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Atakpa EO, Yan B, Okon SU, Liu Q, Zhang D, Zhang C. Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20637-20650. [PMID: 38383925 DOI: 10.1007/s11356-024-32419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.
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Affiliation(s)
- Edidiong Okokon Atakpa
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Bozhi Yan
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Samuel Ukpong Okon
- Institute of Port, Coastal, and Offshore Engineering, Ocean College, Zhejiang University, Zhoushan, 316021, China
- Suzhou Industrial Technological Research Institute of Zhejiang University, Suzhou, 215163, China
| | - Qing Liu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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2
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Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
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Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
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3
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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4
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Pyke R, Fortin N, Wasserscheid J, Tremblay J, Schreiber L, Levesque MJ, Messina-Pacheco S, Whyte L, Wang F, Lee K, Cooper D, Greer CW. Biodegradation potential of residue generated during the in-situ burning of oil in the marine environment. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130439. [PMID: 36437193 DOI: 10.1016/j.jhazmat.2022.130439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
The biodegradability of residues derived from in-situ burning, an oil spill response strategy which involves burning an oil slick on the sea surface, has not yet been fully studied. With a growing risk of oil spills, the fate of the persistent burn residue containing potentially toxic substances must be better understood. Microcosms were used to study the microbial community response and potential biodegradability of in-situ burn residues generated from Ultra Low Sulphur (ULS) marine diesel. Microcosm studies were conducted using residues originating from the burning of unweathered and weathered diesel, with the addition of a fertilizer and a dispersant. Burn residues were incubated for 6 weeks at 7 °C in natural seawater with continual agitation in the dark. Samples were subsequently sacrificed for chemistry as well as 16S rRNA gene amplicon and shotgun metagenomic sequencing. Chemistry analyses revealed a reduction in hydrocarbon concentrations. Medium chain-length n-alkanes (nC16-nC24) decreased by 8% in unweathered burn residue microcosms and up to 26% in weathered burn residue microcosms. A significant decrease in polycyclic aromatic hydrocarbon (PAH) concentrations was observed only for naphthalene, fluorene and their alkylated homologs, in the microcosms amended with residue produced from burning weathered diesel. Decreases of 2-24%, were identified depending on the compound. Microcosms amended with burn residues had distinct microbial communities marked by an increase in relative abundance of putative hydrocarbon degraders as well as an increase of known hydrocarbon-degradation genes. These novel results suggest that if in-situ burning is performed on ULS marine diesel, some of the indigenous bacteria would respond to the newly available carbon source and some of the residual compounds would be biodegraded. Future studies involving longer incubation periods could give a better understanding of the fate of burn residues by shedding light on the potential biodegradability of the more recalcitrant residual compounds.
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Affiliation(s)
- Ruby Pyke
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada
| | - Nathalie Fortin
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Jessica Wasserscheid
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Lars Schreiber
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Marie-Josee Levesque
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | | | - Lyle Whyte
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada
| | - Feiyue Wang
- Centre for Earth Observation Science and Department of Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ottawa, ON, Canada
| | - David Cooper
- SL Ross Environmental Research Ltd., Ottawa, ON, Canada
| | - Charles W Greer
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada; National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada.
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Hafez T, Ortiz-Zarragoitia M, Cagnon C, Cravo-Laureau C, Duran R. Cold sediment microbial community shifts in response to crude oil water-accommodated fraction with or without dispersant: a microcosm study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44640-44656. [PMID: 36694068 DOI: 10.1007/s11356-023-25264-6] [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: 08/05/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
In cold environments, the low temperature slows down microbial metabolisms, such as the biodegradation processes of hydrocarbons, which are often stimulated by the addition of dispersants in oil spill disasters. In this study, we investigated the effects of hydrocarbon water-accommodated fraction (WAF) prepared with and without dispersant on benthic microbial communities in a microcosm experiment in which hydrocarbon removal was observed. Both WAFs contained similar polycyclic aromatic hydrocarbon (PAH) content. The microcosm experiment, set up with either pristine or contaminated sediments, was conducted for 21 days at 4 °C under WAF and WAF + dispersant conditions. The behavior of bacterial communities in response to WAF and WAF + dispersant was examined at both DNA and RNA levels, revealing the effect of WAF and WAF + dispersant on the resident and active communities respectively. The contaminated sediment showed less taxa responsive to the addition of both WAF and WAF + dispersant than the pristine sediment, indicating the legacy effect by the presence hydrocarbon-degrading and dispersant-resistant taxa inhabiting the contaminated sediment.
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Affiliation(s)
- Tamer Hafez
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
| | | | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France.
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6
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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7
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Yang H, Wu J, Du H, Zhang H, Li J, Wei Q. Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River. Front Microbiol 2022; 12:828409. [PMID: 35250916 PMCID: PMC8891936 DOI: 10.3389/fmicb.2021.828409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.
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Affiliation(s)
- Haile Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinming Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Junyi Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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8
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Lyautey E, Bonnineau C, Billard P, Loizeau JL, Naffrechoux E, Tlili A, Topp E, Ferrari BJD, Pesce S. Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination. Front Microbiol 2021; 12:738629. [PMID: 34733255 PMCID: PMC8560053 DOI: 10.3389/fmicb.2021.738629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Lake sediments are natural receptors for a wide range of anthropogenic contaminants including organic matter and toxicants such as trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls that accumulate over time. This contamination can impact benthic communities, including microorganisms which play a crucial role in biogeochemical cycling and food-webs. The present survey aimed at exploring whether anthropogenic contamination, at a large lake scale, can influence the diversity, structure and functions of microbial communities associated to surface sediment, as well as their genetic potential for resistance to metals and antibiotics. Changes in the characteristics of these communities were assessed in surface sediments collected in Lake Geneva from eight sampling sites in October 2017 and May 2018. These sampling sites were characterized by a large concentration range of metal and organic compound contamination. Variation between the two sampling periods were very limited for all sampling sites and measured microbial parameters. In contrast, spatial variations were observed, with two sites being distinct from each other, and from the other six sites. Benthic communities from the most contaminated sampling site (Vidy Bay, near the city of Lausanne) were characterized by the lowest bacterial and archaeal diversity, a distinct community composition, the highest abundance of antibiotic resistance genes and functional (respiration, denitrification, methanogenesis, phosphatase, and beta-glucosidase) activity levels. The second sampling site which is highly influenced by inputs from the Rhône River, exhibited low levels of diversity, a distinct community composition, high abundance of antibiotic resistance genes and the highest bacterial abundance. Overall, our results suggest that local anthropogenic contamination, including organic matter and toxicants, is a major driver of the diversity and functioning of sediment-microbial communities in Lake Geneva. This highlights the need to consider benthic microbial communities and a suite of complementary ecotoxicological endpoints for more effective environmental risk assessments of contaminants in lake sediments.
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Affiliation(s)
- Emilie Lyautey
- INRAE UR RiverLy, Villeurbanne, France.,INRAE, Université Savoie Mont Blanc, CARRTEL, Thonon-les-Bains, France
| | | | | | - Jean-Luc Loizeau
- Department F.A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva, Switzerland
| | | | - Ahmed Tlili
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Edward Topp
- Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, University of Western Ontario, London, ON, Canada
| | - Benoît J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), Lausanne, Switzerland
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9
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States.,Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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10
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Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. MICROBIAL ECOLOGY 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
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Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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11
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Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters. Biodegradation 2020; 31:91-108. [DOI: 10.1007/s10532-020-09896-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/24/2020] [Indexed: 10/24/2022]
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12
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Santisi S, Catalfamo M, Bonsignore M, Gentile G, Di Salvo E, Genovese M, Mahjoubi M, Cherif A, Mancini G, Hassanshahian M, Pioggia G, Cappello S. Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy). J Appl Microbiol 2019; 127:618-629. [PMID: 30848509 DOI: 10.1111/jam.14246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 11/29/2022]
Abstract
The aims of this study were: (i) the characterization of the structure of the indigenous microbial community associated with the sediments under study; (ii) the isolation and characterization of microbial consortia able to degrade the aged hydrocarbons contaminating the sediments, and (iii) the assessment of related biodegradation capability of selected consortia. Samples of surface sediments were collected in Priolo Gargallo harbour (Sicily, Italy). The samples were analysed for physical, chemical (GC-FID analysis) and microbiological characteristics (qualitative (16S rDNA clone library) and quantitative (DAPI, CFU and MPN count) analysis). The sediment samples were used for the selection of two microbial consortia (indicated as PSO and PSM) with high biodegradation capacity for crude oil (∼95%) and PAHs (∼63%) respectively. Genetic analysis showed that Alcanivorax and Cycloclasticus were the dominant genera in both the PSO and PSM consortia. Oil-polluted environments naturally develop an elevated biorecovery potential. The presence of a highly specialized microbial flora (adapted to support the contamination) and their stimulation through favourable induced conditions provides a promising recovery strategy. The chance to identify and select indigenous bacteria and/or consortia with a high biodegradation capacity is fundamental for the development and optimization of bioaugmentation strategies especially for those concerning in situ applications.
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Affiliation(s)
- S Santisi
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - M Catalfamo
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - M Bonsignore
- Faculty of Biological Sciences, University of Messina, Messina, Italy
| | - G Gentile
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - E Di Salvo
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - M Genovese
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy
| | - M Mahjoubi
- Higher Institute for Biotechnology - University of Manouba Biotechpole of Sidi Thabet, Ariana, Tunisia
| | - A Cherif
- Higher Institute for Biotechnology - University of Manouba Biotechpole of Sidi Thabet, Ariana, Tunisia
| | - G Mancini
- Dep. "Ingegneria Industriale", University of Catania, Catania, Italy
| | - M Hassanshahian
- Dep."Biology", Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - G Pioggia
- Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
| | - S Cappello
- Institute for Biological Resources and Marine Biotechnology (IRBIM)-CNR of Messina, Messina, Italy.,Institute of Applied Sciences & Intelligent Systems "Eduardo Caianiello" (ISASI)-CNR of Messina, Messina, Italy
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13
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Louvado A, Coelho FJRC, Oliveira V, Gomes H, Cleary DFR, Simões MMQ, Cunha A, Gomes NCM. Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment. J Appl Microbiol 2019; 127:134-149. [PMID: 30907485 DOI: 10.1111/jam.14261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023]
Abstract
AIM To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment. METHODS AND RESULTS A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22 -C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination. CONCLUSION This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition. SIGNIFICANCE AND IMPACT OF THE STUDY Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.
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Affiliation(s)
- A Louvado
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - V Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - H Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - M M Q Simões
- Department of Chemistry & QOPNA, University of Aveiro, Aveiro, Portugal
| | - A Cunha
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
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14
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Khan MAI, Biswas B, Smith E, Naidu R, Megharaj M. Toxicity assessment of fresh and weathered petroleum hydrocarbons in contaminated soil- a review. CHEMOSPHERE 2018; 212:755-767. [PMID: 30179840 DOI: 10.1016/j.chemosphere.2018.08.094] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/04/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
Soil contamination with total petroleum hydrocarbons (TPH) is widespread throughout the globe due to the massive production of TPH anthropogenically and its occurrence in the soil. TPH is toxic to beneficial soil organisms and humans and thus has become a serious concern among the public. Traditionally TPH toxicity in the soil is estimated based on chemical fractions and a range of bioassays including plants, invertebrates and microorganisms. There is a large inconsistency among ecotoxicology data using these assays due to the nature of TPH and their weathering. Therefore, in this article, we critically reviewed the weathered conditions of TPH, the potential fate in soil and the bioindicators for the assessment of the ecotoxicity. Based on the current research and the state-of-the-art problem, we also highlighted key recommendations for future research scope for the real-world solution of the ecotoxicological studies of hydrocarbons.
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Affiliation(s)
- Muhammad Atikul Islam Khan
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ACT Building, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Bhabananda Biswas
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ACT Building, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Euan Smith
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ACT Building, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ACT Building, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ACT Building, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ACT Building, The University of Newcastle, Callaghan, NSW 2308, Australia.
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15
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Ní Chadhain SM, Miller JL, Dustin JP, Trethewey JP, Jones SH, Launen LA. An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes. MARINE POLLUTION BULLETIN 2018; 136:351-364. [PMID: 30509817 PMCID: PMC6281173 DOI: 10.1016/j.marpolbul.2018.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/26/2018] [Accepted: 09/02/2018] [Indexed: 06/09/2023]
Abstract
Small fringing marshes are ecologically important habitats often impacted by petroleum. We characterized the phylogenetic structure (16S rRNA) and petroleum hydrocarbon degrading alkane hydroxylase genes (alkB and CYP 153A1) in a sediment microbial community from a New Hampshire fringing marsh, using alkane-exposed dilution cultures to enrich for petroleum degrading bacteria. 16S rRNA and alkB analysis demonstrated that the initial sediment community was dominated by Betaproteobacteria (mainly Comamonadaceae) and Gammaproteobacteria (mainly Pseudomonas), while CYP 153A1 sequences predominantly matched Rhizobiales. 24 h of exposure to n-hexane, gasoline, dodecane, or dilution culture alone reduced functional and phylogenetic diversity, enriching for Gammaproteobacteria, especially Pseudomonas. Gammaproteobacteria continued to dominate for 10 days in the n-hexane and no alkane exposed samples, while dodecane and gasoline exposure selected for gram-positive bacteria. The data demonstrate that small fringing marshes in New England harbor petroleum-degrading bacteria, suggesting that petroleum degradation may be an important fringing marsh ecosystem function.
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Affiliation(s)
- Sinéad M Ní Chadhain
- Department of Biology, LSCB 217, University of South Alabama, 5871 USA Drive N., Mobile, AL 36688, USA
| | - Jarett L Miller
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - John P Dustin
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Jeff P Trethewey
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Stephen H Jones
- Department of Natural Resources and the Environment, University of New Hampshire, 285 Rudman Hall, 46 College Rd., Durham, NH 03824, USA
| | - Loren A Launen
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA.
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16
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Sarkar P, Roy A, Pal S, Mohapatra B, Kazy SK, Maiti MK, Sar P. Enrichment and characterization of hydrocarbon-degrading bacteria from petroleum refinery waste as potent bioaugmentation agent for in situ bioremediation. BIORESOURCE TECHNOLOGY 2017; 242:15-27. [PMID: 28533069 DOI: 10.1016/j.biortech.2017.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/30/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Intrinsic biodegradation potential of bacteria from petroleum refinery waste was investigated through isolation of cultivable strains and their characterization. Pseudomonas and Bacillus spp. populated the normal cultivable taxa while prolonged enrichment with hydrocarbons and crude oil yielded hydrocarbonoclastic bacteria of genera Burkholderia, Enterobacter, Kocuria, Pandoraea, etc. Strains isolated through enrichment showed assemblages of superior metabolic properties: utilization of aliphatic (C6-C22) and polyaromatic compounds, anaerobic growth with multiple terminal electron acceptors and higher biosurfactant production. Biodegradation of dodecane was studied thoroughly by GC-MS along with detection of gene encoding alkane hydroxylase (alkB). Microcosms bioaugmented with Enterobacter, Pandoraea and Burkholderia strains showed efficient biodegradation (98% TPH removal) well fitted in first order kinetic model with low rate constants and decreased half-life. This study proves that catabolically efficient bacteria resides naturally in complex petroleum refinery wastes and those can be useful for bioaugmentation based bioremediation.
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Affiliation(s)
- Poulomi Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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17
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Liu Q, Tang J, Liu X, Song B, Zhen M, Ashbolt N. Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations. J Appl Microbiol 2017; 123:875-885. [DOI: 10.1111/jam.13549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Q. Liu
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - J. Tang
- College of Environmental Science and Engineering; Nankai University; Tianjin China
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education); Tianjin China
- Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation; Tianjin China
| | - X. Liu
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - B. Song
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - M. Zhen
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - N.J. Ashbolt
- School of Public Health; University of Alberta; Edmonton AB Canada
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18
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Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D. Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms. Trends Biotechnol 2017; 35:860-870. [PMID: 28511936 DOI: 10.1016/j.tibtech.2017.04.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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Affiliation(s)
- Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Alberto Scoma
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00015 Monterotondo, Italy
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
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19
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Corteselli EM, Aitken MD, Singleton DR. Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov. Int J Syst Evol Microbiol 2017; 67:925-931. [PMID: 27926817 DOI: 10.1099/ijsem.0.001714] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain TR3.2T was isolated from aerobic bioreactor-treated soil from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Salisbury, NC, USA. Strain TR3.2T was identified as a member of 'Pyrene Group 2' or 'PG2', a previously uncultivated cluster of organisms associated with the degradation of high-molecular-weight PAHs by stable-isotope probing. Based on its 16S rRNA gene sequence, the strain was classified as a member of the class Gammaproteobacteria but possessed only 90.5 % gene identity to its closest described relative, Methylococcus capsulatus strain Bath. Strain TR3.2T grew on the PAHs pyrene, phenanthrene, anthracene, benz[a]anthracene and fluorene, as well as the azaarene carbazole, and could additionally metabolize a limited number of organic acids. Optimal growth occurred aerobically under mesophilic temperature, neutral pH and low salinity conditions. Strain TR3.2T was catalase and oxidase positive. Predominant fatty acids were C17 : 0 cyclo and C16 : 0. Genomic G+C content of the single chromosome was 67.79 mol% as determined by complete genome sequencing. Due to the high sequence divergence from any cultivated species and its unique physiological properties compared to its closest relatives, strain TR3.2T is proposed as a representative of a novel order, family, genus and species within the class Gammaproteobacteria, for which the name Immundisolibacter cernigliae gen. nov., sp. nov. is proposed. The associated order and family are therefore proposed as Immundisolibacteralesord. nov. and Immundisolibacteraceaefam. nov. The type strain of the species is TR3.2T (=ATCC TSD-58T=DSM 103040T).
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Affiliation(s)
- Elizabeth M Corteselli
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - David R Singleton
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
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20
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Aubé J, Senin P, Pringault O, Bonin P, Deflandre B, Bouchez O, Bru N, Biritxinaga-Etchart E, Klopp C, Guyoneaud R, Goñi-Urriza M. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. MARINE POLLUTION BULLETIN 2016; 111:115-125. [PMID: 27449831 DOI: 10.1016/j.marpolbul.2016.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 07/11/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination.
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Affiliation(s)
- Johanne Aubé
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Pavel Senin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France; Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Case 093, 34095 Montpellier Cedex 5, France.
| | - Patricia Bonin
- MIO, Institut Méditerranéen d'Océanologie, UMR 7294, F13288 Marseille, France.
| | - Bruno Deflandre
- EPOC, UMR 5805, Université de Bordeaux, F33615 Pessac, France.
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F31326 Castanet-Tolosan, France.
| | - Noëlle Bru
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Edurne Biritxinaga-Etchart
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
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21
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Jeanbille M, Gury J, Duran R, Tronczynski J, Agogué H, Ben Saïd O, Ghiglione JF, Auguet JC. Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats. Front Microbiol 2016; 7:1637. [PMID: 27790213 PMCID: PMC5061854 DOI: 10.3389/fmicb.2016.01637] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.
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Affiliation(s)
- Mathilde Jeanbille
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Jérôme Gury
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Jacek Tronczynski
- Laboratoire Biogéochimie des Contaminants Organiques, Unité Biogéochimie et Ecotoxicologie, Département Ressources Biologiques et Environnement, Ifremer Centre Atlantique Nantes, France
| | - Hélène Agogué
- Littoral, Environnement et Sociétés, UMR 7266 Centre National de la Recherche Scientifique - Université de La Rochelle La Rochelle, France
| | - Olfa Ben Saïd
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'AdourPau, France; Laboratoire de Bio-surveillance de l'Environnement, Faculté des Sciences de BizerteZarzouna, Tunisie
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne, Sorbonne Universités, UMR 7621, Centre National de la Recherche Scientifique-University Pierre and Marie Curie Banyuls sur mer, France
| | - Jean-Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation, UMR Centre National de la Recherche Scientifique 9190 Montpellier, France
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Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01086-16. [PMID: 27795254 PMCID: PMC5054325 DOI: 10.1128/genomea.01086-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described “Pyrene Group 2” (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation.
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23
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Jeanbille M, Gury J, Duran R, Tronczynski J, Ghiglione JF, Agogué H, Saïd OB, Taïb N, Debroas D, Garnier C, Auguet JC. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. Front Microbiol 2016; 7:1303. [PMID: 27594854 PMCID: PMC4990537 DOI: 10.3389/fmicb.2016.01303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/08/2016] [Indexed: 01/11/2023] Open
Abstract
Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.
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Affiliation(s)
- Mathilde Jeanbille
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jérôme Gury
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jacek Tronczynski
- Laboratoire Biogéochimie des Contaminants Organiques, Unité Biogéochimie et Ecotoxicologie, Département Ressources Biologiques et Environnement, Ifremer Centre Atlantique Nantes, France
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne, Sorbonne Universités, CNRS, Université Pierre-et-Marie-Curie, UMR 7621, Observatoire Océanologique Banyuls-sur-mer, France
| | - Hélène Agogué
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - Université de La Rochelle La Rochelle, France
| | - Olfa Ben Saïd
- Laboratoire de Bio-surveillance de l'Environnement, Faculté des Sciences de Bizerte Zarzouna, Tunisia
| | - Najwa Taïb
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Cédric Garnier
- Processus de Transferts et d'Echanges dans l'Environnement, EA 3819, Université de Toulon La Garde, France
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24
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Jiang R, Wang JX, Huang B, Yu KC, Zhang P, Zheng JW, Liu XZ. Phylogenetic analysis of bacterial community composition in sediments with organic contaminants from the Jiaojiang estuary in China. MARINE POLLUTION BULLETIN 2016; 109:558-565. [PMID: 27234368 DOI: 10.1016/j.marpolbul.2016.03.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/17/2016] [Accepted: 03/20/2016] [Indexed: 05/20/2023]
Abstract
The aim of this study was to investigate the bacterial community composition, the concentration of organic contaminants, and their relationship in the sediments of Jiaojiang estuary. Sediments were collected from seven stations and the environmental parameters were analyzed. The results showed that the site closest to the chemical industry zone was the most polluted. Bacterial communities were determined using 16S rRNA clone libraries and phylogenetic analysis. These results revealed that there were 13 known bacterial phyla in the sediments and that Proteobacteria were the dominant group. Using these data, we assessed the correlation between bacterial communities and organic contaminants using cluster, multidimensional scaling, and redundancy analyses. These showed that there was no simple relationship between organic contaminants and bacterial community diversity in the sediments, but polycyclic aromatic hydrocarbons were more influential than the other pollutants and negatively affected Chloroflexi.
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Affiliation(s)
- Ran Jiang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jian-Xin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Kai-Cheng Yu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China
| | - Pan Zhang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jun-Wei Zheng
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xue-Zhu Liu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhoushan 316022, China.
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25
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Marziah Z, Mahdzir A, Musa MN, Jaafar AB, Azhim A, Hara H. Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea. Microbiologyopen 2016; 5:967-978. [PMID: 27256005 PMCID: PMC5221450 DOI: 10.1002/mbo3.380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 12/05/2022] Open
Abstract
This study for the first time provides insight into the bacterial community in the benthic region of the Off‐Terengganu Coastline, which is considered to be anthropogenically polluted due to heavy fishing vessel commotion. Subsurface bacteria were randomly collected from two locations at different depths and were examined using the 16S rDNA V3‐V4 marker gene on the Illumina™ Miseq platform. In addition, the physiochemical parameters of the sediment were also measured. Surprisingly, the results show a high diversity of sulfur‐oxidizing bacteria in the surveyed area, where Sulfurovum sp. was identified to predominate the overall bacterial community. The physiochemical parameters reveal insufficient evidence of hydrothermal vents in the surveyed area. However, there are traces of hydrocarbon pollutants such as gasoline, diesel, and mineral oil in this area. It is assumed that sediment accumulation in the lee of breakwater plays an important role in trapping the runoff from the nearby harbor, which includes oil spills. Based on the common knowledge, Sulvurofum sp. is a native bacterium that exists in deep hydrothermal vents and volcanic territories. Although the reason for the abundance of Sulfurovum sp. in the surveyed area is still unclear, there is a possibility that metabolic adaptation plays an important role in regulating hydrocarbon pollutants for survival. The work presented in this paper therefore has profound implications for future studies on Sulfurovum sp. versatility. However, future research is needed to strengthen the findings of this study and to provide a better evidence regarding the metabolic response of this bacterium toward hydrocarbon pollutants.
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Affiliation(s)
- Zahar Marziah
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia
| | - Akbariah Mahdzir
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia.,Ocean Thermal Energy Centre (OTEC-KL), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia
| | - Md Nor Musa
- Ocean Thermal Energy Centre (OTEC-KL), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia
| | - Abu Bakar Jaafar
- Perdana School of Science, Technology and Innovation Policy, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia
| | - Azran Azhim
- Kuliyyah of Science, International Islamic University Malaysia, Kuantan, 25200, Malaysia
| | - Hirofumi Hara
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, Kuala Lumpur, 54100, Malaysia
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26
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Salem FB, Said OB, Aissa P, Mahmoudi E, Monperrus M, Grunberger O, Duran R. Pesticides in Ichkeul Lake-Bizerta Lagoon Watershed in Tunisia: use, occurrence, and effects on bacteria and free-living marine nematodes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:36-48. [PMID: 26165992 DOI: 10.1007/s11356-015-4991-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
This study aimed to identify the most commonly used agricultural pesticides around Ichkeul Lake-Bizerta Lagoon watershed. First survey of pesticide use on agricultural watershed was performed with farmers, Regional Commissioner for Agricultural Development, and pesticide dealers. Then, sediment contamination by pesticides and response of benthic communities (bacteria and free-living marine nematode) were investigated. The analysis of 22 active organochlorine pesticides in sediments was performed according to quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, biodiversity of indigenous bacterial community sediment was determined by terminal restriction fragment length polymorphism (T-RFLP), and free-living marine nematodes were counted. The results of the field survey showed that iodosulfuron, mesosulfuron, 2,4-dichlorophenoxyacetic acid (2,4 D), glyphosate, and fenoxaprops were the most used herbicides, tebuconazole and epoxiconazole the most used fungicides, and deltamethrin the most used insecticide. Sixteen organochlorine pesticide compounds among the 22 examined were detected in sediments up to 2 ppm in Ichkeul Lake, endrin, dieldrin, and hexachlorocyclohexane being the most detected molecules. The most pesticide-contaminated site in the lake presented the higher density of nematode, but when considering all sites, no clear correlation with organochlorine pesticide (OCP) content could be established. The bacterial community structure in the most contaminated site in the lake was characterized by the terminal restriction fragments (T-RFs) 97, 146, 258, 285, and 335 while the most contaminated site in the lagoon was characterized by the T-RFs 54, 263, 315, 403, and 428. Interestingly, T-RFs 38 and 143 were found in the most contaminated sites of both lake and lagoon ecosystems, indicating that they were resistant to OCPs and able to cope with environmental fluctuation of salinity. In contrast, the T-RFs 63, 100, 118, and 381 in the lake and the T-RFs 40, 60, 80, 158, 300, 321, and 357 in the lagoon were sensitive to OCPs. This study highlighted that the intensive use of pesticides in agriculture, through transfer to aquatic ecosystem, may disturb the benthic ecosystem functioning of the protected area. The free-living marine nematodes and bacterial communities represent useful proxy to follow the ecosystem health and its capacity of resilience.
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Affiliation(s)
- Fida Ben Salem
- Laboratory of Environment Biomonitoring, Faculty of Sciences of Bizerta, University of Carthage, 7021, Zarzouna, Tunisia.
- Equipe Environnement et Microbiologie, MELODY Group, UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau cedex, France.
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, IPREM UMR 5254 CNRS, Université de Pau et des Pays de l'Adour, Pau cedex, France.
| | - Olfa Ben Said
- Laboratory of Environment Biomonitoring, Faculty of Sciences of Bizerta, University of Carthage, 7021, Zarzouna, Tunisia
| | - Patricia Aissa
- Laboratory of Environment Biomonitoring, Faculty of Sciences of Bizerta, University of Carthage, 7021, Zarzouna, Tunisia
| | - Ezzeddine Mahmoudi
- Laboratory of Environment Biomonitoring, Faculty of Sciences of Bizerta, University of Carthage, 7021, Zarzouna, Tunisia
| | - Mathilde Monperrus
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, IPREM UMR 5254 CNRS, Université de Pau et des Pays de l'Adour, Pau cedex, France
| | - Olivier Grunberger
- IRD, UMR-LISAH (IRD-INRA-SupAgro), Bat 24, 2 place Viala, 34060, Montpellier cedex 01, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY Group, UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau cedex, France
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27
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Wang Z, Pan F, Hesham AEL, Gao Y, Zhang Y, Yang M. Impacts of produced water origin on bacterial community structures of activated sludge. J Environ Sci (China) 2015; 37:192-199. [PMID: 26574104 DOI: 10.1016/j.jes.2015.04.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 06/05/2023]
Abstract
The purpose of this study was to reveal how activated sludge communities respond to influent quality and indigenous communities by treating two produced waters from different origins in a batch reactor in succession. The community shift and compositions were investigated using Polymerase Chain Reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and further 16S ribosomal DNA (rDNA) clone library analysis. The abundance of targeted genes for polycyclic aromatic hydrocarbon (PAH) degradation, nahAc/phnAc and C12O/C23O, was tracked to define the metabolic ability of the in situ microbial community by Most Probable Number (MPN) PCR. The biosystem performed almost the same for treatment of both produced waters in terms of removals of chemical oxygen demand (COD) and PAHs. Sludge communities were closely associated with the respective influent bacterial communities (similarity>60%), while one sludge clone library was dominated by the Betaproteobacteria (38%) and Bacteriodetes (30%) and the other was dominated by Gammaproteobacteria (52%). This suggested that different influent and water quality have an effect on sludge community compositions. In addition, the existence of catabolic genes in sludge was consistent with the potential for degradation of PAHs in the treatment of both produced waters.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory for Microorganisms and Functional Molecules, College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Feng Pan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Abd El-Latif Hesham
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Genetics Department, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Yingxin Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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28
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Duran R, Cuny P, Bonin P, Cravo-Laureau C. Microbial ecology of hydrocarbon-polluted coastal sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15195-15199. [PMID: 26381785 DOI: 10.1007/s11356-015-5373-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Philippe Cuny
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Patricia Bonin
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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29
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Ben Said O, Louati H, Soltani A, Preud'homme H, Cravo-Laureau C, Got P, Pringault O, Aissa P, Duran R. Changes of benthic bacteria and meiofauna assemblages during bio-treatments of anthracene-contaminated sediments from Bizerta lagoon (Tunisia). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15319-15331. [PMID: 25618309 DOI: 10.1007/s11356-015-4105-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
Sediments from Bizerta lagoon were used in an experimental microcosm setup involving three scenarios for the bioremediation of anthracene-polluted sediments, namely bioaugmentation, biostimulation, and a combination of both bioaugmentation and biostimulation. In order to investigate the effect of the biotreatments on the benthic biosphere, 16S rRNA gene-based T-RFLP bacterial community structure and the abundance and diversity of the meiofauna were determined throughout the experiment period. Addition of fresh anthracene drastically reduced the benthic bacterial and meiofaunal abundances. The treatment combining biostimulation and bioaugmentation was most efficient in eliminating anthracene, resulting in a less toxic sedimentary environment, which restored meiofaunal abundance and diversity. Furthermore, canonical correspondence analysis showed that the biostimulation treatment promoted a bacterial community favorable to the development of nematodes while the treatment combining biostimulation and bioaugmentation resulted in a bacterial community that advantaged the development of the other meiofauna taxa (copepods, oligochaetes, polychaetes, and other) restoring thus the meiofaunal structure. The results highlight the importance to take into account the bacteria/meiofauna interactions during the implementation of bioremediation treatment.
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Affiliation(s)
- Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia.
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France.
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia.
| | - Hela Louati
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Amel Soltani
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Hugues Preud'homme
- Laboratoire Chimie Analytique BioInorganique Environnement-UMR CNRS IPREM 5254-Helioparc, Université de Pau et des Pays de l'Adour, Pau, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Got
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Olivier Pringault
- Laboratoire Ecosystèmes Marins Côtiers, UMR 5119 CNRS-UM2-IFREMER-IRD-ECOSYM, Université Montpellier 2, Montpellier, France
| | - Patricia Aissa
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021, Zarzouna, Tunisia
| | - Robert Duran
- Equipe Environnement et Microbiologie-MELODY Group-UMR CNRS IPREM 5254-IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
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30
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Duran R, Bielen A, Paradžik T, Gassie C, Pustijanac E, Cagnon C, Hamer B, Vujaklija D. Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15215-29. [PMID: 25712885 DOI: 10.1007/s11356-015-4240-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/13/2015] [Indexed: 05/27/2023]
Abstract
The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
- Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1155, 64013, Pau Cedex, France.
| | - Ana Bielen
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Tina Paradžik
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Claire Gassie
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Emina Pustijanac
- Juraj Dobrila University of Pula, Zagrebačka 30, 52100, Pula, Croatia
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Bojan Hamer
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210, Rovinj, Croatia
| | - Dušica Vujaklija
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
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31
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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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Pringault O, Aube J, Bouchez O, Klopp C, Mariette J, Escudie F, Senin P, Goni-Urriza M. Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat. CHEMOSPHERE 2015; 135:189-201. [PMID: 25957138 DOI: 10.1016/j.chemosphere.2015.04.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/18/2015] [Accepted: 04/14/2015] [Indexed: 06/04/2023]
Abstract
The contamination of polluted environments is often due to a complex mixture of pollutants sometimes at trace levels which nevertheless may have significant effects on the diversity and functioning of organisms. The aim of this study was to assess the functional responses of a microbial mat exposed to a natural complex mixture of PAHs and metals as a function of the maturation stage of the biofilm. Microbial mats sampled in a slightly polluted environment were exposed to contaminated water of a retention basin of an oil refinery. The responses of the microbial mats differed according to season. In spring 2012, strong inhibition of both oxygen production and respiration was observed relative to the control, with rates representing less than 5% of the control after 72 h of incubation. A decrease of microbial activities was followed by a decrease of the coupling between autotrophs and heterotrophs. In contrast, in autumn 2012, no significant changes for oxygen production and respiration were observed and the coupling between autotrophs and heterotrophs was not altered. The differences observed between the spring and autumn mats might be explained by the maturity of the microbial mat with dominance of heterotrophic bacteria in spring, and diatoms and cyanobacteria in autumn, as well as by the differences in the chemical composition of the complex mixture of PAHs and metals.
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Affiliation(s)
- Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS-Université de Montpellier, Place Eugène Bataillon, case 093, 34095 Montpellier cedex 5, France
| | - Johanne Aube
- Equipe Environnement et Microbiologie, UMR IPREM 5254, IBEAS BP 1155, Université de Pau et des Pays de l'Adour, 64013 Pau cedex, France
| | - Olivier Bouchez
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Christophe Klopp
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Jérome Mariette
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Frédéric Escudie
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Pavel Senin
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Marisol Goni-Urriza
- Equipe Environnement et Microbiologie, UMR IPREM 5254, IBEAS BP 1155, Université de Pau et des Pays de l'Adour, 64013 Pau cedex, France
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Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea). BIOMED RESEARCH INTERNATIONAL 2015; 2015:981829. [PMID: 26273661 PMCID: PMC4530241 DOI: 10.1155/2015/981829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/01/2015] [Accepted: 02/01/2015] [Indexed: 11/17/2022]
Abstract
Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.
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Loviso CL, Lozada M, Guibert LM, Musumeci MA, Sarango Cardenas S, Kuin RV, Marcos MS, Dionisi HM. Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments. J Appl Microbiol 2015; 119:411-24. [PMID: 25968322 DOI: 10.1111/jam.12843] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/22/2015] [Accepted: 04/30/2015] [Indexed: 01/18/2023]
Abstract
AIMS To investigate the potential to degrade polycyclic aromatic hydrocarbons (PAHs) of yet-to-be-cultured bacterial populations from chronically polluted intertidal sediments. METHODS AND RESULTS A gene variant encoding the alpha subunit of the catalytic component of an aromatic-ring-hydroxylating oxygenase (RHO) was abundant in intertidal sediments from chronically polluted subantarctic and temperate coastal environments, and its abundance increased after PAH amendment. Conversely, this marker gene was not detected in sediments from a nonimpacted site, even after a short-term PAH exposure. A metagenomic fragment carrying this gene variant was identified in a fosmid library of subantarctic sediments. This fragment contained five pairs of alpha and beta subunit genes and a lone alpha subunit gene of oxygenases, classified as belonging to three different RHO functional classes. In silico structural analysis suggested that two of these oxygenases contain large substrate-binding pockets, capable of accepting high molecular weight PAHs. CONCLUSIONS The identified uncultured micro-organism presents the potential to degrade aromatic hydrocarbons with various chemical structures, and could represent an important member of the PAH-degrading community in these polluted coastal environments. SIGNIFICANCE AND IMPACT OF THE STUDY This work provides valuable information for the design of environmental molecular diagnostic tools and for the biotechnological application of RHO enzymes.
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Affiliation(s)
- C L Loviso
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - L M Guibert
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - S Sarango Cardenas
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - R V Kuin
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M S Marcos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - H M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
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Jemli M, Karray F, Feki F, Loukil S, Mhiri N, Aloui F, Sayadi S. Biological treatment of fish processing wastewater: A case study from Sfax City (Southeastern Tunisia). J Environ Sci (China) 2015; 30:102-112. [PMID: 25872714 DOI: 10.1016/j.jes.2014.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 06/04/2023]
Abstract
The present work presents a study of the biological treatment of fish processing wastewater at salt concentration of 55 g/L. Wastewater was treated by both continuous stirred-tank reactor (CSTR) and membrane bioreactor (MBR) during 50 and 100 days, respectively. These biological processes involved salt-tolerant bacteria from natural hypersaline environments at different organic loading rates (OLRs). The phylogenetic analysis of the corresponding excised DGGE bands has demonstrated that the taxonomic affiliation of the most dominant species includes Halomonadaceae and Flavobacteriaceae families of the Proteobacteria (Gamma-proteobacteria class) and the Bacteroidetes phyla, respectively. The results of MBR were better than those of CSTR in the removal of total organic carbon with efficiencies from 97.9% to 98.6%. Nevertheless, salinity with increasing OLR aggravates fouling that requires more cleaning for a membrane in MBR while leads to deterioration of sludge settleability and effluent quality in CSTR.
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Affiliation(s)
- Meryem Jemli
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia.
| | - Fatma Karray
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
| | - Firas Feki
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
| | - Slim Loukil
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
| | - Najla Mhiri
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
| | - Fathi Aloui
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
| | - Sami Sayadi
- Laboratoire des Bioprocédés Environnementaux, Pôle d'Excellence Régional (PER, AUF), Centre de Biotechnologie de Sfax, Université de Sfax, Route de Sidi Mansour km 6, PO Box 1177, 3018 Sfax, Tunisia
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Ribeiro H, Almeida CMR, Magalhães C, Bordalo AA, Mucha AP. Salt marsh sediment characteristics as key regulators on the efficiency of hydrocarbons bioremediation by Juncus maritimus rhizospheric bacterial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:450-462. [PMID: 25081009 DOI: 10.1007/s11356-014-3388-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/24/2014] [Indexed: 06/03/2023]
Abstract
Mitigation of petroleum hydrocarbons was investigated during a 5-month greenhouse experiment, to assess the rhizoremediation (RR) potential in sediments with different characteristics colonized by Juncus maritimus, a salt marsh plant commonly found in temperate estuaries. Furthermore, the efficiency of two bioremediation treatments namely biostimulation (BS) by the addition of nutrients, and bioaugmentation (BA) by addition of indigenous microorganisms, was tested in combination with RR. The effect of the distinct treatments on hydrocarbon degradation, root biomass weight, and bacterial community structure was assessed. Our result showed higher potential for hydrocarbon degradation (evaluated by total petroleum hydrocarbon analysis) in coarse rhizosediments with low organic matter (OM), than rhizosediments with high OM, and small size particles. Moreover, the bacterial community structure was shaped according to the rhizosediment characteristics, highlighting the importance of specific microbe-particle associations to define the structure of rhizospheric bacterial communities, rather than external factors, such as hydrocarbon contamination or the applied treatments. The potential for hydrocarbon RR seems to depend on root system development and bacterial diversity, since biodegradation efficiencies were positively related with these two parameters. Treatments with higher root biomass, and concomitantly with higher bacterial diversity yielded higher hydrocarbon degradation. Moreover, BS and BA did not enhance hydrocarbons RR. In fact, it was observed that higher nutrient availability might interfere with root growth and negatively influence hydrocarbon degradation performance. Therefore, our results suggested that to conduct appropriate hydrocarbon bioremediation strategies, the effect of sediment characteristics on root growth/exploration should be taken into consideration, a feature not explored in previous studies. Furthermore, strategies aiming for the recovery of bacterial diversity after oil spills may improve the efficiency of hydrocarbon biodegradation in contaminated salt marsh sediments.
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Affiliation(s)
- Hugo Ribeiro
- CIMAR/CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123, Porto, Portugal,
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Abed RMM, Al-Kindi S, Al-Kharusi S. Diversity of bacterial communities along a petroleum contamination gradient in desert soils. MICROBIAL ECOLOGY 2015; 69:95-105. [PMID: 25103912 DOI: 10.1007/s00248-014-0475-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box: 36, 123 Al Khoud, Muscat, Sultanate of Oman,
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Todorova NH, Mironova RS, Karamfilov VK. Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments. MARINE POLLUTION BULLETIN 2014; 83:231-240. [PMID: 24759506 DOI: 10.1016/j.marpolbul.2014.03.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 03/13/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
Molecular analysis was applied to characterize bacterial community structure in sediment samples collected from pristine site and oil-polluted Black Sea harbor. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed a high similarity in the restriction patterns of both samples thus not demonstrating the effect of the pollutant on the structure of the bacterial communities. Constructed 16S rRNA gene libraries gave more detailed assessment of members. Results showed that α- and γ-Proteobacteria were dominant in the oil polluted site, whereas the pristine site was characterized by prevalence of Actinobacteria. The biodegradative potential of the adapted bacterial community in the oil-polluted sediments was demonstrated by the presence of the aromatic ring hydroxylating dioxygenase genes.
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Affiliation(s)
- Nadezhda H Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Y. Gagarin 2 str., 1113 Sofia, Bulgaria.
| | - Roumyana S Mironova
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, G. Bonchev str., bl. 21, 1113 Sofia, Bulgaria.
| | - Ventzislav K Karamfilov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Y. Gagarin 2 str., 1113 Sofia, Bulgaria.
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Genovese M, Crisafi F, Denaro R, Cappello S, Russo D, Calogero R, Santisi S, Catalfamo M, Modica A, Smedile F, Genovese L, Golyshin PN, Giuliano L, Yakimov MM. Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation. Front Microbiol 2014; 5:162. [PMID: 24782850 PMCID: PMC3995047 DOI: 10.3389/fmicb.2014.00162] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/25/2014] [Indexed: 11/13/2022] Open
Abstract
The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs) in coastal sediments. Approximately 1000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6500 ppm). The rapid consumption of oxygen by aerobic heterotrophs created highly reduced conditions in the sediments with subsequent recession of biodegradation rates. As follows, after 3 months of ageing, the anaerobic sediments did not exhibit any significant levels of biodegradation and more than 80% of added Bunker C fuel oil remained buried. Anaerobic microbial community exhibited a strong enrichment in sulfate-reducing PHs-degrading and PHs-associated Deltaproteobacteria. As an effective bioremediation strategy to clean up these contaminated sediments, we applied a Modular Slurry System (MSS) allowing the containment of sediments and their physical-chemical treatment, e.g., aeration. Aeration for 3 months has increased the removal of main PHs contaminants up to 98%. As revealed by CARD-FISH, qPCR, and 16S rRNA gene clone library analyses, addition of Bunker C fuel oil initially affected the activity of autochthonous aerobic obligate marine hydrocarbonoclastic bacteria (OMHCB), and after 1 month more than the third of microbial population was represented by Alcanivorax-, Cycloclasticus-, and Marinobacter-related organisms. In the end of the experiment, the microbial community composition has returned to a status typically observed in pristine marine ecosystems with no detectable OMHCB present. Eco-toxicological bioassay revealed that the toxicity of sediments after treatment was substantially decreased. Thus, our studies demonstrated that petroleum-contaminated anaerobic marine sediments could efficiently be cleaned through an in situ oxygenation which stimulates their self-cleaning potential due to reawakening of allochtonous aerobic OMHCB.
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Affiliation(s)
- Maria Genovese
- Institute for Coastal Marine Environment, CNRMessina, Italy
| | | | - Renata Denaro
- Institute for Coastal Marine Environment, CNRMessina, Italy
| | | | - Daniela Russo
- Institute for Coastal Marine Environment, CNRMessina, Italy
- Department of Biological and Environmental Sciences, University of MessinaMessina, Italy
| | | | - Santina Santisi
- Institute for Coastal Marine Environment, CNRMessina, Italy
- Department of Biological and Environmental Sciences, University of MessinaMessina, Italy
| | | | - Alfonso Modica
- Environmental Laboratory, Syndial SpAPriolo Gargallo, Italy
| | | | | | - Peter N. Golyshin
- Environmental Genomics, School of Biological Sciences, Bangor UniversityBangor, UK
| | - Laura Giuliano
- Institute for Coastal Marine Environment, CNRMessina, Italy
- Mediterranean Science CommissionMonaco, Monaco
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Li J, Li F, Yu S, Qin S, Wang G. Impacts of mariculture on the diversity of bacterial communities within intertidal sediments in the Northeast of China. MICROBIAL ECOLOGY 2013; 66:861-870. [PMID: 23963221 DOI: 10.1007/s00248-013-0272-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
Mariculture is one of the major seafood supplies worldwide and has caused serious environmental concerns on the coastal zone. Its rapid development has been shown to disrupt the sediment ecosystems and thus influence the benthic bacterial communities. Bacterial diversity and community structure within both adjacent farms and non-cultured zones intertidal sediments along the coasts of Qinhuangdao and Dalian, China, were investigated using full-length 16S rRNA gene-based T-RFLP analyses and clone library construction. Richness and Shannon-Wiener index were significantly increased at sites adjacent the mariculture farm with mean values of 29 and 2.97 from peak profiles of T-RFLP result. Clustering analyses suggested that impacts of mariculture on bacterial diversity of sediment were significantly larger than those resulted from temporal and spatial scales. Upon comparisons of RFLP patterns from 602 clones from libraries of the selected five samples, 137 OTUs were retrieved. Members of γ- and δ-Proteobacteria, Bacilli, Flavobacteria, and Actinobacteria were recorded in all libraries. In addition, γ-Proteobacteria were dominant in all samples (21.7~45.0 %). Redundancy analysis revealed that the distribution of bacterial composition seemed to be determined by the variables of salinity, PO4 (3-)-P, NH4 (+)-N, and Chlorophyll a content. The phyla of γ-Proteobacteria, Clostridia, Flavobacteria, Bacilli, and Planctomycetes were principal components to contribute to the bacterial differences of clone libraries. Our finding demonstrated that these phyla could display variations of bacterial composition linked to environmental disturbance resulted from mariculture.
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Affiliation(s)
- Jialin Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
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Louati H, Said OB, Soltani A, Got P, Mahmoudi E, Cravo-Laureau C, Duran R, Aissa P, Pringault O. The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure. CHEMOSPHERE 2013; 93:2535-2546. [PMID: 24206831 DOI: 10.1016/j.chemosphere.2013.09.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 06/02/2023]
Abstract
Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.
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Jho EH, Shin D, Turner SJ, Singhal N. Effect of Fenton reagent shock and recovery periods on anaerobic microbial community structure and degradation of chlorinated aliphatics. Biodegradation 2013; 25:253-64. [DOI: 10.1007/s10532-013-9657-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
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Ribeiro H, Mucha AP, Almeida CMR, Bordalo AA. Bacterial community response to petroleum contamination and nutrient addition in sediments from a temperate salt marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 458-460:568-576. [PMID: 23707865 DOI: 10.1016/j.scitotenv.2013.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 06/02/2023]
Abstract
Microbial communities play an important role in the biodegradation of organic pollutants in sediments, including hydrocarbons. The aim of this study was to evaluate the response of temperate salt marsh microbial communities to petroleum contamination, in terms of community structure, abundance and capacity to degrade hydrocarbons. Sediments un-colonized and colonized (rhizosediments) by Juncus maritimus, Phragmites australis and Triglochin striata were collected in a temperate estuary (Lima, NW Portugal), spiked with petroleum under variable nutritional conditions, and incubated for 15 days. Results showed that plant speciation emerged as the major factor for shaping the rhizosphere community structure, overriding the petroleum influence. Moreover, when exposed to petroleum contamination, the distinct salt marsh microbial communities responded similarly with (i) increased abundance, (ii) changes in structure, and (iii) decreased diversity. Communities, particularly those associated to J. maritimus and P. australis roots displayed a potential to degrade petroleum hydrocarbons, with degradation percentages between 15% and 41%, depending on sediment type and nutritional conditions. In conclusion, distinct salt marsh microbial communities responded similarly to petroleum contamination, but presented different pace, nutritional requirements, and potential for its biodegradation, which should be taken into account when developing bioremediation strategies.
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Affiliation(s)
- Hugo Ribeiro
- Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
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Abstract
A 69-year-old patient presented with a tender, thickly crusted skin lesion of 1 week's duration. A bacterial culture swab taken from the underlying granular tissue yielded a pure isolate of a Gram-negative coccobacillus, presumptively identified as a novel Francisella species via 16S rRNA and multilocus gene sequence analysis.
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Sun MY, Dafforn KA, Johnston EL, Brown MV. Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environ Microbiol 2013; 15:2517-31. [DOI: 10.1111/1462-2920.12133] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 03/19/2013] [Accepted: 03/24/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie Y. Sun
- Evolution and Ecology Research Center; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney; NSW; 2052; Australia
| | - Katherine A. Dafforn
- Evolution and Ecology Research Center; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney; NSW; 2052; Australia
| | - Emma L. Johnston
- Evolution and Ecology Research Center; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney; NSW; 2052; Australia
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Silva-Castro GA, Rodelas B, Perucha C, Laguna J, González-López J, Calvo C. Bioremediation of diesel-polluted soil using biostimulation as post-treatment after oxidation with Fenton-like reagents: assays in a pilot plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 445-446:347-55. [PMID: 23354375 DOI: 10.1016/j.scitotenv.2012.12.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/21/2012] [Accepted: 12/25/2012] [Indexed: 05/20/2023]
Abstract
The present study focuses on the remediation of diesel-polluted soil using modified Fenton treatment coupled with inorganic NPK fertilizer ("Fenton+NPK"). Studies were carried out in a pilot plant containing 1 m(3) of sandy soil contaminated with 20,000 mg kg(-1) of diesel, placed outdoors at a temperature ranging between 5 and 10 °C. Results showed that NPK-fertilizer as post-treatment stimulated culturable degrading bacteria and enhanced dehydrogenase activity. Fenton+NPK treatment increased total petroleum hydrocarbon (TPH) removal efficacy. Natural attenuation removed 49% of TPH in the surface layer, 23% of TPH in the non-saturated layer and 4% of the TPH in the saturated layer, while the percentage removed of TPH after Fenton+NPK treatment was 58%, 57% and 32% respectively. The results from our study showed that, immediately after soil contamination, occurred a specialization and differentiation of the bacterial community, but after this initial modification, no significant changes of bacterial diversity was observed under natural attenuation conditions. In contrast, when the Fenton's reagent was applied a reduction of the bacterial biodiversity was observed. However, the post-biostimulation did enhance the degrading microbiota and stimulated their degrading biological activity. In conclusion, biostimulation, as a post-treatment step in chemical oxidation, is an effective solution to remediate hydrocarbon-polluted sites.
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Affiliation(s)
- Gloria Andrea Silva-Castro
- Department of Microbiology, Institute of Water Research, University of Granada, Spain, C/Ramón y Cajal no 4, 18071 Granada, Spain.
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Louati H, Ben Said O, Got P, Soltani A, Mahmoudi E, Cravo-Laureau C, Duran R, Aissa P, Pringault O. Microbial community responses to bioremediation treatments for the mitigation of low-dose anthracene in marine coastal sediments of Bizerte lagoon (Tunisia). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:300-310. [PMID: 22441697 DOI: 10.1007/s11356-012-0860-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/12/2012] [Indexed: 05/31/2023]
Abstract
PURPOSE The main goals of this study were to investigate (1) the behavior of microbial communities in response to low-dose bioavailable anthracene addition in lightly contaminated sediment from Bizerte Lagoon and (2) the effects of bioremediation treatments on microbial biomass, activity, and community structure. METHODS Sediment microcosms amended with 1 ppm anthracene were incubated in triplicate during 30 days. Biostimulation (addition of nitrogen and phosphorus fertilizer) and bioaugmentation (inoculation of a hydrocarbonoclastic bacterium) were used as bioremediation treatments. Bacterial biomass was estimated using flow cytometry. Sediment oxygen consumption was measured with oxygen microelectrodes. Bacterial community structure was assessed by molecular fingerprints (terminal restriction fragment length polymorphism; T-RFLP) analysis. RESULTS Anthracene contamination resulted in a significant reduction of bacterial abundance with an impact on cell integrity. Concomitantly, sediment oxygen consumption was strongly inhibited. Correspondence analysis on T-RFLP data indicated that bacterial community structures from anthracene-contaminated microcosms were different from that of the control. Interestingly, the changes observed in microbial biomass, structure, and activities as a result of anthracene contamination were not alleviated even with the use of biostimulation and combination of biostimulation and bioaugmentation strategy for anthracene bioremediation. Nevertheless, both treatment methods resulted in different community structures relative to the contaminated and control microcosms with the appearance of distinct populations. CONCLUSION Anthracene spiking severely affected microbial communities, suggesting dominance of nontolerant populations in this lightly-contaminated sediment. Although biostimulation and/or bioaugmentation treatments did not alleviate the anthracene toxic effects, the changes observed in microbial population and structure suggest that the proposed treatments might be promising to promote bacterial growth. Further works are still required to propose a more efficient strategy to stimulate biodegradation that takes into account the complex interactions between species for resource access.
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Affiliation(s)
- Hela Louati
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, 7021 Zarzouna, Bizerte, Tunisia
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Giloteaux L, Duran R, Casiot C, Bruneel O, Elbaz-Poulichet F, Goñi-Urriza M. Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic. FEMS Microbiol Ecol 2012; 83:724-37. [PMID: 23057444 DOI: 10.1111/1574-6941.12028] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022] Open
Abstract
A 3-year survey on sulfate-reducing bacteria (SRB) was conducted in the waters of the arsenic-rich acid mine drainage (AMD) located at Carnoulès (France) to determine the influence of environmental parameters on their community structure. The source (S5 station) exhibited most extreme conditions with pH lowering to ~1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29 593, and 638 mg L(-1), respectively. The conditions were less extreme at the downstream stations S1 (pH ~3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167 mg L(-1), respectively) and COWG (pH ~3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110 mg L(-1), respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of pH, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (pH 1.4) with high iron and arsenic concentrations (6379 and 524 mg L(-1), respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems.
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Affiliation(s)
- Ludovic Giloteaux
- Equipe Environnement et Microbiologie - UMR IPREM5254, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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Guibert LM, Loviso CL, Marcos MS, Commendatore MG, Dionisi HM, Lozada M. Alkane biodegradation genes from chronically polluted subantarctic coastal sediments and their shifts in response to oil exposure. MICROBIAL ECOLOGY 2012; 64:605-616. [PMID: 22580956 DOI: 10.1007/s00248-012-0051-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/27/2012] [Indexed: 05/31/2023]
Abstract
Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.
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Affiliation(s)
- Lilian M Guibert
- Centro Nacional Patagónico (CENPAT - CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
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Pringault O, Viret H, Duran R. Interactions between Zn and bacteria in marine tropical coastal sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:879-892. [PMID: 21953181 DOI: 10.1007/s11356-011-0621-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 09/11/2011] [Indexed: 05/31/2023]
Abstract
PURPOSE The main goals of this study were (1) to examine the effects of zinc on the microbial community structure of anthropogenically impacted sediments in a tropical coastal ecosystem and (2) to determine whether these microbial benthic communities may enhance the adsorption of zinc. METHODS The interactions between zinc and bacteria in tropical sediments were studied in sediment microcosms amended with 2.5 mg L⁻¹ of Zn in the water phase and incubated for 8 days under different environmental conditions, oxic/anoxic and glucose addition. At the end of incubation, microbial structure was assessed by molecular fingerprints (T-RFLP) analysis and Zn speciation in the sediment was determined by sequential extraction. RESULTS In the three studied sediments, Zn spiking resulted in only slight changes in bacterial community structure. In contrast, the addition of low concentrations of glucose (5 mM) strongly modified the bacterial community structure: <20% of similarity with the initial structure concomitant with a strong diminution of the specific richness. Overall, these results suggest that highly labile organic matter has a larger impact on microbial structure than heavy metal. These weak impacts of Zn on bacteria diversity might be partly explained by (1) the strong adsorption of Zn in the presence of bacteria and/or (2) the incorporation of Zn into a nonbioavailable fraction. Nevertheless, Zn spiking resulted in significant changes in nutrient cycles, suggesting that bacterial metabolisms were impacted by the heavy metal. This led to an increase in nutrient supplies to the water column, potentially enhancing eutrophication in a nutrient-limited, oligotrophic ecosystem.
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Affiliation(s)
- Olivier Pringault
- Institut de Recherche pour le Développement, UMR 5119, IRD, CNRS, Université Montpellier 2, Station Méditerranéenne de l'Environnement Littoral 2 Rue des Chantiers, 34200 Sete, France.
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