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Bai X, Han Y, Han L. Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9. PLoS One 2024; 19:e0298303. [PMID: 38358983 PMCID: PMC10868839 DOI: 10.1371/journal.pone.0298303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The plant growth-promoting rhizobacterium Tsukamurella tyrosinosolvens P9 can improve peanut growth. In this study, a co-culture system of strain P9 and peanut was established to analyze the transcriptome of peanut roots interacting with P9 for 24 and 72 h. During the early stage of co-culturing, genes related to mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction, ethylene synthesis, and cell wall pectin degradation were induced, and the up-regulation of phenylpropanoid derivative, flavonoid, and isoflavone synthesis enhanced the defense response of peanut. The enhanced expression of genes associated with photosynthesis and carbon fixation, circadian rhythm regulation, indoleacetic acid (IAA) synthesis, and cytokinin decomposition promoted root growth and development. At the late stage of co-culturing, ethylene synthesis was reduced, whereas Ca2+ signal transduction, isoquinoline alkaloid synthesis, and ascorbate and aldarate metabolism were up-regulated, thereby maintaining root ROS homeostasis. Sugar decomposition and oxidative phosphorylation and nitrogen and fatty acid metabolism were induced, and peanut growth was significantly promoted. Finally, the gene expression of seedlings inoculated with strain P9 exhibited temporal differences. The results of our study, which explored transcriptional alterations of peanut root during interacting with P9, provide a basis for elucidating the growth-promoting mechanism of this bacterial strain in peanut.
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Affiliation(s)
- Xue Bai
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yujie Han
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Lizhen Han
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
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Wang W, Li D, Qiu X, Yang J, Liu L, Wang E, Yuan H. Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. ENVIRONMENTAL MICROBIOME 2024; 19:2. [PMID: 38178261 PMCID: PMC10768371 DOI: 10.1186/s40793-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.
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Affiliation(s)
- Wenqian Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Dongmei Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Xiaoqian Qiu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11340, Ciudad de México, México
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China.
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Liu X, Wang Y, Han L, Xia Y, Xie J. A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice. FEMS Microbiol Ecol 2023; 99:fiad113. [PMID: 37742208 DOI: 10.1093/femsec/fiad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.
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Affiliation(s)
- Xuewei Liu
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yirong Wang
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Lijuan Han
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yuxian Xia
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Jiaqin Xie
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
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Debnath S, Chakraborty S, Langthasa M, Choure K, Agnihotri V, Srivastava A, Rai PK, Tilwari A, Maheshwari DK, Pandey P. Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1152875. [PMID: 37113600 PMCID: PMC10126288 DOI: 10.3389/fpls.2023.1152875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Non-rhizobial endophytes (NREs) are active colonizers inhabiting the root nodules. Though their active role in the lentil agroecosystem is not well defined, here we observed that these NREs might promote the growth of lentils, modulate rhizospheric community structure and could be used as promising organisms for optimal use of rice fallow soil. NREs from root nodules of lentils were isolated and examined for plant growth-promoting traits, exopolysaccharide (EPS) and biofilm production, root metabolites, and the presence of nifH and nifK elements. The greenhouse experiment with the chosen NREs, i.e., Serratia plymuthica 33GS and Serratia sp. R6 significantly increased the germination rate, vigour index, development of nodules (in non-sterile soil) and fresh weight of nodules (33GS 94%, R6 61% growth) and length of the shoot (33GS 86%, R6 51.16%) as well as chlorophyll levels when compared to the uninoculated control. Scanning Electron Microscopy (SEM) revealed that both isolates could successfully colonize the roots and elicit root hair growth. The inoculation of the NREs resulted in specific changes in root exudation patterns. The plants with 33GS and R6 treatment significantly stimulated the exudation of triterpenes, fatty acids, and their methyl esters in comparison to the uninoculated plants, altering the rhizospheric microbial community structure. Proteobacteria dominated the rhizospheric microbiota in all the treatments. Treatment with 33GS or R6 also enhanced the relative abundance of other favourable microbes, including Rhizobium, Mesorhizobium, and Bradyrhizobium. The correlation network analysis of relative abundances resulted in numerous bacterial taxa, which were in cooperation with each other, having a possible role in plant growth promotion. The results indicate the significant role of NREs as plant growth promoters, which also includes their role in root exudation patterns, enhancement of soil nutrient status and modulation of rhizospheric microbiota, suggesting their prospects in sustainable, and bio-based agriculture.
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Affiliation(s)
- Sourav Debnath
- Department of Microbiology, Assam University, Silchar, India
| | | | | | - Kamlesh Choure
- Department of Biotechnology, AKS University, Satna, India
| | | | | | | | - Anita Tilwari
- Department of Microbiology, Barkatullah University, Bhopal, India
| | - D. K. Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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Shamshirgaran R, Malakooti R, Akbarpoor A, Moghaddam AZ. Fabrication of Polyvinylpyrrolidone‐Stabilized Nano Zero‐Valent Iron Supported by Hydrophilic Biochar for Efficient Cr (VI) Removal from Groundwater. ChemistrySelect 2022. [DOI: 10.1002/slct.202202927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Debnath S, Das A, Maheshwari DK, Pandey P. Treatment with atypical rhizobia, Pararhizobium giardinii and Ochrobactrum sp. modulate the rhizospheric bacterial community, and enhances Lens culinaris growth in fallow-soil. Microbiol Res 2022; 267:127255. [PMID: 36434988 DOI: 10.1016/j.micres.2022.127255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/26/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophic nodule isolates are acknowledged promoters of plant growth and rhizospheric community. Consequently, in the lentil agroecosystem, inoculation of atypical rhizobial isolates could be a viable alternative to chemical fertilizers for fallow land usage optimization. The aim of this study is to evaluate and select the rhizobial isolates of lentil nodules with plant-growth-promoting (PGP) attributes and to elucidate their application in rice-fallow soil for determining the growth of lentils and its impact on the rhizospheric bacterial community. Lentil's nodule isolates were identified and screened for their PGP attributes, biofilm, exopolysaccharide (EPS) formation, and early plant growth promotion. The pot experiment with the selected atypical rhizobial isolates Pararhizobium giardinii (P1) and Ochrobactrum sp. (42S) significantly enhanced germination, vigour index, nodule formation (P1 60%, 42S 42% increase), nodule fresh weight, shoot length (65% P1 & 35% 42S), and chlorophyll content as compared to the uninoculated control treatment. The genes for nitrogen fixation nifH and nifK were detected in both isolates. Scanning Electron Microscopy (SEM) revealed successful root and nodule colonization by both isolates, while Transmission Electron Microscopy (TEM) displayed nitrogen-fixing zones within root nodules. Proteobacteria predominated in the lentil rhizosphere of all the treatments. Whereas, application of either P1 or 42S increased Rhizobium, Mesorhizobium, and Bradyrhizobium genra, thus positively modulating rhizospheric community structure. The correlation network analysis revealed an abundance of some interdependent bacterial genera with a possible role in overall plant growth. Functional genes for siderophore biosynthesis and ABC transporter were positively modulated by application of either P1 or 42S. This study showed the significant effect of P. giardinii P1 and Ochrobactrum sp. 42S of L. culinaris on lentil growth, improving fallowsoil health for optimum usage, and modulated rhizospheric community structure which strongly manifest prospects of low-cost, eco-friendly and sustainable biofertilizers.
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Affiliation(s)
- Sourav Debnath
- Department of Microbiology, Assam University, Silchar 788011, India
| | - Ankita Das
- Department of Microbiology, Assam University, Silchar 788011, India
| | - D K Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar 249404, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar 788011, India.
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7
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Siderophore Synthesis Ability of the Nitrogen-Fixing Bacterium (NFB) GXGL-4A is Regulated at the Transcriptional Level by a Transcriptional Factor (trX) and an Aminomethyltransferase-Encoding Gene (amt). Curr Microbiol 2022; 79:369. [PMID: 36253498 DOI: 10.1007/s00284-022-03080-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/07/2022] [Indexed: 11/03/2022]
Abstract
Kosakonia radicincitans GXGL-4A, a gram-negative nitrogen-fixing (NF) bacterial strain is coated with a thick capsulatus on the surface of cell wall, which becomes a physical barrier for exogenous DNA to enter the cell, so the operation of genetic transformation is difficult. In this study, an optimized Tn5 transposon mutagenesis system was established by using a high osmotic HO-1 medium combined with the electroporation transformation. Eventually, a mutant library containing a total of 1633 Tn5 insertional mutants were established. Of these mutants, the mutants M81 and M107 were found to have an enhanced capability to synthesize siderophore through the CAS agar plate assay and the spectrophotometric determination. The bacterial cells of two mutants were applied in cucumber growth-promoting experiment. Cucumber seedlings treated with M81 and M107 cells had a significant increase in biomass including seedling height, seedling fresh weight, root fresh weight, and root length. The whole genome sequencing of the mutants M81 and M107 showed that the integration sites of Tn5 transposon element were located in MmyB-like helix-turn-helix transcription regulator (locus tag: A3780_19720, trX) and aminomethyltransferase-encoding genes (locus tag: A3780_01680, amt) in the genome of GXGL-4A, respectively. The ability of siderophore synthesis of the target mutants was improved by Tn5 insertion mutagenesis, and the mutants obtained showed a good plant growth-promoting effect when applied to the cucumber seedlings. The results suggest that the identified functional genes regulates the biosynthesis of siderophore in azotobacter GXGL-4A, and the specific mechanism needs to be further investigated.
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Nonthakaew N, Panbangred W, Songnuan W, Intra B. Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets’ rhizosphere microbiome. Front Microbiol 2022; 13:967415. [PMID: 36090067 PMCID: PMC9453592 DOI: 10.3389/fmicb.2022.967415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.
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Affiliation(s)
- Napawit Nonthakaew
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
| | - Watanalai Panbangred
- Research, Innovation, and Partnerships Office (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
- *Correspondence: Bungonsiri Intra,
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Nikoo M, Rudiansyah M, Bokov DO, Jainakbaev N, Suksatan W, Ansari MJ, Thangavelu L, Chupradit S, Zamani A, Adili A, Shomali N, Akbari M. Potential of chimeric antigen receptor (CAR)-redirected immune cells in breast cancer therapies: Recent advances. J Cell Mol Med 2022; 26:4137-4156. [PMID: 35762299 PMCID: PMC9344815 DOI: 10.1111/jcmm.17465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/16/2022] [Accepted: 05/28/2022] [Indexed: 11/29/2022] Open
Abstract
Despite substantial developments in conventional treatments such as surgery, chemotherapy, radiotherapy, endocrine therapy, and molecular-targeted therapy, breast cancer remains the leading cause of cancer mortality in women. Currently, chimeric antigen receptor (CAR)-redirected immune cell therapy has emerged as an innovative immunotherapeutic approach to ameliorate survival rates of breast cancer patients by eliciting cytotoxic activity against cognate tumour-associated antigens expressing tumour cells. As a crucial component of adaptive immunity, T cells and NK cells, as the central innate immune cells, are two types of pivotal candidates for CAR engineering in treating solid malignancies. However, the biological distinctions between NK cells- and T cells lead to differences in cancer immunotherapy outcomes. Likewise, optimal breast cancer removal via CAR-redirected immune cells requires detecting safe target antigens, improving CAR structure for ideal immune cell functions, promoting CAR-redirected immune cells filtration to the tumour microenvironment (TME), and increasing the ability of these engineered cells to persist and retain within the immunosuppressive TME. This review provides a concise overview of breast cancer pathogenesis and its hostile TME. We focus on the CAR-T and CAR-NK cells and discuss their significant differences. Finally, we deliver a summary based on recent advancements in the therapeutic capability of CAR-T and CAR-NK cells in treating breast cancer.
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Affiliation(s)
- Marzieh Nikoo
- Department of Immunology, School of MedicineKermanshah University of Medical SciencesKermanshahIran
| | - Mohammad Rudiansyah
- Division of Nephrology & Hypertension, Department of Internal Medicine, Faculty of MedicineUniversitas Lambung Mangkurat / Ulin HospitalBanjarmasinIndonesia
| | - Dmitry Olegovich Bokov
- Institute of PharmacySechenov First Moscow State Medical UniversityMoscowRussian Federation
- Laboratory of Food ChemistryFederal Research Center of Nutrition, Biotechnology and Food SafetyMoscowRussian Federation
| | | | - Wanich Suksatan
- Faculty of Nursing, HRH Princess Chulabhorn College of Medical ScienceChulabhorn Royal AcademyBangkokThailand
| | - Mohammad Javed Ansari
- Department of Pharmaceutics, College of PharmacyPrince Sattam Bin Abdulaziz UniversityAl‐kharjSaudi Arabia
| | - Lakshmi Thangavelu
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical ScienceSaveetha UniversityChennaiIndia
| | - Supat Chupradit
- Department of Occupational Therapy, Faculty of Associated Medical SciencesChiang Mai UniversityChiang MaiThailand
| | - Amir Zamani
- Shiraz Transplant Center, Abu Ali Sina HospitalShiraz University of Medical SciencesShirazIran
| | - Ali Adili
- Department of OncologyTabriz University of Medical SciencesTabrizIran
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South FloridaTampaFloridaUSA
| | - Navid Shomali
- Department of ImmunologyTabriz University of Medical SciencesTabrizIran
| | - Morteza Akbari
- Department of ImmunologyTabriz University of Medical SciencesTabrizIran
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He Y, Guo W, Peng J, Guo J, Ma J, Wang X, Zhang C, Jia N, Wang E, Hu D, Wang Z. Volatile Organic Compounds of Streptomyces sp. TOR3209 Stimulated Tobacco Growth by Up-Regulating the Expression of Genes Related to Plant Growth and Development. Front Microbiol 2022; 13:891245. [PMID: 35668752 PMCID: PMC9164152 DOI: 10.3389/fmicb.2022.891245] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
To investigate the mechanism underlying the plant growth-promoting (PGP) effects of strain Streptomyces sp. TOR3209, PGP traits responsible for indoleacetic acid production, siderophore production, and phosphate solubilization were tested by culturing the strain TOR3209 in the corresponding media. The effects of volatile organic compounds (VOCs) produced by the strain TOR3209 on plant growth were observed by co-culturing this strain with tobacco seedlings in I-plates. Meanwhile, the effects of VOCs on tobacco gene expression were estimated by performing a transcriptome analysis, and VOCs were identified by the solid-phase micro-extraction (SPME) method. The results showed positive reactions for the three tested PGP traits in the culture of strain TOR3209, while the tobacco seedlings co-cultured with strain TOR3209 revealed an increase in the fresh weight by up to 100% when compared to that of the control plants, demonstrating that the production VOCs was also a PGP trait. In transcriptome analysis, plants co-cultured with strain TOR3209 presented the highest up-regulated expression of the genes involved in plant growth and development processes, implying that the bacterial VOCs played a role as a regulator of plant gene expression. Among the VOCs produced by the strain TOR3209, two antifungal molecules, 2,4-bis(1,1-dimethylethyl)-phenol and hexanedioic acid dibutyl ester, were found as the main compounds. Conclusively, up-regulation in the expression of growth- and development-related genes via VOCs production is an important PGP mechanism in strain TOR3209. Further efforts to explore the effective VOCs and investigate the effects of the two main VOCs in the future are recommended.
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Affiliation(s)
- Yuxi He
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Wenyu Guo
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Jieli Peng
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Jinying Guo
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Jia Ma
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xu Wang
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Cuimian Zhang
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Nan Jia
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Dong Hu
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- *Correspondence: Dong Hu
| | - Zhanwu Wang
- Institute of Agro-Resources and Environment/Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- Zhanwu Wang
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Boubekri K, Soumare A, Mardad I, Lyamlouli K, Ouhdouch Y, Hafidi M, Kouisni L. Multifunctional role of Actinobacteria in agricultural production sustainability: a review. Microbiol Res 2022; 261:127059. [DOI: 10.1016/j.micres.2022.127059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/26/2021] [Accepted: 05/01/2022] [Indexed: 12/13/2022]
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12
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Shen MC, Shi YZ, Bo GD, Liu XM. Fungal Inhibition of Agricultural Soil Pathogen Stimulated by Nitrogen-Reducing Fertilization. Front Bioeng Biotechnol 2022; 10:866419. [PMID: 35497365 PMCID: PMC9039341 DOI: 10.3389/fbioe.2022.866419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Plant health is the fundamental of agricultural production, which is threatened by plant pathogens severely. The previous studies exhibited the effects of different pathogen control strategies (physical, chemical, and microbial methods), which resulted from bringing in exogenous additives, on microbial community structures and functions. Nevertheless, few studies focused on the potential inhibitory abilities of native microbial community in the soil, which could be activated or enhanced by different fertilization strategies. In this study, three plant diseases (TMV, TBS, and TBW) of tobacco, fungal community of tobacco rhizosphere soil, and the correlation between them were researched. The results showed that nitrogen-reducing fertilization strategies could significantly decrease the occurrence rate and the disease index of three tobacco diseases. The results of bioinformatics analyses revealed that the fungal communities of different treatments could differentiate the nitrogen-reducing fertilization group and the control group (CK). Furthermore, key genera which were responsible for the variation of fungal community were explored by LEfSe analysis. For instance, Tausonia and Trichocladium increased, while Naganishia and Fusicolla decreased under nitrogen-reducing fertilization conditions. Additionally, the correlation between tobacco diseases and key genera was verified using the Mantel test. Moreover, the causal relationship between key genera and tobacco diseases was deeply explored by PLS–PM analysis. These findings provide a theoretical basis for a nitrogen-reducing fertilization strategy against tobacco diseases without exogenous additives and make contributions to revealing the microbial mechanism of native-valued fungal key taxa against tobacco diseases, which could be stimulated by agricultural fertilization management.
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Affiliation(s)
- Min-Chong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - You-Zhi Shi
- Cigar Institute of China Tobacco Hubei Industrial Co., Ltd., Yichang, China
| | - Guo-Dong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xin-Min Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Xin-Min Liu,
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13
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Ali Q, Ayaz M, Mu G, Hussain A, Yuanyuan Q, Yu C, Xu Y, Manghwar H, Gu Q, Wu H, Gao X. Revealing plant growth-promoting mechanisms of Bacillus strains in elevating rice growth and its interaction with salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:994902. [PMID: 36119605 PMCID: PMC9479341 DOI: 10.3389/fpls.2022.994902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/10/2022] [Indexed: 05/04/2023]
Abstract
Soil salinity is a major environmental stress that has been negatively affecting the growth and productivity of rice. However, various salt-resistant plant growth-promoting rhizobacteria (PGPR) have been known to promote plant growth and alleviate the damaging effects of salt stress via mitigating physio-biochemical and molecular characteristics. This study was conducted to examine the salt stress potential of Bacillus strains identified from harsh environments of the Qinghai-Tibetan plateau region of China. The Bacillus strains NMTD17, GBSW22, and FZB42 were screened for their response under different salt stress conditions (1, 4, 7, 9, 11, 13, and 16%). The screening analysis revealed strains NMTD17, GBSW22, and FZB42 to be high-salt tolerant, moderate-salt tolerant, and salt-sensitive, respectively. The NMTD17 strain produced a strong biofilm, followed by GBSW22 and FZB42. The expression of salt stress-related genes in selected strains was also analyzed through qPCR in various salt concentrations. Further, the Bacillus strains were used in pot experiments to study their growth-promoting ability and antioxidant activities at various concentrations (0, 100, 150, and 200 mmol). The analysis of growth-promoting traits in rice exhibited that NMTD17 had a highly significant effect and GSBW22 had a moderately significant effect in comparison with FZB42. The highly resistant strain NMTD17 that stably promoted rice plant growth was further examined for its function in the composition of rhizobacterial communities. The inoculation of NMTD17 increased the relative abundance and richness of rhizobacterial species. These outcomes propose that NMTD17 possesses the potential of PGPR traits, antioxidants enzyme activities, and reshaping the rhizobacterial community that together mitigate the harmful effects of salinity in rice plants.
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Affiliation(s)
- Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Ayaz
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Guangyuan Mu
- Shenzhen Batian Ecotypic Engineering Co., Ltd., Shenzhen, China
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qiu Yuanyuan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Yujiao Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Qin Gu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Xuewen Gao,
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14
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Wang H, Zhang R, Duan Y, Jiang W, Chen X, Shen X, Yin C, Mao Z. The Endophytic Strain Trichoderma asperellum 6S-2: An Efficient Biocontrol Agent against Apple Replant Disease in China and a Potential Plant-Growth-Promoting Fungus. J Fungi (Basel) 2021; 7:jof7121050. [PMID: 34947033 PMCID: PMC8705406 DOI: 10.3390/jof7121050] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 01/24/2023] Open
Abstract
A study was conducted for endophytic antagonistic fungi obtained from the roots of healthy apple trees growing in nine replanted orchards in Shandong Province, China. The fungi were assessed for their ability to inhibit Fusarium proliferatum f. sp. malus domestica MR5, a fungal strain associated with apple replant disease (ARD). An effective endophyte, designated as strain 6S-2, was isolated and identified as Trichoderma asperellum. Strain 6S-2 demonstrated protease, amylase, cellulase, and laccase activities, which are important for the parasitic and antagonistic functions of pathogenic fungi. The inhibition rate of 6S-2 against Fusarium proliferatum f. sp. malus domestica MR5 was 52.41%. Strain 6S-2 also secreted iron carriers, auxin, ammonia and was able to solubilize phosphorus. Its fermentation extract and volatile substances inhibited the growth of MR5, causing its hyphae to twist, shrink, swell, and rupture. The antifungal activity of the 6S-2 fermentation extract increased with increasing concentrations. It promoted the production and elongation of Arabidopsis thaliana lateral roots, and the strongest effects were seen at a concentration of 50 mg/mL. A GC-MS analysis of the 6S-2 fermentation extract and volatile substances showed that they comprised mainly alkanes, alcohols, and furanones, as well as the specific volatile substance 6-PP. The application of 6S-2 spore suspension to replanted apple orchard soils reduced plant oxidative damage and promoted plant growth in a pot experiment. Therefore, the endophytic strain T. asperellum 6S-2 has the potential to serve as an effective biocontrol fungus for the prevention of ARD in China, and appears to promote plant growth.
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Affiliation(s)
| | | | | | | | | | | | - Chengmiao Yin
- Correspondence: (C.Y.); (Z.M.); Tel.: +86-186-5388-0060 (C.Y.); +86-139-5382-2958 (Z.M.)
| | - Zhiquan Mao
- Correspondence: (C.Y.); (Z.M.); Tel.: +86-186-5388-0060 (C.Y.); +86-139-5382-2958 (Z.M.)
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15
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Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria. Appl Microbiol Biotechnol 2021; 105:8805-8822. [PMID: 34716462 DOI: 10.1007/s00253-021-11659-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.
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16
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Peng J, Ma J, Wei X, Zhang C, Jia N, Wang X, Wang ET, Hu D, Wang Z. Accumulation of beneficial bacteria in the rhizosphere of maize (Zea mays L.) grown in a saline soil in responding to a consortium of plant growth promoting rhizobacteria. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01650-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Purpose
Salt stress reduces plant growth and is now becoming one of the most important factors restricting the agricultural productivity. Inoculation of plant growth-promoting rhizobacteria (PGPR) has been shown to confer plant tolerance against abiotic stress, but the detailed mechanisms of how this occurs remain unclear and the application effects in different reports are unstable. In order to obtain a favorite effect of PGPR inoculation and improve our knowledge about the related mechanism, we performed this study to analyze the mechanism of a PGPR consortium on improving the salt resistance of crops.
Methods
A region-specific (Saline land around Bohai Sea in China) PGPR consortium was selected that contains three strains (Pseudomonas sp. P8, Peribacillus sp. P10, and Streptomyces sp. X52) isolated from rhizosphere of Sonchus brachyotus DC. grown in a saline soil. By inoculation tests, their plant growth-promoting (PGP) traits and ability to improve the salt resistance of maize were investigated and shifting in rhizosphere bacterial community of the inoculated plants was analyzed using the high-throughput sequencing technology.
Results
The three selected strains were salt tolerant, presented several growth promoting properties, and inhibited several phytopathogenic fungi. The inoculation of this consortium promoted the growth of maize plant and enriched the beneficial bacteria in rhizosphere of maize in a saline soil, including the nitrogen fixing bacteria Azotobacter, Sinorhizobium, and Devosia, and the nitrification bacteria Candidatus Nitrososphaera, and Nitrosovibrio.
Conclusions
The bacterial consortium P8/P10/X52 could improve plant growth in a saline soil by both their PGP traits and regulating the rhizosphere bacterial community. The findings provided novel information about how the PGPR helped the plants in the view of microbiome.
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17
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Identification of basmati rice (Oryza sativa L.) rhizobacteria and their effect on plant growth traits for sustainable development in agriculture. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00033-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Zhang H, Ma B, Huang T, Shi Y. Nitrate reduction by the aerobic denitrifying actinomycete Streptomyces sp. XD-11-6-2: Performance, metabolic activity, and micro-polluted water treatment. BIORESOURCE TECHNOLOGY 2021; 326:124779. [PMID: 33535149 DOI: 10.1016/j.biortech.2021.124779] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Aerobic denitrifying bacteria were widely reported in different nitrogen polluted aquatic ecosystem. However, the aerobic denitrification characteristics of actinomycete were not well understood. Here, the actinomycete strain XD-11-6-2 was isolated from reservoir and identified as Streptomyces sp. XD-11-6-2 by DNA sequencing. Strain XD-11-6-2 removed 90.34% of total organic carbon and 93.66% of total nitrogen under aerobic condition. A total of 77.87% of nitrogen was removed as a gaseous product, and 15.67% of nitrogen was converted into biomass. Biolog combined with network model indicated that strain XD-11-6-2 could use six types of carbon sources, and exhibit outstanding capacity to metabolize diverse carbon sources. Moreover, the highest nitrate and total nitrogen removal efficiencies of raw water were 72.29% and 74.86%, respectively. In general, these results provide new insights to understand the potential of actinomycetes in treating micro-polluted water.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yinjie Shi
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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19
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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