1
|
Hepditch SLJ, Gutierrez-Villagomez JM, To TA, Larocque E, Xin Q, Heshka N, Vander Meulen I, Headley JV, Dettman HD, Triffault-Bouchet G, Ahad JME, Langlois VS. Aquatic toxicity and chemical fate of diluted bitumen spills in freshwater under natural weathering. ENVIRONMENT INTERNATIONAL 2024; 190:108944. [PMID: 39151269 DOI: 10.1016/j.envint.2024.108944] [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: 04/15/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Increasing global demands for oils are fueling the production of diluted bitumen (DB) from Canada's oil sands region. More weathered than conventional crude (CC) oils, Alberta bitumen is often diluted with lighter petroleum oils to reduce density and viscosity to meet pipeline specifications for transportation. Being a heavy oil product that is transported in large volumes across Canada and the USA, there has been interest to compare its behavior and toxicity characteristics when spilled to those of CC. To determine the influence of environmental weathering upon DB following a freshwater spill, we conducted separate controlled spills of Cold Lake Blend DB and Mixed Sweet Blend light CC oil in a mesocosm spill-tank system at 24 °C with wave-action for 56 days. DB-contaminated waters remained acutely lethal for a period of 14 days to early life stage fathead minnows (Pimephales promelas) exposed during embryologic development, while CC was lethal for 1 day. However, concentrations of mono- and polycyclic aromatic compounds, often claimed to be principally responsible for the acute and chronic toxicity of crude oils, were consistently higher in CC water compared to DB. Elevated aromatic concentrations in CC water correlated with higher prevalences of developmental malformations, reduced heart and growth rates, and impacts on the aryl hydrocarbon receptor pathway. Organic acids were measured over the course of the studies and O2 containing naphthenic acids were present at greater relative abundances in DB- compared to CC-contaminated water, with their attenuation correlating with reduced acute and sublethal toxicity. Furthermore, organic acid degradation products accumulated with time and likely contributed to the consistently sublethal toxicity of the weathered oils throughout the experiment. Improved characterization of the fractions including organic acids and those organic compounds found within the unresolved complex mixture of fresh and weathered crude oils is necessary to adequately understand and prepare for the risks that accidental petroleum spills pose to aquatic resources.
Collapse
Affiliation(s)
- S L J Hepditch
- Institut national de la recherche scientifique (INRS), 490 rue de la Couronne, Québec City, QC G1K 9A9, Canada; Centre d'expertise en analyse environnementale du Québec, ministère de l'Environnement et de la lutte contre les changements climatiques, de la faune et des forêts (MELCCFP), Québec City, QC H7C 2M7, Canada; Geological Survey of Canada, Natural Resources Canada (NRCan), Québec City, QC G1K 9A9, Canada
| | - J M Gutierrez-Villagomez
- Institut national de la recherche scientifique (INRS), 490 rue de la Couronne, Québec City, QC G1K 9A9, Canada
| | - T A To
- Institut national de la recherche scientifique (INRS), 490 rue de la Couronne, Québec City, QC G1K 9A9, Canada
| | - E Larocque
- Institut national de la recherche scientifique (INRS), 490 rue de la Couronne, Québec City, QC G1K 9A9, Canada
| | - Q Xin
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - N Heshka
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - I Vander Meulen
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, National Hydrology Research Center, 11 Innovation Boulevard, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - J V Headley
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, National Hydrology Research Center, 11 Innovation Boulevard, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - H D Dettman
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - G Triffault-Bouchet
- Centre d'expertise en analyse environnementale du Québec, ministère de l'Environnement et de la lutte contre les changements climatiques, de la faune et des forêts (MELCCFP), Québec City, QC H7C 2M7, Canada
| | - J M E Ahad
- Geological Survey of Canada, Natural Resources Canada (NRCan), Québec City, QC G1K 9A9, Canada
| | - V S Langlois
- Institut national de la recherche scientifique (INRS), 490 rue de la Couronne, Québec City, QC G1K 9A9, Canada.
| |
Collapse
|
2
|
Nai H, Xu S, Chen B, Zhong J, Fang L, Qin S, Sano Y. Generation of secondary microbial methane of high-rank coals: insights from the microbial community and carbon isotope. Front Microbiol 2024; 15:1414379. [PMID: 39149210 PMCID: PMC11324580 DOI: 10.3389/fmicb.2024.1414379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024] Open
Abstract
Secondary microbial methane could provide a valuable energy source if it were better understood. Although coal seam is an ideal environment for investigating secondary microbial methane, there are few studies to trace the secondary microbial methane of high-rank coals. Here, we collected co-produced water samples from coalbeds in the Qinshui Basin (China) and analyzed the microbial community structure by 16S ribosomal RNA (16S rRNA) amplicon sequencing analysis. 16S rRNA sequencing demonstrated abundant methanogens in coalbeds including 6 orders (Methanobacteriales, Methanococcales, Methanofastidiosales, Methanomassiliicoccale, Methanomicrobiales, and Methanosarciniales) and 22 genera of methanogens. Superheavy DIC (δ13CDIC ranging from -4.2‰ to 34.8‰) and abundance of methanogenic microbes in co-produced water revealed the generation of secondary biogenic methane in high-rank coal seams in the Qingshui Basin. Hydrogenotrophic methanogenesis is the main pathway for secondary biogenic methane production. In deeply buried coal seams, biogenic methane is dominated by CO2 and H2 reduction methanogenesis, and in shallow buried coal seams, it may be produced synergistically by hydrocarbon degradation and hydrogenotrophic methanogenic microbes. The study discussed here is important for a better understanding of the generation of secondary microbial methane in high-rank coal.
Collapse
Affiliation(s)
- Hui Nai
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Sheng Xu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Biying Chen
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Jun Zhong
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Lujia Fang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Sirou Qin
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, China
| | - Yuji Sano
- Marine Core Research Institute, Kochi University, Kochi, Japan
| |
Collapse
|
3
|
Bahar MM, Samarasinghe SVAC, Bekele D, Naidu R. Residual hydrocarbons in long-term contaminated soils: implications to risk-based management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22759-22773. [PMID: 38409383 PMCID: PMC10997687 DOI: 10.1007/s11356-024-32593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
Petroleum hydrocarbon (PHC) contamination is a widespread and severe environmental issue affecting many countries' resource sectors. PHCs are mixtures of hydrocarbon compounds with varying molar masses that naturally attenuate at different rates. Lighter fractions attenuate first, followed by medium-molar-mass constituents, while larger molecules remain for longer periods. This results in significant regulatory challenges concerning residual hydrocarbons in long-term contaminated soils. This study examined the potential risks associated with residual PHC and its implications for risk-based management of heavily contaminated soils (23,000-26,000 mg PHC/kg). Ecotoxicological properties, such as seedling emergence and growth of two native plant species-small Flinders grass (Iseilema membranaceum) and ruby saltbush (Enchylaena tomentosa)-and earthworm survival tests in PHC-contaminated soils, were assessed. Additionally, the effects of aging on the attenuation of PHC in contaminated soils were evaluated. Toxicity responses of plant growth parameters were determined as no-observed-effect concentrations: 75%-100% for seedling emergence, < 25%-75% for plant shoot height, and 75%-100% for earthworm survival. After 42 weeks of aging, the total PHC levels in weathered soils decreased by 14% to 30% and by 67% in diesel-spiked soil due to natural attenuation. Dehydrogenase enzyme activity in soils increased during the initial aging period. Furthermore, a clear shift of bacterial communities was observed in the soils following aging, including enrichment of PHC-resistant and -utilizing bacteria-for example, Nocardia sp. This study underscores the potential of natural attenuation for eco-friendly and cost-effective soil management, underlining that its success depends on site-specific factors like water content and nutrient availability. Therefore, we recommend detailed soil assessments to evaluate these conditions prior to adopting a risk-based management approach.
Collapse
Affiliation(s)
- Md Mezbaul Bahar
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia.
- crc for Contamination Assessment and Environmental Remediation (crcCARE), ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
| | - Samarasinghe Vidane Arachchige Chamila Samarasinghe
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
- crc for Contamination Assessment and Environmental Remediation (crcCARE), ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Dawit Bekele
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
- Douglas Partners, West End, QLD, 4101, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
- crc for Contamination Assessment and Environmental Remediation (crcCARE), ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| |
Collapse
|
4
|
Mohamad Shahimin MF, Siddique T. Uncovering Anaerobic Hydrocarbon Biodegradation Pathways in Oil Sands Tailings from Two Different Tailings Ponds via Metabolite and Functional Gene Analyses. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04855-0. [PMID: 38376742 DOI: 10.1007/s12010-024-04855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
Oil sands tailings, a slurry of alkaline water, silt, clay, unrecovered bitumen, and residual hydrocarbons generated during bitumen extraction, are contained in ponds. Indigenous microbes metabolize hydrocarbons and emit greenhouse gases from the tailings. Metabolism of hydrocarbons in tailings ponds of two operators, namely, Canadian Natural Upgrading Limited (CNUL) and Canadian Natural Resources Limited (CNRL), has not been comprehensively investigated. Previous reports have revealed sequential and preferential hydrocarbon degradation of alkanes in primary cultures established from CNUL and CNRL tailings amended separately with mixtures of hydrocarbons (n-alkanes, iso-alkanes, paraffinic solvent, or naphtha). In this study, activation pathway of hydrocarbon biodegradation in these primary cultures was investigated. The functional gene analysis revealed that fumarate addition was potentially the primary activation pathway of alkanes in all cultures. However, the metabolite analysis only detected transient succinylated 2-methylpentane and 2-methylbutane metabolites during initial methanogenic biodegradation of iso-alkanes and paraffinic solvent in all CNUL and CNRL cultures amended with iso-alkanes and paraffinic solvent. Under sulfidogenic conditions (prepared only with CNUL tailings amended with iso-alkanes), succinylated 2-methylpentane persisted throughout incubation period of ~ 1100 days, implying dead-end nature of the metabolite. Though no metabolite was detected in n-alkanes- and naphtha-amended cultures during incubation, assA/masD genes related to Peptococcaceae were amplified in all CNUL and CNRL primary cultures. The findings of this present study suggest that microbial communities in different tailings ponds can biodegrade hydrocarbons through fumarate addition as activation pathway under methanogenic and sulfidogenic conditions.
Collapse
Affiliation(s)
- Mohd Faidz Mohamad Shahimin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada.
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis, Aras 2, Blok S2, UniCITI Alam Campus, 02100, Padang Besar, Perlis, Malaysia.
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada
| |
Collapse
|
5
|
Panwar R, Mathur J. Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower. 3 Biotech 2023; 13:251. [PMID: 37388857 PMCID: PMC10299988 DOI: 10.1007/s13205-023-03664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/06/2023] [Indexed: 07/01/2023] Open
Abstract
Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.
Collapse
Affiliation(s)
- Ritu Panwar
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan 304022 India
| | - Jyoti Mathur
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan 304022 India
| |
Collapse
|
6
|
Zhang H, Liu X, Wang Y, Duan L, Liu X, Zhang X, Dong L. Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:64486-64498. [PMID: 37071357 DOI: 10.1007/s11356-023-26903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/05/2023] [Indexed: 05/11/2023]
Abstract
Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.
Collapse
Affiliation(s)
- Handan Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China.
| | - Yujing Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Linshuai Duan
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiqin Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xin Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
| | - Lu Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
| |
Collapse
|
7
|
Brown DC, Aggarwal N, Turner RJ. Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36190831 DOI: 10.1099/mic.0.001248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.
Collapse
|
8
|
Du J, Liu J, Jia T, Chai B. The relationships between soil physicochemical properties, bacterial communities and polycyclic aromatic hydrocarbon concentrations in soils proximal to coking plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 298:118823. [PMID: 35007680 DOI: 10.1016/j.envpol.2022.118823] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the major channel for their decontamination from different environments. Aerobic and anaerobic biodegradations of PAHs in batch reactors with single or multiple bacterial strains have been intensively studied, but the cooperative mechanism of functional PAH-degrading populations at the community level under field conditions remains to be explored. We determined the composition of PAH-degrading populations in the bacterial community and PAHs in farmland and wasteland soils contaminated by coking plants using high-throughput sequencing and high-performance liquid chromatography (HPLC), respectively. The results indicated that the PAH content of farmland was significantly lower than that of wasteland, which was attributed to the lower content of low molecular weight (LMW) PAHs and benzo [k]fluoranthene. The soil physicochemical properties were significantly different between farmland and wasteland. The naphthalene content was related to the soil organic carbon (SOC) and pH, while phenanthrene was related to the nitrate nitrogen (NO3--N) and water content (WC). The pH, nitrite (NO2--N), SOC, NO3--N and WC were correlated with the content of high molecular weight (HMW) PAHs and total PAHs. The relative abundances of the phyla Actinobacteria, Chloroflexi, Acidobacteria, and Firmicutes and the genera Nocardioides, Bacillus, Lysobacter, Mycobacterium, Streptomyces, and Steroidobacter in farmland soil were higher than those in wasteland soil. The soil physicochemical characteristics of farmland increased the diversities of the PAH degrader and total bacterial communities, which were significantly negatively related to the total PAHs and LMW PAHs. Subsequently, the connectivity and complexity of the network in farmland were lower than those in wasteland, while the module containing a module hub capable of degrading PAHs was identified in the network of farmland soil. Structural equation modelling (SEM) analysis showed that the soil characteristics and optimized abundance and diversity of the bacterial community in farmland were beneficial for the dissipation efficiency of PAHs.
Collapse
Affiliation(s)
- Jingqi Du
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, PR China; Department of Life Sciences, Lüliang University, Lüliang, 033000, PR China
| | - Jinxian Liu
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, PR China
| | - Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, PR China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, PR China.
| |
Collapse
|
9
|
Semenova EM, Grouzdev DS, Sokolova DS, Tourova TP, Poltaraus AB, Potekhina NV, Shishina PN, Bolshakova MA, Avtukh AN, Ianutsevich EA, Tereshina VM, Nazina TN. Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae. Microorganisms 2022; 10:microorganisms10020378. [PMID: 35208832 PMCID: PMC8878594 DOI: 10.3390/microorganisms10020378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2T was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2T grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2T had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4T. The genomic DNA G + C content of strain HO-Ch2T was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2T and Actinotalea genomes were 79.8–82.0% and 20.5–22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2T (= VKM Ac-2850T = KCTC 49656T) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales.
Collapse
Affiliation(s)
- Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Tatiyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | | | - Polina N. Shishina
- Geological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; (P.N.S.); (M.A.B.)
| | - Maria A. Bolshakova
- Geological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; (P.N.S.); (M.A.B.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Vera M. Tereshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
- Correspondence: ; Tel.: +7-499-135-0341
| |
Collapse
|
10
|
A microbial solution to oil sand pollution: Understanding the microbiomes, metabolic pathways and mechanisms involved in naphthenic acid (NA) biodegradation. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Advanced methods for RNA recovery from petroleum impacted soils. MethodsX 2021; 8:101503. [PMID: 34754774 PMCID: PMC8563465 DOI: 10.1016/j.mex.2021.101503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022] Open
Abstract
Microbially-mediated hydrocarbon degradation is well documented. However, how these microbial processes occur in complex subsurface petroleum impacted systems remains unclear, and this knowledge is needed to guide technologies to enhance microbial degradation effectively. Analysis of RNA derived from soils impacted by petroleum liquids would allow for analysis of active microbial communities, and a deeper understanding of the dynamic biochemistry occurring during site remediation. However, RNA analysis in soils impacted with petroleum liquids is challenging due to: (A) RNA being inherently unstable, and (B) petroleum impacted soils containing problematic levels of polymerase chain reaction (PCR) inhibitors that must be removed to yield high-purity RNA for downstream analysis. A previously published soil wash pretreatment step and a commercially available DNA extraction kit protocol were combined and modified to be able to purify RNA from soils containing petroleum liquids.A key modification involved reformulation of the pretreatment solution via replacing water as the diluent with a commercially-available RNA preservation solution. Methods were developed and demonstrated using cryogenically preserved soils from three former petroleum refineries. Results showed the new soil washing approach had no adverse effects on RNA recovery but did improve RNA quality, by PCR inhibitor removal, which in turn allows for characterization of active microbial communities present in petroleum impacted soils. In summary, our method for extracting RNA from petroleum-impacted soils provides a promising new tool for resolving metabolic processes at sites as they progress toward restoration via natural and/or engineered remediation.
Collapse
|
12
|
Sengupta K, Pal S. A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40288-40307. [PMID: 33844144 DOI: 10.1007/s11356-021-13666-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.
Collapse
Affiliation(s)
- Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Pune, 411004, India
| | - Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
| |
Collapse
|
13
|
A Deep Look into the Microbiology and Chemistry of Froth Treatment Tailings: A Review. Microorganisms 2021; 9:microorganisms9051091. [PMID: 34069522 PMCID: PMC8161226 DOI: 10.3390/microorganisms9051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 11/30/2022] Open
Abstract
In Alberta’s Athabasca oil sands region (AOSR), over 1.25 billion m3 of tailings waste from the bitumen extraction process are stored in tailings ponds. Fugitive emissions associated with residual hydrocarbons in tailings ponds pose an environmental concern and include greenhouse gases (GHGs), reduced sulphur compounds (RSCs), and volatile organic compounds (VOCs). Froth treatment tailings (FTT) are a specific type of tailings waste stream from the bitumen froth treatment process that contains bioavailable diluent: either naphtha or paraffins. Tailings ponds that receive FTT are associated with the highest levels of biogenic gas production, as diverse microbial communities biodegrade the residual diluent. In this review, current literature regarding the composition, chemical analysis, and microbial degradation of FTT and its constituents is presented in order to provide a more complete understanding of the complex chemistry and biological processes related to fugitive emissions from tailings ponds receiving FTT. Characterizing the composition and biodegradation of FTT is important from an environmental perspective to better predict emissions from tailings ponds and guide tailings pond management decisions.
Collapse
|
14
|
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| |
Collapse
|
15
|
Borowik A, Wyszkowska J, Kucharski M, Kucharski J. The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity. SENSORS 2020; 20:s20123362. [PMID: 32545819 PMCID: PMC7349710 DOI: 10.3390/s20123362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C6–C12) degradation was higher by 17%; mineral oil (C12–C35), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.
Collapse
|
16
|
Metagenomic Insight Towards Vanillin-Mediated Membrane Biofouling Prevention: In Silico Docking Validation. Curr Microbiol 2020; 77:2233-2247. [PMID: 32382950 DOI: 10.1007/s00284-020-02003-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
Biofouling leads to water quality deterioration and higher maintenance cost for cleaning of membranes. The present study has demonstrated the application of a biomolecule (vanillin) in scrubbing and destabilizing biofilms of drinking water reverse osmosis (RO) membrane module in lab scale reactor set-up. Reverse osmosis membrane reactor was connected with tap water supply and subjected with optimal concentration of vanillin. The pressure drop was delayed by 17-20 days as compared to control reactor. Real-time PCR analysis of metagenome indicated the reduced copy number of functional biofilm-associated genes (bdlA, lasI, pgaC) in treated membrane. SEM and metagenome analysis revealed that the sticky biofilm communities shifted to loosely bound emboli after vanillin treatment. Metagenome sequence analysis revealed the inhibitory activity against major biofouling biota like members of Proteobacteria, Acidobacteria, Acnitobacteria, Bacteroidetes, Candidatus, Nitrospira, and Firmicutes. Biofouled membrane metagenome sequence was also compared with real-life (brackish water, waste water, domestic drinking water) biofouled membrane communities. In silico docking of vanillin to receptor proteins and chemical configuration simulation along with other phenolic derivatives were performed, which suggested that the autoiducer signal capability of vanillin was effective against representative broad spectrum biofilm population. Vanillin exhibited the quorum-quenching mode of action by virtue of docking towards similar amino acid (Thr 131, Ilu 214) responsible of autoinducer signal anchoring in the transcriptional regulatory proteins.
Collapse
|
17
|
Sierra-Garcia IN, Belgini DRB, Torres-Ballesteros A, Paez-Espino D, Capilla R, Santos Neto EV, Gray N, de Oliveira VM. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136646. [PMID: 32014760 DOI: 10.1016/j.scitotenv.2020.136646] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.
Collapse
Affiliation(s)
- Isabel Natalia Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil.
| | - Daiane R B Belgini
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Adriana Torres-Ballesteros
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | | | | | | | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Valeria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil
| |
Collapse
|
18
|
Sousa STPD, Cabral L, Lacerda-Júnior GV, Noronha MF, Ottoni JR, Sartoratto A, Oliveira VMD. Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 189:109974. [PMID: 31761556 DOI: 10.1016/j.ecoenv.2019.109974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.
Collapse
Affiliation(s)
- Sanderson Tarciso Pereira de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Gileno Vieira Lacerda-Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Melline Fontes Noronha
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Júlia Ronzella Ottoni
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Adilson Sartoratto
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| |
Collapse
|
19
|
Nzila A, Razzak SA, Sankara S, Nazal MK, Al-Momani M, Kang GU, Ibal JC, Shin JH. Characterisation and microbial community analysis of lipid utilising microorganisms for biogas formation. PLoS One 2019; 14:e0224989. [PMID: 31703100 PMCID: PMC6839884 DOI: 10.1371/journal.pone.0224989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
In the anaerobic process, fat-oil-grease (FOG) is hydrolysed to long-chain fatty acids (LCFAs) and glycerol (GLYC), which are then used as substrates to produce biogas. The increase in FOG and LCFAs inhibits methanogenesis, and so far, most work investigating this inhibition has been carried out when FOG or LCFAs were used as co-substrates. In the current work, the inhibition of methanogenesis by FOG, LCFAs and GLYC was investigated when used as sole substrates. To gain more insight on the dynamics of this process, the change of microbial community was analysed using 16S rRNA gene amplicon sequencing. The results indicate that, as the concentrations of cooking olive oil (CO, which represents FOG) and LCFAs increase, methanogenesis is inhibited. For instance, at 0.01 g. L-1 of FOG, the rate of biogas formation was around 8 ml.L-1.day-1, and this decreased to <4 ml.L-1.day-1 at 40 g.L-1. Similar results were observed with the use of LCFAs. However, GLYC concentrations up to 100g.L-1 did not affect the rate of biogas formation. Acidic pH, temperature > = 45°C and NaCl > 3% led to a significant decrease in the rate of biogas formation. Microbial community analyses were carried out from samples from 3 different bioreactors (CO, OLEI and GLYC), on day 1, 5 and 15. In each bioreactor, microbial communities were dominated by Proteobacteria, Firmicutes and Bacteroidetes phyla. The most important families were Enterobacteriaceae, Pseudomonadaceae and Shewanellaceae (Proteobacteria phylum), Clostridiacea and Ruminococcaceae (Firmicutes) and Porphyromonadaceae and Bacteroidaceae (Bacteroidetes). In CO bioreactor, Proteobacteria bacteria decreased over time, while those of OLEI and GLYC bioreactors increased. A more pronounced increase in Bacteroidetes and Firmicutes were observed in CO bioreactor. The methanogenic archaea Methanobacteriaceae and Methanocorpusculaceae were identified. This analysis has shown that a set of microbial population is selected as a function of the substrate.
Collapse
Affiliation(s)
- Alexis Nzila
- Department of Life Sciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Shaikh Abdur Razzak
- Departments of Chemical Engineering, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Saravanan Sankara
- Department of Life Sciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Mazen K. Nazal
- Research Institute, Center for Environment and Water, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Marwan Al-Momani
- Departments of Mathematics & Statistics, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Gi-Ung Kang
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
20
|
Daae HL, Heldal KK, Madsen AM, Olsen R, Skaugset NP, Graff P. Occupational exposure during treatment of offshore drilling waste and characterization of microbiological diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:533-540. [PMID: 31121403 DOI: 10.1016/j.scitotenv.2019.05.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
The exposure for workers handling and recycling offshore drilling waste are previously not described, and given the potential for exposure to hazardous components, there is a need for characterizing this occupational exposure. In this study five plants recycling offshore drilling waste with different techniques were included. Measurements were conducted in both winter and summer to include seasonal exposure variations. Altogether >200 personal air-exposure measurements for oil mist, oil vapor, volatile organic compounds (VOC), hydrogen sulfide (H2S) and solvents were carried out respectively. Microorganisms related to drilling waste were identified in bulk samples and in stationary air measurements from two of the plants. The exposure to oil mist and oil vapor were below 10% of the current Norwegian occupational exposure limits (OEL) for all measured components. The plants using the Resoil or TCC method had a statistically significant higher exposure to oil vapor than the plant using complete combustion (p-value <0.05). No statistically significant difference was found between the different treatment methods for oil mist. The exposure to solvents was generally low (additive factor < 0.03). Endotoxin measurements done during winter showed a median concentration of 5.4 endotoxin units (EU)/m3. Levels of H2S above the odor threshold of 0.1 ppm were measured at four plants. Both drill mud and slop water contained a high number and diversity of bacteria (2-4 × 104 colony forming unit (CFU)/mL), where a large fraction was Gram-negative species. Some of the identified microorganisms are classified as potentially infectious pathogens for humans and thus might be a hazard to workers.
Collapse
Affiliation(s)
- Hanne Line Daae
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Kari Kulvik Heldal
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Raymond Olsen
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Nils Petter Skaugset
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Pål Graff
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway.
| |
Collapse
|
21
|
Reid T, Droppo IG, Chaganti SR, Weisener CG. Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:113-124. [PMID: 30772540 DOI: 10.1016/j.scitotenv.2019.02.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY & MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.
Collapse
Affiliation(s)
- Thomas Reid
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada.
| | - Ian G Droppo
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| |
Collapse
|
22
|
Ahad JME, Pakdel H, Gammon PR, Siddique T, Kuznetsova A, Savard MM. Evaluating in situ biodegradation of 13C-labelled naphthenic acids in groundwater near oil sands tailings ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:392-399. [PMID: 29940450 DOI: 10.1016/j.scitotenv.2018.06.159] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Potential seepage of naphthenic acids (NAs) from tailings ponds into surface water and groundwater is one of the main environmental concerns associated with the Canadian Athabasca oil sands mining operations. Here we report the application of 13C-labelled NA surrogate compounds to evaluate intrinsic biodegradation along groundwater flow-paths originating from oil sands tailings ponds at two different sites: a glacio-fluvial aquifer (Site 1) and a low-lying wetland (Site 2). Microcosms containing the carboxyl group labelled (99%) NA surrogates (cyclohexanecarboxylic acid, CHCA; 1,2-cyclohexanedicarboxylic acid, CHDCA; 1-adamantanecarboxylic acid, ACA) were lowered into monitoring wells for several months to allow sufficient time for substrate degradation and formation of a biofilm in conditions characteristic of the local aquifer. Phospholipid fatty acids (PLFAs), biomarkers for the active microbial population, were extracted from the biofilms for stable carbon isotope (δ13C) analysis. At Site 1, highly 13C-enriched δ13C values (up to ~+7100‰) confirmed the in situ microbial breakdown of CHCA and CHDCA. At Site 2, δ13C-PLFA values from -60.6 to -24.5‰ indicated uptake of a 13C-depleted substrate such as biogenic methane and not 13C-labelled ACA. Determination of the microbial community using 16s RNA sequencing confirmed the presence of methane-oxidizing bacteria in the subsurface at Site 2. The in situ biodegradation of NAs at Site 1 demonstrates that the indigenous microbial population in the shallow subsurface near tailings ponds can readily break down some of these compounds prior to surface water discharge. The lack of evidence for microbial uptake of 13C-labelled ACA at Site 2 demonstrates that other NAs, in particular tricyclic diamondoid acids, may persist in the environment following seepage from tailings ponds or natural sources.
Collapse
Affiliation(s)
- Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec, QC G1K 9A9, Canada.
| | - Hooshang Pakdel
- INRS, Centre Eau Terre Environnement, Québec, QC G1K 9A9, Canada
| | - Paul R Gammon
- Geological Survey of Canada, Natural Resources Canada, Ottawa, ON K1A 0E8, Canada
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Alsu Kuznetsova
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Martine M Savard
- Geological Survey of Canada, Natural Resources Canada, Québec, QC G1K 9A9, Canada
| |
Collapse
|
23
|
Kumar V, AlMomin S, Al-Aqeel H, Al-Salameen F, Nair S, Shajan A. Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. PLoS One 2018; 13:e0202127. [PMID: 30092049 PMCID: PMC6084965 DOI: 10.1371/journal.pone.0202127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/27/2018] [Indexed: 01/17/2023] Open
Abstract
The role of rhizosphere microbial communities in the degradation of hydrocarbons remains poorly understood and is a field of active study. We used high throughput sequencing to explore the rhizosphere microbial diversity in the alfalfa and barley planted oil contaminated soil samples. The analysis of 16s rRNA sequences showed Proteobacteria to be the most enriched (45.9%) followed by Bacteriodetes (21.4%) and Actinobacteria (10.4%) phyla. The results also indicated differences in the microbial diversity among the oil contaminated planted soil samples. The oil contaminated planted soil samples showed a higher richness in the microbial flora when compared to that of untreated samples, as indicated by the Chao1 indices. However, the trend was different for the diversity measure, where oil contaminated barley planted soil samples showed slightly lower diversity indices. While the clustering of soil samples grouped the oil contaminated samples within and across the plant types, the clean sandy soil samples formed a separate group. The oil contaminated rhizosphere soil showed an enrichment of known oil-degrading genera, such as Alcanivorax and Aequorivita, later being specifically enriched in the contaminated soil samples planted with barley. Overall, we found a few well known oil-degrading bacterial groups to be enriched in the oil contaminated planted soil samples compared to the untreated samples. Further, phyla such as Thermi and Gemmatimonadetes showed an enrichment in the oil contaminated soil samples, indicating their potential role in hydrocarbon degradation. The findings of the current study will be useful in understanding the rhizosphere microflora responsible for oil degradation and thus can help in designing appropriate phytoremediation strategies for oil contaminated lands.
Collapse
Affiliation(s)
- Vinod Kumar
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
- * E-mail:
| | - Sabah AlMomin
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Hamed Al-Aqeel
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Fadila Al-Salameen
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Sindhu Nair
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Anisha Shajan
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| |
Collapse
|
24
|
Toth CRA, Gieg LM. Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition. Front Microbiol 2018; 8:2610. [PMID: 29354103 PMCID: PMC5758579 DOI: 10.3389/fmicb.2017.02610] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.
Collapse
Affiliation(s)
- Courtney R A Toth
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Foght JM, Gieg LM, Siddique T. The microbiology of oil sands tailings: past, present, future. FEMS Microbiol Ecol 2017; 93:3064888. [PMID: 28334283 DOI: 10.1093/femsec/fix034] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 03/08/2017] [Indexed: 01/30/2023] Open
Abstract
Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behavior of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailings ponds (OSTPs) and tailings reclamation. Historically, microbial impacts on OSTPs were generally discounted, but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions. OSTPs that experienced different processing and management histories have developed distinct microbial communities that influence the behavior and reclamation of the tailings stored therein. In particular, the interactions of Deltaproteobacteria and Firmicutes with methanogenic archaea impact greenhouse gas emissions, sulfur cycling, pore water toxicity, sediment biogeochemistry and densification, water usage and the trajectory of long-term mine waste reclamation. This review summarizes historical data; synthesizes current understanding of microbial diversity and activities in situ and in vitro; predicts microbial effects on tailings remediation and reclamation; and highlights knowledge gaps for future research.
Collapse
Affiliation(s)
- Julia M Foght
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada T6G 2G7
| |
Collapse
|
27
|
VanMensel D, Chaganti SR, Boudens R, Reid T, Ciborowski J, Weisener C. Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective. MICROBIAL ECOLOGY 2017; 74:362-372. [PMID: 28246922 DOI: 10.1007/s00248-017-0953-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p < 0.05) were observed. Chemoorganotrophic organisms dominated in fresh and aged ponds and showed increased relative abundance resulting from GI treatment. GI-treated anaerobic FFTaged reported stimulus of organisms with biodegradation potential (e.g., Pseudomonas, Enterobacter) and methylotrophic capabilities (e.g., Syntrophus, Smithella). In comparison, GI-treated anaerobic FFTfresh stimulated Desulfuromonas as the principle genus at 52 weeks. Under aerobic conditions, GI-treated FFTaged showed stimulation of organisms capable of sulfur and iron cycling (e.g., Geobacter). However, GI-treated aerobic FFTfresh showed no stimulus at 52 weeks. This research provides an enhanced understanding of oil sands tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.
Collapse
Affiliation(s)
- Danielle VanMensel
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
| | - Subba Rao Chaganti
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Ryan Boudens
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Thomas Reid
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Jan Ciborowski
- Department of Biology, University of Windsor, Windsor, Ontario, Canada
| | - Christopher Weisener
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| |
Collapse
|
28
|
Exploring environmental systems and processes through next-generation sequencing technologies: insights into microbial response to petroleum contamination in key environments. THE NUCLEUS 2016. [DOI: 10.1007/s13237-016-0190-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
29
|
Fowler SJ, Toth CRA, Gieg LM. Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments. Front Microbiol 2016; 7:562. [PMID: 27148240 PMCID: PMC4840303 DOI: 10.3389/fmicb.2016.00562] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/04/2016] [Indexed: 11/17/2022] Open
Abstract
The methanogenic biodegradation of crude oil involves the conversion of hydrocarbons to methanogenic substrates by syntrophic bacteria and subsequent methane production by methanogens. Assessing the metabolic roles played by various microbial species in syntrophic communities remains a challenge, but such information has important implications for bioremediation and microbial enhanced energy recovery technologies. Many factors such as changing environmental conditions or substrate variations can influence the composition and biodegradation capabilities of syntrophic microbial communities in hydrocarbon-impacted environments. In this study, a methanogenic crude oil-degrading enrichment culture was successively transferred onto the single long chain fatty acids palmitate or stearate followed by their parent alkanes, hexadecane or octadecane, respectively, in order to assess the impact of different substrates on microbial community composition and retention of hydrocarbon biodegradation genes. 16S rRNA gene sequencing showed that a reduction in substrate diversity resulted in a corresponding loss of microbial diversity, but that hydrocarbon biodegradation genes (such as assA/masD encoding alkylsuccinate synthase) could be retained within a community even in the absence of hydrocarbon substrates. Despite substrate-related diversity changes, all communities were dominated by hydrogenotrophic and acetotrophic methanogens along with bacteria including Clostridium sp., members of the Deltaproteobacteria, and a number of other phyla. Microbial co-occurrence network analysis revealed a dense network of interactions amongst syntrophic bacteria and methanogens that were maintained despite changes in the substrates for methanogenesis. Our results reveal the effect of substrate diversity loss on microbial community diversity, indicate that many syntrophic interactions are stable over time despite changes in substrate pressure, and show that syntrophic interactions amongst bacteria themselves are as important as interactions between bacteria and methanogens in complex methanogenic communities.
Collapse
Affiliation(s)
- S Jane Fowler
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary AB, Canada
| | - Courtney R A Toth
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary AB, Canada
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary AB, Canada
| |
Collapse
|
30
|
Jiménez N, Richnow HH, Vogt C, Treude T, Krüger M. Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies. J Mol Microbiol Biotechnol 2016; 26:227-42. [PMID: 26959375 DOI: 10.1159/000441679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.
Collapse
Affiliation(s)
- Núria Jiménez
- Department of Resource Geochemistry, BGR - Federal Institute for Geosciences and Natural Resources, Hannover, Germany
| | | | | | | | | |
Collapse
|
31
|
Al-Kindi S, Abed RMM. Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil. Front Microbiol 2016; 7:240. [PMID: 26973618 PMCID: PMC4777724 DOI: 10.3389/fmicb.2016.00240] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 02/15/2016] [Indexed: 02/01/2023] Open
Abstract
Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography–mass spectrometry (GC–MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2–3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO2, given the high respiration activities of the soybean meal alone. GC–MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7–1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C14 to C30 alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5–86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95–98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.
Collapse
Affiliation(s)
- Sumaiya Al-Kindi
- Biology Department, College of Science, Sultan Qaboos University Muscat, Oman
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University Muscat, Oman
| |
Collapse
|
32
|
Warren LA, Kendra KE, Brady AL, Slater GF. Sulfur Biogeochemistry of an Oil Sands Composite Tailings Deposit. Front Microbiol 2016; 6:1533. [PMID: 26869997 PMCID: PMC4737920 DOI: 10.3389/fmicb.2015.01533] [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: 10/01/2015] [Accepted: 12/21/2015] [Indexed: 11/13/2022] Open
Abstract
Composite tailings (CT), an engineered, alkaline, saline mixture of oil sands tailings (FFT), processed sand and gypsum (CaSO4; 1 kg CaSO4 per m3 FFT) are used as a dry reclamation strategy in the Alberta Oil Sands Region (AOSR). It is estimated that 9.6 × 108 m3 of CT are either in, or awaiting emplacement in surface pits within the AOSR, highlighting their potential global importance in sulfur cycling. Here, in the first CT sulfur biogeochemistry investigation, integrated geochemical, pyrosequencing and lipid analyses identified high aqueous concentrations of ∑H2S (>300 μM) and highly altered sulfur compounds composition; low cell biomass (3.3 × 106– 6.0 × 106 cells g−1) and modest bacterial diversity (H' range between 1.4 and 1.9) across 5 depths spanning 34 m of an in situ CT deposit. Pyrosequence results identified a total of 29,719 bacterial 16S rRNA gene sequences, representing 131 OTUs spanning19 phyla including 7 candidate divisions, not reported in oil sands tailings pond studies to date. Legacy FFT common phyla, notably, gamma and beta Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi were represented. However, overall CT microbial diversity and PLFA values were low relative to other contexts. The identified known sulfate/sulfur reducing bacteria constituted at most 2% of the abundance; however, over 90% of the 131 OTUs identified are capable of sulfur metabolism. While PCR biases caution against overinterpretation of pyrosequence surveys, bacterial sequence results identified here, align with phospholipid fatty acid (PLFA) and geochemical results. The highest bacterial diversities were associated with the depth of highest porewater [∑H2S] (22–24 m) and joint porewater co-occurrence of Fe2+ and ∑H2S (6–8 m). Three distinct bacterial community structure depths corresponded to CT porewater regions of (1) shallow evident Fe(II) (<6 m), (2) co-occurring Fe(II) and ∑H2S (6–8 m) and (3) extensive ∑H2S (6–34 m) (UniFrac). Candidate divisions GNO2, NKB19 and Spam were present only at 6–8 m associated with co-occurring [Fe(II)] and [∑H2S]. Collectively, results indicate that CT materials are differentiated from other sulfur rich environments by modestly diverse, low abundance, but highly sulfur active and more enigmatic communities (7 candidate divisions present within the 19 phyla identified).
Collapse
Affiliation(s)
- Lesley A Warren
- School of Geography and Earth Sciences, McMaster University Hamilton ON, Canada
| | - Kathryn E Kendra
- School of Geography and Earth Sciences, McMaster University Hamilton ON, Canada
| | - Allyson L Brady
- School of Geography and Earth Sciences, McMaster University Hamilton ON, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University Hamilton ON, Canada
| |
Collapse
|
33
|
Oulas A, Polymenakou PN, Seshadri R, Tripp HJ, Mandalakis M, Paez-Espino AD, Pati A, Chain P, Nomikou P, Carey S, Kilias S, Christakis C, Kotoulas G, Magoulas A, Ivanova NN, Kyrpides NC. Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environ Microbiol 2015; 18:1122-36. [PMID: 26487573 DOI: 10.1111/1462-2920.13095] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/16/2015] [Indexed: 11/27/2022]
Abstract
Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.
Collapse
Affiliation(s)
- Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Rekha Seshadri
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - H James Tripp
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - A David Paez-Espino
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Amrita Pati
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Paraskevi Nomikou
- National and Kapodistrian University of Athens, Faculty of Geology and Geoenvironment, Athens, Greece
| | - Steven Carey
- Graduate School of Oceanography, University of Rhode Island, Kingston, RI, USA
| | - Stephanos Kilias
- National and Kapodistrian University of Athens, Faculty of Geology and Geoenvironment, Athens, Greece
| | - Christos Christakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, Heraklion, Crete, 71003, Greece
| | - Natalia N Ivanova
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos C Kyrpides
- Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Biological Sciences, King Abdulaziz, Jeddah, Saudia Arabia
| |
Collapse
|
34
|
Jimenez-Sanchez G. Genomics innovation: transforming healthcare, business, and the global economy. Genome 2015; 58:511-7. [DOI: 10.1139/gen-2015-0121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomics revolution has generated an unprecedented number of assets to propel innovation. Initial availability of genomics-based applications show a significant potential to contribute addressing global challenges, such as human health, food security, alternative sources of energies, and environmental sustainability. In the last years, most developed and emerging nations have established bioeconomy agendas where genomics plays a major role to meet their local needs. Genomic medicine is one of the most visible areas where genomics innovation is likely to contribute to a more individualized, predictive, and preventive medical practice. Examples in agriculture, dairy and beef, fishery, aquaculture, and forests industries include the effective selection of genetic variants associated to traits of economic value. Some, in addition to producing more and better foods, already represent an important increase in revenues to their respective industries. It is reasonable to predict that genomics applications will lead to a paradigm shift in our ability to ease significant health, economic, and social burdens. However, to successfully benefit from genomics innovations, it is imperative to address a number of hurdles related to generating robust scientific evidence, developing lower-cost sequencing technologies, effective bioinformatics, as well as sensitive ethical, economical, environmental, legal, and social aspects associated with the development and use of genomics innovations.
Collapse
Affiliation(s)
- Gerardo Jimenez-Sanchez
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA; Global Biotech Consulting Group, Mexico
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA; Global Biotech Consulting Group, Mexico
| |
Collapse
|
35
|
Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
Collapse
Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| |
Collapse
|
36
|
Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KYH, Thompson JR. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol 2015; 6:1027. [PMID: 26441948 PMCID: PMC4585245 DOI: 10.3389/fmicb.2015.01027] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022] Open
Abstract
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.
Collapse
Affiliation(s)
- BoonFei Tan
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
| | - Charmaine Ng
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Jean Pierre Nshimyimana
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological UniversitySingapore, Singapore
| | - Lay Leng Loh
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Karina Y.-H. Gin
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Janelle R. Thompson
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, CambridgeMA, USA
| |
Collapse
|
37
|
Pourmohammadbagher A, Shaw JM. Probing Contaminant Transport to and from Clay Surfaces in Organic Solvents and Water Using Solution Calorimetry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10841-10849. [PMID: 26296102 DOI: 10.1021/acs.est.5b02416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Clays, in tailings, are a significant ongoing environmental concern in the mining and oilsands production industries, and clay rehabilitation following contamination poses challenges episodically. Understanding the fundamentals of clay behavior can lead to better environmental impact mitigation strategies. Systematic calorimetric measurements are shown to provide a framework for parsing the synergistic and antagonistic impacts of trace (i.e., parts per million level) components on the surface compositions of clays. The enthalpy of solution of as-received and "contaminated" clays, in as-received and "contaminated" organic solvents and water, at 60 °C and atmospheric pressure, provides important illustrative examples. Clay contamination included pre-saturation of clays with water and organic liquids. Solvent contamination included the addition of trace water to organic solvents and trace organic liquids to water. Enthalpy of solution outcomes are interpreted using a quantitative mass and energy balance modeling framework that isolates terms for solvent and trace contaminant sorption/desorption and surface energy effects. Underlying surface energies are shown to dominate the energetics of the solvent-clay interaction, and organic liquids as solvents or as trace contaminants are shown to displace water from as-received clay surfaces. This approach can be readily extended to include pH, salts, or other effects and is expected to provide mechanistic and quantitative insights underlying the stability of clays in tailings ponds and the behaviors of clays in diverse industrial and natural environments.
Collapse
Affiliation(s)
- Amin Pourmohammadbagher
- Department of Chemical and Materials Engineering, University of Alberta , Edmonton, Alberta T6G 2V4, Canada
| | - John M Shaw
- Department of Chemical and Materials Engineering, University of Alberta , Edmonton, Alberta T6G 2V4, Canada
| |
Collapse
|
38
|
Tan B, Jane Fowler S, Laban NA, Dong X, Sensen CW, Foght J, Gieg LM. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. THE ISME JOURNAL 2015; 9:2028-45. [PMID: 25734684 PMCID: PMC4542035 DOI: 10.1038/ismej.2015.22] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.
Collapse
Affiliation(s)
- Boonfei Tan
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - S Jane Fowler
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nidal Abu Laban
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Visual Genomics Centre, Faculty of Medicine, Calgary, Alberta, Canada
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
39
|
Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops. Appl Environ Microbiol 2015. [PMID: 26209669 DOI: 10.1128/aem.02221-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Oil sands are surface exposed in river valley outcrops in northeastern Alberta, where flat slabs (tablets) of weathered, bitumen-saturated sandstone can be retrieved from outcrop cliffs or from riverbeds. Although the average yearly surface temperature of this region is low (0.7°C), we found that the temperatures of the exposed surfaces of outcrop cliffs reached 55 to 60°C on sunny summer days, with daily maxima being 27 to 31°C. Analysis of the cooccurrence of taxa derived from pyrosequencing of 16S/18S rRNA genes indicated that an aerobic microbial network of fungi and hydrocarbon-, methane-, or acetate-oxidizing heterotrophic bacteria was present in all cliff tablets. Metagenomic analyses indicated an elevated presence of fungal cytochrome P450 monooxygenases in these samples. This network was distinct from the heterotrophic community found in riverbeds, which included fewer fungi. A subset of cliff tablets had a network of anaerobic and/or thermophilic taxa, including methanogens, Firmicutes, and Thermotogae, in the center. Long-term aerobic incubation of outcrop samples at 55°C gave a thermophilic microbial community. Analysis of residual bitumen with a Fourier transform ion cyclotron resonance mass spectrometer indicated that aerobic degradation proceeded at 55°C but not at 4°C. Little anaerobic degradation was observed. These results indicate that bitumen degradation on outcrop surfaces is a largely aerobic process with a minor anaerobic contribution and is catalyzed by a consortium of bacteria and fungi. Bitumen degradation is stimulated by periodic high temperatures on outcrop cliffs, which cause significant decreases in bitumen viscosity.
Collapse
|
40
|
Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation. Appl Microbiol Biotechnol 2015; 99:8751-64. [DOI: 10.1007/s00253-015-6748-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/27/2015] [Accepted: 05/31/2015] [Indexed: 11/25/2022]
|
41
|
West CE, Pureveen J, Scarlett AG, Lengger SK, Wilde MJ, Korndorffer F, Tegelaar EW, Rowland SJ. Can two-dimensional gas chromatography/mass spectrometric identification of bicyclic aromatic acids in petroleum fractions help to reveal further details of aromatic hydrocarbon biotransformation pathways? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1023-32. [PMID: 24677524 DOI: 10.1002/rcm.6876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 05/24/2023]
Abstract
RATIONALE The identification of key acid metabolites ('signature' metabolites) has allowed significant improvements to be made in our understanding of the biodegradation of petroleum hydrocarbons, in reservoir and in contaminated natural systems, such as aquifers and seawater. On this basis, anaerobic oxidation is now more widely accepted as one viable mechanism, for instance. However, identification of metabolites in the complex acid mixtures from petroleum degradation is challenging and would benefit from use of more highly resolving analytical methods. METHODS Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GCxGC/TOFMS) with both nominal mass and accurate mass measurement was used to study the complex mixtures of aromatic acids (as methyl esters) in petroleum fractions. RESULTS Numerous mono- and di-aromatic acid isomers were identified in a commercial naphthenic acids fraction from petroleum and in an acids fraction from a biodegraded petroleum. In many instances, compounds were identified by comparison of mass spectral and retention time data with those of authentic compounds. CONCLUSIONS The identification of a variety of alkyl naphthalene carboxylic and alkanoic and alkyl tetralin carboxylic and alkanoic acids, plus identifications of a range of alkyl indane acids, provides further evidence for 'signature' metabolites of biodegradation of aromatic petroleum hydrocarbons. Identifications such as these now offer the prospect of better differentiation of metabolites of bacterial processes (e.g. aerobic, methanogenic, sulphate-reducing) in polar petroleum fractions.
Collapse
Affiliation(s)
- Charles E West
- Petroleum and Environmental Geochemistry Group, Biogeochemistry Research Centre, Plymouth University, Drake Circus, Plymouth, PL4 8AA, UK
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Yang S, Wen X, Zhao L, Shi Y, Jin H. Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route. PLoS One 2014; 9:e96552. [PMID: 24794099 PMCID: PMC4008593 DOI: 10.1371/journal.pone.0096552] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/08/2014] [Indexed: 11/25/2022] Open
Abstract
The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.
Collapse
Affiliation(s)
- Sizhong Yang
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
- * E-mail:
| | - Xi Wen
- College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, Gansu, China
| | - Liang Zhao
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Yulan Shi
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Huijun Jin
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
| |
Collapse
|