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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. MARINE POLLUTION BULLETIN 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] [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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Ali B, Sajjad W, Ilahi N, Bahadur A, Kang S. Soot biodegradation by psychrotolerant bacterial consortia. Biodegradation 2022; 33:407-418. [PMID: 35666328 DOI: 10.1007/s10532-022-09990-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/02/2022]
Abstract
To probe the bioavailability of soot released into the atmosphere is pivotal to understanding their environmental impacts. Soot aerosol absorbs organic matter, creating a hot spot for biogeochemical transformation and the global carbon cycle. Soot primarily contains condensed aromatics chemically recalcitrant; however, oligotrophic microorganisms might use it as a nutritional source. This study investigated the influence of psychrotolerant bacterial consortia on soot. Significant increase in the bacterial biomass, reduction in water-insoluble organic carbon (OC) and elemental carbon (EC) in soot residues and increase in water-soluble OC in the filtrate signifies the use of soot as a carbon and nutritional source. The influence on morphology and composition of soot was reported using Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy, and Energy Dispersive X-Ray analysis (EDX). The FTIR analysis showed significant variations in the pattern of soot spectra, suggesting degradation. Elemental analysis and EDX showed a reduction in carbon percentage. Besides, the reduction of optical density with incubation time signifies the OC and EC consumption. This study shows that soot can be a substrate and pivotal factor in the microbial food web. Nowadays, soot emission to the environment is growing; therefore, soot involvement in microbe-mediated processes should be closely focused.
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Affiliation(s)
- Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Rd. 320, Lanzhou, 730000, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Rd. 320, Lanzhou, 730000, China
| | - Nikhat Ilahi
- School of Life Sciences, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Rd. 320, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Rd. 320, Lanzhou, 730000, China.
- University of Chinese Academy of Sciences (UCAS), Beijing, China.
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Kriem LS, Wright K, Ccahuana-Vasquez RA, Rupp S. Confocal Raman microscopy to identify bacteria in oral subgingival biofilm models. PLoS One 2020; 15:e0232912. [PMID: 32392236 PMCID: PMC7213720 DOI: 10.1371/journal.pone.0232912] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
The study of oral disease progression, in relation to the accumulation of subgingival biofilm in gingivitis and periodontitis is limited, due to either the ability to monitor plaque in vitro. When compared, optical spectroscopic techniques offer advantages over traditional destructive or biofilm staining approaches, making it a suitable alternative for the analysis and continued development of three-dimensional structures. In this work, we have developed a confocal Raman spectroscopy analysis approach towards in vitro subgingival plaque models. The main objective of this study was to develop a method for differentiating multiple oral subgingival bacterial species in planktonic and biofilm conditions, using confocal Raman microscopy. Five common subgingival bacteria (Fusobacterium nucleatum, Streptococcus mutans, Veillonella dispar, Actinomyces naeslundii and Prevotella nigrescens) were used and differentiated using a 2-way orthogonal Partial Least Square with Discriminant Analysis (O2PLS-DA) for the collected spectral data. In addition to planktonic growth, mono-species biofilms cultured using the 'Zürich Model' were also analyzed. The developed method was successfully used to predict planktonic and mono-species biofilm species in a cross validation setup. The results show differences in the presence and absence of chemical bands within the Raman spectra. The O2PLS-DA model was able to successfully predict 100% of all tested planktonic samples and 90% of all mono-species biofilm samples. Using this approach we have shown that Confocal Raman microscopy can analyse and predict the identity of planktonic and mono-species biofilm species, thus enabling its potential as a technique to map oral multi-species biofilm models.
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Affiliation(s)
- Lukas Simon Kriem
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Kevin Wright
- Procter & Gamble, Egham, England, United Kingdom
| | | | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
- * E-mail:
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Shon JC, Noh YJ, Kwon YS, Kim JH, Wu Z, Seo JS. The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110254. [PMID: 32007746 DOI: 10.1016/j.ecoenv.2020.110254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
The direct interactions of bacterial membranes and polycyclic aromatic hydrocarbons (PAHs) strongly influence the biological processes, such as metabolic activity and uptake of substrates due to changes in membrane lipids. However, the elucidation of adaptation mechanisms as well as membrane phospholipid alterations in the presence of phenanthrene (PHE) from α-proteobacteria has not been fully explored. This study was conducted to define the degradation efficiency of PHE by Sphingopyxis soli strain KIT-001 in a newly isolated from Jeonju river sediments and to characterize lipid profiles in the presence of PHE in comparison to cells grown on glucose using quantitative lipidomic analysis. This strain was able to respectively utilize 1-hydroxy-2-naphthoic acid and salicylic acid as sole carbon source and approximately 90% of PHE (50 mg/L) was rapidly degraded via naphthalene route within 1 day incubation. In the cells grown on PHE, strain KIT-001 appeared to dynamically change profiles of metabolite and lipid in comparison to cells grown on glucose. The levels of primary metabolites, phosphatidylethanolamines (PE), and phosphatidic acids (PA) were significantly decreased, whereas the levels of phosphatidylcholines (PC) and phosphatidylglycerols (PG) were significantly increased. The adaptation mechanism of Sphingopyxis sp. regarded mainly the accumulation of bilayer forming lipids and anionic lipids to adapt more quickly under restricted nutrition and toxicity condition. Hence, these findings are conceivable that strain KIT-001 has a good adaptive ability and biodegradation for PHE through the alteration of phospholipids, and will be helpful for applications for effective bioremediation of PAHs-contaminated sites.
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Affiliation(s)
- Jong Cheol Shon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Ji Noh
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Sang Kwon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Zhexue Wu
- Mass Spectrometry Convergence Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Su Seo
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea.
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