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Bhat A, Sharma R, Desigan K, Lucas MM, Mishra A, Bowers RM, Woyke T, Epstein B, Tiffin P, Pueyo JJ, Paape T. Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiol 2024; 24:247. [PMID: 38971740 PMCID: PMC11227200 DOI: 10.1186/s12866-024-03391-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg. RESULTS Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg. CONCLUSIONS Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.
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Affiliation(s)
- Aditi Bhat
- Brookhaven National Laboratory, Upton, USA
| | | | | | | | - Ankita Mishra
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brendan Epstein
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - José J Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Tim Paape
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA.
- USDA-ARS Children's Nutrition Research Center, Houston, TX, USA.
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Li P, Chen J, Ying S, Chen N, Fang S, Ye M, Zhang C, Li C, Ge Y. Different responses of Sinorhizobium sp. upon Pb and Zn exposure: Mineralization versus complexation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123260. [PMID: 38159637 DOI: 10.1016/j.envpol.2023.123260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Lead (Pb) and zinc (Zn) have been discharged into environment and may negatively impact ecological security. Rhizobia has gained attention due to their involvement in the restoration of metal polluted soils. However, little is known about the responses of rhizobia under Pb and Zn stress, especially the roles played by extracellular polymeric substances (EPS) in the resistance of these two metals. Here, Sinorhizobium sp. C10 was isolated from soil around a mining area and was exposed to a series of Pb/Zn treatments. The cell morphology and surface mineral crystals, EPS content and fluorescent substances were determined. In addition, the extracellular polysaccharides and proteins were characterized by attenuated total reflection infrared spectroscopy (ATR-IR) and X-ray photoelectron spectroscopy (XPS). The results showed that Zn stress induced the synthesis of EPS by C10 cells. Functional groups of polysaccharides (CO) and proteins (C-O/C-N) were involved in complexation with Zn. In contrast, C10 resisted Pb stress by forming lead phosphate (Pb3(PO4)2) on the cell surface. Galactose (Gal) and tyrosine played key roles in resistance to the Zn toxicity, whereas glucosamine (N-Glc) was converted to glucose in large amounts during extracellular Pb precipitation. Together, this study demonstrated that C10 possessed different strategies to detoxify the two metals, and could provide basis for bioremediation of Pb and Zn polluted sites.
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Affiliation(s)
- Peihuan Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiale Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Ying
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nike Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shu Fang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Menglei Ye
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunhua Zhang
- Demonstration Laboratory of Element and Life Science Research, Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chonghua Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ying Ge
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Huang M, Shen S, Meng Z, Si G, Wu X, Feng T, Liu C, Chen J, Duan C. Mechanisms involved in the sequestration and resistance of cadmium for a plant-associated Pseudomonas strain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115527. [PMID: 37806135 DOI: 10.1016/j.ecoenv.2023.115527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/07/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023]
Abstract
Understanding Cd-resistant bacterial cadmium (Cd) resistance systems is crucial for improving microremediation in Cd-contaminated environments. However, these mechanisms are not fully understood in plant-associated bacteria. In the present study, we investigated the mechanisms underlying Cd sequestration and resistance in the strain AN-B15. These results showed that extracellular Cd sequestration by complexation in strain AN-B15 was primarily responsible for the removal of Cd from the solution. Transcriptome analyses have shown that the mechanisms of Cd resistance at the transcriptional level involve collaborative processes involving multiple metabolic pathways. The AN-B15 strain upregulated the expression of genes related to exopolymeric substance synthesis, metal transport, Fe-S cluster biogenesis, iron recruitment, reactive oxygen species oxidative stress defense, and DNA and protein repair to resist Cd-induced stress. Furthermore, inoculation with AN-B15 alleviated Cd-induced toxicity and reduced Cd uptake in the shoots of wheat seedlings, indicating its potential for remediation. Overall, the results improve our understanding of the mechanisms involved in Cd resistance in bacteria and thus have important implications for improving microremediation.
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Affiliation(s)
- Mingyu Huang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Shili Shen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhuang Meng
- School of Agriculture, Yunnan University, Kunming 650091, China
| | - Guangzheng Si
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Xinni Wu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Tingting Feng
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Chang'e Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Jinquan Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Changqun Duan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China; School of Agriculture, Yunnan University, Kunming 650091, China.
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Zheng K, Liu Z, Liu C, Liu J, Zhuang J. Enhancing remediation potential of heavy metal contaminated soils through synergistic application of microbial inoculants and legumes. Front Microbiol 2023; 14:1272591. [PMID: 37840744 PMCID: PMC10571051 DOI: 10.3389/fmicb.2023.1272591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Soil microorganisms play a crucial role in remediating contaminated soils in modern ecosystems. However, the potential of combining microorganisms with legumes to enhance the remediation of heavy metal-contaminated soils remains unexplored. To investigate this, we isolated and purified a highly efficient cadmium and lead-tolerant strain. Through soil-cultivated pot experiments with two leguminous plants (Robinia pseudoacacia L. and Sophora xanthantha), we studied the effects of applying this microbial agent on plant nutrient uptake of soil nutrients, heavy metal accumulation, and the dynamics of heavy metal content. Additionally, we examined the response characteristics of inter-root microbial and bacterial communities. The results demonstrated that microorganisms screened from heavy metal-contaminated soil environments exhibited strong survival and adaptability in heavy metal solutions. The use of the Serratia marcescens WZ14 strain-phytoremediation significantly increased the soil's ammonium nitrogen (AN) and organic carbon (OC) contents compared to monoculture. In addition, the lead (Pb) and cadmium (Cd) contents of the soil significantly decreased after combined remediation than those of the soil before potting. However, the remediation effects on Pb- and Cd-contaminated soils differed between the two legumes following the Serratia marcescens WZ14 inoculation. The combined restoration altered the composition of the plant inter-rhizosphere bacterial community, with the increase in the relative abundance of both Proteobacteria and Firmicutes. Overall, the combined remediation using the tolerant strain WZ14 with legumes proved advantageous. It effectively reduced the heavy metal content of the soil, minimized the risk of heavy metal migration, and enhanced heavy metal uptake, accumulation, and translocation in the legumes of S. xanthantha and R. pseudoacacia. Additionally, it improved the adaptability and resistance of both legumes, leading to an overall improvement in the soil's environmental quality. These studies can offer primary data and technical support for remediating and treating Cd and Pb in soils, as well as rehabilitating mining sites.
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Affiliation(s)
| | | | | | | | - Jiayao Zhuang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China
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Rai PK, Sonne C, Kim KH. Heavy metals and arsenic stress in food crops: Elucidating antioxidative defense mechanisms in hyperaccumulators for food security, agricultural sustainability, and human health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162327. [PMID: 36813200 DOI: 10.1016/j.scitotenv.2023.162327] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The spread of heavy metal(loid)s at soil-food crop interfaces has become a threat to sustainable agricultural productivity, food security, and human health. The eco-toxic effects of heavy metals on food crops can be manifested through reactive oxygen species that have the potential to disturb seed germination, normal growth, photosynthesis, cellular metabolism, and homeostasis. This review provides a critical overview of stress tolerance mechanisms in food crops/hyperaccumulator plants against heavy metals and arsenic (HM-As). The HM-As antioxidative stress tolerance in food crops is associated with changes in metabolomics (physico-biochemical/lipidomics) and genomics (molecular level). Furthermore, HM-As stress tolerance can occur through plant-microbe, phytohormone, antioxidant, and signal molecule interactions. Information regarding the avoidance, tolerance, and stress resilience of HM-As should help pave the way to minimize food chain contamination, eco-toxicity, and health risks. Advanced biotechnological approaches (e.g., genome modification with CRISPR-Cas9 gene editing) in concert with traditional sustainable biological methods are useful options to develop 'pollution safe designer cultivars' with increased climate change resilience and public health risks mitigation. Further, the usage of HM-As tolerant hyperaccumulator biomass in biorefineries (e.g., environmental remediation, value added chemicals, and bioenergy) is advocated to realize the synergy between biotechnological research and socio-economic policy frameworks, which are inextricably linked with environmental sustainability. The biotechnological innovations, if directed toward 'cleaner climate smart phytotechnologies' and 'HM-As stress resilient food crops', should help open the new path to achieve sustainable development goals (SDGs) and a circular bioeconomy.
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Affiliation(s)
- Prabhat Kumar Rai
- Department of Environmental Science, Mizoram University, Aizawl 796004, India
| | - Christian Sonne
- Department of Ecoscience, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Ki-Hyun Kim
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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Mu D, Zheng S, Lin D, Xu Y, Dong R, Pei P, Sun Y. Derivation and validation of soil cadmium thresholds for the safe farmland production of vegetables in high geological background area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162171. [PMID: 36775143 DOI: 10.1016/j.scitotenv.2023.162171] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Excessive dietary intake of cadmium (Cd) poses toxicity risks to human health, and it is therefore essential to establish accurate and regionally appropriate soil Cd thresholds that ensure the safety of agricultural products grown in different areas. This study investigated the differences in the Cd accumulation in 32 vegetable varieties and found that the Cd content ranged from 0.01 to 0.24 mg·kg-1, and decreased in the order of stem and bulb vegetables > leafy vegetables > solanaceous crops > bean cultivars. A correlation analysis and structural equation model showed that pH, soil organic matter, and the cation exchange capacity had significant effects on Cd accumulation in the vegetables and explained 72.1 % of the variance. In addition, species sensitivity distribution (SSD) curves showed that stem and bulb vegetables were more sensitive to Cd than other types of vegetables. Using the Burr Type III function for curve fitting, we derived Cd thresholds of 6.66, 4.15, and 1.57 mg·kg-1 for vegetable soils. These thresholds will ensure that 20 %, 50 %, and 95 % of these vegetable varieties were risk-free, respectively. The predicted threshold of soil Cd was more than twice that of China's current National Soil Quality Standard (GB 15618-2018) for Cd values. Therefore, soil scenarios and cultivars should be considered comprehensively when determining farmland soil thresholds. The present results provide a new model for setting soil Cd criteria in high geological background areas.
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Affiliation(s)
- Demiao Mu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China
| | - Shunan Zheng
- Rural Energy & Environment Agency, MARA, Beijing 100125, China
| | - Dasong Lin
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China
| | - Yingming Xu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China
| | - Ruyin Dong
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China
| | - Penggang Pei
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China
| | - Yuebing Sun
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin 300191, China.
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7
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Diez-Marulanda JC, Brandão PFB. Isolation of urease-producing bacteria from cocoa farms soils in Santander, Colombia, for cadmium remediation. 3 Biotech 2023; 13:98. [PMID: 36860360 PMCID: PMC9968674 DOI: 10.1007/s13205-023-03495-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/25/2023] [Indexed: 03/01/2023] Open
Abstract
Cadmium (Cd) is a toxic heavy metal that causes serious health problems and is present in agriculturally important soils in Colombia, such as the ones used for cocoa farming. Recently, the use of ureolytic bacteria by the Microbiologically Induced Carbonate Precipitation (MICP) activity has been proposed as an alternative to mitigate the availability of Cd in contaminated soils. In this study, 12 urease-positive bacteria able to grow in the presence of Cd(II) were isolated and identified. Three were selected based on urease activity, precipitates formation and growth, with two belonging to the genus Serratia (codes 4.1a and 5b) and one to Acinetobacter (code 6a). These isolates exhibited low urease activity levels (3.09, 1.34 and 0.31 μmol mL-1 h-1, respectively), but could raise the pH to values close to 9.0 and to produce carbonate precipitates. It was shown that the presence of Cd affects the growth of the selected isolates. However, urease activity was not negatively influenced. In addition, the three isolates were observed to efficiently remove Cd from solution. The two Serratia isolates presented maximum removals of 99.70% and 99.62%, with initial 0.05 mM Cd(II) in the culture medium (supplemented with urea and Ca(II)) at 30 °C and 144 h of incubation. For the Acinetobacter isolate, the maximum removal was 91.23% at the same conditions. Thus, this study evidences the potential use of these bacteria for bioremediation treatments in samples contaminated with Cd, and it is one of the few reports that shows the high cadmium removal capacity of bacteria from the genus Serratia. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03495-1.
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Affiliation(s)
- Juan C. Diez-Marulanda
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (GERMINA), Av. Carrera 30 # 45-03, 111321 Bogotá, Colombia
| | - Pedro F. B. Brandão
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (GERMINA), Av. Carrera 30 # 45-03, 111321 Bogotá, Colombia
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Han X, Wang J, Zhang Y, Kong Y, Dong H, Feng X, Li T, Zhou C, Yu J, Xin D, Chen Q, Qi Z. Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129843. [PMID: 36113351 DOI: 10.1016/j.jhazmat.2022.129843] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) is the most widely distributed heavy metal pollutant in soil and has significant negative effects on crop yields and human health. Rhizobia can enhance soybean growth in the presence of heavy metals, and the legume-rhizobia symbiosis has been used to promote heavy-metal phytoremediation, but much remains to be learned about the molecular networks that underlie these effects. Here, we demonstrated that soybean root growth was strongly suppressed after seven days of Cd exposure but that the presence of rhizobia largely eliminated this effect, even prior to nodule development. Moreover, rhizobia did not appear to promote root growth by limiting plant Cd uptake: seedlings with and without rhizobia had similar root Cd concentrations. Previous studies have demonstrated a role for m6A RNA methylation in the response of rice and barley to Cd stress. We therefore performed transcriptome-wide m6A methylation profiling to investigate changes in the soybean RNA methylome in response to Cd with and without rhizobia. Here, we provide some of the first data on transcriptome-wide m6a RNA methylation patterns in soybean; m6A modifications were concentrated at the 3' UTR of transcripts and showed a positive relationship with transcript abundance. Transcriptome-wide m6A RNA methylation peaks increased in the presence of Cd, and the integration of m6A methylome and transcriptome results enabled us to identify 154 genes whose transcripts were both differentially methylated and differentially expressed in response to Cd stress. Annotation results suggested that these genes were associated with Ca2+ homeostasis, ROS pathways, polyamine metabolism, MAPK signaling, hormones, and biotic stress responses. There were 176 differentially methylated and expressed transcripts under Cd stress in the presence of rhizobia. In contrast to the Cd-only gene set, they were also enriched in genes related to auxin, jasmonic acid, and brassinosteroids, as well as abiotic stress tolerance. They contained fewer genes related to Ca2+ homeostasis and also included candidates with known functions in the legume-rhizobia symbiosis. These findings offer new insights into how rhizobia promote soybean root growth under Cd stress; they provide candidate genes for research on plant heavy metal responses and for the use of legumes in phytoremediation.
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Affiliation(s)
- Xue Han
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Jialin Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Youlin Kong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Huiying Dong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Xuezhen Feng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Tianshu Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Changjun Zhou
- Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China
| | - Jidong Yu
- Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
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Elbagory M, El-Nahrawy S, Omara AED. Synergistic Interaction between Symbiotic N 2 Fixing Bacteria and Bacillus strains to Improve Growth, Physiological Parameters, Antioxidant Enzymes and Ni Accumulation in Faba Bean Plants ( Vicia faba) under Nickel Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:1812. [PMID: 35890447 PMCID: PMC9322151 DOI: 10.3390/plants11141812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Several activities in the agriculture sector lead to the accumulation of Nickel (Ni) in soil. Therefore, effective and economical ways to reduce soil bioavailability of Ni must be identified. Five isolates of Rhizobium leguminosarum biovar Viceae (ICARDA 441, ICARDA 36, ICARDA 39, TAL−1148, and ARC−207) and three bacterial strains (Bacillus subtilis, B. circulance, and B. coagulans) were evaluated for tolerance and biosorption of different levels of Ni (0, 20, 40, 60, and 80 mg L−1). Pot experiments were conducted during the 2019/2020 and 2020/2021 seasons using four inoculation treatments (inoculation with the most tolerant Rhizobium (TAL−1148), inoculation with the most tolerant Rhizobium (TAL−1148) + B. subtilis, inoculation with the most tolerant Rhizobium (TAL−1148) + B. circulance, and inoculation with the most tolerant Rhizobium (TAL−1148) + B. coagulans) under different levels of Ni (0, 200, 400, and 600 mg kg−1), and their effects on growth, physiological characteristics, antioxidant enzymes, and Ni accumulation in faba bean plants (Vicia faba C.V. Nobaria 1) were determined. The results showed that Rhizobium (TAL−1148) and B. subtilis were the most tolerant of Ni. In pot trials, inoculation with the most tolerant Rhizobium TAL−1148 + B. subtilis treatment was shown to be more effective in terms of growth parameters (dry weight of plant, plant height, number of nodules, and N2 content), and this was reflected in physiological characteristics and antioxidant enzymes under 600 mg kg−1 Ni compared to the other treatments in the 2019/2020 season. In the second season, 2020/2021, a similar pattern was observed. Additionally, lower concentrations of Ni were found in faba bean plants (roots and shoots). Therefore, a combination of the most tolerant Rhizobium (TAL−1148) + B. subtilis treatment might be used to reduce Ni toxicity.
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Affiliation(s)
- Mohssen Elbagory
- Department of Biology, Faculty of Science and Arts, King Khalid University, Mohail 61321, Assir, Saudi Arabia;
- Agricultural Research Center, Department of Microbiology, Soils, Water and Environment Research Institute, Giza 12112, Egypt;
| | - Sahar El-Nahrawy
- Agricultural Research Center, Department of Microbiology, Soils, Water and Environment Research Institute, Giza 12112, Egypt;
| | - Alaa El-Dein Omara
- Agricultural Research Center, Department of Microbiology, Soils, Water and Environment Research Institute, Giza 12112, Egypt;
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10
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Analysis of Ensifer aridi Mutants Affecting Regulation of Methionine, Trehalose, and Inositol Metabolisms Suggests a Role in Stress Adaptation and Symbiosis Development. Microorganisms 2022; 10:microorganisms10020298. [PMID: 35208753 PMCID: PMC8877191 DOI: 10.3390/microorganisms10020298] [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: 12/20/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Isolated from desert, the nitrogen-fixing bacterium Ensifer aridi LMR001 is capable of survival under particularly harsh environmental conditions. To obtain insights in molecular mechanisms involved in stress adaptation, a recent study using RNAseq revealed that the RpoE2-mediated general stress response was activated under mild saline stress but appeared non-essential for the bacterium to thrive under stress and develop the symbiosis. Functions associated with the stress response included the metabolisms of trehalose, methionine, and inositol. To explore the roles of these metabolisms in stress adaptation and symbiosis development, and the possible regulatory mechanisms involved, mutants were generated notably in regulators and their transcriptions were studied in various mutant backgrounds. We found that mutations in regulatory genes nesR and sahR of the methionine cycle generating S-adenosylmethionine negatively impacted symbiosis, tolerance to salt, and motility in the presence of NaCl. When both regulators were mutated, an increased tolerance to detergent, oxidative, and acid stresses was found, suggesting a modification of the cell wall components which may explain these phenotypes and support a major role of the fine-tuning methylation for symbiosis and stress adaptation of the bacterium. In contrast, we also found that mutations in the predicted trehalose transport and utilization regulator ThuR and the trehalose phosphate phosphatase OtsB-encoding genes improved symbiosis and growth in liquid medium containing 0.4 M of NaCl of LMR001ΔotsB, suggesting that trehalose metabolism control and possibly trehalose-6 phosphate cellular status may be biotechnologically engineered for improved symbiosis under stress. Finally, transcriptional fusions of gfp to promoters of selected genes and expression studies in the various mutant backgrounds suggest complex regulatory interplay between inositol, methionine, and trehalose metabolic pathways.
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Chhetri G, Kim J, Kim I, Kang M, So Y, Seo T. Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants. Antonie van Leeuwenhoek 2021; 114:1925-1934. [PMID: 34491486 DOI: 10.1007/s10482-021-01651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4-95.6%), Aquabacterium (95.9-95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30 °C in the presence of 1-6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8-76.3% and 19.4-21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711 T = NBRC 114717 T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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Ren C, Teng Y, Chen X, Shen Y, Xiao H, Wang H. Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 83:103606. [PMID: 33545380 DOI: 10.1016/j.etap.2021.103606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.
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Affiliation(s)
- Chaolu Ren
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Yiran Teng
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Xiaoyan Chen
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Yujia Shen
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Hui Xiao
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongyuan Wang
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China.
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Rolón-Cárdenas GA, Arvizu-Gómez JL, Pacheco-Aguilar JR, Vázquez-Martínez J, Hernández-Morales A. Cadmium-tolerant endophytic Pseudomonas rhodesiae strains isolated from Typha latifolia modify the root architecture of Arabidopsis thaliana Col-0 in presence and absence of Cd. Braz J Microbiol 2021; 52:349-361. [PMID: 33236245 PMCID: PMC7966613 DOI: 10.1007/s42770-020-00408-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022] Open
Abstract
In this work, we isolated four Cd-tolerant endophytic bacteria from Typha latifolia roots that grow at a Cd-contaminated site. Bacterial isolates GRC065, GRC066, GRC093, and GRC140 were identified as Pseudomonas rhodesiae. These bacterial isolates tolerate cadmium and have abilities for phosphate solubilization, siderophore production, indole acetic acid (IAA) synthesis, and ACC deaminase activity, suggesting that they are plant growth-promoting rhizobacteria. Bacterial inoculation in Arabidopsis thaliana seedlings showed that P. rhodesiae strains increase total fresh weight and number of lateral roots concerning non-inoculated plants. These results indicated that P. rhodesiae strains promote A. thaliana seedlings growth by modifying the root system. On the other hand, in A. thaliana seedlings exposed to 2.5 mg/l of Cd, P. rhodesiae strains increased the number and density of lateral roots concerning non-inoculated plants, indicating that they modify the root architecture of A. thaliana seedlings exposed to cadmium. The results showed that P. rhodesiae strains promote the development of lateral roots in A. thaliana seedlings cultivated in both conditions, with and without cadmium. These results suggest that P. rhodesiae strains could exert a similar role inside the roots of T. latifolia that grow in the Cd-contaminated environment.
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Affiliation(s)
- Gisela Adelina Rolón-Cárdenas
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, Mexico
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, CP 79060, Ciudad Valles, San Luis Potosí, Mexico
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic, Nayarit, Mexico
| | | | - Juan Vázquez-Martínez
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México (TecNM), Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, Mexico
| | - Alejandro Hernández-Morales
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, Mexico.
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, CP 79060, Ciudad Valles, San Luis Potosí, Mexico.
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Edulamudi P, Antony Masilamani AJ, Vanga UR, Divi VRSG, Konada VM. Nickel tolerance and biosorption potential of rhizobia associated with horse gram [ Macrotyloma uniflorum (Lam.) Verdc.]. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:1184-1190. [PMID: 33599156 DOI: 10.1080/15226514.2021.1884182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The rhizobia isolated from root nodules of horse gram were screened for nickel (Ni) tolerance in vitro. The strain HGR-4 could tolerate 1000 µg g-1 of Ni. It was also observed that horse gram plants associated with HGR-4 have shown Ni stress tolerance in Ni amended soils up to a concentration of 100 µg g-1. In another experiment, the plants associated with HGR-4 have shown higher nodulation, nitrogen level, and leghaemoglobin content at 80 µg g-1 of Ni than control plants without HGR-4 inoculation. Analysis of biosorption potential of Ni in horse gram plants inoculated by the strain HGR-4 was done using atomic absorption spectroscopy revealed maximum biosorption in bacterial root nodules. Besides, there was a reduction in the content of the heavy metal in the soil samples which demonstrates a fair amount of heavy metal extraction and accumulation of Ni by rhizobia associated root nodules of the horse gram. This study demonstrates that the strain HGR-4 (GQ483457 Rhizobium sp. ATCC BAA-2335) could be a potential source for phytoextraction of Ni contaminated soils upon its association with horse gram. The study could be of use in phytoremediation of metal (Ni) contaminated soils in the future. Novelty statement: The phytoremediation of nickel (Ni) using of rhizobia associated with horse gram remains unevaluated till now. Horse gram associated with rhizobia could produce nodules and fix nitrogen even in Ni amended soils. The biosorption potential of the rhizobial strains was analyzed from both root nodules and soil. These findings imply that horse gram plants associated with these rhizobial strains could be used to remediate Ni metal in contaminated soils.
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Affiliation(s)
- Prabhavati Edulamudi
- Department of Botany and Microbiology, Acharya Nagarjuna University, Guntur, India
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Wang Q, Li Q, Lin Y, Hou Y, Deng Z, Liu W, Wang H, Xia Z. Biochemical and genetic basis of cadmium biosorption by Enterobacter ludwigii LY6, isolated from industrial contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114637. [PMID: 32380392 DOI: 10.1016/j.envpol.2020.114637] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
In this study, a cadmium-tolerant bacterium, Enterobacter ludwigii LY6, was isolated from cadmium-contaminated soil in Shifang, Sichuan province, China. The cadmium chloride removal rate of the strain LY6 with a treatment of 100 mg/L cadmium chloride reached 56.0%. Scanning electron microscopy showed that exopolysaccharides (EPS) might be the main means of cadmium adsorption by the strain. X-ray powder diffraction (XRD) and energy-dispersive X-ray spectroscopy (EDS) analyses indicated that cadmium sulfide nanoparticles formed on the surface of bacteria cultured in a medium containing 100 mg/L cadmium chloride. In addition, the expression of several genes increased with the increase of the cadmium concentration in the medium, including the multiple antibiotic resistance proteins marA and marR, and the cold shock protein CspA. GO functions, such as the redox activity, respiratory chain and transport functions, and KEGG pathways involved in "bacterial chemotaxis" and "terpenoid backbone biosynthesis" were found to be closely related to bacterial cadmium tolerance and biosorption. This is the first report that E. ludwigii can reduce sulfate to form cadmium sulfide nanoparticles under high concentration cadmium exposure. The genes related to cadmium tolerance identified in this study lay a foundation for the genetic breeding of cadmium-tolerant strains.
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Affiliation(s)
- QiangFeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Yang Lin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Yong Hou
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Ziyuan Deng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Wu Liu
- Sichuan Lanyue Science and Technology Co., Ltd., Chengdu, 610207, Sichuan, China
| | - Haitao Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - ZhongMei Xia
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China.
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Perry BJ, Sullivan JT, Colombi E, Murphy RJT, Ramsay JP, Ronson CW. Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings. Microb Genom 2020; 6. [PMID: 32845829 PMCID: PMC7643969 DOI: 10.1099/mgen.0.000426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mesorhizobium is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). Mesorhizobium strains that nodulate Lotus spp. have been divided into host-range groupings. Group I (GI) strains nodulate L. corniculatus and L. japonicus ecotype Gifu, while group II (GII) strains have a broader host range, which includes L. pedunculatus. To identify the basis of this extended host range, and better understand Mesorhizobium and ICESym genomics, the genomes of eight Mesorhizobium strains were completed using hybrid long- and short-read assembly. Bioinformatic comparison with previously sequenced mesorhizobia genomes indicated host range was not predicted by Mesorhizobium genospecies but rather by the evolutionary relationship between ICESym symbiotic regions. Three radiating lineages of Loteae ICESyms were identified on this basis, which correlate with Lotus spp. host-range grouping and have lineage-specific nod gene complements. Pangenomic analysis of the completed GI and GII ICESyms identified 155 core genes (on average 30.1 % of a given ICESym). Individual GI or GII ICESyms carried diverse accessory genes with an average of 34.6 % of genes unique to a given ICESym. Identification and comparative analysis of NodD symbiotic regulatory motifs – nod boxes – identified 21 branches across the NodD regulons. Four of these branches were associated with seven genes unique to the five GII ICESyms. The nod boxes preceding the host-range gene nodZ in GI and GII ICESyms were disparate, suggesting regulation of nodZ may differ between GI and GII ICESyms. The broad host-range determinant(s) of GII ICESyms that confer nodulation of L. pedunculatus are likely present amongst the 53 GII-unique genes identified.
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Affiliation(s)
- Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Elena Colombi
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Riley J T Murphy
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Joshua P Ramsay
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Meier MJ, Dodge AE, Samarajeewa AD, Beaudette LA. Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113816. [PMID: 31864930 DOI: 10.1016/j.envpol.2019.113816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 05/20/2023]
Abstract
Anthropogenic activities can disrupt soil ecosystems, normally resulting in reduced soil microbial health. Regulatory agencies need to determine the effects of uncharacterized substances on soil microbial health to establish the safety of these chemicals if they end up in the environment. Previous work has focused on measuring traditional ecotoxicologial endpoints within the categories of microbial biomass, activity, and community structure/diversity. Because these tests can be labor intensive, lengthy to conduct, and cannot measure changes in individual gene functions, we wanted to establish whether metatranscriptomics could be used as a more sensitive endpoint and provide a perspective on community function that is more informative than taxonomic identification of microbes alone. We spiked a freshly collected sandy loam soil (Vulcan, Alberta, Canada) with 0, 60, 145, 347, 833, and 2000 mg kg-1 of silver nanoparticles (AgNPs), a known antagonist of microorganisms due to its propensity for dissolution of toxic silver ions. Assessments performed in our previous work using traditional tests demonstrated the toxicity of AgNPs on soil microbial processes. We expanded this analysis with genomics-based tests by measuring changes in community taxonomic structure and function using 16S rDNA profiling and metatranscriptomics. In addition to identifying bacterial taxa affected by AgNPs, we found that genes involved in heavy metal resistance (e.g., the CzcA efflux pump) and other toxicity response pathways were highly upregulated in the presence of silver. Dose-response analysis using BMDExpress2 software successfully modeled many physiologically relevant genes responding to low concentrations of AgNPs. We found that the transcriptomic point of departure (BMD50) was lower than the IC50s calculated using the traditional tests in our previous work. These results suggest that dose-response modeling of metatranscriptomic gene expression is a useful tool in soil microbial health assessment. SUMMARY: Genomics-based endpoints for the assessment of soil microbial health can be used to perform quantitative dose-response modeling, and soil-based RNAseq adds functional insights.
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Affiliation(s)
- Matthew J Meier
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada.
| | - Annette E Dodge
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Ajith Dias Samarajeewa
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Lee A Beaudette
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
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Rai PK, Kim KH, Lee SS, Lee JH. Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135858. [PMID: 31846820 DOI: 10.1016/j.scitotenv.2019.135858] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.
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Affiliation(s)
- Prabhat Kumar Rai
- Department of Environmental Science, Mizoram University, Aizawl 796004, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Sang Soo Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26494, Republic of Korea.
| | - Jin-Hong Lee
- Department of Environmental Engineering, Chungnam National University, Daejeon 34148, Republic of Korea
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Armendariz AL, Talano MA, Olmos Nicotra MF, Escudero L, Breser ML, Porporatto C, Agostini E. Impact of double inoculation with Bradyrhizobium japonicum E109 and Azospirillum brasilense Az39 on soybean plants grown under arsenic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 138:26-35. [PMID: 30831360 DOI: 10.1016/j.plaphy.2019.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Inoculation practice with plant growth-promoting bacteria (PGPB) has been proposed as a good biotechnological tool to enhance plant performance and alleviate heavy metal/metalloid stress. Soybean is often cultivated in soil with high arsenic (As) content or irrigated with As-contaminated groundwater, which causes deleterious effects on its growth and yield, even when it was inoculated with rhizobium. Thus, the effect of double inoculation with known PGPB strains, Bradyrhizobium japonicum E109 and Azospirillum brasilense Az39 was evaluated in plants grown in pots under controlled conditions and treated with As. First, the viability of these co-cultivated bacteria was assayed using a flow cytometry analysis using SYTO9 and propidium iodide (PI) dyes. This was performed in vitro to evaluate the bacterial population dynamic under 25 μM AsV and AsIII treatment. A synergistic effect was observed when bacteria were co-cultured, since mortality diminished, compared to each growing alone. Indole acetic acid (IAA) produced by A. brasilense Az39 would be one of the main components involved in B. japonicum E109 mortality reduction, mainly under AsIII treatment. Regarding in vivo assays, under As stress, plant growth improvement, nodule number and N content increase were observed in double inoculated plants. Furthermore, double inoculation strategy reduced As translocation to aerial parts thus improving As phytostabilization potential of soybean plants. These results suggest that double inoculation with B. japonicum E109 and A. brasilense Az39 could be a safe and advantageous practice to improve growth and yield of soybean exposed to As, accompanied by an important metalloid phytostabilization.
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Affiliation(s)
- Ana L Armendariz
- Molecular Biology Department, Faculty of Exact, Physical, Chemical and Natural Sciences, National University of Río Cuarto, Ruta Nacional 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
| | - Melina A Talano
- Molecular Biology Department, Faculty of Exact, Physical, Chemical and Natural Sciences, National University of Río Cuarto, Ruta Nacional 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
| | - María Florencia Olmos Nicotra
- Molecular Biology Department, Faculty of Exact, Physical, Chemical and Natural Sciences, National University of Río Cuarto, Ruta Nacional 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
| | - Leticia Escudero
- Laboratory of Analytical Chemistry for Research and Development (QUIANID), Interdisciplinary Institute of Basic Sciences (ICB), UNCUYO-CONICET, Faculty of Natural and Exact Sciences, National University of Cuyo, Padre J. Contreras 1300, CP 5500, Mendoza, Argentina.
| | - María Laura Breser
- Research and Transference Center of Villa María (CITVM-CONICET), National University of Villa María, Arturo Jauretche 1555, CP 5900, Villa María, Córdoba, Argentina.
| | - Carina Porporatto
- Research and Transference Center of Villa María (CITVM-CONICET), National University of Villa María, Arturo Jauretche 1555, CP 5900, Villa María, Córdoba, Argentina.
| | - Elizabeth Agostini
- Molecular Biology Department, Faculty of Exact, Physical, Chemical and Natural Sciences, National University of Río Cuarto, Ruta Nacional 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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Chen Y, Ding Q, Chao Y, Wei X, Wang S, Qiu R. Structural development and assembly patterns of the root-associated microbiomes during phytoremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1591-1601. [PMID: 30743871 DOI: 10.1016/j.scitotenv.2018.07.095] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 05/20/2023]
Abstract
Successful in situ phytoremediation depends on beneficial interactions between roots and microbes. However, the assembly strategies of root-associated microbiome during phytoremediation are not well known. Here we investigated the assembly patterns of root-associated microbiomes during phytoremediation as well as its regulation by both plants and heavy metals. Plant cultivation and soil amendment increased microbial diversity and restructured microbial communities. Rhizo-compartmentalization was the largest source of variation in root-associated microbiomes, with endosphere being the most independent and exclusive compartment. Soil type explained a larger amount of microbiomes variation in bulk soil and rhizosphere than that in endosphere. A specific core root microbiome was likely to be selected by the metal-tolerant plant H. cannabinus, with Enterobacteriaceae, Pseudomonadaceae and Comamonadaceae which contain a large number of metal-tolerant and plant growth-promoting bacteria (PGPB) being the most abundant families. The root-associated microbial community tended to proceed a niche-assembled patterns and formed a smaller bacterial pool dominant by Proteobacteria, Actinobacteria and Chloroflexi under metal-contaminated conditions. Among these genera, potential metal-tolerant PGPB species have taken up the keystone positions in the microbial co-occurrence networks, revealing their key roles in metal-contaminated environment due to niche selection. We also detected a keystone functional group reducing metal bioavailability which might work as vanguards and devote to maintaining the structure and function of the whole microbial community. In conclusion, this study suggested a specific assembly pattern of root-associated microbiomes of the metal-tolerant plant H. cannabinus during phytoremediation, showing the directional selections of the associated microbiomes by both the plant and metal-contaminated conditions in such a system.
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Affiliation(s)
- Yanmei Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Qiaobei Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China.
| | - Xiange Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
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Transcriptome Response to Heavy Metals in Sinorhizobium meliloti CCNWSX0020 Reveals New Metal Resistance Determinants That Also Promote Bioremediation by Medicago lupulina in Metal-Contaminated Soil. Appl Environ Microbiol 2017; 83:AEM.01244-17. [PMID: 28778889 DOI: 10.1128/aem.01244-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 07/26/2017] [Indexed: 01/16/2023] Open
Abstract
The symbiosis of the highly metal-resistant Sinorhizobium meliloti CCNWSX0020 and Medicago lupulina has been considered an efficient tool for bioremediation of heavy metal-polluted soils. However, the metal resistance mechanisms of S. meliloti CCNWSX00200 have not been elucidated in detail. Here we employed a comparative transcriptome approach to analyze the defense mechanisms of S. meliloti CCNWSX00200 against Cu or Zn exposure. Six highly upregulated transcripts involved in Cu and Zn resistance were identified through deletion mutagenesis, including genes encoding a multicopper oxidase (CueO), an outer membrane protein (Omp), sulfite oxidoreductases (YedYZ), and three hypothetical proteins (a CusA-like protein, a FixH-like protein, and an unknown protein), and the corresponding mutant strains showed various degrees of sensitivity to multiple metals. The Cu-sensitive mutant (ΔcueO) and three mutants that were both Cu and Zn sensitive (ΔyedYZ, ΔcusA-like, and ΔfixH-like) were selected for further study of the effects of these metal resistance determinants on bioremediation. The results showed that inoculation with the ΔcueO mutant severely inhibited infection establishment and nodulation of M. lupulina under Cu stress, while inoculation with the ΔyedYZ and ΔfixH-like mutants decreased just the early infection frequency and nodulation under Cu and Zn stresses. In contrast, inoculation with the ΔcusA-like mutant almost led to loss of the symbiotic capacity of M. lupulina to even grow in uncontaminated soil. Moreover, the antioxidant enzyme activity and metal accumulation in roots of M. lupulina inoculated with all mutants were lower than those with the wild-type strain. These results suggest that heavy metal resistance determinants may promote bioremediation by directly or indirectly influencing formation of the rhizobium-legume symbiosis.IMPORTANCE Rhizobium-legume symbiosis has been promoted as an appropriate tool for bioremediation of heavy metal-contaminated soils. Considering the plant-growth-promoting traits and survival advantage of metal-resistant rhizobia in contaminated environments, more heavy metal-resistant rhizobia and genetically manipulated strains were investigated. In view of the genetic diversity of metal resistance determinants in rhizobia, their effects on phytoremediation by the rhizobium-legume symbiosis must be different and depend on their specific assigned functions. Our work provides a better understanding of the mechanism of heavy metal resistance determinants involved in the rhizobium-legume symbiosis, and in further studies, genetically modified rhizobia harboring effective heavy metal resistance determinants may be engineered for the practical application of rhizobium-legume symbiosis for bioremediation in metal-contaminated soils.
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Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
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Dreiseikelmann B, Bunk B, Spröer C, Rohde M, Nimtz M, Wittmann J. Characterization and genome comparisons of three Achromobacter phages of the family Siphoviridae. Arch Virol 2017; 162:2191-2201. [PMID: 28357512 DOI: 10.1007/s00705-017-3347-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 03/17/2017] [Indexed: 11/30/2022]
Abstract
In this study, we present the characterization and genomic data of three Achromobacter phages belonging to the family Siphoviridae. Phages 83-24, JWX and JWF were isolated from sewage samples in Paris and Braunschweig, respectively, and infect Achromobacter xylosoxidans, an emerging nosocomial pathogen in cystic fibrosis patients. Analysis of morphology and growth parameters revealed that phages 83-24 and JWX have similar properties, both have nearly the same head and tail measurements, and both have a burst size between 85 and 100 pfu/cell. In regard to morphological properties, JWF had a much longer and more flexible tail compared to other phages. The linear double-stranded DNAs of all three phages are terminally redundant and not circularly permutated. The complete nucleotide sequences consist of 81,541 bp for JWF, 49,714 bp for JWX and 48,216 bp for 83-24. Analysis of the genome sequences showed again that phages JWX and 83-24 are quite similar. Comparison to the GenBank database via BLASTN revealed partial similarities to Roseobacter phage RDJL phi1 and Burkholderia phage BcepGomr. In contrast, BLASTN analysis of the genome sequence of phage JWF revealed only few similarities to non-annotated prophage regions in different strains of Burkholderia and Mesorhizobium.
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Affiliation(s)
- Brigitte Dreiseikelmann
- Department of Microbiology/Genetechnology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Manfred Nimtz
- Protein Analytics Platform, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany.
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Ancient Heavy Metal Contamination in Soils as a Driver of Tolerant Anthyllis vulneraria Rhizobial Communities. Appl Environ Microbiol 2016; 83:AEM.01735-16. [PMID: 27793823 DOI: 10.1128/aem.01735-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023] Open
Abstract
Anthyllis vulneraria is a legume associated with nitrogen-fixing rhizobia that together offer an adapted biological material for mine-soil phytostabilization by limiting metal pollution. To find rhizobia associated with Anthyllis at a given site, we evaluated the genetic and phenotypic properties of a collection of 137 rhizobia recovered from soils presenting contrasting metal levels. Zn-Pb mine soils largely contained metal-tolerant rhizobia belonging to Mesorhizobium metallidurans or to another sister metal-tolerant species. All of the metal-tolerant isolates harbored the cadA marker gene (encoding a metal-efflux PIB-type ATPase transporter). In contrast, metal-sensitive strains were taxonomically distinct from metal-tolerant populations and consisted of new Mesorhizobium genospecies. Based on the symbiotic nodA marker, the populations comprise two symbiovar assemblages (potentially related to Anthyllis or Lotus host preferences) according to soil geographic locations but independently of metal content. Multivariate analysis showed that soil Pb and Cd concentrations differentially impacted the rhizobial communities and that a rhizobial community found in one geographically distant site was highly divergent from the others. In conclusion, heavy metal levels in soils drive the taxonomic composition of Anthyllis-associated rhizobial populations according to their metal-tolerance phenotype but not their symbiotic nodA diversity. In addition to heavy metals, local soil physicochemical and topoclimatic conditions also impact the rhizobial beta diversity. Mesorhizobium communities were locally adapted and site specific, and their use is recommended for the success of phytostabilization strategies based on Mesorhizobium-legume vegetation. IMPORTANCE Phytostabilization of toxic mine spoils limits heavy metal dispersion and environmental pollution by establishing a sustainable plant cover. This eco-friendly method is facilitated by the use of selected and adapted cover crop legumes living in symbiosis with rhizobia that can stimulate plant growth naturally through biological nitrogen fixation. We studied microsymbiont partners of a metal-tolerant legume, Anthyllis vulneraria, which is tolerant to very highly metal-polluted soils in mining and nonmining sites. Site-specific rhizobial communities were linked to taxonomic composition and metal tolerance capacity. The rhizobial species Mesorhizobium metallidurans was dominant in all Zn-Pb mines but one. It was not detected in unpolluted sites where other distinct Mesorhizobium species occur. Given the different soil conditions at the respective mining sites, including their heavy-metal contamination, revegetation strategies based on rhizobia adapting to local conditions are more likely to succeed over the long term compared to strategies based on introducing less-well-adapted strains.
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Park HR, Oh R, Wagner P, Panganiban R, Lu Q. New Insights Into Cellular Stress Responses to Environmental Metal Toxicants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 331:55-82. [PMID: 28325215 DOI: 10.1016/bs.ircmb.2016.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exposures to metal toxicants in the environment disrupt normal physiological functions and have been linked to the development of a myriad of human diseases. While the molecular and cellular mechanisms underlying metal toxicities remain to be fully understood, it is well appreciated that metal toxicants induce cellular stresses and that how cells respond to the stresses plays an important role in metal toxicity. In this review, we focus on how metal exposures induce stresses in the endoplasmic reticulum (ER) to elicit the unfolded protein response (UPR). We document the emerging evidence that induction of ER stress and UPR in the development of human diseases is associated with metal exposures. We also discuss the role of the interplay between ER stress and oxidative stress in metal toxicity. Finally, we review recent advances in functional genomics approaches and discuss how applications of these new tools could help elucidate the molecular mechanisms underlying cellular stresses induced by environmental metal toxicants.
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Affiliation(s)
- H-R Park
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - R Oh
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - P Wagner
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - R Panganiban
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Q Lu
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
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27
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RETRACTED ARTICLE: Cadmium permeates through calcium channels and activates transcriptomic complexity in wheat roots in response to cadmium stress. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0488-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Surface Properties of Wild-Type Rhizobium leguminosarum bv. trifolii Strain 24.2 and Its Derivatives with Different Extracellular Polysaccharide Content. PLoS One 2016; 11:e0165080. [PMID: 27760230 PMCID: PMC5070845 DOI: 10.1371/journal.pone.0165080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii is a soil bacterium able to establish symbiosis with agriculturally important legumes, i.e., clover plants (Trifolium spp.). Cell surface properties of rhizobia play an essential role in their interaction with both biotic and abiotic surfaces. Physicochemical properties of bacterial cells are underpinned by the chemical composition of their envelope surrounding the cells, and depend on various environmental conditions. In this study, we performed a comprehensive characterization of cell surface properties of a wild-type R. leguminosarum bv. trifolii strain 24.2 and its derivatives producing various levels of exopolysaccharide (EPS), namely, pssA mutant Rt5819 deficient in EPS synthesis, rosR mutant Rt2472 producing diminished amounts of this polysaccharide, and two EPS-overproducing strains, Rt24.2(pBA1) and Rt24.2(pBR1), under different growth conditions (medium type, bacterial culture age, cell viability, and pH). We established that EPS plays an essential role in the electrophoretic mobility of rhizobial cells, and that higher amounts of EPS produced resulted in greater negative electrophoretic mobility and higher acidity (lower pKapp,av) of the bacterial cell surface. From the tested strains, the electrophoretic mobility was lowest in EPS-deficient pssA mutant. Moreover, EPS produced by rhizobial strains resulted not only in an increase of negative surface charge but also in increased hydrophobicity of bacterial cell surface. This was determined by measurements of water contact angle, surface free energy, and free energy of bacterial surface-water-bacterial surface interaction. Electrophoretic mobility of the studied strains was also affected by the structure of the bacterial population (i.e., live/dead cell ratio), medium composition (ionic strength and mono- and divalent cation concentrations), and pH.
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Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME JOURNAL 2016; 11:248-262. [PMID: 27420027 PMCID: PMC5315480 DOI: 10.1038/ismej.2016.88] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 01/18/2023]
Abstract
The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil. Our study uses whole-genome sequencing to describe the pan-genome of a focal clade of wild mesorhizobia that show contrasting levels of nickel adaptation despite high relatedness (99.8% identity at 16S). We observe ecotypic specialization within an otherwise genomically cohesive population, rather than finding distinct specialized bacterial lineages in contrasting soil types. This finding supports recent reports that heterogeneous environments impose selection that maintains differentiation only at a small fraction of the genome. Our work further uses a genome-wide association study to propose candidate genes for nickel adaptation. Several candidates show homology to genetic systems involved in nickel tolerance and one cluster of candidates correlates perfectly with soil origin, which validates our approach of ascribing genomic variation to adaptive divergence.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Peter L Chang
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Plant Pathology and Nematology, University of California, Davis, CA, USA
| | - Christopher A Conow
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joseph P Dunham
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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Icgen B, Yilmaz F. Design a cadA-targeted DNA probe for screening of potential bacterial cadmium biosorbents. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5743-5752. [PMID: 26585451 DOI: 10.1007/s11356-015-5810-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Due to their metal removal ability, bacterial biosorbents can be effectively used for the treatment of wastewaters containing heavy metals. Searching for bacterial biosorbents for hazardous heavy metals like cadmium is a pivotal for remediation efforts. The gene cadA, that mediates resistance to cadmium over an ATP-dependent efflux mechanism, provides a good target for the selection of potential cadmium biosorbents. For this reason, in this study, a 36-mer-oligonucleotide DNA probe based on the entire 3.5-kb BglII-XbaI fragment of cadA operon from staphylococcal plasmid pI258 was prepared by using Vector NTI Express software. Under the hybridization conditions of 46 °C, 50 % formamide, and 0.028 M NaCl, the designed cadA probe appeared to be highly specific to the cadA-positive Staphylococcus warneri and Delftia acidovorans isolates tested. The results indicated that the newly designed cadA-targeted DNA probe has potential as a specific, sensitive, and quantitative tool in selecting and in situ screening of potential cadmium biosorbents.
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Affiliation(s)
- Bulent Icgen
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey.
| | - Fadime Yilmaz
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey
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31
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Cui L, Zhang YJ, Huang WE, Zhang BF, Martin FL, Li JY, Zhang KS, Zhu YG. Surface-Enhanced Raman Spectroscopy for Identification of Heavy Metal Arsenic(V)-Mediated Enhancing Effect on Antibiotic Resistance. Anal Chem 2016; 88:3164-70. [PMID: 26885563 DOI: 10.1021/acs.analchem.5b04490] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacterial antibiotic resistance poses a threat to global public health. Restricted usage of antibiotics does not necessarily prevent its continued emergence. Rapid and sensitive screening of triggers, in addition to antibiotic, and exploring the underlying mechanism are still major challenges. Herein, by developing a homogeneous vacuum filtration-based bacterial sample fabrication enabling high surface-enhanced Raman scattering (SERS) reproducibility across multiple bacterial samples and negating interfering spectral variations from inhomogeneous sample geometry and SERS enhancement, SERS was employed to study heavy metal arsenic [As(V)]-mediated antibiotic resistance in a robust, sensitive, and rapid fashion. Independent and robust spectral changes representing phenotypic bacterial responses, combined with multivariate analysis, clearly identified that As(V) enhanced antibiotic resistance to tetracycline (Tet). Similar spectral alteration profile to As(V) and Tet indicated that cross-resistance, whereby As(V)-induced bacterial resistance simultaneously blocked Tet action, could account for the enhanced resistance. The sensitive, robust, and rich phenotypic profile provided by SERS, combined with additional advantages in imposing no need to cultivate bacteria and single-cell sensitivity, can be further exploited to evaluate resistance-intervening factors in real microbiota.
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Affiliation(s)
- Li Cui
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Ying-Jiao Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford , Oxford OX1 3PJ, U.K
| | - Bi-Feng Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Francis L Martin
- Lancaster Environment Centre, Lancaster University , Lancaster LA1 4YQ, U.K
| | - Jun-Yi Li
- Lancaster Environment Centre, Lancaster University , Lancaster LA1 4YQ, U.K
| | - Kai-Song Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
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Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress. Appl Environ Microbiol 2016; 82:1734-1744. [PMID: 26729719 DOI: 10.1128/aem.03689-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/29/2015] [Indexed: 11/20/2022] Open
Abstract
Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion.
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33
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Rachwał K, Matczyńska E, Janczarek M. Transcriptome profiling of a Rhizobium leguminosarum bv. trifolii rosR mutant reveals the role of the transcriptional regulator RosR in motility, synthesis of cell-surface components, and other cellular processes. BMC Genomics 2015; 16:1111. [PMID: 26715155 PMCID: PMC4696191 DOI: 10.1186/s12864-015-2332-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
Background Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with red clover (Trifolium pratense). The presence of surface polysaccharides and other extracellular components as well as motility and competitiveness are essential traits for both adaptation of this bacterium to changing environmental conditions and successful infection of host plant roots. The R. leguminosarum bv. trifolii rosR gene encodes a protein belonging to the family of Ros/MucR transcriptional regulators, which contain a Cys2His2-type zinc-finger motif and are involved in the regulation of exopolysaccharide synthesis in several rhizobial species. Previously, it was established that a mutation in the rosR gene significantly decreased exopolysaccharide synthesis, increased bacterial sensitivity to some stress factors, and negatively affected infection of clover roots. Results RNA-Seq analysis performed for the R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt2472 carrying a rosR mutation identified a large number of genes which were differentially expressed in these two backgrounds. A considerable majority of these genes were up-regulated in the mutant (63.22 %), indicating that RosR functions mainly as a repressor. Transcriptome profiling of the rosR mutant revealed a role of this regulator in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Moreover, it was established that the Rt2472 strain was characterized by a longer generation time and showed an increased aggregation ability, but was impaired in motility as a result of considerably reduced flagellation of its cells. Conclusions The comparative transcriptome analysis of R. leguminosarum bv. trifolii wild-type Rt24.2 and the Rt2472 mutant identified a set of genes belonging to the RosR regulon and confirmed the important role of RosR in the regulatory network. The data obtained in this study indicate that this protein affects several cellular processes and plays an important role in bacterial adaptation to environmental conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2332-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kamila Rachwał
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Ewa Matczyńska
- Department of Mathematics and Computer Science, Institute of Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348, Cracow, Poland.,Genomed SA, Ponczowa 12, 02-971, Warsaw, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
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Alías-Villegas C, Cubo MT, Lara-Dampier V, Bellogín RA, Camacho M, Temprano F, Espuny MR. Rhizobial strains isolated from nodules of Medicago marina in southwest Spain are abiotic-stress tolerant and symbiotically diverse. Syst Appl Microbiol 2015; 38:506-14. [DOI: 10.1016/j.syapm.2015.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/05/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
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Hao X, Xie P, Zhu YG, Taghavi S, Wei G, Rensing C. Copper tolerance mechanisms of Mesorhizobium amorphae and its role in aiding phytostabilization by Robinia pseudoacacia in copper contaminated soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2328-2340. [PMID: 25594414 DOI: 10.1021/es504956a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The legume-rhizobium symbiosis has been proposed as an important system for phytoremediation of heavy metal contaminated soils due to its beneficial activity of symbiotic nitrogen fixation. However, little is known about metal resistant mechanism of rhizobia and the role of metal resistance determinants in phytoremediation. In this study, copper resistance mechanisms were investigated for a multiple metal resistant plant growth promoting rhizobium, Mesorhizobium amorphae 186. Three categories of determinants involved in copper resistance were identified through transposon mutagenesis, including genes encoding a P-type ATPase (CopA), hypothetical proteins, and other proteins (a GTP-binding protein and a ribosomal protein). Among these determinants, copA played the dominant role in copper homeostasis of M. amorphae 186. Mutagenesis of a hypothetical gene lipA in mutant MlipA exhibited pleiotropic phenotypes including sensitivity to copper, blocked symbiotic capacity and inhibited growth. In addition, the expression of cusB encoding part of an RND-type efflux system was induced by copper. To explore the possible role of copper resistance mechanism in phytoremediation of copper contaminated soil, the symbiotic nodulation and nitrogen fixation abilities were compared using a wild-type strain, a copA-defective mutant, and a lipA-defective mutant. Results showed that a copA deletion did not affect the symbiotic capacity of rhizobia under uncontaminated condition, but the protective role of copA in symbiotic processes at high copper concentration is likely concentration-dependent. In contrast, inoculation of a lipA-defective strain led to significant decreases in the functional nodule numbers, total N content, plant biomass and leghemoglobin expression level of Robinia pseudoacacia even under conditions of uncontaminated soil. Moreover, plants inoculated with lipA-defective strain accumulated much less copper than both the wild-type strain and the copA-defective strain, suggesting an important role of a healthy symbiotic relationship between legume and rhizobia in phytostabilization.
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Affiliation(s)
- Xiuli Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
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Lafuente A, Pérez-Palacios P, Doukkali B, Molina-Sánchez MD, Jiménez-Zurdo JI, Caviedes MA, Rodríguez-Llorente ID, Pajuelo E. Unraveling the effect of arsenic on the model Medicago-Ensifer interaction: a transcriptomic meta-analysis. THE NEW PHYTOLOGIST 2015; 205:255-272. [PMID: 25252248 DOI: 10.1111/nph.13009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
The genetic regulation underlying the effect of arsenic (As(III)) on the model symbiosis Medicago-Ensifer was investigated using a combination of physiological (split-roots), microscopy and genetic (microarrays, qRT-PCR and composite plants) tools. Nodulation was very sensitive to As(III) (median inhibitory dose (ID50) = 20 μM). The effect on root elongation and on nodulation was local (nonsystemic). A battery of stress (salt, drought, heat shock, metals, etc.)-related genes were induced. Glutathione played a pivotal role in tolerance/detoxification, together with secondary metabolites ((iso)flavonoids and phenylpropanoids). However, antioxidant enzymes were not activated. Concerning the symbiotic interaction, molecular evidence suggesting that rhizobia alleviate As stress is for the first time provided. Chalcone synthase (which is involved in the first step of the legume-rhizobia cross-talk) was strongly enhanced, suggesting that the plants are biased to establish symbiotic interactions under As(III) stress. In contrast, 13 subsequent nodulation genes (involved in nodulation factors (Nod factors) perception, infection, thread initiation and progression, and nodule morphogenesis) were repressed. Overexpression of the ethylene responsive factor ERN in composite plants reduced root stress and partially restored nodulation, whereas overexpression of the early nodulin ENOD12 enhanced nodulation both in the presence and, particularly, in the absence of As, without affecting root elongation. Several transcription factors were identified, which could be additional targets for genetic engineering aiming to improve nodulation and/or alleviate root stress induced by this toxic.
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Affiliation(s)
- Alejandro Lafuente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González 2, 41012, Sevilla, Spain
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Teng Y, Wang X, Li L, Li Z, Luo Y. Rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils. FRONTIERS IN PLANT SCIENCE 2015; 6:32. [PMID: 25699064 PMCID: PMC4318275 DOI: 10.3389/fpls.2015.00032] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/13/2015] [Indexed: 05/20/2023]
Abstract
Environmental pollutants have received considerable attention due to their serious effects on human health. There are physical, chemical, and biological means to remediate pollution; among them, bioremediation has become increasingly popular. The nitrogen-fixing rhizobia are widely distributed in the soil and root ecosystems and can increase legume growth and production by supplying nitrogen, resulting in the reduced need for fertilizer applications. Rhizobia also possess the biochemical and ecological capacity to degrade organic pollutants and are resistant to heavy metals, making them useful for rehabilitating contaminated soils. Moreover, rhizobia stimulate the survival and action of other biodegrading bacteria, thereby lowering the concentration of pollutants. The synergistic action of multiple rhizobial strains enhances both plant growth and the availability of pollutants ranging from heavy metals to persistent organic pollutants. Because phytoremediation has some restrictions, the beneficial interaction between plants and rhizobia provides a promising option for remediation. This review describes recent advances in the exploitation of rhizobia for the rehabilitation of contaminated soil and the biochemical and molecular mechanisms involved, thereby promoting further development of this novel bioremediation strategy into a widely accepted technique.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
- *Correspondence: Ying Teng, Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, Jiangsu 210008, China e-mail:
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Lina Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Yongming Luo
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China
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Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform. Appl Microbiol Biotechnol 2014; 99:3233-42. [DOI: 10.1007/s00253-014-6213-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/22/2023]
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Ammendola S, Cerasi M, Battistoni A. Deregulation of transition metals homeostasis is a key feature of cadmium toxicity in Salmonella. Biometals 2014; 27:703-14. [DOI: 10.1007/s10534-014-9763-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
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Maynaud G, Brunel B, Yashiro E, Mergeay M, Cleyet-Marel JC, Le Quéré A. CadA of Mesorhizobium metallidurans isolated from a zinc-rich mining soil is a PIB-2-type ATPase involved in cadmium and zinc resistance. Res Microbiol 2014; 165:175-89. [DOI: 10.1016/j.resmic.2014.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
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Visioli G, D'Egidio S, Sanangelantoni AM. The bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy. FRONTIERS IN PLANT SCIENCE 2014; 5:752. [PMID: 25709609 PMCID: PMC4285865 DOI: 10.3389/fpls.2014.00752] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/08/2014] [Indexed: 05/20/2023]
Abstract
Hyperaccumulators are plants that can extract heavy metal ions from the soil and translocate those ions to the shoots, where they are sequestered and detoxified. Hyperaccumulation depends not only on the availability of mobilized metal ions in the soil, but also on the enhanced activity of metal transporters and metal chelators which may be provided by the plant or its associated microbes. The rhizobiome is captured by plant root exudates from the complex microbial community in the soil, and may colonize the root surface or infiltrate the root cortex. This community can increase the root surface area by inducing hairy root proliferation. It may also increase the solubility of metals in the rhizosphere and promote the uptake of soluble metals by the plant. The bacterial rhizobiome, a subset of specialized microorganisms that colonize the plant rhizosphere and endosphere, makes an important contribution to the hyperaccumulator phenotype. In this review, we discuss classic and more recent tools that are used to study the interactions between hyperaccumulators and the bacterial rhizobiome, and consider future perspectives based on the use of omics analysis and microscopy to study plant metabolism in the context of metal accumulation. Recent data suggest that metal-resistant bacteria isolated from the hyperaccumulator rhizosphere and endosphere could be useful in applications such as phytoextraction and phytoremediation, although more research is required to determine whether such properties can be transferred successfully to non-accumulator species.
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Affiliation(s)
- Giovanna Visioli
- *Correspondence: Giovanna Visioli, Department of Life Sciences, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy e-mail:
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Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiol Res 2014; 169:2-17. [DOI: 10.1016/j.micres.2013.09.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/24/2022]
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