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Martinez-Varela A, Casas G, Berrojalbiz N, Lundin D, Piña B, Dachs J, Vila-Costa M. Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:119988-119999. [PMID: 37934408 DOI: 10.1007/s11356-023-30650-1] [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: 07/12/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.
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Affiliation(s)
- Alicia Martinez-Varela
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Gemma Casas
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Naiara Berrojalbiz
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, 35195, Kalmar, Sweden
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain.
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2
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Iriarte J, Dachs J, Casas G, Martínez-Varela A, Berrojalbiz N, Vila-Costa M. Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1625-1636. [PMID: 36655903 PMCID: PMC9893724 DOI: 10.1021/acs.est.2c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 05/28/2023]
Abstract
The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.
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Martinez-Varela A, Casas G, Berrojalbiz N, Piña B, Dachs J, Vila-Costa M. Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica. Front Microbiol 2022; 13:907265. [PMID: 35910648 PMCID: PMC9329070 DOI: 10.3389/fmicb.2022.907265] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.
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Affiliation(s)
| | | | | | | | | | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Spain
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4
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Bagi A, Knapik K, Baussant T. Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes - Potential for use in detection of marine oil pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152238. [PMID: 34896501 DOI: 10.1016/j.scitotenv.2021.152238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.
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Affiliation(s)
- Andrea Bagi
- NORCE Norwegian Research Centre, Bergen, Norway.
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5
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Dell’ Anno F, Rastelli E, Sansone C, Brunet C, Ianora A, Dell’ Anno A. Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era. Microorganisms 2021; 9:1695. [PMID: 34442774 PMCID: PMC8400010 DOI: 10.3390/microorganisms9081695] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022] Open
Abstract
Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.
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Affiliation(s)
- Filippo Dell’ Anno
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy; (C.S.); (C.B.); (A.I.)
| | - Antonio Dell’ Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Oyetibo GO, Ige OO, Obinani PK, Amund OO. Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112563. [PMID: 33852998 DOI: 10.1016/j.jenvman.2021.112563] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/26/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Oluwatobi O Ige
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
| | - Peace K Obinani
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
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Martinez-Varela A, Cerro-Gálvez E, Auladell A, Sharma S, Moran MA, Kiene RP, Piña B, Dachs J, Vila-Costa M. Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean. Environ Microbiol 2021; 23:4532-4546. [PMID: 34169620 DOI: 10.1111/1462-2920.15646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
Thousands of man-made synthetic chemicals are released to oceans and compose the anthropogenic dissolved organic carbon (ADOC). Little is known about the effects of this chronic pollution on marine microbiome activities. In this study, we measured the pollution level at three sites in the Northeast Subarctic Pacific Ocean (NESAP) and investigated how mixtures of three model families of ADOC at different environmentally relevant concentrations affected naturally occurring marine bacterioplankton communities' structure and metabolic functioning. The offshore northernmost site (North) had the lowest concentrations of hydrocarbons, as well as organophosphate ester plasticizers, contrasting with the two other continental shelf sites, the southern coastal site (South) being the most contaminated. At North, ADOC stimulated bacterial growth and promoted an increase in the contribution of some Gammaproteobacteria groups (e.g. Alteromonadales) to the 16 rRNA pool. These groups are described as fast responders after oil spills. In contrast, minor changes in South microbiome activities were observed. Gene expression profiles at Central showed the coexistence of ADOC degradation and stress-response strategies to cope with ADOC toxicities. These results show that marine microbial communities at three distinct domains in NESAP are influenced by background concentrations of ADOC, expanding previous assessments for polar and temperate waters.
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Affiliation(s)
- Alícia Martinez-Varela
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Elena Cerro-Gálvez
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Adrià Auladell
- Department of Marine Biology and Oceanography, Marine Science Institute, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Shalabh Sharma
- Department of Marine Sciences, University of Georgia, Marine Sciences Building, Athens, GA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Marine Sciences Building, Athens, GA, USA
| | - Ronald P Kiene
- Department of Marine Sciences, University of South Alabama, Mobile, AL, USA
| | - Benjamí Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
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Thomas GE, Brant JL, Campo P, Clark DR, Coulon F, Gregson BH, McGenity TJ, McKew BA. Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession. Microorganisms 2021; 9:microorganisms9061200. [PMID: 34206054 PMCID: PMC8229435 DOI: 10.3390/microorganisms9061200] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude-oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon-degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h. A succession of obligate hydrocarbonoclastic bacteria (OHCB), driven by metabolite niche partitioning, is demonstrated. Importantly, this succession has revealed how the OHCB Oleispira, hitherto considered to be a psychrophile, can dominate in the early stages of oil-spill response (1 and 3 days), outcompeting all other OHCB, at the relatively high temperature of 16 °C. Additionally, we demonstrate how some dispersants or biosurfactants can select for specific bacterial genera, especially the biosurfactant rhamnolipid, which appears to provide an advantageous compatibility with Pseudomonas, a genus in which some species synthesize rhamnolipid in the presence of hydrocarbons.
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Affiliation(s)
- Gareth E. Thomas
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; (D.R.C.); (B.H.G.); (T.J.M.); (B.A.M.)
- Correspondence: ; Tel.: +44-1206-873333 (ext. 2918)
| | - Jan L. Brant
- Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK;
| | - Pablo Campo
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK; (P.C.); (F.C.)
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; (D.R.C.); (B.H.G.); (T.J.M.); (B.A.M.)
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK; (P.C.); (F.C.)
| | - Benjamin H. Gregson
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; (D.R.C.); (B.H.G.); (T.J.M.); (B.A.M.)
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; (D.R.C.); (B.H.G.); (T.J.M.); (B.A.M.)
| | - Boyd A. McKew
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; (D.R.C.); (B.H.G.); (T.J.M.); (B.A.M.)
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Thomas GE, Cameron TC, Campo P, Clark DR, Coulon F, Gregson BH, Hepburn LJ, McGenity TJ, Miliou A, Whitby C, McKew BA. Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece. Front Microbiol 2020; 11:1706. [PMID: 32765479 PMCID: PMC7379155 DOI: 10.3389/fmicb.2020.01706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.
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Affiliation(s)
- Gareth E. Thomas
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Tom C. Cameron
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Pablo Campo
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex, United Kingdom
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | | | - Leanne J. Hepburn
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Corinne Whitby
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Boyd A. McKew
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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10
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Knapik K, Bagi A, Krolicka A, Baussant T. Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP). Microorganisms 2020; 8:E744. [PMID: 32429288 PMCID: PMC7284936 DOI: 10.3390/microorganisms8050744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022] Open
Abstract
The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.
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Affiliation(s)
| | | | | | - Thierry Baussant
- NORCE Environment, NORCE Norwegian Research Centre AS, 4070 Randaberg, Norway; (K.K.); (A.B.); (A.K.)
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11
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Gu Z, Yang LE, Chen Z, Chen W. Comparative analysis of different DNA barcodes for applications in the identification and production of Pyropia. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environ Microbiol 2020; 22:1870-1883. [PMID: 32090431 PMCID: PMC7318663 DOI: 10.1111/1462-2920.14956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
In cold marine environments, the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8, which utilizes aliphatic alkanes almost exclusively as substrates, dominates microbial communities following oil spills. In this study, LC–MS/MS shotgun proteomics was used to identify changes in the proteome induced during growth on n‐alkanes and in cold temperatures. Specifically, proteins with significantly higher relative abundance during growth on tetradecane (n‐C14) at 16°C and 4°C have been quantified. During growth on n‐C14, O. antarctica expressed a complete pathway for the terminal oxidation of n‐alkanes including two alkane monooxygenases, two alcohol dehydrogenases, two aldehyde dehydrogenases, a fatty‐acid‐CoA ligase, a fatty acid desaturase and associated oxidoreductases. Increased biosynthesis of these proteins ranged from 3‐ to 21‐fold compared with growth on a non‐hydrocarbon control. This study also highlights mechanisms O. antarctica may utilize to provide it with ecological competitiveness at low temperatures. This was evidenced by an increase in spectral counts for proteins involved in flagella structure/output to overcome higher viscosity, flagella rotation to accumulate cells and proline metabolism to counteract oxidative stress, during growth at 4°C compared with 16°C. Such species‐specific understanding of the physiology during hydrocarbon degradation can be important for parameterizing models that predict the fate of marine oil spills.
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Affiliation(s)
- Benjamin H Gregson
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Peter N Golyshin
- School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, UK.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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Hamdan HZ, Salam DA, Saikaly PE. Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation. MARINE POLLUTION BULLETIN 2019; 149:110508. [PMID: 31425842 DOI: 10.1016/j.marpolbul.2019.110508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
In this study, the shoreline of Lebanon, which extends over 225 km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).
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Affiliation(s)
- Hamdan Z Hamdan
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon
| | - Darine A Salam
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
| | - Pascal E Saikaly
- Division of Biological and Environmental Sciences and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Buttigieg PL, Fadeev E, Bienhold C, Hehemann L, Offre P, Boetius A. Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Curr Opin Microbiol 2018; 43:169-185. [PMID: 29477022 DOI: 10.1016/j.mib.2018.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 02/07/2023]
Abstract
Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. While this first synthesis shows that notable efforts exist, vast regions such as the ocean depths, the open ocean, the polar oceans, and most of the Southern Hemisphere lack consistent observation. To secure a coordinated future for a global microbial observing system, existing long-term efforts must be better networked to generate shared bioindicators of the Global Ocean's state and health.
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Affiliation(s)
- Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany.
| | - Eduard Fadeev
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Christina Bienhold
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Laura Hehemann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany
| | - Pierre Offre
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Antje Boetius
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany; MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, D-28334 Bremen, Germany.
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15
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Pan Y, Chen J, Zhou H, Tam NFY. Changes in microbial community during removal of BDE-153 in four types of aquatic sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:644-652. [PMID: 28934686 DOI: 10.1016/j.scitotenv.2017.09.130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Indigenous microorganisms in sediments could degrade polybrominated diphenyl ethers (PBDEs), but how the microbial communities respond to PBDEs was seldom reported. The effect of BDE-153, a common congener in aquatic environments, on the microbial communities in four types of aquatic sediments was evaluated during the 150days' incubation under an anaerobic condition. The intrinsic potential to remove BDE-153 varied significantly among four sediment types, and the removal rates of mangrove, mudflat, marine and freshwater sediments were 0.013, 0.013, 0.011, and 0.009day-1, respectively. The observed microbial species, Simpson, Shannon, and Chao1 indices in all sediments were rather stable and were not changed significantly by BDE-153 amendment. However, BDE-153 amendment altered the microbial community compositions in three saline sediments at the end of the incubation period. Distance-based multivariate multiple regression analysis revealed that salinity, total organic carbon (TOC) and BDE-52, the major debromination product of BDE-153, were the three main factors explaining the variations in microbial community compositions in BDE-treated sediments; whereas salinity, TOC and pH were the main contributing factors in control sediments without BDE-153. The daughter congeners generated during anaerobic debromination process need more attention, especially their effect on the microbial communities in aquatic sediments.
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Affiliation(s)
- Ying Pan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road, Nanjing 210098, China
| | - Haichao Zhou
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Futian-CityU Mangrove R&D Centre, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; College of Life Sciences and Oceanography, Shenzhen University, Nanhai Avenue, 518060, China
| | - Nora F Y Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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Aylagas E, Borja Á, Tangherlini M, Dell'Anno A, Corinaldesi C, Michell CT, Irigoien X, Danovaro R, Rodríguez-Ezpeleta N. A bacterial community-based index to assess the ecological status of estuarine and coastal environments. MARINE POLLUTION BULLETIN 2017; 114:679-688. [PMID: 27784536 DOI: 10.1016/j.marpolbul.2016.10.050] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 05/27/2023]
Abstract
Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.
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Affiliation(s)
- Eva Aylagas
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain.
| | - Ángel Borja
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain.
| | - Michael Tangherlini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Craig T Michell
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Xabier Irigoien
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain; Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Acosta-González A, Marqués S. Bacterial diversity in oil-polluted marine coastal sediments. Curr Opin Biotechnol 2016; 38:24-32. [PMID: 26773654 DOI: 10.1016/j.copbio.2015.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022]
Abstract
Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.
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Affiliation(s)
- Alejandro Acosta-González
- Grupo de Investigación en Bioprospección (GIBP), Facultad de Ingeniería, Universidad de La Sabana, Autopista Norte km 7, Chía, Cundinamarca, Colombia
| | - Silvia Marqués
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, Profesor Albareda 1, E-18008 Granada, Spain.
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18
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Caruso G, La Ferla R, Azzaro M, Zoppini A, Marino G, Petochi T, Corinaldesi C, Leonardi M, Zaccone R, Fonda Umani S, Caroppo C, Monticelli L, Azzaro F, Decembrini F, Maimone G, Cavallo RA, Stabili L, Hristova Todorova N, K. Karamfilov V, Rastelli E, Cappello S, Acquaviva MI, Narracci M, De Angelis R, Del Negro P, Latini M, Danovaro R. Microbial assemblages for environmental quality assessment: Knowledge, gaps and usefulness in the European Marine Strategy Framework Directive. Crit Rev Microbiol 2015; 42:883-904. [DOI: 10.3109/1040841x.2015.1087380] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Antizar-Ladislao B, Bhattacharya BD, Ray Chaudhuri S, Sarkar SK. Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment. MARINE POLLUTION BULLETIN 2015; 99:104-111. [PMID: 26231062 DOI: 10.1016/j.marpolbul.2015.07.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/19/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure.
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Affiliation(s)
| | - B D Bhattacharya
- Department of Marine Science, University of Calcutta, 35 Ballygunge Circular Road, Calcutta 700019, India
| | - S Ray Chaudhuri
- West Bengal University of Technology, BF 142, Sector I, Salt Lake, Calcutta 700064, India
| | - S K Sarkar
- Department of Marine Science, University of Calcutta, 35 Ballygunge Circular Road, Calcutta 700019, India
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