1
|
Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
Collapse
Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| |
Collapse
|
2
|
Louvado A, Coelho FJRC, Oliveira V, Gomes H, Cleary DFR, Simões MMQ, Cunha A, Gomes NCM. Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment. J Appl Microbiol 2019; 127:134-149. [PMID: 30907485 DOI: 10.1111/jam.14261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023]
Abstract
AIM To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment. METHODS AND RESULTS A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22 -C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination. CONCLUSION This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition. SIGNIFICANCE AND IMPACT OF THE STUDY Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.
Collapse
Affiliation(s)
- A Louvado
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - V Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - H Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - M M Q Simões
- Department of Chemistry & QOPNA, University of Aveiro, Aveiro, Portugal
| | - A Cunha
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| |
Collapse
|
3
|
Khanolkar D, Dubey SK, Naik MM. Tributyltin chloride (TBTCl)-enhanced exopolysaccharide and siderophore production in an estuarine Alcaligenes faecalis strain. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 68:612-621. [PMID: 25612551 DOI: 10.1007/s00244-014-0120-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Tributyltin chloride (TBTCl) has been used extensively as an antifouling agent in ship paints, which results in the contamination of aquatic sites. These contaminated sites serve as enrichment areas for TBTCl-resistant bacterial strains. One TBTCl-resistant bacterial strain was isolated from the sediments of Zuari estuary, Goa, India, which is a major hub of various ship-building activities. Based on biochemical characteristics and 16S rDNA sequence analysis, this bacterial strain was identified as Alcaligenes faecalis and designated as strain SD5. It could degrade ≥3 mM TBTCl by using it as a sole carbon source and transform it into the less toxic dibutyltin chloride, which was confirmed by nuclear magnetic resonance and mass spectroscopy. Interestingly, this bacterial strain also showed enhanced exopolysaccharide and siderophore production when cells were exposed to toxic levels of TBTCl, suggesting their involvement in conferring resistance to this antifouling biocide as well as degradative capability respectively.
Collapse
Affiliation(s)
- Dnyanada Khanolkar
- Laboratory of Molecular Microbiology and Environmental Biotechnology, Department of Microbiology, Goa University, Taleigao Plateau, Bambolim, 403206, Goa, India
| | | | | |
Collapse
|
4
|
Khanolkar DS, Naik MM, Dubey SK. Biotransformation of Tributyltin chloride by Pseudomonas stutzeri strain DN2. Braz J Microbiol 2015; 45:1239-45. [PMID: 25763027 PMCID: PMC4323296 DOI: 10.1590/s1517-83822014000400014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 04/17/2014] [Indexed: 11/21/2022] Open
Abstract
A bacterial isolate capable of utilizing tributyltin chloride (TBTCl) as sole carbon source was isolated from estuarine sediments of west coast of India and identified as Pseudomonas stutzeri based on biochemical tests and Fatty acid methyl ester (FAME) analysis. This isolate was designated as strain DN2. Although this bacterial isolate could resist up to 3 mM TBTCl level, it showed maximum growth at 2 mM TBTCl in mineral salt medium (MSM). Pseudomonas stutzeri DN2 exposed to 2 mM TBTCl revealed significant alteration in cell morphology as elongation and shrinkage in cell size along with roughness of cell surface. FTIR and NMR analysis of TBTCl degradation product extracted using chloroform and purified using column chromatography clearly revealed biotransformation of TBTCl into Dibutyltin dichloride (DBTCl2) through debutylation process. Therefore, Pseudomonas stutzeri strain DN2 may be used as a potential bacterial strain for bioremediation of TBTCl contaminated aquatic environmental sites.
Collapse
Affiliation(s)
- Dnyanada S Khanolkar
- Laboratory of Bacterial Genetics and Environmental Biotechnology Department of Microbiology Goa University Goa India Laboratory of Bacterial Genetics and Environmental Biotechnology, Department of Microbiology, Goa University, Goa, India
| | - Milind Mohan Naik
- Laboratory of Bacterial Genetics and Environmental Biotechnology Department of Microbiology Goa University Goa India Laboratory of Bacterial Genetics and Environmental Biotechnology, Department of Microbiology, Goa University, Goa, India
| | - Santosh Kumar Dubey
- Laboratory of Bacterial Genetics and Environmental Biotechnology Department of Microbiology Goa University Goa India Laboratory of Bacterial Genetics and Environmental Biotechnology, Department of Microbiology, Goa University, Goa, India
| |
Collapse
|
5
|
Visualizing tributyltin (TBT) in bacterial aggregates by specific rhodamine-based fluorescent probes. Anal Chim Acta 2015; 853:514-520. [DOI: 10.1016/j.aca.2014.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 01/07/2023]
|
6
|
Filipkowska A, Kowalewska G, Pavoni B. Organotin compounds in surface sediments of the Southern Baltic coastal zone: a study on the main factors for their accumulation and degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:2077-2087. [PMID: 24026206 PMCID: PMC3906560 DOI: 10.1007/s11356-013-2115-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/29/2013] [Indexed: 05/05/2023]
Abstract
Sediment samples were collected in the Gulf of Gdańsk, and the Vistula and Szczecin Lagoons-all located in the coastal zone of the Southern Baltic Sea-just after the total ban on using harmful organotins in antifouling paints on ships came into force, to assess their butyltin and phenyltin contamination extent. Altogether, 26 sampling stations were chosen to account for different potential exposure to organotin pollution and environmental conditions: from shallow and well-oxygenated waters, shipping routes and river mouths, to deep and anoxic sites. Additionally, the organic carbon content, pigment content, and grain size of all the sediment samples were determined, and some parameters of the near-bottom water (oxygen content, salinity, temperature) were measured as well. Total concentrations of butyltin compounds ranged between 2 and 182 ng Sn g(-1) d.w., whereas phenyltins were below the detection limit. Sediments from the Gulf of Gdańsk and Vistula Lagoon were found moderately contaminated with tributyltin, whereas those from the Szczecin Lagoon were ranked as highly contaminated. Butyltin degradation indices prove a recent tributyltin input into the sediments adjacent to sites used for dumping for dredged harbor materials and for anchorage in the Gulf of Gdańsk (where two big international ports are located), and into those collected in the Szczecin Lagoon. Essential factors affecting the degradation and distribution of organotins, based on significant correlations between butyltins and environmental variables, were found in the study area.
Collapse
Affiliation(s)
- Anna Filipkowska
- Marine Pollution Laboratory, Institute of Oceanology, Polish Academy of Sciences, ul. Powstańców Warszawy 55, 81-712, Sopot, Poland.
| | - Grażyna Kowalewska
- Marine Pollution Laboratory, Institute of Oceanology, Polish Academy of Sciences, ul. Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Bruno Pavoni
- Department of Environmental Sciences, Informatics and Statistics, University of Venice, Calle Larga S. Marta 2137, 30123, Venice, Italy
| |
Collapse
|
7
|
Biochemical basis of mercury remediation and bioaccumulation by Enterobacter sp. EMB21. Appl Biochem Biotechnol 2012. [PMID: 23179279 DOI: 10.1007/s12010-012-9970-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The aims of this study were to isolate metal bioaccumulating bacterial strains and to study their applications in removal of environmental problematic heavy metals like mercury. Five bacterial strains belonging to genera Enterobacter, Bacillus, and Pseudomonas were isolated from oil-spilled soil. Among these, one of the strains Enterobacter sp. EMB21 showed mercury bioaccumulation inside the cells simultaneous to its bioremediation. The bioaccumulation of remediated mercury was confirmed by transmission electron microscopy and energy dispersive X-ray. The mercury-resistant loci in the Enterobacter sp. EMB21 cells were plasmid-mediated as confirmed by transformation of mercury-sensitive Escherichia coli DH5α by Enterobacter sp. EMB21 plasmid. Effect of different culture parameters viz-a-viz inoculum size, pH, carbon, and nitrogen source revealed that alkaline pH and presence of dextrose and yeast extract favored better remediation. The results indicated the usefulness of Enterobacter sp. EMB21 for the effective remediation of mercury in bioaccumulated form. The Enterobacter sp. EMB21 seems promising for heavy metal remediation wherein the remediated metal can be trapped inside the cells. The process can further be developed for the synthesis of valuable high-end functional alloy, nanoparticles, or metal conjugates from the metal being remediated.
Collapse
|