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Comprehensive Genomic Characterization of Marine Bacteria Thalassospira spp. Provides Insights into Their Ecological Roles in Aromatic Hydrocarbon-Exposed Environments. Microbiol Spectr 2022; 10:e0314922. [PMID: 36190412 PMCID: PMC9604089 DOI: 10.1128/spectrum.03149-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The marine bacterial genus Thalassospira has often been identified as an abundant member of polycyclic aromatic hydrocarbon (PAH)-exposed microbial communities. However, despite their potential usability for biotechnological applications, functional genes that are conserved in their genomes have barely been investigated. Thus, the goal of this study was to comprehensively examine the functional genes that were potentially responsible for aromatic hydrocarbon biodegradation in the Thalassospira genomes available from databases, including a new isolate of Thalassospira, strain GO-4, isolated from a phenanthrene-enriched marine bacterial consortium. Strain GO-4 was used in this study as a model organism to link the genomic data and their metabolic functions. Strain GO-4 growth assays confirmed that it utilized a common phenanthrene biodegradation intermediate 2-carboxybenzaldehyde (CBA) as the sole source of carbon and energy, but did not utilize phenanthrene. Consistently, strain GO-4 was found to possess homologous genes of phdK, pht, and pca that encode enzymes for biodegradation of CBA, phthalic acid, and protocatechuic acid, respectively. Further comprehensive genomic analyses for 33 Thalassospira genomes from databases showed that a gene cluster that consisted of phdK and pht homologs was conserved in 13 of the 33 strains. pca gene homologs were found in all examined genomes; however, homologs of the known PAH-degrading genes, such as the pah, phn, or nah genes, were not found. Possibly Thalassospira spp. co-occupy niches with other PAH-degrading bacteria that provide them with PAH degradation intermediates and facilitated their inhabitation in PAH-exposed microbial ecosystems. IMPORTANCE Comprehensive investigation of multiple genomic data sets from targeted microbial taxa deposited in databases may provide substantial information to predict metabolic capabilities and ecological roles in different environments. This study is the first report that details the functional profiling of Thalassospira spp. that have repeatedly been found in polycyclic aromatic hydrocarbon (PAH)-exposed marine bacterial communities by using genomic data from a new isolate, Thalassospira strain GO-4, and other strains in databases. Through screening of functional genes potentially involved in aromatic hydrocarbon biodegradation across 33 Thalassospira genomes and growth assays for strain GO-4, it was suggested that Thalassospira spp. unexceptionally conserved the ability to metabolize single-ring, PAH biodegradation intermediates, while being incapable of utilizing PAHs. This expanded our understanding of this potentially important contributing member to PAH-degrading microbial ecosystems; such species are considered to be specialized in driving downstream reactions of PAH biodegradation.
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Gao D, Zhao H, Wang L, Li Y, Tang T, Bai Y, Liang H. Current and emerging trends in bioaugmentation of organic contaminated soils: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115799. [PMID: 35930885 DOI: 10.1016/j.jenvman.2022.115799] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.
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Affiliation(s)
- Dawen Gao
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Huan Zhao
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Litao Wang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Ying Li
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Teng Tang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Yuhong Bai
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Hong Liang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
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Beste DJV. New perspectives on an ancient pathogen: thoughts for World Tuberculosis Day 2022. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35357305 PMCID: PMC9558351 DOI: 10.1099/mic.0.001178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dany J V Beste
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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