1
|
Nies DH, Schleuder G, Galea D, Herzberg M. A flow equilibrium of zinc in cells of Cupriavidus metallidurans. J Bacteriol 2024; 206:e0008024. [PMID: 38661374 PMCID: PMC11112998 DOI: 10.1128/jb.00080-24] [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: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
The hypothesis was tested that a kinetical flow equilibrium of uptake and efflux reactions is responsible for balancing the cellular zinc content. The experiments were done with the metal-resistant bacterium Cupriavidus metallidurans. In pulse-chase experiments, the cells were loaded with radioactive 65Zn and chased with the 100-fold concentration of non-radioactive zinc chloride. In parallel, the cells were loaded with isotope-enriched stable 67Zn and chased with non-enriched zinc to differentiate between zinc pools in the cell. The experiments demonstrated the existence of a kinetical flow equilibrium, resulting in a constant turnover of cell-bound zinc ions. The absence of the metal-binding cytoplasmic components, polyphosphate and glutathione, metal uptake, and metal efflux systems influenced the flow equilibrium. The experiments also revealed that not all zinc uptake and efflux systems are known in C. metallidurans. Cultivation of the cells under zinc-replete, zinc-, and zinc-magnesium-starvation conditions influenced zinc import and export rates. Here, magnesium starvation had a stronger influence compared to zinc starvation. Other metal cations, especially cobalt, affected the cellular zinc pools and zinc export during the chase reaction. In summary, the experiments with 65Zn and 67Zn demonstrated a constant turnover of cell-bound zinc. This indicated that simultaneously occurring import and export reactions in combination with cytoplasmic metal-binding components resulted in a kinetical flow equilibrium that was responsible for the adjustment of the cellular zinc content. IMPORTANCE Understanding the biochemical action of a single enzyme or transport protein is the pre-requisite to obtain insight into its cellular function but this is only one half of the coin. The other side concerns the question of how central metabolic functions of a cell emerge from the interplay of different proteins and other macromolecules. This paper demonstrates that a flow equilibrium of zinc uptake and efflux reactions is at the core of cellular zinc homeostasis and identifies the most important contributors to this flow equilibrium: the uptake and efflux systems and metal-binding components of the cytoplasm.
Collapse
Affiliation(s)
- Dietrich H. Nies
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Grit Schleuder
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Diana Galea
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| |
Collapse
|
2
|
Kwiatos N, Waldron KJ. In a state of flux: new insight into the transport processes that maintain bacterial metal homeostasis. J Bacteriol 2024; 206:e0014624. [PMID: 38712925 PMCID: PMC11112988 DOI: 10.1128/jb.00146-24] [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] [Indexed: 05/08/2024] Open
Abstract
A new study by Nies et al. (J Bacteriol 206:e00080-24, 2024, https://doi.org/10.1128/jb.00080-24) provides a rich, quantitative data set of zinc accumulation by cells of Cupriavidus metallidurans, including of mutant bacterial strains lacking import or efflux genes, and comparison of zinc accumulation by cells previously starved of metal with those of zinc-replete cells. The data surprisingly demonstrate the concomitant activity of both active metal import and metal efflux systems. They present a flow equilibrium model to describe zinc homeostasis in bacteria.
Collapse
Affiliation(s)
- Natalia Kwiatos
- Laboratory of Metalloprotein Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kevin J. Waldron
- Laboratory of Metalloprotein Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
3
|
Rahal S, Menaa B, Chekireb D. Screening of heavy metal-resistant rhizobial and non-rhizobial microflora isolated from Trifolium sp. growing in mining areas. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:283. [PMID: 38372826 DOI: 10.1007/s10661-024-12445-0] [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: 06/20/2023] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can promote plant growth and development with several beneficial effects, especially in challenging environmental conditions, such as the presence of toxic contaminants. In this study, 49 isolates obtained from Trifolium sp. nodules growing on a Pb/Zn mine site were characterized for PGP traits including siderophores production, phosphate solubilization, extracellular enzymes production, and antifungal activity. The isolates were also screened for their ability to grow at increasing concentrations of NaCl and heavy metals, including lead, zinc, cobalt, copper, nickel, cadmium, and chromium. The findings of our study indicated that isolates Cupriavidus paucula RSCup01-RSCup08, Providencia rettgeri RSPro01, Pseudomonas putida RSPs01, Pseudomonas thivervalensis RSPs03-RSPs09, and Acinetobacter beijerinckii RSAci01 showed several key traits crucial for promoting plant growth, thus demonstrating the greatest potential. Most isolates displayed resistance to salt and heavy metals. Notably, Staphylococcus xylosus RSSta01, Pseudomonas sp. RSPs02, Micrococcus yunnanensis RSMicc01, and Kocuria dechangensis RSKoc01 demonstrated a significant capacity to grow at salt concentrations ranging from 10 to 20%, and isolates including Cupravidus paucula RSCup01-RSCup08 exhibited resistance to high levels of heavy metals, up to 1300 mg/L Pb++, 1200 mg/L Zn++, 1000 mg/L Ni++, 1000 mg/L Cd++, 500 mg/L Cu++, 400 mg/L Co++, and 50 mg/L CrVI+. Additionally, the analysis revealed that metal-resistant genes pbrA, czcD, and nccA were exclusively detected in the Cupriavidus paucula RSCup01 strain. The results of this study provide insights into the potential of plant growth-promoting rhizobacteria strains that might be used as inoculants to improve phytoremediation in heavy metal-contaminated soils.
Collapse
Affiliation(s)
- Sarah Rahal
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Sciences, Department of Biochemistry, University Badji Mokhtar Annaba, B.P. 12, Sidi Amar, 23200, Annaba, Algeria.
| | - Belkis Menaa
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Sciences, Department of Biochemistry, University Badji Mokhtar Annaba, B.P. 12, Sidi Amar, 23200, Annaba, Algeria
| | - Djamel Chekireb
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Sciences, Department of Biochemistry, University Badji Mokhtar Annaba, B.P. 12, Sidi Amar, 23200, Annaba, Algeria
| |
Collapse
|
4
|
Pazos-Rojas LA, Cuellar-Sánchez A, Romero-Cerón AL, Rivera-Urbalejo A, Van Dillewijn P, Luna-Vital DA, Muñoz-Rojas J, Morales-García YE, Bustillos-Cristales MDR. The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria. Microorganisms 2023; 12:39. [PMID: 38257865 PMCID: PMC10818521 DOI: 10.3390/microorganisms12010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Many bacteria have the ability to survive in challenging environments; however, they cannot all grow on standard culture media, a phenomenon known as the viable but non-culturable (VBNC) state. Bacteria commonly enter the VBNC state under nutrient-poor environments or under stressful conditions. This review explores the concept of the VBNC state, providing insights into the beneficial bacteria known to employ this strategy. The investigation covers different chemical and physical factors that can induce the latency state, cell features, and gene expression observed in cells in the VBNC state. The review also covers the significance and applications of beneficial bacteria, methods of evaluating bacterial viability, the ability of bacteria to persist in environments associated with higher organisms, and the factors that facilitate the return to the culturable state. Knowledge about beneficial bacteria capable of entering the VBNC state remains limited; however, beneficial bacteria in this state could face adverse environmental conditions and return to a culturable state when the conditions become suitable and continue to exert their beneficial effects. Likewise, this unique feature positions them as potential candidates for healthcare applications, such as the use of probiotic bacteria to enhance human health, applications in industrial microbiology for the production of prebiotics and functional foods, and in the beer and wine industry. Moreover, their use in formulations to increase crop yields and for bacterial bioremediation offers an alternative pathway to harness their beneficial attributes.
Collapse
Affiliation(s)
- Laura Abisaí Pazos-Rojas
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Alma Cuellar-Sánchez
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Ana Laura Romero-Cerón
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - América Rivera-Urbalejo
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
| | - Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Diego Armando Luna-Vital
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
| | - Yolanda Elizabeth Morales-García
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
- Faculty of Biological Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico
| | - María del Rocío Bustillos-Cristales
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
| |
Collapse
|
5
|
Mahmoud SM, Barakat OS, Kotram LE. Stimulation the immune response through ξ potential on core-shell 'calcium oxide/magnetite iron oxides' nanoparticles. Anim Biotechnol 2023; 34:2657-2673. [PMID: 35981058 DOI: 10.1080/10495398.2022.2111310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This study investigated the role of ξ Potential on Monometallic (MM) and Bimetallic (BM) Calcium Oxide/Magnetite Iron Oxides nanoparticles to stimulate the immune response. Metallic nanoparticles (MNPs) were biosynthesis using Pseudomonas fluorescens S48. MNPs characterization was carried out by UV-Vis spectra, XRD analysis, Zeta potential and Particles size, SEM-EDS, and TEM, and the concentrations were calculated by ICP-AES. The immune system activity was measured by estimation of lymphocytes transformation, phagocytic activity. The end point was in evaluating the toxicity of Metallic NPs by comet assay. SEM-EDS and TEM micrographs showed that MM CaO and Fe3O4 represent a perfect example of zero-dimensional (0-D) NPs with cubic and spherical particles in shape, while BM CaO/Fe3O4 NPs appeared in the form of Core-shell structure. The variations effect of novelty MM, BM CaO/Fe3O4 NPs in enhancing immune activity were based on the ξ Potential whereas negatively and positively charged. These findings demonstrate that the cationic CaO/Fe3O4 NPs are inefficient in stimulating the immune system which causes a high cytotoxic effect. But the anionic CaO/Fe3O4 NPs have advantages in targeting the immune system because of enhanced delivery to the cells through adsorptive endocytosis as well as the half-life clearance from the blood.
Collapse
Affiliation(s)
- Sara Mohamed Mahmoud
- Biotechnology Department, Faculty of Graduate Studies and Environmental Researches, Ain Shams University, Cairo, Egypt
| | - Olfat S Barakat
- Agricultural Microbiology Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Laila E Kotram
- Immunity Department, Animal Reproduction Research Institute (ARRI), Agriculture Research Center (ARC), Giza, Egypt
| |
Collapse
|
6
|
Mukherjee S, Bhattacharjee S, Paul S, Nath S, Paul S. Biofilm-a Syntrophic Consortia of Microbial Cells: Boon or Bane? Appl Biochem Biotechnol 2023; 195:5583-5604. [PMID: 35829902 DOI: 10.1007/s12010-022-04075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Biofilm is the conglomeration of microbial cells which is associated with a surface. In the recent times, the study of biofilm has gained popularity and vivid research is being done to know about the effects of biofilm and that it consists of many organisms which are symbiotic in nature, some of which are human pathogens. Here, in this study, we have discussed about biofilms, its formation, relevance of its presence in the biosphere, and the possible remediations to cope up with its negative effects. Since removal of biofilm is difficult, emphasis has been made to suggest ways to prevent biofilm formation and also to devise ways to utilize biofilm in an economically and environment-friendly method.
Collapse
Affiliation(s)
- Susmita Mukherjee
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Shreya Bhattacharjee
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Sharanya Paul
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Somava Nath
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Sonali Paul
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India.
| |
Collapse
|
7
|
Biełło KA, Olaya-Abril A, Cabello P, Rodríguez-Caballero G, Sáez LP, Moreno-Vivián C, Luque-Almagro VM, Roldán MD. Quantitative Proteomic Analysis of Cyanide and Mercury Detoxification by Pseudomonas pseudoalcaligenes CECT 5344. Microbiol Spectr 2023; 11:e0055323. [PMID: 37432117 PMCID: PMC10433974 DOI: 10.1128/spectrum.00553-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT 5344 uses cyanide and different metal-cyanide complexes as the sole nitrogen source. Under cyanotrophic conditions, this strain was able to grow with up to 100 μM mercury, which was accumulated intracellularly. A quantitative proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been applied to unravel the molecular basis of the detoxification of both cyanide and mercury by the strain CECT 5344, highlighting the relevance of the cyanide-insensitive alternative oxidase CioAB and the nitrilase NitC in the tolerance and assimilation of cyanide, independently of the presence or absence of mercury. Proteins overrepresented in the presence of cyanide and mercury included mercury transporters, mercuric reductase MerA, transcriptional regulator MerD, arsenate reductase and arsenical resistance proteins, thioredoxin reductase, glutathione S-transferase, proteins related to aliphatic sulfonates metabolism and sulfate transport, hemin import transporter, and phosphate starvation induced protein PhoH, among others. A transcriptional study revealed that from the six putative merR genes present in the genome of the strain CECT 5344 that could be involved in the regulation of mercury resistance/detoxification, only the merR2 gene was significantly induced by mercury under cyanotrophic conditions. A bioinformatic analysis allowed the identification of putative MerR2 binding sites in the promoter regions of the regulatory genes merR5, merR6, arsR, and phoR, and also upstream from the structural genes encoding glutathione S-transferase (fosA and yghU), dithiol oxidoreductase (dsbA), metal resistance chaperone (cpxP), and amino acid/peptide extruder involved in quorum sensing (virD), among others. IMPORTANCE Cyanide, mercury, and arsenic are considered very toxic chemicals that are present in nature as cocontaminants in the liquid residues generated by different industrial activities like mining. Considering the huge amounts of toxic cyanide- and mercury-containing wastes generated at a large scale and the high biotechnological potential of P. pseudoalcaligenes CECT 5344 in the detoxification of cyanide present in these industrial wastes, in this work, proteomic, transcriptional, and bioinformatic approaches were used to characterize the molecular response of this bacterium to cyanide and mercury, highlighting the mechanisms involved in the simultaneous detoxification of both compounds. The results generated could be applied for developing bioremediation strategies to detoxify wastes cocontaminated with cyanide, mercury, and arsenic, such as those generated at a large scale in the mining industry.
Collapse
Affiliation(s)
- Karolina A Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Gema Rodríguez-Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara P Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor Manuel Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| |
Collapse
|
8
|
He Y, Luo Y, Wei C, Long L, Wang C, Wu Y. Effects of dissolved organic matter derived from cow manure on heavy metal(loid)s and bacterial community dynamics in mercury-thallium mining waste slag. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:5857-5877. [PMID: 37178440 DOI: 10.1007/s10653-023-01607-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Organic amendments in aided phytostabilization of waste slag containing high levels of heavy metal (loid)s (HMs) are an important way to control the release of HMs in situ. However, the effects of dissolved organic matter (DOM) derived from organic amendments on HMs and microbial community dynamics in waste slag are still unclear. Here, the effect of DOM derived from organic amendments (cow manure) on the geochemical behaviour of HMs and the bacterial community dynamics in mercury (Hg)-thallium (Tl) mining waste slag were investigated. The results showed that the Hg-Tl mining waste slag without the addition of DOM continuously decreased the pH and increased the EC, Eh, SO42-, Hg, and Tl levels in the leachate with increasing incubation time. The addition of DOM significantly increased the pH, EC, SO42-, and arsenic (As) levels but decreased the Eh, Hg, and Tl levels. The addition of DOM significantly increased the diversity and richness of the bacterial community. The dominant bacterial phyla (Proteobacteria, Firmicutes, Acidobacteriota, Actinobacteriota, and Bacteroidota) and genera (Bacillus, Acinetobacter, Delftia, Sphingomonas, and Enterobacter) were changed in association with increases in DOM content and incubation time. The DOM components in the leachate were humic-like substances (C1 and C2), and the DOC content and maximum fluorescence intensity (FMax) values of C1 and C2 in the leachate decreased and first increased and then decreased with increasing incubation time. The correlations between HMs and DOM and the bacterial community showed that the geochemical behaviours of HMs in Hg-Tl mining waste slag were directly influenced by DOM-mediated properties and indirectly influenced by DOM regulation of bacterial community changes. Overall, these results indicated that DOM properties associated with bacterial community changes increased As mobilization but decreased Hg and Tl mobilization from Hg-Tl mining waste slag.
Collapse
Affiliation(s)
- Yu He
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Youfa Luo
- Key Laboratory of Kast Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Hostile Environment Ecological Restoration Technology Engineering Research Centre, Guizhou University, Guiyang, 550025, China.
| | - Chaoxiao Wei
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Licui Long
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Chi Wang
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Yonggui Wu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Hostile Environment Ecological Restoration Technology Engineering Research Centre, Guizhou University, Guiyang, 550025, China
| |
Collapse
|
9
|
Joshi S, Gangola S, Bhandari G, Bhandari NS, Nainwal D, Rani A, Malik S, Slama P. Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies. Front Microbiol 2023; 14:1229828. [PMID: 37555069 PMCID: PMC10405491 DOI: 10.3389/fmicb.2023.1229828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.
Collapse
Affiliation(s)
- Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Geeta Bhandari
- Department of Biosciences, Himalayan School of Bio Sciences, Swami Rama Himalayan University, Dehradun, India
| | | | - Deepa Nainwal
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Anju Rani
- Department of Life Sciences, Graphic Era (Deemed to be) University, Dehradun, Uttarakhand, India
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
- Guru Nanak College of Pharmaceutical Sciences, Dehradun, Uttarakhand, India
- Department of Applied Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| |
Collapse
|
10
|
Ariute JC, Felice AG, Soares S, da Gama MAS, de Souza EB, Azevedo V, Brenig B, Aburjaile F, Benko-Iseppon AM. Characterization and Association of Rips Repertoire to Host Range of Novel Ralstonia solanacearum Strains by In Silico Approaches. Microorganisms 2023; 11:microorganisms11040954. [PMID: 37110377 PMCID: PMC10144018 DOI: 10.3390/microorganisms11040954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/24/2022] [Accepted: 01/28/2023] [Indexed: 04/29/2023] Open
Abstract
Ralstonia solanacearum species complex (RSSC) cause several phytobacteriosis in many economically important crops around the globe, especially in the tropics. In Brazil, phylotypes I and II cause bacterial wilt (BW) and are indistinguishable by classical microbiological and phytopathological methods, while Moko disease is caused only by phylotype II strains. Type III effectors of RSSC (Rips) are key molecular actors regarding pathogenesis and are associated with specificity to some hosts. In this study, we sequenced and characterized 14 newly RSSC isolates from Brazil's Northern and Northeastern regions, including BW and Moko ecotypes. Virulence and resistance sequences were annotated, and the Rips repertoire was predicted. Confirming previous studies, RSSC pangenome is open as α≅0.77. Genomic information regarding these isolates matches those for R. solanacearum in NCBI. All of them fit in phylotype II with a similarity above 96%, with five isolates in phylotype IIB and nine in phylotype IIA. Almost all R. solanacearum genomes in NCBI are actually from other species in RSSC. Rips repertoire of Moko IIB was more homogeneous, except for isolate B4, which presented ten non-shared Rips. Rips repertoire of phylotype IIA was more diverse in both Moko and BW, with 43 common shared Rips among all 14 isolates. New BW isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. Rips not shared with other isolates might contribute to individual virulence, but commonly shared Rips are good avirulence candidates. The high number of Rips shared by new Moko and BW isolates suggests they are actually Moko isolates infecting solanaceous hosts. Finally, infection assays and Rips expression on different hosts are needed to better elucidate the association between Rips repertoire and host specificities.
Collapse
Affiliation(s)
- Juan Carlos Ariute
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
- Genetics Department, Universidade Federal de Pernambuco, Recife 50740-600, Pernambuco, Brazil
| | - Andrei Giachetto Felice
- Institute of Biological and Natural Sciences, Universidade Federal do Triângulo Mineiro, Uberaba 38025-180, Minas Gerais, Brazil
| | - Siomar Soares
- Institute of Biological and Natural Sciences, Universidade Federal do Triângulo Mineiro, Uberaba 38025-180, Minas Gerais, Brazil
| | | | - Elineide Barbosa de Souza
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife 52171-900, Pernambuco, Brazil
| | - Vasco Azevedo
- Genetics, Ecology and Evolution Department, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University Göttingen, 37077 Göttingen, Germany
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Ana Maria Benko-Iseppon
- Genetics Department, Universidade Federal de Pernambuco, Recife 50740-600, Pernambuco, Brazil
| |
Collapse
|
11
|
Li Q, Zhang W, Liao S, Xing D, Xiao Y, Zhou D, Yang Q. Mechanism of lead adsorption by a Bacillus cereus strain with indole-3-acetic acid secretion and inorganic phosphorus dissolution functions. BMC Microbiol 2023; 23:57. [PMID: 36869296 PMCID: PMC9985246 DOI: 10.1186/s12866-023-02795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Heavy metal pollution has become a major source of environmental pollution because of increasing industrialization. Microbial remediation is a promising approach to remediate lead-contaminated environments owing to its cost-effective, environment-friendly, ecologically sustainable, and highly efficient properties. In this study, the growth-promoting functions and lead-adsorption ability of Bacillus cereus SEM-15 were examined, and the functional mechanism of the strain was preliminarily identified using scanning electron microscopy, energy spectrum, infrared spectrum, and genome analyses, providing theoretical support for utilization of B. cereus SEM-15 in heavy metals remediation. RESULTS B. cereus SEM-15 showed strong ability to dissolve inorganic phosphorus and secrete indole-3-acetic acid. The lead adsorption efficiency of the strain at lead ion concentration of 150 mg/L was more than 93%. Single factor analysis revealed the optimal conditions for heavy metal adsorption by B. cereus SEM-15 (adsorption time, initial lead ion concentration, pH, and inoculum amount were 10 min, 50-150 mg/L, 6-7, and 5 g/L, respectively) in nutrient-free environment, with the lead adsorption rate reaching 96.58%. Scanning electron microscopy of B. cereus SEM-15 cells before and after lead adsorption showed adherence of a large number of granular precipitates to the cell surface after lead adsorption. X-Ray photoelectron spectroscopy and Fourier transform infrared spectroscopy results indicated the characteristic peaks of Pb-O, Pb-O-R (R = functional group), and Pb-S bonds after lead adsorption, and a shift in the characteristic peaks of bonds and groups related to C, N, and O. Genome annotation results showed the presence of genes related to heavy metals tolerance and plant growth promotion in B. cereus SEM-15, providing a molecular basis for the strain's heavy metals tolerance and plant growth promotion functions. CONCLUSIONS This study analyzed the lead adsorption characteristics of B. cereus SEM-15 and the associated influencing factors, and discussed the adsorption mechanism and related functional genes, providing a basis for clarifying the underlying molecular mechanism and offering a reference for further research on plant-microorganisms combined remediation of heavy metals polluted environments.
Collapse
Affiliation(s)
- Qingrong Li
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China.,Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, GuangZhou, 510610, China
| | - Wenbo Zhang
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China
| | - Sentai Liao
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China
| | - Dongxu Xing
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China.,Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, GuangZhou, 510610, China
| | - Yang Xiao
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China.,Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, GuangZhou, 510610, China
| | - Donglai Zhou
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China
| | - Qiong Yang
- Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China. .,Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, GuangZhou, 510610, China.
| |
Collapse
|
12
|
Wang L, Yan L, Ye L, Chen J, Li Y, Zhang Q, Jing C. Identification and Characterization of a Au(III) Reductase from Erwinia sp. IMH. JACS AU 2022; 2:1435-1442. [PMID: 35783184 PMCID: PMC9241155 DOI: 10.1021/jacsau.2c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms contribute to the formation of secondary gold (Au) deposits through enzymatic reduction of Au(III) to Au(0). However, the enzyme that catalyzes the reduction of Au(III) remains enigmatic. Here, we identified and characterized a previously unknown Au reductase (GolR) in the cytoplasm of Erwinia sp. IMH. The expression of golR was strongly up-regulated in response to increasing Au(III) concentrations and exposure time. Mutant with in-frame deletion of golR was incapable of reducing Au(III), and the capability was rescued by reintroducing wild-type golR into the mutant strain. The Au(III) reduction was determined to occur in the cytoplasmic space by comparing the TEM images of the wild-type, mutant, and complemented strains. In vitro assays of the purified GolR protein confirmed its ability to reduce Au(III) to Au nanoparticles. Molecular dynamic simulations demonstrated that the hydrophobic cavity of GolR may selectively bind AuCl2(OH)2 -, the predominant auric chloride species at neutral pH. Density functional theory calculations revealed that AuCl2(OH)2 - may be coordinated at the Fe-containing active site of GolR and is probably reduced via three consecutive proton-coupled electron transfer processes. The new class of reductase, GolR, opens the chapter for the mechanistic understanding of Au(III) bioreduction.
Collapse
Affiliation(s)
- Liying Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
| | - Li Yan
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
| | - Li Ye
- School
of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jinfeng Chen
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Yanwei Li
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Qingzhu Zhang
- Environment
Research Institute, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
- School
of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| |
Collapse
|
13
|
Lu Z, Su H. Employing gene chip technology for monitoring and assessing soil heavy metal pollution. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:2. [PMID: 34862584 DOI: 10.1007/s10661-021-09650-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.
Collapse
Affiliation(s)
- ZiChun Lu
- College of Hehai, Chongqing University of Technology, Chongqing, 400717, China
| | - HaiFeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Natural and Resources, Xi'an, Shanxi, 710075, China.
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China.
| |
Collapse
|
14
|
Mu HM, Wan YY, Wu BC, Tian Y, Dong HL, Xian CG, Li Y. A rapid change in microbial communities of the shale gas drilling fluid from 3548 m depth to the above-ground storage tank. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147009. [PMID: 33901962 DOI: 10.1016/j.scitotenv.2021.147009] [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] [Received: 11/15/2020] [Revised: 03/11/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Despite the growing body of studies on the various fracturing phrases, the research on the differences between subterranean and surface microorganisms at shale gas drilling sites is still limited. Generally, shale gas development and the production process are divided into drilling and fracturing. The distribution of microbial communities in the latter has been paid some attention, but a deficit remains in terms of our understanding of the microbial community in the former, especially for the phase of drilling flowback and drilling flowback surface. In this study, four drilling flowback fluids (DFFs) (H230-flowback drilling cuttings, H23G-flowback drilling mud, H240-flowback drilling sediment, and H21F-flowback drilling water) from the outlet of subterranean pipeline to the inlet of storage tank were successively collected from H2 shale gas field during its initial drilling in Sichuan, China. Natural mountain water (H10W) used as the injection water of H2 was also sampled. Illumina MiSeq 16S rRNA gene sequencing revealed a total of 8 phyla, 17 classes, 36 orders, 62 families, and 98 genera that were recovered from these samples with uneven distribution. The majority of the obtained sequences belonged to the phyla Proteobacteria (75.36%), Bacteroidetes (10.75%), and Firmicutes (5.64%), with significant differences found in DFFs and injection water. The richness of microorganisms gradually increased with the increasing flowback flowing distance (H230 < H23G < H240 < H21F < H10W), which was employed to reveal a rapid change in microbiota that was evident in samples along the flow path aboveground from a depth of 3548 m. The findings of this study could expand our understanding of the ecological role of microorganisms during the shale gas drilling phase. Furthermore, the study highlights the temporal-spatial trajectory of microbial communities from subterranean environments to the surface in a short period of 30 days.
Collapse
Affiliation(s)
- Hong Mei Mu
- State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China
| | - Yun Yang Wan
- State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China.
| | - Bai Chun Wu
- State Key Laboratory of Petroleum Pollution Control, CNPC Research Institute of Safety and Environmental Technology, Beijing 102206, China
| | - Yan Tian
- State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China
| | - Hai Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA
| | - Cheng Gang Xian
- State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China
| | - Yang Li
- State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China; China Petroleum & Chemical Corporation, Beijing 100728, China.
| |
Collapse
|
15
|
Huang J, Liu C, Price GW, Li Y, Wang Y. Identification of a novel heavy metal resistant Ralstonia strain and its growth response to cadmium exposure. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125942. [PMID: 34492869 DOI: 10.1016/j.jhazmat.2021.125942] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/02/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
A novel Ralstonia Bcul-1 strain was isolated from soil samples that was closest to Ralstonia pickettii. Broad-spectrum resistance was identified to a group of heavy metal ions and tolerance to concentrations of Cd2+ up to 400 mg L-1. Low concentrations of heavy metal ions did not have distinctive impact on heavy metal resistance genes and appeared to induce greater expression. Under exposure to Cd2+, cell wall components were significantly enhanced, and some proteins were also simultaneously expressed allowing the bacteria to adapt to the high Cd2+ living environment. The maximum removal rate of Cd2+ by the Ralstonia Bcul-1 strain was 78.97% in the culture medium supplemented with 100 mg L-1 Cd2+. Ralstonia Bcul-1 was able to survive and grow in a low nutrient and cadmium contaminated (0.42 mg kg-1) vegetable soil, and the cadmium removal rate was up to 65.76% in 9th growth. Ralstonia Bcul-1 mixed with biochar could maintain sustainable growth of this strain in the soil up to 75 d and the adsorption efficiency of cadmium increased by 16.23-40.80% as compared to biochar application alone. Results from this work suggests that Ralstonia Bcul-1 is an ideal candidate for bioremediation of nutrient deficient heavy metal contaminated soil.
Collapse
Affiliation(s)
- Jiaqing Huang
- Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences (FAAS), Fuzhou 350013, China; Fujian Key Laboratory of Agricultural Ecological Process of Red Soil Mountain, Fuzhou 350013, China
| | - Cenwei Liu
- Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences (FAAS), Fuzhou 350013, China; Fujian Key Laboratory of Agricultural Ecological Process of Red Soil Mountain, Fuzhou 350013, China
| | - G W Price
- Department of Engineering, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Yanchun Li
- Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences (FAAS), Fuzhou 350013, China; Fujian Key Laboratory of Agricultural Ecological Process of Red Soil Mountain, Fuzhou 350013, China
| | - Yixiang Wang
- Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences (FAAS), Fuzhou 350013, China; Fujian Key Laboratory of Agricultural Ecological Process of Red Soil Mountain, Fuzhou 350013, China.
| |
Collapse
|
16
|
Pushkar B, Sevak P, Parab S, Nilkanth N. Chromium pollution and its bioremediation mechanisms in bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 287:112279. [PMID: 33706095 DOI: 10.1016/j.jenvman.2021.112279] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/10/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Environment pollution is at its peak and is creating havoc for living beings. Industrial wastes containing toxic pollutants have contributed to a great extent in this disastrous environment pollution. Chromium (Cr3+/Cr6+) is highly toxic and one of the most common environmental pollutants because of its extensive use in industries especially tanneries. Lack of efficient treatment methods has resulted in extensive chromium pollution. Bioremediation of chromium using bacteria is very thoughtful due to its eco-friendly and cost-effective outcome. Bacteria possess numerous mechanisms such as biosorption, reduction, efflux or bioaccumulation, naturally or acquired to counter the toxicity of chromium. This review focuses on the bacterial responses against chromium toxicity and scope for their application in bioremediation. The differences and similarities between Gram negative and positive bacteria against chromium are also highlighted. Further, the knowledge gap and future prospects are also discussed in order to fill these gaps and overcome the problem associated with real-time applicability of bacterial bioremediation.
Collapse
Affiliation(s)
- Bhupendra Pushkar
- Department of Biotechnology, University of Mumbai, Kalina, Santacruz (E), Mumbai, 400098, Maharashtra, India; Global Biotech Forum, Maharashtra, India.
| | - Pooja Sevak
- Department of Biotechnology, University of Mumbai, Kalina, Santacruz (E), Mumbai, 400098, Maharashtra, India; Society for Innovations in Biosciences, Maharashtra, India
| | - Sejal Parab
- Department of Biotechnology, University of Mumbai, Kalina, Santacruz (E), Mumbai, 400098, Maharashtra, India
| | - Nikita Nilkanth
- Department of Biotechnology, University of Mumbai, Kalina, Santacruz (E), Mumbai, 400098, Maharashtra, India
| |
Collapse
|
17
|
Clavero-León C, Ruiz D, Cillero J, Orlando J, González B. The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper. PeerJ 2021; 9:e11373. [PMID: 34040892 PMCID: PMC8127957 DOI: 10.7717/peerj.11373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/07/2021] [Indexed: 11/20/2022] Open
Abstract
Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
Collapse
Affiliation(s)
- Claudia Clavero-León
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Daniela Ruiz
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Javier Cillero
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| |
Collapse
|
18
|
Hamida RS, Ali MA, Abdelmeguid NE, Al-Zaban MI, Baz L, Bin-Meferij MM. Lichens-A Potential Source for Nanoparticles Fabrication: A Review on Nanoparticles Biosynthesis and Their Prospective Applications. J Fungi (Basel) 2021; 7:291. [PMID: 33921411 PMCID: PMC8069866 DOI: 10.3390/jof7040291] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Green synthesis of nanoparticles (NPs) is a safe, eco-friendly, and relatively inexpensive alternative to conventional routes of NPs production. These methods require natural resources such as cyanobacteria, algae, plants, fungi, lichens, and naturally extracted biomolecules such as pigments, vitamins, polysaccharides, proteins, and enzymes to reduce bulk materials (the target metal salts) into a nanoscale product. Synthesis of nanomaterials (NMs) using lichen extracts is a promising eco-friendly, simple, low-cost biological synthesis process. Lichens are groups of organisms including multiple types of fungi and algae that live in symbiosis. Until now, the fabrication of NPs using lichens has remained largely unexplored, although the role of lichens as natural factories for synthesizing NPs has been reported. Lichens have a potential reducible activity to fabricate different types of NMs, including metal and metal oxide NPs and bimetallic alloys and nanocomposites. These NPs exhibit promising catalytic and antidiabetic, antioxidant, and antimicrobial activities. To the best of our knowledge, this review provides, for the first time, an overview of the main published studies concerning the use of lichen for nanofabrication and the applications of these NMs in different sectors. Moreover, the possible mechanisms of biosynthesis are discussed, together with the various optimization factors influencing the biological synthesis and toxicity of NPs.
Collapse
Affiliation(s)
- Reham Samir Hamida
- Molecular Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21500, Egypt; (R.S.H.); (N.E.A.)
| | - Mohamed Abdelaal Ali
- Biotechnology Unit, Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh 11543, Saudi Arabia;
- Plant Production Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria 21934, Egypt
| | - Nabila Elsayed Abdelmeguid
- Molecular Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21500, Egypt; (R.S.H.); (N.E.A.)
| | - Mayasar Ibrahim Al-Zaban
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11543, Saudi Arabia;
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mashael Mohammed Bin-Meferij
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11543, Saudi Arabia;
| |
Collapse
|
19
|
Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
Collapse
Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| |
Collapse
|
20
|
Van Houdt R, Vandecraen J, Leys N, Monsieurs P, Aertsen A. Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter. Microorganisms 2021; 9:microorganisms9020309. [PMID: 33540705 PMCID: PMC7912956 DOI: 10.3390/microorganisms9020309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/30/2022] Open
Abstract
Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterization of CH34ZnR revealed that it was also more resistant to cadmium, and that it incurred seven insertion sequence-mediated mutations. Among these, an IS1088 disruption of the glpR gene (encoding a DeoR-type transcriptional repressor) resulted in the constitutive expression of the neighboring ATP-binding cassette (ABC)-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34ZnR with the parental glpR gene further demonstrated that loss of GlpR function and concomitant derepression of the adjacent ABC transporter is pivotal for the observed resistance phenotype. Importantly, addition of glycerol, presumably by glycerol-mediated attenuation of GlpR activity, also promoted increased zinc and cadmium resistance in the parental CH34 strain. Upregulation of this ABC-type transporter is therefore proposed as a new adaptation route towards metal resistance.
Collapse
Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (J.V.); (N.L.); (P.M.)
- Correspondence:
| | - Joachim Vandecraen
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (J.V.); (N.L.); (P.M.)
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (J.V.); (N.L.); (P.M.)
| | - Pieter Monsieurs
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (J.V.); (N.L.); (P.M.)
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;
| |
Collapse
|
21
|
Rajeev M, Sushmitha TJ, Aravindraja C, Toleti SR, Pandian SK. Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111808. [PMID: 33360289 DOI: 10.1016/j.ecoenv.2020.111808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/12/2023]
Abstract
One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.
Collapse
Affiliation(s)
- Meora Rajeev
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - T J Sushmitha
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | | | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam 603 102, Tamil Nadu, India
| | | |
Collapse
|
22
|
Meena M, Sonigra P, Yadav G. Biological-based methods for the removal of volatile organic compounds (VOCs) and heavy metals. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2485-2508. [PMID: 33095900 DOI: 10.1007/s11356-020-11112-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The current scenario of increased population and industrial advancement leads to the spoliation of freshwater and tapper of the quality of water. These results decrease in freshwater bodies near all of the areas. Besides, organic and inorganic compounds discharged from different sources into the available natural water bodies are the cause of pollution. The occurrence of heavy metals in water and volatile organic compounds (VOCs) in the air is responsible for a vast range of negative impacts on the atmosphere and human health. Nonetheless, high uses of heavy metals for human purposes may alter the biochemical and geochemical equilibrium. The major air contaminants which are released into the surroundings known as VOCs are produced through different kinds of sources, such as petrochemical and pharmaceutical industries. VOCs are known to cause various health hazards. VOCs are a pivotal group of chemicals that evaporate readily at room temperature. To get over this problem, biofiltration technology has been evolved for the treatment of heavy metals using biological entities such as plants, algae, fungi, and bacteria. Biofiltration technology is a beneficial and sustainable method for the elimination of toxic pollutants from the aquatic environment. Various types of biological technologies ranging from biotrickling filters to biofilters have been developed and they are cost-effective, simple to fabricate, and easy to perform. A significant advantage of this process is the pollutant that is transformed into biodegradable trashes which can decompose within an average time period, thus yielding no secondary pollutants. The aim of this article is to scrutinize the role of biofiltration in the removal of heavy metals in wastewater and VOCs and also to analyze the recent bioremediation technologies and methods.
Collapse
Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| |
Collapse
|
23
|
Patel A, Enman J, Gulkova A, Guntoro PI, Dutkiewicz A, Ghorbani Y, Rova U, Christakopoulos P, Matsakas L. Integrating biometallurgical recovery of metals with biogenic synthesis of nanoparticles. CHEMOSPHERE 2021; 263:128306. [PMID: 33297243 DOI: 10.1016/j.chemosphere.2020.128306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
Industrial activities, such as mining, electroplating, cement production, and metallurgical operations, as well as manufacturing of plastics, fertilizers, pesticides, batteries, dyes or anticorrosive agents, can cause metal contamination in the surrounding environment. This is an acute problem due to the non-biodegradable nature of metal pollutants, their transformation into toxic and carcinogenic compounds, and bioaccumulation through the food chain. At the same time, platinum group metals and rare earth elements are of strong economic interest and their recovery is incentivized. Microbial interaction with metals or metals-bearing minerals can facilitate metals recovery in the form of nanoparticles. Metal nanoparticles are gaining increasing attention due to their unique characteristics and application as antimicrobial and antibiofilm agents, biocatalysts, in targeted drug delivery, for wastewater treatment, and in water electrolysis. Ideally, metal nanoparticles should be homogenous in shape and size, and not toxic to humans or the environment. Microbial synthesis of nanoparticles represents a safe, and environmentally friendly alternative to chemical and physical methods. In this review article, we mainly focus on metal and metal salts nanoparticles synthesized by various microorganisms, such as bacteria, fungi, microalgae, and yeasts, as well as their advantages in biomedical, health, and environmental applications.
Collapse
Affiliation(s)
- Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Josefine Enman
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | | | - Pratama Istiadi Guntoro
- Mineral Processing, Division of Minerals and Metallurgical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Agata Dutkiewicz
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Yousef Ghorbani
- Mineral Processing, Division of Minerals and Metallurgical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87, Luleå, Sweden.
| |
Collapse
|
24
|
Mahdi ZS, Talebnia Roshan F, Nikzad M, Ezoji H. Biosynthesis of zinc oxide nanoparticles using bacteria: a study on the characterization and application for electrochemical determination of bisphenol A. INORG NANO-MET CHEM 2020. [DOI: 10.1080/24701556.2020.1835962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zahra Sadat Mahdi
- Faculty of Chemical Engineering, Babol Noshirvani University of Technology, Babol, Iran
| | - Farid Talebnia Roshan
- Faculty of Chemical Engineering, Babol Noshirvani University of Technology, Babol, Iran
| | - Maryam Nikzad
- Faculty of Chemical Engineering, Babol Noshirvani University of Technology, Babol, Iran
| | - Hoda Ezoji
- Faculty of Chemical Engineering, Babol Noshirvani University of Technology, Babol, Iran
| |
Collapse
|
25
|
Nourmohammadi E, Hosseinkhani S, Nedaeinia R, Khoshdel-Sarkarizi H, Nedaeinia M, Ranjbar M, Ebrahimi N, Farjami Z, Nourmohammadi M, Mahmoudi A, Goli M, Ferns GA, Sadeghizadeh M. Construction of a sensitive and specific lead biosensor using a genetically engineered bacterial system with a luciferase gene reporter controlled by pbr and cadA promoters. Biomed Eng Online 2020; 19:79. [PMID: 33076919 PMCID: PMC7574304 DOI: 10.1186/s12938-020-00816-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/05/2020] [Indexed: 12/04/2022] Open
Abstract
Background A bacterial biosensor refers to genetically engineered bacteria that produce an assessable signal in the presence of a physical or chemical agent in the environment. Methods We have designed and evaluated a bacterial biosensor expressing a luciferase reporter gene controlled by pbr and cadA promoters in Cupriavidus metallidurans (previously termed Ralstonia metallidurans) containing the CH34 and pI258 plasmids of Staphylococcus aureus, respectively, and that can be used for the detection of heavy metals. In the present study, we have produced and evaluated biosensor plasmids designated pGL3-luc/pbr biosensor and pGL3-luc/cad biosensor, that were based on the expression of luc+ and under the control of the cad promoter and the cadC gene of S. aureus plasmid pI258 and pbr promoter and pbrR gene from plasmid pMOL30 of Cupriavidus metallidurans. Results We found that the pGL3-luc/pbr biosensor may be used to measure lead concentrations between 1–100 μM in the presence of other metals, including zinc, cadmium, tin and nickel. The latter metals did not result in any significant signal. The pGL3-luc/cad biosensor could detect lead concentrations between 10 nM to 10 μM. Conclusions This biosensor was found to be specific for measuring lead ions in both environmental and biological samples.
Collapse
Affiliation(s)
- Esmail Nourmohammadi
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hoda Khoshdel-Sarkarizi
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Mozhdeh Nedaeinia
- Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Ranjbar
- Advanced Materials Research Center, Department of Materials Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Neshat Ebrahimi
- Laboratory of Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zahra Farjami
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Nourmohammadi
- Department of Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Mahmoudi
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Goli
- Department of Food Science and Technology, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Gordon A Ferns
- Brighton and Sussex Medical School, Division of Medical Education, Falmer, Brighton, BN1 9PH, Sussex, UK
| | - Majid Sadeghizadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
26
|
Arroyo-Herrera I, Rojas-Rojas FU, Lozano-Cervantes KD, Larios-Serrato V, Vásquez-Murrieta MS, Whtiman WB, Ibarra JA, Estrada-de Los Santos P. Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. 3 Biotech 2020; 10:242. [PMID: 32405446 DOI: 10.1007/s13205-020-02210-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 11/27/2022] Open
Abstract
Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.
Collapse
Affiliation(s)
- Ivan Arroyo-Herrera
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Fernando Uriel Rojas-Rojas
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
- 2Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, León, Guanajuato, Mexico
| | - Karla Daniela Lozano-Cervantes
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Violeta Larios-Serrato
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - María Soledad Vásquez-Murrieta
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | | | - J Antonio Ibarra
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Paulina Estrada-de Los Santos
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| |
Collapse
|
27
|
Ducret V, Gonzalez MR, Leoni S, Valentini M, Perron K. The CzcCBA Efflux System Requires the CadA P-Type ATPase for Timely Expression Upon Zinc Excess in Pseudomonas aeruginosa. Front Microbiol 2020; 11:911. [PMID: 32477311 PMCID: PMC7242495 DOI: 10.3389/fmicb.2020.00911] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Zinc (Zn) is a trace element essential for life but can be toxic if present in excess. While cells have import systems to guarantee a vital Zn intracellular concentration, they also rely on export systems to avoid lethal Zn overload. In particular, the opportunistic pathogen Pseudomonas aeruginosa possesses four Zn export systems: CadA, CzcCBA, CzcD, and YiiP. In this work, we compare the importance for bacterial survival of each export system at high Zn concentrations. We show that the P-type ATPase CadA, and the efflux pump CzcCBA are the main efflux systems affecting the bacterium tolerance to Zn. In addition, cadA and czcCBA genes expression kinetics revealed a hierarchical organization and interdependence. In the presence of high Zn concentrations, cadA expression is very rapidly induced (<1 min), while czcCBA expression occurs subsequently (>15 min). Our present data show that the fast responsiveness of cadA to Zn excess is due to its transcriptional activator, CadR, which is constitutively present on its promoter and promptly activating cadA gene expression upon Zn binding. Moreover, we showed that CadA is essential for a timely induction of the CzcCBA efflux system. Finally, we observed an induction of cadA and czcCBA efflux systems upon phagocytosis of P. aeruginosa by macrophages, in which a toxic metal boost is discharged into the phagolysosome to intoxicate microbes. Importantly, we demonstrated that the regulatory link between induction of the CzcCBA system and the repression of the OprD porin responsible for carbapenem antibiotic resistance, is maintained in the macrophage environment.
Collapse
Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Manuel R Gonzalez
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| |
Collapse
|
28
|
Jia X, Ma Y, Bu R, Zhao T, Wu K. Directed evolution of a transcription factor PbrR to improve lead selectivity and reduce zinc interference through dual selection. AMB Express 2020; 10:67. [PMID: 32277291 PMCID: PMC7148400 DOI: 10.1186/s13568-020-01004-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/04/2020] [Indexed: 11/25/2022] Open
Abstract
Directed evolution has been proven as a powerful tool for developing proteins and strains with novel or enhanced features. In this study, a dual selection system was designed to tune the binding specificity of a transcription factor to a particular ligand with the ampicillin resistance gene amp (ON selection) as the positive selection marker and the levansucrase gene sacB (OFF selection) as the negative selection marker. It was applied to the lead responsive transcription factor PbrR in a whole-cell lead biosensor previously constructed in our lab (Jia et al. in Fems Microbiol Lett 365:fny157, 2018). After multiple rounds of ON–OFF selection, two mutants with higher specificity for lead were selected. Structural analysis revealed that the mutation C134 located on the metal-binding loop at the C-terminal of PbrR is likely associated with the enhanced binding to both lead and cadmium. The double mutations D64A and L68S close to the metal-binding residue C79 may lead to the reduced binding specificity toward zinc ions. This dual selection system can be applied to engineer the specificity of other transcription factors and provide fine-tuned tools to synthetic biology.
Collapse
|
29
|
Abstract
Soils are home to more than 25% of the earth’s total biodiversity and supports life on land and water, nutrient cycling and retention, food production, pollution remediation, and climate regulation. Accumulating evidence demonstrates that multiple sustainability goals can be simultaneously addressed when soil biota are put at the center of land management assessments; this is because the activity and interactions of soil organisms are intimately tied to multiple processes that ecosystems and society rely on. With soil biodiversity at the center of multiple globally relevant sustainability programs, we will be able to more efficiently and holistically achieve the Sustainable Development Goals and Aichi Biodiversity Targets. Here we review scenarios where soil biota can clearly support global sustainability targets, global changes and pressures that threaten soil biodiversity, and actions to conserve soil biodiversity and advance sustainability goals. This synthesis shows how the latest empirical evidence from soil biological research can shape tangible actions around the world for a sustainable future.
Collapse
|
30
|
Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. RESULTS The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. CONCLUSIONS STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
Collapse
Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| |
Collapse
|
31
|
Mazhar SH, Herzberg M, Ben Fekih I, Zhang C, Bello SK, Li YP, Su J, Xu J, Feng R, Zhou S, Rensing C. Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. Front Microbiol 2020; 11:47. [PMID: 32117100 PMCID: PMC7019866 DOI: 10.3389/fmicb.2020.00047] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold–copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid – pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.
Collapse
Affiliation(s)
- Sohaib H Mazhar
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenkang Zhang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Suleiman Kehinde Bello
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junming Su
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqiang Xu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
32
|
Luziatelli F, Ficca AG, Cardarelli M, Melini F, Cavalieri A, Ruzzi M. Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals. Microorganisms 2020; 8:microorganisms8020153. [PMID: 31979031 PMCID: PMC7074716 DOI: 10.3390/microorganisms8020153] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/03/2020] [Accepted: 01/20/2020] [Indexed: 11/20/2022] Open
Abstract
Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.
Collapse
Affiliation(s)
- Francesca Luziatelli
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
| | - Anna Grazia Ficca
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
| | | | - Francesca Melini
- CREA Research Centre for Food and Nutrition, Via Ardeatina 546, I-00178 Rome, Italy;
| | - Andrea Cavalieri
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark;
| | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
- Correspondence: ; Tel.: +39-0761-357-317
| |
Collapse
|
33
|
Tolbatov I, Re N, Coletti C, Marrone A. Determinants of the Lead(II) Affinity in pbrR Protein: A Computational Study. Inorg Chem 2019; 59:790-800. [DOI: 10.1021/acs.inorgchem.9b03059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iogann Tolbatov
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| |
Collapse
|
34
|
Podder M, Majumder C. Bacteria immobilization on neem leaves/MnFe2O4 composite surface for removal of As(III) and As(V) from wastewater. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2015.08.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
35
|
Paul T, Mukherjee SK. Induction of inflammatory response in human cell lines by arsenic-contaminated soil-isolated bacterium Micrococcus sp. KUMAs15. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
36
|
El-Seedi HR, El-Shabasy RM, Khalifa SAM, Saeed A, Shah A, Shah R, Iftikhar FJ, Abdel-Daim MM, Omri A, Hajrahand NH, Sabir JSM, Zou X, Halabi MF, Sarhan W, Guo W. Metal nanoparticles fabricated by green chemistry using natural extracts: biosynthesis, mechanisms, and applications. RSC Adv 2019; 9:24539-24559. [PMID: 35527869 PMCID: PMC9069627 DOI: 10.1039/c9ra02225b] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Nanoparticles (NPs) are new inspiring clinical targets that have emerged from persistent efforts with unique properties and diverse applications. However, the main methods currently utilized in their production are not environmentally friendly. With the aim of promoting a green approach for the synthesis of NPs, this review describes eco-friendly methods for the preparation of biogenic NPs and the known mechanisms for their biosynthesis. Natural plant extracts contain many different secondary metabolites and biomolecules, including flavonoids, alkaloids, terpenoids, phenolic compounds and enzymes. Secondary metabolites can enable the reduction of metal ions to NPs in eco-friendly one-step synthetic processes. Moreover, the green synthesis of NPs using plant extracts often obviates the need for stabilizing and capping agents and yields biologically active shape- and size-dependent products. Herein, we review the formation of metallic NPs induced by natural extracts and list the plant extracts used in the synthesis of NPs. In addition, the use of bacterial and fungal extracts in the synthesis of NPs is highlighted, and the parameters that influence the rate of particle production, size, and morphology are discussed. Finally, the importance and uniqueness of NP-based products are illustrated, and their commercial applications in various fields are briefly featured.
Collapse
Affiliation(s)
- Hesham R El-Seedi
- Pharmacognosy Group, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre Box 574 SE-751 23 Uppsala Sweden +46 18 4714207
- College of Food and Biological Engineering, Jiangsu University Zhenjiang 212013 China
- Al-Rayan Research and Innovation Center, Al-Rayan Colleges Medina 42541 Saudi Arabia
- Department of Chemistry, Faculty of Science, Menoufia University Egypt
| | - Rehan M El-Shabasy
- Department of Chemistry, Faculty of Science, Menoufia University Egypt
- Ecological Chemistry Group, Department of Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology Stockholm Sweden
| | - Shaden A M Khalifa
- Clinical Research Centre, Karolinska University Hospital Huddinge Sweden
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE 106 91 Stockholm Sweden
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University 45320 Islamabad Pakistan
| | - Afzal Shah
- Department of Chemistry, College of Science, University of Bahrain Sakhir 32038 Bahrain
| | - Raza Shah
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
| | - Faiza Jan Iftikhar
- Department of Chemistry, Quaid-i-Azam University 45320 Islamabad Pakistan
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University Ismailia 41522 Egypt
| | - Abdelfatteh Omri
- Center of Excellence in Bionoscience Research, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
| | - Nahid H Hajrahand
- Center of Excellence in Bionoscience Research, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
| | - Jamal S M Sabir
- Center of Excellence in Bionoscience Research, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU) Jeddah 21589 Saudi Arabia
| | - Xiaobo Zou
- College of Food and Biological Engineering, Jiangsu University Zhenjiang 212013 China
| | - Mohammed F Halabi
- Al-Rayan Research and Innovation Center, Al-Rayan Colleges Medina 42541 Saudi Arabia
| | | | - Weisheng Guo
- Translational Medicine Center, The Second Affiliated Hospital, Guangzhou Medical University Guangzhou 510260 China +86-020-34153830
| |
Collapse
|
37
|
Hosny AEDM, Rasmy SA, Aboul-Magd DS, Kashef MT, El-Bazza ZE. The increasing threat of silver-resistance in clinical isolates from wounds and burns. Infect Drug Resist 2019; 12:1985-2001. [PMID: 31372006 PMCID: PMC6636436 DOI: 10.2147/idr.s209881] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/13/2019] [Indexed: 01/08/2023] Open
Abstract
Purpose The widespread use of silver-containing compounds has led to emergence of silver-resistant bacteria. Few studies are available on the detectability of plasmid-mediated silver-resistance in developing countries. Therefore, we aimed to detect silver-resistance in isolates from wounds and burns, and to genetically characterize plasmid-mediated silver-resistance genes (sil genes). Methods One hundred and fifty clinical isolates were obtained from burns and wounds. They were identified using the suitable Analytical Profile Index and MicroScan identification systems. Their antimicrobial susceptibility was tested by the disk diffusion and broth microdilution methods. Their silver nitrate (AgNO3) minimum inhibitory concentration (MIC) was determined using the broth macrodilution method. The presence of different sil genes on plasmids extracted from silver-resistant isolates and the replicon types of the extracted plasmids were investigated using polymerase chain reaction (PCR). The ability of these plasmids to impart silver-resistance was tested by transformation. Results All except two isolates were multidrug-resistant. Nineteen silver-resistant bacterial isolates (12.6%) were detected; with AgNO3 MIC ≥512 µg/mL. They were identified as Klebsiella pneumoniae (n=7), Staphylococcus aureus (n=4), Escherichia coli (n=2), Enterobacter cloacae (n=2), Pseudomonas aeruginosa (n=2) and Acinetobacter baumannii (n=2). PCR revealed the presence of different sil genes on the extracted plasmids. Plasmid transformation resulted in the transfer of silver-resistance to the resulting transformants. The extracted plasmids had different replicon types. Conclusion Plasmid-mediated silver-resistance was detected for the first time, in clinical P. aeruginosa, A. baumannii and S. aureus isolates; in addition to its detection in K. pneumoniae, E. coli and Enterobacter cloacae. Therefore, strict monitoring on the use of silver compounds in medical settings is required; with implementation of an approved standardized method for silver-resistance detection.
Collapse
Affiliation(s)
- Alaa El-Dien Ms Hosny
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Salwa A Rasmy
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Dina S Aboul-Magd
- Drug Radiation Research Department, National Center for Radiation Research and Technology, Atomic Energy Authority, Cairo, Egypt
| | - Mona T Kashef
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Zeinab E El-Bazza
- Drug Radiation Research Department, National Center for Radiation Research and Technology, Atomic Energy Authority, Cairo, Egypt
| |
Collapse
|
38
|
Remenár M, Kamlárová A, Harichová J, Zámocký M, Ferianc P. The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia. Pol J Microbiol 2019; 67:191-201. [PMID: 30015457 PMCID: PMC7256691 DOI: 10.21307/pjm-2018-022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/18/2022] Open
Abstract
A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp) sequences tentatively assigned to CzcA family heavy metal efflux pump [YP_001899332] from Ralstonia picketii 12J with 99% similarity. In this study the bacterium MR-CH-I2 and its heavy-metal resistance determinant were more precisely identified. This bacterial isolate was on the base of phylogenetic analysis of almost the whole (1,500 bp) 16S rDNA (16S rRNA) sequence, MR-CH-I2 [MF102046], and sequence for gyrB gene and its product respectively, MR-CH-I2-gyrB [MF134666], assigned to R. picketii 12J [CP001068] with 99 and 100% similarities, respectively. In addition, the whole nccA-like heavy-metal resistance gene sequence (3,192 bp), marked as MR-CH-I2-nccA [KR476581], was obtained and on the base of phylogenetic analysis its assignment was confirmed to MULTISPECIES: cation efflux system protein CzcA [WP_004635342] from Burkholderiaceae with 98% similarity. Furthermore, although the bacterium carried one high molecular plasmid of about 50 kb in size, nccA-like gene was not located on this plasmid. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.
Collapse
Affiliation(s)
- Matej Remenár
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Anna Kamlárová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Jana Harichová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia.,Metalloprotein Research Group, Division of Biochemistry, Department of Chemistry, University of Natural Resources and Applied Life Sciences,Vienna,Austria
| | - Peter Ferianc
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| |
Collapse
|
39
|
Nongkhlaw M, Joshi SR. Molecular insight into the expression of metal transporter genes in Chryseobacterium sp. PMSZPI isolated from uranium deposit. PLoS One 2019; 14:e0216995. [PMID: 31120947 PMCID: PMC6532875 DOI: 10.1371/journal.pone.0216995] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/02/2019] [Indexed: 11/18/2022] Open
Abstract
Metal tolerant bacterium Chryseobacterium sp. PMSZPI previously isolated and characterized from uranium ore deposit was studied for elucidating the role of metal transporter genes belonging to the Cation Diffusion Facilitator (CDF), Root-Nodulation-Division (RND) and PIB-type ATPase family in cadmium and uranium tolerance. The bacterium showed tolerance towards cadmium (MIC~6mM) and uranium (MIC~2mM) and was found to harbor metal transporter genes belonging to CDF, RND and PIB-type ATPase family of proteins. Expression studies by real-time PCR showed an upregulation of czcA(RND), czcD(CDF) and cadA(PIB-type ATPase) genes in presence of cadmium or uranium. Higher expression of czcA and czcD was found when the bacterium was treated with cadmium and uranium respectively. This study provides significant insight into the molecular mechanism that plays a role in cadmium and uranium tolerance in bacteria.
Collapse
Affiliation(s)
- Macmillan Nongkhlaw
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Mawlai, Umshing, Shillong, Meghalaya, India
| | - Santa Ram Joshi
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Mawlai, Umshing, Shillong, Meghalaya, India
- * E-mail:
| |
Collapse
|
40
|
Gutiérrez-Barranquero JA, Cazorla FM, de Vicente A. Pseudomonas syringae pv. syringae Associated With Mango Trees, a Particular Pathogen Within the "Hodgepodge" of the Pseudomonas syringae Complex. FRONTIERS IN PLANT SCIENCE 2019; 10:570. [PMID: 31139201 PMCID: PMC6518948 DOI: 10.3389/fpls.2019.00570] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/15/2019] [Indexed: 05/29/2023]
Abstract
The Pseudomonas syringae complex comprises different genetic groups that include strains from both agricultural and environmental habitats. This complex group has been used for decades as a "hodgepodge," including many taxonomically related species. More than 60 pathovars of P. syringae have been described based on distinct host ranges and disease symptoms they cause. These pathovars cause disease relying on an array of virulence mechanisms. However, P. syringae pv. syringae (Pss) is the most polyphagous bacterium in the P. syringae complex, based on its wide host range, that primarily affects woody and herbaceous host plants. In early 1990s, bacterial apical necrosis (BAN) of mango trees, a critical disease elicited by Pss in Southern Spain was described for the first time. Pss exhibits important epiphytic traits and virulence factors, which may promote its survival and pathogenicity in mango trees and in other plant hosts. Over more than two decades, Pss strains isolated from mango trees have been comprehensively investigated to elucidate the mechanisms that governs their epiphytic and pathogenic lifestyles. In particular, the vast majority of Pss strains isolated from mango trees produce an antimetabolite toxin, called mangotoxin, whose leading role in virulence has been clearly demonstrated. Moreover, phenotypic, genetic and phylogenetic approaches support that Pss strains producers of BAN symptoms on mango trees all belong to a single phylotype within phylogroup 2, are adapted to the mango host, and produce mangotoxin. Remarkably, a genome sequencing project of the Pss model strain UMAF0158 revealed the presence of other factors that may play major roles in its different lifestyles, such as the presence of two different type III secretion systems, two type VI secretion systems and an operon for cellulose biosynthesis. The role of cellulose in increasing mango leaf colonization and biofilm formation, and impairing virulence of Pss, suggests that cellulose may play a pivotal role with regards to the balance of its different lifestyles. In addition, 62-kb plasmids belonging to the pPT23A-family of plasmids (PFPs) have been strongly associated with Pss strains that inhabit mango trees. Further, complete sequence and comparative genomic analyses revealed major roles of PFPs in detoxification of copper compounds and ultraviolet radiation resistance, both improving the epiphytic lifestyle of Pss on mango surfaces. Hence, in this review we summarize the research that has been conducted on Pss by our research group to elucidate the molecular mechanisms that underpin the epiphytic and pathogenic lifestyle on mango trees. Finally, future directions in this particular plant-pathogen story are discussed.
Collapse
|
41
|
Kutralam-Muniasamy G, Pérez-Guevara F. Comparative genome analysis of completely sequenced Cupriavidus genomes provides insights into the biosynthetic potential and versatile applications of Cupriavidus alkaliphilus ASC-732. Can J Microbiol 2019; 65:575-595. [PMID: 31022352 DOI: 10.1139/cjm-2019-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genome analysis of microorganisms provides valuable information to endorse more extensive research on their potential applications. In this paper, the genome of Cupriavidus alkaliphilus ASC-732, isolated from agave rhizosphere in northeastern Mexico, was analyzed and compared with the genomes of other Cupriavidus species to gain better insight into the parts in the genetic makeup responsible for essential metabolic pathways and others of biotechnological importance. Here, the key genes related to glycolysis, pentose phosphate, and the Entner-Doudoroff and tricarboxylic acid cycle pathways were predicted. Comparative genome analysis revealed that the key genes for hydrogenotrophic growth and carbon fixation pathway, i.e., those coding for hydrogenase and enzymes Calvin-Benson-Bassham cycle, are absent in C. alkaliphilus ASC-732. Furthermore, capabilities for producing polyhydroxyalkanoates and extracellular polysaccharide matrix and degrading xenobiotics were found, and the related pathways are explained. Moreover, biofilm formation and the production of exopolysaccharides and polyhydroxyalkanoates were corroborated with crystal violet staining, calcofluor, and Nile red fluorochromes, confirming the presence of the products of the active genes in these pathways and their related metabolic routes, respectively. Additionally, a large group of genes essential for the resistance and detoxification of several heavy metals were also found. Thus, the present study demonstrates that this strain can respond to various environmental signals, such as energy source, nutrient limitations, virulence, and extreme metals concentration, indicating the possibility to foster C. alkaliphilus ASC-732 in diverse biotechnological applications.
Collapse
Affiliation(s)
- Gurusamy Kutralam-Muniasamy
- a Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
| | - Fermín Pérez-Guevara
- a Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, Mexico.,b Nanoscience and Nanotechnology Program, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
| |
Collapse
|
42
|
Kaplan H, Ratering S, Felix-Henningsen P, Schnell S. Stability of in situ immobilization of trace metals with different amendments revealed by microbial 13C-labelled wheat root decomposition and efflux-mediated metal resistance of soil bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:1082-1089. [PMID: 31096323 DOI: 10.1016/j.scitotenv.2018.12.441] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/14/2018] [Accepted: 12/28/2018] [Indexed: 05/16/2023]
Abstract
The aim of the present study was to prove the long-term efficiency of the amendments zerovalent iron grit, zeolite, and Divergan® for trace metal remediation in heavily contaminated soils and to attain a recovery of microbial functionality and diversity by remediation. For immobilization of the trace metals the amendments zerovalent iron grit, natural zeolite, and Divergan® were used. Trace metal total and mobile contents were determined and bacterial communities were assessed after a SIP experiment with 13C-labelled wheat root by Ion-Torrent Sequencing targeting the bacterial 16S rRNA gene and two trace metal resistant genes for copper and cadmium (copA and czcA gene). The results show that the remediation effect of the three amendments is still stable after five years. The mobile trace metal contents were significantly (≤0.001) reduced in all treatments, except the Cu content in the zeolite treatment. A higher diversity in active metabolizing and growing soil bacteria was observed in remediated soils as compared to the non-remediated control, especially for the Divergan® treatment. The bacterial genera Kribbella, Glycomyces, Inquilinus, Nocardioides, and Lysobacter are the most significantly enriched genera in the 13C fractions of the treated samples. The occurrence of bacterial families, which could be identified carrying efflux-mediated metal resistance genes for Cd/Zn and Cu, were reduced in the remediated soils as compared to the non-remediated control. The most abundant bacterial family for the copA and the czcA gene is Xanthomonadaceae. The pH-value and the trace metal concentration could be identified as key drivers of bacterial community composition, and functions in trace metal contaminated soils and remediated soils.
Collapse
Affiliation(s)
- Hülya Kaplan
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany; Institute of Soil Science and Soil Conservation, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Peter Felix-Henningsen
- Institute of Soil Science and Soil Conservation, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University, 35392 Giessen, Germany.
| |
Collapse
|
43
|
Ramos-Zúñiga J, Gallardo S, Martínez-Bussenius C, Norambuena R, Navarro CA, Paradela A, Jerez CA. Response of the biomining Acidithiobacillus ferrooxidans to high cadmium concentrations. J Proteomics 2019; 198:132-144. [DOI: 10.1016/j.jprot.2018.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/28/2022]
|
44
|
Liu JL, Yao J, Wang F, Min N, Gu JH, Li ZF, Sunahara G, Duran R, Solevic-Knudsen T, Hudson-Edwards KA, Alakangas L. Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:98-107. [PMID: 30669085 DOI: 10.1016/j.envpol.2018.12.045] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/08/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.
Collapse
Affiliation(s)
- Jian-Li Liu
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Fei Wang
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ning Min
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Ji-Hai Gu
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Zi-Fu Li
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Tatjana Solevic-Knudsen
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoseva 12, PO Box 473, 11001, Belgrade, Serbia
| | - Karen A Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, UK
| | - Lena Alakangas
- Department of Chemical Engineering and Geosciences, Luleå University of Technology, SE-97187 Luleå, Sweden
| |
Collapse
|
45
|
Litvinenko LV. Ability of the Dietzia, Gordonia and Rhodococcus Actinobacteria to Accumulate Nickel Ions. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
46
|
Ali MM, Provoost A, Maertens L, Leys N, Monsieurs P, Charlier D, Van Houdt R. Genomic and Transcriptomic Changes that Mediate Increased Platinum Resistance in Cupriavidus metallidurans. Genes (Basel) 2019; 10:E63. [PMID: 30669395 PMCID: PMC6357080 DOI: 10.3390/genes10010063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
The extensive anthropogenic use of platinum, a rare element found in low natural abundance in the Earth's continental crust and one of the critical raw materials in the EU innovation partnership framework, has resulted in increased concentrations in surface environments. To minimize its spread and increase its recovery from the environment, biological recovery via different microbial systems is explored. In contrast, studies focusing on the effects of prolonged exposure to Pt are limited. In this study, we used the metal-resistant Cupriavidus metallidurans NA4 strain to explore the adaptation of environmental bacteria to platinum exposure. We used a combined Nanopore⁻Illumina sequencing approach to fully resolve all six replicons of the C. metallidurans NA4 genome, and compared them with the C. metallidurans CH34 genome, revealing an important role in metal resistance for its chromid rather than its megaplasmids. In addition, we identified the genomic and transcriptomic changes in a laboratory-evolved strain, displaying resistance to 160 µM Pt4+. The latter carried 20 mutations, including a large 69.9 kb deletion in its plasmid pNA4_D (89.6 kb in size), and 226 differentially-expressed genes compared to its parental strain. Many membrane-related processes were affected, including up-regulation of cytochrome c and a lytic transglycosylase, down-regulation of flagellar and pili-related genes, and loss of the pNA4_D conjugative machinery, pointing towards a significant role in the adaptation to platinum.
Collapse
Affiliation(s)
- Md Muntasir Ali
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussel, Belgium.
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| | - Laurens Maertens
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
- Research Unit in Biology of Microorganisms (URBM), Faculty of Sciences, UNamur, 5000 Namur, Belgium.
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussel, Belgium.
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| |
Collapse
|
47
|
Wu Z, Kong Z, Lu S, Huang C, Huang S, He Y, Wu L. Isolation, characterization and the effect of indigenous heavy metal-resistant plant growth-promoting bacteria on sorghum grown in acid mine drainage polluted soils. J GEN APPL MICROBIOL 2019; 65:254-264. [DOI: 10.2323/jgam.2018.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zijun Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Shina Lu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Cheng Huang
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Shaoyi Huang
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Yinghui He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University
| |
Collapse
|
48
|
Mijnendonckx K, Ali MM, Provoost A, Janssen P, Mergeay M, Leys N, Charlier D, Monsieurs P, Van Houdt R. Spontaneous mutation in the AgrRS two-component regulatory system ofCupriavidus metalliduransresults in enhanced silver resistance. Metallomics 2019; 11:1912-1924. [DOI: 10.1039/c9mt00123a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cupriavidus metalliduransis able to adapt to toxic silver concentrations and previously uncharacterized periplasmic proteins played a crucial role in this adaptation process.
Collapse
Affiliation(s)
| | - Md Muntasir Ali
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
- Research Group of Microbiology
| | - Ann Provoost
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Paul Janssen
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Max Mergeay
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Natalie Leys
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Daniël Charlier
- Research Group of Microbiology
- Department of Bioengineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussel
- Belgium
| | - Pieter Monsieurs
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Rob Van Houdt
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| |
Collapse
|
49
|
Li YP, Carraro N, Yang N, Liu B, Xia X, Feng R, Saquib Q, Al-Wathnani HA, van der Meer JR, Rensing C. Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine. Genes (Basel) 2018; 9:genes9120573. [PMID: 30477188 PMCID: PMC6316836 DOI: 10.3390/genes9120573] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative PIB-1-ATPase, 5 putative PIB-3-ATPase, 4 putative Zn(II)/Cd(II) PIB-4 type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.
Collapse
Affiliation(s)
- Yuan Ping Li
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne 1015, Switzerland.
| | - Nan Yang
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Bixiu Liu
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Renwei Feng
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Hend A Al-Wathnani
- Department of Botany & Microbiology, College of Sciences, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | | | - Christopher Rensing
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academic of Sciences, 361021 Xiamen, China.
| |
Collapse
|
50
|
Millacura FA, Janssen PJ, Monsieurs P, Janssen A, Provoost A, Van Houdt R, Rojas LA. Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance. Genes (Basel) 2018; 9:E551. [PMID: 30428624 PMCID: PMC6266692 DOI: 10.3390/genes9110551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 12/04/2022] Open
Abstract
For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.
Collapse
Affiliation(s)
- Felipe A Millacura
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK.
| | - Paul J Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Pieter Monsieurs
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Provoost
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Rob Van Houdt
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Luis A Rojas
- Chemistry Department, Faculty of Sciences, Universidad Católica del Norte, UCN, Antofagasta 1240000, Chile.
| |
Collapse
|