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Kumar R, De M. Simultaneous bioremediation of diesel-contaminated soil and water ecosystems using mixed culture of Acinetobacter baumannii IITG19 and Providencia vermicola IITG20. ENVIRONMENTAL TECHNOLOGY 2024:1-18. [PMID: 38837716 DOI: 10.1080/09593330.2024.2361171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Diesel degradation and bacterial growth were investigated in soil, marine water, and freshwater ecosystems using Acinetobacter baumannii IITG19, Providencia vermicola IITG20, and their mixed culture. Both bacteria were found to be effective in all three ecosystems, with the best degradation occurring in freshwater. Acinetobacter baumannii IITG19 showed higher degradation (59%, 62%, and 76%) than Providencia vermicola IITG20 (31%, 57%, and 67%) in soil, marine water, and freshwater, respectively. Alkanes showed higher degradation than naphthenes and aromatics for both strains. The mixed culture showed higher diesel degradation efficiency than individual strains in all ecosystems. The overall degradation was similar in soil and marine water (66%), while freshwater showed the highest degradation of 81%. In the presence of the mixed culture, the degradation of alkanes was more than 90%. Bacterial growth was highest in freshwater and lowest in soil for both bacteria and the mixed culture. Metabolite analysis confirmed alcoholic degradation for alkanes and cyclo-alcoholic degradation for naphthenes. The degradation rate for mixed culture was higher than that of both the individual strains. The mixed culture had highest degradation rate constant in freshwater at 0.11 day-1 followed by that in marine ecosystem at 0.078 day-1. The rate constant was lowest for soil ecosystem at 0.066 day-1. Thus the mixed culture showed effectiveness in all three ecosystems, with its highest effectiveness observed in the freshwater ecosystem.
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Affiliation(s)
- Rahul Kumar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Mahuya De
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, India
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Saiyam D, Dubey A, Malla MA, Kumar A. Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications. Braz J Microbiol 2024; 55:281-295. [PMID: 38216798 PMCID: PMC10920585 DOI: 10.1007/s42770-023-01228-3] [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: 05/24/2023] [Accepted: 12/21/2023] [Indexed: 01/14/2024] Open
Abstract
Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.
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Affiliation(s)
- Diksha Saiyam
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
| | - Muneer Ahmad Malla
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India.
- Metagenomics and Secretomics Research Laboratory, Department of Botany, University of Allahabad (A Central University), Prayagraj, 211002, UP, India.
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Sarfo MK, Gyasi SF, Kabo-Bah AT, Adu B, Mohktar Q, Appiah AS, Serfor-Armah Y. Isolation and characterization of crude-oil-dependent bacteria from the coast of Ghana using oxford nanopore sequencing. Heliyon 2023; 9:e13075. [PMID: 36785818 PMCID: PMC9918745 DOI: 10.1016/j.heliyon.2023.e13075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
The utilization and improper use of crude oil can have irreparable damage on the environment and human populations. This study sought to isolate hydrocarbon utilizing bacteria from 1% v/v pristine seawater and 1% v/v crude oil using enrichment culture techniques. Whole genome sequencing of DNA using the Oxford Nanopore sequencing technique with Fastq WIMP as the workflow at 3% abundance was undertaken. The results showed that the most abundant isolates identified using this technique at specific sampling sites were, Acinetobacter junii (51.9%), Alcanivarax pacificus (15.8%), Acinetobacter haemolyticus (21.6%), Pseudomonas aeruginosa (23.4%), Alcanivorax xenomutans (24.7%), Alcanivorax xenomutans (23.0%) Acinetobacter baumannii (40.0%) and Acinetobacter junii (14.2%). Cumulatively, the most abundant isolates in the 8 sampling sites were Acinetobacter junii (17.91%), Alcanivorax xenomutans (11.68%), Pseudomonas aeruginosa (7.68%), Escherichia coli (7.67%), Acinetobacter haemolyticus (3.40%), and Alkanivorax pacificus (3.10%). Spearman's rank correlation analysis to examine the strength of relationship between the physicochemical parameters and type of bacteria isolated, revealed that salinity (0.8046) and pH (0.7252) were the highest. Isolated bacteria from pristine seawater, especially Escherichia coli have shown their capacity for bioremediating oil spill pollution in oceanic environments in Ghana.
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Affiliation(s)
- Mark Kwasi Sarfo
- Regional Center for Energy and Environmental Sustainability, Department of Civil and Environmental Engineering, University of Energy and Natural Resources, Sunyani, Ghana,Corresponding author.
| | - Samuel Fosu Gyasi
- Department of Biological Science, University of Energy and Natural Resources, Sunyani, Ghana,Centre for Research in Applied Biology, University of Energy and Natural Resources, Sunyani, Ghana
| | - Amos Tiereyangn Kabo-Bah
- Regional Center for Energy and Environmental Sustainability, Department of Civil and Environmental Engineering, University of Energy and Natural Resources, Sunyani, Ghana
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University Of Ghana, Ghana
| | - Quaneeta Mohktar
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University Of Ghana, Ghana
| | - Andrew Sarkodie Appiah
- Biotechnology Center, Biotechnology and Nuclear Agricultural Research Institute, Ghana Atomic Energy Commission, Ghana
| | - Yaw Serfor-Armah
- School of Nuclear and Allied Sciences, University of Ghana, Legon, Ghana
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Mai Y, Peng S, Lai Z, Wang X. Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21981-21997. [PMID: 34775557 DOI: 10.1007/s11356-021-17449-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.
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Affiliation(s)
- Yongzhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Songyao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zini Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510070, China.
| | - Xuesong Wang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 100 Xianlie Middle Road, 510070, China.
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Diallo MM, Vural C, Cay H, Ozdemir G. Enhanced biodegradation of crude oil in soil by a developed bacterial consortium and indigenous plant growth promoting bacteria. J Appl Microbiol 2020; 130:1192-1207. [PMID: 32916758 DOI: 10.1111/jam.14848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/08/2020] [Accepted: 09/01/2020] [Indexed: 10/23/2022]
Abstract
AIMS This study aimed to develop an efficient, cost-effective and eco-friendly bacterial consortium to degrade petroleum sludge. METHODS AND RESULTS Four bacterial strains belonging to genera Acinetobacter and Pseudomonas were selected to constitute three different consortia based on their initial concentration. The highest degradation rate (78%) of 1% (v/v) crude oil after 4 weeks of incubation was recorded when the concentration of biosurfactant (BS) producing isolate was high. Genes, such as alkB, almA, cyp153, pah-rhdGN, nah, phnAC and cat23 were detected using the polymerase chain reaction method and their induction levels were optimal at pH 7·0. A crude oil sludge was artificially constituted, and its bacterial composition was investigated using 16S rRNA gene amplicon sequencing. The results showed that the soil bacterial community was dominated by plant growth-promoting bacteria (PGPB) after crude oil treatment. CONCLUSIONS Our findings indicate the decontamination of the crude oil contaminated soil was more effective in the presence of both the constituted consortium and PGPB compared to the presence of PGPB alone. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed that the PGPB (Taibaiella) present in petroleum uncontaminated soil can promote the soil decontamination. The addition of both efficient hydrocarbon-degrading and BS producing bacteria is also necessary to improve the decontamination.
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Affiliation(s)
- M M Diallo
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
| | - C Vural
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey.,Department of Biology, Molecular Biology Section, Faculty of Science and Arts, Pamukkale University Kinikli Campus, Denizli, Turkey
| | - H Cay
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
| | - G Ozdemir
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
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Ho MT, Li MSM, McDowell T, MacDonald J, Yuan ZC. Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil. BMC Biotechnol 2020; 20:39. [PMID: 32711499 PMCID: PMC7477861 DOI: 10.1186/s12896-020-00632-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas. Results Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (CnHn + 2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16. Conclusions The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments.
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Affiliation(s)
- Margaret T Ho
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Michelle S M Li
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada
| | - Jacqueline MacDonald
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Ze-Chun Yuan
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada. .,London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada.
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