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"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. ISME JOURNAL 2019; 13:2129-2134. [PMID: 30952995 DOI: 10.1038/s41396-019-0400-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name "Candidatus Macondimonas diazotrophica" gen. nov., sp. nov. "Ca. M. diazotrophica" appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.
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52
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Cerro-Gálvez E, Casal P, Lundin D, Piña B, Pinhassi J, Dachs J, Vila-Costa M. Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environ Microbiol 2019; 21:1466-1481. [PMID: 30838733 DOI: 10.1111/1462-2920.14580] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/21/2019] [Accepted: 03/03/2019] [Indexed: 11/29/2022]
Abstract
Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.
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Affiliation(s)
- Elena Cerro-Gálvez
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Paulo Casal
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 39182, Kalmar, Sweden
| | - Benjamin Piña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 39182, Kalmar, Sweden
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Catalunya, Spain
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53
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Neethu CS, Saravanakumar C, Purvaja R, Robin RS, Ramesh R. Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices. Sci Rep 2019; 9:1354. [PMID: 30718727 PMCID: PMC6361881 DOI: 10.1038/s41598-018-37903-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.
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Affiliation(s)
- C S Neethu
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India
| | - C Saravanakumar
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
| | - R Purvaja
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
| | - R S Robin
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai, 600025, India.
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54
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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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55
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Storey S, Ashaari MM, Clipson N, Doyle E, de Menezes AB. Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study. Front Microbiol 2018; 9:2815. [PMID: 30519226 PMCID: PMC6258822 DOI: 10.3389/fmicb.2018.02815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.
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Affiliation(s)
- Sean Storey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Mardiana Mohd Ashaari
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Malaysia, Malaysia
| | - Nicholas Clipson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Alexandre B de Menezes
- Microbiology, School of Natural Sciences, Ryan Institute, National University of Ireland, Galway, Ireland
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56
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Urakawa H, Rajan S, Feeney ME, Sobecky PA, Mortazavi B. Ecological response of nitrification to oil spills and its impact on the nitrogen cycle. Environ Microbiol 2018; 21:18-33. [DOI: 10.1111/1462-2920.14391] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/11/2018] [Accepted: 08/17/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Hidetoshi Urakawa
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Suja Rajan
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Megan E. Feeney
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Patricia A. Sobecky
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Behzad Mortazavi
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
- Dauphin Island Sea Lab Dauphin Island AL, 36528 USA
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57
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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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58
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Tiralerdpanich P, Sonthiphand P, Luepromchai E, Pinyakong O, Pokethitiyook P. Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis. MARINE POLLUTION BULLETIN 2018; 133:595-605. [PMID: 30041354 DOI: 10.1016/j.marpolbul.2018.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/22/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.
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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
| | - Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand.
| | - Ekawan Luepromchai
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand
| | - Prayad Pokethitiyook
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
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59
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Sekar R, DiChristina TJ. Degradation of the recalcitrant oil spill components anthracene and pyrene by a microbially driven Fenton reaction. FEMS Microbiol Lett 2018; 364:4222791. [PMID: 29029043 DOI: 10.1093/femsle/fnx203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/23/2017] [Indexed: 12/30/2022] Open
Abstract
Oil spill components include a range of toxic saturated, aromatic and polar hydrocarbons, including pyrene and anthracene. Such contaminants harm natural ecosystems, adversely affect human health and negatively impact tourism and the fishing industries. Current physical, chemical and biological remediation technologies are often unable to completely remove recalcitrant oil spill components, which accumulate at levels greater than regulatory limits set by the Environmental Protection Agency. In the present study, a microbially driven Fenton reaction, previously shown to produce hydroxyl (HO • ) radicals that degrade chlorinated solvents and associated solvent stabilizers, was also found to degrade source zone concentrations of the oil spill components, pyrene (10 μM) and anthracene (1 μM), at initial rates of 0.82 and 0.20 μM h -1 , respectively. The pyrene- and anthracene-degrading Fenton reaction was driven by the metal-reducing facultative anaerobe Shewanella oneidensis exposed to alternating aerobic and anaerobic conditions in the presence of Fe(III). Similar to the chlorinated solvent degradation system, the pyrene and anthracene degradation systems required neither the continual supply of exogenous H 2 O 2 nor UV-induced Fe(III) reduction to regenerate Fe(II). The microbially driven Fenton reaction provides the foundation for the development of alternate ex situ and in situ oil and gas spill remediation technologies.
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Affiliation(s)
- Ramanan Sekar
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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60
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Xie Y, Zhang X, Yang J, Kim S, Hong S, Giesy JP, Yim UH, Shim WJ, Yu H, Khim JS. eDNA-based bioassessment of coastal sediments impacted by an oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:739-748. [PMID: 29625298 DOI: 10.1016/j.envpol.2018.02.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments.
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Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Seonjin Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Biological Sciences, University of Hong Kong, Hong Kong, SAR, China; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Won Joon Shim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
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Babilonia J, Conesa A, Casaburi G, Pereira C, Louyakis AS, Reid RP, Foster JS. Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia. Front Microbiol 2018; 9:1359. [PMID: 29988640 PMCID: PMC6027182 DOI: 10.3389/fmicb.2018.01359] [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: 01/07/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
Stromatolites are organosedimentary build-ups that have formed as a result of the sediment trapping, binding and precipitating activities of microbes. Today, extant systems provide an ideal platform for understanding the structure, composition, and interactions between stromatolite-forming microbial communities and their respective environments. In this study, we compared the metagenomes of three prevalent stromatolite-forming microbial mat types in the Spaven Province of Hamelin Pool, Shark Bay located in Western Australia. These stromatolite-forming mat types included an intertidal pustular mat as well as a smooth and colloform mat types located in the subtidal zone. Additionally, the metagenomes of an adjacent, non-lithifying mat located in the upper intertidal zone were also sequenced for comparative purposes. Taxonomic and functional gene analyses revealed distinctive differences between the lithifying and non-lithifying mat types, which strongly correlated with water depth. Three distinct populations emerged including the upper intertidal non-lithifying mats, the intertidal pustular mats associated with unlaminated carbonate build-ups, and the subtidal colloform and smooth mat types associated with laminated structures. Functional analysis of metagenomes revealed that amongst stromatolite-forming mats there was an enrichment of photosynthesis pathways in the pustular stromatolite-forming mats. In the colloform and smooth stromatolite-forming mats, however, there was an increase in the abundance of genes associated with those heterotrophic metabolisms typically associated with carbonate mineralization, such as sulfate reduction. The comparative metagenomic analyses suggest that stromatolites of Hamelin Pool may form by two distinctive processes that are highly dependent on water depth. These results provide key insight into the potential adaptive strategies and synergistic interactions between microbes and their environments that may lead to stromatolite formation and accretion.
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Affiliation(s)
- Joany Babilonia
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Ana Conesa
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Cecile Pereira
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,EURA NOVA, Marseille, France
| | - Artemis S Louyakis
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - R Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
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Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides. Appl Environ Microbiol 2018; 84:AEM.00197-18. [PMID: 29654181 DOI: 10.1128/aem.00197-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 12/31/2022] Open
Abstract
Benzalkonium chlorides (BAC) are commonly used biocides in broad-spectrum disinfectant solutions. How microorganisms cope with BAC exposure remains poorly understood, despite its importance for disinfection and disinfectant-induced antibiotic resistance. To provide insights into these issues, we exposed two isolates of an opportunistic pathogen, Pseudomonas aeruginosa, to increasing concentrations of BAC. One isolate was preadapted to BAC, as it originated from a bioreactor fed with subinhibitory concentrations of BAC for 3 years, while the other originated from a bioreactor that received no BAC. Replicated populations of both isolates were able to survive high concentrations of BAC, up to 1,200 and 1,600 mg/liter for the non- and preadapted strains, respectively, exceeding typical application doses. Transcriptome sequencing (RNA-seq) analysis revealed upregulation of efflux pump genes and decreased expression of porins related to BAC transport as well as reduced growth rate. Increased expression of spermidine (a polycation) synthase genes and mutations in the pmrB (polymyxin resistance) gene, which cause a reduction in membrane negative charge, suggested that a major adaptation to exposure to the cationic surfactant BAC was to actively stabilize cell surface charge. Collectively, these results revealed that P. aeruginosa adapts to BAC exposure by a combination of mechanisms and provided genetic markers to monitor BAC-resistant organisms that may have applications in the practice of disinfection.IMPORTANCE BAC are widely used as biocides in disinfectant solutions, food-processing lines, domestic households, and health care facilities. Due to their wide use and mode of action, there has been rising concern that BAC may promote antibiotic resistance. Consistent with this idea, at least 40 outbreaks have been attributed to infection by disinfectant- and antibiotic-resistant pathogens such as P. aeruginosa However, the underlying molecular mechanisms that bacteria use to deal with BAC exposure remain poorly elucidated. Elucidating these mechanisms may be important for monitoring and limiting the spread of disinfectant-resistant pathogens. Using an integrated approach that combined genomics and transcriptomics with physiological characterization of BAC-adapted isolates, this study provided a comprehensive understanding of the BAC resistance mechanisms in P. aeruginosa Our findings also revealed potential genetic markers to detect and monitor the abundance of BAC-resistant pathogens across clinical or environmental settings. This work contributes new knowledge about high concentrations of benzalkonium chlorides disinfectants-resistance mechanisms at the whole-cell genomic and transcriptomic level.
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Ribicic D, Netzer R, Hazen TC, Techtmann SM, Drabløs F, Brakstad OG. Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater. MARINE POLLUTION BULLETIN 2018; 129:370-378. [PMID: 29680562 DOI: 10.1016/j.marpolbul.2018.02.034] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/30/2018] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.
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Affiliation(s)
- Deni Ribicic
- NTNU Norwegian University of Science and Technology, Department of Clinical and Molecular Medicine, Trondheim, Norway.
| | | | - Terry C Hazen
- University of Tennessee Knoxville, Department of Civil and Environmental Engineering, Knoxville, TN, USA
| | - Stephen M Techtmann
- Michigan Technological University, Department of Biological Sciences, Houghton, MI, USA
| | - Finn Drabløs
- NTNU Norwegian University of Science and Technology, Department of Clinical and Molecular Medicine, Trondheim, Norway
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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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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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Tribelli PM, Rossi L, Ricardi MM, Gomez-Lozano M, Molin S, Raiger Iustman LJ, Lopez NI. Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach. ACTA ACUST UNITED AC 2018; 45:15-23. [DOI: 10.1007/s10295-017-1987-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/01/2017] [Indexed: 01/25/2023]
Abstract
Abstract
Diesel fuel is one of the most important sources of hydrocarbon contamination worldwide. Its composition consists of a complex mixture of n-alkanes, branched alkanes and aromatic compounds. Hydrocarbon degradation in Pseudomonas species has been mostly studied under aerobic conditions; however, a dynamic spectrum of oxygen availability can be found in the environment. Pseudomonas extremaustralis, an Antarctic bacterium isolated from a pristine environment, is able to degrade diesel fuel and presents a wide microaerophilic metabolism. In this work RNA-deep sequence experiments were analyzed comparing the expression profile in aerobic and microaerophilic cultures. Interestingly, genes involved in alkane degradation, including alkB, were over-expressed in micro-aerobiosis in absence of hydrocarbon compounds. In minimal media supplemented with diesel fuel, n-alkanes degradation (C13–C19) after 7 days was observed under low oxygen conditions but not in aerobiosis. In-silico analysis of the alkB promoter zone showed a putative binding sequence for the anaerobic global regulator, Anr. Our results indicate that some diesel fuel components can be utilized as sole carbon source under microaerophilic conditions for cell maintenance or slow growth in a Pseudomonas species and this metabolism could represent an adaptive advantage in polluted environments.
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Affiliation(s)
- Paula M Tribelli
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Leticia Rossi
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Martiniano M Ricardi
- 0000 0001 0056 1981 grid.7345.5 Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires C1428EGA Buenos Aires Argentina
| | - Maria Gomez-Lozano
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Søren Molin
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Laura J Raiger Iustman
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Nancy I Lopez
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
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Huettel M, Overholt WA, Kostka JE, Hagan C, Kaba J, Wells WB, Dudley S. Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping. MARINE POLLUTION BULLETIN 2018; 126:488-500. [PMID: 29421130 DOI: 10.1016/j.marpolbul.2017.10.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 09/25/2017] [Accepted: 10/21/2017] [Indexed: 06/08/2023]
Abstract
After Deepwater Horizon oil reached the Florida coast, oil was buried in Pensacola Beach (PB) sands to ~70cm depth, resulting in Total Petroleum Hydrocarbon (TPH) concentrations up to ~2kg per meter of beach. This study followed the decomposition of the buried oil and the factors influencing its degradation. The abundance of bacteria in oiled sand increased by 2 orders of magnitude within one week after oil burial, while diversity decreased by ~50%. Half-lives of aliphatic and aromatic hydrocarbons reached 25 and 22days, respectively. Aerobic microbial oil decomposition, promoted by tidal pumping, and human cleaning activities effectively removed oil from the beach. After one year, concentrations of GC-amenable hydrocarbons at PB were similar to those in the uncontaminated reference beach at St. George Island/FL, and microbial populations that disappeared after the oil contamination had reestablished. Yet, oxihydrocarbons can be found at PB to the present day.
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Affiliation(s)
- Markus Huettel
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Will A Overholt
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States.
| | - Joel E Kostka
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States.
| | - Christopher Hagan
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - John Kaba
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Wm Brian Wells
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Stacia Dudley
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
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Oh S, Hammes F, Liu WT. Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. WATER RESEARCH 2018; 128:278-285. [PMID: 29107912 DOI: 10.1016/j.watres.2017.10.054] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 05/08/2023]
Abstract
Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.
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Affiliation(s)
- Seungdae Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Frederik Hammes
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstr. 133, CH-8600 Dübendorf, Switzerland
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
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Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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Orellana LH, Rodriguez-R LM, Konstantinidis KT. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res 2017; 45:e14. [PMID: 28180325 PMCID: PMC5388429 DOI: 10.1093/nar/gkw900] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 09/25/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles and related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N2O, to inert N2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.
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Affiliation(s)
- Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, GA, USA
| | - Luis M Rodriguez-R
- Center for Bioinformatics and Computational Genomics and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, GA, USA.,Center for Bioinformatics and Computational Genomics and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, GA, USA
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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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73
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Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. ISME JOURNAL 2017; 11:2569-2583. [PMID: 28777379 DOI: 10.1038/ismej.2017.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/10/2017] [Accepted: 05/30/2017] [Indexed: 11/09/2022]
Abstract
The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.
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Affiliation(s)
- K M Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.,Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA
| | - Y M Piceno
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - P Hu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - L M Tom
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - O U Mason
- Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - G L Andersen
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - J A Gilbert
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.,Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA.,The Microbiome Center, Department of Surgery, The University of Chicago, Chicago, IL, USA
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74
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Harriman BH, Zito P, Podgorski DC, Tarr MA, Suflita JM. Impact of Photooxidation and Biodegradation on the Fate of Oil Spilled During the Deepwater Horizon Incident: Advanced Stages of Weathering. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7412-7421. [PMID: 28570062 DOI: 10.1021/acs.est.7b01278] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While the biogeochemical forces influencing the weathering of spilled oil have been investigated for decades, the environmental fate and effects of "oxyhydrocarbons" in sand patties deposited on beaches are not well-known. We collected sand patties deposited in the swash zone on Gulf of Mexico beaches following the Deepwater Horizon oil spill. When sand patties were exposed to simulated sunlight, a larger concentration of dissolved organic carbon was leached into seawater than the corresponding dark controls. This result was consistent with the general ease of movement of seawater through the sand patties as shown with a 35SO42- radiotracer. Ultrahigh-resolution mass spectrometry, as well as optical measurements revealed that the chemical composition of dissolved organic matter (DOM) leached from the sand patties under dark and irradiated conditions were substantially different, but neither had a significant inhibitory influence on the endogenous rate of aerobic or anaerobic microbial respiratory activity. Rather, the dissolved organic photooxidation products stimulated significantly more microbial O2 consumption (113 ± 4 μM) than either the dark (78 ± 2 μM) controls or the endogenous (38 μM ± 4) forms of DOM. The changes in the DOM quality and quantity were consistent with biodegradation as an explanation for the differences. These results confirm that sand patties undergo a gradual dissolution of DOM in both the dark and in the light, but photooxidation accelerates the production of water-soluble polar organic compounds that are relatively more amenable to aerobic biodegradation. As such, these processes represent previously unrecognized advanced weathering stages that are important in the ultimate transformation of spilled crude oil.
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Affiliation(s)
- Brian H Harriman
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019
- Institute for Energy and the Environment, University of Oklahoma , Norman, Oklahoma 73019
| | - Phoebe Zito
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310-3706
| | - David C Podgorski
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310-3706
- Department of Earth, Ocean and Atmospheric Science, Florida State University , Tallahassee, Florida 32306
| | - Matthew A Tarr
- Department of Chemistry, University of New Orleans , New Orleans, Louisiana 70148
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019
- Institute for Energy and the Environment, University of Oklahoma , Norman, Oklahoma 73019
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75
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Miller M, Zhu C, Bromberg Y. clubber: removing the bioinformatics bottleneck in big data analyses. J Integr Bioinform 2017; 14:/j/jib.ahead-of-print/jib-2017-0020/jib-2017-0020.xml. [PMID: 28609295 PMCID: PMC5929469 DOI: 10.1515/jib-2017-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/27/2017] [Indexed: 11/17/2022] Open
Abstract
With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.
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76
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Ferguson RMW, Gontikaki E, Anderson JA, Witte U. The Variable Influence of Dispersant on Degradation of Oil Hydrocarbons in Subarctic Deep-Sea Sediments at Low Temperatures (0-5 °C). Sci Rep 2017; 7:2253. [PMID: 28533547 PMCID: PMC5440406 DOI: 10.1038/s41598-017-02475-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/11/2017] [Indexed: 01/23/2023] Open
Abstract
The microbial degradation of petroleum hydrocarbons at low temperatures was investigated in subarctic deep-sea sediments in the Faroe Shetland Channel (FSC). The effect of the marine oil dispersant, Superdispersant 25 on hydrocarbon degradation was also examined. Sediments collected at 500 and 1000 m depth were spiked with a model oil containing 20 hydrocarbons and incubated at ambient temperature (5 and 0 °C, respectively) with and without marine dispersant. Treatment of sediments with hydrocarbons resulted in the enrichment of Gammaproteobacteria, and specifically the genera Pseudoalteromonas, Pseudomonas, Halomonas, and Cobetia. Hydrocarbon degradation was faster at 5 °C (500 m) with 65–89% of each component degraded after 50 days compared to 0–47% degradation at 0 °C (1000 m), where the aromatic hydrocarbons fluoranthene, anthracene, and Dibenzothiophene showed no degradation. Dispersant significantly increased the rate of degradation at 1000 m, but had no effect at 500 m. There was no statistically significant effect of Superdispersant 25 on the bacterial community structure at either station. These results show that the indigenous bacterial community in the FSC has the capacity to mitigate some of the effects of a potential oil spill, however, the effect of dispersant is ambiguous and further research is needed to understand the implications of its use.
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Affiliation(s)
- Robert M W Ferguson
- Institute of Biological and Environmental Science, Oceanlab, University of Aberdeen, Newburgh, AB41 6AA, UK. .,Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Science, Oceanlab, University of Aberdeen, Newburgh, AB41 6AA, UK
| | - James A Anderson
- Surface Chemistry and Catalysis Group, School of Engineering, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Ursula Witte
- Institute of Biological and Environmental Science, Oceanlab, University of Aberdeen, Newburgh, AB41 6AA, UK
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77
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Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D. Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms. Trends Biotechnol 2017; 35:860-870. [PMID: 28511936 DOI: 10.1016/j.tibtech.2017.04.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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Affiliation(s)
- Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Alberto Scoma
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00015 Monterotondo, Italy
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
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78
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Daghio M, Aulenta F, Vaiopoulou E, Franzetti A, Arends JBA, Sherry A, Suárez-Suárez A, Head IM, Bestetti G, Rabaey K. Electrobioremediation of oil spills. WATER RESEARCH 2017; 114:351-370. [PMID: 28279880 DOI: 10.1016/j.watres.2017.02.030] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/27/2017] [Accepted: 02/14/2017] [Indexed: 05/20/2023]
Abstract
Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process.
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Affiliation(s)
- Matteo Daghio
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo, RM, Italy
| | - Eleni Vaiopoulou
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Jan B A Arends
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Angela Sherry
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ana Suárez-Suárez
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ian M Head
- School of Civil Engineering & Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Giuseppina Bestetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium.
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79
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Chen C, Liu Q, Liu C, Yu J. Effect of different enrichment strategies on microbial community structure in petroleum-contaminated marine sediment in Dalian, China. MARINE POLLUTION BULLETIN 2017; 117:274-282. [PMID: 28189367 DOI: 10.1016/j.marpolbul.2017.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/04/2017] [Accepted: 02/04/2017] [Indexed: 06/06/2023]
Abstract
An oil spill occurred at Xingang Port, Dalian, China in 2010. Four years after this spill, oil contamination was still detected in samples collected nearby. In this study, the strains that evolved in the sediment were screened by high-throughput sequencing technology. Most of these strains were genera reported to have functions associated with crude oil biodegradation. The diversities and numbers of microbes were monitored through enrichment culturing; the dominant strains propagated at first, but the enrichment could not be continued, which indicated that the prolonged culture was not effective in the enrichment of the micro-consortium. Oxygen was also observed to affect the propagation of the dominant microbes. The results showed the role of culture strategies and oxygen in the enrichment of the petroleum-degrading microbes. Therefore, dominant strains could be screened by optimizing both the enrichment time and oxygen concentration used for culturing to facilitate oil biodegradation in the marine ecosystem.
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Affiliation(s)
- Chao Chen
- College of Life Science, Dalian Nationalities University, Dalian 116600, PR China
| | - Qiu Liu
- College of Life Science, Dalian Nationalities University, Dalian 116600, PR China.
| | - Changjian Liu
- College of Life Science, Dalian Nationalities University, Dalian 116600, PR China
| | - Jicheng Yu
- College of Life Science, Dalian Nationalities University, Dalian 116600, PR China.
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80
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Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. Appl Environ Microbiol 2017; 83:AEM.03321-16. [PMID: 28258138 DOI: 10.1128/aem.03321-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/01/2017] [Indexed: 01/01/2023] Open
Abstract
A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.
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81
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Zhao JK, Li XM, Ai GM, Deng Y, Liu SJ, Jiang CY. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:90-98. [PMID: 27415596 DOI: 10.1016/j.jhazmat.2016.06.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the primary process of removing PAHs from environments. The metabolic pathway of PAHs in pure cultures has been intensively studied, but cooperative metabolisms at community-level remained to be explored. In this study, we determined the dynamic composition of a microbial community and its metabolic intermediates during fluoranthene degradation using high-throughput metagenomics and gas chromatography-mass spectrometry (GC-MS), respectively. Subsequently, a cooperative metabolic network for fluoranthene degradation was constructed. The network shows that Mycobacterium contributed the majority of ring-hydroxylating and -cleavage dioxygenases, while Diaphorobacter contributed most of the dehydrogenases. Hyphomicrobium, Agrobacterium, and Sphingopyxis contributed to genes encoding enzymes involved in downstream reactions of fluoranthene degradation. The contributions of various microbial groups were calculated with the PICRUSt program. The contributions of Hyphomicrobium to alcohol dehydrogenases were 62.4% in stage 1 (i.e., when fluoranthene was rapidly removed) and 76.8% in stage 3 (i.e., when fluoranthene was not detectable), respectively; the contribution of Pseudomonas were 6.6% in stage 1 and decreased to 1.2% in subsequent stages. To the best of the author's knowledge, this report describes the first cooperative metabolic network to predict the contributions of various microbial groups during PAH-degradation at community-level.
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Affiliation(s)
- Jian-Kang Zhao
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ming Li
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Ye Deng
- Research Center of Ecological and Environmental Science, CAS, Beijing, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
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82
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Bouhajja E, Agathos SN, George IF. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnol Adv 2016; 34:1413-1426. [PMID: 27825829 DOI: 10.1016/j.biotechadv.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 12/23/2022]
Abstract
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
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Affiliation(s)
- Emna Bouhajja
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium
| | - Spiros N Agathos
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador
| | - Isabelle F George
- Université Libre de Bruxelles, Laboratoire d'Ecologie des Systèmes Aquatiques, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
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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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84
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Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel. Extremophiles 2016; 20:747-57. [PMID: 27444744 DOI: 10.1007/s00792-016-0864-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
Stability of microbial communities can impact the ability of dispersed cells to colonize a new habitat. Saturated brines and their halophile communities are presumed to be steady state systems due to limited environmental perturbations. In this study, the bacteriorhodopsin-containing fraction of the haloarchaeal community from Eilat salt crystallizer ponds was sampled five times over 3 years. Analyses revealed the existence of a constant core as several OTUs were found repeatedly over the length of the study: OTUs comprising 52 % of the total cloned and sequenced PCR amplicons were found in every sample, and OTUs comprising 89 % of the total sequences were found in more than one, and often more than two samples. LIBSHUFF and UNIFRAC analyses showed statistical similarity between samples and Spearman's coefficient denoted significant correlations between OTU pairs, indicating non-random patterns in abundance and co-occurrence of detected OTUs. Further, changes in the detected OTUs were statistically linked to deviations in salinity. We interpret these results as indicating the existence of an ever-present core bacteriorhodopsin-containing Eilat crystallizer community that fluctuates in population densities, which are controlled by salinity rather than the extinction of some OTUs and their replacement through immigration and colonization.
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85
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Warden JG, Casaburi G, Omelon CR, Bennett PC, Breecker DO, Foster JS. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. Front Microbiol 2016; 7:1064. [PMID: 27458453 PMCID: PMC4933708 DOI: 10.3389/fmicb.2016.01064] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/24/2016] [Indexed: 12/02/2022] Open
Abstract
Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.
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Affiliation(s)
- John G Warden
- Department of Geological Sciences, University of Texas at Austin, AustinTX, USA; Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt IslandFL, USA
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
| | - Christopher R Omelon
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Philip C Bennett
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Daniel O Breecker
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
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86
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Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. Appl Environ Microbiol 2016; 82:2872-2883. [PMID: 26969701 DOI: 10.1128/aem.03529-15] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on water pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities are only beginning to be explored by culture-independent techniques that circumvent the limitations of conventional monitoring efforts. Hence, theories regarding the frequency of opportunistic pathogens in DW biofilms and how biofilm members withstand high doses of disinfectants and/or chlorine residuals in the water supply remain speculative. The aim of this study was to characterize the composition of microbial communities growing on five hospital shower hoses using both 16S rRNA gene sequencing of bacterial isolates and whole-genome shotgun metagenome sequencing. The resulting data revealed a Mycobacterium-like population, closely related to Mycobacterium rhodesiae and Mycobacterium tusciae, to be the predominant taxon in all five samples, and its nearly complete draft genome sequence was recovered. In contrast, the fraction recovered by culture was mostly affiliated with Proteobacteria, including members of the genera Sphingomonas, Blastomonas, and Porphyrobacter.The biofilm community harbored genes related to disinfectant tolerance (2.34% of the total annotated proteins) and a lower abundance of virulence determinants related to colonization and evasion of the host immune system. Additionally, genes potentially conferring resistance to β-lactam, aminoglycoside, amphenicol, and quinolone antibiotics were detected. Collectively, our results underscore the need to understand the microbiome of DW biofilms using metagenomic approaches. This information might lead to more robust management practices that minimize the risks associated with exposure to opportunistic pathogens in hospitals.
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87
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Morais D, Pylro V, Clark IM, Hirsch PR, Tótola MR. Responses of microbial community from tropical pristine coastal soil to crude oil contamination. PeerJ 2016; 4:e1733. [PMID: 26925341 PMCID: PMC4768689 DOI: 10.7717/peerj.1733] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/02/2016] [Indexed: 02/01/2023] Open
Abstract
Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.
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Affiliation(s)
- Daniel Morais
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; AgroEcology Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Center (CPqRR-FIOCRUZ) , Belo Horizonte, Minas Gerais , Brazil
| | - Ian M Clark
- AgroEcology Department, Rothamsted Research , Harpenden, Hertfordshire , United Kingdom
| | - Penny R Hirsch
- AgroEcology Department, Rothamsted Research , Harpenden, Hertfordshire , United Kingdom
| | - Marcos R Tótola
- Department of Microbiology, Universidade Federal de Viçosa , Viçosa, Minas Gerais , Brazil
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88
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Acosta-González A, Marqués S. Bacterial diversity in oil-polluted marine coastal sediments. Curr Opin Biotechnol 2016; 38:24-32. [PMID: 26773654 DOI: 10.1016/j.copbio.2015.12.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022]
Abstract
Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.
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Affiliation(s)
- Alejandro Acosta-González
- Grupo de Investigación en Bioprospección (GIBP), Facultad de Ingeniería, Universidad de La Sabana, Autopista Norte km 7, Chía, Cundinamarca, Colombia
| | - Silvia Marqués
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, Profesor Albareda 1, E-18008 Granada, Spain.
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89
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Guibert LM, Loviso CL, Borglin S, Jansson JK, Dionisi HM, Lozada M. Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments. MICROBIAL ECOLOGY 2016; 71:100-112. [PMID: 26547568 DOI: 10.1007/s00248-015-0698-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
We aimed to gain insight into the alkane degradation potential of microbial communities from chronically polluted sediments of a subantarctic coastal environment using a combination of metagenomic approaches. A total of 6178 sequences annotated as alkane-1-monooxygenases (EC 1.14.15.3) were retrieved from a shotgun metagenomic dataset that included two sites analyzed in triplicate. The majority of the sequences binned with AlkB described in Bacteroidetes (32 ± 13 %) or Proteobacteria (29 ± 7 %), although a large proportion remained unclassified at the phylum level. Operational taxonomic unit (OTU)-based analyses showed small differences in AlkB distribution among samples that could be correlated with alkane concentrations, as well as with site-specific variations in pH and salinity. A number of low-abundance OTUs, mostly affiliated with Actinobacterial sequences, were found to be only present in the most contaminated samples. On the other hand, the molecular screening of a large-insert metagenomic library of intertidal sediments from one of the sampling sites identified two genomic fragments containing novel alkB gene sequences, as well as various contiguous genes related to lipid metabolism. Both genomic fragments were affiliated with the phylum Planctomycetes, and one could be further assigned to the genus Rhodopirellula due to the presence of a partial sequence of the 23S ribosomal RNA (rRNA) gene. This work highlights the diversity of bacterial groups contributing to the alkane degradation potential and reveals patterns of functional diversity in relation with environmental stressors in a chronically polluted, high-latitude coastal environment. In addition, alkane biodegradation genes are described for the first time in members of Planctomycetes.
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Affiliation(s)
- Lilian M Guibert
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Claudia L Loviso
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina.
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90
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Hydrocarbon-Degrading Bacteria Exhibit a Species-Specific Response to Dispersed Oil while Moderating Ecotoxicity. Appl Environ Microbiol 2015; 82:518-27. [PMID: 26546426 DOI: 10.1128/aem.02379-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022] Open
Abstract
The Deepwater Horizon blowout in April 2010 represented the largest accidental marine oil spill and the largest release of chemical dispersants into the environment to date. While dispersant application may provide numerous benefits to oil spill response efforts, the impacts of dispersants and potential synergistic effects with crude oil on individual hydrocarbon-degrading bacteria are poorly understood. In this study, two environmentally relevant species of hydrocarbon-degrading bacteria were utilized to quantify the response to Macondo crude oil and Corexit 9500A-dispersed oil in terms of bacterial growth and oil degradation potential. In addition, specific hydrocarbon compounds were quantified in the dissolved phase of the medium and linked to ecotoxicity using a U.S. Environmental Protection Agency (EPA)-approved rotifer assay. Bacterial treatment significantly and drastically reduced the toxicity associated with dispersed oil (increasing the 50% lethal concentration [LC50] by 215%). The growth and crude oil degradation potential of Acinetobacter were inhibited by Corexit by 34% and 40%, respectively; conversely, Corexit significantly enhanced the growth of Alcanivorax by 10% relative to that in undispersed oil. Furthermore, both bacterial strains were shown to grow with Corexit as the sole carbon and energy source. Hydrocarbon-degrading bacterial species demonstrate a unique response to dispersed oil compared to their response to crude oil, with potentially opposing effects on toxicity. While some species have the potential to enhance the toxicity of crude oil by producing biosurfactants, the same bacteria may reduce the toxicity associated with dispersed oil through degradation or sequestration.
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91
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Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015; 3:e1319. [PMID: 26500826 PMCID: PMC4614810 DOI: 10.7717/peerj.1319] [Citation(s) in RCA: 1011] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022] Open
Abstract
Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
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Affiliation(s)
- A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States ; Department of Medicine, The University of Chicago , Chicago, IL , United States
| | - Özcan C Esen
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Christopher Quince
- Warwick Medical School, University of Warwick , Coventry , United Kingdom
| | - Joseph H Vineis
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Tom O Delmont
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
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92
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Abstract
Dispersants provide a reliable large-scale response to catastrophic oil spills that can be used when the preferable option of recapturing the oil cannot be achieved. By allowing even mild wave action to disperse floating oil into tiny droplets (<70 μm) in the water column, seabirds, reptiles, and mammals are protected from lethal oiling at the surface, and microbial biodegradation is dramatically increased. Recent work has clarified how dramatic this increase is likely to be: beached oil has an environmental residence of years, whereas dispersed oil has a half-life of weeks. Oil spill response operations endorse the concept of net environmental benefit, that any environmental costs imposed by a response technique must be outweighed by the likely benefits. This critical review discusses the potential environmental debits and credits from dispersant use and concludes that, in most cases, the potential environmental costs of adding these chemicals to a polluted area are likely outweighed by the much shorter residence time, and hence integrated environmental impact, of the spilled oil in the environment.
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Affiliation(s)
- Roger C Prince
- ExxonMobil Biomedical Sciences, Inc., Annandale, New Jersey 08801 United States
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