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Kundu K, Van Landuyt J, Mattelin V, Martin B, Neyts M, Parmentier K, Boon N. Enhanced removal of warfare agent tri-nitro-toluene by a Methylophaga-dominated microbiome. MARINE POLLUTION BULLETIN 2023; 190:114866. [PMID: 37001405 DOI: 10.1016/j.marpolbul.2023.114866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Historical exposure of the marine environment to 2,4,6-trinitrotoluene (TNT) happened due to the dumping of left-over munitions. Despite significant research on TNT decontamination, the potential of marine microbiome for TNT degradation remains only little explored. In this study, TNT degradation experiments were conducted with sediment located near the World War I munition dumpsite - Paardenmarkt in the Belgian part of North Sea. A slow removal was observed using TNT as sole source of C and N, which could be enhanced by adding methanol. Degradation was reflected in nitro-reduced metabolites and microbial growth. 16S Illumina sequencing analysis revealed several enriched genera that used TNT as a sole source of C and N - Colwellia, Thalossospira, and Methylophaga. Addition of methanol resulted in increased abundance of Methylophaga, which corresponded to the rapid removal of TNT. Methanol enhanced the degradation by providing additional energy and establishing syntrophic association between methanol-utilizing and TNT-utilizing bacteria.
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Affiliation(s)
- Kankana Kundu
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium.
| | - Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium
| | - Bram Martin
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium
| | - Marijke Neyts
- Royal Belgian Institute of Natural Science (RBIN), 3de en 23ste Linieregimentsplein, 8400 Oostende, Belgium
| | - Koen Parmentier
- Royal Belgian Institute of Natural Science (RBIN), 3de en 23ste Linieregimentsplein, 8400 Oostende, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium; Centre for Advanced Process Technology for Urban Resource recovery (CAPTURE), Ghent, Belgium.
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2
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Fahmi AM, Summers S, Jones M, Bowler B, Hennige S, Gutierrez T. Effect of ocean acidification on the growth, response and hydrocarbon degradation of coccolithophore-bacterial communities exposed to crude oil. Sci Rep 2023; 13:5013. [PMID: 36973465 PMCID: PMC10042988 DOI: 10.1038/s41598-023-31784-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Hydrocarbon-degrading bacteria, which can be found living with eukaryotic phytoplankton, play a pivotal role in the fate of oil spillage to the marine environment. Considering the susceptibility of calcium carbonate-bearing phytoplankton under future ocean acidification conditions and their oil-degrading communities to oil exposure under such conditions, we investigated the response of non-axenic E. huxleyi to crude oil under ambient versus elevated CO2 concentrations. Under elevated CO2 conditions, exposure to crude oil resulted in the immediate decline of E. huxleyi, with concomitant shifts in the relative abundance of Alphaproteobacteria and Gammaproteobacteria. Survival of E. huxleyi under ambient conditions following oil enrichment was likely facilitated by enrichment of oil-degraders Methylobacterium and Sphingomonas, while the increase in relative abundance of Marinobacter and unclassified Gammaproteobacteria may have increased competitive pressure with E. huxleyi for micronutrient acquisition. Biodegradation of the oil was not affected by elevated CO2 despite a shift in relative abundance of known and putative hydrocarbon degraders. While ocean acidification does not appear to affect microbial degradation of crude oil, elevated mortality responses of E. huxleyi and shifts in the bacterial community illustrates the complexity of microalgal-bacterial interactions and highlights the need to factor these into future ecosystem recovery projections.
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Affiliation(s)
- Afiq Mohd Fahmi
- School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Fakulti Sains dan Sekitaran Marin, Universiti Malaysia Terengganu, 21030, Kuala, Terengganu, Malaysia
| | - Stephen Summers
- School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- The Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Martin Jones
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, NE17RU, UK
| | - Bernard Bowler
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, NE17RU, UK
| | - Sebastian Hennige
- School of Geosciences, University of Edinburgh, Edinburgh, EH9 3JW, UK.
| | - Tony Gutierrez
- School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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3
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [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: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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4
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Liu Y, Chen S, Xie Z, Zhang L, Wang J, Fang J. Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench. Microorganisms 2023; 11:microorganisms11030630. [PMID: 36985204 PMCID: PMC10052102 DOI: 10.3390/microorganisms11030630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518000, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Li Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Correspondence: (J.W.); (J.F.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
- Correspondence: (J.W.); (J.F.)
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5
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Gomez NCF, Onda DFL. Potential of sediment bacterial communities from Manila Bay (Philippines) to degrade low-density polyethylene (LDPE). Arch Microbiol 2022; 205:38. [PMID: 36565350 DOI: 10.1007/s00203-022-03366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/02/2022] [Accepted: 12/02/2022] [Indexed: 12/25/2022]
Abstract
The persistence of plastics and its effects in different environments where they accumulate, particularly in coastal areas, is of serious concern. These plastics exhibit signs of degradation, possibly mediated by microorganisms. In this study, we investigated the potential of sediment microbial communities from Manila Bay, Philippines, which has a severe plastics problem, to degrade low-density polyethylene (LDPE). Plastics in selected sites were quantified and sediment samples from sites with the lowest and highest plastic accumulation were collected. These sediments were then introduced and incubated with LDPE in vitro for a period of 91 days. Fourier transform infrared spectroscopy detected the appearance of carbonyl and vinyl products on the plastic surface, indicating structural surface modifications attributed to polymer degradation. Communities attached to the plastics were profiled using high-throughput sequencing of the V4-V5 region of the 16S rRNA gene. Members of the phylum Proteobacteria dominated the plastic surface throughout the experiment. Several bacterial taxa associated with hydrocarbon degradation were also enriched, with some taxa positively correlating with the biodegradation indices, suggesting potential active roles in the partial biodegradation of plastics. Other taxa were also present, which might be consuming by-products or providing nourishment for other groups, indicating synergy in utilizing the plastic as the main carbon source and creation of a microenvironment within the plastics biofilm. This study showed that sediment microbes from Manila Bay may have naturally occurring microbial groups potentially capable of partially degrading plastics, supporting previous studies that the biodegradation potential for plastics is ubiquitously present in marine microbial assemblages.
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Affiliation(s)
- Norchel Corcia F Gomez
- Microbial Oceanography Laboratory, The Marine Science Institute, University of the Philippines Diliman, Velasquez St., 1101, Quezon City, Philippines
| | - Deo Florence L Onda
- Microbial Oceanography Laboratory, The Marine Science Institute, University of the Philippines Diliman, Velasquez St., 1101, Quezon City, Philippines.
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6
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Tiralerdpanich P, Nasaree S, Pinyakong O, Sonthiphand P. Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117849. [PMID: 34325096 DOI: 10.1016/j.envpol.2021.117849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/07/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg-1), moderate (600 mg kg-1), and high (1200 mg kg-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg-1 sediment day-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg-1 sediment day-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.
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Affiliation(s)
- Parichaya Tiralerdpanich
- International Postgraduate Program in Hazardous Substance and Environmental Management, Chulalongkorn University, 9th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand
| | - Sirawit Nasaree
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Rachadhavi, Bangkok, 10400, Thailand
| | - Onruthai Pinyakong
- Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok, 10330, Thailand
| | - Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Rachadhavi, Bangkok, 10400, Thailand.
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7
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Babich TL, Semenova EM, Sokolova DS, Tourova TP, Bidzhieva SK, Loiko NG, Avdonin GI, Lutsenko NI, Nazina TN. Phylogenetic Diversity and Potential Activity of Bacteria and Fungi in the Deep Subsurface Horizons of an Uranium Deposit. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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8
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Cerro-Gálvez E, Dachs J, Lundin D, Fernández-Pinos MC, Sebastián M, Vila-Costa M. Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9609-9621. [PMID: 33606522 PMCID: PMC8491159 DOI: 10.1021/acs.est.0c07262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 05/23/2023]
Abstract
Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Jordi Dachs
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Daniel Lundin
- Centre
for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar 35195, Sweden
| | | | - Marta Sebastián
- Department
of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya 08003, Spain
| | - Maria Vila-Costa
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
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9
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Thompson HF, Summers S, Yuecel R, Gutierrez T. Hydrocarbon-Degrading Bacteria Found Tightly Associated with the 50-70 μm Cell-Size Population of Eukaryotic Phytoplankton in Surface Waters of a Northeast Atlantic Region. Microorganisms 2020; 8:microorganisms8121955. [PMID: 33317100 PMCID: PMC7763645 DOI: 10.3390/microorganisms8121955] [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: 11/19/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022] Open
Abstract
The surface of marine eukaryotic phytoplankton can harbour communities of hydrocarbon-degrading bacteria; however, this algal–bacterial association has, hitherto, been only examined with non-axenic laboratory cultures of micro-algae. In this study, we isolated an operationally-defined community of phytoplankton, of cell size 50–70 μm, from a natural community in sea surface waters of a subarctic region in the northeast Atlantic. Using MiSeq 16S rRNA sequencing, we identified several recognized (Alcanivorax, Marinobacter, Oleispira, Porticoccus, Thalassospira) and putative hydrocarbon degraders (Colwelliaceae, Vibrionaceae) tightly associated with the phytoplankton population. We combined fluorescence in situ hybridisation with flow-cytometry (FISH-Flow) to examine the association of Marinobacter with this natural eukaryotic phytoplankton population. About 1.5% of the phytoplankton population contained tightly associated Marinobacter. The remaining Marinobacter population were loosely associated with either eukaryotic phytoplankton cells or non-chlorophyll particulate material. This work is the first to show the presence of obligate, generalist and putative hydrocarbonoclastic bacteria associated with natural populations of eukaryotic phytoplankton directly from sea surface water samples. It also highlights the suitability of FISH-Flow for future studies to examine the spatial and temporal structure and dynamics of these and other algal–bacterial associations in natural seawater samples.
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Affiliation(s)
- Haydn Frank Thompson
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
| | - Stephen Summers
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Raif Yuecel
- Iain Fraser Cytometry Centre, Institute of Medical Sciences IMS, University of Aberdeen, Aberdeen AB25 2ZD, UK;
- Exeter Centre for Cytomics (EXCC), College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Tony Gutierrez
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
- Correspondence:
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10
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Bera G, Doyle S, Passow U, Kamalanathan M, Wade TL, Sylvan JB, Sericano JL, Gold G, Quigg A, Knap AH. Biological response to dissolved versus dispersed oil. MARINE POLLUTION BULLETIN 2020; 150:110713. [PMID: 31757392 DOI: 10.1016/j.marpolbul.2019.110713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/21/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
The water-soluble compounds of oil (e.g. low molecular weight PAHs) dissolve as a function of their physicochemical properties and environmental conditions, while the non-soluble compounds exist as dispersed droplets. Both the chemical and physical form of oil will affect the biological response. We present data from a mesocosm study comparing the microbial response to the water-soluble fraction (WSF), versus a water-accommodated fraction of oil (WAF), which contains both dispersed and dissolved oil components. WAF and WSF contained similar concentrations of low molecular weight PAHs, but concentrations of 4- and 5-ring PAHs were higher in WAF compared to WSF. Microbial communities were significantly different between WSF and WAF treatments, primary productivity was reduced more in WSF than in WAF, and concentrations of transparent exopolymeric particles were highest in WSF and lowest in the controls. These differences highlight the importance of dosing strategy for mesocosm and toxicity tests.
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Affiliation(s)
- Gopal Bera
- Texas A & M University, College Station, TX, USA.
| | - Shawn Doyle
- Texas A & M University, College Station, TX, USA
| | | | | | - Terry L Wade
- Texas A & M University, College Station, TX, USA
| | | | | | - Gerardo Gold
- Texas A & M University, College Station, TX, USA
| | - Antonietta Quigg
- Texas A & M University, College Station, TX, USA; Texas A & M University at Galveston, Galveston, TX, USA
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11
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Muangchinda C, Rungsihiranrut A, Prombutara P, Soonglerdsongpha S, Pinyakong O. 16S metagenomic analysis reveals adaptability of a mixed-PAH-degrading consortium isolated from crude oil-contaminated seawater to changing environmental conditions. JOURNAL OF HAZARDOUS MATERIALS 2018; 357:119-127. [PMID: 29870896 DOI: 10.1016/j.jhazmat.2018.05.062] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/10/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
A bacterial consortium, named SWO, was enriched from crude oil-contaminated seawater from Phrao Bay in Rayong Province, Thailand, after a large oil spill in 2013. The bacterial consortium degraded a polycyclic aromatic hydrocarbon (PAH) mixture consisting of phenanthrene, anthracene, fluoranthene, and pyrene (50 mg L-1 each) by approximately 73%, 69%, 52%, and 48%, respectively, within 21 days. This consortium exhibited excellent adaptation to a wide range of environmental conditions. It could degrade a mixture of four PAHs under a range of pH values (4.0-9.0), temperatures (25 °C-37 °C), and salinities (0-10 g L-1 with NaCl). In addition, this consortium degraded 20-30% of benzo[a]pyrene and perylene (10 mg L-1 each), high molecular weight PAHs, in the presence of other PAHs within 35 days, and degraded 40% of 2% (v/v) crude oil within 20 days. The 16S rRNA gene amplicon sequencing analysis demonstrated that Pseudomonas and Methylophaga were the dominant genera of consortium SWO in almost all treatments, while Pseudidiomarina, Thalassospira and Alcanivorax were predominant under higher salt concentrations. Moreover, Pseudomonas and Alcanivorax were dominant in the crude oil-degradation treatment. Our results suggest that the consortium SWO maintained its biodegradation ability by altering the bacterial community profile upon encountering changes in the environmental conditions.
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Affiliation(s)
- Chanokporn Muangchinda
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Thailand
| | - Adisan Rungsihiranrut
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Thailand
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Thailand
| | - Suwat Soonglerdsongpha
- Environmental Technology Research Department, PTT Research and Technology Institute, PTT Public Company Limited, Ayutthaya, Thailand
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Thailand.
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12
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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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13
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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14
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Shiller AM, Chan EW, Joung DJ, Redmond MC, Kessler JD. Light rare earth element depletion during Deepwater Horizon blowout methanotrophy. Sci Rep 2017; 7:10389. [PMID: 28871146 PMCID: PMC5583346 DOI: 10.1038/s41598-017-11060-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022] Open
Abstract
Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation samples revealed that LREE-containing MDHs were present. Our field and laboratory observations provide further insight into the biochemical pathways of methanotrophy during the DWH blowout. Additionally, our results are the first observations of direct biological alteration of REE distributions in oceanic systems. In view of the ubiquity of LREE-containing MDHs in oceanic systems, our results suggest that biological uptake of LREEs is an overlooked aspect of the oceanic geochemistry of this group of elements previously thought to be biologically inactive and an unresolved factor in the flux of methane, a potent greenhouse gas, from the ocean.
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Affiliation(s)
- A M Shiller
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States.
| | - E W Chan
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
| | - D J Joung
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States
| | - M C Redmond
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - J D Kessler
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
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15
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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16
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Fradet DT, Tavormina PL, Orphan VJ. Members of the methanotrophic genus Methylomarinum inhabit inland mud pots. PeerJ 2016; 4:e2116. [PMID: 27478692 PMCID: PMC4950536 DOI: 10.7717/peerj.2116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 11/24/2022] Open
Abstract
Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling.
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Affiliation(s)
- Danielle T Fradet
- Flintridge Sacred Heart Academy , La Canada Flintridge, CA , United States
| | - Patricia L Tavormina
- Geological and Planetary Sciences, California Institute of Technology , Pasadena, CA , United States
| | - Victoria J Orphan
- Geological and Planetary Sciences, California Institute of Technology , Pasadena, CA , United States
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17
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Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, Hazen TC, Alm EJ. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments. PLoS One 2016; 11:e0154804. [PMID: 27152415 PMCID: PMC4859510 DOI: 10.1371/journal.pone.0154804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/19/2016] [Indexed: 01/16/2023] Open
Abstract
Many microbial ecology experiments use sequencing data to measure a community’s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method’s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of “bottle effects”.
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Affiliation(s)
- Scott W Olesen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Suhani Vora
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Stephen M Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America
| | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America.,Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Juan R Bastidas-Oyanedel
- Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, Abu Dhabi, UAE
| | - Jorge Rodríguez
- Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, Abu Dhabi, UAE
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America.,Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
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18
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Mishamandani S, Gutierrez T, Berry D, Aitken MD. Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons. Environ Microbiol 2015; 18:1817-33. [PMID: 26184578 DOI: 10.1111/1462-2920.12988] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 01/22/2023]
Abstract
Emerging evidence shows that hydrocarbonoclastic bacteria (HCB) may be commonly found associated with phytoplankton in the ocean, but the ecology of these bacteria and how they respond to crude oil remains poorly understood. Here, we used a natural diatom-bacterial assemblage to investigate the diversity and response of HCB associated with a cosmopolitan marine diatom, Skeletonema costatum, to crude oil. Pyrosequencing analysis and qPCR revealed a dramatic transition in the diatom-associated bacterial community, defined initially by a short-lived bloom of Methylophaga (putative oil degraders) that was subsequently succeeded by distinct groups of HCB (Marinobacter, Polycyclovorans, Arenibacter, Parvibaculum, Roseobacter clade), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential. Interestingly, these oil-enriched organisms contributed to the apparent and exclusive biodegradation of substituted and non-substituted polycyclic aromatic hydrocarbons (PAHs), thereby suggesting that the HCB community associated with the diatom is tuned to specializing in the degradation of PAHs. Furthermore, the formation of marine oil snow (MOS) in oil-amended incubations was consistent with its formation during the Deepwater Horizon oil spill. This work highlights the phycosphere of phytoplankton as an underexplored biotope in the ocean where HCB may contribute importantly to the biodegradation of hydrocarbon contaminants in marine surface waters.
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Affiliation(s)
- Sara Mishamandani
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Tony Gutierrez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,School of Life Sciences, Heriot-Watt University, Edinburgh, UK
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
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20
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Sauret C, Böttjer D, Talarmin A, Guigue C, Conan P, Pujo-Pay M, Ghiglione JF. Top-Down Control of Diesel-Degrading Prokaryotic Communities. MICROBIAL ECOLOGY 2015; 70:445-458. [PMID: 25805213 DOI: 10.1007/s00248-015-0596-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/08/2015] [Indexed: 06/04/2023]
Abstract
Biostimulation through the addition of inorganic nutrients has been the most widely practiced bioremediation strategy in oil-polluted marine waters. However, little attention has so far been paid to the microbial food web and the impact of top-down control that directly or indirectly influences the success of the bioremediation. We designed a mesocosm experiment using pre-filtered (<50 μm) surface seawater from the Bay of Banyuls-sur-Mer (North-Western Mediterranean Sea) and examined the top-down effect exerted by heterotrophic nanoflagellates (HNF) and virus-like particles (VLP) on prokaryotic abundance, activity and diversity in the presence or absence of diesel fuel. Prokaryotes, HNF and VLP abundances showed a predator-prey succession, with a co-development of HNF and VLP. In the polluted system, we observed a stronger impact of viral lysis on prokaryotic abundances than in the control. Analysis of the diversity revealed that a bloom of Vibrio sp. occurred in the polluted mesocosm. That bloom was rapidly followed by a less abundant and more even community of predation-resistant bacteria, including known hydrocarbon degraders such as Oleispira spp. and Methylophaga spp. and opportunistic bacteria such as Percisivirga spp., Roseobacter spp. and Phaeobacter spp. The shift in prokaryotic dominance in response to viral lysis provided clear evidence of the 'killing the winner' model. Nevertheless, despite clear effects on prokaryotic abundance, activity and diversity, the diesel degradation was not impacted by top-down control. The present study investigates for the first time the functioning of a complex microbial network (including VLP) using a nutrient-based biostimulation strategy and highlights some key processes useful for tailoring bioremediation.
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Affiliation(s)
- Caroline Sauret
- UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, 66650, Banyuls-sur-mer, France
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21
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Gutierrez T, Biddle JF, Teske A, Aitken MD. Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments. Front Microbiol 2015. [PMID: 26217326 PMCID: PMC4493657 DOI: 10.3389/fmicb.2015.00695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [13C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled PHE and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea.
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Affiliation(s)
- Tony Gutierrez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ; School of Life Sciences, Heriot-Watt University, Edinburgh UK
| | - Jennifer F Biddle
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
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22
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Kostka JE, Teske AP, Joye SB, Head IM. The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems. Front Microbiol 2014; 5:471. [PMID: 25237309 PMCID: PMC4154464 DOI: 10.3389/fmicb.2014.00471] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022] Open
Affiliation(s)
- Joel E Kostka
- School of Biology and Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina Chapel Hill, NC, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia Athens, GA, USA
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
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23
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Gutierrez T, Aitken MD. Role of methylotrophs in the degradation of hydrocarbons during the Deepwater Horizon oil spill. ISME JOURNAL 2014; 8:2543-5. [PMID: 24865772 DOI: 10.1038/ismej.2014.88] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/15/2014] [Indexed: 11/09/2022]
Abstract
The role of methylotrophic bacteria in the fate of the oil and gas released into the Gulf of Mexico during the Deepwater Horizon oil spill has been controversial, particularly in relation to whether organisms such as Methylophaga had contributed to the consumption of methane. Whereas methanotrophy remains unqualified in these organisms, recent work by our group using DNA-based stable-isotope probing coupled with cultivation-based methods has uncovered hydrocarbon-degrading Methylophaga. Recent findings have also shown that methylotrophs, including Methylophaga, were in a heightened state of metabolic activity within oil plume waters during the active phase of the spill. Taken collectively, these findings suggest that members of this group may have participated in the degradation of high-molecular-weight hydrocarbons in plume waters. The discovery of hydrocarbon-degrading Methylophaga also highlights the importance of considering these organisms in playing a role to the fate of oil hydrocarbons at oil-impacted sites.
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Affiliation(s)
- Tony Gutierrez
- 1] School of Life Sciences, Heriot-Watt University, Edinburgh, UK [2] Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
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