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Zhong S, Feng J, Kong J, Huang Y, Chen X, Zhang S. Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep. Microorganisms 2023; 11:3001. [PMID: 38138145 PMCID: PMC10745737 DOI: 10.3390/microorganisms11123001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.
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Affiliation(s)
- Song Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
| | - Jingchun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Kong
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yongji Huang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiao Chen
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Si Zhang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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Mukherji S, Imchen M, Mondal S, Bhattacharyya A, Siddhardha B, Kumavath R, Ghosh A. Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban. CHEMOSPHERE 2022; 309:136806. [PMID: 36220439 DOI: 10.1016/j.chemosphere.2022.136806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Sangita Mondal
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anish Bhattacharyya
- School of Biological Sciences, Division of Genomics and Evolution, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periye P.O., Kasaragod, Kerala, 671316, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014 India.
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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Mandal A, Dutta A, Das R, Mukherjee J. Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review. MARINE POLLUTION BULLETIN 2021; 170:112626. [PMID: 34153859 DOI: 10.1016/j.marpolbul.2021.112626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 05/16/2023]
Abstract
Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm-2y-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.
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Affiliation(s)
- Abhishek Mandal
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Ahana Dutta
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Reshmi Das
- School of Environmental Studies, Jadavpur University, 700032, India.
| | - Joydeep Mukherjee
- School of Environmental Studies, Jadavpur University, 700032, India.
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4
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Zhang X, Wang L, Zhou W, Feng L, Hu M, Hu J, Liu Z. Mixing of plant litters strengthens their remediation effects on crude oil-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:12753-12765. [PMID: 33094455 DOI: 10.1007/s11356-020-11299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
To investigate the effects of the mixing of litters on their remediation efficiency in petroleum-contaminated soil, litters from two common plants in the petroleum-contaminated region of Northern Shaanxi, China, Bothriochloa ischaemum (L.) Keng and Sophora davidii Kom. ex Pavol., and their mixture were mixed with 45 g/kg petroleum-contaminated soil. Based on these, a 150-day simulated remediation experiment was conducted at 25 °C and consistent moisture conditions. The effects on the degradation of petroleum components and the restoration of nutrient contents, pH, and enzymatic activity in the disturbed soil were detected. The effects of the litter treatments on the community structure and carbon source utilization characteristics of soil microorganisms were also studied. The results indicated that all litter treatments significantly accelerated the degradation of petroleum components, while the mixing of litter exhibited significant synergistic effects, leading to significantly higher degradation rates of saturated hydrocarbons, aromatic hydrocarbons, and nonhydrocarbon substances than the observed rates in the single-litter treatments and the predicted rates based on the single-litter treatments. Litter treatment significantly increased the N and P contents and enzymatic activity of contaminated soil. The effects of mixed litter on soil chemical and biological properties fell between the effects of the 2 types of single-litter treatments. However, the mixing of litters exhibited significant synergistic effects in supplementing available P and increasing sucrase, dehydrogenase, lignin peroxidase, and laccase activity, while it exhibited significant antagonistic effects in supplementing nitrate nitrogen and increasing urease, phosphatase, polyphenol oxidase, and manganese peroxidase activity. Litter treatment significantly altered the community structure of soil microorganisms. The relative abundances of some petroleum-degrading microbial phyla or genera in mixed litter-treated soil were significantly different from those in single litter-treated soils, which might contribute to the strengthened remediation effects of mixed litter treatment. The results might provide a theoretical basis for the more effect utilization of biomass resources in the remediation of petroleum-contaminated soil.
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Affiliation(s)
- Xiaoxi Zhang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Lijie Wang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Wenxing Zhou
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Liaoliao Feng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Man Hu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Jiawei Hu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Zengwen Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
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5
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Krolicka A, Gomiero A, Baussant T. qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139527. [PMID: 32497879 DOI: 10.1016/j.scitotenv.2020.139527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Today's benthic offshore biological monitoring of oil & gas (O&G) activities relies on macrofauna taxa enumeration. For the future, analysis of DNA isolated directly from sediments holds great potential for multi-trophic biodiversity surveys and the monitoring of a larger spectrum of benthic taxa, including micro-fauna. Here, we evaluate more specifically the potential of microfauna-specific gene quantification in relation to both petroleum-related discharge compounds and other seafloor environmental properties. We carried out this evaluation using sediment samples collected at drilling Region III on the Norwegian continental shelf where DNA metabarcoding of eukaryotic diversity was already performed. Generally, the quantification of microfauna indicator taxa related well to the gradient of contamination on the seafloor. Contrary to eukaryotic Euplotida, metabarcoding data and qPCR numbers for indicative prokaryotic taxa showed the same relationship to offshore contaminants (both showed positive relationship). We found absolute numbers of SSU rRNA gene copies of (1) Dinophyceae, Bacillariophyceae and Alcanivorax were correlated with the level of petroleum-related compounds but not with other environmental variables, (2) bacteria closely related to Shewanella were correlated with the concentration of Ba, PAH, as well to percent of gravel, (3) Desulfobacteriales correlated with petroleum-related contaminants, but as well with percent of gravel and grain size. Findings from our study suggest that biomonitoring surveys of O&G activities on benthos could benefit from quantification of specific micro-fauna indicators that is simpler and faster than the methods currently used for impact assessment of benthos.
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Affiliation(s)
- Adriana Krolicka
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway.
| | - Alessio Gomiero
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| | - Thierry Baussant
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
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Pinto M, Polania Zenner P, Langer TM, Harrison J, Simon M, Varela MM, Herndl GJ. Putative degraders of low-density polyethylene-derived compounds are ubiquitous members of plastic-associated bacterial communities in the marine environment. Environ Microbiol 2020; 22:4779-4793. [PMID: 32935476 PMCID: PMC7702132 DOI: 10.1111/1462-2920.15232] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/12/2020] [Indexed: 11/28/2022]
Abstract
It remains unknown whether and to what extent marine prokaryotic communities are capable of degrading plastic in the ocean. To address this knowledge gap, we combined enrichment experiments employing low‐density polyethylene (LDPE) as the sole carbon source with a comparison of bacterial communities on plastic debris in the Pacific, the North Atlantic and the northern Adriatic Sea. A total of 35 operational taxonomic units (OTUs) were enriched in the LDPE‐laboratory incubations after 1 year, of which 20 were present with relative abundances > 0.5% in at least one plastic sample collected from the environment. From these, OTUs classified as Cognatiyoonia, Psychrobacter, Roseovarius and Roseobacter were found in the communities of plastics collected at all oceanic sites. Additionally, OTUs classified as Roseobacter, Pseudophaeobacter, Phaeobacter, Marinovum and Cognatiyoonia, also enriched in the LDPE‐laboratory incubations, were enriched on LDPE communities compared to the ones associated to glass and polypropylene in in‐situ incubations in the northern Adriatic Sea after 1 month of incubation. Some of these enriched OTUs were also related to known alkane and hydrocarbon degraders. Collectively, these results demonstrate that there are prokaryotes capable of surviving with LDPE as the sole carbon source living on plastics in relatively high abundances in different water masses of the global ocean.
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Affiliation(s)
- Maria Pinto
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Research Platform 'Plastics in the Environment and Society', University of Vienna, Vienna, Austria
| | - Paula Polania Zenner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Teresa M Langer
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Jesse Harrison
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, A Coruña, Spain
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Research Platform 'Plastics in the Environment and Society', University of Vienna, Vienna, Austria.,NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
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7
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Thomas GE, Cameron TC, Campo P, Clark DR, Coulon F, Gregson BH, Hepburn LJ, McGenity TJ, Miliou A, Whitby C, McKew BA. Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece. Front Microbiol 2020; 11:1706. [PMID: 32765479 PMCID: PMC7379155 DOI: 10.3389/fmicb.2020.01706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.
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Affiliation(s)
- Gareth E. Thomas
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Tom C. Cameron
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Pablo Campo
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex, United Kingdom
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | | | - Leanne J. Hepburn
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Corinne Whitby
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Boyd A. McKew
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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8
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Domingues PM, Oliveira V, Serafim LS, Gomes NCM, Cunha Â. Biosurfactant Production in Sub-Oxic Conditions Detected in Hydrocarbon-Degrading Isolates from Marine and Estuarine Sediments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17051746. [PMID: 32156011 PMCID: PMC7084516 DOI: 10.3390/ijerph17051746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/16/2022]
Abstract
Hydrocarbon bioremediation in anoxic sediment layers is still challenging not only because it involves metabolic pathways with lower energy yields but also because the production of biosurfactants that contribute to the dispersion of the pollutant is limited by oxygen availability. This work aims at screening populations of culturable hydrocarbonoclastic and biosurfactant (BSF) producing bacteria from deep sub-seafloor sediments (mud volcanos from Gulf of Cadiz) and estuarine sub-surface sediments (Ria de Aveiro) for strains with potential to operate in sub-oxic conditions. Isolates were retrieved from anaerobic selective cultures in which crude oil was provided as sole carbon source and different supplements were provided as electron acceptors. Twelve representative isolates were obtained from selective cultures with deep-sea and estuary sediments, six from each. These were identified by sequencing of 16S rRNA gene fragments belonging to Pseudomonas, Bacillus, Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera. BSF production by the isolates was tested by atomized oil assay, surface tension measurement and determination of the emulsification index. All isolates were able to produce BSFs under aerobic and anaerobic conditions, except for isolate DS27 which only produced BSF under aerobic conditions. These isolates presented potential to be applied in bioremediation or microbial enhanced oil recovery strategies under conditions of oxygen limitation. For the first time, members of Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera are described as anaerobic producers of BSFs.
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Affiliation(s)
- Patrícia M. Domingues
- Department of Chemistry and CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Newton C. M. Gomes
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +351-234-370-784
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9
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Baltar F, Gutiérrez-Rodríguez A, Meyer M, Skudelny I, Sander S, Thomson B, Nodder S, Middag R, Morales SE. Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria. Front Microbiol 2018; 9:3190. [PMID: 30619234 PMCID: PMC6306045 DOI: 10.3389/fmicb.2018.03190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/10/2018] [Indexed: 01/26/2023] Open
Abstract
Marine microbes are an important control on the biogeochemical cycling of trace metals, but simultaneously, these metals can control the growth of microorganisms and the cycling of major nutrients like C and N. However, studies on the response/limitation of microorganisms to trace metals have traditionally focused on the response of autotrophic phytoplankton to Fe fertilization. Few reports are available on the response of heterotrophic prokaryotes to Fe, and even less to other biogeochemically relevant metals. We performed the first study coupling dark incubations with next generation sequencing to specifically target the functional and phylogenetic response of heterotrophic prokaryotes to Fe enrichment. Furthermore, we also studied their response to Co, Mn, Ni, Zn, Cu (individually and mixed), using surface and deep samples from either coastal or open-ocean waters. Heterotrophic prokaryotic activity was stimulated by Fe in surface open–ocean, as well as in coastal, and deep open-ocean waters (where Zn also stimulated). The most susceptible populations to trace metals additions were uncultured bacteria (e.g., SAR324, SAR406, NS9, and DEV007). Interestingly, hydrocarbon-degrading bacteria (e.g., Thalassolituus, Marinobacter, and Oleibacter) benefited the most from metal addition across all waters (regions/depths) revealing a predominant role in the cycling of metals and organic matter in the ocean.
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Affiliation(s)
- Federico Baltar
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Department of Marine Science, University of Otago, Dunedin, New Zealand.,National Institute of Water and Atmospheric Research (NIWA)/University of Otago Research Centre for Oceanography, University of Otago, Dunedin, New Zealand
| | | | - Moana Meyer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Isadora Skudelny
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Sylvia Sander
- National Institute of Water and Atmospheric Research (NIWA)/University of Otago Research Centre for Oceanography, University of Otago, Dunedin, New Zealand.,Environment Laboratories, Department of Nuclear Sciences and Applications, International Atomic Energy Agency (IAEA), Monaco, Monaco
| | - Blair Thomson
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Scott Nodder
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Rob Middag
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research, Yerseke, Netherlands
| | - Sergio E Morales
- Department of Microbiology and Immunology, Otago School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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10
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Wang W, Wang L, Shao Z. Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 PMCID: PMC6193391 DOI: 10.1128/aem.01261-18 10.1016/j.biotechadv.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 06/12/2023] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lin Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 DOI: 10.1128/aem.01261-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by Cycloclasticus Cycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in Cycloclasticus IMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Yan L, Yu D, Hui N, Naanuri E, Viggor S, Gafarov A, Sokolov SL, Heinaru A, Romantschuk M. Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination. Front Microbiol 2018; 9:15. [PMID: 29410652 PMCID: PMC5787342 DOI: 10.3389/fmicb.2018.00015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.
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Affiliation(s)
- Lijuan Yan
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Dan Yu
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Nan Hui
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Eve Naanuri
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Signe Viggor
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Arslan Gafarov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Sergei L Sokolov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Ain Heinaru
- Faculty of Science and Technology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Martin Romantschuk
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland.,Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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13
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Viggi CC, Matturro B, Frascadore E, Insogna S, Mezzi A, Kaciulis S, Sherry A, Mejeha OK, Head IM, Vaiopoulou E, Rabaey K, Rossetti S, Aulenta F. Bridging spatially segregated redox zones with a microbial electrochemical snorkel triggers biogeochemical cycles in oil-contaminated River Tyne (UK) sediments. WATER RESEARCH 2017; 127:11-21. [PMID: 29020640 DOI: 10.1016/j.watres.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 09/19/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Marine sediments represent an important sink for a number of anthropogenic organic contaminants, including petroleum hydrocarbons following an accidental oil spill. Degradation of these compounds largely depends on the activity of sedimentary microbial communities linked to biogeochemical cycles, in which abundant elements such as iron and sulfur are shuttled between their oxidized and reduced forms. Here we show that introduction of a small electrically conductive graphite rod ("the electrochemical snorkel") into an oil-contaminated River Tyne (UK) sediment, so as to create an electrochemical connection between the anoxic contaminated sediment and the oxygenated overlying water, has a large impact on the rate of metabolic reactions taking place in the bulk sediment. The electrochemical snorkel accelerated sulfate reduction processes driven by organic contaminant oxidation and suppressed competitive methane-producing reactions. The application of a comprehensive suite of chemical, spectroscopic, biomolecular and thermodynamic analyses suggested that the snorkel served as a scavenger of toxic sulfide via a redox interaction with the iron cycle. Taken as a whole, the results of this work highlight a new strategy for controlling biological processes, such as bioremediation, through the manipulation of the electron flows in contaminated sediments.
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Affiliation(s)
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Italy
| | | | | | - Alessio Mezzi
- Institute for the Study of Nanostructured Materials (ISMN), National Research Council (CNR), Italy
| | - Saulius Kaciulis
- Institute for the Study of Nanostructured Materials (ISMN), National Research Council (CNR), Italy
| | - Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Obioma K Mejeha
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Eleni Vaiopoulou
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Italy.
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14
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Terrisse F, Cravo-Laureau C, Noël C, Cagnon C, Dumbrell AJ, McGenity TJ, Duran R. Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes. Front Microbiol 2017; 8:1549. [PMID: 28861063 PMCID: PMC5562018 DOI: 10.3389/fmicb.2017.01549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/31/2017] [Indexed: 12/26/2022] Open
Abstract
Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.
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Affiliation(s)
- Fanny Terrisse
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cristiana Cravo-Laureau
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cyril Noël
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Christine Cagnon
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Alex J Dumbrell
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Terry J McGenity
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
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15
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Lee J, Han I, Kang BR, Kim SH, Sul WJ, Lee TK. Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community. MARINE POLLUTION BULLETIN 2017; 114:296-301. [PMID: 27671845 DOI: 10.1016/j.marpolbul.2016.09.043] [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: 06/23/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Crude oil spills, Hebei Spirit in South Korea, is considered as one of the worst environmental disasters of the region. Our understanding on activation of oil-degrading bacteria and resilience of microbial community in oil contaminated sites are limited due to scarcity of such event. In the present study, tidal flat sediment contaminated by the oil spill were investigated for duration of 13months to identify temporal change in microbial community and functional genes responsible for PAH-degradation. The results showed predominance of previously known oil-degrading genera, such as Cycloclasticus, Alcanivorax, and Thalassolituus, displaying significant increase within first four months of the accident. The disturbance caused by the oil spill altered the microbial community and its functional structures, but they were almost restored to the original state after 13months. Present study demonstrated high detoxification capacity of indigenous bacterial populations in the tidal flat sediments and its resilience of microbial community.
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Affiliation(s)
- Jaejin Lee
- Unit of Antarctic K-route Expedition, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Il Han
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Bo Ram Kang
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Seong Heon Kim
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Woo Jun Sul
- Department of System Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea.
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16
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Leal AJ, Rodrigues EM, Leal PL, Júlio ADL, Fernandes RDCR, Borges AC, Tótola MR. Changes in the microbial community during bioremediation of gasoline-contaminated soil. Braz J Microbiol 2016; 48:342-351. [PMID: 28034596 PMCID: PMC5470457 DOI: 10.1016/j.bjm.2016.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/26/2016] [Accepted: 10/05/2016] [Indexed: 01/11/2023] Open
Abstract
We aimed to verify the changes in the microbial community during bioremediation of gasoline-contaminated soil. Microbial inoculants were produced from successive additions of gasoline to municipal solid waste compost (MSWC) previously fertilized with nitrogen-phosphorous. To obtain Inoculant A, fertilized MSWC was amended with gasoline every 3 days during 18 days. Inoculant B received the same application, but at every 6 days. Inoculant C included MSWC fertilized with N–P, but no gasoline. The inoculants were applied to gasoline-contaminated soil at 10, 30, or 50 g/kg. Mineralization of gasoline hydrocarbons in soil was evaluated by respirometric analysis. The viability of the inoculants was evaluated after 103 days of storage under refrigeration or room temperature. The relative proportions of microbial groups in the inoculants and soil were evaluated by FAME. The dose of 50 g/kg of inoculants A and B led to the largest CO2 emission from soil. CO2 emissions in treatments with inoculant C were inversely proportional to the dose of inoculant. Heterotrophic bacterial counts were greater in soil treated with inoculants A and B. The application of inoculants decreased the proportion of actinobacteria and increased of Gram-negative bacteria. Decline in the density of heterotrophic bacteria in inoculants occurred after storage. This reduction was bigger in inoculants stored at room temperature. The application of stored inoculants in gasoline-contaminated soil resulted in a CO2 emission twice bigger than that observed in uninoculated soil. We concluded that MSWC is an effective material for the production of microbial inoculants for the bioremediation of gasoline-contaminated soil.
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Affiliation(s)
- Aline Jaime Leal
- Instituto Federal Sul-rio-grandense, Bagé, Rio Grande do Sul, Brazil
| | - Edmo Montes Rodrigues
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil.
| | - Patrícia Lopes Leal
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil
| | - Aline Daniela Lopes Júlio
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil
| | - Rita de Cássia Rocha Fernandes
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil
| | - Arnaldo Chaer Borges
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil
| | - Marcos Rogério Tótola
- Universidade Federal de Viçosa, Departamento de Microbiologia, Laboratório de Biotecnologia Ambiental e Biodiversidade, Viçosa, Minas Gerais, Brazil.
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17
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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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18
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Meng L, Liu H, Bao M, Sun P. Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters. MARINE POLLUTION BULLETIN 2016; 111:203-212. [PMID: 27485782 DOI: 10.1016/j.marpolbul.2016.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
This study tracked structure shifts of bacterial compositions before, during and after invading by crude oil to determine the microbial response and explore how temperature, dispersants and nutrients affect the composition of microbial communities or their activities of biodegradation in artificial marine environment. During petroleum hydrocarbons exposed, the composition and functional dynamics of marine microbial communities were altered, favoring bacteria that could utilize this rich carbon source such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes phyla. Low temperature as a dominant factor decreased bacterial richness and catabolic diversity due to abated enzymes activities in correlation with the process of biodegradation. Dispersants exerted no negative consequences on microbial composition, however, bacterial composition by the Chloroflexi, TM6, OP8, Cyanobacteria and Gemmatimonadetes phyla increased. It seemed that more frequent fertilizer application could be equally safe to bacteria and increased significantly the abundance of bacterial strains but Actinobacteria phyla decreased.
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Affiliation(s)
- Long Meng
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Han Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China.
| | - Peiyan Sun
- Key Laboratory of Marine Spill Oil Identification and Damage Assessment Technology, North China Sea Environmental Monitoring Center, State Oceanic Administration, Qingdao 266033, China
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19
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Sarkar J, Kazy SK, Gupta A, Dutta A, Mohapatra B, Roy A, Bera P, Mitra A, Sar P. Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge. Front Microbiol 2016; 7:1407. [PMID: 27708623 PMCID: PMC5030240 DOI: 10.3389/fmicb.2016.01407] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022] Open
Abstract
Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community’s composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N2 fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O2 and increase in oxidation-reduction potential (ORP) marked with an enrichment of N2 fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.
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Affiliation(s)
- Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Avishek Dutta
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Paramita Bera
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Adinpunya Mitra
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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20
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Jeanbille M, Gury J, Duran R, Tronczynski J, Ghiglione JF, Agogué H, Saïd OB, Taïb N, Debroas D, Garnier C, Auguet JC. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. Front Microbiol 2016; 7:1303. [PMID: 27594854 PMCID: PMC4990537 DOI: 10.3389/fmicb.2016.01303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/08/2016] [Indexed: 01/11/2023] Open
Abstract
Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.
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Affiliation(s)
- Mathilde Jeanbille
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jérôme Gury
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jacek Tronczynski
- Laboratoire Biogéochimie des Contaminants Organiques, Unité Biogéochimie et Ecotoxicologie, Département Ressources Biologiques et Environnement, Ifremer Centre Atlantique Nantes, France
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne, Sorbonne Universités, CNRS, Université Pierre-et-Marie-Curie, UMR 7621, Observatoire Océanologique Banyuls-sur-mer, France
| | - Hélène Agogué
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - Université de La Rochelle La Rochelle, France
| | - Olfa Ben Saïd
- Laboratoire de Bio-surveillance de l'Environnement, Faculté des Sciences de Bizerte Zarzouna, Tunisia
| | - Najwa Taïb
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Cédric Garnier
- Processus de Transferts et d'Echanges dans l'Environnement, EA 3819, Université de Toulon La Garde, France
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Rodrigues EM, Kalks KHM, Fernandes PL, Tótola MR. Bioremediation strategies of hydrocarbons and microbial diversity in the Trindade Island shoreline--Brazil. MARINE POLLUTION BULLETIN 2015; 101:517-525. [PMID: 26522160 DOI: 10.1016/j.marpolbul.2015.10.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
This study analyzed the microbial diversity colonizing the surface of an oil sample during its contact with water, off the Trindade Island coast and simulated the efficiency of eight different bioremediation strategies for this environment. The diversity analysis was performed using acrylic coupons that served as the support for an oil inclusion at sea. The coupons were sampled over 30 days, and T-RFLP multiplex was employed to access the diversity of fungi, Bacteria and Archaea present on the oil surface. The bioremediation strategies were simulated in a respirometer. The results showed that the bacterial domain was the most dominant in oil colonization and that the richness of the species attached to the oil gradually increases with the exposure time of the coupons. The combination of biostimulation and bioaugmentation with a native population was proven to be an effective strategy for the remediation of oil off the Trindade Island shoreline.
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Affiliation(s)
- Edmo M Rodrigues
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Karlos H M Kalks
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Péricles L Fernandes
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos R Tótola
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
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Duran R, Cuny P, Bonin P, Cravo-Laureau C. Microbial ecology of hydrocarbon-polluted coastal sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15195-15199. [PMID: 26381785 DOI: 10.1007/s11356-015-5373-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Philippe Cuny
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Patricia Bonin
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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