosphere-Associated Microbial Communities Reveal Adaptive Mechanisms of Dioclea apurensis Kunth in Eastern Amazon’s Rehabilitating Minelands. Plants (Basel, Switzerland), 2022;11(5). [Google Scholar]
Kumar SS, Ghosh P, Malyan SK, Sharma J, Kumar V. A comprehensive review on enzymatic degradation of the organophosphate pesticide malathion in the environment. Journal of Environmental Science and Health Part C-Environmental Carcinogenesis & Ecotoxicology Reviews. 2019;37(4):288-329. [CrossRef] [Google Scholar]

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[1] O. Tyc, M. van den Berg, S. Gerards, J.A. van Veen, J.M. Raaijmakers, W. de Boer, et al. Impact of interspecific interactions on antimicrobial activity among soil bacteria. Frontiers in Microbiology. 2014:5. [Google Scholar]

[2] A. Zelezniak, S. Andrejev, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(20):6449-54. [CrossRef] [Google Scholar]

[3] J. Kramer, Oezkaya O, Kuemmerli R. Bacterial siderophores in community and host interactions. Nature Reviews Microbiology. 2020;18(3):152-63. [CrossRef] [Google Scholar]

[4] K. Velmourougane, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. Journal of Basic Microbiology. 2017;57(7):548-73. [CrossRef] [Google Scholar]

[5] J.E. Berleman, Kirby J.R. Deciphering the hunting strategy of a bacterial wolfpack. Fems Microbiology Reviews. 2009;33(5):942-57. [CrossRef] [Google Scholar]

[6] J. Moran, McGrath C. Comparison of methods for mapping rhizosphere processes in the context of their surrounding root and soil environments. Biotechniques. 2021;71(6). [Google Scholar]

[7] S.J. Shi, Nuccio E.E. , Shi Z.J. , He Z.L. , Zhou J.Z. , Firestone M.K. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecology Letters. 2016;19(8):926-36. [CrossRef] [Google Scholar]

[8] H.Z. Kang, Gao HH, Yu WJ, Yi Y, Wang Y, Ning ML. Changes in soil microbial community structure and function after afforestation depend on species and age: Case study in a subtropical alluvial island. Science of the Total Environment. 2018;625:1423-32. [CrossRef] [Google Scholar]

[9] M. Altaf-Ul-Amin, Afendi FM, Kiboi SK, Kanaya S. Systems Biology in the Context of Big Data and Networks. Biomed Research International. 2014;2014. [Google Scholar]

[10] D.S. Lundberg, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488(7409):86-+. [CrossRef] [Google Scholar]

[11] J.Y. Zhang, Zhang N, Liu YX, Zhang XN, Hu B, Qin Y, et al. Root microbiota shift in rice correlates with resident time in the field and developmental stage. Science China-Life Sciences. 2018;61(6):613-21. [CrossRef] [Google Scholar]

[12] H. Toju, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS. Network modules and hubs in plant-root fungal biomes. Journal of the Royal Society Interface. 2016;13(116). [Google Scholar]

[13] M.A. Hassani, Duran P, Hacquard S. Microbial interactions within the plant holobiont. Microbiome. 2018;6. [CrossRef] [Google Scholar]

[14] C.E. Lawson, Wu S, Bhattacharjee AS, Hamilton JJ, McMahon KD, Goel R, et al. Metabolic network analysis reveals microbial community interactions in anammox granules. Nature Communications. 2017;8. [CrossRef] [Google Scholar]

[15] G. D’Souza, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Natural Product Reports. 2018;35(5):455-88. [CrossRef] [Google Scholar]

[16] K. Wang, Li X, Yang CX, Song SA, Cui CY, Zhou XF, et al. A LysR Family Transcriptional Regulator Modulates Burkholderia cenocepacia Biofilm Formation and Protease Production. Applied and Environmental Microbiology. 2021;87(12). [Google Scholar]

[17] Schmidt R., Etalo D.W., de Jager V., Gerards S., Zweers H., de Boer W., et al. Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions. Frontiers in Microbiology, 2016. [Google Scholar]

[18] Nadell C.D., Drescher K., Foster K.R. Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 2016, 14(9):589-600. [CrossRef] [Google Scholar]

[19] Madsen J.S., Burmolle M., Hansen L.H. , Sorensen SJ. The interconnection between biofilm formation and horizontal gene transfer. Fems Immunology and Medical Microbiology. 2012;65(2):183-95. [CrossRef] [Google Scholar]

[20] Viollet A., Pivato B., Mougel C., Cleyet-Marel J.C., Gubry-Rangin C., Lemanceau P., et al. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza. 2017;27(1):23-33. [CrossRef] [Google Scholar]

[21] Duran D., Bernal P., Vazquez-Arias D., BlancoRomero E., Garrido-Sanz D., Redondo-Nieto M., et al. Pseudomonas fluorescens F113 type VI secretion systems mediate bacterial killing and adaption to the rhizosphere microbiome. Scientific Reports. 2021;11(1). [CrossRef] [Google Scholar]

[22] Mei K., Wu G.R., Liu J.C, Wu J.J. , Hong H.L. , Lu H.L. , et al. Dynamics of low-molecular-weight organic acids for the extraction and sequestration of arsenic species and heavy metals using mangrove sediments. Chemosphere. 2022;286. [Google Scholar]

[23] Nascimento SVd, Costa PHdO, Herrera H., Caldeira C.F., Gastauer M., Ramos S.J. , et al. Proteomic Profiling and Rhizosphere-Associated Microbial Communities Reveal Adaptive Mechanisms of Dioclea apurensis Kunth in Eastern Amazon’s Rehabilitating Minelands. Plants (Basel, Switzerland), 2022;11(5). [Google Scholar]

[24] Kumar SS, Ghosh P, Malyan SK, Sharma J, Kumar V. A comprehensive review on enzymatic degradation of the organophosphate pesticide malathion in the environment. Journal of Environmental Science and Health Part C-Environmental Carcinogenesis & Ecotoxicology Reviews. 2019;37(4):288-329. [CrossRef] [Google Scholar]