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Liang S, Li H, Wu H, Yan B, Song A. Microorganisms in coastal wetland sediments: a review on microbial community structure, functional gene, and environmental potential. Front Microbiol 2023; 14:1163896. [PMID: 37333635 PMCID: PMC10272453 DOI: 10.3389/fmicb.2023.1163896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Coastal wetlands (CW) are the junction of the terrestrial and marine ecosystems and have special ecological compositions and functions, which are important for maintaining biogeochemical cycles. Microorganisms inhabiting in sediments play key roles in the material cycle of CW. Due to the variable environment of CW and the fact that most CW are affected by human activities and climate change, CW are severely degraded. In-depth understanding of the community structure, function, and environmental potential of microorganisms in CW sediments is essential for wetland restoration and function enhancement. Therefore, this paper summarizes microbial community structure and its influencing factors, discusses the change patterns of microbial functional genes, reveals the potential environmental functions of microorganisms, and further proposes future prospects about CW studies. These results provide some important references for promoting the application of microorganisms in material cycling and pollution remediation of CW.
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Affiliation(s)
- Shen Liang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huai Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Baixing Yan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Aiwen Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Hafez T, Ortiz-Zarragoitia M, Cagnon C, Cravo-Laureau C, Duran R. Cold sediment microbial community shifts in response to crude oil water-accommodated fraction with or without dispersant: a microcosm study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44640-44656. [PMID: 36694068 DOI: 10.1007/s11356-023-25264-6] [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: 08/05/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
In cold environments, the low temperature slows down microbial metabolisms, such as the biodegradation processes of hydrocarbons, which are often stimulated by the addition of dispersants in oil spill disasters. In this study, we investigated the effects of hydrocarbon water-accommodated fraction (WAF) prepared with and without dispersant on benthic microbial communities in a microcosm experiment in which hydrocarbon removal was observed. Both WAFs contained similar polycyclic aromatic hydrocarbon (PAH) content. The microcosm experiment, set up with either pristine or contaminated sediments, was conducted for 21 days at 4 °C under WAF and WAF + dispersant conditions. The behavior of bacterial communities in response to WAF and WAF + dispersant was examined at both DNA and RNA levels, revealing the effect of WAF and WAF + dispersant on the resident and active communities respectively. The contaminated sediment showed less taxa responsive to the addition of both WAF and WAF + dispersant than the pristine sediment, indicating the legacy effect by the presence hydrocarbon-degrading and dispersant-resistant taxa inhabiting the contaminated sediment.
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Affiliation(s)
- Tamer Hafez
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
| | | | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France.
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3
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Tombuloglu H, Yaman C, Boudellioua I, Cevik E, Anil I, Aga O, Yaman AB, Qureshi A, Gunday ST. Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation. 3 Biotech 2023; 13:40. [PMID: 36636577 PMCID: PMC9829945 DOI: 10.1007/s13205-023-03460-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03460-y.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Cevat Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Imane Boudellioua
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, P.O. Box 2205, Dhahran, 31261 Saudi Arabia
| | - Emre Cevik
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
| | - Ismail Anil
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Omer Aga
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Ayse B. Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Aleem Qureshi
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Seyda Tugba Gunday
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
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Mathur V, Ulanova D. Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02073-x. [PMID: 35867138 DOI: 10.1007/s00248-022-02073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.
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Affiliation(s)
- Vartika Mathur
- Animal Plant Interactions Lab, Department of Zoology, Sri Venkateswara College, Benito Juarez Marg, Dhaula Kuan, New Delhi-110021, India.
| | - Dana Ulanova
- Department of Marine Resource Sciences, Faculty of Agriculture and Marine Science, Kochi University, Monobe, Nankoku city, Kochi, 783-8502, Japan.
- Center for Advanced Marine Core Research, Kochi University, Monobe, Nankoku city, Kochi, 783-8502, Japan.
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Salt flat microbial diversity and dynamics across salinity gradient. Sci Rep 2022; 12:11293. [PMID: 35788147 PMCID: PMC9253026 DOI: 10.1038/s41598-022-15347-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.
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Schultz J, Argentino ICV, Kallies R, Nunes da Rocha U, Rosado AS. Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano. Front Microbiol 2022; 13:885557. [PMID: 35602031 PMCID: PMC9114708 DOI: 10.3389/fmicb.2022.885557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 01/19/2023] Open
Abstract
Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.
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Affiliation(s)
- Júnia Schultz
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Alexandre Soares Rosado
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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7
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Akbari A, David C, Rahim AA, Ghoshal S. Salt selected for hydrocarbon-degrading bacteria and enhanced hydrocarbon biodegradation in slurry bioreactors. WATER RESEARCH 2021; 202:117424. [PMID: 34332190 DOI: 10.1016/j.watres.2021.117424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/12/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Hydrocarbon and salt contamination of surface and groundwater resources often co-occur from oil production activities. However, salt is often considered as a potential inhibitor of microbial activity. The feasibility of microbiome-based biotechnologies to treat the hydrocarbon contamination is contingent on the ability of the indigenous community to adapt to saline conditions. Here, we demonstrate enhanced hydrocarbon biodegradation in soil slurries under saline conditions of up to ~1 M (5%) compared to non-saline systems and the underlying causes. The mineralization extent of hexadecane was enhanced by salinity in the absence of nutrients. Salinity, similar to nutrients, enhanced the mineralization but through ecological selection. Microbial community analysis indicated a significant enrichment of Actinobacteria phylum and an increase in the absolute abundance of the hydrocarbon-degrading Dietzia genus, but a decrease in the total population size with salinity. Moreover, the in situ expression of alkane hydroxylases genes of Dietzia was generally increased with salinity. The data demonstrate that indigenous halotolerant hydrocarbon degraders were enriched, and their hydrocarbon degradation genes upregulated under saline conditions. These findings have positive implications for engineered biotreatment approaches for hydrocarbons in saline environments such as those affected with produced waters and oil sands tailing ponds.
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Affiliation(s)
- Ali Akbari
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Carolyn David
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Arshath Abdul Rahim
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada.
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8
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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9
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Effect of pyrene and phenanthrene in shaping bacterial communities in seagrass meadows sediments. Arch Microbiol 2021; 203:4259-4272. [PMID: 34100100 DOI: 10.1007/s00203-021-02410-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), originating from anthropogenic and natural sources, are highly concerned environmental pollutants. This study investigated the impact of two model PAHs (pyrene and phenanthrene) on bacterial community succession in the seagrass meadows sediment in a lab-scale microcosm. Halophila ovalis sediment slurry microcosms were established, one group was placed as a control, and the other two were treated with pyrene and phenanthrene. Bacterial community succession in response to respective PAHs was investigated by 16S rRNA amplicon sequencing. The results demonstrated that bacterial diversity decrease in each microcosm during the incubation process; however, the composition of bacterial communities in each microcosm was significantly different. Proteobacteria (37-89%), Firmicutes (9-41%), and Bacteroides (7-21%) were the predominant group at the phylum levels. Their abundance varies during the incubation process. Several previously reported hydrocarbon-degrading genera, such as Pseudomonas, Spinghobium, Sphingobacterium, Mycobacterium, Pseudoxanthomonas, Idiomarina, Stenotrophomonas, were detected in higher abundance in pyrene- and phenanthrene-treated microcosms. However, these genera were distinctly distributed in the pyrene and phenanthrene treatments, suggesting that certain bacterial groups favorably degrade different PAHs. Statistical analyses, such as ANOSIM and PERMANOVA, also revealed that significant differences existed among the treatments' bacterial consortia (P < 0.05). This work showed that polycyclic aromatic hydrocarbon significantly affects bacterial community succession, and different PAHs might influence the bacterial community succession differently.
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10
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, 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, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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11
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Bôto ML, Magalhães C, Perdigão R, Alexandrino DAM, Fernandes JP, Bernabeu AM, Ramos S, Carvalho MF, Semedo M, LaRoche J, Almeida CMR, Mucha AP. Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast. Front Microbiol 2021; 12:633659. [PMID: 33967978 PMCID: PMC8102992 DOI: 10.3389/fmicb.2021.633659] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
Oil spills are among the most catastrophic events to marine ecosystems and current remediation techniques are not suitable for ecological restoration. Bioremediation approaches can take advantage of the activity of microorganisms with biodegradation capacity thus helping to accelerate the recovery of contaminated environments. The use of native microorganisms can increase the bioremediation efficiency since they have higher potential to survive in the natural environment while preventing unpredictable ecological impacts associated with the introduction of non-native organisms. In order to know the geographical scale to which a native bioremediation consortium can be applied, we need to understand the spatial heterogeneity of the natural microbial communities with potential for hydrocarbon degradation. In the present study, we aim to describe the genetic diversity and the potential of native microbial communities to degrade petroleum hydrocarbons, at an early stage of bioremediation, along the NW Iberian Peninsula coast, an area particularly susceptible to oil spills. Seawater samples collected in 47 sites were exposed to crude oil for 2 weeks, in enrichment experiments. Seawater samples collected in situ, and samples collected after the enrichment with crude oil, were characterized for prokaryotic communities by using 16S rRNA gene amplicon sequencing and predictive functional profiling. Results showed a drastic decrease in richness and diversity of microbial communities after the enrichment with crude oil. Enriched microbial communities were mainly dominated by genera known to degrade hydrocarbons, namely Alcanivorax, Pseudomonas, Acinetobacter, Rhodococcus, Flavobacterium, Oleibacter, Marinobacter, and Thalassospira, without significant differences between geographic areas and locations. Predictive functional profiling of the enriched microbial consortia showed a high potential to degrade the aromatic compounds aminobenzoate, benzoate, chlorocyclohexane, chlorobenzene, ethylbenzene, naphthalene, polycyclic aromatic compounds, styrene, toluene, and xylene. Only a few genera contributed for more than 50% of this genetic potential for aromatic compounds degradation in the enriched communities, namely Alcanivorax, Thalassospira, and Pseudomonas spp. This work is a starting point for the future development of prototype consortia of hydrocarbon-degrading bacteria to mitigate oil spills in the Iberian NW coast.
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Affiliation(s)
- Maria L Bôto
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Catarina Magalhães
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Faculty of Sciences (FCUP), University of Porto, Porto, Portugal.,Ocean Frontier Institute, Dalhousie University, Halifax, NS, Canada
| | - Rafaela Perdigão
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Diogo A M Alexandrino
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Joana P Fernandes
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Ana M Bernabeu
- Marine and Environmental Geology (GEOMA) Group, Department of Marine Geosciences, University of Vigo, Vigo, Spain
| | - Sandra Ramos
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Maria F Carvalho
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Miguel Semedo
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - C Marisa R Almeida
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Faculty of Sciences (FCUP), University of Porto, Porto, Portugal
| | - Ana P Mucha
- Bioremediation and Ecosystems Functioning (EcoBioTec), CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Faculty of Sciences (FCUP), University of Porto, Porto, Portugal
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12
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Chernikova TN, Bargiela R, Toshchakov SV, Shivaraman V, Lunev EA, Yakimov MM, Thomas DN, Golyshin PN. Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Front Microbiol 2020; 11:572931. [PMID: 33193176 PMCID: PMC7655873 DOI: 10.3389/fmicb.2020.572931] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.
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Affiliation(s)
- Tatyana N Chernikova
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | | | - Evgenii A Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Michail M Yakimov
- Institute for Marine Biological Resources and Biotechnology of the National Research Council, IRBIM-CNR, Messina, Italy
| | - David N Thomas
- School of Ocean Sciences, Bangor University, Menai Bridge, United Kingdom
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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13
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Wei Z, Wang JJ, Gaston LA, Li J, Fultz LM, DeLaune RD, Dodla SK. Remediation of crude oil-contaminated coastal marsh soil: Integrated effect of biochar, rhamnolipid biosurfactant and nitrogen application. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122595. [PMID: 32298868 DOI: 10.1016/j.jhazmat.2020.122595] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Decontamination of oil spills from coastal wetland soils requires a delicate approach. A microcosm study was carried out to investigate the impact of integrated application of biochar, rhamnolipid (RL) biosurfactant and nitrogen (N) on petroleum hydrocarbon remediation in a Louisiana coastal saline marsh and their impact on soil microbial community. The soil was artificially contaminated with crude oil and subjected to treatments of different combinations of sugarcane residue biochar, RL, and coated urea. Total petroleum hydrocarbons (TPH) in the contaminated soil were analyzed periodically using gas chromatograph and associated soil bacterial community was studied using 16 s rRNA sequencing technologies. Results showed that integrated application of biochar + RL, biochar + N, and biochar + N+RL reduced 32.3%, 73.2%, 80.9% of TPH, respectively, and exhibited synergic interaction with higher efficiency than application individually. Combined treatments showed distinct functions that biochar increased the sorption of aromatic compounds, while RL and N enhanced the degradation of heavy and light aliphatic compounds. All remediation treatments caused reduction of soil bacterial diversity while RL and N shifted the microbial community to higher abundances of Proteobacteria and Bacteroidetes, respectively. Overall, the findings of this study demonstrate the positivity of applying integrated biochar, biosurfactant, and N treatment in oil remediation in wetland soils.
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Affiliation(s)
- Zhuo Wei
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jim J Wang
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.
| | - Lewis A Gaston
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jifeng Li
- Department of Life Sciences, Louisiana State University. Baton Rouge, LA 70803, USA
| | - Lisa M Fultz
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Ronald D DeLaune
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Syam K Dodla
- Red River Research Station, Louisiana State University Agricultural Center, Bossier City, LA 71112, USA
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14
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Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways. mSystems 2020; 5:5/4/e00668-20. [PMID: 32843540 PMCID: PMC7449609 DOI: 10.1128/msystems.00668-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments. Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil and chemically dispersed oil in coastal and offshore surface waters from the Texas-Louisiana continental shelf. Using a combination of analytical chemistry and 16S rRNA amplicon and metatranscriptomic sequencing, we provide a broad, comparative overview of the ecological response of hydrocarbon-degrading bacteria and their expression of hydrocarbon-degrading genes in marine surface waters over time between two oceanic biomes. We found evidence for the existence of different ecotypes of several commonly described hydrocarbon-degrading bacterial taxa which behaved differentially in coastal and offshore shelf waters despite being exposed to similar concentrations of oil, dispersants, and nutrients. This resulted in the differential expression of catabolic pathways for n-alkanes and polycyclic aromatic hydrocarbons (PAHs)—the two major categories of compounds found in crude oil—with preferential expression of n-alkane degradation genes in coastal waters while offshore microbial communities trended more toward the expression of PAH degradation genes. This was unexpected as it contrasts with the generally held view that n-alkanes, being more labile, are attacked before the more refractory PAHs. Collectively, our results provide new insights into the existence and potential consequences of niche partitioning of hydrocarbon-degrading taxa between neighboring marine environments. IMPORTANCE In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.
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15
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Miller JI, Techtmann S, Joyner D, Mahmoudi N, Fortney J, Fordyce JA, GaraJayeva N, Askerov FS, Cravid C, Kuijper M, Pelz O, Hazen TC. Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth. mBio 2020; 11:e01448-20. [PMID: 32817104 PMCID: PMC7439485 DOI: 10.1128/mbio.01448-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 11/20/2022] Open
Abstract
The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.
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Affiliation(s)
- John I Miller
- Bredesen Center, University of Tennessee, Knoxville, Tennessee, USA
| | - Stephen Techtmann
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Dominique Joyner
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nagissa Mahmoudi
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Julian Fortney
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - James A Fordyce
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | | | | | | | | | - Oliver Pelz
- BP International, Sunbury on Thames, United Kingdom
| | - Terry C Hazen
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
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16
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Araújo WJ, Oliveira JS, Araújo SCS, Minnicelli CF, Silva-Portela RCB, da Fonseca MMB, Freitas JF, Silva-Barbalho KK, Napp AP, Pereira JES, Peralba MCR, Passaglia LMP, Vainstein MH, Agnez-Lima LF. Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes. Front Bioeng Biotechnol 2020; 8:962. [PMID: 32850771 PMCID: PMC7431673 DOI: 10.3389/fbioe.2020.00962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/24/2020] [Indexed: 11/29/2022] Open
Abstract
The waste produced by petrochemical industries has a significant environmental impact. Biotechnological approaches offer promising alternatives for waste treatment in a sustainable and environment-friendly manner. Microbial consortia potentially clean up the wastes through degradation of hydrocarbons using biosurfactants as adjuvants. In this work, microbial consortia were obtained from a production water (PW) sample from a Brazilian oil reservoir using enrichment and selection approaches in the presence of oil as carbon source. A consortium was obtained using Bushnell-Haas (BH) mineral medium with petroleum. In parallel, another consortium was obtained in yeast extract peptone dextrose (YPD)-rich medium and was subsequently compared to the BH mineral medium with petroleum. Metagenomic sequencing of these microbial communities showed that the BH consortium was less diverse and predominantly composed of Brevibacillus genus members, while the YPD consortium was taxonomically more diverse. Functional annotation revealed that the BH consortium was enriched with genes involved in biosurfactant synthesis, while the YPD consortium presented higher abundance of hydrocarbon degradation genes. The comparison of these two consortia against consortia available in public databases confirmed the enrichment of biosurfactant genes in the BH consortium. Functional assays showed that the BH consortium exhibits high cellular hydrophobicity and formation of stable emulsions, suggesting that oil uptake by microorganisms might be favored by biosurfactants. In contrast, the YPD consortium was more efficient than the BH consortium in reducing interfacial tension. Despite the genetic differences between the consortia, analysis by a gas chromatography-flame ionization detector showed few significant differences regarding the hydrocarbon degradation rates. Specifically, the YPD consortium presented higher degradation rates of C12 to C14 alkanes, while the BH consortium showed a significant increase in the degradation of some polycyclic aromatic hydrocarbons (PAHs). These data suggest that the enrichment of biosurfactant genes in the BH consortium could promote efficient hydrocarbon degradation, despite its lower taxonomical diversity compared to the consortium enriched in YPD medium. Together, these results showed that cultivation in a minimal medium supplemented with oil was an efficient strategy in selecting biosurfactant-producing microorganisms and highlighted the biotechnological potential of these bacterial consortia in waste treatment and bioremediation of impacted areas.
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Affiliation(s)
- W J Araújo
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - J S Oliveira
- INESC-ID/IST - Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - S C S Araújo
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - C F Minnicelli
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - R C B Silva-Portela
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - M M B da Fonseca
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - J F Freitas
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - K K Silva-Barbalho
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
| | - A P Napp
- Laboratório de Fungos de Importância Médica e Biotecnológica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - J E S Pereira
- Laboratório de Fungos de Importância Médica e Biotecnológica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - M C R Peralba
- Laboratório de Química Analítica e Ambiental, Departamento de Química, Instituto de Química, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L M P Passaglia
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biociência, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - M H Vainstein
- Laboratório de Fungos de Importância Médica e Biotecnológica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L F Agnez-Lima
- Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazi
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17
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Thomas GE, Cameron TC, Campo P, Clark DR, Coulon F, Gregson BH, Hepburn LJ, McGenity TJ, Miliou A, Whitby C, McKew BA. Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece. Front Microbiol 2020; 11:1706. [PMID: 32765479 PMCID: PMC7379155 DOI: 10.3389/fmicb.2020.01706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.
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Affiliation(s)
- Gareth E. Thomas
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Tom C. Cameron
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Pablo Campo
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex, United Kingdom
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | | | - Leanne J. Hepburn
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Corinne Whitby
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Boyd A. McKew
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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18
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Lumibao CY, Bernik BM, Formel SK, Kandalepas D, Mighell KL, Pardue J, Van Bael SA, Blum MJ. Rhizosphere microbial communities reflect genotypic and trait variation in a salt marsh ecosystem engineer. AMERICAN JOURNAL OF BOTANY 2020; 107:941-949. [PMID: 32533589 DOI: 10.1002/ajb2.1497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
PREMISE There is growing recognition that intraspecific genetic variation in plants can influence associated soil microbial communities, but the functional bridges linking plant genotype with microbial community structure are not well understood. This deficit is due in part to a prevailing focus on characterizing relationships between microbial communities and functional trait variation among plant species or across plant communities, rather than within a single species. METHODS We examined whether and how spatiotemporal variation in salt marsh rhizosphere microbial communities reflect plant provenance (genotypic variation) and associated trait variation within an ecosystem engineer, Spartina alterniflora. We planted S. alterniflora from four genetically distinct source populations in replicate sets of experimental plots across a shoreline in southeastern Louisiana, USA. After 2 years, we measured functional plant traits and profiled microbial communities. RESULTS Bacterial and fungal α-diversity and richness were significantly higher in winter than in summer and corresponded to plant trait variation associated with provenance. Notably, 20% of the variation in fungal community composition was explained by trait differences while bacterial community structure did not reflect plant provenance or trait variation. However, evidence was found suggesting that bacterial communities are indirectly shaped by the influence of plant provenance on soil physicochemical properties. CONCLUSIONS This study illustrates that intraspecific genetic and corresponding trait variation in an ecosystem engineer can shape rhizosphere microbial communities, with fungal communities being more responsive than bacteria to the influence of plant provenance and associated trait variation. Our results highlight the potential relevance of plant intraspecific variation in plant-microbe-soil feedbacks shaping naturally depauperate ecosystems like salt marshes.
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Affiliation(s)
- Candice Y Lumibao
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Brittany M Bernik
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
- Tulane University, The ByWater Institute, New Orleans, LA, 70118, USA
| | - Stephen K Formel
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Demetra Kandalepas
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
- Tulane University, The ByWater Institute, New Orleans, LA, 70118, USA
| | - Kimberly L Mighell
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - John Pardue
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Sunshine A Van Bael
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Michael J Blum
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
- Tulane University, The ByWater Institute, New Orleans, LA, 70118, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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19
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Viggor S, Jõesaar M, Soares-Castro P, Ilmjärv T, Santos PM, Kapley A, Kivisaar M. Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates. Microorganisms 2020; 8:E652. [PMID: 32365784 PMCID: PMC7285258 DOI: 10.3390/microorganisms8050652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/30/2023] Open
Abstract
The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro Soares-Castro
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Tanel Ilmjärv
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro M. Santos
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Atya Kapley
- Director’s Research Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India;
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
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20
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Bruckberger MC, Morgan MJ, Bastow TP, Walsh T, Prommer H, Mukhopadhyay A, Kaksonen AH, Davis GB, Puzon GJ. Investigation into the microbial communities and associated crude oil-contamination along a Gulf War impacted groundwater system in Kuwait. WATER RESEARCH 2020; 170:115314. [PMID: 31835139 DOI: 10.1016/j.watres.2019.115314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
During the First Gulf War (1991) a large number of oil wells were destroyed and oil fires subsequently extinguished with seawater. As a result Kuwait's sparse fresh groundwater resources were severely contaminated with crude oil. Since then limited research has focused on the microbial community ecology of the groundwater and their impact on the associated contamination. Here, the microbial community ecology (bacterial, archaeal and eukaryotic) and how it relates to the characteristics of the hydrocarbon contaminants were examined for the first time since the 1991 event. This study was conducted using 15 wells along the main groundwater flow direction and detected several potential hydrocarbon degrading microorganisms such as Hyphomicrobiaceae, Porphyromonadaceae and Eurotiomycetes. The beta diversity of the microbial communities correlated significantly with total petroleum hydrocarbon (TPH) concentrations and salinity. The TPH consisted mainly of polar compounds present as an unresolved complex mixture (UCM) of a highly recalcitrant nature. Based on the proportions of TPH to dissolved organic carbon (DOC), the results indicate that some minor biodegradation has occurred within highly contaminated aquifer zones. However, overall the results from this study suggest that the observed variations in TPH concentrations among the sampled wells are mainly induced by mixing/dilution with pristine groundwater rather than by biodegradation of the contaminants. The findings make an important contribution to better understand the fate of the groundwater pollution in Kuwait, with important implications for the design of future remediation efforts.
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Affiliation(s)
- Melanie C Bruckberger
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; University of Western Australia, School of Agriculture and Environment, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | | | - Trevor P Bastow
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Canberra, ACT, Australia
| | - Henning Prommer
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; University of Western Australia, School of Earth Sciences, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Amitabha Mukhopadhyay
- Water Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, 13109, Safat, Kuwait
| | - Anna H Kaksonen
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Greg B Davis
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia
| | - Geoffrey J Puzon
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia.
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21
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Tai X, Li R, Zhang B, Yu H, Kong X, Bai Z, Deng Y, Jia L, Jin D. Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds. Microorganisms 2020; 8:microorganisms8020311. [PMID: 32102406 PMCID: PMC7074964 DOI: 10.3390/microorganisms8020311] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.
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Affiliation(s)
- Xin Tai
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China;
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
| | - Rui Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao Zhang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Hao Yu
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China;
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- Correspondence: (H.Y.); (D.J.); Tel.: +86-183-4184-9989 (H.Y.); +86-152-1009-8966 (D.J.)
| | - Xiao Kong
- School of Health and Public, Qingdao University, Qingdao 266071, China;
| | - Zhihui Bai
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lan Jia
- Research Institute of Mineral Resources Development and Utilization Technology and Equipment, Liaoning Technical University, Fuxin 123000, China;
| | - Decai Jin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (H.Y.); (D.J.); Tel.: +86-183-4184-9989 (H.Y.); +86-152-1009-8966 (D.J.)
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22
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Ramírez D, Vega-Alvarado L, Taboada B, Estradas-Romero A, Soto L, Juárez K. Bacterial diversity in surface sediments from the continental shelf and slope of the North West gulf of Mexico and the presence of hydrocarbon degrading bacteria. MARINE POLLUTION BULLETIN 2020; 150:110590. [PMID: 31718861 DOI: 10.1016/j.marpolbul.2019.110590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 06/10/2023]
Abstract
Bacteria play an important role in ecological processes in oil contaminated marine sediments. In this work, bacterial diversity studies with surface sediment samples from the NW Gulf of Mexico were performed, two from continental shelf and two from upper slope. The bacterial communities seem significantly influenced by depth, distance from the shoreline, temperature, dissolved oxygen and aluminum. The most abundant Phylum was Proteobacteria, Class Gammaproteobacteria. However, Class Deltaproteobacteria, Order Desulfuromonadales predominated in continental shelf and Order Alteromonadales (Gammaproteobacteria) prevailed in the upper slope sediments. Many potential hydrocarbon degrading bacterial genera were identified, 71 of the assigned genera were associated to hydrocarbon degradation processes. The genera Desulfobulbus and Haliea were confined to continental inner-shelf, while Shewanella and Fusibacter were mostly detected in deeper sediments. The occurrence and abundance of putative hydrocarbon degrading bacteria in this area, could be indicative of an impacted zone caused by the presence hydrocarbons in the environment.
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Affiliation(s)
- Diana Ramírez
- Posgrado en Ciencias del Mar y Limnología, UNAM, Circuito, Ciudad Universitaria, Coyoacán, D.F, C.P. 04510, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, UNAM, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, D.F, C.P. 04510, Mexico
| | - Blanca Taboada
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Campus Morelos, Av. Universidad 2001, Cuernavaca Morelos, C.P. 62210, Mexico
| | - Alejandro Estradas-Romero
- Facultad de Ciencias, UNAM. Circuito Exterior s/n, Coyoacán, Ciudad Universitaria, Coyoacán, Ciudad de México, C. P. 04510, Mexico
| | - Luis Soto
- Instituto de Ciencias del Mar y Limnología, UNAM, Circuito, Ciudad Universitaria, Coyoacán, D.F, C.P. 04510, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Campus Morelos, Av. Universidad 2001, Cuernavaca Morelos, C.P. 62210, Mexico.
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23
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Hackbusch S, Noirungsee N, Viamonte J, Sun X, Bubenheim P, Kostka JE, Müller R, Liese A. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico. MARINE POLLUTION BULLETIN 2020; 150:110683. [PMID: 31753565 DOI: 10.1016/j.marpolbul.2019.110683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.
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Affiliation(s)
- Steffen Hackbusch
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Nuttapol Noirungsee
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Juan Viamonte
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Xiaoxu Sun
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Paul Bubenheim
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Joel E Kostka
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
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24
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Bernhard AE, Chelsky A, Giblin AE, Roberts BJ. Influence of local and regional drivers on spatial and temporal variation of ammonia-oxidizing communities in Gulf of Mexico salt marshes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:825-834. [PMID: 31646752 DOI: 10.1111/1758-2229.12802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
We characterized ammonia-oxidizing archaea (AOA) and bacteria (AOB) from salt marsh sediments in the Gulf of Mexico over 5 years to identify environmental drivers of nitrifying community patterns following the Deepwater Horizon oil spill. Samples were collected from oiled and unoiled sites in July of 2012-2016 from 12 marshes spanning three regions on the Louisiana coast. No consistent oil effect was detected for either AOA or AOB abundance or community composition. At the local scale, abundance was correlated with changes in marsh elevation, suggesting that oxygen may be an important driver. Regional differences in abundance were best explained by salinity and soil moisture, while interannual variation may be more linked to changes in climate and Mississippi River discharge. Variation of AOA communities was correlated with organic sediment nutrients, while AOB communities were correlated with soil extractable nutrients. AOA and AOB diversity and AOB abundance decreased in 2014 in all regions, suggesting that broad-scale drivers, such as climate, may explain synchronous shifts throughout the coastal area. Our results provide insights about large-scale disturbances on nitrifying microbes in the Gulf of Mexico, and suggest that nitrogen cycling may be controlled primarily by local factors, but large-scale drivers might override these localized differences at times.
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Affiliation(s)
| | - Ariella Chelsky
- Louisiana Universities Marine Consortium, Chauvin, LA
- San Francisco Estuary Institute, Richmond, CA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA
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25
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Sun X, Chu L, Mercando E, Romero I, Hollander D, Kostka JE. Dispersant Enhances Hydrocarbon Degradation and Alters the Structure of Metabolically Active Microbial Communities in Shallow Seawater From the Northeastern Gulf of Mexico. Front Microbiol 2019; 10:2387. [PMID: 31749769 PMCID: PMC6842959 DOI: 10.3389/fmicb.2019.02387] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 10/01/2019] [Indexed: 01/23/2023] Open
Abstract
Dispersant application is a primary emergency oil spill response strategy and yet the efficacy and unintended consequences of this approach in marine ecosystems remain controversial. To address these uncertainties, ex situ incubations were conducted to quantify the impact of dispersant on petroleum hydrocarbon (PHC) biodegradation rates and microbial community structure at as close as realistically possible to approximated in situ conditions [2 ppm v/v oil with or without dispersant, at a dispersant to oil ratio (DOR) of 1:15] in surface seawater. Biodegradation rates were not substantially affected by dispersant application at low mixing conditions, while under completely dispersed conditions, biodegradation was substantially enhanced, decreasing the overall half-life of total PHC compounds from 15.4 to 8.8 days. While microbial respiration and growth were not substantially altered by dispersant treatment, RNA analysis revealed that dispersant application resulted in pronounced changes to the composition of metabolically active microbial communities, and the abundance of nitrogen-fixing prokaryotes, as determined by qPCR of nitrogenase (nifH) genes, showed a large increase. While the Gammaproteobacteria were enriched in all treatments, the Betaproteobacteria and different families of Alphaproteobacteria predominated in the oil and dispersant treatment, respectively. Results show that mixing conditions regulate the efficacy of dispersant application in an oil slick, and the quantitative increase in the nitrogen-fixing microbial community indicates a selection pressure for nitrogen fixation in response to a readily biodegradable, nitrogen-poor substrate.
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Affiliation(s)
- Xiaoxu Sun
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science and Technology, Guangzhou, China
| | - Lena Chu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Elisa Mercando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Isabel Romero
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
| | - David Hollander
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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26
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Turner RE, Rabalais NN, Overton EB, Meyer BM, McClenachan G, Swenson EM, Besonen M, Parsons ML, Zingre J. Oiling of the continental shelf and coastal marshes over eight years after the 2010 Deepwater Horizon oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1367-1376. [PMID: 31254894 DOI: 10.1016/j.envpol.2019.05.134] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/18/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
We measured the temporal and spatial trajectory of oiling from the April, 2010, Deepwater Horizon oil spill in water from Louisiana's continental shelf, the estuarine waters of Barataria Bay, and in coastal marsh sediments. The concentrations of 28 target alkanes and 43 target polycyclic aromatic hydrocarbons were determined in water samples collected on 10 offshore cruises, in 19 water samples collected monthly one km offshore at 13 inshore stations in 2010 and 2013, and in 16-60 surficial marsh sediment samples collected on each of 26 trips. The concentration of total aromatics in offshore waters peaked in late summer, 2010, at 100 times above the May, 2010 values, which were already slightly contaminated. There were no differences in surface or bottom water samples. The concentration of total aromatics declined at a rate of 73% y-1 to 1/1000th of the May 2010 values by summer 2016. The concentrations inside the estuary were proportional to those one km offshore, but were 10-30% lower. The oil concentrations in sediments were initially different at 1 and 10 m distance into the marsh, but became equal after 2 years. Thus, the distinction between oiled and unoiled sites became blurred, if not non-existent then, and oiling had spread over an area wider than was visible initially. The concentrations of oil in sediments were 100-1000 times above the May 2010 values, and dropped to 10 times higher after 8 years, thereafter, demonstrating a long-term contamination by oil or oil residues that will remain for decades. The chemical signature of the oil residues offshore compared to in the marsh reflects the more aerobic offshore conditions and water-soluble tendencies of the dissolved components, whereas the anaerobic marsh sediments will retain the heavier molecular components for a long time, and have a consequential effect on the ecosystems.
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Affiliation(s)
- R Eugene Turner
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Nancy N Rabalais
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Edward B Overton
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Buffy M Meyer
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Giovanna McClenachan
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA; Presently, Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Erick M Swenson
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Mark Besonen
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University - Corpus Christi, Corpus Christi, TX, 78412, USA
| | - Michael L Parsons
- Coastal Watershed Institute, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
| | - Jeffrey Zingre
- Coastal Watershed Institute, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
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27
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Miller JI, Techtmann S, Fortney J, Mahmoudi N, Joyner D, Liu J, Olesen S, Alm E, Fernandez A, Gardinali P, GaraJayeva N, Askerov FS, Hazen TC. Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities. Front Microbiol 2019; 10:995. [PMID: 31143165 PMCID: PMC6521576 DOI: 10.3389/fmicb.2019.00995] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/18/2019] [Indexed: 12/03/2022] Open
Abstract
The Caspian Sea, which is the largest landlocked body of water on the planet, receives substantial annual hydrocarbon input from anthropogenic sources (e.g., industry, agriculture, oil exploration, and extraction) and natural sources (e.g., mud volcanoes and oil seeps). The Caspian Sea also receives substantial amounts of runoff from agricultural and municipal sources, containing nutrients that have caused eutrophication and subsequent hypoxia in the deep, cold waters. The effect of decreasing oxygen saturation and cold temperatures on oil hydrocarbon biodegradation by a microbial community is not well characterized. The purpose of this study was to investigate the effect of oxic and anoxic conditions on oil hydrocarbon biodegradation at cold temperatures by microbial communities derived from the Caspian Sea. Water samples were collected from the Caspian Sea for study in experimental microcosms. Major taxonomic orders observed in the ambient water samples included Flavobacteriales, Actinomycetales, and Oceanospirillales. Microcosms were inoculated with microbial communities from the deepest waters and amended with oil hydrocarbons for 17 days. Hydrocarbon degradation and shifts in microbial community structure were measured. Surprisingly, oil hydrocarbon biodegradation under anoxic conditions exceeded that under oxic conditions; this was particularly evident in the degradation of aromatic hydrocarbons. Important microbial taxa associated with the anoxic microcosms included known oil degraders such as Oceanospirillaceae. This study provides knowledge about the ambient community structure of the Caspian Sea, which serves as an important reference point for future studies. Furthermore, this may be the first report in which anaerobic biodegradation of oil hydrocarbons exceeds aerobic biodegradation.
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Affiliation(s)
- John I Miller
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Stephen Techtmann
- Biosciences Division, Michigan Technological University, Houghton, MI, United States
| | - Julian Fortney
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC, Canada
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jiang Liu
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Scott Olesen
- Harvard School of Public Health, Cambridge, MA, United States
| | - Eric Alm
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Adolfo Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Piero Gardinali
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | | | | | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
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28
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Fernandes C, Kankonkar H, Meena RM, Menezes G, Shenoy BD, Khandeparker R. Metagenomic analysis of tarball-associated bacteria from Goa, India. MARINE POLLUTION BULLETIN 2019; 141:398-403. [PMID: 30955749 DOI: 10.1016/j.marpolbul.2019.02.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.
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Affiliation(s)
- Clafy Fernandes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Harshada Kankonkar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Ram Murti Meena
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Gilda Menezes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Belle Damodara Shenoy
- CSIR-National Institute of Oceanography Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam, 530017, Andhra Pradesh, India
| | - Rakhee Khandeparker
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India.
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Asemoloye MD, Jonathan SG, Ahmad R. Degradation of 2, 2-Dichlorovinyl dimethyl phosphate (dichlorvos) through the rhizosphere interaction between Panicum maximum Jacq and some selected fungi. CHEMOSPHERE 2019; 221:403-411. [PMID: 30648645 DOI: 10.1016/j.chemosphere.2019.01.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Many fungi have been reported to enhance the plant responses and degradation of several persistent pollutants in soils. In this study, five dominant fungi strains were identified from a pesticides polluted soil in Nigeria and screened for the expression of phosphoesterase (opd and mpd) and catechol 1, 2-dioxygenase (afk2 and afk4) genes using Reverse Transcriptase-PCR technique. Their rhizosphere interaction with plant (Panicum maximum) was further studied for the degradation of 2, 2 Dichlorovinyl dimethyl phosphate (dichlorvos). Fungal strains were mixed with Spent Mushroom Compost (SMC) of Pleurotus ostreatus in 1:100 w/w and then applied to a sterilized pesticide polluted soil (5 kg) at increasing concentrations of 10, 20, 30 and 40% with two controls (plant only and fungi-SMC mixture only). Degradation efficiency (DE), degradation rate (K1) and half-life (t1/2) of dichlorvos was calculated in each treatment after 90-day of planting. All the strains were registered at NCBI gene-bank with accession numbers KY693969, KY488464, KY488465, KY693971 and KY693972: they all possess the tested genes although mpd and opd were over-expressed in all the strains while afk2 and afk4 were moderately expressed. The plant-fungi-SMC interaction synergistically sped-up dichlorvos degradation rate in less time period, appreciable loss of dichlorvos at 72.23 and 82.70% DE were observed in 30 and 40% treatments respectively as compared to controls 1 and 2 having 62.20 ± 3.07 and 62.33 ± 4.69% DE respectively. In the same way, the 40% treatment gave the best k1 and t1/2 of 1.755 and 0.40 ± 0.02/day respectively.
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Affiliation(s)
- Michael Dare Asemoloye
- Mycology/Fungal Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria.
| | | | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, 22060 Abbottabad, Pakistan.
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Biodegradability of legacy crude oil contamination in Gulf War damaged groundwater wells in Northern Kuwait. Biodegradation 2019; 30:71-85. [DOI: 10.1007/s10532-019-09867-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/19/2019] [Indexed: 10/27/2022]
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Shin B, Kim M, Zengler K, Chin KJ, Overholt WA, Gieg LM, Konstantinidis KT, Kostka JE. Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment. Sci Rep 2019; 9:1239. [PMID: 30718896 PMCID: PMC6361983 DOI: 10.1038/s41598-018-36567-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, 92093, USA
| | - Kuk-Jeong Chin
- Department of Biology, Georgia State University, Atlanta, 30302, USA
| | - Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, USA.
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Ní Chadhain SM, Miller JL, Dustin JP, Trethewey JP, Jones SH, Launen LA. An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes. MARINE POLLUTION BULLETIN 2018; 136:351-364. [PMID: 30509817 PMCID: PMC6281173 DOI: 10.1016/j.marpolbul.2018.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/26/2018] [Accepted: 09/02/2018] [Indexed: 06/09/2023]
Abstract
Small fringing marshes are ecologically important habitats often impacted by petroleum. We characterized the phylogenetic structure (16S rRNA) and petroleum hydrocarbon degrading alkane hydroxylase genes (alkB and CYP 153A1) in a sediment microbial community from a New Hampshire fringing marsh, using alkane-exposed dilution cultures to enrich for petroleum degrading bacteria. 16S rRNA and alkB analysis demonstrated that the initial sediment community was dominated by Betaproteobacteria (mainly Comamonadaceae) and Gammaproteobacteria (mainly Pseudomonas), while CYP 153A1 sequences predominantly matched Rhizobiales. 24 h of exposure to n-hexane, gasoline, dodecane, or dilution culture alone reduced functional and phylogenetic diversity, enriching for Gammaproteobacteria, especially Pseudomonas. Gammaproteobacteria continued to dominate for 10 days in the n-hexane and no alkane exposed samples, while dodecane and gasoline exposure selected for gram-positive bacteria. The data demonstrate that small fringing marshes in New England harbor petroleum-degrading bacteria, suggesting that petroleum degradation may be an important fringing marsh ecosystem function.
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Affiliation(s)
- Sinéad M Ní Chadhain
- Department of Biology, LSCB 217, University of South Alabama, 5871 USA Drive N., Mobile, AL 36688, USA
| | - Jarett L Miller
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - John P Dustin
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Jeff P Trethewey
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Stephen H Jones
- Department of Natural Resources and the Environment, University of New Hampshire, 285 Rudman Hall, 46 College Rd., Durham, NH 03824, USA
| | - Loren A Launen
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA.
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Bae HS, Huang L, White JR, Wang J, DeLaune RD, Ogram A. Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 241:136-147. [PMID: 29804046 DOI: 10.1016/j.envpol.2018.05.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities play vital roles in the biogeochemistry of nutrients in coastal saltmarshes, ultimately controlling water quality, nutrient cycling, and detoxification. We determined the structure of microbial populations inhabiting coastal saltmarsh sediments from northern Barataria Bay, Louisiana, USA to gain insight into impacts on the biogeochemical cycles affected by Macondo oil from the 2010 Deepwater Horizon well blowout two years after the accident. Quantitative PCR directed toward specific functional genes revealed that oiled marshes were greatly diminished in the population sizes of diazotrophs, denitrifiers, nitrate-reducers to ammonia, methanogens, sulfate-reducers and anaerobic aromatic degraders, and harbored elevated numbers of alkane-degraders. Illumina 16S rRNA gene sequencing indicated that oiling greatly changed the structure of the microbial communities, including significant decreases in diversity. Oil-driven changes were also demonstrated in the structure of two functional populations, denitrifying and sulfate reducing prokaryotes, using nirS and dsrB as biomarkers, respectively. Collectively, the results from 16S rRNA and functional genes indicated that oiling not only markedly altered the microbial community structures, but also the sizes and structures of populations involved in (or regulating) a number of important nutrient biogeochemical cycles in the saltmarshes. Alterations such as these are associated with potential deterioration of ecological services, and further studies are necessary to assess the trajectory of recovery of microbial-mediated ecosystem functions over time in oiled saltmarsh sediment.
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Affiliation(s)
- Hee-Sung Bae
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611-0290, USA.
| | - Laibin Huang
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611-0290, USA
| | - John R White
- College of the Coast and Environment, Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jim Wang
- School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Ronald D DeLaune
- College of the Coast and Environment, Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Andrew Ogram
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611-0290, USA
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Sánchez-Soto Jiménez MF, Cerqueda-García D, Montero-Muñoz JL, Aguirre-Macedo ML, García-Maldonado JQ. Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. PeerJ 2018; 6:e5583. [PMID: 30225176 PMCID: PMC6139248 DOI: 10.7717/peerj.5583] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 08/14/2018] [Indexed: 12/31/2022] Open
Abstract
The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto Jiménez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM). Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida. Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Jorge L Montero-Muñoz
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Ma Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida. Departamento de Recursos del Mar, Mérida, Yucatán, México
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Recovery of horse fly populations in Louisiana marshes following the Deepwater Horizon oil spill. Sci Rep 2018; 8:13777. [PMID: 30213957 PMCID: PMC6137066 DOI: 10.1038/s41598-018-31442-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/16/2018] [Indexed: 12/03/2022] Open
Abstract
The Deepwater Horizon oil spill in April 2010 had unprecedented impact on the Gulf of Mexico. We established the greenhead horse fly (Tabanus nigrovittatus Macquart) as a bioindicator of marsh health. This species is bound to coastal marshes, since its larvae develop as top invertebrate predators in the marsh soil. Immediately after the oil spill (2010–2011), populations of this horse fly declined in oiled areas of Louisiana marshes with significant impacts on genetic structure. In this follow-up study five years after the catastrophic event (2015–2016), we now report signs of recovery of populations in formerly oiled areas. Fly numbers increased compared to previous counts. Previously detected genetic bottlenecks in oiled populations have disappeared. Migration into oiled areas began to replenish formerly depleted horse fly populations in impacted regions with populations from non-oiled areas as an important source of migrants. Parameters of family structure that had been impacted by the oil spill (number of breeding parents, effective population size, number of family clusters) rebounded to levels similar to or exceeding those in non-oiled control areas.
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Lu Y, Yuan J, Lu X, Su C, Zhang Y, Wang C, Cao X, Li Q, Su J, Ittekkot V, Garbutt RA, Bush S, Fletcher S, Wagey T, Kachur A, Sweijd N. Major threats of pollution and climate change to global coastal ecosystems and enhanced management for sustainability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:670-680. [PMID: 29709838 DOI: 10.1016/j.envpol.2018.04.016] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Coastal zone is of great importance in the provision of various valuable ecosystem services. However, it is also sensitive and vulnerable to environmental changes due to high human populations and interactions between the land and ocean. Major threats of pollution from over enrichment of nutrients, increasing metals and persistent organic pollutants (POPs), and climate change have led to severe ecological degradation in the coastal zone, while few studies have focused on the combined impacts of pollution and climate change on the coastal ecosystems at the global level. A global overview of nutrients, metals, POPs, and major environmental changes due to climate change and their impacts on coastal ecosystems was carried out in this study. Coasts of the Eastern Atlantic and Western Pacific were hotspots of concentrations of several pollutants, and mostly affected by warming climate. These hotspots shared the same features of large populations, heavy industry and (semi-) closed sea. Estimation of coastal ocean capital, integrated management of land-ocean interaction in the coastal zone, enhancement of integrated global observation system, and coastal ecosystem-based management can play effective roles in promoting sustainable management of coastal marine ecosystems. Enhanced management from the perspective of mitigating pollution and climate change was proposed.
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Affiliation(s)
- Yonglong Lu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jingjing Yuan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaotian Lu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Su
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yueqing Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenchen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianghui Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qifeng Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jilan Su
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | | | | | - Simon Bush
- Environmental Policy Group, Wageningen University, Wageningen, 6706 KN, The Netherlands
| | - Stephen Fletcher
- UNEP World Conservation Monitoring Centre, Cambridge, CB3 0DL, UK; Centre for Marine Conservation Policy Research, Plymouth University, Plymouth Devon, PL4 8AA, UK
| | - Tonny Wagey
- Centre for Coastal and Marine Resources Study, Bogor Agricultural University, Bogor, 16680, West Java, Indonesia
| | - Anatolii Kachur
- Pacific Institute of Geography, Far East Branch, Russian Academy of Sciences, Vladivostok, 690041, Russia
| | - Neville Sweijd
- Council for Scientific and Industrial Research (CSIR), Pretoria, 0001, South Africa
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Bruckberger MC, Bastow TP, Morgan MJ, Gleeson D, Banning N, Davis G, Puzon GJ. Biodegradability of polar compounds formed from weathered diesel. Biodegradation 2018; 29:443-461. [DOI: 10.1007/s10532-018-9841-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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Noh J, Kim H, Lee C, Yoon SJ, Chu S, Kwon BO, Ryu J, Kim JJ, Lee H, Yim UH, Giesy JP, Khim JS. Bioaccumulation of Polycyclic Aromatic Hydrocarbons (PAHs) by the Marine Clam, Mactra veneriformis, Chronically Exposed to Oil-Suspended Particulate Matter Aggregates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7910-7920. [PMID: 29898595 DOI: 10.1021/acs.est.7b06692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dispersion and biodegradation of petroleum hydrocarbons are significantly enhanced by formation of oil-suspended particulate matter aggregates (OSAs), but little is known about their adverse effects on benthic invertebrates or microbes. In this study, we investigated: (1) bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) by the marine bivalve, Mactra veneriformis and (2) changes in composition and relative abundances of microbes, during 50-d of an OSAs feeding experiment. Total concentrations of PAHs increased more rapidly during the first week of exposure, peaked at Day 30, then gradually declined to the end of experiment. While bioaccumulation of PAHs by clams varied among the 20 target compounds, two major groups of PAHs were identified by cluster analysis. One group including 3-methylphenanthrene, 1,6-dimethylphenanthrene, 1,2,6,9-tetramethylphenanthrene, and benzo[ a]anthracene showed a fairly constant rate of accumulation, while the second group including 2-methyldibenzothiophene, 2,4-dimethyldibenzothiophene, 2,4,7-trimethyldibenzothiophene, 3-methylchrysene, 6-ethylchrysene, and 1,3,6-trimethylchrysene exhibited a bell-shaped pattern. Bioaccumulation of PAHs by clams was dependent on changes in abundance of Gammaproteobacteria, indicating active degradations of hydrocarbons by selected species. Six key species included: Porticoccus litoralis, Porticoccus hydrocarbonoclasticus, Cycloclasticus spirillensus, Alcanivorax borkumensis, Alcanivorax dieselolei, and Alkalimarinus sediminis. These results are the first to demonstrate interactions of OSAs and macrofauna/microbe in oil cleanup operations.
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Affiliation(s)
- Junsung Noh
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Hosang Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Changkeun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seo Joon Yoon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seungoh Chu
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Bong-Oh Kwon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Jongseong Ryu
- Department of Marine Biotechnology , Anyang University , Ganghwa-gun , Incheon Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Un Hyuk Yim
- Oil and POPs Research Group , Korea Institute of Ocean Science and Technology , Geoje , Republic of Korea
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan Canada
- Department of Zoology, and Center for Integrative Toxicology , Michigan State University , East Lansing , Michigan United States
- School of Biological Sciences , University of Hong Kong , Hong Kong , SAR China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , People's Republic of China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
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Membrane Fatty Acid Composition and Cell Surface Hydrophobicity of Marine Hydrocarbonoclastic Alcanivorax borkumensis SK2 Grown on Diesel, Biodiesel and Rapeseed Oil as Carbon Sources. Molecules 2018; 23:molecules23061432. [PMID: 29899233 PMCID: PMC6100348 DOI: 10.3390/molecules23061432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/06/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022] Open
Abstract
The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is well known for its ability to successfully degrade various mixtures of n-alkanes occurring in marine oil spills. For effective growth on these compounds, the bacteria possess the unique capability not only to incorporate but also to modify fatty intermediates derived from the alkane degradation pathway. High efficiency of both these processes provides better competitiveness for a single bacteria species among hydrocarbon degraders. To examine the efficiency of A. borkumensis to cope with different sources of fatty acid intermediates, we studied the growth rates and membrane fatty acid patterns of this bacterium cultivated on diesel, biodiesel and rapeseed oil as carbon and energy source. Obtained results revealed significant differences in both parameters depending on growth substrate. Highest growth rates were observed with biodiesel, while growth rates on rapeseed oil and diesel were lower than on the standard reference compound (hexadecane). The most remarkable observation is that cells grown on rapeseed oil, biodiesel, and diesel showed significant amounts of the two polyunsaturated fatty acids linoleic acid and linolenic acid in their membrane. By direct incorporation of these external fatty acids, the bacteria save energy allowing them to degrade those pollutants in a more efficient way. Such fast adaptation may increase resilience of A. borkumensis and allow them to strive and maintain populations in more complex hydrocarbon degrading microbial communities.
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Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China. Syst Appl Microbiol 2018; 41:516-527. [PMID: 29934111 DOI: 10.1016/j.syapm.2018.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/24/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Actinobacteria from special habitats are of interest due to their producing of bioactive compounds and diverse ecological functions. However, little is known of the diversity and functional traits of actinobacteria inhabiting coastal salt marsh soils. We assessed actinobacterial diversity from eight coastal salt marsh rhizosphere soils from Jiangsu Province, China, using culture-based and 16S rRNA gene high throughput sequencing (HTS) methods, in addition to evaluating their plant growth-promoting (PGP) traits of isolates. Actinobacterial sequences represented 2.8%-43.0% of rhizosphere bacterial communities, as determined by HTS technique. The actinobacteria community comprised 34 families and 79 genera. In addition, 196 actinobacterial isolates were obtained, of which 92 representative isolates were selected for further 16S rRNA gene sequencing and phylogenetic analysis. The 92 strains comprised seven suborders, 12 families, and 20 genera that included several potential novel species. All representative strains were tested for their ability of producing indole acetic acid (IAA), siderophores, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), hydrolytic enzymes, and phosphate solubilization. Based on the presence of multiple PGP traits, two strains, Streptomyces sp. KLBMP S0051 and Micromonospora sp. KLBMP S0019 were selected for inoculation of wheat seeds grown under salt stress. Both strains promoted seed germination, and KLBMP S0019 significantly enhanced seedling growth under NaCl stress. Our study demonstrates that coastal salt marsh rhizosphere soils harbor a diverse reservoir of actinobacteria that are potential resources for the discovery of novel species and functions. Moreover, several of the isolates identified here are good candidates as PGP bacteria that may contribute to plant adaptions to saline soils.
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Plewniak F, Crognale S, Rossetti S, Bertin PN. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. Front Microbiol 2018; 9:820. [PMID: 29755441 PMCID: PMC5932151 DOI: 10.3389/fmicb.2018.00820] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simona Rossetti
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
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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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Zhang S, Hu Z, Wang H. A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill. Front Microbiol 2018; 9:520. [PMID: 29628913 PMCID: PMC5876298 DOI: 10.3389/fmicb.2018.00520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/08/2018] [Indexed: 12/19/2022] Open
Abstract
The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.
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Affiliation(s)
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, China
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Alegbeleye OO, Opeolu BO, Jackson VA. Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation. ENVIRONMENTAL MANAGEMENT 2017; 60:758-783. [PMID: 28573478 DOI: 10.1007/s00267-017-0896-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/23/2017] [Indexed: 05/21/2023]
Abstract
The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.
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Affiliation(s)
- Oluwadara Oluwaseun Alegbeleye
- Department of Environmental and Occupational Studies, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa.
| | - Beatrice Oluwatoyin Opeolu
- Extended Curriculum Programmes, Faculty of Applied Sciences, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa
| | - Vanessa Angela Jackson
- Department of Biotechnology and Consumer Science, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa
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Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill. Appl Environ Microbiol 2017; 83:AEM.00784-17. [PMID: 28778895 DOI: 10.1128/aem.00784-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 11/20/2022] Open
Abstract
Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria (Rhizobiales), Chloroflexi (Dehalococcoidia), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts.IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The Deepwater Horizon oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to in situ environmental changes, aside from oil exposure.
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Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
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Asemoloye MD, Ahmad R, Jonathan SG. Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action. PLoS One 2017; 12:e0183373. [PMID: 28859100 PMCID: PMC5578508 DOI: 10.1371/journal.pone.0183373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 11/19/2022] Open
Abstract
Fungi are usually involved in degradation/deterioration of many anthropogenic wastes due to their verse enzyme secretions and adaptive capabilities. In this study, five dominant fungal strains were isolated from an aged lindane polluted site, they were all mixed (100 mg each) together with pent mushroom compost (SMC) and applied to lindane polluted soil (5 kg) at 10, 20, 30, 40% and control 0% (soil with no treatment), these were used to grow M. maximus Jacq for 3 months. To establish lindane degradation, deductions such as Degradation rate (K1), Half-life (t1/2) and Degradation efficiency (DE) were made based on the analyzed lindane concentrations before and after the experiment. We also tested the presence and expressions of phosphoesterases (mpd and opd-A) and catechol 1,2-dioxygenases (efk2 and efk4) genes in the strains. The stains were identified as Aspergillus niger (KY693970); Talaromyces atroroseus (KY488464), Talaromyces purpurogenus (KY488468), Yarrowia lipolytica (KY488469) and Aspergillus flavus (KY693973) through morphological and molecular methods. Combined rhizospheric action of M. maximus and fungi speed up lindane degradation rate, initially detected lindane concentration of 45 mg/kg was reduced to 11.26, 9.34 and 11.23 mg/kg in 20, 30 and 40% treatments respectively making 79.76, 85.93 and 88.67% degradation efficiencies. K1 of 1.29 was recorded in control while higher K1 of 1.60, 1.96 and 2.18 /day were recorded in 20, 30 and 40% treatments respectively. The best t1/2 of 0.32 and 0.35 /day were recorded in 40 and 30% compared to control (0.54 /day). All the strains were also affirmed to possess the tested genes; opd was overexpressed in all the strains except KY693973 while mpd was overexpressed in KY693970, KY488464 but moderately expressed in KY488468, KY488469 and KY693973. However, efk genes were under-expressed in most of the strains except KY488469 and KY693973 which showed moderate expression of efk4. This work suggests that the synergistic association of the identified rhizospheric fungi and M. maximus roots could be used to remove lindane in soil at a limited time period and this combination could be used at large scale.
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Affiliation(s)
- Michael Dare Asemoloye
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
| | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Segun Gbolagade Jonathan
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
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Duran R, Cravo-Laureau C. Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment. FEMS Microbiol Rev 2016; 40:814-830. [PMID: 28201512 PMCID: PMC5091036 DOI: 10.1093/femsre/fuw031] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/28/2015] [Accepted: 07/24/2016] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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Bourguignon N, Bargiela R, Rojo D, Chernikova TN, de Rodas SAL, García-Cantalejo J, Näther DJ, Golyshin PN, Barbas C, Ferrero M, Ferrer M. Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. World J Microbiol Biotechnol 2016; 32:201. [PMID: 27785708 DOI: 10.1007/s11274-016-2163-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.
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Affiliation(s)
- Natalia Bourguignon
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | | | - Sara A López de Rodas
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jesús García-Cantalejo
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniela J Näther
- Institute for Microbiology, Biocentre, Goethe University, Frankfurt, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | - Marcela Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
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Molaei M, Sheng J. Succeed escape: Flow shear promotes tumbling of Escherichia colinear a solid surface. Sci Rep 2016; 6:35290. [PMID: 27752062 PMCID: PMC5082759 DOI: 10.1038/srep35290] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022] Open
Abstract
Understanding how bacteria move close to a surface under various stimuli is crucial for a broad range of microbial processes including biofilm formation, bacterial transport and migration. While prior studies focus on interactions between single stimulus and bacterial suspension, we emphasize on compounding effects of flow shear and solid surfaces on bacterial motility, especially reorientation and tumble. We have applied microfluidics and digital holographic microscopy to capture a large number (>105) of 3D Escherichia coli trajectories near a surface under various flow shear. We find that near-surface flow shear promotes cell reorientation and mitigates the tumble suppression and re-orientation confinement found in a quiescent flow, and consequently enhances surface normal bacterial dispersion. Conditional sampling suggests that two complimentary hydrodynamic mechanisms, Jeffrey Orbit and shear-induced flagella unbundling, are responsible for the enhancement in bacterial tumble motility. These findings imply that flow shear may mitigate cell trapping and prevent biofilm initiation.
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Affiliation(s)
- Mehdi Molaei
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas, United States of America
| | - Jian Sheng
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas, United States of America
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