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Lumibao CY, Liu Y. Long-Term Contaminant Exposure Alters Functional Potential and Species Composition of Soil Bacterial Communities in Gulf Coast Prairies. Microorganisms 2024; 12:1460. [PMID: 39065226 DOI: 10.3390/microorganisms12071460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Environmental pollution is a persistent threat to coastal ecosystems worldwide, adversely affecting soil microbiota. Soil microbial communities perform critical functions in many coastal processes, yet they are increasingly subject to oil and heavy metal pollution. Here, we assessed how small-scale contamination by oil and heavy metal impacts the diversity and functional potential of native soil bacterial communities in the gulf coast prairie dunes of a barrier island in South Texas along the northern Gulf of Mexico. We analyzed the bacterial community structure and their predicted functional profiles according to contaminant history and examined linkages between species diversity and functional potential. Overall, contaminants altered bacterial community compositions without affecting richness, leading to strongly distinct bacterial communities that were accompanied by shifts in functional potential, i.e., changes in predicted metabolic pathways across oiled, metal, and uncontaminated environments. We also observed that exposure to different contaminants can either lead to strengthened or decoupled linkages between species diversity and functional potential. Taken together, these findings indicate that bacterial communities might recover their diversity levels after contaminant exposure, but with consequent shifts in community composition and function. Furthermore, the trajectory of bacterial communities can depend on the nature or type of disturbance.
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Affiliation(s)
- Candice Y Lumibao
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Yue Liu
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
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2
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Ghaderi D. Mapping the shoreline risk assessment of oil spill in the eastern region of Qeshm channel. MARINE POLLUTION BULLETIN 2024; 206:116714. [PMID: 39002217 DOI: 10.1016/j.marpolbul.2024.116714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/06/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
The northern shores of the Strait of Hormuz constitute one of the most diverse shorelines in the Persian Gulf, characterized by both utility and environmental richness. Situated in the Qeshm channel, which hosts the largest mangrove habitat, major industries, and commercial port, these shores are subject to the occurrence of oil spills, posing potential substantial harm. This study employs General NOAA Operational Modeling Environment (GNOME) and numerical modeling to assess the potential risks to shorelines from hypothetical oil spills, considering the distinctive features of the shores and their environmental sensitivity. The results indicate that high-risk levels are not excessively prevalent overall and are confined to approximately 24 km. The shape of the channel and hydrodynamic conditions highlight the eastern sector of the Bandar Abbas urban area as particularly susceptible to oil spill entrapment. The findings indicate that high-risk areas are predominantly located away from industrial-oil shores and primarily consist of muddy shores. Therefore, internal strategies of Oil Spill Contingency Plan (OSCP) of companies are deemed insufficient and necessitate comprehensive planning initiatives.
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Affiliation(s)
- Danial Ghaderi
- Physical Oceanography, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran; Center Providing Consultation And Simulation Services For Coastal And Marine Environments (NPDS Company), Bandar Abbas, Iran.
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3
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Xu C, Lu S, Cidan Y, Wang H, Sun G, Saleem MU, Ataya FS, Zhu Y, Wangdui-Basang, Li K. Microbiome analysis reveals alteration in water microbial communities due to livestock activities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34334-2. [PMID: 38995335 DOI: 10.1007/s11356-024-34334-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The Baihe River, a tributary of the Yellow River located in the Ngawa Tibetan and Qiang Autonomous Prefecture in Northern Sichuan, is surrounded by natural resources suitable for animal development. However, the impact of livestock activities water microbiome in this area remains unexplored. This study collected water samples from areas with captive yaks and sheep (NS and YS) and compared them with water samples from Hongyuan Baihe River. Through amplicon sequencing, we investigated the impact of livestock activities on aquatic microorganisms. Diversity analysis, significance analysis, and microbial phenotype prediction indicated a significant decrease in microbial community diversity and function in the NS and YS groups. Pathogenic microorganisms such as Bacteroidales and Thelebolaceae and antibiotic-resistant bacteria genes such as Flavobacteriales and Burkholderiaceae were significantly higher in livestock breeding areas. Additionally, bacteria adapted to acidification, hypoxia, and eutrophication (e.g., Acidobacteria, Flavobacteriales, Deltaproteobacteria, Rhodobacterales) were more abundant in these areas. Our results demonstrate that livestock activities significantly alter the structure and function of microbial communities in surrounding water bodies, deteriorating water quality.
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Affiliation(s)
- Chang Xu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Sijia Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yangji Cidan
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, People's Republic of China
| | - Hongzhuang Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, People's Republic of China
| | - Guangming Sun
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, People's Republic of China
| | - Muhammad Usman Saleem
- Department of Biosciences, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Farid Shokry Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, People's Republic of China
| | - Wangdui-Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, People's Republic of China
| | - Kun Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Zhou Y, Wang Y, Yao S, Zhao X, Kong Q, Cui L, Zhang H. Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135060. [PMID: 38943887 DOI: 10.1016/j.jhazmat.2024.135060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.
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Affiliation(s)
- Yumiao Zhou
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shudi Yao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xinyu Zhao
- Laoshan Laboratory, Qingdao 266237, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lihua Cui
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China.
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Ghezzi D, Jiménez-Morillo NT, Foschi L, Donini E, Chiarini V, De Waele J, Miller AZ, Cappelletti M. The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter. ENVIRONMENTAL MICROBIOME 2024; 19:25. [PMID: 38659019 PMCID: PMC11040949 DOI: 10.1186/s40793-024-00562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota. RESULTS Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development. CONCLUSIONS The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Nicasio Tomás Jiménez-Morillo
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Pólo da Mitra Apartado 94, Évora, 7006-554, Portugal
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. de la Reina Mercedes, 10, Sevilla, 41012, Spain
| | - Lisa Foschi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Eva Donini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Veronica Chiarini
- Department of Geosciences, University of Padova, via Gradenigo 6, Padua, 35131, Italy
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy
| | - Ana Zélia Miller
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. de la Reina Mercedes, 10, Sevilla, 41012, Spain.
- HERCULES Laboratory, University of Évora, Largo dos Colegiais 2, Évora, 7004-516, Portugal.
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy.
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Monjezi SD, Bakhtiyari AR, Alavi-Yeganeh MS. Sourcing aliphatic and polycyclic aromatic hydrocarbons (PAHs) in Jinga shrimp (Metapenaeus affinis) muscle tissues and surface sediments (study case: Northwest Persian Gulf). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28644-28657. [PMID: 38558344 DOI: 10.1007/s11356-024-32738-8] [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: 10/01/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
This study addresses the sources of aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of the northwestern Persian Gulf and the muscle tissues of Jinga shrimp (Metapenaeus affinis), a commercially important aquatic species. In November 2018, 28 Jinga shrimp samples were systematically collected from four key fishing areas in Behrgan and Khormusi: Imam Khomeini Port (S1), Mahshahr Port (S2), Sejafi (S3), and Behrgan Wharf (S4). Additionally, sediment samples were collected from these locations, and AHs and PAHs concentrations were analyzed using gas chromatography-mass spectrometry (GC-MS). The average aliphatic concentration in Jinga shrimp was 4800.32 (μg g-1 DW), exceeding the sediment samples' 2496.69 (μg g-1 DW) estimate. Hydrocarbon component analysis revealed EPA priority list (PAH-16) and measured PAHs (PAH-29) concentrations in Jinga shrimp ranging from 1095.8 to 2698.3 (ng g-1 DW) and in sediments from 653.6 to 1019.5 (ng g-1 DW). Elevated AHs and PAHs in Jinga shrimp, compared to sediments, suggest a petrogenic source, notably at station S4 near Behrgansar and Nowruz oil fields. Low molecular weight (LMW) compounds dominated in both shrimp and sediment PAHs. Aliphatic composition profiles in shrimps closely mirrored sediment profiles, illustrating an even-to-odd carbon dominance gradient. Diagnostic ratio examinations of hydrocarbons indicated pervasive petroleum derivatives in the environment. This study establishes a direct correlation between hydrocarbon concentrations in shrimp and sediment samples and the corresponding aliphatic groups, PAH-16, and PAH-29. The findings underscore the potential of Jinga shrimp as a reliable indicator of hydrocarbon pollution in the northwestern Persian Gulf.
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Affiliation(s)
- Shaghayegh Davodi Monjezi
- Department of Environmental Science, Faculty of Natural Resources and Marine Science, Tarbiat Modares University, Noor, Iran
| | - Alireaza Riyahi Bakhtiyari
- Department of Environmental Science, Faculty of Natural Resources and Marine Science, Tarbiat Modares University, Noor, Iran.
| | - Mohammad Sadegh Alavi-Yeganeh
- Department of Marine Biology, Faculty of Natural Resources and Marine Science, Tarbiat Modares University, Noor, Iran
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7
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Campbell BC, Greenfield P, Barnhart EP, Gong S, Midgley DJ, Paulsen IT, George SC. Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams. mBio 2024; 15:e0173523. [PMID: 38345372 PMCID: PMC10936416 DOI: 10.1128/mbio.01735-23] [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: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.
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Affiliation(s)
- Bronwyn C. Campbell
- Environment Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Western Australia, Australia
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul Greenfield
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - Elliott P. Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, Montana, USA
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - David J. Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Simon C. George
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
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8
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Luter HM, Laffy P, Flores F, Brinkman DL, Fisher R, Negri AP. Molecular responses of sponge larvae exposed to partially weathered condensate oil. MARINE POLLUTION BULLETIN 2024; 199:115928. [PMID: 38141581 DOI: 10.1016/j.marpolbul.2023.115928] [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: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
Anthropogenic inputs of petroleum hydrocarbons into the marine environment can have long lasting impacts on benthic communities. Sponges form an abundant and diverse component of benthic habitats, contributing a variety of important functional roles; however, their responses to petroleum hydrocarbons are largely unknown. This study combined a traditional ecotoxicological experimental design and endpoint with global gene expression profiling and microbial indicator species analysis to examine the effects of a water accommodated fraction (WAF) of condensate oil on a common Indo-Pacific sponge, Phyllospongia foliascens. A no significant effect concentration (N(S)EC) of 2.1 % WAF was obtained for larval settlement, while gene-specific (N(S)EC) thresholds ranged from 3.4 % to 8.8 % WAF. Significant shifts in global gene expression were identified at WAF treatments ≥20 %, with larvae exposed to 100 % WAF most responsive. Results from this study provide an example on the incorporation of non-conventional molecular and microbiological responses into ecotoxicological studies on petroleum hydrocarbons.
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Affiliation(s)
- Heidi M Luter
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia.
| | - Patrick Laffy
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia
| | - Florita Flores
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia
| | - Diane L Brinkman
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia
| | - Rebecca Fisher
- Australian Institute of Marine Science, Crawley 6009, WA, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville 4810, QLD, Australia; AIMS@JCU, Division of Research & Innovation, James Cook University, Townsville 4811, QLD, Australia
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9
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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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10
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Chen Q, Li Z, Chen Y, Liu M, Yang Q, Zhu B, Mu J, Feng L, Chen Z. Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments. MARINE POLLUTION BULLETIN 2024; 199:115925. [PMID: 38113802 DOI: 10.1016/j.marpolbul.2023.115925] [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: 09/05/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.
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Affiliation(s)
- Qingguo Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhenzhen Li
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Yu Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mei Liu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Qiao Yang
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Baikang Zhu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jun Mu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572022, PR China.
| | - Lijuan Feng
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhi Chen
- Department of Building, Civil and Environmental Engineering, Faculty of Engineering & Computer Sciences, Concordia University, Montreal, Quebec H3G1M8, Canada
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11
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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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12
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Zhou P, Tian L, Siddique MS, Song S, Graham NJD, Zhu YG, Yu W. Divergent Fate and Roles of Dissolved Organic Matter from Spatially Varied Grassland Soils in China During Long-Term Biogeochemical Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1164-1176. [PMID: 38164759 DOI: 10.1021/acs.est.3c08046] [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: 01/03/2024]
Abstract
Terrestrial dissolved organic matter (DOM) is critical to global carbon and nutrient cycling, climate change, and human health. However, how the spatial and compositional differences of soil DOM affect its dynamics and fate in water during the carbon cycle is largely unclear. Herein, the biodegradation of DOM from 14 spatially distributed grassland soils in China with diverse organic composition was investigated by 165 days of incubation experiments. The results showed that although the high humified fraction (high-HS) regions were featured by high humic-like fractions of 4-25 kDa molecular weight, especially the abundant condensed aromatics and tannins, they unexpectedly displayed greater DOM degradation during 45-165 days. In contrast, the unique proteinaceous and 25-100 kDa fractions enriched in the low humified fraction (low-HS) regions were drastically depleted and improved the decay of bulk DOM but only during 0-45 days. Together, DOM from the high-HS regions would cause lower CO2 outgassing to the atmosphere but higher organic loads for drinking water production in the short term than that from the low-HS regions. However, this would be reversed for the two regions during the long-term transformation processes. These findings highlight the importance of spatial and temporal variability of DOM biogeochemistry to mitigate the negative impacts of grassland soil DOM on climate, waters, and humans.
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Affiliation(s)
- Peng Zhou
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Saboor Siddique
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shian Song
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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13
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Antonioli R, de Faria Poloni J, Riveros Escalona MA, Dorn M. Functional response of microbial communities in lab-controlled oil-contaminated marine sediment. Mol Omics 2023; 19:756-768. [PMID: 37477619 DOI: 10.1039/d3mo00007a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.
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Affiliation(s)
- Regis Antonioli
- Center for Biotechnology, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
| | - Joice de Faria Poloni
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, 90619-900, Porto Alegre, Brazil
| | | | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
- National Institute of Science and Technology - Forensic Science, Porto Alegre, Brazil
- Institute of Informatics, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil.
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14
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Khishdost M, Dobaradaran S, Goudarzi G, Takdastan A, Babaei AA. Contaminant occurrence, distribution and ecological risk assessment of phthalate esters in the Persian Gulf. PLoS One 2023; 18:e0287504. [PMID: 37418450 PMCID: PMC10328224 DOI: 10.1371/journal.pone.0287504] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/04/2023] [Indexed: 07/09/2023] Open
Abstract
Due to the increasing population of the world, the presence of harmful compounds, especially phthalate esters (PAEs), are one of the important problems of environmental pollution. These compounds are known as carcinogenic compounds and Endocrine-disrupting chemicals (EDCs) for humans. In this study, the occurrence of PAEs and the evaluation of its ecological risks were carried out in the Persian Gulf. Water samples were collected from two industrial sites, a rural site and an urban site. Samples were analyzed using magnetic solid phase extraction (MSPE) and gas chromatography-mass spectrometry (GC/MS) technique to measure seven PAEs including Di(2-ethylhexyl) phthalate (DEHP), butyl benzyl phthalate (BBP), diethyl phthalate (DEP), dibutyl phthalate (DBP), Dimethyl phthalate (DMP), di-n-octyl phthalate (DNOP), and Di-iso-butyl phthalate (DIBP). The BBP was not detected in any of the samples. The total concentration of six PAEs (Σ6PAEs) ranged from 7.23 to 23.7 μg/L, with a mean concentration of 13.7μg/L. The potential ecological risk of each target PAEs was evaluated by using the risk quotient (RQ) method in seawater samples, and the relative results declined in the sequence of DEHP >DIBP > DBP > DEP > DMP in examined water samples. DEHP had a high risk to algae, crustaceans and fish at all sites. While DMP and DEP showed lower risk for all mentioned trophic levels. The results of this study will be helpful for the implementation of effective control measures and remedial strategies for PAEs pollution in the Persian Gulf.
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Affiliation(s)
- Maria Khishdost
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sina Dobaradaran
- Systems Environmental Health and Energy Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
- Department of Environmental Health Engineering, Faculty of Health and Nutrition, Bushehr University of Medical Sciences, Bushehr, Iran
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gholamreza Goudarzi
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Air Pollution and Respiratory Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Takdastan
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Akbar Babaei
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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15
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Shih CY, Chen SY, Hsu CR, Chin CH, Chiu WC, Chang MH, Kang LK, Yang CH, Pai TW, Hu CH, Hsu PH, Tzou WS. Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. PLoS One 2023; 18:e0284022. [PMID: 37294811 PMCID: PMC10256201 DOI: 10.1371/journal.pone.0284022] [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: 09/23/2022] [Accepted: 03/21/2023] [Indexed: 06/11/2023] Open
Abstract
Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.
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Affiliation(s)
- Chi-Yu Shih
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
| | - Shiow-Yi Chen
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chun-Ru Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Ching-Hsiang Chin
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Wei-Chih Chiu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | | | - Lee-Kuo Kang
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Cing-Han Yang
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Chin-Hwa Hu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Pang-Hung Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Wen-Shyong Tzou
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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16
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Ferreira NM, Coutinho R, de Oliveira LS. Emerging studies on oil pollution biomonitoring: A systematic review. MARINE POLLUTION BULLETIN 2023; 192:115081. [PMID: 37236096 DOI: 10.1016/j.marpolbul.2023.115081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
In the last decade, several methods were applied to monitor the impact of oil pollution on marine organisms. Recent studies showed an eminent need to standardize these methods to produce comparable results. Here we present the first thorough systematic review of the literature on oil pollution monitoring methods in the last decade. The literature search resulted on 390 selected original articles, categorized according to the analytical method employed. Except for Ecosystem-level analyses, most methods are used on short-term studies. The combination of Biomarker and Bioaccumulation analysis is the most frequently adopted strategy for oil pollution biomonitoring, followed by Omic analyses. This systematic review describes the principles of the most frequently used monitoring tools, presents their advantages, limitations, and main findings and, as such, could be used as a guideline for future researches on the field.
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Affiliation(s)
- Nícollas Menezes Ferreira
- Department of Marine Biotechnology, Instituto de Estudos do Mar Almirante Paulo Moreira-IEAPM, Arraial do Cabo, RJ 28930000, Brazil; Marine Biotecnology Graduate Program, Instituto de Estudos do Mar Almirante Paulo Moreia-IEAPM and Universidade Federal Fluminense-UFF, Niterói, RJ 24220900, Brazil
| | - Ricardo Coutinho
- Department of Marine Biotechnology, Instituto de Estudos do Mar Almirante Paulo Moreira-IEAPM, Arraial do Cabo, RJ 28930000, Brazil; Marine Biotecnology Graduate Program, Instituto de Estudos do Mar Almirante Paulo Moreia-IEAPM and Universidade Federal Fluminense-UFF, Niterói, RJ 24220900, Brazil
| | - Louisi Souza de Oliveira
- Department of Marine Biotechnology, Instituto de Estudos do Mar Almirante Paulo Moreira-IEAPM, Arraial do Cabo, RJ 28930000, Brazil; Marine Biotecnology Graduate Program, Instituto de Estudos do Mar Almirante Paulo Moreia-IEAPM and Universidade Federal Fluminense-UFF, Niterói, RJ 24220900, Brazil.
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17
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Yavari-Bafghi M, Rezaei Somee M, Amoozegar MA, Dastgheib SMM, Shavandi M. Genome-resolved analyses of oligotrophic groundwater microbial communities along phenol pollution in a continuous-flow biodegradation model system. Front Microbiol 2023; 14:1147162. [PMID: 37065124 PMCID: PMC10090433 DOI: 10.3389/fmicb.2023.1147162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Groundwater pollution is one of the major environmental concerns. The entrance of pollutants into the oligotrophic groundwater ecosystems alters native microbial community structure and metabolism. This study investigated the application of innovative Small Bioreactor Chambers and CaO2 nanoparticles for phenol removal within continuous-flow sand-packed columns for 6 months. Scanning electron microscopy and confocal laser scanning microscopy analysis were conducted to indicate the impact of attached biofilm on sand surfaces in bioremediation columns. Then, the influence of each method on the microbial biodiversity of the column’s groundwater was investigated by next-generation sequencing of the 16S rRNA gene. The results indicated that the simultaneous application of biostimulation and bioaugmentation completely eliminated phenol during the first 42 days. However, 80.2% of phenol remained in the natural bioremediation column at the end of the experiment. Microbial diversity was decreased by CaO2 injection while order-level groups known for phenol degradation such as Rhodobacterales and Xanthomonadales dominated in biostimulation columns. Genome-resolved comparative analyses of oligotrophic groundwater prokaryotic communities revealed that Burkholderiales, Micrococcales, and Cytophagales were the dominant members of the pristine groundwater. Six-month exposure of groundwater to phenol shifted the microbial population towards increasing the heterotrophic members of Desulfobacterales, Pseudomonadales, and Xanthomonadales with the degradation potential of phenol and other hydrocarbons.
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Affiliation(s)
- Maryam Yavari-Bafghi
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Rezaei Somee
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Mohammad Ali Amoozegar,
| | - Seyed Mohammad Mehdi Dastgheib
- Microbiology and Biotechnology Group, Environment and Biotechnology Research Division, Research Institute of Petroleum Industry, Tehran, Iran
| | - Mahmoud Shavandi
- Microbiology and Biotechnology Group, Environment and Biotechnology Research Division, Research Institute of Petroleum Industry, Tehran, Iran
- *Correspondence: Mahmoud Shavandi,
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18
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Shi Y, Xue H, Li J, Yao Y, Liu R, Niu Q. Response of methanogenic system to long-term polycyclic aromatic hydrocarbon exposure: Adsorption and biodegradation, performance variation, and microbial function assessment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 329:117010. [PMID: 36603323 DOI: 10.1016/j.jenvman.2022.117010] [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: 08/29/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Phenanthrene (PHE) as a typical polycyclic aromatic hydrocarbon (PAH) is prevalent and harmful to organisms in petroleum-polluted sites. The effects of PHE concentration levels on performance, microbial community and functions in methanogenic system were comprehensively investigated by an operation of UASB reactor (198 days) and a series of batch tests. The results found that PHE was prone to accumulate in reactor by sludge adsorption (Final concentration = 12.53 mg/g TS Sludge), which posed significant influences on methanogenic system. The removal of chemical oxygen demand (COD), NH4+-N and volatile fatty acids (VFAs) in reactor were reduced with PHE accumulation. Meanwhile, microbes with higher ATPase secrete more EPS activity to self-protect against PHE toxicity. Sequencing analysis showed that PHE interfered significantly diversity and structure of microbial community. For bacteria, PHE was toxic to Bacteroidetes and Latescibacteria, while syntrophs (f_Syntrophaceae, Syntrophorhabdus, etc.) involved in VFAs oxidation and aromatic organics degradation were tolerant of PHE stress. For archaea, acetoclastic methanogens (Methanosaeta) abundance was continuously diminished by 45.1% under long-term PHE exposure. Further functions analysis suggested that microbial community accelerated amino acid metabolism, energy metabolism and xenobiotics biodegradation & metabolism to satisfy physiological demanding under PHE stress. Combining batch tests of methanogenic metabolism proved that acetoclastic methanogenesis was negatively affected by PHE due to inhibition of functional enzymes (acetate kinase, phosphate acetyltransferase, etc.) expression. These findings may provide the basis for enhancing bioremediation of PAH pollution in anaerobic environment.
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Affiliation(s)
- Yongsen Shi
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Hanhan Xue
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Jingyi Li
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Yilin Yao
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China; China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China.
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19
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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20
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Somee MR, Amoozegar MA, Dastgheib SMM, Shavandi M, Maman LG, Bertilsson S, Mehrshad M. Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 2022; 23:690. [PMID: 36203131 PMCID: PMC9535955 DOI: 10.1186/s12864-022-08906-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08906-w.
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Affiliation(s)
- Maryam Rezaei Somee
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | | | - Mahmoud Shavandi
- Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Leila Ghanbari Maman
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden.
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Song J, Beule L, Jongmans-Hochschulz E, Wichels A, Gerdts G. The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient. ISME COMMUNICATIONS 2022; 2:35. [PMID: 37938248 PMCID: PMC9723596 DOI: 10.1038/s43705-022-00117-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 05/28/2023]
Abstract
Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.
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Affiliation(s)
- Jessica Song
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany.
| | - Lukas Beule
- Julius Kühn Institute-Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Strasse 19, 14195, Berlin, Germany
| | - Elanor Jongmans-Hochschulz
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
| | - Antje Wichels
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
| | - Gunnar Gerdts
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
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Pandey N, Ojha U. Bio‐based polydimethylsiloxane porous sponge materials with programmable hydrophobicity and porosity for efficient separation of hydrophobic liquids from water. J Appl Polym Sci 2022. [DOI: 10.1002/app.51823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Niharika Pandey
- Department of Chemistry Rajiv Gandhi Institute of Petroleum Technology Jais India
| | - Umaprasana Ojha
- Department of Chemistry Rajiv Gandhi Institute of Petroleum Technology Jais India
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Schreiber L, Fortin N, Tremblay J, Wasserscheid J, Sanschagrin S, Mason J, Wright CA, Spear D, Johannessen SC, Robinson B, King T, Lee K, Greer CW. In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions. FEMS Microbiol Ecol 2021; 97:fiab082. [PMID: 34124756 PMCID: PMC8213973 DOI: 10.1093/femsec/fiab082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022] Open
Abstract
Douglas Channel and the adjacent Hecate Strait (British Columbia, Canada) are part of a proposed route to ship diluted bitumen (dilbit). This study presents how two types of dilbit naturally degrade in this environment by using an in situ microcosm design based on dilbit-coated beads. We show that dilbit-associated n-alkanes were microbially biodegraded with estimated half-lives of 57-69 days. n-Alkanes appeared to be primarily degraded using the aerobic alkB, ladA and CYP153 pathways. The loss of dilbit polycyclic aromatic hydrocarbons (PAHs) was slower than of n-alkanes, with half-lives of 89-439 days. A biodegradation of PAHs could not be conclusively determined, although a significant enrichment of the phnAc gene (a marker for aerobic PAH biodegradation) was observed. PAH degradation appeared to be slower in Hecate Strait than in Douglas Channel. Microcosm-associated microbial communities were shaped by the presence of dilbit, deployment location and incubation time but not by dilbit type. Metagenome-assembled genomes of putative dilbit-degraders were obtained and could be divided into populations of early, late and continuous degraders. The majority of the identified MAGs could be assigned to the orders Flavobacteriales, Methylococcales, Pseudomonadales and Rhodobacterales. A high proportion of the MAGs represent currently unknown lineages or lineages with currently no cultured representative.
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Affiliation(s)
- Lars Schreiber
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Nathalie Fortin
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Sylvie Sanschagrin
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Jennifer Mason
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Cynthia A Wright
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - David Spear
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - Sophia C Johannessen
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - Brian Robinson
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas King
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada (DFO), 200 Kent St, Ottawa,ON K1A 0E6, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
- Department of Natural Resource Sciences, McGill University, Macdonald-Stewart Building, McGill, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
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