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Fang X, Zhang M, Zheng P, Wang H, Wang K, Lv J, Shi F. Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil. Front Microbiol 2024; 15:1343366. [PMID: 38835489 PMCID: PMC11148334 DOI: 10.3389/fmicb.2024.1343366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024] Open
Abstract
Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.
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Affiliation(s)
- Xin Fang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Mei Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Pufan Zheng
- Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Research Center of Agricultural Products Preservation Engineering and Technology (Tianjin)), Tianjin, China
| | - Haomin Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Lv
- School of Environmental Science and Engineering, Tiangong University, Tianjin, China
| | - Fuchen Shi
- College of Life Sciences, Nankai University, Tianjin, China
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Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [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: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
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Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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Wietz M, Engel A, Ramondenc S, Niwano M, von Appen WJ, Priest T, von Jackowski A, Metfies K, Bienhold C, Boetius A. The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone. Environ Microbiol 2024; 26:e16568. [PMID: 38268397 DOI: 10.1111/1462-2920.16568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anja Engel
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Simon Ramondenc
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matomo Niwano
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anabel von Jackowski
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Shi H, Gao W, Zheng Y, Yang L, Han B, Zhang Y, Zheng L. Distribution and abundance of oil-degrading bacteria in seawater of the Yellow Sea and Bohai Sea, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166038. [PMID: 37562632 DOI: 10.1016/j.scitotenv.2023.166038] [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: 04/12/2023] [Revised: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Petroleum hydrocarbons are widespread in seawater. As an important sea area in northern China, the content and distribution of petroleum hydrocarbons in seawater need our attention because of the high toxicity and lasting polluting effects on the ecological environment of the Yellow Sea and Bohai Sea. In addition, there are few reports comparing the diversity of oil-degrading bacteria before and after enrichment. Therefore, we collected surface seawater from 10 sites in the Yellow Sea and Bohai Sea in the autumn of 2020 to study the distribution characteristics of total petroleum hydrocarbons (TPH) and the diversity of oil-degrading bacteria. The concentration of TPH was 81.65 μg/L-139.55 μg/L at ten sites in the Bohai Sea and the Yellow Sea, which conformed to the China Grade II water quality standard (GB3097-1997). Moreover, the pristine/phytane (PR/PH) value of most sites was close to 1, indicating that the area was obviously polluted by exogenous petroleum hydrocarbons. We found that oil-degrading bacteria in the seawater of the Yellow Sea and the Bohai Sea had a good degradation effect on C11-C14 short chain alkanes (degradation rate of 59.19-73.22 %) and C1-C4 phenanthrene (degradation rate of 48.19-60.74 %). In terms of the diversity of oil-degrading bacteria, Gammaproteobacteria and Alphaproteobacteria dominated the enriched bacterial communities. Notably, the relative abundance of Alcanivorax changed significantly before and after enrichment. We proposed that surface seawater in the Bohai Sea and Yellow Sea could form oil-degrading bacteria mainly composed of Alcanivorax, which had great potential for oil pollution remediation.
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Affiliation(s)
- Haolei Shi
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Wei Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Yunchao Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Lin Yang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bin Han
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yanchao Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Li Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Ortmann AC, Cobanli SE, Wohlgeschaffen G, Poon HY, Ryther C, Greer CW, Wasserscheid J, Elias M, Robinson B, King TL. Factors that affect water column hydrocarbon concentrations have minor impacts on microbial responses following simulated diesel fuel spills. MARINE POLLUTION BULLETIN 2023; 194:115358. [PMID: 37567129 DOI: 10.1016/j.marpolbul.2023.115358] [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: 02/01/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
Effects of season and mixing on hydrocarbon concentrations and the microbial community response was explored in a series of mesocosm experiments simulating surface spills of diesel into coastal waters. Mixing of any amount contributed to hydrocarbons entering the water column, but diesel fuel composition had a significant effect on hydrocarbon concentrations. Higher initial concentrations of aromatic hydrocarbons resulted in higher water column concentrations, with minimal differences among seasons due to high variability. Regardless of the concentrations of hydrocarbons, prokaryotes increased and there were higher relative abundances of hydrocarbon affiliated bacteria with indications of biodegradation within 4 d of exposure. As concentrations decreased over time, the eukaryote community shifted from the initial community to one which appeared to be composed of organisms with some resilience to hydrocarbons. This series of experiments demonstrates the wide range of conditions under which natural attenuation of diesel fuel is an effective response.
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Affiliation(s)
- Alice C Ortmann
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada.
| | - Susan E Cobanli
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Gary Wohlgeschaffen
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Ho Yin Poon
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Camilla Ryther
- Dalhousie University, 6299 South Street, Halifax, NS B3H 4R2, Canada
| | - Charles W Greer
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Jessica Wasserscheid
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Miria Elias
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Brian Robinson
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas L King
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
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6
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Succession Patterns of Microbial Composition and Activity following the Diesel Spill in an Urban River. Microorganisms 2023; 11:microorganisms11030698. [PMID: 36985271 PMCID: PMC10058704 DOI: 10.3390/microorganisms11030698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled diesel has not been well-documented in river water. Using a combination of 14C-/3H--based radiotracer assays, analytical chemistry, MiSeq sequencing, and simulation-based microcosm incubation approaches, we demonstrated succession patterns of microbial diesel-degrading activities, and bacterial and fungal community compositions. The biodegradation activities of alkanes and polycyclic aromatic hydrocarbons (PAHs) were induced within 24 h after diesel addition, and reached their maximum after incubation for 7 days. Potential diesel-degrading bacteria Perlucidibaca, Acinetobacter, Pseudomonas, Acidovorax, and Aquabacterium dominated the community initially (day 3 and day 7), but later community structure (day 21) was dominated by bacteria Ralstonia and Planctomyces. The key early fungi responders were Aspergillus, Mortierella, and Phaeoacremonium by day 7, whereas Bullera and Basidiobolus dominated the fungal community at day 21. These results directly characterize the rapid response of microbial community to diesel spills, and suggest that the progression of diesel microbial degradation is performed by the cooperative system of the versatile obligate diesel-degrading and some general heterotrophic microorganisms in river diesel spills.
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7
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Yang F, Zhao F. Mechanism of visible light enhances microbial degradation of Bisphenol A. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130214. [PMID: 36327837 DOI: 10.1016/j.jhazmat.2022.130214] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bisphenol A (BPA) is a toxic endocrine disruptor detected in various environments. Microbial metabolic/enzymatic degradation has been thought to be the main pathway for BPA attenuation in natural environments. In this study, we found that under visible light conditions, superoxide produced by bacteria was the main reason for the rapid removal of BPA, accounting for 57 % of the total removal rate. With visible light, the bacteria degraded BPA at a rate of 0.22 mg/L/d, and the total removal within 8 days reached 85 %, which is 4.7 times compared with that of dark culture. The intermediate product 4-iso-propenylphenol, which was considered as an end-product of microbial degradation of BPA in previous reports, was detected in large quantities at 24 h in culture but gradually decreased in our experiment. Community analysis suggested bacteria with aromatic hydrocarbon degradation ability were more enriched under light incubation. Moreover, the bacteria showed well degradation ability to various pharmaceutically active but nonbiodegradable compounds including diclofenac and fluoxetine, with a removal rate of 88 % and 20 %, respectively. Our study revealed the organic pollutant transformation pathway under the combined action of light and microorganisms, providing new insights into the microbial treatment of aromatic hydrocarbon pollutants.
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Affiliation(s)
- Fan Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China.
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8
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Lyu L, Li J, Chen Y, Mai Z, Wang L, Li Q, Zhang S. Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea. Front Microbiol 2022; 13:920067. [PMID: 36338091 PMCID: PMC9626528 DOI: 10.3389/fmicb.2022.920067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Lina Lyu,
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Si Zhang,
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9
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Zhou Y, Kong Q, Zhao X, Lin Z, Zhang H. Dynamic changes in the microbial community in the surface seawater of Jiaozhou Bay after crude oil spills: An in situ microcosm study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119496. [PMID: 35594998 DOI: 10.1016/j.envpol.2022.119496] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
The changes in the composition and structure of microbial communities in Jiaozhou Bay are strongly affected by marine oil pollution, but the outcomes of the microbial responses and effects of dispersant application remain unclear. Herein, we performed an in situ microcosm study to investigate the response of the indigenous microbial community under crude oil alone and combined oil and dispersant treatment in the surface seawater of a semi-enclosed marine area of Jiaozhou Bay. The dynamics of the bacterial classification based on 16s rDNA sequencing were used to assess the changes with the crude oil concentration, dispersant use, and time. The crude oil resulted in a high abundance of the genera Pseudohongiella, Cycloclasticus, Marivita, and C1-B045 from the Gammaproteobacteria and Alphaproteobacteria classes, suggesting for hydrocarbon degradation. However, the dispersant treatment was more advantageous for Pacificibacter, Marivita, and Loktanella. Besides accelerating the rate of bacterial community succession, the dispersants had significantly stronger effects on the structure of the bacterial community and the degradation functions than the oil. A higher dose of oil exposure corresponded to fewer dominant species with a high relative abundance. Our study provides information for screening potential degradation bacteria and assessing the risks that oil spills pose to marine ecosystems.
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Affiliation(s)
- Yumiao Zhou
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China
| | - Xinyu Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Zhihao Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China.
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10
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Chen J, Zang Y, Yang Z, Qu T, Sun T, Liang S, Zhu M, Wang Y, Tang X. Composition and Functional Diversity of Epiphytic Bacterial and Fungal Communities on Marine Macrophytes in an Intertidal Zone. Front Microbiol 2022; 13:839465. [PMID: 35369473 PMCID: PMC8972133 DOI: 10.3389/fmicb.2022.839465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Marine macrophytes (seagrasses and macroalgae) and their epiphytic microorganisms play an important role in the ecological and biochemical processes of coastal oceans. However, simultaneous comparative studies on the biodiversity and functions of epiphytic bacteria and fungi associated with marine macrophytes have not been conducted. In this study, high-throughput sequencing technology was used to describe the epiphytic bacterial and fungal communities of 11 common macroalgae and 2 seagrasses from an intertidal zone of northern China and compare them with seawater communities. The results showed that Proteobacteria and Bacteroidota were the dominant bacterial phyla in marine macrophytes, whereas Ascomycota, Chytridiomycota, and Basidiomycota were the dominant fungal phyla. The alpha diversity of the bacterial and fungal communities in seagrasses was the highest of all macrophyte samples. This may have been related to their ability to recruit microorganisms from multiple sources. Host phylogeny may influence bacterial community structure, and geographical differences may influence fungal community structure. The FAPROTAX data indicated that C metabolic microbes were enriched in marine macrophytes, while the FUNGuild data indicated that undefined saprotroph, which participated in organic matter degradation, were also enriched in marine macrophytes. These findings provide a theoretical basis regarding the epiphytic microorganisms of macrophytes and may offer new insights to support the improved ecological restoration of seagrass and macroalgae beds.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tongfei Qu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shuo Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Ellis M, Altshuler I, Schreiber L, Chen YJ, Okshevsky M, Lee K, Greer CW, Whyte LG. Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage. MARINE POLLUTION BULLETIN 2022; 174:113288. [PMID: 35090274 DOI: 10.1016/j.marpolbul.2021.113288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.
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Affiliation(s)
- Madison Ellis
- Department of Natural Resource Sciences, McGill University, Quebec, Canada.
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Faculty of Biosciences, Norwegian University of Life Sciences NMBU, Ås, Norway
| | - Lars Schreiber
- Energy, Mining and Environment Research Centre, National Research Council of Canada, Quebec, Canada
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Mira Okshevsky
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Department of Human Health Therapeutics Research Centre, National Research Council of Canada, Quebec, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada, Ottawa, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council of Canada, Quebec, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
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12
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Fu X, Qiao Y, Xue J, Cheng D, Chen C, Bai Y, Jiang Q. Analyses of community structure and role of immobilized bacteria system in the bioremediation process of diesel pollution seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149439. [PMID: 34375874 DOI: 10.1016/j.scitotenv.2021.149439] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Immobilized bacteria system plays an important role during degradation process in oil contaminated seawater. Although the immobilized bacteria system can be recycled to avoid pollution after remediation, it remains an open question on whether or not the secondary pollution occurs during the degradation process. Additionally, the research on the role of immobilized bacteria system in the process of oil removal is not clear enough. In this study, both the diesel degradation rate of diesel by immobilized bacteria system and changes in marine microbial community structure were determined to explore the role of immobilized bacteria system. The immobilized bacteria system was added to the diesel polluted seawater (1% diesel) for 30 days. The degradation performance was investigated during the process, and the microbial community structure was analyzed simultaneously. The results illustrated that the degradation rate of diesel by immobilized bacteria system reached 78.39% after 30 days, and Alcanivorax (59.09%), Achromobacter (24.34%) and Thalassospira (9.84%) were the dominant genera in the immobilized bacteria system. The addition of immobilized bacteria system increased the content of nitrogen and phosphorus, and then promoted the growth of oil-degrading bacteria. Thus, functional genes related to oil degradation increased. Additionally, there was little difference in the microbial composition between the treated seawater and the unpolluted seawater. Based on all results, it can be inferred that immobilized bacteria system triggered and stimulated diesel degradation process. This study provides a promising way to improve the removal of oil, and provides theoretical support for the wide application of immobilized microorganism technology.
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Affiliation(s)
- Xinge Fu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yanlu Qiao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China
| | - Jianliang Xue
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China.
| | - Dongle Cheng
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Chuan Chen
- School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yu Bai
- Chinaunicom System Integration Co., Ltd, No.131, Xidan North Road, Beijing 100085, China
| | - Qing Jiang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China
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13
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Odobel C, Dussud C, Philip L, Derippe G, Lauters M, Eyheraguibel B, Burgaud G, Ter Halle A, Meistertzheim AL, Bruzaud S, Barbe V, Ghiglione JF. Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater. Front Microbiol 2021; 12:734782. [PMID: 34867851 PMCID: PMC8637277 DOI: 10.3389/fmicb.2021.734782] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
The microorganisms living on plastics called "plastisphere" have been classically described as very abundant, highly diverse, and very specific when compared to the surrounding environments, but their potential ability to biodegrade various plastic types in natural conditions have been poorly investigated. Here, we follow the successive phases of biofilm development and maturation after long-term immersion in seawater (7 months) on conventional [fossil-based polyethylene (PE) and polystyrene (PS)] and biodegradable plastics [biobased polylactic acid (PLA) and polyhydroxybutyrate-co-hydroxyvalerate (PHBV), or fossil-based polycaprolactone (PCL)], as well as on artificially aged or non-aged PE without or with prooxidant additives [oxobiodegradable (OXO)]. First, we confirmed that the classical primo-colonization and growth phases of the biofilms that occurred during the first 10 days of immersion in seawater were more or less independent of the plastic type. After only 1 month, we found congruent signs of biodegradation for some bio-based and also fossil-based materials. A continuous growth of the biofilm during the 7 months of observation (measured by epifluorescence microscopy and flow cytometry) was found on PHBV, PCL, and artificially aged OXO, together with a continuous increase in intracellular (3H-leucine incorporation) and extracellular activities (lipase, aminopeptidase, and β-glucosidase) as well as subsequent changes in biofilm diversity that became specific to each polymer type (16S rRNA metabarcoding). No sign of biodegradation was visible for PE, PS, and PLA under our experimental conditions. We also provide a list of operational taxonomic units (OTUs) potentially involved in the biodegradation of these polymers under natural seawater conditions, such as Pseudohongiella sp. and Marinobacter sp. on PCL, Marinicella litoralis and Celeribacter sp. on PHBV, or Myxococcales on artificially aged OXO. This study opens new routes for a deeper understanding of the polymers' biodegradability in seawaters, especially when considering an alternative to conventional fossil-based plastics.
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Affiliation(s)
- Charlene Odobel
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Claire Dussud
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Lena Philip
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France.,SAS Plastic@Sea, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Gabrielle Derippe
- CNRS, UMR 6027, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, Lorient, France
| | - Marion Lauters
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Boris Eyheraguibel
- CNRS, UMR 6296, Institut de Chimie de Clermont-Ferrand (ICCF), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Gaëtan Burgaud
- CNRS, EA 3882, Université de Brest, Laboratoire Universitaire de Biodiversité et d'Ecologie Microbionne (LUBEM), Plouzané, France
| | - Alexandra Ter Halle
- CNRS, UMR 5623, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), Université de Toulouse, Toulouse, France
| | | | - Stephane Bruzaud
- CNRS, UMR 6027, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, Lorient, France
| | - Valerie Barbe
- CEA, CNRS, Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Francois Ghiglione
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne (LOMIC), Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
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14
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Bodor A, Bounedjoum N, Feigl G, Duzs Á, Laczi K, Szilágyi Á, Rákhely G, Perei K. Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125996. [PMID: 33992922 DOI: 10.1016/j.jhazmat.2021.125996] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.
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Affiliation(s)
- Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Feigl
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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15
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Jacquin J, Callac N, Cheng J, Giraud C, Gorand Y, Denoual C, Pujo-Pay M, Conan P, Meistertzheim AL, Barbe V, Bruzaud S, Ghiglione JF. Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks. Front Microbiol 2021; 12:604395. [PMID: 34335485 PMCID: PMC8321090 DOI: 10.3389/fmicb.2021.604395] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
The European Parliament recently approved a new law banning single-use plastic items for 2021 such as plastic plates, cutlery, straws, cotton swabs, and balloon sticks. Transition to a bioeconomy involves the substitution of these banned products with biodegradable materials. Several materials such as polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), poly(butylene succinate) (PBS), polyhydroxybutyrate-valerate (PHBV), Bioplast, and Mater-Bi could be good candidates to substitute cotton swabs, but their biodegradability needs to be tested under marine conditions. In this study, we described the microbial life growing on these materials, and we evaluated their biodegradability in seawater, compared with controls made of non-biodegradable polypropylene (PP) or biodegradable cellulose. During the first 40 days in seawater, we detected clear changes in bacterial diversity (Illumina sequencing of 16S rRNA gene) and heterotrophic activity (incorporation of 3H-leucine) that coincided with the classic succession of initial colonization, growth, and maturation phases of a biofilm. Biodegradability of the cotton swab sticks was then tested during another 94 days under strict diet conditions with the different plastics as sole carbon source. The drastic decrease of the bacterial activity on PP, PLA, and PBS suggested no bacterial attack of these materials, whereas the bacterial activity in PBAT, Bioplast, Mater-Bi, and PHBV presented similar responses to the cellulose positive control. Interestingly, the different bacterial diversity trends observed for biodegradable vs. non-biodegradable plastics allowed to describe potential new candidates involved in the degradation of these materials under marine conditions. This better understanding of the bacterial diversity and activity dynamics during the colonization and biodegradation processes contributes to an expanding baseline to understand plastic biodegradation in marine conditions and provide a foundation for further decisions on the replacement of the banned single-used plastics.
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Affiliation(s)
- Justine Jacquin
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France.,Innovation Plasturgie et Composites, Biopole Clermont Limagne, Saint-Beauzire, France
| | - Nolwenn Callac
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France.,CNRS, UMR 9220 ENTROPIE, Ifremer (LEAD-NC), IRD, Univ Nouvelle-Calédonie, Univ La Réunion, Nouméa, New Caledonia
| | - Jingguang Cheng
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France
| | - Carolane Giraud
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France.,CNRS, UMR 9220 ENTROPIE, Ifremer (LEAD-NC), IRD, Univ Nouvelle-Calédonie, Univ La Réunion, Nouméa, New Caledonia
| | - Yonko Gorand
- Plateforme EnRMAT, Laboratoire PROMES, Rembla de la Thermodynamique, Perpignan, France
| | - Clement Denoual
- UMR CNRS 6027, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, Lorient, France
| | - Mireille Pujo-Pay
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France
| | - Pascal Conan
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France
| | | | - Valerie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphane Bruzaud
- UMR CNRS 6027, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, Lorient, France
| | - Jean-François Ghiglione
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Sorbonne Université, Paris, France
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16
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Ruocco N, Esposito R, Bertolino M, Zazo G, Sonnessa M, Andreani F, Coppola D, Giordano D, Nuzzo G, Lauritano C, Fontana A, Ianora A, Verde C, Costantini M. A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges. Mar Drugs 2021; 19:173. [PMID: 33810171 PMCID: PMC8004616 DOI: 10.3390/md19030173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.
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Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Roberta Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia 21, 80126 Napoli, Italy
| | - Marco Bertolino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, Corso Europa 26, 16132 Genova, Italy;
| | - Gianluca Zazo
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Michele Sonnessa
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Federico Andreani
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Daniela Giordano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Genoveffa Nuzzo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Angelo Fontana
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Cinzia Verde
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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17
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Hidalgo KJ, Sierra-Garcia IN, Dellagnezze BM, de Oliveira VM. Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain. Front Microbiol 2020; 11:561506. [PMID: 33072021 PMCID: PMC7530279 DOI: 10.3389/fmicb.2020.561506] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 02/01/2023] Open
Abstract
Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.
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Affiliation(s)
- Kelly J. Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabel N. Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Biology Department & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bruna M. Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
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