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Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Arnold J, Joye SB. Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant. Appl Environ Microbiol 2024; 90:e0108324. [PMID: 39041797 DOI: 10.1128/aem.01083-24] [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: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 07/24/2024] Open
Abstract
Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the "mobilome," potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments' heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.
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Affiliation(s)
- Tito D Peña-Montenegro
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
- Grupo de Investigación y Desarrollo en Ciencias, Tecnología e Innovación (BioGRID), Sociedad de Doctores e Investigadores de Colombia (SoPhIC), Bogotá, Colombia
| | - Sara Kleindienst
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, Georgia, 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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Kottuparambil S, Ashok A, López P, Amad MH, Duarte CM, Agusti S. High temperature and solar radiation in the Red Sea enhance the dissolution of crude oil from surface films. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:42034-42048. [PMID: 38856854 PMCID: PMC11219460 DOI: 10.1007/s11356-024-33864-z] [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: 12/30/2022] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The Red Sea is a hotspot of biodiversity susceptible to oil pollution. Besides, it is one of the warmest seas on the Earth with highly transparent waters. In this study, we estimated the oil dissolution rates under natural sunlight spectra and temperature conditions using coastal oil slicks collected after the 2019 Sabiti oil spill in the Red Sea. Optical analyses revealed the significant interactive effect of sunlight and temperature in enhancing the dissolution of oil into dissolved organic matter (DOM). The highest oil dissolution rate (38.68 g C m-3 d-1) was observed in full-spectrum sunlight. Oil dissolution significantly enhanced total organic carbon (TOC) and polycyclic aromatic hydrocarbons (PAHs) in seawater. High nucleic acid (HNA) bacteria, likely the oil degraders, proliferated from 30 to 70 - 90% after 4 days. The heavier stable carbon isotopic composition of methane (δ13C-CH4) and lighter stable carbon isotopic composition of carbon dioxide (δ13C-CO2) indicate the putative role of bacterial processes in the natural degradation of crude oil. The results indicated that the combined effect of temperature and solar radiation enhanced the biological and photochemical dissolution of oil on the Red Sea surface.
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Affiliation(s)
- Sreejith Kottuparambil
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Mubadala Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.
| | - Ananya Ashok
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Patricia López
- King Abdullah University of Science and Technology (KAUST), Core Labs, 23955-6900, Thuwal, Saudi Arabia
| | - Maan H Amad
- King Abdullah University of Science and Technology (KAUST), Core Labs, 23955-6900, Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Susana Agusti
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
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4
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Perdigão R, Tomasino MP, Magalhães C, Carvalho MF, Almeida CMR, Mucha AP. Microbial response to a port fuel spill: Community dynamics and potential for bioremediation. MARINE POLLUTION BULLETIN 2024; 203:116434. [PMID: 38713928 DOI: 10.1016/j.marpolbul.2024.116434] [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: 01/31/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.
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Affiliation(s)
- Rafaela Perdigão
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal.
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
| | - Ana P Mucha
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
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Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
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Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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6
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Charalampous G, Fragkou E, Kalogerakis N, Antoniou E, Gontikaki E. Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea. MARINE POLLUTION BULLETIN 2024; 202:116275. [PMID: 38564821 DOI: 10.1016/j.marpolbul.2024.116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024]
Abstract
Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Efsevia Fragkou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
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7
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Langeloh H, Greer CW, Vergeynst L, Hakvåg S, Øverjordet IB, Bakke I, Sørensen L, Brakstad OG. Comparison of two field systems for determination of crude oil biodegradation in cold seawater. MARINE POLLUTION BULLETIN 2024; 199:115919. [PMID: 38134872 DOI: 10.1016/j.marpolbul.2023.115919] [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: 09/27/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Marine oil spills have devastating environmental impacts and extrapolation of experimental fate and impact data from the lab to the field remains challenging due to the lack of comparable field data. In this work we compared two field systems used to study in situ oil depletion with emphasis on biodegradation and associated microbial communities. The systems were based on (i) oil impregnated clay beads and (ii) hydrophobic Fluortex adsorbents coated with thin oil films. The bacterial communities associated with the two systems displayed similar compositions of dominant bacterial taxa. Initial abundances of Oceanospirillales were observed in both systems with later emergences of Flavobacteriales, Alteromonadales and Rhodobacterales. Depletion of oil compounds was significantly faster in the Fluortex system and most likely related to the greater bioavailability of oil compounds as compared to the clay bead system.
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Affiliation(s)
- Hendrik Langeloh
- The Norwegian University of Science and Technology (NTNU), Dept. of Biotechnology and Food Science, Sem Sælandsvei 6/8, 7491 Trondheim, Norway.
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, 75 Bd de Mortagne, Boucherville, QC J4B 6Y4, Montreal, Canada; McGill University, Natural Resource Sciences, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9 Montreal, Quebec, Canada.
| | - Leendert Vergeynst
- Arctic Research Centre, Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus, Denmark; Aarhus University Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds vej 10 D, 8000 Aarhus, Denmark.
| | - Sigrid Hakvåg
- SINTEF Ocean, Department of Climate and Environment, Brattørkaia 17b, 7010 Trondheim, Norway.
| | - Ida B Øverjordet
- SINTEF Ocean, Department of Climate and Environment, Brattørkaia 17b, 7010 Trondheim, Norway.
| | - Ingrid Bakke
- SINTEF Ocean, Department of Climate and Environment, Brattørkaia 17b, 7010 Trondheim, Norway.
| | - Lisbet Sørensen
- SINTEF Ocean, Department of Climate and Environment, Brattørkaia 17b, 7010 Trondheim, Norway.
| | - Odd G Brakstad
- SINTEF Ocean, Department of Climate and Environment, Brattørkaia 17b, 7010 Trondheim, Norway.
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8
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Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
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Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
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9
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Chai G, Li J, Li Z. The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics. Microbiol Res 2024; 278:127542. [PMID: 37979302 DOI: 10.1016/j.micres.2023.127542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.
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Affiliation(s)
- Guangjun Chai
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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10
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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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11
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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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12
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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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13
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Zhao S, Liu R, Wang J, Lv S, Zhang B, Dong C, Shao Z. Biodegradation of polyethylene terephthalate (PET) by diverse marine bacteria in deep-sea sediments. Environ Microbiol 2023; 25:2719-2731. [PMID: 37421171 DOI: 10.1111/1462-2920.16460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/19/2023] [Indexed: 07/09/2023]
Abstract
PET plastic waste entering the oceans is supposed to take hundreds of years to degrade and tends to accumulate in the deep sea. However, we know little about the bacteria capable of plastic degradation therein. To determine whether PET-degrading bacteria are present in deep-sea sediment, we collected the samples from the eastern central Pacific Ocean and initiated microbial incubation with PET as the carbon source. After enrichment with PET for 2 years, we gained all 15 deep-sea sediment communities at five oceanic sampling sites. Bacterial isolation for pure culture and further growth tests confirmed that diverse bacteria possess degradation ability including Alcanivorax xenomutans BC02_1_A5, Marinobacter sediminum BC31_3_A1, Marinobacter gudaonensis BC06_2_A6, Thalassospira xiamenensis BC02_2_A1 and Nocardioides marinus BC14_2_R3. Furthermore, four strains were chosen as representatives to reconfirm the PET degradation capability by SEM, weight loss and UPLC-MS. The results showed that after 30-day incubation, 1.3%-1.8% of PET was lost. De-polymerization of PET by the four strains was confirmed by the occurrence of the PET monomer of MHET and TPA as the key degradation products. Bacterial consortia possessing PET-degrading potential are prevalent and diverse and might play a key role in the removal of PET pollutants in deep oceans.
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Affiliation(s)
- Sufang Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
| | - Juan Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
| | - Shiwei Lv
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
| | - Benjuan Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Fisheries and Life, Shanghai Ocean University, Shanghai, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
- School of Fisheries and Life, Shanghai Ocean University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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14
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Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Sánchez-Calderón JD, Arnold J, Joye SB. Species-specific responses of marine bacteria to environmental perturbation. ISME COMMUNICATIONS 2023; 3:99. [PMID: 37736763 PMCID: PMC10516948 DOI: 10.1038/s43705-023-00310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.
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Affiliation(s)
- Tito D Peña-Montenegro
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Grupo de Investigación y Desarrollo en Ciencias, Tecnología e Innovación (BioGRID), Sociedad de Doctores e Investigadores de Colombia (SoPhIC), Bogotá, Colombia
| | - Sara Kleindienst
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Bandtäle 2, 70569, Stuttgart, Germany
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, University of Oldenburg, Oldenburg, 26129, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Juan D Sánchez-Calderón
- Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional Barranquilla, Barranquilla, Colombia
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Department of Genetics, University of Georgia, 120 Green St., Athens, GA, 30602-7223, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA.
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15
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Frates ES, Spietz RL, Silverstein MR, Girguis P, Hatzenpichler R, Marlow JJ. Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment. Front Microbiol 2023; 14:1235906. [PMID: 37744927 PMCID: PMC10512730 DOI: 10.3389/fmicb.2023.1235906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.
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Affiliation(s)
- Erin S. Frates
- Department of Biology, Boston University, Boston, MA, United States
| | - Rachel L. Spietz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | | | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
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16
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Booth AM, Sørensen L, Brakstad OG, Ribicic D, Creese M, Arey JS, Lyon DY, Redman AD, Martin-Aparicio A, Camenzuli L, Wang N, Gros J. Comprehensive Two-Dimensional Gas Chromatography with Peak Tracking for Screening of Constituent Biodegradation in Petroleum UVCB Substances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12583-12593. [PMID: 37590158 PMCID: PMC10469455 DOI: 10.1021/acs.est.3c01624] [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: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023]
Abstract
Petroleum substances, as archetypical UVCBs (substances of unknown or variable composition, complex reaction products, or biological substances), pose a challenge for chemical risk assessment as they contain hundreds to thousands of individual constituents. It is particularly challenging to determine the biodegradability of petroleum substances since each constituent behaves differently. Testing the whole substance provides an average biodegradation, but it would be effectively impossible to obtain all constituents and test them individually. To overcome this challenge, comprehensive two-dimensional gas chromatography (GC × GC) in combination with advanced data-handling algorithms was applied to track and calculate degradation half-times (DT50s) of individual constituents in two dispersed middle distillate gas oils in seawater. By tracking >1000 peaks (representing ∼53-54% of the total mass across the entire chromatographic area), known biodegradation patterns of oil constituents were confirmed and extended to include many hundreds not currently investigated by traditional one-dimensional GC methods. Approximately 95% of the total tracked peak mass biodegraded after 64 days. By tracking the microbial community evolution, a correlation between the presence of functional microbial communities and the observed progression of DT50s between chemical classes was demonstrated. This approach could be used to screen the persistence of GC × GC-amenable constituents of petroleum substance UVCBs.
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Affiliation(s)
| | | | | | | | | | - J. Samuel Arey
- Oleolytics
LLC, Lebanon, New Jersey 08833, United States
| | | | - Aaron D. Redman
- ExxonMobil
Biomedical Sciences, Inc., Annandale, New Jersey 08801, United States
- Concawe, Brussels 1160, Belgium
| | | | - Louise Camenzuli
- ExxonMobil
Petroleum & Chemical B.V., Machelen 1831, Belgium
- Concawe, Brussels 1160, Belgium
| | | | - Jonas Gros
- Scientific
Consultant, Villars-sur-Glâne 1752, Switzerland
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17
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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18
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Guo Z, Kang Y, Wu H, Li M, Hu Z, Zhang J. Enhanced removal of phenanthrene and nutrients in wetland sediment with metallic biochar: Performance and mechanisms. CHEMOSPHERE 2023; 327:138523. [PMID: 36990361 DOI: 10.1016/j.chemosphere.2023.138523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/16/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Polycyclic aromatic hydrocarbon (PAHs) are persistent organic pollutants and pose high risk in aquatic environment. The utilization of biochar is a strategy for PAHs-contaminated remediation but is challenging due to the adsorption saturation and reoccurrence of PAHs desorbed back into water. In this study, iron (Fe) and manganese (Mn) were provided as electron acceptors for biochar modification to enhance anaerobic biodegradation of phenanthrene (Phe). Results revealed that, the Mn(Ⅳ) and Fe(Ⅲ) modification improved the removal of Phe by 24.2% and 31.4% than that of biochar, respectively. Additionally, nitrate removal was improved by 19.5% with Fe(Ⅲ) amendment. The Mn-and Fe-biochar decreased Phe contents by 8.7% and 17.4% in sediment, 10.3% and 13.8% in biochar than that of biochar. Much higher DOC contents were observed with Mn- and Fe-biochar, which provided bioavailable carbon source for microbes and contributed to microbial degradation of Phe. The greater degree of humification, higher proportions of humic and fulvic acid like components in metallic biochar participated in electron transport and further enhancing the degradation of PAHs. Microbial analysis proved the high abundance of Phe-degrading bacteria (e.g. PAH-RHDα, Flavobacterium and Vibrio), nitrogen removal microbes (e.g. amoA, nxrA, and nir), Fe and Mn bioreduction or oxidation (e. g. Bacillus, Thermomonas, Deferribacter) with metallic biochar. Based on the results, the Fe and Mn modification, especially Fe-modified biochar provided well performance for PAHs removal in aquatic sediment.
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Affiliation(s)
- Zizhang Guo
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Yan Kang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Haiming Wu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Mei Li
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Zhen Hu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
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19
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Vigneron A, Cruaud P, Lovejoy C, Vincent WF. Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes. MICROBIOME 2023; 11:104. [PMID: 37173775 PMCID: PMC10176705 DOI: 10.1186/s40168-023-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. RESULTS Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. CONCLUSIONS Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada.
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
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20
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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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21
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Tonteri O, Reunamo A, Nousiainen A, Koskinen L, Nuutinen J, Truu J, Jørgensen KS. Effects of Dispersant on the Petroleum Hydrocarbon Biodegradation and Microbial Communities in Seawater from the Baltic Sea and Norwegian Sea. Microorganisms 2023; 11:microorganisms11040882. [PMID: 37110305 PMCID: PMC10142239 DOI: 10.3390/microorganisms11040882] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Dispersants have been used in several oil spill accidents, but little information is available on their effectiveness in Baltic Sea conditions with low salinity and cold seawater. This study investigated the effects of dispersant use on petroleum hydrocarbon biodegradation rates and bacterial community structures. Microcosm experiments were conducted at 5 °C for 12 days with North Sea crude oil and dispersant Finasol 51 with open sea Gulf of Bothnia and coastal Gulf of Finland and Norwegian Sea seawater. Petroleum hydrocarbon concentrations were analysed with GC-FID. Bacterial community structures were studied using 16S rDNA gene amplicon sequencing, and the abundance of genes involved in hydrocarbon degradation with quantitative PCR. The highest oil degradation gene abundances and oil removal were observed in microcosms with coastal seawater from the Gulf of Bothnia and Gulf of Finland, respectively, and the lowest in the seawater from the Norwegian Sea. Dispersant usage caused apparent effects on bacterial communities in all treatments; however, the dispersant’s effect on the biodegradation rate was unclear due to uncertainties with chemical analysis and variation in oil concentrations used in the experiments.
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Affiliation(s)
- Ossi Tonteri
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
- Correspondence:
| | - Anna Reunamo
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Aura Nousiainen
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Laura Koskinen
- Laboratory Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Jari Nuutinen
- Laboratory Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Jaak Truu
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Kirsten S. Jørgensen
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
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22
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Pyke R, Fortin N, Wasserscheid J, Tremblay J, Schreiber L, Levesque MJ, Messina-Pacheco S, Whyte L, Wang F, Lee K, Cooper D, Greer CW. Biodegradation potential of residue generated during the in-situ burning of oil in the marine environment. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130439. [PMID: 36437193 DOI: 10.1016/j.jhazmat.2022.130439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
The biodegradability of residues derived from in-situ burning, an oil spill response strategy which involves burning an oil slick on the sea surface, has not yet been fully studied. With a growing risk of oil spills, the fate of the persistent burn residue containing potentially toxic substances must be better understood. Microcosms were used to study the microbial community response and potential biodegradability of in-situ burn residues generated from Ultra Low Sulphur (ULS) marine diesel. Microcosm studies were conducted using residues originating from the burning of unweathered and weathered diesel, with the addition of a fertilizer and a dispersant. Burn residues were incubated for 6 weeks at 7 °C in natural seawater with continual agitation in the dark. Samples were subsequently sacrificed for chemistry as well as 16S rRNA gene amplicon and shotgun metagenomic sequencing. Chemistry analyses revealed a reduction in hydrocarbon concentrations. Medium chain-length n-alkanes (nC16-nC24) decreased by 8% in unweathered burn residue microcosms and up to 26% in weathered burn residue microcosms. A significant decrease in polycyclic aromatic hydrocarbon (PAH) concentrations was observed only for naphthalene, fluorene and their alkylated homologs, in the microcosms amended with residue produced from burning weathered diesel. Decreases of 2-24%, were identified depending on the compound. Microcosms amended with burn residues had distinct microbial communities marked by an increase in relative abundance of putative hydrocarbon degraders as well as an increase of known hydrocarbon-degradation genes. These novel results suggest that if in-situ burning is performed on ULS marine diesel, some of the indigenous bacteria would respond to the newly available carbon source and some of the residual compounds would be biodegraded. Future studies involving longer incubation periods could give a better understanding of the fate of burn residues by shedding light on the potential biodegradability of the more recalcitrant residual compounds.
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Affiliation(s)
- Ruby Pyke
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada
| | - Nathalie Fortin
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Jessica Wasserscheid
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Lars Schreiber
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | - Marie-Josee Levesque
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada
| | | | - Lyle Whyte
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada
| | - Feiyue Wang
- Centre for Earth Observation Science and Department of Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ottawa, ON, Canada
| | - David Cooper
- SL Ross Environmental Research Ltd., Ottawa, ON, Canada
| | - Charles W Greer
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, QC, Canada; National Research Council Canada, Energy, Mining and Environment Research Centre, Montréal, QC, Canada.
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23
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Liu Y, Chen S, Xie Z, Zhang L, Wang J, Fang J. Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench. Microorganisms 2023; 11:microorganisms11030630. [PMID: 36985204 PMCID: PMC10052102 DOI: 10.3390/microorganisms11030630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518000, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Li Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Correspondence: (J.W.); (J.F.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
- Correspondence: (J.W.); (J.F.)
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24
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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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25
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Brock ML, Richardson R, Ederington-Hagy M, Nigro L, Snyder RA, Jeffrey WH. Temporal variability of microbial response to crude oil exposure in the northern Gulf of Mexico. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1096880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Oil spills are common occurrences in the United States and can result in extensive ecological damage. The 2010 Deepwater Horizon oil spill in the Gulf of Mexico was the largest accidental spill recorded. Many studies were performed in deep water habitats to understand the microbial response to the released crude oil. However, much less is known about how planktonic coastal communities respond to oil spills and whether that response might vary over the course of the year. Understanding this temporal variability would lend additional insight into how coastal Florida habitats may have responded to the Deepwater Horizon oil spill. To assess this, the temporal response of planktonic coastal microbial communities to acute crude oil exposure was examined from September 2015 to September 2016 using seawater samples collected from Pensacola Beach, Florida, at 2-week intervals. A standard oil exposure protocol was performed using water accommodated fractions made from MC252 surrogate oil under photo-oxidizing conditions. Dose response curves for bacterial production and primary production were constructed from 3H-leucine incorporation and 14C-bicarbonate fixation, respectively. To assess drivers of temporal patterns in inhibition, a suite of biological and environmental parameters was measured including bacterial counts, chlorophyll a, temperature, salinity, and nutrients. Additionally, 16S rRNA sequencing was performed on unamended seawater to determine if temporal variation in the in situ bacterial community contributed to differences in inhibition. We observed that there is temporal variation in the inhibition of primary and bacterial production due to acute crude oil exposure. We also identified significant relationships of inhibition with environmental and biological parameters that quantitatively demonstrated that exposure to water-soluble crude oil constituents was most detrimental to planktonic microbial communities when temperature was high, when there were low inputs of total Kjeldahl nitrogen, and when there was low bacterial diversity or low phytoplankton biomass.
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26
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Ghosh S, Chhabria MT, Roy K. Exploring quantitative structure-property relationship models for environmental fate assessment of petroleum hydrocarbons. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:26218-26233. [PMID: 36355241 DOI: 10.1007/s11356-022-23904-x] [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: 06/22/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
The rate and extent of biodegradation of petroleum hydrocarbons in the different aquatic environments is an important element to address. The major avenue for removing petroleum hydrocarbons from the environment is thought to be biodegradation. The present study involves the development of predictive quantitative structure-property relationship (QSPR) models for the primary biodegradation half-life of petroleum hydrocarbons that may be used to forecast the biodegradation half-life of untested petroleum hydrocarbons within the established models' applicability domain. These models use easily computable two-dimensional (2D) descriptors to investigate important structural characteristics needed for the biodegradation of petroleum hydrocarbons in freshwater (dataset 1), temperate seawater (dataset 2), and arctic seawater (dataset 3). All the developed models follow OECD guidelines. We have used double cross-validation, best subset selection, and partial least squares tools for model development. In addition, the small dataset modeler tool has been successfully used for the dataset with very few compounds (dataset 3 with 17 compounds), where dataset division was not possible. The resultant models are robust, predictive, and mechanistically interpretable based on both internal and external validation metrics (R2 range of 0.605-0.959. Q2(Loo) range of 0.509-0.904, and Q2F1 range of 0.526-0.959). The intelligent consensus predictor tool has been used for the improvement of the prediction quality for test set compounds which provided superior outcomes to those from individual partial least squares models based on several metrics (Q2F1 = 0.808 and Q2F2 = 0.805 for dataset 1 in freshwater). Molecular size and hydrophilic factor for freshwater, frequency of two carbon atoms at topological distance 4 for temperate seawater, and electronegative atom count relative to size for arctic seawater were found to be the most significant descriptors responsible for the regulation of biodegradation half-life of petroleum hydrocarbons.
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Affiliation(s)
- Sulekha Ghosh
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009, Gujarat, India
| | - Mahesh T Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009, Gujarat, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, India.
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27
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Iriarte J, Dachs J, Casas G, Martínez-Varela A, Berrojalbiz N, Vila-Costa M. Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1625-1636. [PMID: 36655903 PMCID: PMC9893724 DOI: 10.1021/acs.est.2c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 05/28/2023]
Abstract
The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.
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28
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Kokate PP, Bales E, Joyner D, Hazen TC, Techtmann SM. Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates. FEMS Microbiol Lett 2023; 370:fnad081. [PMID: 37573136 DOI: 10.1093/femsle/fnad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.
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Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Erika Bales
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Terry C Hazen
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
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29
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Dell'Anno F, Joaquim van Zyl L, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell'Anno A, Rastelli E. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120772. [PMID: 36455775 DOI: 10.1016/j.envpol.2022.120772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
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Affiliation(s)
- Filippo Dell'Anno
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Antonio Cannavacciuolo
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Milva Pepi
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK.
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
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30
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Ryther CM, Ortmann AC, Wohlgeschaffen G, Robinson BJ. Temperate Coastal Microbial Communities Rapidly Respond to Low Concentrations of Partially Weathered Diesel. MICROBIAL ECOLOGY 2022; 84:1122-1132. [PMID: 34888738 PMCID: PMC9747835 DOI: 10.1007/s00248-021-01939-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/05/2021] [Indexed: 05/23/2023]
Abstract
Diesel is frequently encountered in coastal ecosystems due to land run-off from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a run-off event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel run-off can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.
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Affiliation(s)
- Camilla M Ryther
- Biology Department, Dalhousie University, 6299 South Street, Halifax, NS, B3H 4R2, Canada
| | - Alice C Ortmann
- Centre for Offshore Oil, Gas and Energy Research Laboratory, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS, B2Y 4A2, Canada.
| | - Gary Wohlgeschaffen
- Centre for Offshore Oil, Gas and Energy Research Laboratory, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS, B2Y 4A2, Canada
| | - Brian J Robinson
- Centre for Offshore Oil, Gas and Energy Research Laboratory, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS, B2Y 4A2, Canada
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Zhu Z, Merlin F, Yang M, Lee K, Chen B, Liu B, Cao Y, Song X, Ye X, Li QK, Greer CW, Boufadel MC, Isaacman L, Zhang B. Recent advances in chemical and biological degradation of spilled oil: A review of dispersants application in the marine environment. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129260. [PMID: 35739779 DOI: 10.1016/j.jhazmat.2022.129260] [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: 03/24/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Growing concerns over the risk of accidental releases of oil into the marine environment have emphasized our need to improve both oil spill preparedness and response strategies. Among the available spill response options, dispersants offer the advantages of breaking oil slicks into small oil droplets and promoting their dilution, dissolution, and biodegradation within the water column. Thus dispersants can reduce the probability of oil slicks at sea from reaching coastal regions and reduce their direct impact on mammals, sea birds and shoreline ecosystems. To facilitate marine oil spill response operations, especially addressing spill incidents in remote/Arctic offshore regions, an in-depth understanding of the transportation, fate and effects of naturally/chemically dispersed oil is of great importance. This review provides a synthesis of recent research results studies related to the application of dispersants at the surface and in the deep sea, the fate and transportation of naturally and chemically dispersed oil, and dispersant application in the Arctic and ice-covered waters. Future perspectives have been provided to identify the research gaps and help industries and spill response organizations develop science-based guidelines and protocols for the application of dispersants application.
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Affiliation(s)
- Zhiwen Zhu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | | | - Min Yang
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Bo Liu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Yiqi Cao
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Xing Song
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Xudong Ye
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Qingqi K Li
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Michel C Boufadel
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Lisa Isaacman
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada.
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Kim T, Lee C, Lee J, Bae H, Noh J, Hong S, Kwon BO, Kim JJ, Yim UH, Chang GS, Giesy JP, Khim JS. Best available technique for the recovery of marine benthic communities in a gravel shore after the oil spill: A mesocosm-based sediment triad assessment. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128945. [PMID: 35500340 DOI: 10.1016/j.jhazmat.2022.128945] [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: 03/10/2022] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Ecotoxicological effects of spilled oils are well documented, but study of recovery of marine benthic communities is limited. Long-term recovery of hard bottom communities during physical and biological remediations after a spill was monitored. A 60-day experiment was conducted using a mesocosm with monitoring of eight endpoints by use of the sediment quality triad (SQT). First, physical treatment of hot water + high pressure flushing maximally removed residual oils (max=93%), showing the greatest recovery among SQT variables (mean=72%). Physical cleanup generally involved adverse effects such as depression of the microphytobenthic community during the initial period. Next, biological treatments, such as fertilizer, emulsifier, enzyme and augmentation of the microbes, all facilitated removal of oil (max=66%) enhancing ecological recovery. Analysis of the microbiome confirmed that oil-degrading bacteria, such as Dietzia sp. and Rosevarius sp. were present. A mixed bioremediation, including fertilizer + multi-enzyme + microbes (FMeM) maximized efficacy of remediation as indicated by SQT parameters (mean=47%). Natural attenuation with "no treatment" showed comparable recovery to other remediations. Considering economic availability, environmental performance, and technical applicability, of currently available techniques, combined treatments of physical removal via hand wiping followed by FMeM could be most effective for recovery of the rocky shore benthic community.
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Affiliation(s)
- Taewoo Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Changkeun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Junghyun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Hanna Bae
- GeoSystem Research Corporation, Gunpo 15807, Republic of Korea
| | - Junsung Noh
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Bong-Oh Kwon
- Department of Marine Biotechnology, Kunsan National University, Kunsan 54150, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Gap Soo Chang
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK S7N5E2, Canada
| | - John P Giesy
- Department of Veterinary Biomedical Sciences & Toxicology Centre, University of Saskatchewan,Saskatoon, SK S7N5B3, Canada; Environmental Sciences Department, Baylor University, Waco, TX 76798-7266, United States
| | - 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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Martinez-Varela A, Casas G, Berrojalbiz N, Piña B, Dachs J, Vila-Costa M. Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica. Front Microbiol 2022; 13:907265. [PMID: 35910648 PMCID: PMC9329070 DOI: 10.3389/fmicb.2022.907265] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.
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Affiliation(s)
| | | | | | | | | | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Spain
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Ahmad S, Pinto AP, Hai FI, Badawy METI, Vazquez RR, Naqvi TA, Munis FH, Mahmood T, Chaudhary HJ. Dimethoate residues in Pakistan and mitigation strategies through microbial degradation: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:51367-51383. [PMID: 35616845 DOI: 10.1007/s11356-022-20933-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Organophosphate pesticides (OPs) are used extensively for crop protection worldwide due to their high water solubility and relatively low persistence in the environment compared to other pesticides, such as organochlorines. Dimethoate is a broad-spectrum insecticide that belongs to the thio-organophosphate group of OPs. It is applied to cash crops, animal farms, and houses. It has been used in Pakistan since the 1960s, either alone or in a mixture with other OPs or pyrethroids. However, the uncontrolled use of this pesticide has resulted in residual accumulation in water, soil, and tissues of plants via the food chain, causing toxic effects. This review article has compiled and analyzed data reported in the literature between 1998 and 2021 regarding dimethoate residues and their microbial bioremediation. Different microorganisms such as bacteria, fungi, and algae have shown potential for bioremediation. However, an extensive role of bacteria has been observed compared to other microorganisms. Twenty bacterial, three fungal, and one algal genus with potential for the remediation of dimethoate have been assessed. Active bacterial biodegraders belong to four classes (i) alpha-proteobacteria, (ii) gamma-proteobacteria, (iii) beta-proteobacteria, and (iv) actinobacteria and flavobacteria. Microorganisms, especially bacterial species, are a sustainable technology for dimethoate bioremediation from environmental samples. Yet, new microbial species or consortia should be explored.
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Affiliation(s)
- Saliha Ahmad
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ana Paula Pinto
- Environment and Development, Institute for Advanced Studies and Research, MED, Mediterranean Institute for Agriculture, Evora University, Polo da Mitra, Ap. 94, 7006-554, Evora, Portugal
| | - Faisal Ibney Hai
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Mohamed El-Taher Ibrahim Badawy
- Department of Pesticide Chemistry and Technology, Faculty of Agriculture, Alexandria University, 21545-El Shatby, Aflaton St, Alexandria, Egypt
| | - Refugio Rodriguez Vazquez
- Center for Research and Advanced Studies of the National Polytechnic Institute, Av. Instituto Politécnico Nacional No. 2508, C.P. 07360, Mexico City, Mexico
| | - Tatheer Alam Naqvi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Farooq Hussain Munis
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Tariq Mahmood
- Department of Agriculture, Hazara University, Mansehra, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation. Microorganisms 2022; 10:microorganisms10071289. [PMID: 35889007 PMCID: PMC9324126 DOI: 10.3390/microorganisms10071289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 12/04/2022] Open
Abstract
The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.
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Emulating Deep-Sea Bioremediation: Oil Plume Degradation by Undisturbed Deep-Sea Microbial Communities Using a High-Pressure Sampling and Experimentation System. ENERGIES 2022. [DOI: 10.3390/en15134525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hydrocarbon biodegradation rates in the deep-sea have been largely determined under atmospheric pressure, which may lead to non-representative results. In this work, we aim to study the response of deep-sea microbial communities of the Eastern Mediterranean Sea (EMS) to oil contamination at in situ environmental conditions and provide representative biodegradation rates. Seawater from a 600 to 1000 m depth was collected using a high-pressure (HP) sampling device equipped with a unidirectional check-valve, without depressurization upon retrieval. The sample was then passed into a HP-reactor via a piston pump without pressure disruption and used for a time-series oil biodegradation experiment at plume concentrations, with and without dispersant application, at 10 MPa and 14 °C. The experimental results demonstrated a high capacity of indigenous microbial communities in the deep EMS for alkane degradation regardless of dispersant application (>70%), while PAHs were highly degraded when oil was dispersed (>90%) and presented very low half-lives (19.4 to 2.2 days), compared to published data. To our knowledge, this is the first emulation study of deep-sea bioremediation using undisturbed deep-sea microbial communities.
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Sharma V, Vashishtha A, Jos ALM, Khosla A, Basu N, Yadav R, Bhatt A, Gulani A, Singh P, Lakhera S, Verma M. Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships. Curr Microbiol 2022; 79:224. [PMID: 35704242 DOI: 10.1007/s00284-022-02910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
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Affiliation(s)
- Vaibhav Sharma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Vashishtha
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Arsha Liz M Jos
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshita Khosla
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Nirmegh Basu
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Rishabh Yadav
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Bhatt
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshanshi Gulani
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Pushpa Singh
- Swami Shraddhanand College, University of Delhi, Alipur, New Delhi, Delhi, 110036, India
| | - Sanidhya Lakhera
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Mansi Verma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India. .,Department of Zoology, Sri Venkateswara College, South Campus, University of Delhi, New Delhi, Delhi, 110021, India.
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Jayasinghe SA, Kennedy F, McMinn A, Martin A. Bacterial Utilisation of Aliphatic Organics: Is the Dwarf Planet Ceres Habitable? Life (Basel) 2022; 12:life12060821. [PMID: 35743852 PMCID: PMC9224870 DOI: 10.3390/life12060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
The regolith environment and associated organic material on Ceres is analogous to environments that existed on Earth 3–4 billion years ago. This has implications not only for abiogenesis and the theory of transpermia, but it provides context for developing a framework to contrast the limits of Earth’s biosphere with extraterrestrial environments of interest. In this study, substrate utilisation by the ice-associated bacterium Colwellia hornerae was examined with respect to three aliphatic organic hydrocarbons that may be present on Ceres: dodecane, isobutyronitrile, and dioctyl-sulphide. Following inoculation into a phyllosilicate regolith spiked with a hydrocarbon (1% or 20% organic concentration wt%), cell density, electron transport activity, oxygen consumption, and the production of ATP, NADPH, and protein in C. hornerae was monitored for a period of 32 days. Microbial growth kinetics were correlated with changes in bioavailable carbon, nitrogen, and sulphur. We provide compelling evidence that C. hornerae can survive and grow by utilising isobutyronitrile and, in particular, dodecane. Cellular growth, electron transport activity, and oxygen consumption increased significantly in dodecane at 20 wt% compared to only minor growth at 1 wt%. Importantly, the reduction in total carbon, nitrogen, and sulphur observed at 20 wt% is attributed to biotic, rather than abiotic, processes. This study illustrates that short-term bacterial incubation studies using exotic substrates provide a useful indicator of habitability. We suggest that replicating the regolith environment of Ceres warrants further study and that this dwarf planet could be a valid target for future exploratory missions.
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Affiliation(s)
- Sahan A. Jayasinghe
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
| | - Fraser Kennedy
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
- Correspondence: (A.M.); (A.M.)
| | - Andrew Martin
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Correspondence: (A.M.); (A.M.)
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Unzueta-Martínez A, Scanes E, Parker LM, Ross PM, O'Connor W, Bowen JL. Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission. Anim Microbiome 2022; 4:32. [PMID: 35590396 PMCID: PMC9118846 DOI: 10.1186/s42523-022-00186-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. Results We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. Conclusion Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00186-9.
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Affiliation(s)
- Andrea Unzueta-Martínez
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Elliot Scanes
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Laura M Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Wayne O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, NSW, 2316, Australia
| | - Jennifer L Bowen
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA
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From Surface Water to the Deep Sea: A Review on Factors Affecting the Biodegradation of Spilled Oil in Marine Environment. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.
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Bagi A, Knapik K, Baussant T. Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes - Potential for use in detection of marine oil pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152238. [PMID: 34896501 DOI: 10.1016/j.scitotenv.2021.152238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.
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Affiliation(s)
- Andrea Bagi
- NORCE Norwegian Research Centre, Bergen, Norway.
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 2022; 10:microorganisms10020328. [PMID: 35208784 PMCID: PMC8879337 DOI: 10.3390/microorganisms10020328] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.
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Dispersed Crude Oil Induces Dysbiosis in the Red Snapper Lutjanus campechanus External Microbiota. Microbiol Spectr 2022; 10:e0058721. [PMID: 35080447 PMCID: PMC8791192 DOI: 10.1128/spectrum.00587-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The fish external microbiota competitively excludes primary pathogens and prevents the proliferation of opportunists. A shift from healthy microbiota composition, known as dysbiosis, may be triggered by environmental stressors and increases host susceptibility to disease. The Deepwater Horizon (DWH) oil spill was a significant stressor event in the Gulf of Mexico. Despite anecdotal reports of skin lesions on fishes following the oil spill, little information is available on the impact of dispersed oil on the fish external microbiota. In this study, juvenile red snapper (Lutjanus campechanus) were exposed to a chemically enhanced water-accommodated fraction (CEWAF) of Corexit 9500/DWH oil (CEWAF) and/or the bacterial pathogen Vibrio anguillarum in treatments designed to detect changes in and recovery of the external microbiota. In fish chronically exposed to CEWAF, immunoglobulin M (IgM) expression significantly decreased between 2 and 4 weeks of exposure, coinciding with elevated liver total polycyclic aromatic hydrocarbons (PAHs). Dysbiosis was detected on fish chronically exposed to CEWAF compared to seawater controls, and addition of a pathogen challenge altered the final microbiota composition. Dysbiosis was prevented by returning fish to clean seawater for 21 days after 1 week of CEWAF exposure. Four fish exhibited lesions during the trial, all of which were exposed to CEWAF but not all of which were exposed to V. anguillarum. This study indicates that month-long exposure to dispersed oil leads to dysbiosis in the external microbiota. As the microbiota is vital to host health, these effects should be considered when determining the total impacts of pollutants in aquatic ecosystems. IMPORTANCE Fish skin is an immunologically active tissue. It harbors a complex community of microorganisms vital to host homeostasis as, in healthy fish, they competitively exclude pathogens found in the surrounding aquatic environment. Crude oil exposure results in immunosuppression in marine animals, altering the relationship between the host and its microbial community. An alteration of the healthy microbiota, a condition known as dysbiosis, increases host susceptibility to pathogens. Despite reports of external lesions on fishes following the DWH oil spill and the importance of the external microbiota to fish health, there is little information on the effect of dispersed oil on the external microbiota of fishes. This research provides insight into the impact of a stressor event such as an oil spill on dysbiosis and enhances understanding of long-term sublethal effects of exposure to aid in regulatory decisions for protecting fish populations during recovery.
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Ahmad S, Chaudhary HJ, Damalas CA. Microbial detoxification of dimethoate through mediated hydrolysis by Brucella sp. PS4: molecular profiling and plant growth-promoting traits. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:2420-2431. [PMID: 34374007 DOI: 10.1007/s11356-021-15806-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
High toxicity of dimethoate requires efficient ways for detoxification and removal of its residues in contaminated environments. Microbial remediation is a process that utilizes the degradation potential of microbes to provide a cost-effective and reliable approach for pesticide abatement. For this purpose, a dimethoate-degrading bacterium Brucella sp. was isolated from a contaminated agricultural soil sample in Multan, Pakistan. This isolate was found to tolerate up to 100 ppm of dimethoate in minimal salt medium and was further evaluated for plant growth-promoting traits. The strain gave positive results for amylase, ammonia, and catalase production, while other traits such as indole acetic acid production and potassium solubilization were also confirmed. Thus, the strain could play an important role for plant nutrient transmission in the plant rhizosphere. Optimization of growth parameters (i.e., pH and temperature) depicted the potential of PS4 to be best tolerating dimethoate, with maximum cell density at λ 600 nm. Optimum pH and temperature for growth were found to be 6 and 35 °C, respectively. Based on optimization results as well as different attributes, the rhizospheric bacterial isolate PS4 was further subjected to a batch degradation experiment under different concentrations of dimethoate (25, 50, 75, and 100 ppm). This promising dimethoate-degrading isolate was found to degrade 83% of dimethoate (at 100 ppm) within a period of 7 days. In addition, it degraded 88% of dimethoate at 50 ppm, indicating that the bacterial isolate utilized dimethoate solely as a source of energy. The strain followed the first order reaction kinetics, depicting its dependence on dimethoate as energy and carbon source. Molecular profiling further supported its role in plant growth promotion and multi-stress tolerance. This research showed that Brucella sp. is capable of degrading dimethoate, and therefore, it would be useful in the investigation of novel bioremediation techniques at pesticide-polluted sites.
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Affiliation(s)
- Saliha Ahmad
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Christos A Damalas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
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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: 23] [Impact Index Per Article: 11.5] [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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Lofthus S, Bakke I, Greer CW, Brakstad OG. Biodegradation of weathered crude oil by microbial communities in solid and melted sea ice. MARINE POLLUTION BULLETIN 2021; 172:112823. [PMID: 34454387 DOI: 10.1016/j.marpolbul.2021.112823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Oil spilled in the Arctic may drift into ice-covered areas and become trapped until the ice melts. To determine if exposure to oil during freezing may have a priming effect on degradation of the oil, weathered dispersed oil (2-3 mg/L) was frozen into solid ice for 200 days at -10 °C, then melted and incubated for 64 days at 4 °C. No degradation was measured in oil frozen into ice prior to melting. Both total amount of oil and target compounds were biotransformed by the microbial community from the melted ice. However, oil released from melted ice was degraded at a slower rate than oil incubated in fresh seawater at the same temperature (4 °C), and by a different microbial community. These data suggest negligible biodegradation of oil frozen in sea ice, while oil-degrading bacteria surviving in the ice may contribute to biodegradation when the ice melts.
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Affiliation(s)
- Synnøve Lofthus
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway; SINTEF Ocean AS, Climate and Environment, Trondheim, Norway.
| | - Ingrid Bakke
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Centre, Montreal, Quebec, Canada
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Achberger AM, Doyle SM, Mills MI, Holmes CP, Quigg A, Sylvan JB. Bacteria-Oil Microaggregates Are an Important Mechanism for Hydrocarbon Degradation in the Marine Water Column. mSystems 2021; 6:e0110521. [PMID: 34609162 PMCID: PMC8547462 DOI: 10.1128/msystems.01105-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Following oil spills in aquatic environments, oil-associated flocculants observed within contaminated waters ultimately lead to the sedimentation of oil as marine oil snow (MOS). To better understand the role of aggregates in hydrocarbon degradation and transport, we experimentally produced a MOS sedimentation event using Gulf of Mexico coastal waters amended with oil or oil plus dispersant. In addition to the formation of MOS, smaller micrometer-scale (10- to 150-μm) microbial aggregates were observed. Visual inspection of these microaggregates revealed that they were most abundant in the oil-amended treatments and frequently associated with oil droplets, linking their formation to the presence of oil. The peak abundance of the microaggregates coincided with the maximum rates of biological hydrocarbon oxidation estimated by the mineralization of 14C-labeled hexadecane and naphthalene. To elucidate the potential of microaggregates to serve as hot spots for hydrocarbon degradation, we characterized the free-living and aggregate-associated microbial assemblages using 16S rRNA gene sequencing. The microaggregate population was found to be bacterially dominated and enriched with putative hydrocarbon-degrading taxa. Direct observation of some of these taxa using catalyzed reporter deposition fluorescence in situ hybridization confirmed their greater abundance within microaggregates relative to the surrounding seawater. Metagenomic sequencing of these bacteria-oil microaggregates (BOMAs) further supported their community's capacity to utilize a wide variety of hydrocarbon compounds. Taken together, these data highlight that BOMAs are inherent features in the biological response to oil spills and likely important hot spots for hydrocarbon oxidation in the ocean. IMPORTANCE Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment. In addition to MOS, we observed micrometer-scale (10- to 150-μm) aggregates whose abundance coincided with maximum rates of hydrocarbon degradation and whose composition was dominated by hydrocarbon-degrading bacteria with the genetic potential to metabolize a range of these compounds. This targeted study examining the role of these bacteria-oil microaggregates in hydrocarbon degradation reveals details of this fundamental component of the biological response to oil spills, and with it, alterations to biogeochemical cycling in the ocean.
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Affiliation(s)
- Amanda M. Achberger
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Shawn M. Doyle
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Makeda I. Mills
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Charles P. Holmes
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Antonietta Quigg
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
- Department of Marine Biology, Texas A&M University-Galveston, Galveston, Texas, USA
| | - Jason B. Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
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Nikolova C, Ijaz UZ, Gutierrez T. Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant-assisted oil biodegradation. Ecol Evol 2021; 11:13862-13874. [PMID: 34707823 PMCID: PMC8525123 DOI: 10.1002/ece3.8091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Assembly processes in marine microbial communities amended with crude oil and chemical dispersant are poorly understood and even more so when biosurfactants are used. We set up a microcosm experiment in which microbiome structure was analyzed using 16S rRNA gene amplicon sequencing and six null models to better understand and quantify the mechanisms and patterns controlling the assembly of a marine crude oil degrading microbial community in the presence of chemical dispersant or rhamnolipid biosurfactant. Although each null model quantifies different aspects of the community assembly, there was a general agreement that neither purely stochastic nor purely deterministic processes dominated the microbial communities, and their influence was variable over time. Determinism was dominant in the early phase of incubation, while stochasticity was prevalent in the middle and late stages. There was faster recruitment of phylogenetically distant species in the dispersant-amended community compared to oil-only or rhamnolipid-amended communities. This analysis provides important insights of how chemical dispersants and rhamnolipid influence microbial communities' dynamics and identified which groups may be excluded-an important consideration for biodegradation process and oil spill response.
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Affiliation(s)
- Christina Nikolova
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | | | - Tony Gutierrez
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
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