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Huang ZS, Tan XQ, Yang HB, Zeng Y, Chen SJ, Wei ZS, Huang YQ. Mechanistic insights into tris(2-chloroisopropyl) phosphate biomineralization coupled with lead (II) biostabilization driven by denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173927. [PMID: 38901584 DOI: 10.1016/j.scitotenv.2024.173927] [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: 04/11/2024] [Revised: 05/24/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
The ubiquity and persistence of organophosphate esters (OPEs) and heavy metal (HMs) pose global environmental risks. This study explored tris(2-chloroisopropyl)phosphate (TCPP) biomineralization coupled to lead (Pb2+) biostabilization driven by denitrifying bacteria (DNB). The domesticated DNB achieved synergistic bioremoval of TCPP and Pb2+ in the batch bioreactor (efficiency: 98 %).TCPP mineralized into PO43- and Cl-, and Pb2+ precipitated with PO43-. The TCPP-degrading/Pb2+-resistant DNB: Achromobacter, Pseudomonas, Citrobacter, and Stenotrophomonas, dominated the bacterial community, and synergized TCPP biomineralization and Pb2+ biostabilization. Metagenomics and metaproteomics revealed TCPP underwent dechlorination, hydrolysis, the TCA cycle-based dissimilation, and assimilation; Pb2+ was detoxified via bioprecipitation, bacterial membrane biosorption, EPS biocomplexation, and efflux out of cells. TCPP, as an initial donor, along with NO3-, as the terminal acceptor, formed a respiratory redox as the primary energy metabolism. Both TCPP and Pb2+ can stimulate phosphatase expression, which established the mutual enhancements between their bioconversions by catalyzing TCPP dephosphorylation and facilitating Pb2+ bioprecipitation. TCPP may alleviate the Pb2+-induced oxidative stress by aiding protein phosphorylation. 80 % of Pb2+ converted into crystalized pyromorphite. These results provide the mechanistic foundations and help develop greener strategies for synergistic bioremediation of OPEs and HMs.
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Affiliation(s)
- Zhen-Shan Huang
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Xiu-Qin Tan
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, MEE, Guangzhou 510530, China
| | - Han-Biao Yang
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Yuan Zeng
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - She-Jun Chen
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Zai-Shan Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Yu-Qi Huang
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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2
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Abdeljelil N, Ben Miloud Yahia N, Landoulsi A, Chatti A, Wattiez R, Gillan D, Van Houdt R. Proteomic and morphological insights into the exposure of Cupriavidus metallidurans CH34 planktonic cells and biofilms to aluminium. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133403. [PMID: 38215523 DOI: 10.1016/j.jhazmat.2023.133403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
Aluminium (Al) is one of the most popular materials for industrial and domestic use. Nevertheless, research has proven that this metal can be toxic to most organisms. This light metal has no known biological function and to date very few aluminium-specific biological pathways have been identified. In addition, information about the impact of this metal on microbial life is scarce. Here, we aimed to study the effect of aluminium on the metal-resistant soil bacterium Cupriavidus metallidurans CH34 in different growth modes, i.e. planktonic cells, adhered cells and mature biofilms. Our results indicated that despite a significant tolerance to aluminium (minimal inhibitory concentration of 6.25 mM Al₂(SO₄)₃.18H₂O), the exposure of C. metallidurans to a sub-inhibitory dose (0.78 mM) caused early oxidative stress and an increase in hydrolytic activity. Changes in the outer membrane surface of planktonic cells were observed, in addition to a rapid disruption of mature biofilms. On protein level, aluminium exposure increased the expression of proteins involved in metabolic activity such as pyruvate kinase, formate dehydrogenase and poly(3-hydroxybutyrate) polymerase, whereas proteins involved in chemotaxis, and the production and transport of iron scavenging siderophores were significantly downregulated.
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Affiliation(s)
- Nissem Abdeljelil
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium; Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium; Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | | | - Ahmed Landoulsi
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Abdelwaheb Chatti
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium.
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3
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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Raghavan D, Patinharekkara SC, Elampilay ST, Payatatti VKI, Charles S, Veeraraghavan S, Kadiyalath J, Vandana S, Purayil SK, Prasadam H, Anitha SJ. New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115222. [PMID: 37418939 DOI: 10.1016/j.ecoenv.2023.115222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
Accumulation of nano ZnO (nZnO) in soils could be toxic to bacterial communities through disruption of Zn homeostasis. Under such conditions, bacterial communities strive to maintain cellular Zn levels by accentuation of appropriate cellular machinery. In this study, soil was exposed to a gradient (50-1000 mg Zn kg-1) of nZnO for evaluating their effects on genes involved in Zn homeostasis (ZHG). The responses were compared with similar levels of its bulk counterpart (bZnO). It was observed that ZnO (as nZnO or bZnO) induced a plethora of influx and efflux transporters as well as metallothioneins (MTs) and metallochaperones mediated by an array of Zn sensitive regulatory proteins. Major influx system identified was the ZnuABC transporter, while important efflux transporters identified were CzcCBA, ZntA, YiiP and the major regulator was Zur. The response of communities was dose- dependent at lower concentrations (<500 mg Zn kg-1 as nZnO or bZnO). However, at 1000 mg Zn kg-1, a size-dependent threshold of gene/gene family abundances was evident. Under nZnO, a poor adaptation to toxicity induced anaerobic conditions due to deployment of major influx and secondary detoxifying systems as well as poor chelation of free Zn ions was evident. Moreover, Zn homeostasis related link with biofilm formation and virulence were accentuated under nZnO than bZnO. While these findings were verified by PCoA and Procrustes analysis, Network analysis and taxa vs ZHG associations also substantiated that a stronger Zn shunting mechanism was induced under nZnO due to higher toxicity. Molecular crosstalks with systems governing Cu and Fe homeostasis were also evident. Expression analysis of important resistance genes by qRT-PCR showed good alignment with the predictive metagenome data, thereby validating our findings. From the study it was evident that the induction of detoxifying and resistant genes was greatly lowered under nZnO, which markedly hampered Zn homeostasis among the soil bacterial communities.
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Affiliation(s)
- Dinesh Raghavan
- ICAR-Indian Institute of Spices Research, Marikunnu PO, Kozhikode, Kerala, India
| | | | | | | | - Sona Charles
- ICAR-Indian Institute of Spices Research, Marikunnu PO, Kozhikode, Kerala, India
| | | | - Jayarajan Kadiyalath
- ICAR-Indian Institute of Spices Research, Marikunnu PO, Kozhikode, Kerala, India
| | - Sajith Vandana
- National Institute of Technology, NIT Campus PO, Kozhikode, Kerala, India
| | | | - Haritha Prasadam
- ICAR-Indian Institute of Spices Research, Marikunnu PO, Kozhikode, Kerala, India
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5
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Ridene S, Werfelli N, Mansouri A, Landoulsi A, Abbes C. Bioremediation potential of consortium Pseudomonas Stutzeri LBR and Cupriavidus Metallidurans LBJ in soil polluted by lead. PLoS One 2023; 18:e0284120. [PMID: 37319245 PMCID: PMC10270627 DOI: 10.1371/journal.pone.0284120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 03/23/2023] [Indexed: 06/17/2023] Open
Abstract
Pollution by lead (Pb) is an environmental and health threat due to the severity of its toxicity. Microbial bioremediation is an eco-friendly technique used to remediate contaminated soils. This present study was used to evaluate the effect of two bacterial strains isolated and identified from Bizerte lagoon: Cupriavidus metallidurans LBJ (C. metallidurans LBJ) and Pseudomonas stutzeri LBR (P. stutzeri LBR) on the rate of depollution of soil contaminated with Pb from Tunisia. To determine this effect, sterile and non-sterile soil was bioaugmented by P. stutzeri LBR and C. metallidurans LBJ strains individually and in a mixture for 25 days at 30°C. Results showed that the bioaugmentation of the non-sterile soil by the mixture of P. stutzeri LBR and C. metallidurans LBJ strains gave the best rate of reduction of Pb of 71.02%, compared to a rate of 58.07% and 46.47% respectively for bioaugmentation by the bacterial strains individually. In the case of the sterile soil, results showed that the reduction rate of lead was in the order of 66.96% in the case of the mixture of the two bacterial strains compared with 55.66% and 41.86% respectively for the addition of the two strains individually. These results are confirmed by analysis of the leachate from the sterile and non-sterile soil which showed an increase in the mobility and bioavailability of Pb in soil. These promising results offer another perspective for a soil bioremediation bioprocess applying bacterial bioremediation.
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Affiliation(s)
- Sirine Ridene
- University of Carthage, Biochemistry and Molecular Biology Laboratory of Faculty of Sciences of Bizerte, Risks Related to Environmental Stress, Struggle and Prevention (UR17ES20), Bizerte, Zarzouna, Tunisia
| | - Naima Werfelli
- International Center For Environmental Technologies, Boulevard Leader Yasser Arafat, Tunis, Tunisia
| | - Ahlem Mansouri
- University of Carthage, Biochemistry and Molecular Biology Laboratory of Faculty of Sciences of Bizerte, Risks Related to Environmental Stress, Struggle and Prevention (UR17ES20), Bizerte, Zarzouna, Tunisia
| | - Ahmed Landoulsi
- University of Carthage, Biochemistry and Molecular Biology Laboratory of Faculty of Sciences of Bizerte, Risks Related to Environmental Stress, Struggle and Prevention (UR17ES20), Bizerte, Zarzouna, Tunisia
| | - Chiraz Abbes
- University of Carthage, Biochemistry and Molecular Biology Laboratory of Faculty of Sciences of Bizerte, Risks Related to Environmental Stress, Struggle and Prevention (UR17ES20), Bizerte, Zarzouna, Tunisia
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6
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Hirth N, Gerlach MS, Wiesemann N, Herzberg M, Große C, Nies DH. Full Copper Resistance in Cupriavidus metallidurans Requires the Interplay of Many Resistance Systems. Appl Environ Microbiol 2023:e0056723. [PMID: 37191542 DOI: 10.1128/aem.00567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
The metal-resistant bacterium Cupriavidus metallidurans uses its copper resistance components to survive the synergistic toxicity of copper ions and gold complexes in auriferous soils. The cup, cop, cus, and gig determinants encode as central component the Cu(I)-exporting PIB1-type ATPase CupA, the periplasmic Cu(I)-oxidase CopA, the transenvelope efflux system CusCBA, and the Gig system with unknown function, respectively. The interplay of these systems with each other and with glutathione (GSH) was analyzed. Copper resistance in single and multiple mutants up to the quintuple mutant was characterized in dose-response curves, Live/Dead-staining, and atomic copper and glutathione content of the cells. The regulation of the cus and gig determinants was studied using reporter gene fusions and in case of gig also RT-PCR studies, which verified the operon structure of gigPABT. All five systems contributed to copper resistance in the order of importance: Cup, Cop, Cus, GSH, and Gig. Only Cup was able to increase copper resistance of the Δcop Δcup Δcus Δgig ΔgshA quintuple mutant but the other systems were required to increase copper resistance of the Δcop Δcus Δgig ΔgshA quadruple mutant to the parent level. Removal of the Cop system resulted in a clear decrease of copper resistance in most strain backgrounds. Cus cooperated with and partially substituted Cop. Gig and GSH cooperated with Cop, Cus, and Cup. Copper resistance is thus the result of an interplay of many systems. IMPORTANCE The ability of bacteria to maintain homeostasis of the essential-but-toxic "Janus"-faced element copper is important for their survival in many natural environments but also in case of pathogenic bacteria in their respective host. The most important contributors to copper homeostasis have been identified in the last decades and comprise PIB1-type ATPases, periplasmic copper- and oxygen-dependent copper oxidases, transenvelope efflux systems, and glutathione; however, it is not known how all these players interact. This publication investigates this interplay and describes copper homeostasis as a trait emerging from a network of interacting resistance systems.
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Affiliation(s)
- Niklas Hirth
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | | | - Nicole Wiesemann
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Martin Herzberg
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Cornelia Große
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Dietrich H Nies
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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7
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Hasani Zadeh P, Fermoso FG, Collins G, Serrano A, Mills S, Abram F. Impacts of metal stress on extracellular microbial products, and potential for selective metal recovery. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114604. [PMID: 36758509 DOI: 10.1016/j.ecoenv.2023.114604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Harnessing microbial capabilities for metal recovery from secondary waste sources is an eco-friendly and sustainable approach for the management of metal-containing wastes. Soluble microbial products (SMP) and extracellular polymeric substances (EPS) are the two main groups of extracellular compounds produced by microorganisms in response to metal stress that are of great importance for remediation and recovery of metals. These include various high-, and low, molecular weight components, which serve various functional and structural roles. These compounds often contain functional groups with metal binding potential that can attenuate metal stress by sequestering metal ions, making them less bioavailable. Microorganisms can regulate the content and composition of EPS and SMP in response to metal stress in order to increase the compounds specificity and capacity for metal binding. Thus, EPS and SMP represent ideal candidates for developing technologies for selective metal recovery from complex wastes. To discover highly metal-sorptive compounds with specific metal binding affinity for metal recovery applications, it is necessary to investigate the metal binding affinity of these compounds, especially under metal stressed conditions. In this review we critically reviewed microbial EPS and SMP production as a response to metal stress with a particular emphasis on the metal binding properties of these compounds and their role in altering metal bioavailability. Furthermore, for the first time, we compiled the available data on potential application of these compounds for selective metal recovery from waste streams.
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Affiliation(s)
- Parvin Hasani Zadeh
- Bioprocesses for the Circular Economy Group, Instituto de la Grasa, Spanish National Research Council (CSIC), Seville, Spain; Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Fernando G Fermoso
- Bioprocesses for the Circular Economy Group, Instituto de la Grasa, Spanish National Research Council (CSIC), Seville, Spain
| | - Gavin Collins
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Antonio Serrano
- Institute of Water Research, University of Granada, Granada 18071, Spain; Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Granada 18071, Spain
| | - Simon Mills
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Florence Abram
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
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8
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Cobalt(II), Nickel(II), Palladium(II) and Zinc(II) Metallothiosemicarbazones: Synthesis, Characterization, X-ray Structures and Biological Activity. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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9
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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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10
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Wang M, Zhang W, Zhao J, Yang Z, Guo X, Ji H. Distinct structural strategies with similar functional responses of abundant and rare subcommunities regarding heavy metal pollution in the Beiyun river basin. CHEMOSPHERE 2022; 309:136659. [PMID: 36202374 DOI: 10.1016/j.chemosphere.2022.136659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Bacteria within a metacommunity could be partitioned into different subcommunities ecological assemblages in light of potential importance for the community function. It is unknown how abundant and rare microbial subcommunities in urban river sediments respond to heavy metal pollutants. Using high-throughput sequencing, we analyzed these response patterns in the heavliy polluted (Beijing, China). We found that this river faces substantial ecological risks, owing to high rates of Cd and Hg pollution from urban activities. Surprisingly, abundant and rare subcommunity structures showed opposite responses to heavy metals. Abundant taxa, such as Crenarchaeota and Euryarchaeota, are resistant to heavy metal pollution through the synergistic of ammonia nitrogen (NH4+-N) and total phosphorus (TP). By contrast, rare taxa, such as Verrucomicrobia, Fibrobacteres, Berkelbacteria, and Euryarchaeota, had a high synergy with NH4+-N and TP with high a resilience to heavy metal pollution. However, the functions of both abundant and rare subcommunities showed a similar response to heavy metal pollutants, especially in denitrification processes. The abundant taxa responded to heavy metal pollution through methanogenesis by CO2 reduction with H2, human pathogens nosocomia, sulfate respiration, photoheterotrophy, and dark sulfide oxidation synergy with NH4+-N and TP. The rare taxa responded to heavy metals through methanogenesis by CO2 reduction with H2, cellulolysis, sulfate respiration, intracellular parasites, nitrate reduction and plant pathogen. We observed distinct patterns between the structural and functional responses of microbial subcommunities to heavy metal pollutants. Our findings support the concept that denitrification processes are sensitive to but not inhibited by high levels of heavy metals pollution. We propose that the structures and functions of the abundant and rare microbial subcommunities could inform the management of pollutants in heavily polluted urban river ecosystems at fine geographical scales.
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Affiliation(s)
- Min Wang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Wei Zhang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Junying Zhao
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Zirou Yang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Xiaoyu Guo
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China.
| | - Hongbing Ji
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China; School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.
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11
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Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori. mBio 2022; 13:e0163322. [PMID: 36154274 PMCID: PMC9601102 DOI: 10.1128/mbio.01633-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial antibiotic resistance is a major threat to human health. A combination of antibiotics with metals is among the proposed alternative treatments. Only one such combination is successfully used in clinics; it associates antibiotics with the metal bismuth to treat infections by Helicobacter pylori. This bacterial pathogen colonizes the human stomach and is associated with gastric cancer, killing 800,000 individuals yearly. The effect of bismuth in H. pylori treatment is not well understood in particular for sublethal doses such as those measured in the plasma of treated patients. We addressed this question and observed that bismuth induces the formation of homogeneously sized membrane vesicles (MVs) with unique protein cargo content enriched in bismuth-binding proteins, as shown by quantitative proteomics. Purified MVs of bismuth-exposed bacteria were strongly enriched in bismuth as measured by inductively coupled plasma optical emission spectrometry (ICP-OES), unlike bacterial cells from which they originate. Thus, our results revealed a novel function of MVs in bismuth detoxification, where secreted MVs act as tool to discard bismuth from the bacteria. Bismuth also induces the formation of intracellular polyphosphate granules that are associated with changes in nucleoid structure. Nucleoid compaction in response to bismuth was established by immunogold electron microscopy and refined by the first chromosome conformation capture (Hi-C) analysis of H. pylori. Our results reveal that even low doses of bismuth induce profound changes in H. pylori physiology and highlight a novel defense mechanism that involves MV-mediated bismuth extrusion from the bacteria and a probable local DNA protective response where polyphosphate granules are associated with nucleoid compaction.
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12
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Yu H, Huang L, Zhang G, Zhou P. Physiological metabolism of electrochemically active bacteria directed by combined acetate and Cd(II) in single-chamber microbial electrolysis cells. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127538. [PMID: 34736191 DOI: 10.1016/j.jhazmat.2021.127538] [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: 09/02/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
It is of great interest to explore physiological metabolism of electrochemically active bacteria (EAB) for combined organics and heavy metals in single-chamber microbial electrolysis cells (MECs). Four pure culture EAB varying degrees responded to the combined acetate (1.0-5.0 g/L) and Cd(II) (20-150 mg/L) at different initial concentrations in the single-chamber MECs, shown as significant relevance of Cd(II) removal (2.57-7.35 mg/L/h) and H2 production (0-0.0011 m3/m3/h) instead of acetate removal (73-130 mg/L/h), to these EAB species at initial Cd(II) below 120 mg/L and initial acetate below 3.0 g/L. A high initial acetate (5.0 g/L) compensated the Cd(II) inhibition and broadened the removal of Cd(II) to 150 mg/L. These EAB physiologically released variable amounts of extracellular polymeric substances with a compositional diversity in response to the changes of initial Cd(II) and circuital current whereas the activities of typical intracellular enzymes were more apparently altered by the initial Cd(II) than the circuital current. These results provide experimental validation of the presence, the metabolic plasticity and the physiological response of these EAB directed by the changes of initial Cd(II) and acetate concentrations in the single-chamber MECs, deepening our understanding of EAB physiological coping strategies in metallurgical microbial electro-ecological cycles.
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Affiliation(s)
- Haihang Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Liping Huang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Guoquan Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Peng Zhou
- College of Chemistry, Dalian University of Technology, Dalian 116024, China
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13
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Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031484. [PMID: 35162506 PMCID: PMC8835105 DOI: 10.3390/ijerph19031484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.
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S, Misra M, Ghosh Sachan S. Nanobioremediation of heavy metals: Perspectives and challenges. J Basic Microbiol 2021. [DOI: 10.1002/jobm.202100384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Sunanda
- Department of Bioengineering and Biotechnology Birla Institute of Technology, Mesra Ranchi Jharkhand India
| | - Modhurima Misra
- Department of Bioengineering and Biotechnology Birla Institute of Technology, Mesra Ranchi Jharkhand India
| | - Shashwati Ghosh Sachan
- Department of Bioengineering and Biotechnology Birla Institute of Technology, Mesra Ranchi Jharkhand India
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15
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Lin Y, Wang L, Xu K, Li K, Ren H. Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics. MICROBIOME 2021; 9:67. [PMID: 33752740 PMCID: PMC7986553 DOI: 10.1186/s40168-021-01016-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/02/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Denitrifying phosphorus removal sludge (DPRS) is widely adopted for nitrogen and phosphorus removal in wastewater treatment but faces threats from heavy metals. However, a lack of understanding of the taxon-specific heavy metal-resistance mechanisms hinders the targeted optimization of DPRS's robustness in nutrient removal. RESULTS We obtained 403 high- or medium-quality metagenome-assembled genomes from DPRS treated by elevating cadmium, nickel, and chromium pressure. Then, the proteomic responses of individual taxa under heavy metal pressures were characterized, with an emphasis on functions involving heavy metal resistance and maintenance of nutrient metabolism. When oxygen availability was constrained by high-concentration heavy metals, comammox Nitrospira overproduced highly oxygen-affinitive hemoglobin and electron-transporting cytochrome c-like proteins, underpinning its ability to enhance oxygen acquisition and utilization. In contrast, Nitrosomonas overexpressed ammonia monooxygenase and nitrite reductase to facilitate the partial nitrification and denitrification process for maintaining nitrogen removal. Comparisons between phosphorus-accumulating organisms (PAOs) demonstrated different heavy metal-resistance mechanisms adopted by Dechloromonas and Candidatus Accumulibacter, despite their high genomic similarities. In particular, Dechloromonas outcompeted the canonical PAO Candidatus Accumulibacter in synthesizing polyphosphate, a potential public good for heavy metal detoxification. The superiority of Dechloromonas in energy utilization, radical elimination, and damaged cell component repair also contributed to its dominance under heavy metal pressures. Moreover, the enrichment analysis revealed that functions involved in extracellular polymeric substance formation, siderophore activity, and heavy metal efflux were significantly overexpressed due to the related activities of specific taxa. CONCLUSIONS Our study demonstrates that heavy metal-resistance mechanisms within a multipartite community are highly heterogeneous between different taxa. These findings provide a fundamental understanding of how the heterogeneity of individual microorganisms contributes to the metabolic versatility and robustness of microbiomes inhabiting dynamic environments, which is vital for manipulating the adaptation of microbial assemblages under adverse environmental stimuli. Video abstract.
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Affiliation(s)
- Yuan Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Liye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
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16
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Hemmat-Jou MH, Safari-Sinegani AA, Che R, Mirzaie-Asl A, Tahmourespour A, Tahmasbian I. Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4845-4856. [PMID: 32949366 DOI: 10.1007/s11356-020-10824-x] [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: 03/01/2020] [Accepted: 09/13/2020] [Indexed: 05/27/2023]
Abstract
This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.
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Affiliation(s)
| | | | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650091, China
| | - Asghar Mirzaie-Asl
- Department of Biotechnology, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - Arezoo Tahmourespour
- Department of Basic Medical Sciences, Islamic Azad University (Isfahan Branch), Isfahan, Iran
| | - Iman Tahmasbian
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, QLD, 4350, Australia
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Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
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18
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Minari GD, Saran LM, Lima Constancio MT, Correia da Silva R, Rosalen DL, José de Melo W, Carareto Alves LM. Bioremediation potential of new cadmium, chromium, and nickel-resistant bacteria isolated from tropical agricultural soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111038. [PMID: 32739674 DOI: 10.1016/j.ecoenv.2020.111038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 05/26/2023]
Abstract
Soil management using fertilizers can modify soil chemical, biochemical and biological properties, including the concentration of trace-elements as cadmium (Cd), chromium (Cd) and nickel (Ni). Bacterial isolates from Cd, Cr, and Ni-contaminated soil were evaluated for some characteristics for their use in bioremediation. Isolates (592) were obtained from soil samples (19) of three areas used in three maize cultivation systems: no-tillage and conventional tillage with the application of mineral fertilizers; minimum tillage with the application of sewage sludge. Four isolates were resistant to Cr3+ (3.06 mmol dm-3) and Cd2+ (2.92 mmol dm-3). One isolate was resistant to the three metals at 0.95 mmol dm-3. All isolates developed in a medium of Cd2+, Cr3+ and Ni2+ at 0.5 mmol dm-3, and removed Cd2+ (17-33%) and Cr6+ (60-70%). They were identified by sequencing of the gene 16S rRNA, as bacteria of the genera Paenibacillus, Burkholderia, Ensifer, and two Cupriavidus. One of the Cupriavidus isolate was able to remove 60% of Cr6+ from the culture medium and showed high indole acetic acid production capacity. We evaluated it in a microbe-plant system that could potentially be deployed in bioremediation by removing toxic metals from contaminated soil.
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Affiliation(s)
- Guilherme Deomedesse Minari
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil
| | - Luciana Maria Saran
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil.
| | - Milena Tavares Lima Constancio
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil
| | - Rafael Correia da Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil
| | - David Luciano Rosalen
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Rural Engineering, Jaboticabal, Brazil
| | - Wanderley José de Melo
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil; Brasil University, Descalvado, Brazil
| | - Lúcia Maria Carareto Alves
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Technology, Jaboticabal, Brazil
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Assessment of the tolerance to Fe, Cu and Zn of a sulfidogenic sludge generated from hydrothermal vents sediments as a basis for its application on metals precipitation. Mol Biol Rep 2020; 47:6165-6177. [PMID: 32749633 DOI: 10.1007/s11033-020-05690-2] [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: 02/19/2020] [Accepted: 07/26/2020] [Indexed: 10/23/2022]
Abstract
A paramour factor limiting metal-microorganism interaction is the metal ion concentration, and the metal precipitation efficiency driven by microorganisms is sensitive to metal ion concentration. The aim of the work was to determine the tolerance of the sulfidogenic sludge generated from hydrothermal vent sediments at microcosms level to different concentrations of Fe, Cu and Zn and the effect on the microbial community. In this study the chemical oxygen demand (COD) removal, sulfate-reducing activity (SRA) determination, inhibition effect through the determination of IC50, and the characterization of the bacterial community´s diversity were conducted. The IC50 on SRA was 34 and 81 mg/L for Zn and Cu, respectively. The highest sulfide concentration (H2S mg/L) and % of sulfate reduction obtained were: 511.30 ± 0.75 and 35.34 ± 0.51 for 50 mg/L of Fe, 482.48 ± 6.40 and 33.35 ± 0.44 for 10 mg/L of Cu, 442.26 ± 17.1 and 30.57 ± 1.18 for 10 mg/L of Zn, respectively. The COD removal rates were of 71.81 ± 7.6, 53.92 ± 1.07 and 57.68 ± 10.2 mg COD/ L d for Fe (50 mg/L), Cu (40 mg/L) and Zn (20 mg/L), respectively. Proteobacteria, Firmicutes, Chloroflexi and Actinobacteria were common phyla to four microcosms (stabilized sulfidogenic and added with Fe, Cu or Zn). The dsrA genes of Desulfotomaculum acetoxidans, Desulfotomaculum gibsoniae and Desulfovibrio desulfuricans were expressed in the microcosms supporting the SRA results. The consortia could be explored for ex-situ bioremediation purposes in the presence of the metals tested in this work.
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20
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Yu X, Ding Z, Ji Y, Zhao J, Liu X, Tian J, Wu N, Fan Y. An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. BMC Microbiol 2020; 20:18. [PMID: 31964334 PMCID: PMC6975044 DOI: 10.1186/s12866-020-1705-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance. RESULTS In this study, we isolated two different Cd2+ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25, which could be grown in the presence of Cd2+ at concentration up to 0.3 mM and 0.8 mM, respectively. According to the genomic sequencing, transcriptome analysis under cadmium stress, and other related experiments, a gene cluster in plasmid p25 was found to be a major contributor to Cd2+ resistance in B. marisflavi 151-25. The cluster in p25 contained orf4802 and orf4803 which encodes an ATPase transporter and a transcriptional regulator protein, respectively. Although 151-6 has much lower Cd2+ resistance than 151-25, they contained similar gene cluster, but in different locations. A gene cluster on the chromosome containing orf4111, orf4112 and orf4113, which encodes an ATPase transporter, a cadmium efflux system accessory protein and a cadmium resistance protein, respectively, was found to play a major role on the Cd2+ resistance for B. vietamensis 151-6. CONCLUSIONS This work described cadmium resistance mechanisms in newly isolated Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. Based on homologies to the cad system (CadA-CadC) in Staphylococcus aureus and analysis of transcriptome under Cd2+ induction, we inferred that the mechanisms of cadmium resistance in B. marisflavi 151-25 was as same as the cad system in S. aureus. Although Bacillus vietamensis 151-6 also had the similar gene cluster to B. marisflavi 151-25 and S. aureus, its transcriptional regulatory mechanism of cadmium resistance was not same. This study explored the cadmium resistance mechanism for B. vietamensis 151-6 and B. marisflavi 151-25 and has expanded our understanding of the biological effects of cadmium.
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Affiliation(s)
- Xiaoxia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zundan Ding
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyang Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Jintong Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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21
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Liu J, Yao J, Sunahara G, Wang F, Li Z, Duran R. Nonferrous metal (loid) s mediate bacterial diversity in an abandoned mine tailing impoundment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:24806-24818. [PMID: 31240654 DOI: 10.1007/s11356-019-05092-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Migration and transformation of toxic metal (loid) s in tailing sites inevitably lead to ecological disturbances and serious threats to the surroundings. However, the horizontal and vertical distribution of bacterial diversity has not been determined in nonferrous metal (loid) tailing ponds, especially in Guangxi China, where the world's largest and potentially most toxic sources of metal (loid) s are located. Distribution of bacterial communities was stable at horizontal levels. At the surface (0-10 cm), the stability was most attributed to Bacillus and Enterococcus, while bacterial communities at the subsurface (50 cm) were mainly contributed by Nitrospira and Sulfuricella. Variable vertical distribution of bacterial communities has led to the occurrence of specific genera and specific predicted functions (such as transcription regulation factors). Sulfurifustis (a S-oxidizing and inorganic carbon fixing bacteria) genera were specific at the surface, whereas Streptococcus-related genera were found at the surface and subsurface, but were more abundant in the latter depth. Physical-chemical parameters, such as pH, TN, and metal (loid) (As, Cd, Pb, Cu, and Zn) concentrations were the main drivers of bacterial community abundance, diversity, composition, and metabolic functions. These results increase our understanding of the physical-chemical effects on the spatial distribution of bacterial communities and provide useful insight for the bioremediation and site management of nonferrous metal (loid) tailings.
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Affiliation(s)
- Jianli Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, H9X3V9, Quebec, Canada
| | - Fei Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zifu Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
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22
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Huang N, Mao J, Zhao Y, Hu M, Wang X. Multiple Transcriptional Mechanisms Collectively Mediate Copper Resistance in Cupriavidus gilardii CR3. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4609-4618. [PMID: 30920814 DOI: 10.1021/acs.est.8b06787] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacteria resist copper (Cu) stress by implementing several metabolic mechanisms. However, these mechanisms are not fully understood. We investigated the mechanism of Cu resistance in Cupriavidus gilardii CR3, a Cu-resistant bacterium with a fully sequenced, annotated genome. The growth of CR3 was inhibited by higher Cu concentrations (≥1.0 mM) but not by lower ones (≤0.5 mM). CR3 accumulated Cu intracellularly (ratios of intercellular to extracellular Cu were 11.6, 4.24, and 3.9 in 0.1, 0.5, and 1.5 mM Cu treatments, respectively). A comparative transcriptome analysis of CR3 respectively revealed 310 and 413 differentially expressed genes under 0.5 and 1.5 mM Cu stress, most of which were up-regulated under Cu treatment. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses uncovered several genotype-specific biological processes related to Cu stress. Besides revealing known Cu resistance-related genes, our global transcriptomics approach indicated that sulfur metabolism, iron-sulfur cluster, and cell secretion systems are involved in mediating Cu resistance in strain CR3. These results suggest that bacteria collectively use multiple systems to cope with Cu stress. Our findings concerning the global transcriptome response to Cu stress in CR3 provide new information for understanding the intricate regulatory network of Cu homeostasis in prokaryotes.
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Affiliation(s)
| | | | - Yan Zhao
- School of Chemistry and Environmental Engineering , Changchun University of Science and Technology , Changchun 130022 , P. R. China
| | - Mingzhong Hu
- School of Chemical Engineering , Changchun University of Technology , Changchun 130012 , P. R. China
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23
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Ali I, Peng C, Khan ZM, Naz I, Sultan M, Ali M, Abbasi IA, Islam T, Ye T. Overview of microbes based fabricated biogenic nanoparticles for water and wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 230:128-150. [PMID: 30286344 DOI: 10.1016/j.jenvman.2018.09.073] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/14/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Treatment of toxic and emerging pollutants (T&EPs) is increasing the threats to the survival of conventional wastewater treatment (WWTs) technologies. The high installation and operational costs of advanced treatment technologies have shifted the research interest to the development of economical and reliable technology for management of T&EPs. Thus, recently biogenic nanoparticles (BNPs) fabricated using microbes/microorganisms are getting tremendous research interest due to their unique properties (i.e. high specific surface area, desired morphology, catalytic reactivity) for the biodegradation and biosorption of T&EPs. In addition, BNPs can be manufactured using metal contaminated water which indicates a hidden potential for resource recovery and utilization. Therefore, the present study discusses the adsorptive and catalytic performance of BNPs in the removal of T&EPs from water (W) and wastewater (WW). In addition, inspired by the superior performance of BNPs in advance WWT, a model of BNPs based WWT resource recovery and utilization process is also proposed. Finally, main issues i.e. mass production, leaching, poisoning/toxicity, regeneration, reusability and fabrication costs and process optimization are discussed which are main hinders in the transfer of BNPs based WWT technologies from laboratory to commercial scale.
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Affiliation(s)
- Imran Ali
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Changsheng Peng
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing 526061, China.
| | - Zahid M Khan
- Department of Agricultural Engineering, Bahauddin Zakariya University, Bosan Road, Multan 60800, Pakistan
| | - Iffat Naz
- Department of Biology, Qassim University, Buraidah 51452, Saudi Arabia
| | - Muhammad Sultan
- Department of Agricultural Engineering, Bahauddin Zakariya University, Bosan Road, Multan 60800, Pakistan.
| | - Mohsin Ali
- Department of Environmental Engineering, Middle East Technical University, Ankara 0600, Turkey
| | - Irfan A Abbasi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tariqul Islam
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tong Ye
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
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Yu X, Wei S, Yang Y, Ding Z, Wang Q, Zhao J, Liu X, Chu X, Tian J, Wu N, Fan Y. Identification of cadmium-binding proteins from rice (Oryza sativa L.). Int J Biol Macromol 2018; 119:597-603. [DOI: 10.1016/j.ijbiomac.2018.07.190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/02/2018] [Accepted: 07/30/2018] [Indexed: 01/02/2023]
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25
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Jacquiod S, Cyriaque V, Riber L, Al-Soud WA, Gillan DC, Wattiez R, Sørensen SJ. Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:299-307. [PMID: 29055834 DOI: 10.1016/j.jhazmat.2017.09.046] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/11/2017] [Accepted: 09/25/2017] [Indexed: 05/19/2023]
Abstract
Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.
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Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Leise Riber
- Section of Functional Genomics, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 Copenhagen N, Denmark.
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - David C Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
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26
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Gillan DC, Van Camp C, Mergeay M, Provoost A, Thomas N, Vermard L, Billon G, Wattiez R. Paleomicrobiology to investigate copper resistance in bacteria: isolation and description ofCupriavidus necatorB9 in the soil of a medieval foundry. Environ Microbiol 2017; 19:770-787. [DOI: 10.1111/1462-2920.13645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Max Mergeay
- Molecular & Cellular Biology; Unit of Microbiology SCK•CEN; Mol Belgium
| | - Ann Provoost
- Molecular & Cellular Biology; Unit of Microbiology SCK•CEN; Mol Belgium
| | - Nicolas Thomas
- Médiévistique occidentale, Université Paris 1 Panthéon-Sorbonne-CNRS; Inrap-UMR 8589 Lamop France
- Institut National de Recherches Archéologiques Préventives (INRAP); France
| | - Laurent Vermard
- Institut National de Recherches Archéologiques Préventives (INRAP); France
| | - Gabriel Billon
- Université de Lille 1, Sciences & Technologies, LASIR (UMR CNRS 8516); Villeneuve d'Ascq France
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27
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Majumder ELW, Wall JD. Uranium Bio-Transformations: Chemical or Biological Processes? ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ojic.2017.72003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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García-Depraect O, Guerrero-Barajas C, Jan-Roblero J, Ordaz A. Characterization of a Marine Microbial Community Used for Enhanced Sulfate Reduction and Copper Precipitation in a Two-Step Process. Appl Biochem Biotechnol 2016; 182:452-467. [DOI: 10.1007/s12010-016-2337-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/16/2016] [Indexed: 11/24/2022]
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29
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Martínez-Bussenius C, Navarro CA, Jerez CA. Microbial copper resistance: importance in biohydrometallurgy. Microb Biotechnol 2016; 10:279-295. [PMID: 27790868 PMCID: PMC5328820 DOI: 10.1111/1751-7915.12450] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/29/2022] Open
Abstract
Industrial biomining has been extensively used for many years to recover valuable metals such as copper, gold, uranium and others. Furthermore, microorganisms involved in these processes can also be used to bioremediate places contaminated with acid and metals. These uses are possible due to the great metal resistance that these extreme acidophilic microorganisms possess. In this review, the most recent findings related to copper resistance mechanisms of bacteria and archaea related to biohydrometallurgy are described. The recent search for novel metal resistance determinants is not only of scientific interest but also of industrial importance, as reflected by the genomic sequencing of microorganisms present in mining operations and the search of those bacteria with extreme metal resistance to improve the extraction processes used by the biomining companies.
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Affiliation(s)
- Cristóbal Martínez-Bussenius
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Claudio A Navarro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Carlos A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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30
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Rea MA, Zammit CM, Reith F. Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold. FEMS Microbiol Ecol 2016; 92:fiw082. [PMID: 27098381 DOI: 10.1093/femsec/fiw082] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2016] [Indexed: 01/21/2023] Open
Abstract
The biogeochemical cycling of gold (Au), i.e. its solubilization, transport and re-precipitation, leading to the (trans)formation of Au grains and nuggets has been demonstrated under a range of environmental conditions. Biogenic (trans)formations of Au grains are driven by (geo)biochemical processes mediated by distinct biofilm consortia living on these grains. This review summarizes the current knowledge concerning the composition and functional capabilities of Au-grain communities, and identifies contributions of key-species involved in Au-cycling. To date, community data are available from grains collected at 10 sites in Australia, New Zealand and South America. The majority of detected operational taxonomic units detected belong to the α-, β- and γ-Proteobacteria and the Actinobacteria. A range of organisms appears to contribute predominantly to biofilm establishment and nutrient cycling, some affect the mobilization of Au via excretion of Au-complexing ligands, e.g. organic acids, thiosulfate and cyanide, while a range of resident Proteobacteria, especially Cupriavidus metallidurans and Delftia acidovorans, have developed Au-specific biochemical responses to deal with Au-toxicity and reductively precipitate mobile Au-complexes. This leads to the biomineralization of secondary Au and drives the environmental cycle of Au.
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Affiliation(s)
- Maria Angelica Rea
- School of Biological Sciences, The Sprigg Geobiology Centre, The University of Adelaide, Adelaide, South Australia 5005, Australia CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
| | - Carla M Zammit
- School of Earth Sciences, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Frank Reith
- School of Biological Sciences, The Sprigg Geobiology Centre, The University of Adelaide, Adelaide, South Australia 5005, Australia CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
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