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Cabrera MÁ, Márquez SL, Pérez-Donoso JM. New insights into xenobiotic tolerance of Antarctic bacteria: transcriptomic analysis of Pseudomonas sp. TNT3 during 2,4,6-trinitrotoluene biotransformation. Environ Sci Pollut Res Int 2024; 31:17256-17274. [PMID: 38337121 DOI: 10.1007/s11356-024-32298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
The xenobiotic 2,4,6-trinitrotoluene (TNT) is a highly persistent environmental contaminant, whose biotransformation by microorganisms has attracted renewed attention. In previous research, we reported the discovery of Pseudomonas sp. TNT3, the first described Antarctic bacterium with the ability to biotransform TNT. Furthermore, through genomic analysis, we identified distinctive features in this isolate associated with the biotransformation of TNT and other xenobiotics. However, the metabolic pathways and genes active during TNT exposure in this bacterium remained unexplored. In the present transcriptomic study, we used RNA-sequencing to investigate gene expression changes in Pseudomonas sp. TNT3 exposed to 100 mg/L of TNT. The results showed differential expression of 194 genes (54 upregulated and 140 downregulated), mostly encoding hypothetical proteins. The most highly upregulated gene (> 1000-fold) encoded an azoreductase enzyme not previously described. Other significantly upregulated genes were associated with (nitro)aromatics detoxification, oxidative, thiol-specific, and nitrosative stress responses, and (nitro)aromatic xenobiotic tolerance via efflux pumps. Most of the downregulated genes were involved in the electron transport chain, pyrroloquinoline quinone (PQQ)-related alcohol oxidation, and motility. These findings highlight a complex cellular response to TNT exposure, with the azoreductase enzyme likely playing a crucial role in TNT biotransformation. Our study provides new insights into the molecular mechanisms of TNT biotransformation and aids in developing effective TNT bioremediation strategies. To the best of our knowledge, this report is the first transcriptomic response analysis of an Antarctic bacterium during TNT biotransformation.
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Affiliation(s)
- Ma Ángeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Sebastián L Márquez
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile.
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Hussain N, Muccee F, Hammad M, Mohiuddin F, Bunny SM, Shahab A. Molecular and metabolic characterization of petroleum hydrocarbons degrading Bacillus cereus. Pol J Microbiol 2024; 73:107-120. [PMID: 38437466 PMCID: PMC10911661 DOI: 10.33073/pjm-2024-012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID™ ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), o-nitrophenyl-β-D-galactosidase (ONPG), p-nitrophenyl-β-D-glucosidase (βGLU), p-nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, o-, p- and m-cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and m-tolualdehyde), carboxylic acid (methanoic acid, cis,cis-muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, cis,cis-muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in B. cereus.
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Affiliation(s)
- Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain Campus, Al Ain, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi Campus, Abu Dhabi, United Arab Emirates
| | - Fatima Muccee
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Muhammad Hammad
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Farhan Mohiuddin
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Saboor Muarij Bunny
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Aansa Shahab
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
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Chai G, Li J, Li Z. The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics. Microbiol Res 2024; 278:127542. [PMID: 37979302 DOI: 10.1016/j.micres.2023.127542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.
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Affiliation(s)
- Guangjun Chai
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Ganesh Kumar A, Manisha D, Nivedha Rajan N, Sujitha K, Magesh Peter D, Kirubagaran R, Dharani G. Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation. Mar Pollut Bull 2023; 194:115151. [PMID: 37453166 DOI: 10.1016/j.marpolbul.2023.115151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/28/2023] [Accepted: 06/04/2023] [Indexed: 07/18/2023]
Abstract
A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India.
| | - D Manisha
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - N Nivedha Rajan
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - K Sujitha
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - D Magesh Peter
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - R Kirubagaran
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - G Dharani
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
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Das N, Das A, Das S, Bhatawadekar V, Pandey P, Choure K, Damare S, Pandey P. Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. Fermentation 2023; 9:196. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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Muriel-Millán LF, Millán-López S, Pardo-López L. Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics. Appl Microbiol Biotechnol 2021; 105:7171-7185. [PMID: 34515846 DOI: 10.1007/s00253-021-11569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad Universitaria, CDMX, Mexico.
| | - Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
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Ganesh Kumar A, Manisha D, Sujitha K, Magesh Peter D, Kirubagaran R, Dharani G. Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil. Sci Rep 2021; 11:9347. [PMID: 33931710 PMCID: PMC8087790 DOI: 10.1038/s41598-021-88525-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.
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Affiliation(s)
- A. Ganesh Kumar
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Manisha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - K. Sujitha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Magesh Peter
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - R. Kirubagaran
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - G. Dharani
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
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