1
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Carlsen ECL, Hjelset S, Gomes T, Igartua A, Sørensen L, Booth AM, Hylland K, Eiler A. Synthetic and natural rubber associated chemicals drive functional and structural changes as well as adaptations to antibiotics in in vitro marine microbiomes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116134. [PMID: 38387143 DOI: 10.1016/j.ecoenv.2024.116134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
The leaching of additives from plastics and elastomers (rubbers) has raised concerns due to their potential negative impacts on the environment and the development of antibiotic resistance. In this study, we investigated the effects of chemicals extracted from two types of rubber on microbiomes derived from a benthic sea urchin and two pelagic fish species. Additionally, we examined whether bacterial communities preconditioned with rubber-associated chemicals displayed adaptations to antibiotics. At the highest tested concentrations of chemicals, we observed reduced maximum growth rates and yields, prolonged lag phases, and increased alpha diversity. While the effects on alpha and beta diversity were not always conclusive, several bacterial genera were significantly influenced by chemicals from the two rubber sources. Subsequent exposure of sea urchin microbiomes preconditioned with rubber chemicals to the antibiotic ciprofloxacin resulted in decreased maximum growth rates. This indicates a more sensitive microbiome to ciprofloxacin when preconditioned with rubber chemicals. Although no significant interaction effects between rubber chemicals and ciprofloxacin exposure were observed in bacterial alpha and beta diversity, we observed log-fold changes in two bacterial genera in response to ciprofloxacin exposure. These findings highlight the structural and functional alterations in microbiomes originating from various marine species when exposed to rubber-associated chemicals and underscore the potential risks posed to marine life.
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Affiliation(s)
- Eira Catharine Lødrup Carlsen
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway
| | - Sverre Hjelset
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway; Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Økernveien 94, Oslo 0579, Norway
| | - Tânia Gomes
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Økernveien 94, Oslo 0579, Norway
| | - Amaia Igartua
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Lisbet Sørensen
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Andy M Booth
- Department of Climate and Environment, SINTEF Ocean, SINTEF Sealab, Brattørkaia 17C, Trondheim 7010, Norway
| | - Ketil Hylland
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway
| | - Alexander Eiler
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo 0371, Norway.
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2
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Bharali P, Gogoi B, Sorhie V, Acharjee SA, Walling B, Alemtoshi, Vishwakarma V, Shah MP. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments. Biodegradation 2024; 35:1-46. [PMID: 37436665 DOI: 10.1007/s10532-023-10042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023]
Abstract
Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.
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Affiliation(s)
- Pranjal Bharali
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India.
| | - Bhagyudoy Gogoi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Viphrezolie Sorhie
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Shiva Aley Acharjee
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Bendangtula Walling
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Alemtoshi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Galgotias University, Greater Noida, NCR Delhi, India
| | - Maulin Pramod Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India
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3
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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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4
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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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5
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Hung H, Halsall C, Ball H, Bidleman T, Dachs J, De Silva A, Hermanson M, Kallenborn R, Muir D, Sühring R, Wang X, Wilson S. Climate change influence on the levels and trends of persistent organic pollutants (POPs) and chemicals of emerging Arctic concern (CEACs) in the Arctic physical environment - a review. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1577-1615. [PMID: 35244108 DOI: 10.1039/d1em00485a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Climate change brings about significant changes in the physical environment in the Arctic. Increasing temperatures, sea ice retreat, slumping permafrost, changing sea ice regimes, glacial loss and changes in precipitation patterns can all affect how contaminants distribute within the Arctic environment and subsequently impact the Arctic ecosystems. In this review, we summarized observed evidence of the influence of climate change on contaminant circulation and transport among various Arctic environment media, including air, ice, snow, permafrost, fresh water and the marine environment. We have also drawn on parallel examples observed in Antarctica and the Tibetan Plateau, to broaden the discussion on how climate change may influence contaminant fate in similar cold-climate ecosystems. Significant knowledge gaps on indirect effects of climate change on contaminants in the Arctic environment, including those of extreme weather events, increase in forests fires, and enhanced human activities leading to new local contaminant emissions, have been identified. Enhanced mobilization of contaminants to marine and freshwater ecosystems has been observed as a result of climate change, but better linkages need to be made between these observed effects with subsequent exposure and accumulation of contaminants in biota. Emerging issues include those of Arctic contamination by microplastics and higher molecular weight halogenated natural products (hHNPs) and the implications of such contamination in a changing Arctic environment is explored.
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Affiliation(s)
- Hayley Hung
- Air Quality Processes Research Section, Environment and Climate Change Canada, 4905 Dufferin Street, Toronto, Ontario M5P 1W4, Canada.
| | - Crispin Halsall
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Hollie Ball
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Terry Bidleman
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - Jordi Dachs
- Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDAEA-CSIC), Barcelona, Catalonia 08034, Spain
| | - Amila De Silva
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7S 1A1, Canada
| | - Mark Hermanson
- Hermanson & Associates LLC, 2000 W 53rd Street, Minneapolis, Minnesota 55419, USA
| | - Roland Kallenborn
- Department of Arctic Technology, University Centre in Svalbard (UNIS), Longyearbyen, 9171, Norway
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås, 1432, Norway
| | - Derek Muir
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7S 1A1, Canada
| | - Roxana Sühring
- Department for Environmental Science, Stockholm University, 114 19 Stockholm, Sweden
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario M5B 2K3, Canada
| | - Xiaoping Wang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon Wilson
- Arctic Monitoring and Assessment Programme Secretariat, The Fram Centre, 9296 Tromsø, Norway
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Vila-Costa M, Lundin D, Casamayor EO, Meijer SN, Fernández P, Dachs J. Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119592. [PMID: 35688389 DOI: 10.1016/j.envpol.2022.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/20/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.
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Affiliation(s)
- Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain.
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Sweden
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes, CEAB-CSIC, Blanes, Catalunya, Spain
| | - Sandra N Meijer
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pilar Fernández
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
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7
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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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8
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Wu JY, Hua ZL, Gu L, Li XQ, Gao C, Liu YY. Perfluorinated compounds (PFCs) in regional industrial rivers: Interactions between pollution flux and eukaryotic community phylosymbiosis. ENVIRONMENTAL RESEARCH 2022; 203:111876. [PMID: 34400162 DOI: 10.1016/j.envres.2021.111876] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Perfluorinated compounds (PFCs) pose serious threats to aquatic ecosystems, especially their microbial communities. However, little is known about the phylosymbiosis of aquatic fungal and viridiplantae communities in response to PFC accumulation. We quantified the distribution of 14 PFCs in rivers and found that PFBA was dominant in the transition from water to sediment. High through-put sequencing revealed that phyla Ascomycota, Basidiomycota, Anthophyta, and Chlorophyta were the predominant in eukaryotic community. The effects of PFCs on spatial community coalescence at taxonomic and phylogenetic levels (p < 0.05) were revealed. Fungal community coalescence triggered the spatial assembly of fungal and viridiplantae communities in riverine environments (p < 0.05). Null modeling indicated that PFBA, PFTrDA and PFOS, etc, mediated phylogenetic assembly (p < 0.05) and stochastic processes (86.67-100%) maintain phylogenetic turnover in the fungal community. Meanwhile, variable selection (27.78-54.44%) explained the viridiplantae community assemblage. Finally, we identified fungal genera Hannaella, Naganishia, Purpureocillium and Stachybotrys as indicators for PFC pollution (p < 0.001). These results help explain the effects of PFCs on riverine ecological remediation.
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Affiliation(s)
- Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
| | - Xiao-Qing Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Chang Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Yuan-Yuan Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
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9
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Cerro-Gálvez E, Dachs J, Lundin D, Fernández-Pinos MC, Sebastián M, Vila-Costa M. Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9609-9621. [PMID: 33606522 PMCID: PMC8491159 DOI: 10.1021/acs.est.0c07262] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 05/23/2023]
Abstract
Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Jordi Dachs
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Daniel Lundin
- Centre
for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar 35195, Sweden
| | | | - Marta Sebastián
- Department
of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya 08003, Spain
| | - Maria Vila-Costa
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
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10
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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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11
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Yap HS, Zakaria NN, Zulkharnain A, Sabri S, Gomez-Fuentes C, Ahmad SA. Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation. BIOLOGY 2021; 10:biology10050354. [PMID: 33922046 PMCID: PMC8143585 DOI: 10.3390/biology10050354] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions. Abstract The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.
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Affiliation(s)
- How Swen Yap
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence:
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12
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Brunel C, Pouteau R, Dawson W, Pester M, Ramirez KS, van Kleunen M. Towards Unraveling Macroecological Patterns in Rhizosphere Microbiomes. TRENDS IN PLANT SCIENCE 2020; 25:1017-1029. [PMID: 32467065 DOI: 10.1016/j.tplants.2020.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 05/26/2023]
Abstract
It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales.
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Affiliation(s)
- Caroline Brunel
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; IRD, IPME, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France.
| | - Robin Pouteau
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; AMAP, IRD, CNRS, CIRAD, INRA, Université de Montpellier, 34398 Montpellier Cedex 05, France
| | - Wayne Dawson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Michael Pester
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany; Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, 38106 Braunschweig, Germany
| | - Kelly S Ramirez
- Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; University of Texas at El Paso, Department of Biological Sciences, 500 W University Ave, El Paso, TX 79968, USA
| | - Mark van Kleunen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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13
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Martinez-Varela A, Casas G, Piña B, Dachs J, Vila-Costa M. Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica). Front Microbiol 2020; 11:571983. [PMID: 33013806 PMCID: PMC7516020 DOI: 10.3389/fmicb.2020.571983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/14/2020] [Indexed: 01/04/2023] Open
Abstract
The composition of bacteria inhabiting the sea-surface microlayer (SML) is poorly characterized globally and yet undescribed for the Southern Ocean, despite their relevance for the biogeochemistry of the surface ocean. We report the abundances and diversity of bacteria inhabiting the SML and the subsurface waters (SSL) determined from a unique sample set from a polar coastal ecosystem (Livingston Island, Antarctica). From early to late austral summer (January–March 2018), we consistently found a higher abundance of bacteria in the SML than in the SSL. The SML was enriched in some Gammaproteobacteria genus such as Pseudoalteromonas, Pseudomonas, and Colwellia, known to degrade a wide range of semivolatile, hydrophobic, and surfactant-like organic pollutants. Hydrocarbons and other synthetic chemicals including surfactants, such as perfluoroalkyl substances (PFAS), reach remote marine environments by atmospheric transport and deposition and by oceanic currents, and are known to accumulate in the SML. Relative abundances of specific SML-enriched bacterial groups were significantly correlated to concentrations of PFASs, taken as a proxy of hydrophobic anthropogenic pollutants present in the SML and its stability. Our observations provide evidence for an important pollutant-bacteria interaction in the marine SML. Given that pollutant emissions have increased during the Anthropocene, our results point to the need to assess chemical pollution as a factor modulating marine microbiomes in the contemporaneous and future oceans.
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Affiliation(s)
- Alícia Martinez-Varela
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Gemma Casas
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
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14
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Anthropogenic dissolved organic carbon and marine microbiomes. ISME JOURNAL 2020; 14:2646-2648. [PMID: 32647311 DOI: 10.1038/s41396-020-0712-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/12/2020] [Accepted: 06/30/2020] [Indexed: 11/08/2022]
Abstract
Thousands of synthetic chemicals and hydrocarbons are released to the marine environment composing the anthropogenic dissolved organic carbon (ADOC). Most ADOC is disproportionally hydrophobic, and consequently, its concentrations in the cell membranes are between a thousand and hundred million fold higher than those in the dissolved phase. Marine microorganisms respond to ADOC by multiple strategies ranging from ADOC degradation to detoxifying metabolisms. We argue that the increasing concentrations of ADOC in the oceans deriving from rivers, atmospheric deposition, and plastic leachates can have an effect on the health of the oceans and influence the major biogeochemical cycles, thus influencing the Earth system during the Anthropocene.
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15
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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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16
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Montgomery MT, Boyd TJ, Hall NS, Paerl HW, Osburn CL. Ecosystem Capacity for Microbial Biodegradation of Munitions Compounds and Phenanthrene in Three Coastal Waterways in North Carolina, United States. ACS OMEGA 2020; 5:7326-7341. [PMID: 32280874 PMCID: PMC7144167 DOI: 10.1021/acsomega.9b04188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
Munitions compounds (i.e., 2,4,6-trinitrotoluene (TNT), octahy-dro-1,3,5,7-tetranitro-1,3,5,7-tetrazocin (HMX), and hexadydro-1,3,5-trinitro-1,3,5-triazin (RDX), also called energetics) were originally believed to be recalcitrant to microbial biodegradation based on historical groundwater chemical attenuation data and laboratory culture work. More recently, it has been established that natural bacterial assemblages in coastal waters and sediment can rapidly metabolize these organic nitrogen sources and even incorporate their carbon and nitrogen into bacterial biomass. Here, we report on the capacity of natural microbial assemblages in three coastal North Carolina (United States) estuaries to metabolize energetics and phenanthrene (PHE), a proxy for terrestrial aromatic compounds. Microbial assemblages generally had the highest ecosystem capacity (mass of the compound mineralized per average estuarine residence time) for HMX (21-5463 kg) > RDX (1.4-5821 kg) ≫ PHE (0.29-660 kg) > TNT (0.25-451 kg). Increasing antecedent precipitation tended to decrease the ecosystem capacity to mineralize TNT in the Newport River Estuary, and PHE and TNT mineralization were often highest with increasing salinity. There was some evidence from the New River Estuary that increased N-demand (due to a phytoplankton bloom) is associated with increased energetic mineralization rates. Using this type of analysis to determine the ecosystem capacity to metabolize energetics can explain why these compounds are rarely detected in seawater and marine sediment, despite the known presence of unexploded ordnance or recent use in military training exercises. Overall, measuring the ecosystem capacity may help predict the effects of climate change (warming and altered precipitation patterns) and other perturbations on exotic compound fate and transport within ecosystems and provide critical information for managers and decision-makers to develop management strategies based on these changes.
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Affiliation(s)
- Michael T. Montgomery
- Chemistry
Division, Naval Research Laboratory, 4555 Overlook Avenue Southwest, Washington, District of Columbia 20375, United States
| | - Thomas J. Boyd
- Chemistry
Division, Naval Research Laboratory, 4555 Overlook Avenue Southwest, Washington, District of Columbia 20375, United States
| | - Nathan S. Hall
- Institute
of Marine Sciences, University of North
Carolina, Morehead City, North Carolina 28557, United States
| | - Hans W. Paerl
- Institute
of Marine Sciences, University of North
Carolina, Morehead City, North Carolina 28557, United States
| | - Christopher L. Osburn
- Department
of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
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17
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Cerro-Gálvez E, Roscales JL, Jiménez B, Sala MM, Dachs J, Vila-Costa M. Microbial responses to perfluoroalkyl substances and perfluorooctanesulfonate (PFOS) desulfurization in the Antarctic marine environment. WATER RESEARCH 2020; 171:115434. [PMID: 31927092 DOI: 10.1016/j.watres.2019.115434] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 05/27/2023]
Abstract
Perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) acids are ubiquitous in the oceans, including remote regions, and are toxic to fish and mammals. The impact to the lowest trophic levels of the food web, however, remains unknown. We challenged natural bacterial communities inhabiting Antarctic coastal waters (Deception Island) with PFOS and PFOA concentrations ranging from 2 ng/L to 600 ng/L that selected for tolerant taxa. After 48 h, concentrations of PFOS decreased by more than 50% and sulfur metabolism-related transcripts were significantly enriched in the treatments suggesting desulfurization of PFOS. Conversely, no significant differences were found between initial and final PFOA concentrations. Gammaproteobacteria and Roseobacter, two abundant groups of marine bacteria, increased their relative activity after 24 h of incubation, whereas Flavobacteriia became the main contributor in the treatments after 6 days. Community activities (extracellular enzyme activity and absolute number of transcripts) were higher in the treatments than in the controls, while bacterial abundances were lower in the treatments, suggesting a selection of PFOS and PFOA tolerant community in the exposed treatments. Our results show a direct effect of PFOS and PFOA exposure on the composition and functionality of natural Antarctic marine microbial communities. While no evidence of defluorination of PFOS or PFOA was detected, probable desulfurization of PFOS depicts a direct link with the sulfur biogeochemistry of the ocean.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalunya, Spain
| | - Jose L Roscales
- Department of Instrumental Analysis and Environmental Chemistry, Institute of Organic Chemistry, (IQOG-CSIC), Madrid, Spain
| | - Begoña Jiménez
- Department of Instrumental Analysis and Environmental Chemistry, Institute of Organic Chemistry, (IQOG-CSIC), Madrid, Spain
| | - M Montserrat Sala
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-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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18
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Pascoal F, Magalhães C, Costa R. The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Front Microbiol 2020; 11:231. [PMID: 32140148 PMCID: PMC7042395 DOI: 10.3389/fmicb.2020.00231] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022] Open
Abstract
Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.
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Affiliation(s)
- Francisco Pascoal
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science & Engineering, University of Waikato, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Halitax, NS, Canada
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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19
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Krolicka A, Boccadoro C, Nilsen MM, Demir-Hilton E, Birch J, Preston C, Scholin C, Baussant T. Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:133715. [PMID: 31470316 DOI: 10.1016/j.scitotenv.2019.133715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
In this paper, a molecular analytical approach for detecting hydrocarbonoclastic bacteria in water is suggested as a proxy measurement for tracking petroleum discharges in industrialized or pristine aquatic environments. This approach is tested for general application in cold marine regions (freezing to 5 °C). We used amplicon sequencing and qPCR to quantify 16S rRNA and GyrB genes from oleophilic bacteria in seawater samples from two different crude oil enrichments. The first experiment was conducted in a controlled environment using laboratory conditions and natural North Sea fjord seawater (NSC) at a constant temperature of 5 °C. The second was performed in the field with natural Arctic seawater (ARC) and outdoor temperature conditions from -7 °C to around 4 °C. Although the experimental conditions for NSC and ARC differed, the temporal changes in bacterial communities were comparable and reflected oil biotransformation processes. The common bacterial OTUs for NSC and ARC had the highest identity to Colwellia rossensis and Oleispira antarctica rRNA sequences and were enriched within a few days in both conditions. Other typical oil degrading bacteria such as Alcanivorax (n-alkane degrader) and Cycloclasticus (polycyclic aromatic hydrocarbons degrader) were rapidly enriched only in NSC conditions. Both the strong correlation between Oleispira SSU gene copies and oil concentration, and the specificity of the Oleispira assay suggest that this organism is a robust bioindicator for seawater contaminated by petroleum in cold water environments. Further optimization for automation of the Oleispira assay for in situ analysis with a genosensing device is underway. The assay for Colwellia quantification requires more specificity to fewer Colwellia OTUs and a well-established dose-response relationship before those taxa are used for oil tracking purposes.
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Affiliation(s)
- Adriana Krolicka
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway.
| | - Catherine Boccadoro
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| | - Mari Mæland Nilsen
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| | - Elif Demir-Hilton
- Monterey Bay Aquarium Research Institute, Sandholdt Road, Moss Landing, CA, USA
| | - Jim Birch
- Monterey Bay Aquarium Research Institute, Sandholdt Road, Moss Landing, CA, USA
| | - Christina Preston
- Monterey Bay Aquarium Research Institute, Sandholdt Road, Moss Landing, CA, USA
| | - Chris Scholin
- Monterey Bay Aquarium Research Institute, Sandholdt Road, Moss Landing, CA, USA
| | - Thierry Baussant
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
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20
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González-Gaya B, Casal P, Jurado E, Dachs J, Jiménez B. Vertical transport and sinks of perfluoroalkyl substances in the global open ocean. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1957-1969. [PMID: 31393489 DOI: 10.1039/c9em00266a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ubiquitous occurrence of perfluoroalkyl substances (PFAS) in the open ocean has been previously documented, but their vertical transport and oceanic sinks have not been comprehensively characterized and quantified at the oceanic scale. During the Malaspina 2010 circumnavigation expedition, 21 PFAS were measured at the surface and at the deep chlorophyll maximum (DCM) in the Atlantic, Indian and Pacific oceans. In this work, we report an extended data set of PFAS dissolved phase concentrations at the DCM. ∑PFAS at the DCM varied from 130 to 11 000 pg L-1, with a global average value of 500 pg L-1. Perfluorooctanesulfonate (PFOS) abundance contributed 39% of ∑PFAS, followed by perfluorodecanoate (PFDA, 17%), and perfluorohexanoate (PFHxA, 12%). The relative contribution of the remaining compounds was below 10%, with perfluorooctanoate (PFOA) contributing only 5% to PFAS measured at the DCM. Estimates of vertical diffusivity, derived from microstructure turbulence observations in the upper (<300 m) water column, allowed the derivation of PFAS eddy diffusive fluxes from concurrent field measurements of eddy diffusivity and PFAS concentrations. The PFAS concentrations at the DCM predicted from an eddy diffusivity model were lower than field-measured concentrations, suggesting a relevant role of other vertical transport mechanisms. Settling fluxes of organic matter bound PFAS (biological pump), oceanic circulation and potential, yet un-reported, biological transformations are discussed.
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Affiliation(s)
- Belén González-Gaya
- Department of Instrumental Analysis and Environmental Chemistry, Institute of Organic Chemistry (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain. and Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain and Department of Analytical Chemistry, Plentzia Marine Station of the University of the Basque Country (EHU/UPV), Areatza Pasealekua 47, 48620 Plentzia, Basque Country, Spain
| | - Paulo Casal
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Elena Jurado
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain and Engineering Department, La Salle Campus Barcelona, Ramon Llull University (URL), Sant Joan de la Salle, 42, 08022 Barcelona, Catalonia, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Begoña Jiménez
- Department of Instrumental Analysis and Environmental Chemistry, Institute of Organic Chemistry (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
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21
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Karlsson CMG, Cerro‐Gálvez E, Lundin D, Karlsson C, Vila‐Costa M, Pinhassi J. Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341. Microb Biotechnol 2019; 12:892-906. [PMID: 31270938 PMCID: PMC6680617 DOI: 10.1111/1751-7915.13441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 11/29/2022] Open
Abstract
Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.
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Affiliation(s)
- Christofer M. G. Karlsson
- Centre for Ecology and Evolution in Microbial Model SystemsEEMiSLinnaeus UniversityStuvaregatan 4Kalmar39231Sweden
| | - Elena Cerro‐Gálvez
- Department of Environmental ChemistryIDAEA‐CSICJordi Girona 18‐26Barcelona08034CatalunyaSpain
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model SystemsEEMiSLinnaeus UniversityStuvaregatan 4Kalmar39231Sweden
| | - Camilla Karlsson
- Centre for Ecology and Evolution in Microbial Model SystemsEEMiSLinnaeus UniversityStuvaregatan 4Kalmar39231Sweden
| | - Maria Vila‐Costa
- Department of Environmental ChemistryIDAEA‐CSICJordi Girona 18‐26Barcelona08034CatalunyaSpain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model SystemsEEMiSLinnaeus UniversityStuvaregatan 4Kalmar39231Sweden
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Cerro-Gálvez E, Sala MM, Marrasé C, Gasol JM, Dachs J, Vila-Costa M. Modulation of microbial growth and enzymatic activities in the marine environment due to exposure to organic contaminants of emerging concern and hydrocarbons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 678:486-498. [PMID: 31077927 DOI: 10.1016/j.scitotenv.2019.04.361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 05/06/2023]
Abstract
Organic pollutants are continuously being introduced in seawater with uncharacterized impacts on the engines of the marine biogeochemical cycles, the microorganisms. The effects on marine microbial communities were assessed for perfluoroalkyl substances, organophosphate esters flame retardants and plasticizers, polycyclic aromatic hydrocarbons, and n-alkanes. Dose-response experiments were performed at three stations and at three depths in the NW Mediterranean with contrasted nutrient and pollutant concentrations. In these experiments, the microbial growth rates, the abundances of the main bacterial groups, measured by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH), and extracellular enzymatic activities, were quantified. Increasing concentrations of organic pollutants (OPs) promoted different responses in the communities that were compound, organism and nutrient availability (trophic status). The largest differences between OP treatments and controls in the growth rates of both heterotrophic and phototrophic microbial groups were observed in seawater from the deep chlorophyll maxima. Furthermore, there was a compound specific stimulation of different extracellular enzymatic activities after the exposure to OPs. Our results revealed that marine microbial communities reacted not only to hydrocarbons, known to be used as a carbon source, but also to low concentrations of organic pollutants of emerging concern in a complex manner, reflecting the variability of various environmental variables. Multiple linear regressions suggested that organic pollutants modulated the bacterial growth and extracellular enzymatic activities, but this modulation was of lower magnitude than the observed pronounced response of the microbial community to nutrient availability.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Department of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Cèlia Marrasé
- Department of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain.
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