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Mahjoubi M, Cherif H, Aliyu H, Chouchane H, Cappello S, Neifar M, Mapelli F, Souissi Y, Borin S, Cowan DA, Cherif A. Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production. Int Microbiol 2024:10.1007/s10123-024-00540-8. [PMID: 38867105 DOI: 10.1007/s10123-024-00540-8] [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: 08/30/2023] [Revised: 01/22/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm-1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.
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Affiliation(s)
- Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hanene Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Habibu Aliyu
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Habib Chouchane
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Simone Cappello
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM)-CNR of Messina., Sp. San Raineri, 86, 98122, Messina, Italy
| | - Mohamed Neifar
- Common Services Unit "Bioreactor Coupled With an Ultrafilter"; APVA‑LR16ES20; ENIS, University of Sfax, Sfax, Tunisia
| | | | - Yasmine Souissi
- Department of Engineering, German University of Technology in Oman, P.O. Box 1816, PC 130, Muscat, Sultanate of Oman
| | - Sara Borin
- Common Services Unit "Bioreactor Coupled With an Ultrafilter"; APVA‑LR16ES20; ENIS, University of Sfax, Sfax, Tunisia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [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: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
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Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
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Wang J, Zhang Y, Ding Y, Song H, Liu T, Zhang Y, Xu W, Shi Y. Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater. CHEMOSPHERE 2023; 311:137173. [PMID: 36356804 DOI: 10.1016/j.chemosphere.2022.137173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/29/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Hewei Song
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Ting Liu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yujia Shi
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
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Pseudomonas veronii strain 7-41 degrading medium-chain n-alkanes and polycyclic aromatic hydrocarbons. Sci Rep 2022; 12:20527. [PMID: 36443410 PMCID: PMC9705281 DOI: 10.1038/s41598-022-25191-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Pollution of the environment by crude oil and oil products (represented by various types of compounds, mainly aliphatic, mono- and polyaromatic hydrocarbons) poses a global problem. The strain Pseudomonas veronii 7-41 can grow on medium-chain n-alkanes (C8-C12) and polycyclic aromatic hydrocarbons such as naphthalene. We performed a genetic analysis and physiological/biochemical characterization of strain 7-41 cultivated in a mineral medium with decane, naphthalene or a mixture of the hydrocarbons. The genes responsible for the degradation of alkanes and PAHs are on the IncP-7 conjugative plasmid and are organized into the alk and nah operons typical of pseudomonads. A natural plasmid carrying functional operons for the degradation of two different classes of hydrocarbons was first described. In monosubstrate systems, 28.4% and 68.8% of decane and naphthalene, respectively, were biodegraded by the late stationary growth phase. In a bisubstrate system, these parameters were 25.4% and 20.8% by the end of the exponential growth phase. Then the biodegradation stopped, and the bacterial culture started dying due to the accumulation of salicylate (naphthalene-degradation metabolite), which is toxic in high concentrations. The activity of the salicylate oxidation enzymes was below the detection limit. These results indicate that the presence of decane and a high concentration of salicylate lead to impairment of hydrocarbon degradation by the strain.
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Rana R, Ferdous J, Rahman M, Rahman F, Huq A, Ali Y, Huda N, Mukhles MB, Rafi MH. Biosynthesis and chemical composition of nanomaterials in agricultural soil bioremediation: a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:730. [PMID: 36066693 DOI: 10.1007/s10661-022-10315-1] [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: 05/03/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Nanomaterials (NMs) are currently being used in agricultural soils as part of a new bioremediation (BR) process. In this study, we reviewed the biosynthesis of NMs, as well as their chemical composition and prospective strategies for helpful and sustainable agricultural soil bioremediation (BR). Different types of NMs, such as nanoparticles, nanocomposites, nanocrystals, nano-powders, and nanotubes, are used in agricultural soil reclamation, and they reflect the toxicity of NMs to microorganisms. Plants (Sargassum muticum, Dodonaea viscose, Aloe Vera, Rosemarinus officinalis, Azadirachta indica, Green tea, and so on) and microorganisms (Escherichia coli, Shewanella oneidensis, Pleurotus sp., Klebsiella oxytoca, Aspergillus clavatus, and so on) are the primary sources for the biosynthesis of NMs. By using the BR process, microorganisms, such as bacteria and plants, can immobilize metals and change both inorganic and organic contaminants in the soil. Combining NMs with bioremediation techniques for agricultural soil remediation will be a valuable long-term solution.
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Affiliation(s)
- Rasel Rana
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Jannatul Ferdous
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh.
| | - Fahida Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resources, Chung-Ang University, Gyeonggi-do, Anseong-si, 17546, Republic of Korea
| | - Yousof Ali
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Nazmul Huda
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Muntaha Binte Mukhles
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Meherab Hossain Rafi
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
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Wang J, Zhang Y, Ding Y, Song H, Liu T. Analysis of microbial community resistance mechanisms in groundwater contaminated with SAs and high NH 4+-Fe-Mn. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:153036. [PMID: 35026256 DOI: 10.1016/j.scitotenv.2022.153036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 05/05/2023]
Abstract
The resistance mechanism of microbial communities in contaminated groundwater under the combined stress of sulfonamide antibiotics (SAs), NH4+, and Fe-Mn exceeding the standard levels was studied in an agricultural area along the Songhua River in Northeast China with developed livestock and poultry breeding. Representative points were selected in the study area to explore the response of environmental parameters and microbial communities, and microscopic experiments with different SA concentrations were conducted with background groundwater. The results showed a complex relationship between microbial communities and environmental factors. The environmental factors SM, SM2, SMX, DOC, NO3-, Fe, Mn, and HCO3- significantly affected the microbial community, with SMX, DOC, and Mn having the greatest effect. Three types of antibiotics with similar properties had different effects on the microbial community, and these effects were not simply additive or superimposed. After adding SAs, Proteobacteria with multi-resistance (99.85%) became the dominant phylum, and Acinetobacter (98.68%) became the dominant genus with SA resistance. SAs have a significant influence on bacterial chemotaxis, transporters, substance transport, and metabolism. Microorganisms resist the influence of SAs via a series of resistance mechanisms, such as enhancing the synthesis of relevant enzymes, generating new biochemical reactions, and reducing the transport of harmful substances through cell membranes. We also found that the proportion of exogenous compound degradation and metabolism-related functional genes in the presence of high SA concentrations increased significantly, which may be related to the degradation of SAs by microorganisms.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Hewei Song
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Ting Liu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
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Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. Int J Mol Sci 2021; 23:ijms23010214. [PMID: 35008639 PMCID: PMC8745256 DOI: 10.3390/ijms23010214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.
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