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Fukui Y, Nakamura Y, Imaizumi H, Kamoshida M. Microbial influence on the larval survival of Japanese eel Anguilla japonica: Antibiotic-mediated alterations and biomarker isolation. PLoS One 2024; 19:e0306634. [PMID: 38976712 PMCID: PMC11230566 DOI: 10.1371/journal.pone.0306634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
In rearing systems for the Japanese eel Anguilla japonica, although it is assumed that microorganisms influence larval survival and mortality, particularly during the early stages of growth, the effects of bacterial communities on larval survival have yet to be sufficiently determined. In this study, we compared the bacterial communities associated with larval survival at three stages of eel growth. To artificially alter bacterial communities and assess larval survival, eel larvae were treated with 11 types of antibiotic, and larval survival and bacterial characteristics were compared between the antibiotic-treated and antibiotic-free control groups. Throughout the three growth stages, eels treated with four antibiotics (polymyxin B, tetracycline, novobiocin, and erythromycin) had survival rates higher than those in the control groups. The bacterial communities of surviving larvae in the control and antibiotic groups and dead larvae in the control groups were subsequently analyzed using 16S rRNA gene amplicon sequencing. PERMANOVA analysis indicated that these three larval groups were characterized by significantly different bacterial communities. We identified 14 biomarker amplicon sequence variants (ASVs) of bacterial genera such as Oceanobacter, Alcanivorax, Marinobacter, Roseibium, and Sneathiella that were enriched in surviving larvae in the antibiotic treatment groups. In contrast, all four biomarker ASVs enriched in dead larvae of the control groups were from bacteria in the genus Vibrio. Moreover, 52 bacterial strains corresponding to nine biomarkers were isolated using a culture method. To the best of our knowledge, this is the first study to evaluate the bacterial communities associated with the survival and mortality of larvae in during the early stages of Japanese eel growth and to isolate biomarker bacterial strains. These findings will provide valuable insights for enhancing larval survival in the eel larval rearing systems from a microbiological perspective.
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Affiliation(s)
- Youhei Fukui
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Minamiise, Japan
| | - Yoji Nakamura
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Hitoshi Imaizumi
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Minamiizu, Japan
| | - Masaaki Kamoshida
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Japan
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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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Olivera C, Laura Tondo M, Girardi V, Sol Herrero M, Lucía Balaban C, Matías Salvatierra L. High-performance diesel biodegradation using biogas digestate as microbial inoculum in lab-scale solid supported bioreactors. CHEMOSPHERE 2024; 352:141384. [PMID: 38350516 DOI: 10.1016/j.chemosphere.2024.141384] [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: 06/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/15/2024]
Abstract
Industrial anaerobic digestion (AD) produces biogas and a digestate that is usually applied as a biofertilizer. However, the study and application of this by-product in terms of its rich microbial diversity and high metabolic activity have been barely investigated. In this work, the digestate regarded as an inoculum-without any further manipulation-was faced to a target hydrocarbon (i.e., diesel oil) to explore its biodegradation capability and potential application in bioaugmentation strategies. Lab-scale single batch bioreactors with solid support (i.e., sand or gravel) embedded with the inoculum and diesel were used to improve bioaccessibility and biofilm formation. In addition, different experimental conditions were assayed varying the initial diesel concentration, microbial load, type of solid support, inoculum aging time, and presence or absence of oxygen. Remaining diesel concentration, dehydrogenase activity and microbial community structure were periodically determined. Remarkably, this low-cost consortium was capable of a significant reduction (>90%) in the concentration of diesel, within 14 days and when the initial load was as high as 6950 mg/kg dry solid support. Furthermore, a 10-fold increment in dehydrogenase activity, alongside an increase in the abundance of hydrocarbon-degrading bacterial groups, and the enrichment of genes for alkane monooxygenase and aromatic ring-hydroxylating dioxygenases, encourage further study of this consortium for bioremediation purposes.
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Affiliation(s)
- Camila Olivera
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Laura Tondo
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Valentina Girardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Sol Herrero
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina
| | - Cecilia Lucía Balaban
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Lucas Matías Salvatierra
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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4
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Koike H, Miyamoto K, Teramoto M. Alcanivorax bacteria as important polypropylene degraders in mesopelagic environments. Appl Environ Microbiol 2023; 89:e0136523. [PMID: 37982621 PMCID: PMC10734414 DOI: 10.1128/aem.01365-23] [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: 08/11/2023] [Accepted: 09/19/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE PP biodegradation has not been clearly shown (it has been uncertain whether the PP structure is actually biodegraded or not). This is the first report on the obvious biodegradation of PP. At the same time, this study shows that Alcanivorax bacteria could be major degraders of PP in mesopelagic environments. Moreover, PP biodegradation has been investigated by using solid PP as the sole carbon source. However, this study shows that PP would not be used as a sole carbon and energy source. Our data thus provide very important and key knowledge for PP bioremediation.
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Affiliation(s)
- Hiroki Koike
- Department of Marine Resource Science, Kochi University, Nankoku, Kochi, Japan
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Maki Teramoto
- Department of Marine Resource Science, Kochi University, Nankoku, Kochi, Japan
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5
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Dong C, Wei L, Wang J, Lai Q, Huang Z, Shao Z. Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus. Front Microbiol 2022; 13:1051202. [PMID: 36605514 PMCID: PMC9807766 DOI: 10.3389/fmicb.2022.1051202] [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: 09/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 T and 59MF3M-4 T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Lin Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China,*Correspondence: Zongze Shao,
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6
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Wang W, Sun J, Hao J. Spatial Variability of Bacterial Community Compositions in the Mariana Trench. Can J Microbiol 2022; 68:633-642. [PMID: 35926233 DOI: 10.1139/cjm-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hadal microorganisms play an important role in the biogeochemical processes in marine ecosystems and act as a valuable resource for industrial applications. This paper presents the bacterial community analysis of samples taken from the Challenger Deep within the Mariana Trench, which is the deepest site in the ocean. High-throughput 16S rRNA gene amplicon sequencing was used to reveal that the vertically sampled bacterial populations at eight stations varied at the surface to 10 km depth. The surface water samples harbored a distinct bacterial assemblage, while the mesopelagic and bathyal samples manifested different bacterial community composition, which was not consistent with previous studies. Gammaproteobacteria was the most abundant bacteria in the bathyal and hadal water. The hadal bacterial community consisted mostly of Alteromonadales and Oceanospirillales. The former was widely spread in the water column, which might suggest habitat partitioning at the genus and OTU levels, while the latter might represent hadal-enriched hydrocarbon degraders. The present work complements the current knowledge and understanding of the bathyal and hadal bacterial communities of the Mariana Trench.
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Affiliation(s)
- Wei Wang
- Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute, 117919, Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Qingdao, Shandong, China;
| | - Jingjing Sun
- Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute, 117919, Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Qingdao, Shandong, China;
| | - Jianhua Hao
- Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute, 117919, Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Qingdao, Shandong, China;
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7
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Alvillo-Rivera AJ, Garrido-Hoyos SE, Buitrón G. Cyanide treatment of mining tailings using suspended biomass and moving bed biomass reactors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37458-37470. [PMID: 35066824 DOI: 10.1007/s11356-021-18166-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Mexico is the top producer of silver and is on the eighth place from producing gold in the world. For instance, the hydrometallurgical extraction process produces wastewater (mining tailing) characterized by being composed with varying concentrations of cyanide and heavy metals. The purpose of this research was to study the biodegradation of cyanide contained in mining tailings by means of a bacterial consortium isolated from a tailings dam. For this purpose, three types of Eckendfelder reactors were used, one with suspended biomass (BS) and two moving bed biofilter reactors, one with biomass immobilized on Kaldnes (BK) supports, and the other on polyurethane cubes (BCP). Three experimental stages were worked; in each of them, the concentrations of total cyanide were varied. In the first one, it was 26 ± 2 mg·L-1; in the second one 40 ± 4 mg·L-1; and the third one 55 ± 4 mg·L-1. During the whole operation, the pH and temperature were maintained at 9.5 units and 25 °C. After 141 days of operation, biodegradation of the total cyanide contained in the mining tailings was 69% (17 mg·L-1) in the BS reactor, while in the BK reactor, it was 93% (3.9 mg·L-1) and in the BCP reactor 95% (2.5 mg·L-1). The predominant families in each of the reactors, as well as their respective relative abundances, were for the BS and for the BK of Cyclobacteriaceae (20.65% and 24.64%) and Rhizobiaceae (18.48% and 14.01%) and Halomonadaceae (46.97%) and Hyphomonadaceae (24.94%) in the BCP.
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Affiliation(s)
- Angélica Julieta Alvillo-Rivera
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, Campus Morelos (Instituto Mexicano de Tecnología del Agua), Jiutepec, Morelos, México.
| | | | - Germán Buitrón
- Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla, Querétaro, México
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8
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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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9
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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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10
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Oceanobacter mangrovi Sp. Nov., a Novel Poly-β-hydroxybutyrate Accumulating Bacterium Isolated from Mangrove Sediment. Curr Microbiol 2022; 79:100. [PMID: 35150341 DOI: 10.1007/s00284-022-02798-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/01/2022] [Indexed: 11/03/2022]
Abstract
A Gram-stain-negative, rod-shaped, motile, mesophilic, and aerobic bacterial strain, designated SM2-42 T was isolated from a mangrove sediment. Catalase activity and oxidase activity were positive. Growth was observed at 20 °C-40 °C, pH 6.0-8.0, and in the presence of 0.5-5.0% NaCl. Cells of strain SM2-42 T contained poly-β-hydroxybutyrate granules. The 16S rRNA gene of strain SM2-42 T had maximum sequence similarity with Oceanobacter kriegii 197 T of 97.1%. Phylogenetic analysis based on 16S rRNA gene sequence and 120 conserved concatenated proteins indicated that strain SM2-42 T was affiliated to the genus Oceanobacter and formed a monophyletic branch with O. kriegii 197 T. The average nucleotide identity and digital DNA-DNA hybridization values between strain SM2-42 T and O. kriegii 197 T were 76.43% and 21.60%, respectively. The major isoprenoid quinone was Q-8. The major fatty acids (> 10%) comprised C16:0, summed feature 8 (C18:1ω7c and C18:1 ω6c), C18:0, and summed feature 3 (C16:1ω7c and/or C16:1 ω6c). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The draft genome size was 5,115,008 bp with DNA G + C content of 54.3%. Based on phylogenetic analyses and whole genomic comparisons, strain SM2-42 T represented a novel species, for which the name Oceanobacter mangrovi sp. nov. was proposed. The type strain was SM2-42 T (= MCCC 1K06300T = KCTC 82938 T).
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11
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Hansen J, Melchiorsen J, Ciacotich N, Gram L, Sonnenschein EC. Effect of polymer type on the colonization of plastic pellets by marine bacteria. FEMS Microbiol Lett 2021; 368:6152281. [PMID: 33640965 DOI: 10.1093/femsle/fnab026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Plastic is omnipresent in the oceans and serves as a surface for biofilm-forming microorganisms. Plastic debris comprises different polymers, which may influence microbial colonization; here, we evaluated whether polymer type affects bacterial biofilm formation. Quantifying the biofilm on polyethylene (PE), polypropylene (PP) or polystyrene (PS) pellets by six marine bacterial strains (Vibrio,Pseudoalteromonas,Phaeobacter) demonstrated that each strain had a unique colonization behavior with either a preference for PS or PP over the other polymer types or no preference for a specific plastic type. PE, PP and PS pellets were exposed to natural seawater microbiota using free-living or total communities as inoculum. Microbial assembly as determined by 16S rRNA (V4) amplicon sequencing was affected by the composition of the initial inoculum and also by the plastic type. Known polymer and hydrocarbon degraders such as Paraglaciecola, Oleibacter and Hydrogenophaga were found in the plastic biofilms. Thus, on a community level, bacterial colonization on plastic is influenced by the microorganisms as well as the polymer type, and also individual strains can demonstrate polymer-specific colonization.
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Affiliation(s)
- Josefine Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs Lyngby, Denmark
| | - Jette Melchiorsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs Lyngby, Denmark
| | - Nicole Ciacotich
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs Lyngby, Denmark
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12
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Hernández-López EL, Gasperin J, Bernáldez-Sarabia J, Licea-Navarro AF, Guerrero A, Lizárraga-Partida ML. Detection of Alcanivorax spp., Cycloclasticus spp., and Methanomicrobiales in water column and sediment samples in the Gulf of Mexico by qPCR. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:35131-35139. [PMID: 31680200 PMCID: PMC6900280 DOI: 10.1007/s11356-019-06551-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Water column and sediment samples were collected in the southern Gulf of Mexico (GoMex) during 3 oceanographic cruises: XIXIMI-04 (September 2015), XIXIMI-05 (June 2016), and XIXIMI-06 (August 2017). DNA that was extracted from the samples was analyzed by qPCR to detect and quantify bacterial groups that have been reported to metabolize alkanes (Alcanivorax) and aromatic hydrocarbons (Cycloclasticus) and are involved in methane production (Methanomicrobiales). The results were then analyzed with regard to the water masses that are currently detected in the GoMex. Generally, we observed a decrease in the proportion of Alcanivorax and a rise in those of Cycloclasticus and Methanomicrobiales in samples from the surface to deep waters and in sediment samples. Scatterplots of the results showed that the relative abundance of the 3 groups was higher primarily from the surface to 1000 m, but the levels of Cycloclasticus and Methanomicrobiales were high in certain water samples below 1000 m and in sediments. In conclusion, oil-degrading bacteria are distributed widely from the surface to deep waters and sediments throughout the southern GoMex, representing a potential inoculum of bacteria for various hydrocarbon fractions that are ready for proliferation and degradation in the event of an oil spill from the seafloor or along the water column.
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Affiliation(s)
- Edna L Hernández-López
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México
| | - Jahaziel Gasperin
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México
| | - Johanna Bernáldez-Sarabia
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México
| | - Alexei F Licea-Navarro
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México
| | - Abraham Guerrero
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México
| | - Marcial Leonardo Lizárraga-Partida
- Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, zona Playitas, 22860, Ensenada, Baja California, México.
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13
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Valencia-Agami SS, Cerqueda-García D, Putzeys S, Uribe-Flores MM, García-Cruz NU, Pech D, Herrera-Silveira J, Aguirre-Macedo ML, García-Maldonado JQ. Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale. Microorganisms 2019; 7:microorganisms7100441. [PMID: 31614583 PMCID: PMC6843455 DOI: 10.3390/microorganisms7100441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/28/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r2 = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r2 = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.
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Affiliation(s)
- Sonia S Valencia-Agami
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Sébastien Putzeys
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - María Magdalena Uribe-Flores
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Norberto Ulises García-Cruz
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Lerma Campeche, Campeche 24500, Mexico.
| | - Jorge Herrera-Silveira
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - M Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
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14
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Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord. Microbiol Resour Announc 2019; 8:8/30/e00596-19. [PMID: 31346022 PMCID: PMC6658692 DOI: 10.1128/mra.00596-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes. Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.
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15
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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16
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Kim HS, Dong K, Kim J, Lee SS. Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment. Microbiologyopen 2018; 8:e00754. [PMID: 30338941 PMCID: PMC6562140 DOI: 10.1002/mbo3.754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 01/01/2023] Open
Abstract
Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty‐one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7 days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell‐Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n‐alkane degradation in the genome of Gordonia sp. Co17, revealed alkane‐1‐monooxygenase, alcohol dehydrogenase, and Baeyer–Villiger monooxygenase. Specially, for confirmation of gene‐level, alkB gene encoding alkane hydroxylase (alkane‐1‐monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125‐fold after 18 hr accompany with the removal of n‐alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil‐contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.
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Affiliation(s)
- Hyun-Sook Kim
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea
| | - Ke Dong
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Jinsoo Kim
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Sang-Seob Lee
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea.,Department of Life Science, Kyonggi University, Suwon-si, Korea
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17
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Teramoto M. A gene cluster for fatty alcohol synthesis from a Reinekea-related bacterium that accumulates fatty alcohols. FEBS Lett 2018; 592:3421-3428. [PMID: 30223312 DOI: 10.1002/1873-3468.13254] [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: 07/06/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 11/09/2022]
Abstract
This study reports on a marine bacterium that accumulates fatty alcohols (C14,16,18 ) at more than 1% (w/w) of the dry cell weight. This unique bacterium, designated as strain 1-4, is related to the genus Reinekea. A novel gene cluster for fatty alcohol synthesis, phsAB, is identified from strain 1-4. The phsA product shows significant homology to fatty acyl-CoA reductase (51% identity), whereas the phsB product shows very low homology to lipases. Interestingly, phsA alone causes Escherichia coli to accumulate fatty alcohols at 19% (w/w) of the dry cell weight. Moreover, the phsA-containing E. coli accumulate more fatty alcohols (24%) and grow faster after phsB is introduced, indicating that phsAB could greatly assist the mass production of fatty alcohols.
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18
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Rodrigues EM, Morais DK, Pylro VS, Redmile-Gordon M, de Oliveira JA, Roesch LFW, Cesar DE, Tótola MR. Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater. MICROBIAL ECOLOGY 2018; 75:688-700. [PMID: 28971238 DOI: 10.1007/s00248-017-1078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-14C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-14C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.
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Affiliation(s)
- Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Daniel Kumazawa Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Institute of Sciences (CAS), Prague, Czech Republic
| | - Victor Satler Pylro
- Soil Microbiology Laboratory, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, ESALQ/USP, Piracicaba, São Paulo, Brazil
| | - Marc Redmile-Gordon
- Department of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Juraci Alves de Oliveira
- Laboratório de Biofísica Ambiental, Departamento de Biologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Luiz Fernando Wurdig Roesch
- Centro para Pesquisa Interdisciplinar em Biotecnologia, CIP-Biotec, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Dionéia Evangelista Cesar
- Laboratório de Ecologia e Biologia Molecular de Microrganismos, Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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19
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Shtratnikova VY, Belalov I, Kasianov AS, Schelkunov MI, Logacheva Maria DA, Novikov AD, Shatalov AA, Gerasimova TV, Yanenko AS, Makeev VJ. The complete genome of the oil emulsifying strain Thalassolituus oleivorans K-188 from the Barents Sea. Mar Genomics 2018; 37:18-20. [PMID: 33250120 DOI: 10.1016/j.margen.2017.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022]
Abstract
Gammaproteobacterium Thalassolituus oleivorans plays an important role in oil degradation in sea water through emulsifying crude oil and alkanes at low temperatures in polar sea environment. Here we report the complete genome sequence of K-188 strain (VKPM B-9394) isolated in the Barents Sea and compare it with other known Thalassolituus oleivorans strains. The Thalassolituus strains are differed in orthologs number of the genes of alkane degradation, transport proteins, genes of sugar utilization, endonucleases, signaling proteins, transcriptional regulators and presence of CRISPR/Cas locus. Also only the genome of K-188 contains the 3-hydroxyalkanoate synthetase.
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Affiliation(s)
- Victoria Yu Shtratnikova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation.
| | - Ilya Belalov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., h. 33, b. 2, Moscow 119071, Russian Federation.
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Gubkina str., h. 3, Moscow 119991, Russian Federation.
| | - Mikhail I Schelkunov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation; Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow 127051, Russian Federation.
| | - D A Logacheva Maria
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation.
| | - Andrey D Novikov
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Alexey A Shatalov
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Tatyana V Gerasimova
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation
| | - Alexander S Yanenko
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Gubkina str., h. 3, Moscow 119991, Russian Federation; State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russian Federation.
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20
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Kesy K, Hentzsch A, Klaeger F, Oberbeckmann S, Mothes S, Labrenz M. Fate and stability of polyamide-associated bacterial assemblages after their passage through the digestive tract of the blue mussel Mytilus edulis. MARINE POLLUTION BULLETIN 2017; 125:132-138. [PMID: 28807417 DOI: 10.1016/j.marpolbul.2017.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
We examined whether bacterial assemblages inhabiting the synthetic polymer polyamide are selectively modified during their passage through the gut of Mytilus edulis in comparison to the biopolymer chitin with focus on potential pathogens. Specifically, we asked whether bacterial biofilms remained stable over a prolonged period of time and whether polyamide could thus serve as a vector for potential pathogenic bacteria. Bacterial diversity and identity were analysed by 16S rRNA gene fingerprints and sequencing of abundant bands. The experiments revealed that egested particles were rapidly colonised by bacteria from the environment, but the taxonomic composition of the biofilms on polyamide and chitin did not differ. No potential pathogens could be detected exclusively on polyamide. However, after 7days of incubation of the biofilms in seawater, the species richness of the polyamide assemblage was lower than that of the chitin assemblage, with yet unknown impacts on the functioning of the biofilm community.
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Affiliation(s)
- Katharina Kesy
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany
| | - Alexander Hentzsch
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany
| | - Franziska Klaeger
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany
| | - Sonja Oberbeckmann
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany
| | - Stephanie Mothes
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany
| | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Seestrasse 15, 18119 Rostock, Warnemuende, Germany.
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21
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Draft Genome Sequence of Marinobacter vinifirmus Type Strain FB1. GENOME ANNOUNCEMENTS 2017; 5:5/39/e01058-17. [PMID: 28963221 PMCID: PMC5624767 DOI: 10.1128/genomea.01058-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gammaproteobacterium Marinobacter vinifirmus is associated with moderately saline environments and is often found in marine ecosystems. Here, we report the draft genome sequence of M. vinifirmus type strain FB1 (3.8 Mbp, 3,588 predicted genes). The presented sequence will improve our understanding of the taxonomy and evolution of the genus Marinobacter.
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22
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Lydon KA, Glinski DA, Westrich JR, Henderson WM, Lipp EK. Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms. ELEMENTA (WASHINGTON, D.C.) 2017; 5:1-16. [PMID: 35178461 PMCID: PMC8849560 DOI: 10.1525/elementa.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68-1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to use triclosan as a carbon source. The results further suggest the potential for selection of Vibrio in coastal environments, especially sediments, where triclosan may accumulate at high levels.
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Affiliation(s)
- Keri Ann Lydon
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, US
| | - Donna A. Glinski
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, US
- Oak Ridge Institute of Science and Education, U.S. Environmental Protection Agency, Athens, Georgia, US
| | - Jason R. Westrich
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, US
| | - W. Matthew Henderson
- U.S. Environmental Protection Agency, Office of Research and Development, NERL/EMMD, Athens, Georgia, US
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, US
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23
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Crisafi F, Genovese M, Smedile F, Russo D, Catalfamo M, Yakimov M, Giuliano L, Denaro R. Bioremediation technologies for polluted seawater sampled after an oil-spill in Taranto Gulf (Italy): A comparison of biostimulation, bioaugmentation and use of a washing agent in microcosm studies. MARINE POLLUTION BULLETIN 2016; 106:119-126. [PMID: 26992747 DOI: 10.1016/j.marpolbul.2016.03.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
Abstract
One of the main challenges of bioremediation is to define efficient protocols having a low environmental impact. We have investigated the effect of three treatments in oily-seawater after a real oil-spill occurred in the Gulf of Taranto (Italy). Biostimulation with inorganic nutrients allowed the biodegradation of the 73±2.4% of hydrocarbons, bioaugmentation with a selected hydrocarbonoclastic consortium consisting of Alcanivorax borkumensis, Alcanivorax dieselolei, Marinobacter hydrocarbonoclasticus, Cycloclasticus sp. 78-ME and Thalassolituus oleivorans degraded 79±3.2%, while the addition of nutrients and a washing agent has allowed the degradation of the 69±2.6%. On the other hand, microbial community was severely affected by the addition of the washing agent and the same product seemed to inhibit the growth of the majority of strains composing the selected consortium at the tested concentration. The use of dispersant should be accurately evaluated also considering its effect on the principal actors of biodegradation.
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Affiliation(s)
- F Crisafi
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - M Genovese
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - F Smedile
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - D Russo
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - M Catalfamo
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - M Yakimov
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - L Giuliano
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy
| | - R Denaro
- Institute for Coastal Marine Environment CNR, Sp.ta S. Raineri 86, 98122 Messina, Italy.
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24
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Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol 2015; 6:1270. [PMID: 26635742 PMCID: PMC4656828 DOI: 10.3389/fmicb.2015.01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
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Affiliation(s)
- Rafael Bargiela
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | - Manuel Ferrer
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
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Teramoto M, Onodera KI, Moriyama H, Komatsu A, Akakabe M, Nishijima M. Aurantiacicella marina gen. nov., sp. nov., a myxol-producing bacterium from surface seawater. Int J Syst Evol Microbiol 2015; 66:248-254. [PMID: 26493321 DOI: 10.1099/ijsem.0.000706] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2A-8T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced myxol as a major carotenoid. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and was related most closely to the genus Aquimarina (91.0-94.4 % 16S rRNA gene sequence similarity to the type strains of species of this genus). The DNA G+C content was 35 mol%. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and five unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-8T represents a novel genus and species, for which the name Aurantiacicella marina gen. nov., sp. nov. is proposed. The type strain of Aurantiacicella marina is 2A-8T ( = NBRC 111187T = KCTC 42676T).
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Ken-Ichi Onodera
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Hironori Moriyama
- Kochi Prefectural Industrial Technology Center, Nunoshida 3992-3, Kochi 781-5101, Japan
| | - Ayumi Komatsu
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Mai Akakabe
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Miyuki Nishijima
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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Teramoto M, Nishijima M. Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater. Int J Syst Evol Microbiol 2014; 65:799-804. [PMID: 25481292 DOI: 10.1099/ijs.0.000018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of β-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9 % similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7(T) represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7(T) ( = NBRC 110145(T) = KCTC 42197(T)).
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Miyuki Nishijima
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
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Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2014; 64:4016-4020. [DOI: 10.1099/ijs.0.065847-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, designated strain 2-3T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. This strain grew well with starch. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family
Rhodobacteraceae
and that the strain was related most closely to the genus
Pacificibacter
(94.0 % sequence similarity to the type strain). The DNA G+C content was 52.4 mol%. The major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The major isoprenoid quinone was Q-10. Strain 2-3T did not grow at 4 or 35 °C, while the type strain of the type species of the genus
Pacificibacter
grows at both temperatures. From the taxonomic data obtained in this study, it is proposed that strain 2-3T be placed into a novel genus and species named Amylibacter marinus gen. nov., sp. nov. in the family
Rhodobacteraceae
. The type strain of Amylibacter marinus is 2-3T ( = NBRC 110140T = LMG 28364T).
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Teramoto M, Yagyu KI, Nishijima M. Perspicuibacter marinus gen. nov., sp. nov., a semi-transparent bacterium isolated from surface seawater, and description of Arenicellaceae fam. nov. and Arenicellales ord. nov. Int J Syst Evol Microbiol 2014; 65:353-358. [PMID: 25355707 DOI: 10.1099/ijs.0.064683-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2-9(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain was transparent on 1/5 strength marine broth plate but became easily visible when the plate was supplemented with pyruvate. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the strain fell within the class Gammaproteobacteria and was most closely related to the genus Arenicella (92.7-93.0 % 16S rRNA gene sequence similarities to type strains of species of this genus) of an unclassified order within this class. The DNA G+C content of strain 2-9(T) was 41.7 mol%. The major fatty acids were C18 : 1ω7c (37.6 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3; 19.1 %), C18 : 0 (10.8 %), C16 : 0 (10.2 %) and an unidentified fatty acid with an equivalent chain-length value of 11.799 (9.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. Ubiquinone-8 (Q-8) was detected as the sole isoprenoid quinone. From these taxonomic data, it is proposed that strain 2-9(T) represents a novel species of a new genus, Perspicuibacter marinus gen. nov., sp. nov. The type strain of the type species is 2-9(T) ( = NBRC 110144(T) = KCTC 42196(T)). A new family, Arenicellaceae fam. nov. (type genus Arenicella), and order, Arenicellales ord. nov., of the class Gammaproteobacteria are proposed to accommodate the novel taxon.
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Ken-Ichi Yagyu
- The Facility for Research Instruments, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Miyuki Nishijima
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
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Chronopoulou PM, Sanni GO, Silas-Olu DI, van der Meer JR, Timmis KN, Brussaard CPD, McGenity TJ. Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea. Microb Biotechnol 2014; 8:434-47. [PMID: 25251384 PMCID: PMC4408176 DOI: 10.1111/1751-7915.12176] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/29/2022] Open
Abstract
The aim of this work was to determine the effect of light crude oil on bacterial communities during an experimental oil spill in the North Sea and in mesocosms (simulating a heavy, enclosed oil spill), and to isolate and characterize hydrocarbon-degrading bacteria from the water column. No oil-induced changes in bacterial community (3 m below the sea surface) were observed 32 h after the experimental spill at sea. In contrast, there was a decrease in the dominant SAR11 phylotype and an increase in Pseudoalteromonas spp. in the oiled mesocosms (investigated by 16S rRNA gene analysis using denaturing gradient gel electrophoresis), as a consequence of the longer incubation, closer proximity of the samples to oil, and the lack of replenishment with seawater. A total of 216 strains were isolated from hydrocarbon enrichment cultures, predominantly belonging to the genus Pseudoaltero monas; most strains grew on PAHs, branched and straight-chain alkanes, as well as many other carbon sources. No obligate hydrocarbonoclastic bacteria were isolated or detected, highlighting the potential importance of cosmopolitan marine generalists like Pseudoalteromonas spp. in degrading hydrocarbons in the water column beneath an oil slick, and revealing the susceptibility to oil pollution of SAR11, the most abundant bacterial clade in the surface ocean.
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Temperatibacter marinus gen. nov., sp. nov., a mesophilic bacterium isolated from surface seawater and description of Temperatibacteraceae fam. nov. in the class Alphaproteobacteria. Int J Syst Evol Microbiol 2014; 64:3075-3080. [DOI: 10.1099/ijs.0.063685-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 5-11T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain exhibited a narrow growth temperature range of 20–30 °C. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the order
Kordiimonadales
in the class
Alphaproteobacteria
and was related most closely to the genus
Kordiimonas
(up to 91.2 % similarity to the type strains of species of the genus) but branched deeply from species of
Kordiimonas
. The major fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. Ubiquinone-10 (Q-10) was detected as the sole isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. Although strains of
Kordiimonas
have been shown to contain unidentified glycolipids, they were not detected from strain 5-11T. The DNA G+C content of strain 5-11T was 44.3 mol%, a value that was lower than those of strains of
Kordiimonas
(50–58 mol%) and was relatively low for the members of the class
Alphaproteobacteria
. On the basis of phenotypic, genotypic and chemotaxonomic data, it is proposed that strain 5-11T represents a novel species of a new genus, Temperatibacter marinus gen. nov., sp. nov., within a new family Temperatibacteraceae fam. nov. The type strain of Temperatibacter marinus is 5-11T ( = NBRC 110045T = LMG 28278T).
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Wang G, Jia Q, Li T, Dai S, Wu H, He H, Fan J, Xiang W, Li X. Bacterioplanes sanyensis gen. nov., sp. nov., a PHB-accumulating bacterium isolated from a pool of Spirulina platensis cultivation. Arch Microbiol 2014; 196:739-44. [DOI: 10.1007/s00203-014-1009-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/08/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Teramoto M, Nishijima M. Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater. Int J Syst Evol Microbiol 2014; 64:2416-2423. [PMID: 24763604 DOI: 10.1099/ijs.0.061150-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8(T), was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (≤ 94.0% similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8(T) represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8(T) ( = NBRC 110023(T) = LMG 28167(T)).
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Miyuki Nishijima
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
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Enhanced bioremediation of oil spills in the sea. Curr Opin Biotechnol 2014; 27:191-4. [PMID: 24657912 DOI: 10.1016/j.copbio.2014.02.004] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 11/23/2022]
Abstract
Hydrocarbon-degrading bacteria are ubiquitous in the sea, including hydrocarbonoclastic bacteria that utilize hydrocarbons almost exclusively as carbon and energy sources. However, the rates at which they naturally degrade petroleum following an oil spill appear to be too slow to prevent oil from reaching the shore and causing environmental damage, as has been documented in the Exxon Valdez and Gulf of Mexico disasters. Unfortunately, there is, at present, no experimentally demonstrated methodology for accelerating the degradation of hydrocarbons in the sea. The rate-limiting factor for petroleum degradation in the sea is availability of nitrogen and phosphorus. Oleophilic fertilizers, such as Inipol EAP 22 and urea-formaldehyde polymers, have stimulated hydrocarbon degradation on shorelines but are less effective in open systems. We suggest uric acid as a potentially useful fertilizer enhancing bioremediation at sea.
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35
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Smith CB, Tolar BB, Hollibaugh JT, King GM. Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton. Front Microbiol 2013; 4:370. [PMID: 24376439 PMCID: PMC3860262 DOI: 10.3389/fmicb.2013.00370] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/20/2013] [Indexed: 11/13/2022] Open
Abstract
Natural and anthropogenic activities introduce alkanes into marine systems where they are degraded by alkane hydroxylases expressed by phylogenetically diverse bacteria. Partial sequences for alkB, one of the structural genes of alkane hydroxylase, have been used to assess the composition of alkane-degrading communities, and to determine their responses to hydrocarbon inputs. We present here the first spatially extensive analysis of alkB in bacterioplankton of the northern Gulf of Mexico (nGoM), a region that experiences numerous hydrocarbon inputs. We have analyzed 401 partial alkB gene sequences amplified from genomic extracts collected during March 2010 from 17 water column samples that included surface waters and bathypelagic depths. Previous analyses of 16S rRNA gene sequences for these and related samples have shown that nGoM bacterial community composition and structure stratify strongly with depth, with distinctly different communities above and below 100 m. Although we hypothesized that alkB gene sequences would exhibit a similar pattern, PCA analyses of operational protein units (OPU) indicated that community composition did not vary consistently with depth or other major physical-chemical variables. We observed 22 distinct OPUs, one of which was ubiquitous and accounted for 57% of all sequences. This OPU clustered with AlkB sequences from known hydrocarbon oxidizers (e.g., Alcanivorax and Marinobacter). Some OPUs could not be associated with known alkane degraders, however, and perhaps represent novel hydrocarbon-oxidizing populations or genes. These results indicate that the capacity for alkane hydrolysis occurs widely in the nGoM, but that alkane degrader diversity varies substantially among sites and responds differently than bulk communities to physical-chemical variables.
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Affiliation(s)
- Conor B. Smith
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - Bradley B. Tolar
- Department of Marine Studies, University of GeorgiaAthens, GA, USA
| | | | - Gary M. King
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
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Mahmoudi N, Porter TM, Zimmerman AR, Fulthorpe RR, Kasozi GN, Silliman BR, Slater GF. Rapid degradation of Deepwater Horizon spilled oil by indigenous microbial communities in Louisiana saltmarsh sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:13303-13312. [PMID: 24219093 DOI: 10.1021/es4036072] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Deepwater Horizon oil spill led to the severe contamination of coastal environments in the Gulf of Mexico. A previous study detailed coastal saltmarsh erosion and recovery in a number of oil-impacted and nonimpacted reference sites in Barataria Bay, Louisiana over the first 18 months after the spill. Concentrations of alkanes and polyaromatic hydrocarbons (PAHs) at oil-impacted sites significantly decreased over this time period. Here, a combination of DNA, lipid, and isotopic approaches confirm that microbial biodegradation was contributing to the observed petroleum mass loss. Natural abundance (14)C analysis of microbial phospholipid fatty acids (PLFA) reveals that petroleum-derived carbon was a primary carbon source for microbial communities at impacted sites several months following oil intrusion when the highest concentrations of oil were present. Also at this time, microbial community analysis suggests that community structure of all three domains has shifted with the intrusion of oil. These results suggest that Gulf of Mexico marsh sediments have considerable biodegradation potential and that natural attenuation is playing a role in impacted sites.
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Affiliation(s)
- Nagissa Mahmoudi
- School of Geography and Earth Sciences, McMaster University , 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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Hydrocarbon biodegradation in intertidal wetland sediments. Curr Opin Biotechnol 2013; 27:46-54. [PMID: 24863896 DOI: 10.1016/j.copbio.2013.10.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 12/23/2022]
Abstract
Intertidal wetlands, primarily salt marsh, mangrove and mudflats, which provide many essential ecosystem services, are under threat on numerous fronts; a situation that is made worse by crude-oil pollution. Microbes are the main vehicle for remediation of such sediments, and new discoveries, such as novel biodegradation pathways, means of accessing oil, multi-species interactions, and community-level responses to oil addition, are helping us to understand, predict and monitor the fate of oil. Despite this, there are many challenges, not least because of the heterogeneity of these ecosystems and the complexity of crude oil. For example, there is growing awareness about the toxicity of the oxygenated products that result from crude-oil weathering, which are difficult to degrade. This review highlights how developments in areas as diverse as systems biology, microbiology, ecology, biogeochemistry and analytical chemistry are enhancing our understanding of hydrocarbon biodegradation and thus bioremediation of oil-polluted intertidal wetlands.
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Al-Awadhi H, Dashti N, Khanafer M, Al-Mailem D, Ali N, Radwan S. Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria. SPRINGERPLUS 2013; 2:369. [PMID: 24040582 PMCID: PMC3769543 DOI: 10.1186/2193-1801-2-369] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022]
Abstract
Culture-dependent methods for bacterial community analysis are currently considered obsolete; therefore, molecular techniques are usually used instead. The results of the current study on hydrocarbonoclastic bacteria in various oily habitats in Kuwait showed however, that the bacterial identities varied dramatically according to the analytical approach used. For six desert and six seawater samples used in this study, the culture-independent and culture-dependent techniques each led to a unique bacterial composition. Problems related to the culture-dependent technique are well known. The results of the current study highlighted bias problems other than those already recorded in the literature for the molecular approaches. Thus, for example, in contrast to the culture-dependent technique, the primers used in the molecular approach preferentially amplified the 16S rDNAs of hydrocarbonoclastic bacteria in total genomic DNAs of all the studied environmental samples, and in addition, failed to reveal in any environmental sample members of the Actinobacteria. The primers used in the molecular approach also amplified certain “pure” 16S rDNAs, but failed to do so when these DNAs were in mixture. In view of these results, it is recommended that the two analytical approaches should be used simultaneously because their combined results would reflect the bacterial community composition more precisely than either of them can do alone.
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Affiliation(s)
- Husain Al-Awadhi
- Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, Safat, 13060 Kuwait
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Bacterial community response to petroleum hydrocarbon amendments in freshwater, marine, and hypersaline water-containing microcosms. Appl Environ Microbiol 2013; 79:5927-35. [PMID: 23872573 DOI: 10.1128/aem.02251-13] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.
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Teramoto M, Queck SY, Ohnishi K. Specialized Hydrocarbonoclastic Bacteria Prevailing in Seawater around a Port in the Strait of Malacca. PLoS One 2013; 8:e66594. [PMID: 23824553 PMCID: PMC3688937 DOI: 10.1371/journal.pone.0066594] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/08/2013] [Indexed: 11/18/2022] Open
Abstract
Major degraders of petroleum hydrocarbons in tropical seas have been indicated only by laboratory culturing and never through observing the bacterial community structure in actual environments. To demonstrate the major degraders of petroleum hydrocarbons spilt in actual tropical seas, indigenous bacterial community in seawater at Sentosa (close to a port) and East Coast Park (far from a port) in Singapore was analyzed. Bacterial species was more diverse at Sentosa than at the Park, and the composition was different: γ-Proteobacteria (57.3%) dominated at Sentosa, while they did not at the Park. Specialized hydrocarbonoclastic bacteria (SHCB), which use limited carbon sources with a preference for petroleum hydrocarbons, were found as abundant species at Sentosa, indicating petroleum contamination. On the other hand, SHCB were not the abundant species at the Park. The abundant species of SHCB at Sentosa were Oleibacter marinus and Alcanivorax species (strain 2A75 type), which have previously been indicated by laboratory culturing as important petroleum-aliphatic-hydrocarbon degraders in tropical seas. Together with the fact that SHCB have been identified as major degraders of petroleum hydrocarbons in marine environments, these results demonstrate that the O. marinus and Alcanivorax species (strain 2A75 type) would be major degraders of petroleum aliphatic hydrocarbons spilt in actual tropical seas.
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi, Japan
- * E-mail:
| | - Shu Yeong Queck
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi, Japan
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Marine bacteria: potential candidates for enhanced bioremediation. Appl Microbiol Biotechnol 2012; 97:561-71. [DOI: 10.1007/s00253-012-4584-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 11/08/2012] [Accepted: 11/09/2012] [Indexed: 11/26/2022]
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Alain K, Harder J, Widdel F, Zengler K. Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate. MICROBIOLOGY-SGM 2012; 158:2946-2957. [PMID: 23038808 DOI: 10.1099/mic.0.061598-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Aromatic hydrocarbons are among the main constituents of crude oil and represent a major fraction of biogenic hydrocarbons. Anthropogenic influences as well as biological production lead to exposure and accumulation of these toxic chemicals in the water column and sediment of marine environments. The ability to degrade these compounds in situ has been demonstrated for oxygen- and sulphate-respiring marine micro-organisms. However, if and to what extent nitrate-reducing bacteria contribute to the degradation of hydrocarbons in the marine environment and if these organisms are similar to their well-studied freshwater counterparts has not been investigated thoroughly. Here we determine the potential of marine prokaryotes from different sediments of the Atlantic Ocean and Mediterranean Sea to couple nitrate reduction to the oxidation of aromatic hydrocarbons. Nitrate-dependent oxidation of toluene as an electron donor in anoxic enrichment cultures was elucidated by analyses of nitrate, nitrite and dinitrogen gas, accompanied by cell proliferation. The metabolically active members of the enriched communities were identified by RT-PCR of their 16S rRNA genes and subsequently quantified by fluorescence in situ hybridization. In all cases, toluene-grown communities were dominated by members of the Gammaproteobacteria, followed in some enrichments by metabolically active alphaproteobacteria as well as members of the Bacteroidetes. From these enrichments, two novel denitrifying toluene-degrading strains belonging to the Gammaproteobacteria were isolated. Two additional toluene-degrading denitrifying strains were isolated from sediments from the Black Sea and the North Sea. These isolates belonged to the Alphaproteobacteria and Gammaproteobacteria. Serial dilutions series with marine sediments indicated that up to 2.2×10(4) cells cm(-3) were able to degrade hydrocarbons with nitrate as the electron acceptor. These results demonstrated the hitherto unrecognized capacity of alpha- and gammaproteobacteria in marine sediments to oxidize toluene using nitrate.
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Affiliation(s)
- Karine Alain
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,NRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Friedrich Widdel
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Karsten Zengler
- University of California, San Diego, Department of Bioengineering, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
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Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 2012; 14:2405-16. [DOI: 10.1111/j.1462-2920.2012.02780.x] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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McGenity TJ, Folwell BD, McKew BA, Sanni GO. Marine crude-oil biodegradation: a central role for interspecies interactions. AQUATIC BIOSYSTEMS 2012; 8:10. [PMID: 22591596 PMCID: PMC3465203 DOI: 10.1186/2046-9063-8-10] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/25/2012] [Indexed: 05/11/2023]
Abstract
The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
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Affiliation(s)
- Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Benjamin D Folwell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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Central role of dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 2012; 78:3638-48. [PMID: 22407688 DOI: 10.1128/aem.00072-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mudflats and salt marshes are habitats at the interface of aquatic and terrestrial systems that provide valuable services to ecosystems. Therefore, it is important to determine how catastrophic incidents, such as oil spills, influence the microbial communities in sediment that are pivotal to the function of the ecosystem and to identify the oil-degrading microbes that mitigate damage to the ecosystem. In this study, an oil spill was simulated by use of a tidal chamber containing intact diatom-dominated sediment cores from a temperate mudflat. Changes in the composition of bacteria and diatoms from both the sediment and tidal biofilms that had detached from the sediment surface were monitored as a function of hydrocarbon removal. The hydrocarbon concentration in the upper 1.5 cm of sediments decreased by 78% over 21 days, with at least 60% being attributed to biodegradation. Most phylotypes were minimally perturbed by the addition of oil, but at day 21, there was a 10-fold increase in the amount of cyanobacteria in the oiled sediment. Throughout the experiment, phylotypes associated with the aerobic degradation of hydrocarbons, including polycyclic aromatic hydrocarbons (PAHs) (Cycloclasticus) and alkanes (Alcanivorax, Oleibacter, and Oceanospirillales strain ME113), substantively increased in oiled mesocosms, collectively representing 2% of the pyrosequences in the oiled sediments at day 21. Tidal biofilms from oiled cores at day 22, however, consisted mostly of phylotypes related to Alcanivorax borkumensis (49% of clones), Oceanospirillales strain ME113 (11% of clones), and diatoms (14% of clones). Thus, aerobic hydrocarbon biodegradation is most likely to be the main mechanism of attenuation of crude oil in the early weeks of an oil spill, with tidal biofilms representing zones of high hydrocarbon-degrading activity.
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Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl Environ Microbiol 2011; 77:7962-74. [PMID: 21948834 DOI: 10.1128/aem.05402-11] [Citation(s) in RCA: 472] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecological and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chemical analysis revealed weathered oil petroleum hydrocarbon (C₈ to C₄₀) concentrations ranging from 3.1 to 4,500 mg kg⁻¹ in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ∼10-fold higher in oiled (0.44 × 10⁷ to 10.2 × 10⁷ copies g⁻¹) versus clean (0.024 × 10⁷ to 1.4 × 10⁷ copies g⁻¹) sand. Community analysis revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community composition of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degradation there.
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Alonso-Gutiérrez J, Teramoto M, Yamazoe A, Harayama S, Figueras A, Novoa B. Alkane-degrading properties of Dietzia sp. H0B, a key player in the Prestige oil spill biodegradation (NW Spain). J Appl Microbiol 2011; 111:800-10. [PMID: 21767337 DOI: 10.1111/j.1365-2672.2011.05104.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Investigation of the alkane-degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. METHODS AND RESULTS Using molecular and chemical analyses, the alkane-degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n-alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8-Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane-degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR-amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. CONCLUSIONS The results from this study suggest novel alkane-degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil-degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. SIGNIFICANCE AND IMPACT OF THE STUDY This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.
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Teramoto M, Ohuchi M, Hatmanti A, Darmayati Y, Widyastuti Y, Harayama S, Fukunaga Y. Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment. Int J Syst Evol Microbiol 2011; 61:375-380. [DOI: 10.1099/ijs.0.018671-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-negative, motile, mesophilic, aerobic, rod-shaped bacterial strains, designated 2O1T, 1O14 and 1O18, were isolated from Indonesian seawater after enrichment with crude oil and a continuous supply of supplemented seawater. The strains exhibited high n-alkane-degrading activity, which indicated that the strains were important degraders of petroleum aliphatic hydrocarbons in tropical marine environments. Phylogenetic analyses based on 16S rRNA gene sequences of members of the Gammaproteobacteria showed that the isolates formed a coherent and distinct cluster in a stable lineage containing Oceanobacter kriegii IFO 15467T (96.4–96.5 % 16S rRNA gene sequence similarity) and Thalassolituus oleivorans MIL-1T. DNA G +C content was 53.0–53.1 mol%. The major fatty acids were C16 : 0, C16 : 1
ω7 and C18 : 1
ω9 and the hydroxy fatty acids were C12 : 0 3-OH and C10 : 0 3-OH. The polar lipids were phosphatidylglycerol, a ninhydrin-positive phospholipid(s) and glycolipids. The major quinone was Q-9 (97–99 %), which distinguished the isolates from Oceanobacter kriegii NBRC 15467T (Q-8; 91 %). On the basis of phenotypic, genotypic and chemotaxonomic data, including DNA–DNA hybridization, the isolates represent a novel genus and species, for which the name Oleibacter marinus gen. nov., sp. nov. is proposed. The type strain of Oleibacter marinus is 2O1T (=NBRC 105760T =BTCC B-675T).
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Affiliation(s)
- Maki Teramoto
- NITE Biotechnology Development Center (NBDC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Motoyuki Ohuchi
- NITE Biotechnology Development Center (NBDC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ariani Hatmanti
- Research Center for Oceanography, Indonesian Institute of Sciences (LIPI), Jakarta Utara 14430, Indonesia
| | - Yeti Darmayati
- Research Center for Oceanography, Indonesian Institute of Sciences (LIPI), Jakarta Utara 14430, Indonesia
| | | | - Shigeaki Harayama
- NITE Biotechnology Development Center (NBDC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yukiyo Fukunaga
- NITE Biotechnology Development Center (NBDC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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Teramoto M, Suzuki M, Hatmanti A, Harayama S. The potential of Cycloclasticus and Altererythrobacter strains for use in bioremediation of petroleum-aromatic-contaminated tropical marine environments. J Biosci Bioeng 2010; 110:48-52. [PMID: 20541115 DOI: 10.1016/j.jbiosc.2009.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/18/2009] [Accepted: 12/18/2009] [Indexed: 11/29/2022]
Abstract
Cycloclasticus sp. A5, which has been suggested to be a major degrader of petroleum aromatics spilled in temperate seas, showed higher degrading activities for petroleum aromatics, at both 25 degrees C and tropical sea temperature 30 degrees C, than the novel aromatic-degrading isolates, related to Altererythrobacter epoxidivorans (97.5% similarity in the almost full-length 16S rRNA gene sequence) and Rhodovulum iodosum (96.3% similarity), obtained after enrichment on crude oil in a continuous supply of Indonesian seawater. Cycloclasticus A5 degraded petroleum aromatics at a similar rate or faster at 30 degrees C as compared to 25 degrees C, but its growth on acetate was severely inhibited at 30 degrees C. These results suggest that, although their abundance would be low in tropical seas not contaminated with aromatics, the Cycloclasticus strains could be major degraders of petroleum aromatics spilled in tropical seas. The 16S rRNA gene of the Cycloclasticus strains has been identified from Indonesian seawater, and the gene fragments showed 96.7-96.8% similarities to that of Cycloclasticus A5. Introducing Cycloclasticus A5 may be an ecologically advantageous bioremediation strategy for petroleum-aromatic-contaminated tropical seas because strain A5 would disappear at 30 degrees C after complete consumption of the aromatics. Altererythrobacter and Rhodovulum-related isolates grew well on pyruvate in 10% strength marine broth at 30 degrees C whereas Cycloclasticus A5 did not grow well on acetate in the broth at 30 degrees C. These growth results, along with its petroleum-aromatic-degrading activity, suggest that the Altererythrobacter isolate could be an important petroleum-aromatic degrader in and around nutrient-rich tropical marine environments.
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Affiliation(s)
- Maki Teramoto
- NITE Biotechnology Development Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.
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