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Howe KL, Zaugg J, Mason OU. Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean. Appl Environ Microbiol 2024; 90:e0122424. [PMID: 39177328 PMCID: PMC11409719 DOI: 10.1128/aem.01224-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.
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Affiliation(s)
- Kathryn L. Howe
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Olivia U. Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
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2
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Harrison SJ, Malkin SY, Joye SB. Dispersant addition, but not nutrients, stimulated blooms of multiple hydrocarbonoclastic genera in nutrient-replete coastal marine surface waters. MARINE POLLUTION BULLETIN 2024; 204:116490. [PMID: 38843703 DOI: 10.1016/j.marpolbul.2024.116490] [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: 12/03/2023] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/17/2024]
Abstract
The range of impacts of chemical dispersants on indigenous marine microbial communities and their activity remains poorly constrained. We tested the response of nearshore surface waters chronically exposed to oil leakage from a downed platform and supplied with nutrients by the Mississippi River to Corexit dispersant and nutrient additions. As assessed using 14C-labeled tracers, hexadecane mineralization potential was orders of magnitude higher in all unamended samples than in previously assessed bathypelagic communities. Nutrient additions stimulated microbial mortality but did not affect community composition and had no generalizable effect on hydrocarbon mineralization potential. By contrast, Corexit amendments caused a rapid shift in community composition and a drawdown of inorganic nitrogen and orthophosphate though no generalizable effect on hydrocarbon mineralization potential. The hydrocarbonoclastic community's response to dispersants is largely driven by the relative availability of organic substrates and nutrients, underscoring the role of environmental conditions and multiple interacting stressors on hydrocarbon degradation potential.
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Affiliation(s)
- Sarah J Harrison
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Sairah Y Malkin
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.
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3
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Muhammad R, Boothman C, Song H, Lloyd JR, van Dongen BE. Assessing the impacts of oil contamination on microbial communities in a Niger Delta soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171813. [PMID: 38513868 DOI: 10.1016/j.scitotenv.2024.171813] [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: 12/08/2023] [Revised: 02/22/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
Oil spills are a global challenge, contaminating the environment with organics and metals known to elicit toxic effects. Ecosystems within Nigeria's Niger Delta have suffered from prolonged severe spills for many decades but the level of impact on the soil microbial community structure and the potential for contaminant bioremediation remains unclear. Here, we assessed the extent/impact of an oil spill in this area 6 months after the accident on both the soil microbial community/diversity and the distribution of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDGNα) genes, responsible for encoding enzymes involved in the degradation of PAHs, across the impacted area. Analyses confirmed the presence of oil contamination, including metals such as Cr and Ni, across the whole impacted area and at depth. The contamination impacted on the microbial community composition, resulting in a lower diversity in all contaminated soils. Gamma-, Delta-, Alpha- proteobacteria and Acidobacteriia dominated 16S rRNA gene sequences across the contaminated area, while Ktedonobacteria dominated the non-contaminated soils. The PAH-RHDαGN genes were only detected in the contaminated area, highlighting a clear relationship with the oil contamination/hydrocarbon metabolism. Correlation analysis indicated significant positive relationships between the oil contaminants (organics, Cr and Ni), PAH-RHDαGN gene, and the presence of bacteria/archaea such as Anaerolinea, Spirochaetia Bacteroidia Thermoplasmata, Methanomicrobia, and Methanobacteria indicating that the oil contamination not only impacted the microbial community/diversity present, but that the microbes across the impacted area and at depth were potentially playing an important role in degrading the oil contamination present. These findings provide new insights on the level of oil contamination remaining 6 months after an oil spill, its impacts on indigenous soil microbial communities and their potential for in situ bioremediation within a Niger Delta's ecosystem. It highlights the strength of using a cross-disciplinary approach to assess the extent of oil pollution in a single study.
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Affiliation(s)
- Rakiya Muhammad
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, University of Manchester, M13 9PL, UK
| | - Christopher Boothman
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, University of Manchester, M13 9PL, UK
| | - Hokyung Song
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, University of Manchester, M13 9PL, UK
| | - Bart E van Dongen
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, University of Manchester, M13 9PL, UK.
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4
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Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
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Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
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5
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Zhong S, Feng J, Kong J, Huang Y, Chen X, Zhang S. Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep. Microorganisms 2023; 11:3001. [PMID: 38138145 PMCID: PMC10745737 DOI: 10.3390/microorganisms11123001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.
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Affiliation(s)
- Song Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
| | - Jingchun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Kong
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yongji Huang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiao Chen
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Si Zhang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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6
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Arrington EC, Tarn J, Kittner HE, Kivenson V, Liu RM, Valentine DL. Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov). Environ Microbiol 2023; 25:2958-2971. [PMID: 37599091 DOI: 10.1111/1462-2920.16474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.
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Affiliation(s)
- Eleanor C Arrington
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Jonathan Tarn
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Hailie E Kittner
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, USA
| | - Rachel M Liu
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - David L Valentine
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California-Santa Barbara, Santa Barbara, California, USA
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7
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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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8
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Vogel AL, Thompson KJ, Straub D, App CB, Gutierrez T, Löffler FE, Kleindienst S. Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation. Front Microbiol 2023; 14:1185619. [PMID: 37455737 PMCID: PMC10338962 DOI: 10.3389/fmicb.2023.1185619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10-2, 1.80 × 10-3, and 3.20 × 10-3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10-1). The other marker genes-rhd3α and pahE-were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.
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Affiliation(s)
- Anjela L. Vogel
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Katharine J. Thompson
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Constantin B. App
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Sara Kleindienst
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
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9
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Zhou Y, Wang Y, Yang L, Kong Q, Zhang H. Microbial degradation mechanisms of surface petroleum contaminated seawater in a typical oil trading port. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121420. [PMID: 36906058 DOI: 10.1016/j.envpol.2023.121420] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/14/2023] [Accepted: 03/04/2023] [Indexed: 05/25/2023]
Abstract
Petroleum hydrocarbons are significant new persistent organic pollutants for marine oil spill risk areas. Oil trading ports, in turn, have become major bearers of the risk of offshore oil pollution. However, studies on the molecular mechanisms of microbial degradation of petroleum pollutants by natural seawater are limited. Here, an in situ microcosm study was conducted. Combined with metagenomics, differences in metabolic pathways and in the gene abundances of total petroleum hydrocarbons (TPH) are revealed under different conditions. About 88% degradation of TPH was shown after 3 weeks of treatment. The positive responders to TPH were concentrated in the genera Cycloclasticus, Marivita and Sulfitobacter of the orders Rhodobacterales and Thiotrichales. The genera Marivita, Roseobacter, Lentibacter and Glaciecola were key degradation species when mixing dispersants with oil, and all of the above are from the Proteobacteria phylum. The analysis showed that the biodegradability of aromatic compounds, polycyclic aromatic hydrocarbon and dioxin were enhanced after the oil spill, and genes with higher abundances of bphAa, bsdC, nahB, doxE and mhpD were found, but the photosynthesis-related mechanism was inhibited. The dispersant treatment effectively stimulated the microbial degradation of TPH and then accelerated the succession of microbial communities. Meanwhile, functions such as bacterial chemotaxis and carbon metabolism (cheA, fadeJ and fadE) were better developed, but the degradation of persistent organic pollutants such as polycyclic aromatic hydrocarbons was weakened. Our study provides insights into the metabolic pathways and specific functional genes for oil degradation by marine microorganisms and will help improve the application and practice of bioremediation.
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Affiliation(s)
- Yumiao Zhou
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Likun Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan, 250000, China.
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10
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Gofstein TR, Leigh MB. Metatranscriptomic shifts suggest shared biodegradation pathways for Corexit 9500 components and crude oil in Arctic seawater. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:51-59. [PMID: 36177554 PMCID: PMC10103760 DOI: 10.1111/1758-2229.13127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 09/12/2022] [Indexed: 05/20/2023]
Abstract
While the genes and pathways responsible for petroleum biodegradation in marine environments have received substantial attention, considerably less is known about those active in the biodegradation of the commonly applied chemical dispersant Corexit 9500. Yet, their fate in the Arctic marine environment is an increasingly important unknown. To elucidate the genes and pathways active in the biodegradation of oil and dispersants, we performed metatranscriptomic sequencing on microbial communities in Arctic seawater exposed to oil, Corexit, or both for 0, 5, and 30 days in a mesocosm incubation experiment. While oil and Corexit stimulated significantly different metatranscriptomic profiles overall, both enriched a suite of fatty acid degradation gene transcripts. Based on the gene transcripts observed and the chemical structures of Corexit 9500 surfactant components, we propose a hypothetical pathway for Corexit surfactant biodegradation in which surfactant ester groups are transformed into fatty acids that are then funnelled into the β-oxidation fatty acid degradation pathway. Several microbial taxa within Oceanospirillales, Pseudomonadales, and Alteromonadales were associated with either oil-only or Corexit-only exposure, potentially implicating them in the degradation of these mixtures. Metabolic gene transcripts were associated with diverse gammaproteobacterial lineages, with many genera exhibiting functional redundancy. These findings offer new insight into the potential genes, pathways, and microbial consortia involved in the biodegradation of Corexit 9500 in the Arctic marine environment.
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Affiliation(s)
- Taylor R. Gofstein
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAlaskaUSA
- Department of Chemistry & BiochemistryUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Mary Beth Leigh
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAlaskaUSA
- Department of Biology and WildlifeUniversity of Alaska FairbanksFairbanksAlaskaUSA
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11
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Ganesan M, Mani R, Sai S, Kasivelu G, Awasthi MK, Rajagopal R, Wan Azelee NI, Selvi PK, Chang SW, Ravindran B. Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes. CHEMOSPHERE 2022; 303:134956. [PMID: 35588873 DOI: 10.1016/j.chemosphere.2022.134956] [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: 03/18/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.
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Affiliation(s)
- Mirunalini Ganesan
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Ravi Mani
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Sakthinarenderan Sai
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Govindaraju Kasivelu
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, PR China.
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Nur Izyan Wan Azelee
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, 81310, Johor, Malaysia
| | - P K Selvi
- Central Pollution Control Board, Nisarga Bhawan, Shivanagar, Bengaluru, India
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea; Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602 105, Tamil Nadu, India.
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12
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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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13
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Gaur VK, Gautam K, Sharma P, Gupta P, Dwivedi S, Srivastava JK, Varjani S, Ngo HH, Kim SH, Chang JS, Bui XT, Taherzadeh MJ, Parra-Saldívar R. Sustainable strategies for combating hydrocarbon pollution: Special emphasis on mobil oil bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155083. [PMID: 35395309 DOI: 10.1016/j.scitotenv.2022.155083] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 05/21/2023]
Abstract
The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.
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Affiliation(s)
- Vivek Kumar Gaur
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea; Centre for Energy and Environmental Sustainability, Lucknow, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Krishna Gautam
- Centre for Energy and Environmental Sustainability, Lucknow, India
| | - Poonam Sharma
- Department of Bioengineering, Integral University, Lucknow, India
| | - Pallavi Gupta
- Bioscience and Biotechnology Department, Banasthali University, Rajasthan, India
| | | | | | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382 010, India.
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Xuan-Thanh Bui
- Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Viet Nam; Key Laboratory of Advanced Waste Treatment Technology, Vietnam National University Ho Chi Minh (VNU-HCM), Linh Trung ward, Thu Duc district, Ho Chi Minh City 700000, Viet Nam
| | | | - Roberto Parra-Saldívar
- Escuela de Ingeniería y Ciencias-Centro de Biotecnología-FEMSA, Tecnológico de Monterrey, Campus Monterrey, Mexico
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14
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Cabral L, Giovanella P, Pellizzer EP, Teramoto EH, Kiang CH, Sette LD. Microbial communities in petroleum-contaminated sites: Structure and metabolisms. CHEMOSPHERE 2022; 286:131752. [PMID: 34426136 DOI: 10.1016/j.chemosphere.2021.131752] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
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Affiliation(s)
- Lucélia Cabral
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Patricia Giovanella
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elias Hideo Teramoto
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Chang Hung Kiang
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara Durães Sette
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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15
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Nanjappa D, Liang Y, Bretherton L, Brown C, Quigg A, Irwin AJ, Finkel ZV. Contrasting transcriptomic responses of a microbial eukaryotic community to oil and dispersant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 288:117774. [PMID: 34274645 DOI: 10.1016/j.envpol.2021.117774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Dispersants can aid dispersion and biodegradation of oil in seawater, but the wider ecotoxicological effects of oil and dispersant to the base of marine food webs is unclear. Here we apply a metatranscriptomic approach to identify molecular responses of a natural marine microbial eukaryotic community to oil and chemically dispersed oil. Oil exposure stimulated the upregulation of ketogenesis in the eukaryotic community, which may alleviate carbon- and energy-limitation and reduce oxidative stress. In contrast, a chemically dispersed oil treatment stimulated eukaryotic genes and pathways consistent with nitrogen and oxygen depletion. These results suggest that the addition of dispersant may elevate bacterial biodegradation of crude oil, indirectly increasing competition for nitrogen between prokaryotic and eukaryotic communities as oxygen consumption induces bacterial anaerobic respiration and denitrification. Eukaryotic microbial communities may mitigate some of the negative effects of oil exposure such as reduced photosynthesis and elevated oxidative stress, through ketosis, but the addition of dispersant to the oil fundamentally alters the environmental and ecological conditions and therefore the biochemical response of the eukaryotic community.
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Affiliation(s)
- Deepak Nanjappa
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada.
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Laura Bretherton
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Chris Brown
- Environmental Science Program, Mount Allison University, Sackville, NB, Canada
| | - Antonietta Quigg
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA
| | - Andrew J Irwin
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada; Department of Mathematics & Statistics, Dalhousie University, Halifax, NS, Canada
| | - Zoe V Finkel
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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16
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Murphy SMC, Bautista MA, Cramm MA, Hubert CRJ. Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea. Appl Environ Microbiol 2021; 87:e0080021. [PMID: 34378990 PMCID: PMC8478444 DOI: 10.1128/aem.00800-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/24/2021] [Indexed: 11/20/2022] Open
Abstract
Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.
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Affiliation(s)
- Sean M. C. Murphy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - María A. Bautista
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Margaret A. Cramm
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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17
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do Carmo Linhares D, Saia FT, Duarte RTD, Nakayama CR, de Melo IS, Pellizari VH. Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil. MICROBIAL ECOLOGY 2021; 81:954-964. [PMID: 33392629 DOI: 10.1007/s00248-020-01659-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.
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Affiliation(s)
- Débora do Carmo Linhares
- Laboratory of Industrial Biotechnology, Institute for Technological Research of São Paulo, 05508-901, São Paulo, SP, Brazil.
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil.
| | - Flávia Talarico Saia
- Institute of Marine Sciences, Federal University of São Paulo, Av. Dr. Carvalho de Mendonça, 144, Encruzilhada, Santos, SP, 11070-102, Brazil
| | - Rubens Tadeu Delgado Duarte
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Cristina Rossi Nakayama
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, Rua São Nicolau, 210, Diadema, SP, 09913-030, Brazil
| | | | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil
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18
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Michán C, Blasco J, Alhama J. High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microb Biotechnol 2021; 14:870-885. [PMID: 33559398 PMCID: PMC8085945 DOI: 10.1111/1751-7915.13763] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
| | - Julián Blasco
- Department of Ecology and Coastal ManagementICMAN‐CSICCampus Rio San PedroPuerto Real (Cádiz)E‐11510Spain
| | - José Alhama
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
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19
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Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders. Genes (Basel) 2021; 12:genes12010098. [PMID: 33466668 PMCID: PMC7828808 DOI: 10.3390/genes12010098] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
Environmental contamination by petroleum hydrocarbons is of concern due to the carcinogenicity and neurotoxicity of these compounds. Successful bioremediation of organic contaminants requires bacterial populations with degradative capacity for these contaminants. Through successive enrichment of microorganisms from a petroleum-contaminated soil using diesel fuel as the sole carbon and energy source, we successfully isolated a bacterial consortium that can degrade diesel fuel hydrocarbons. Metagenome analysis revealed the specific roles of different microbial populations involved in the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), and the metabolic pathways involved in these reactions. One hundred and five putative coding DNA sequences were identified as responsible for both the activation of BTEX and central metabolism (ring-cleavage) of catechol and alkylcatechols during BTEX degradation. The majority of the Coding DNA sequences (CDSs) were affiliated to Acidocella, which was also the dominant bacterial genus in the consortium. The inoculation of diesel fuel contaminated soils with the consortium resulted in approximately 70% hydrocarbon biodegradation, indicating the potential of the consortium for environmental remediation of petroleum hydrocarbons.
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20
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Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation. Microorganisms 2020; 9:microorganisms9010003. [PMID: 33374976 PMCID: PMC7822026 DOI: 10.3390/microorganisms9010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022] Open
Abstract
The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.
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21
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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: 11] [Impact Index Per Article: 2.8] [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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22
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Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways. mSystems 2020; 5:5/4/e00668-20. [PMID: 32843540 PMCID: PMC7449609 DOI: 10.1128/msystems.00668-20] [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] [Indexed: 12/28/2022] Open
Abstract
In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments. Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil and chemically dispersed oil in coastal and offshore surface waters from the Texas-Louisiana continental shelf. Using a combination of analytical chemistry and 16S rRNA amplicon and metatranscriptomic sequencing, we provide a broad, comparative overview of the ecological response of hydrocarbon-degrading bacteria and their expression of hydrocarbon-degrading genes in marine surface waters over time between two oceanic biomes. We found evidence for the existence of different ecotypes of several commonly described hydrocarbon-degrading bacterial taxa which behaved differentially in coastal and offshore shelf waters despite being exposed to similar concentrations of oil, dispersants, and nutrients. This resulted in the differential expression of catabolic pathways for n-alkanes and polycyclic aromatic hydrocarbons (PAHs)—the two major categories of compounds found in crude oil—with preferential expression of n-alkane degradation genes in coastal waters while offshore microbial communities trended more toward the expression of PAH degradation genes. This was unexpected as it contrasts with the generally held view that n-alkanes, being more labile, are attacked before the more refractory PAHs. Collectively, our results provide new insights into the existence and potential consequences of niche partitioning of hydrocarbon-degrading taxa between neighboring marine environments. IMPORTANCE In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.
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23
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Zhou Z, Liu Y, Pan J, Cron BR, Toner BM, Anantharaman K, Breier JA, Dick GJ, Li M. Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. ISME JOURNAL 2020; 14:3136-3148. [PMID: 32820229 DOI: 10.1038/s41396-020-00745-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
Deep-sea hydrothermal plumes are considered natural laboratories for understanding ecological and biogeochemical interactions. Previous studies focused on interactions between microorganisms and inorganic, reduced hydrothermal inputs including sulfur, hydrogen, iron, and manganese. However, little is known about transformations of organic compounds, especially methylated, sulfur-containing compounds, and petroleum hydrocarbons. Here, we reconstructed nine gammaproteobacterial metagenome-assembled genomes, affiliated with Methylococcales, Methylophaga, and Cycloclasticus, from three hydrothermal ecosystems. We present evidence that these three groups have high transcriptional activities of genes encoding cycling of C1-compounds, petroleum hydrocarbons, and organic sulfur in hydrothermal plumes. This includes oxidation of methanethiol, the simplest thermochemically-derived organic sulfur, for energy metabolism in Methylococcales and Cycloclasticus. Together with active transcription of genes for thiosulfate and methane oxidation in Methylococcales, these results suggest an adaptive strategy of versatile and simultaneous use of multiple available electron donors. Meanwhile, the first near-complete MAG of hydrothermal Methylophaga aminisulfidivorans and its transcriptional profile point to active chemotaxis targeting small organic compounds. Petroleum hydrocarbon-degrading Cycloclasticus are abundant and active in plumes of oil spills as well as deep-sea vents, suggesting that they are indigenous and effectively respond to stimulus of hydrocarbons in the deep sea. These findings suggest that these three groups of Gammaproteobacteria transform organic carbon and sulfur compounds via versatile and opportunistic metabolism and modulate biogeochemistry in plumes of hydrothermal systems as well as oil spills, thus contributing broad ecological impact to the deep ocean globally.
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Affiliation(s)
- Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Brandi R Cron
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Brandy M Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.,Department of Soil, Water, and Climate, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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24
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Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. MICROBIAL ECOLOGY 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
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Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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25
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Sala MM, Ruiz-González C, Borrull E, Azúa I, Baña Z, Ayo B, Álvarez-Salgado XA, Gasol JM, Duarte CM. Prokaryotic Capability to Use Organic Substrates Across the Global Tropical and Subtropical Ocean. Front Microbiol 2020; 11:918. [PMID: 32582044 PMCID: PMC7287293 DOI: 10.3389/fmicb.2020.00918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean.
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Affiliation(s)
- Maria Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Zuriñe Baña
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain.,Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | | | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados-Universitat de les Illes Balears, Consejo Superior de Investigaciones Científicas, Esporles, Spain
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26
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Zhao Y, Chen W, Wen D. The effects of crude oil on microbial nitrogen cycling in coastal sediments. ENVIRONMENT INTERNATIONAL 2020; 139:105724. [PMID: 32305744 DOI: 10.1016/j.envint.2020.105724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.
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Affiliation(s)
- Yanan Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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27
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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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28
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Nimnoi P, Pongsilp N. Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform. BMC Microbiol 2020; 20:19. [PMID: 31973711 PMCID: PMC6979385 DOI: 10.1186/s12866-020-1701-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
Background The total bacterial community plays an important role in aquatic ecosystems. In this study, bacterial communities and diversity along the shores of the Upper Gulf of Thailand were first characterized. The association between bacterial communities and types of land use was also evaluated. Results The bacterial communities and diversity of seawater in the Upper Gulf of Thailand, with regard to types of land use, were first revealed by using Illumina next-generation sequencing. A total of 4953 OTUs were observed from all samples in which 554 OTUs were common. The bacterial communities in sampling sites were significantly different from each other. The run-off water from three types of land use significantly affected the community richness and diversity of marine bacteria. Aquaculture sites contained the highest levels of community richness and diversity, followed by mangrove forests and tourist sites. Seawater physicochemical parameters including salinity, turbidity, TSS, total N, and BOD5, were significantly different when grouped by land use. The bacterial communities were mainly determined by salinity, total N, and total P. The species richness estimators and OTUs were positively correlated with turbidity. The top ten most abundant phyla and genera as well as the distribution of bacterial classes were characterized. The Proteobacteria constituted the largest proportions in all sampling sites, ranging between 67.31 and 78.80%. The numbers of the Marinobacterium, Neptuniibacter, Synechococcus, Candidatus Thiobios, hgcI clade (Actinobacteria), and Candidatus Pelagibacter were significantly different when grouped by land use. Conclusions Type of land use significantly affected bacterial communities and diversity along the Upper Gulf of Thailand. Turbidity was the most influential parameter affecting the variation in bacterial community composition. Salinity, total N, and P were the ones of the important factors that shaped the bacterial communities. In addition, the variations of bacterial communities from site-to-site were greater than within-site. The Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia, Euryarchaeota, Planctomycetes, Firmicutes, Deep Sea DHVEG-6, and Marinimicrobia were the most and common phyla distributed across the Upper Gulf of Thailand.
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Affiliation(s)
- Pongrawee Nimnoi
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom, Thailand
| | - Neelawan Pongsilp
- Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand.
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29
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Hackbusch S, Noirungsee N, Viamonte J, Sun X, Bubenheim P, Kostka JE, Müller R, Liese A. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico. MARINE POLLUTION BULLETIN 2020; 150:110683. [PMID: 31753565 DOI: 10.1016/j.marpolbul.2019.110683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.
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Affiliation(s)
- Steffen Hackbusch
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Nuttapol Noirungsee
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Juan Viamonte
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Xiaoxu Sun
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Paul Bubenheim
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Joel E Kostka
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
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30
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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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31
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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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Tremblay J, Fortin N, Elias M, Wasserscheid J, King TL, Lee K, Greer CW. Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants. Environ Microbiol 2019; 21:2307-2319. [PMID: 30927379 DOI: 10.1111/1462-2920.14609] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 01/02/2023]
Abstract
Oil biodegradation has been extensively studied in the wake of the deepwater horizon spill, but the application of dispersant to oil spills in marine environments remains controversial. Here, we report metagenomic (MG) and metatranscriptomic (MT) data mining from microcosm experiments investigating the oil degrading potential of Canadian west and east coasts to estimate the gene abundance and activity of oil degrading bacteria in the presence of dispersant. We found that the addition of dispersant to crude oil mainly favours the abundance of Thalassolituus in the summer and Oleispira in the winter, two key natural oil degrading bacteria. We found a high abundance of genes related not only to n-alkane and aromatics degradation but also associated with transporters, two-component systems, bacterial motility, secretion systems and bacterial chemotaxis.
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Affiliation(s)
- Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Nathalie Fortin
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Miria Elias
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Thomas L King
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Fisheries and Oceans Canada, Dartmouth, Nova Scotia, B2Y4A2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, PO Box 1006, Dartmouth, Nova Scotia, B2Y4A2, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
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33
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Liu J, Zheng Y, Lin H, Wang X, Li M, Liu Y, Yu M, Zhao M, Pedentchouk N, Lea-Smith DJ, Todd JD, Magill CR, Zhang WJ, Zhou S, Song D, Zhong H, Xin Y, Yu M, Tian J, Zhang XH. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. MICROBIOME 2019; 7:47. [PMID: 30975208 PMCID: PMC6460516 DOI: 10.1186/s40168-019-0652-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/22/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. RESULTS Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from - 79 to - 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. CONCLUSIONS These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.
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Affiliation(s)
- Jiwen Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xuchen Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Yu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Nikolai Pedentchouk
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Wei-Jia Zhang
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Shun Zhou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haohui Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yu Xin
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
- Marine Dynamic Process and Climate Function Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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34
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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35
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Cerro-Gálvez E, Casal P, Lundin D, Piña B, Pinhassi J, Dachs J, Vila-Costa M. Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environ Microbiol 2019; 21:1466-1481. [PMID: 30838733 DOI: 10.1111/1462-2920.14580] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/21/2019] [Accepted: 03/03/2019] [Indexed: 11/29/2022]
Abstract
Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Paulo Casal
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 39182, Kalmar, Sweden
| | - Benjamin Piña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 39182, Kalmar, Sweden
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
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36
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Easson CG, Lopez JV. Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico. Front Microbiol 2019; 9:3175. [PMID: 30662434 PMCID: PMC6328475 DOI: 10.3389/fmicb.2018.03175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/07/2018] [Indexed: 02/01/2023] Open
Abstract
The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0-200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.
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Affiliation(s)
- Cole G. Easson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, United States
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37
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Xu X, Liu W, Tian S, Wang W, Qi Q, Jiang P, Gao X, Li F, Li H, Yu H. Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis. Front Microbiol 2018; 9:2885. [PMID: 30559725 PMCID: PMC6287552 DOI: 10.3389/fmicb.2018.02885] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.
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Affiliation(s)
- Xingjian Xu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Wenming Liu
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Shuhua Tian
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Wei Wang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Qige Qi
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Pan Jiang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Xinmei Gao
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Fengjiao Li
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Haiyan Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China
| | - Hongwen Yu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China
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38
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Thomson NM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ. Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria. PLoS One 2018; 13:e0206544. [PMID: 30462661 PMCID: PMC6248924 DOI: 10.1371/journal.pone.0206544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ-proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches.
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Affiliation(s)
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Mark J. Pallen
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
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39
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Gontikaki E, Potts L, Anderson J, Witte U. Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel). J Appl Microbiol 2018; 125:1040-1053. [PMID: 29928773 PMCID: PMC6849767 DOI: 10.1111/jam.14030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/16/2018] [Accepted: 06/18/2018] [Indexed: 02/04/2023]
Abstract
AIMS The aim of this study was the baseline description of oil-degrading sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments. METHODS AND RESULTS Oil-degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well-known oil-degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold-water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m. CONCLUSIONS The genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep-sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general. SIGNIFICANCE AND IMPACT OF THE STUDY Oil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.
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Affiliation(s)
- E. Gontikaki
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - L.D. Potts
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - J.A. Anderson
- Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of EngineeringUniversity of AberdeenAberdeenUK
| | - U. Witte
- School of Biological SciencesUniversity of AberdeenAberdeenUK
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40
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Noh J, Kim H, Lee C, Yoon SJ, Chu S, Kwon BO, Ryu J, Kim JJ, Lee H, Yim UH, Giesy JP, Khim JS. Bioaccumulation of Polycyclic Aromatic Hydrocarbons (PAHs) by the Marine Clam, Mactra veneriformis, Chronically Exposed to Oil-Suspended Particulate Matter Aggregates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7910-7920. [PMID: 29898595 DOI: 10.1021/acs.est.7b06692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dispersion and biodegradation of petroleum hydrocarbons are significantly enhanced by formation of oil-suspended particulate matter aggregates (OSAs), but little is known about their adverse effects on benthic invertebrates or microbes. In this study, we investigated: (1) bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) by the marine bivalve, Mactra veneriformis and (2) changes in composition and relative abundances of microbes, during 50-d of an OSAs feeding experiment. Total concentrations of PAHs increased more rapidly during the first week of exposure, peaked at Day 30, then gradually declined to the end of experiment. While bioaccumulation of PAHs by clams varied among the 20 target compounds, two major groups of PAHs were identified by cluster analysis. One group including 3-methylphenanthrene, 1,6-dimethylphenanthrene, 1,2,6,9-tetramethylphenanthrene, and benzo[ a]anthracene showed a fairly constant rate of accumulation, while the second group including 2-methyldibenzothiophene, 2,4-dimethyldibenzothiophene, 2,4,7-trimethyldibenzothiophene, 3-methylchrysene, 6-ethylchrysene, and 1,3,6-trimethylchrysene exhibited a bell-shaped pattern. Bioaccumulation of PAHs by clams was dependent on changes in abundance of Gammaproteobacteria, indicating active degradations of hydrocarbons by selected species. Six key species included: Porticoccus litoralis, Porticoccus hydrocarbonoclasticus, Cycloclasticus spirillensus, Alcanivorax borkumensis, Alcanivorax dieselolei, and Alkalimarinus sediminis. These results are the first to demonstrate interactions of OSAs and macrofauna/microbe in oil cleanup operations.
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Affiliation(s)
- Junsung Noh
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Hosang Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Changkeun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seo Joon Yoon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seungoh Chu
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Bong-Oh Kwon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Jongseong Ryu
- Department of Marine Biotechnology , Anyang University , Ganghwa-gun , Incheon Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Un Hyuk Yim
- Oil and POPs Research Group , Korea Institute of Ocean Science and Technology , Geoje , Republic of Korea
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan Canada
- Department of Zoology, and Center for Integrative Toxicology , Michigan State University , East Lansing , Michigan United States
- School of Biological Sciences , University of Hong Kong , Hong Kong , SAR China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , People's Republic of China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
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41
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Gemmell BJ, Bacosa HP, Dickey BO, Gemmell CG, Alqasemi LR, Buskey EJ. Rapid alterations to marine microbiota communities following an oil spill. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:505-516. [PMID: 29556940 DOI: 10.1007/s10646-018-1923-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/24/2018] [Indexed: 06/08/2023]
Abstract
Field data from the first several days after an oil spill is rare but crucial for our understanding of a spill's impact on marine microbiota given their short generation times. Field data collected within days of the Texas City "Y" oil spill showed that exposure to crude oil can rapidly imbalance populations of marine microbiota, which leads to the proliferation of more resistant organisms. Vibrionales bacteria were up to 48 times higher than background concentrations at the most impacted sites and populations of the dinoflagellate Prorocentrum texanum increased significantly as well. Laboratory microcosm experiments with a natural plankton community showed that P. texanum grew significantly faster under oiled conditions but monocultures of P. texanum did not. Additional laboratory experiments with natural communities from Tampa Bay, Florida showed similar results although a different species dominated, P. minimum. In both cases, tolerance to the presence of crude oil was enhanced by higher sensitivity of grazers led to a release from grazing pressure and allows Prorocentrum species to dominate after an oil spill. The results suggest careful monitoring for Vibrionales and Prorocentrum during future spills would be beneficial given the potential implications to human health.
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Affiliation(s)
- Brad J Gemmell
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
| | - Hernando P Bacosa
- Marine Science Department, University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Ben O Dickey
- Marine Science Department, University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Colbi G Gemmell
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
- Marine Science Department, University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Lama R Alqasemi
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Edward J Buskey
- Marine Science Department, University of Texas at Austin, Port Aransas, TX, 78373, USA
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42
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Xie Y, Zhang X, Yang J, Kim S, Hong S, Giesy JP, Yim UH, Shim WJ, Yu H, Khim JS. eDNA-based bioassessment of coastal sediments impacted by an oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:739-748. [PMID: 29625298 DOI: 10.1016/j.envpol.2018.02.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments.
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Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Seonjin Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Biological Sciences, University of Hong Kong, Hong Kong, SAR, China; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Won Joon Shim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
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43
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The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico. Sci Rep 2018; 8:9057. [PMID: 29955123 PMCID: PMC6023898 DOI: 10.1038/s41598-018-27350-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/01/2018] [Indexed: 11/18/2022] Open
Abstract
More than 2,000 historic shipwrecks spanning 500 years of history, rest on the Gulf of Mexico seafloor. Shipwrecks serve as artificial reefs and hotspots of biodiversity by providing hard substrate, something rare in deep ocean regions. The Deepwater Horizon (DWH) spill discharged crude oil into the deep Gulf. Because of physical, biological, and chemical interactions, DWH oil was deposited on the seafloor, where historic shipwrecks are present. This study examined sediment microbiomes at seven historic shipwrecks. Steel-hulled, World War II-era shipwrecks and wooden-hulled, 19th century shipwrecks within and outside of the surface oiled area and subsurface plume were examined. Analysis of 16S rRNA sequence libraries, sediment radiocarbon age data, sedimentation rates, and hydrocarbons revealed that the German U-boat U-166 and the wooden-hulled sailing vessel known as the Mardi Gras Wreck, both in the Mississippi Canyon leasing area, were exposed to deposited oil during a rapid sedimentation event. Impacts to shipwreck microbiomes included a significant increase in Piscirickettsiaceae-related sequences in surface sediments, and reduced biodiversity relative to unimpacted sites. This study is the first to address the impact of the spill on shipwreck-associated microbiomes, and to explore how shipwrecks themselves influence microbiome diversity in the deep sea.
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44
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Park C, Park W. Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential. Front Microbiol 2018; 9:1081. [PMID: 29910779 PMCID: PMC5992423 DOI: 10.3389/fmicb.2018.01081] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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45
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Gao W, Yin X, Mi T, Zhang Y, Lin F, Han B, Zhao X, Luan X, Cui Z, Zheng L. Microbial diversity and ecotoxicity of sediments 3 years after the Jiaozhou Bay oil spill. AMB Express 2018; 8:79. [PMID: 29744605 PMCID: PMC5943202 DOI: 10.1186/s13568-018-0603-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/25/2018] [Indexed: 12/13/2022] Open
Abstract
In 2013, the “Qingdao oil pipeline explosion” released an estimated 2000 tons of oil into the environment. Sediment samples were collected from ten sites in Jiaozhou Bay and Shilaoren Beach to evaluate the influence of the spilled oil on the benthic environment 3 years after the oil spill accident. The compositions of oil, bacterial diversity and biotoxicity were examined in this study. The results showed that the concentration of total petroleum hydrocarbons (TPHs) peaked near the oil leak point and gradually decreased along the coastline, ranging from 21.5 to 133.2 μg/g. The distribution of polycyclic aromatic hydrocarbons (PAHs) was correlated with TPH, and naphthalenes were dominant in the 20 detected PAHs. The bacterial diversities in seriously polluted and slightly polluted sediments were completely different. As degrading bacteria, Alcanivorax and Lutibacter were the main genera at the oil-polluted sites. The analysis of biotoxicity by the luminescent bacteria method showed great differences among the polluted sites, the control site in Jiaozhou Bay, and the non-polluted site outside of Jiaozhou Bay. The biotoxicity also peaked at the site near the oil leak point. These results indicate that the oil spill that occurred 3 years ago still affects the environment and impacts the bacterial communities in the sediments.
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46
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Marietou A, Chastain R, Beulig F, Scoma A, Hazen TC, Bartlett DH. The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill. Front Microbiol 2018; 9:808. [PMID: 29755436 PMCID: PMC5932198 DOI: 10.3389/fmicb.2018.00808] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/10/2018] [Indexed: 01/13/2023] Open
Abstract
The Deepwater Horizon oil spill was one of the largest and deepest oil spills recorded. The wellhead was located at approximately 1500 m below the sea where low temperature and high pressure are key environmental characteristics. Using cells collected 4 months following the Deepwater Horizon oil spill at the Gulf of Mexico, we set up Macondo crude oil enrichments at wellhead temperature and different pressures to determine the effect of increasing depth/pressure to the in situ microbial community and their ability to degrade oil. We observed oil degradation under all pressure conditions tested [0.1, 15, and 30 megapascals (MPa)], although oil degradation profiles, cell numbers, and hydrocarbon degradation gene abundances indicated greatest activity at atmospheric pressure. Under all incubations the growth of psychrophilic bacteria was promoted. Bacteria closely related to Oleispira antarctica RB-8 dominated the communities at all pressures. At 30 MPa we observed a shift toward Photobacterium, a genus that includes piezophiles. Alphaproteobacterial members of the Sulfitobacter, previously associated with oil-degradation, were also highly abundant at 0.1 MPa. Our results suggest that pressure acts synergistically with low temperature to slow microbial growth and thus oil degradation in deep-sea environments.
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Affiliation(s)
- Angeliki Marietou
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Roger Chastain
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Felix Beulig
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Douglas H Bartlett
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
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47
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Doyle SM, Whitaker EA, De Pascuale V, Wade TL, Knap AH, Santschi PH, Quigg A, Sylvan JB. Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit. Front Microbiol 2018; 9:689. [PMID: 29696005 PMCID: PMC5904270 DOI: 10.3389/fmicb.2018.00689] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/23/2018] [Indexed: 12/15/2022] Open
Abstract
During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure.
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Affiliation(s)
- Shawn M Doyle
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Emily A Whitaker
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Veronica De Pascuale
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Terry L Wade
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Anthony H Knap
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Peter H Santschi
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Department of Marine Science, Texas A&M University at Galveston, Galveston, TX, United States
| | - Antonietta Quigg
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, United States
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48
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Ribicic D, Netzer R, Hazen TC, Techtmann SM, Drabløs F, Brakstad OG. Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater. MARINE POLLUTION BULLETIN 2018; 129:370-378. [PMID: 29680562 DOI: 10.1016/j.marpolbul.2018.02.034] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/30/2018] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.
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Affiliation(s)
- Deni Ribicic
- NTNU Norwegian University of Science and Technology, Department of Clinical and Molecular Medicine, Trondheim, Norway.
| | | | - Terry C Hazen
- University of Tennessee Knoxville, Department of Civil and Environmental Engineering, Knoxville, TN, USA
| | - Stephen M Techtmann
- Michigan Technological University, Department of Biological Sciences, Houghton, MI, USA
| | - Finn Drabløs
- NTNU Norwegian University of Science and Technology, Department of Clinical and Molecular Medicine, Trondheim, Norway
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49
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Fasca H, de Castilho LVA, de Castilho JFM, Pasqualino IP, Alvarez VM, de Azevedo Jurelevicius D, Seldin L. Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions. Microbiologyopen 2018; 7:e00550. [PMID: 29057585 PMCID: PMC5912000 DOI: 10.1002/mbo3.550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/05/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023] Open
Abstract
The effect of pressure and temperature on microbial communities of marine environments contaminated with petroleum hydrocarbons is understudied. This study aims to reveal the responses of marine bacterial communities to low temperature, high pressure, and contamination with petroleum hydrocarbons using seawater samples collected near an offshore Brazilian platform. Microcosms containing only seawater and those containing seawater contaminated with 1% crude oil were subjected to three different treatments of temperature and pressure as follows: (1) 22°C/0.1 MPa; (2) 4°C/0.1 MPa; and (3) 4°C/22 MPa. The effect of depressurization followed by repressurization on bacterial communities was also evaluated (4°C/22 MPaD). The structure and composition of the bacterial communities in the different microcosms were analyzed by PCR-DGGE and DNA sequencing, respectively. Contamination with oil influenced the structure of the bacterial communities in microcosms incubated either at 4°C or 22°C and at low pressure. Incubation at low temperature and high pressure greatly influenced the structure of bacterial communities even in the absence of oil contamination. The 4°C/22 MPa and 4°C/22 MPaD treatments resulted in similar DGGE profiles. DNA sequencing (after 40 days of incubation) revealed that the diversity and relative abundance of bacterial genera were related to the presence or absence of oil contamination in the nonpressurized treatments. In contrast, the variation in the relative abundances of bacterial genera in the 4°C/22 MPa-microcosms either contaminated or not with crude oil was less evident. The highest relative abundance of the phylum Bacteroidetes was observed in the 4°C/22 MPa treatment.
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Affiliation(s)
- Hanna Fasca
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Livia V. A. de Castilho
- Laboratório de Tecnologia Submarina/PENO/COPPEUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | | | - Ilson P. Pasqualino
- Laboratório de Tecnologia Submarina/PENO/COPPEUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Vanessa M. Alvarez
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Diogo de Azevedo Jurelevicius
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Lucy Seldin
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
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50
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Shiller AM, Chan EW, Joung DJ, Redmond MC, Kessler JD. Light rare earth element depletion during Deepwater Horizon blowout methanotrophy. Sci Rep 2017; 7:10389. [PMID: 28871146 PMCID: PMC5583346 DOI: 10.1038/s41598-017-11060-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022] Open
Abstract
Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation samples revealed that LREE-containing MDHs were present. Our field and laboratory observations provide further insight into the biochemical pathways of methanotrophy during the DWH blowout. Additionally, our results are the first observations of direct biological alteration of REE distributions in oceanic systems. In view of the ubiquity of LREE-containing MDHs in oceanic systems, our results suggest that biological uptake of LREEs is an overlooked aspect of the oceanic geochemistry of this group of elements previously thought to be biologically inactive and an unresolved factor in the flux of methane, a potent greenhouse gas, from the ocean.
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Affiliation(s)
- A M Shiller
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States.
| | - E W Chan
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
| | - D J Joung
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States
| | - M C Redmond
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - J D Kessler
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
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