1
|
Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [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: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
Collapse
Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | | |
Collapse
|
2
|
Vlaanderen EJ, Ghaly TM, Moore LR, Focardi A, Paulsen IT, Tetu SG. Plastic leachate exposure drives antibiotic resistance and virulence in marine bacterial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121558. [PMID: 37019264 DOI: 10.1016/j.envpol.2023.121558] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/14/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
Collapse
Affiliation(s)
- Eric J Vlaanderen
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - Timothy M Ghaly
- School of Natural Sciences Macquarie University, Sydney, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Lisa R Moore
- School of Natural Sciences Macquarie University, Sydney, Australia
| | - Amaranta Focardi
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Ian T Paulsen
- School of Natural Sciences Macquarie University, Sydney, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Sasha G Tetu
- School of Natural Sciences Macquarie University, Sydney, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Cheng J, Xing D, Wang P, Tang S, Cai Z, Zhou J, Zhu X. Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments. JOURNAL OF HAZARDOUS MATERIALS 2023; 449:131038. [PMID: 36821901 PMCID: PMC9938759 DOI: 10.1016/j.jhazmat.2023.131038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5-10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.
Collapse
Affiliation(s)
- Jingguang Cheng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Daochao Xing
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Pu Wang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Si Tang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhonghua Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jin Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
| | - Xiaoshan Zhu
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; College of Ecology and Environment, Hainan University, Haikou 570228, PR China.
| |
Collapse
|
5
|
Dede B, Priest T, Bach W, Walter M, Amann R, Meyerdierks A. High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean. THE ISME JOURNAL 2023; 17:600-610. [PMID: 36721059 PMCID: PMC10030979 DOI: 10.1038/s41396-023-01366-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 104 cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.
Collapse
Affiliation(s)
- Bledina Dede
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wolfgang Bach
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Geoscience Department, University of Bremen, Bremen, Germany
| | - Maren Walter
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Institute of Environmental Physics, University of Bremen, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | |
Collapse
|
6
|
Wei M, Zeng X, Han X, Shao Z, Xie Q, Dong C, Wang Y, Qiu Z. Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field. Front Microbiol 2022; 13:930601. [PMID: 36316996 PMCID: PMC9616709 DOI: 10.3389/fmicb.2022.930601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13CVPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.
Collapse
Affiliation(s)
- Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiqiu Han
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Xiqiu Han,
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Xie
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanqi Dong
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhongyan Qiu
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| |
Collapse
|
7
|
Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. Microorganisms 2021; 10:microorganisms10010066. [PMID: 35056515 PMCID: PMC8779447 DOI: 10.3390/microorganisms10010066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022] Open
Abstract
The genome of Exiguobacterium aurantiacum SW-20 (E. aurantiacum SW-20), a salt-tolerant microorganism with petroleum hydrocarbon-degrading ability isolated from the Changqing Oilfield, was sequenced and analyzed. Genomic data mining even comparative transcriptomics revealed that some genes existed in SW-20 might be related to the salt tolerance. Besides, genes related to petroleum hydrocarbon degradation discovered in genomic clusters were also found in the genome, indicating that these genes have a certain potential in the bioremediation of petroleum pollutants. Multiple natural product biosynthesis gene clusters were detected, which was critical for survival in the extreme conditions. Transcriptomic studies revealed that some genes were significantly up-regulated as salinity increased, implying that these genes might be related to the salt tolerance of SW-20 when living in a high salt environment. In our study, gene clusters including salt tolerance, heavy metal tolerance and alkane degradation were all compared. When the same functional gene clusters from different strains, it was discovered that the gene composition differed. Comparative genomics and in-depth analysis provided insights into the physiological features and adaptation strategies of E. aurantiacum SW-20 in the oilfield environment. Our research increased the understanding of niches adaption of SW-20 at genomic level.
Collapse
|
8
|
Wang H, Sha X, Li R, Li Y, Khaleque HN, Zhang Y, Bohu T, Bai Z, Zhuang X. Comparative Genome Analysis Provides Molecular Evidence for Reclassification of the Photosynthetic Bacterium Rhodobacter sphaeroides EBL0706 as a Strain of Luteovulum azotoformans. Microorganisms 2021; 9:microorganisms9081754. [PMID: 34442833 PMCID: PMC8398827 DOI: 10.3390/microorganisms9081754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we conducted a genome-wide comparative analysis of a former Rhodobacter sphaeroides strain EBL0706, which is now recorded as Luteovulum sphaeroides EBL0706. The genome of EBL0706 was compared with that of Luteovulum azotoformans ATCC 17025, Luteovulum azotoformans KA25, and Luteovulum sphaeroides 2.4.1. The average nucleotide identity (ANI), tetra nucleotide signatures (Tetra), digital DNA–DNA hybridization (dDDH) values, comparative genome, and phylogenetic analysis proposed that EBL0706 is a strain of Luteovulum azotoformans. Functional annotations identified a total of 4034 protein-coding genes in the genome of EBL0706, including a complete photosynthetic gene cluster. This study provides genomic molecular verification for the strain EBL0706 to be reclassified to Luteovulum azotoformans.
Collapse
Affiliation(s)
- Haoyu Wang
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, China;
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
| | - Xiaoling Sha
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Huachen Jiguang Technology, Co. Ltd., Beijing 101407, China
| | - Yijing Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, China;
- Correspondence: (Y.Z.); (T.B.); Tel.: +86-10-6233-1792 (Y.Z.); +853-6855-7877 (T.B.)
| | - Tsing Bohu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa 999078, Macao
- CSIRO Mineral Resources, Australian Resources and Research Centre, Kensington, WA 6151, Australia
- Correspondence: (Y.Z.); (T.B.); Tel.: +86-10-6233-1792 (Y.Z.); +853-6855-7877 (T.B.)
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
9
|
Dell’ Anno F, Rastelli E, Sansone C, Brunet C, Ianora A, Dell’ Anno A. Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era. Microorganisms 2021; 9:1695. [PMID: 34442774 PMCID: PMC8400010 DOI: 10.3390/microorganisms9081695] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022] Open
Abstract
Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.
Collapse
Affiliation(s)
- Filippo Dell’ Anno
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Antonio Dell’ Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
10
|
Kong W, Zhao C, Gao X, Wang L, Tian Q, Liu Y, Xue S, Han Z, Chen F, Wang S. Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126365. [PMID: 34208299 PMCID: PMC8296198 DOI: 10.3390/ijerph18126365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.
Collapse
Affiliation(s)
- Weina Kong
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Cheng Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Xingwang Gao
- Hulangmao Oil Production Area in No.3 Oil Production Plant of Changqing Oilfield Company, Yan’an 717500, China;
| | - Liping Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Qianqian Tian
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Yu Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Shuwen Xue
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
| | - Fulin Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
| |
Collapse
|