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Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [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: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Mohamad Shahimin MF, Siddique T. Biodegradation of 2-methylpentane in fluid fine tailings amended with a mixture of iso-alkanes under sulfate-reducing conditions. Can J Microbiol 2023; 69:362-368. [PMID: 37235883 DOI: 10.1139/cjm-2023-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Anaerobic microorganisms in Canada Natural Upgrading Limited (CNUL) fluid fine tailings (FFT) are sustained by residual solvent hydrocarbons. Although FFT are methanogenic in nature, sulfate-reducing microorganisms represent a significant portion of FFT bacterial community. In this study, we examined biodegradation of three iso-alkanes (2-methylbutane, 2-methylpentane, and 3-methylpentane), representing major iso-alkanes in paraffinic solvent, in CNUL FFT under sulfate-reducing conditions. During ∼1100 days of incubation, only 2-methylpentane was degraded partially, whereas 2-methylbutane and 3-methylpentane were not degraded. During active degradation of 2-methylpentane, the bacterial community was dominated by Anaerolineaceae followed by Syntrophaceae, Peptococcaceae, Desulfobacteraceae, and Desulfobulbaceae. The archaeal community was co-dominated by acetoclastic (Methanosaetaceae) and hydrogenotrophic (Methanobacteriaceae) methanogens. This study underlines the limited capability of the microbial community indigenous to CNUL FFT in degrading recalcitrant iso-alkanes under sulfate-reducing conditions.
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Affiliation(s)
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2G7, Canada
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3
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Arslan M, Müller JA, Gamal El-Din M. Aerobic naphthenic acid-degrading bacteria in petroleum-coke improve oil sands process water remediation in biofilters: DNA-stable isotope probing reveals methylotrophy in Schmutzdecke. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:151961. [PMID: 34843771 DOI: 10.1016/j.scitotenv.2021.151961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
There is an increasing interest in treatment of oil sands process water (OSPW) via biofiltration with petroleum coke (PC) as a substratum. In fixed bed biofilters (FBBs) with PC, the dominance of anaerobic digestion of dissolved organics results in poor removal of naphthenic acids (NAs) along with a high degree of methanogenesis. In this study, the operation of FBBs was modified to improve OSPW remediation by supporting the filtering bed with aerobic naphthenic acid-degrading bacteria treating aerated OSPW (FBBbioaugmentation). The results were compared with a biofilter operated under controlled conditions (FBBcontrol). To this end, a consortium of three aerobic NAs-degrading bacterial strains was immobilized on PC as a top layer (10 cm). These bacteria were pre-screened for growth on 15 different NAs surrogates as a sole carbon source, and for the presence of catabolic genes coding alkane hydroxylase (CYP153) and alkane monooxygenase (alkB) enzymes. The results illustrated that biofiltration in FBBbioaugmentation removed 32% of classical NAs in 15 days; while in the FBBcontrol, degradation was limited to 19%. The degradation of fluorophore (aromatic) compounds was also improved from 16% to 39% for single ring (OI), 22% to 29% for double ring (OII), and 15% to 23% for three rings (OIII) compounds. DNA-Stable Isotope Probing revealed that potential hydrocarbons degraders such as Pseudomonas (inoculated), Pseudoxanthomonas (indigenous) were present up to 9.0% in the 13C-labelled DNA fraction. Furthermore, a high abundance of methylotrophs was observed in the Schmutzdecke, with Methylobacillus comprising more than two-third of the total community. This study shows that bioaugmentation rapidly improved OSPW remediation. Aeration mostly contributed to methane consumption in the top layer, thus minimizing its release into the environment.
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Affiliation(s)
- Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada.
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Hu J, Hellgeth N, Cabay C, Clark J, Oliaro FJ, Van Bonn W, Hartmann EM. Towards understanding microbial degradation of chloroquine in large saltwater systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150532. [PMID: 34606868 DOI: 10.1016/j.scitotenv.2021.150532] [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: 06/14/2021] [Revised: 08/30/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Circulating saltwater aquariums hosting marine animals contain a wide range of microorganisms, which have strong implications on promoting animal health. In this study, we investigated the degradation of chloroquine phosphate, an anti-parasitic bath pharmaceutical used in saltwater quarantine and exhibition systems, and attributed the reduction in drug concentration to microbial degradation of chloroquine associated with pipeline microbial communities. To advance our knowledge on chloroquine degradation in aquatic systems, we conducted microbial and chemical analyses on three tropical saltwater systems. Our findings show that aquarium microbiome composition is shaped by sampling location (i.e., tank water and pipeline; PERMANOVA R2 = 0.09992, p = 0.0134), chloroquine dosing (PERMANOVA R2 = 0.05700, p = 0.0030), and whether the aquarium is occupied by marine animals (PERMANOVA R2 = 0.07019, p = 0.0009). Several microbial taxa belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria, along with functional genes related to pathways such as phenylethylamine degradation and denitrification, appeared to have differential (relative) abundance between samples where chloroquine degradation was observed and those without degradation (Benjamini-Hochberg adjusted p-value <0.05). Together, these results provide practical mitigation options to prevent or delay the development of chloroquine-degrading microbial communities in saltwater aquariums. Our results further demonstrate the need to improve our understanding of the interactions between nitrogen availability and microbial activity in saltwater systems.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Chrissy Cabay
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - James Clark
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Francis J Oliaro
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - William Van Bonn
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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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.
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Machado LF, de Assis Leite DC, da Costa Rachid CTC, Paes JE, Martins EF, Peixoto RS, Rosado AS. Tracking Mangrove Oil Bioremediation Approaches and Bacterial Diversity at Different Depths in an in situ Mesocosms System. Front Microbiol 2019; 10:2107. [PMID: 31572322 PMCID: PMC6753392 DOI: 10.3389/fmicb.2019.02107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022] Open
Abstract
In this study, oil spills were simulated in field-based mangrove mesocosms to compare the efficiency of bioremediation strategies and to characterize the presence of the alkB, ndo, assA, and bssA genes and the ecological structures of microbial communities in mangrove sediments at two different depths, (D1) 1–10 cm and (D2) 25–35 cm. The results indicated that the hydrocarbon degradation efficiency was higher in superficial sediment layers, although no differences in the hydrocarbon degradation rates or in the abundances of the alkB and ndo genes were detected among the tested bioremediation strategies at this depth. Samples from the deeper layer exhibited higher abundances of the analyzed genes, except for assA and bssA, which were not detected in our samples. For all of the treatments and depths, the most abundant phyla were Proteobacteria, Firmicutes and Bacteroidetes, with Gammaproteobacteria, Flavobacteriales and Clostridiales being the most common classes. The indicator species analysis (ISA) results showed strong distinctions among microbial taxa in response to different treatments and in the two collection depths. Our results indicated a high efficiency of the monitored natural attenuation (MNA) for oil consumption in the tested mangrove sediments, revealing the potential of this strategy for environmental decontamination and suggesting that environmental and ecological factors may select for specific bacterial populations in distinct niches.
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Affiliation(s)
- Laís Feitosa Machado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jorge Eduardo Paes
- Research Center Leopoldo Américo Miguez de Mello, Rio de Janeiro, Brazil
| | - Edir Ferreira Martins
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| | - Alexandre Soares Rosado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
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Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer. Microorganisms 2019; 7:microorganisms7020046. [PMID: 30744114 PMCID: PMC6406676 DOI: 10.3390/microorganisms7020046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ.
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Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms 2018; 6:microorganisms6030065. [PMID: 29996505 PMCID: PMC6164631 DOI: 10.3390/microorganisms6030065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 11/23/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.
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Ranchou‐Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou‐Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2017; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.
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Affiliation(s)
- Magali Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Cyrielle Gasc
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Marion Guignard
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Thomas Aüllo
- TIGF – Transport et Infrastructures Gaz France40 Avenue de l'Europe, CS2052264000PauFrance
| | - David Dequidt
- STORENGY – Geosciences DepartmentBois‐ColombesFrance
| | - Pierre Peyret
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Anthony Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
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Lueders T. The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. FEMS Microbiol Ecol 2016; 93:fiw220. [PMID: 27810873 PMCID: PMC5400083 DOI: 10.1093/femsec/fiw220] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.
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Affiliation(s)
- Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Coyotzi S, Pratscher J, Murrell JC, Neufeld JD. Targeted metagenomics of active microbial populations with stable-isotope probing. Curr Opin Biotechnol 2016; 41:1-8. [DOI: 10.1016/j.copbio.2016.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/09/2016] [Accepted: 02/13/2016] [Indexed: 02/02/2023]
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Vogt C, Lueders T, Richnow HH, Krüger M, von Bergen M, Seifert J. Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders. J Mol Microbiol Biotechnol 2016; 26:195-210. [DOI: 10.1159/000440806] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using <sup>13</sup>C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.
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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.
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Affiliation(s)
- Núria Jiménez
- Department of Resource Geochemistry, BGR - Federal Institute for Geosciences and Natural Resources, Hannover, Germany
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14
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von Netzer F, Kuntze K, Vogt C, Richnow HH, Boll M, Lueders T. Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments. J Mol Microbiol Biotechnol 2016; 26:180-94. [PMID: 26959523 DOI: 10.1159/000441946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments.
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Affiliation(s)
- Frederick von Netzer
- Helmholtz Zentrum Mx00FC;nchen - German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg, Germany
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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).
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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
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Foght JM. Microbial metagenomics of oil sands tailings ponds: small bugs, big data. Genome 2015; 58:507-10. [DOI: 10.1139/gen-2015-0146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Julia M. Foght
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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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.
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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
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