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Irianni-Renno M, Rico JL, Key TA, De Long SK. Evaluating Natural Source Zone Depletion and Enhanced Source Zone Depletion in laboratory columns via soil redox continuous sensing and microbiome characterization. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135059. [PMID: 39053064 DOI: 10.1016/j.jhazmat.2024.135059] [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: 11/13/2023] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
To optimally employ Natural Source Zone Depletion (NSZD) and Enhanced Source Zone Depletion (ESZD) at sites impacted by light non-aqueous phase liquids (LNAPL), monitoring strategies are required. Emerging use of subsurface oxidation-reduction potential (ORP) sensors shows promise for tracking redox evolution, which reflects ongoing biogeochemical processes. However, further understanding of how soil redox dynamics relate to subsurface microbial activity and LNAPL degradation pathways is needed. In this work, soil ORP sensors and DNA and RNA sequencing-based microbiome analysis were combined to elucidate NSZD and ESZD (biostimulation via periodic sulfate addition and biosparging) processes in columns containing LNAPL-impacted soils from a former petroleum refinery. Results show expected relationships between continuous soil redox and active microbial communities. Continuous data revealed spatial and temporal detail that informed interpretation of the hydrocarbon biodegradation data. Redox increases were transient for sulfate addition, and sequencing revealed how hydrocarbon concentration and composition impacted microbiome structure and naphthalene degradation. Periodic biosparging did not result in fully aerobic conditions suggesting observed biodegradation improvements could be explained by alternative anaerobic metabolisms (e.g., iron reduction due to air oxidizing reduced iron). Collectively, data suggest combining continuous redox sensing with microbiome analysis provides insights beyond those possible with either monitoring tool alone.
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Affiliation(s)
- Maria Irianni-Renno
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Jorge L Rico
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Trent A Key
- ExxonMobil Environmental and Property Solutions Company, 22777 Springwoods Village Pkwy, Spring, TX 77389, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, USA.
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2
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Wu Z, Ji Y, Liu G, Yu X, Shi K, Liang B, Freilich S, Jiang J. Electro-stimulation modulates syntrophic interactions in methanogenic toluene-degrading microbiota for enhanced functionality. WATER RESEARCH 2024; 260:121898. [PMID: 38865893 DOI: 10.1016/j.watres.2024.121898] [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: 03/06/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Syntrophy achieved via microbial cooperation is vital for anaerobic hydrocarbon degradation and methanogenesis. However, limited understanding of the metabolic division of labor and electronic interactions in electro-stimulated microbiota has impeded the development of enhanced biotechnologies for degrading hydrocarbons to methane. Here, compared to the non-electro-stimulated methanogenic toluene-degrading microbiota, electro-stimulation at 800 mV promoted toluene degradation and methane production efficiencies by 11.49 %-14.76 % and 75.58 %-290.11 %, respectively. Hydrocarbon-degrading gene bamA amplification and metagenomic sequencing analyses revealed that f_Syntrophobacteraceae MAG116 may act as a toluene degrader in the non-electro-stimulated microbiota, which was proposed to establish electron syntrophy with the acetoclastic methanogen Methanosarcina spp. (or Methanothrix sp.) through e-pili or shared acetate. In the electro-stimulated microbiota, 37.22 ± 4.33 % of Desulfoprunum sp. (affiliated f_Desulfurivibrionaceae MAG10) and 58.82 ± 3.74 % of the hydrogenotrophic methanogen Methanobacterium sp. MAG74 were specifically recruited to the anode and cathode, respectively. The potential electrogen f_Desulfurivibrionaceae MAG10 engaged in interspecies electron transfer with both syntroph f_Syntrophobacteraceae MAG116 and the anode, which might be facilitated by c-type cytochromes (e.g., ImcH, OmcT, and PilZ). Moreover, upon capturing electrons from the external circuit, the hydrogen-producing electrotroph Aminidesulfovibrio sp. MAG60 could share electrons and hydrogen with the methanogen Methanobacterium sp. MAG74, which uniquely harbored hydrogenase genes ehaA-R and ehbA-P. This study elucidates the microbial interaction mechanisms underlying the enhanced metabolic efficiency of the electro-stimulated methanogenic toluene-degrading microbiota, and emphasizes the significance of metabolic and electron syntrophic interactions in maintaining the stability of microbial community functionality.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China; College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yanhan Ji
- Department of Microbiology, College of Life Sciences, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Shiri Freilich
- Newe-Ya'ar Research Center, Agricultural Research Organization, Ministry of Agriculture, Israel
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China.
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3
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Yu T, Fu L, Wang Y, Dong Y, Chen Y, Wegener G, Cheng L, Wang F. Thermophilic Hadarchaeota grow on long-chain alkanes in syntrophy with methanogens. Nat Commun 2024; 15:6560. [PMID: 39095478 PMCID: PMC11297162 DOI: 10.1038/s41467-024-50883-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Methanogenic hydrocarbon degradation can be carried out by archaea that couple alkane oxidation directly to methanogenesis, or by syntrophic associations of bacteria with methanogenic archaea. However, metagenomic analyses of methanogenic environments have revealed other archaea with potential for alkane degradation but apparent inability to form methane, suggesting the existence of other modes of syntrophic hydrocarbon degradation. Here, we provide experimental evidence supporting the existence of a third mode of methanogenic degradation of hydrocarbons, mediated by syntrophic cooperation between archaeal partners. We collected sediment samples from a hot spring sediment in Tengchong, China, and enriched Hadarchaeota under methanogenic conditions at 60 °C, using hexadecane as substrate. We named the enriched archaeon Candidatus Melinoarchaeum fermentans DL9YTT1. We used 13C-substrate incubations, metagenomic, metatranscriptomic and metabolomic analyses to show that Ca. Melinoarchaeum uses alkyl-coenzyme M reductases (ACRs) to activate hexadecane via alkyl-CoM formation. Ca. Melinoarchaeum likely degrades alkanes to carbon dioxide, hydrogen and acetate, which can be used as substrates by hydrogenotrophic and acetoclastic methanogens such as Methanothermobacter and Methanothrix.
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Affiliation(s)
- Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Lin Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yijing Dong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China.
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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4
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Hidalgo-Martinez K, Giachini AJ, Schneider M, Soriano A, Baessa MP, Martins LF, de Oliveira VM. Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33663-33684. [PMID: 38687451 DOI: 10.1007/s11356-024-33304-y] [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: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.
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Affiliation(s)
- Kelly Hidalgo-Martinez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil.
- Programa de Pós-Graduação de Genética E Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, CEP 13083-970, Brazil.
| | - Admir José Giachini
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Marcio Schneider
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Adriana Soriano
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Marcus Paulus Baessa
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Luiz Fernando Martins
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil
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5
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Kharey GS, Palace V, Whyte L, Greer CW. Native freshwater lake microbial community response to an in situ experimental dilbit spill. FEMS Microbiol Ecol 2024; 100:fiae055. [PMID: 38650064 PMCID: PMC11068069 DOI: 10.1093/femsec/fiae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.
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Affiliation(s)
- Gurpreet S Kharey
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Vince Palace
- International Institute for Sustainable Development – Experimental Lakes Area, Pine Rd, Kenora, Unorganized Ontario, P0V 2V0, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
- National Research Council Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave., Montreal, Quebec, H4P 2R2, Canada
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6
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Gou Y, Song Y, Li P, Wei W, Luo N, Wang H. Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133265. [PMID: 38113745 DOI: 10.1016/j.jhazmat.2023.133265] [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: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.
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Affiliation(s)
- Yaling Gou
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yun Song
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Peizhong Li
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Wenxia Wei
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Nan Luo
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Hongqi Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
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Xu J, Wang L, Lv W, Song X, Nie Y, Wu XL. Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions. Front Microbiol 2023; 14:1305731. [PMID: 38188585 PMCID: PMC10766756 DOI: 10.3389/fmicb.2023.1305731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under high-pressure conditions, we established methanogenic and sulfate-reducing enrichment cultures under high-pressure conditions using production water from the Jilin Oilfield in China. We utilized a metagenomics approach to analyze the microbial community after a 90-day incubation period. Under methanogenic conditions, Firmicutes, Deferribacteres, Ignavibacteriae, Thermotogae, and Nitrospirae, in association with the hydrogenotrophic methanogen Archaeoglobaceae and acetoclastic Methanosaeta, were highly represented. Genomes for Ca. Odinarchaeota and the hydrogen-dependent methylotrophic Ca. Methanosuratus were also recovered from the methanogenic culture. The sulfate-reducing community was dominated by Firmicutes, Thermotogae, Nitrospirae, Archaeoglobus, and several candidate taxa including Ca. Bipolaricaulota, Ca. Aminicenantes, and Candidate division WOR-3. These candidate taxa were key pantothenate producers for other community members. The study expands present knowledge of the metabolic roles of petroleum-degrading microbial communities under high-pressure conditions. Our results also indicate that microbial community interactions were shaped by syntrophic metabolism and the exchange of amino acids and cofactors among members. Furthermore, incubation under in situ pressure conditions has the potential to reveal the roles of microbial dark matter.
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Affiliation(s)
- Jinbo Xu
- School of Earth and Space Sciences, Peking University, Beijing, China
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Lu Wang
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Weifeng Lv
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Xinmin Song
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, China
- Institute of Ecology, Peking University, Beijing, China
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Kumari S, Das S. Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:79676-79705. [PMID: 37330441 DOI: 10.1007/s11356-023-28130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Ramezanzadeh M, Slowinski S, Rezanezhad F, Murr K, Lam C, Smeaton C, Alibert C, Vandergriendt M, Van Cappellen P. Effects of freeze-thaw cycles on methanogenic hydrocarbon degradation: Experiment and modeling. CHEMOSPHERE 2023; 325:138405. [PMID: 36931401 DOI: 10.1016/j.chemosphere.2023.138405] [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: 11/19/2022] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Cold regions are warming much faster than the global average, resulting in more frequent and intense freeze-thaw cycles (FTCs) in soils. In hydrocarbon-contaminated soils, FTCs modify the biogeochemical and physical processes controlling petroleum hydrocarbon (PHC) biodegradation and the associated generation of methane (CH4) and carbon dioxide (CO2). Thus, understanding the effects of FTCs on the biodegradation of PHCs is critical for environmental risk assessment and the design of remediation strategies for contaminated soils in cold regions. In this study, we developed a diffusion-reaction model that accounts for the effects of FTCs on toluene biodegradation, including methanogenic biodegradation. The model is verified against data generated in a 215 day-long batch experiment with soil collected from a PHC contaminated site in Ontario, Canada. The fully saturated soil incubations with six different treatments were exposed to successive 4-week FTCs, with temperatures oscillating between -10 °C and +15 °C, under anoxic conditions to stimulate methanogenic biodegradation. We measured the headspace concentrations and 13C isotope compositions of CH4 and CO2 and analyzed the porewater for pH, acetate, dissolved organic and inorganic carbon, and toluene. The numerical model represents solute diffusion, volatilization, sorption, as well as a reaction network of 13 biogeochemical processes. The model successfully simulates the soil porewater and headspace concentration time series data by representing the temperature dependencies of microbial reaction and gas diffusion rates during FTCs. According to the model results, the observed increases in the headspace concentrations of CH4 and CO2 by 87% and 136%, respectively, following toluene addition are explained by toluene fermentation and subsequent methanogenesis reactions. The experiment and the numerical simulation show that methanogenic degradation is the primary toluene attenuation mechanism under the electron acceptor-limited conditions experienced by the soil samples, representing 74% of the attenuation, with sorption contributing to 11%, and evaporation contributing to 15%. Also, the model-predicted contribution of acetate-based methanogenesis to total produced CH4 agrees with that derived from the 13C isotope data. The freezing-induced soil matrix organic carbon release is considered as an important process causing DOC increase following each freezing period according to the calculations of carbon balance and SUVA index. The simulation results of a no FTC scenario indicate that, in the absence of FTCs, CO2 and CH4 generation would decrease by 29% and 26%, respectively, and that toluene would be biodegraded 23% faster than in the FTC scenario. Because our modeling approach represents the dominant processes controlling PHC biodegradation and the associated CH4 and CO2 fluxes, it can be used to analyze the sensitivity of these processes to FTC frequency and duration driven by temperature fluctuations.
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Affiliation(s)
- Mehdi Ramezanzadeh
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada.
| | - Stephanie Slowinski
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Fereidoun Rezanezhad
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Kathleen Murr
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Christina Lam
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Christina Smeaton
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland, Canada
| | - Clement Alibert
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Marianne Vandergriendt
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and Water Institute, University of Waterloo, Canada
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10
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Song YC, Holland SI, Lee M, Chen G, Löffler FE, Manefield MJ, Hugenholtz P, Kappler U. A comparative genome analysis of the Bacillota ( Firmicutes) class Dehalobacteriia. Microb Genom 2023; 9:mgen001039. [PMID: 37294008 PMCID: PMC10327494 DOI: 10.1099/mgen.0.001039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/25/2023] [Indexed: 06/10/2023] Open
Abstract
Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.
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Affiliation(s)
- Young C. Song
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, Queensland, 4072, Australia
| | - Sophie I. Holland
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
- Present address: School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Matthew Lee
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Gao Chen
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Frank E. Löffler
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, Department of Bioengineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee, USA
| | - Michael J. Manefield
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, Queensland, 4072, Australia
| | - Ulrike Kappler
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, 4072, Australia
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11
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Wang D, Hunt KA, Candry P, Tao X, Wofford NQ, Zhou J, McInerney MJ, Stahl DA, Tanner RS, Zhou A, Winkler M, Pan C. Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane. mBio 2023; 14:e0318922. [PMID: 36847519 PMCID: PMC10128006 DOI: 10.1128/mbio.03189-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 03/01/2023] Open
Abstract
Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt to changing environments. Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture cooperated via cross-feeding to produce methane using cellulose as the only carbon source and electron donor. The community metabolism of the quad-culture was compared with those of the R. cellulolyticum-containing tri-cultures, bi-cultures, and mono-culture. Methane production was higher in the quad-culture than the sum of the increases in the tri-cultures, which was attributed to a positive synergy of four species. In contrast, cellulose degradation by the quad-culture was lower than the additive effects of the tri-cultures which represented a negative synergy. The community metabolism of the quad-culture was compared between a control condition and a treatment condition with sulfate addition using metaproteomics and metabolic profiling. Sulfate addition enhanced sulfate reduction and decreased methane and CO2 productions. The cross-feeding fluxes in the quad-culture in the two conditions were modeled using a community stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. cellulolyticum to M. concilii and D. vulgaris and intensified substrate competition between M. hungatei and D. vulgaris. Overall, this study uncovered emergent properties of higher-order microbial interactions using a four-species synthetic community. IMPORTANCE A synthetic community was designed using four microbial species that together performed distinct key metabolic processes in the anaerobic degradation of cellulose to methane and CO2. The microorganisms exhibited expected interactions, such as cross-feeding of acetate from a cellulolytic bacterium to an acetoclastic methanogen and competition of H2 between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This validated our rational design of the interactions between microorganisms based on their metabolic roles. More interestingly, we also found positive and negative synergies as emergent properties of high-order microbial interactions among three or more microorganisms in cocultures. These microbial interactions can be quantitatively measured by adding and removing specific members. A community stoichiometric model was constructed to represent the fluxes in the community metabolic network. This study paved the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems.
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Affiliation(s)
- Dongyu Wang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Kristopher A. Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Xuanyu Tao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Neil Q. Wofford
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Ralph S. Tanner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Aifen Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Mari Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Chongle Pan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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12
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Cruz Viggi C, Tucci M, Resitano M, Palushi V, Crognale S, Matturro B, Petrangeli Papini M, Rossetti S, Aulenta F. Enhancing the Anaerobic Biodegradation of Petroleum Hydrocarbons in Soils with Electrically Conductive Materials. Bioengineering (Basel) 2023; 10:bioengineering10040441. [PMID: 37106628 PMCID: PMC10135592 DOI: 10.3390/bioengineering10040441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Anaerobic bioremediation is a relevant process in the management of sites contaminated by petroleum hydrocarbons. Recently, interspecies electron transfer processes mediated by conductive minerals or particles have been proposed as mechanisms through which microbial species within a community share reducing equivalents to drive the syntrophic degradation of organic substrates, including hydrocarbons. Here, a microcosm study was set up to investigate the effect of different electrically conductive materials (ECMs) in enhancing the anaerobic biodegradation of hydrocarbons in historically contaminated soil. The results of a comprehensive suite of chemical and microbiological analyses evidenced that supplementing the soil with (5% w/w) magnetite nanoparticles or biochar particles is an effective strategy to accelerate the removal of selected hydrocarbons. In particular, in microcosms supplemented with ECMs, the removal of total petroleum hydrocarbons was enhanced by up to 50% relative to unamended controls. However, chemical analyses suggested that only a partial bioconversion of contaminants occurred and that longer treatment times would have probably been required to drive the biodegradation process to completion. On the other hand, biomolecular analyses confirmed the presence of several microorganisms and functional genes likely involved in hydrocarbon degradation. Furthermore, the selective enrichment of known electroactive bacteria (i.e., Geobacter and Geothrix) in microcosms amended with ECMs, clearly pointed to a possible role of DIET (Diet Interspecies Electron Transfer) processes in the observed removal of contaminants.
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Affiliation(s)
- Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Valentina Palushi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
| | | | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
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13
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Madison AS, Sorsby SJ, Wang Y, Key TA. Increasing in situ bioremediation effectiveness through field-scale application of molecular biological tools. Front Microbiol 2023; 13:1005871. [PMID: 36845972 PMCID: PMC9950576 DOI: 10.3389/fmicb.2022.1005871] [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: 07/28/2022] [Accepted: 12/28/2022] [Indexed: 02/12/2023] Open
Abstract
Leveraging the capabilities of microorganisms to reduce (degrade or transform) concentrations of pollutants in soil and groundwater can be a cost-effective, natural remedial approach to manage contaminated sites. Traditional design and implementation of bioremediation strategies consist of lab-scale biodegradation studies or collection of field-scale geochemical data to infer associated biological processes. While both lab-scale biodegradation studies and field-scale geochemical data are useful for remedial decision-making, additional insights can be gained through the application of Molecular Biological Tools (MBTs) to directly measure contaminant-degrading microorganisms and associated bioremediation processes. Field-scale application of a standardized framework pairing MBTs with traditional contaminant and geochemical analyses was successfully performed at two contaminated sites. At a site with trichloroethene (TCE) impacted groundwater, framework application informed design of an enhanced bioremediation approach. Baseline abundances of 16S rRNA genes for a genus of obligate organohalide-respiring bacteria (i.e., Dehalococcoides) were measured at low abundances (101-102 cells/mL) within the TCE source and plume areas. In combination with geochemical analyses, these data suggested that intrinsic biodegradation (i.e., reductive dechlorination) may be occurring, but activities were limited by electron donor availability. The framework was utilized to support development of a full-scale enhanced bioremediation design (i.e., electron donor addition) and to monitor remedial performance. Additionally, the framework was applied at a second site with residual petroleum hydrocarbon (PHC) impacted soils and groundwater. MBTs, specifically qPCR and 16S gene amplicon rRNA sequencing, were used to characterize intrinsic bioremediation mechanisms. Functional genes associated with anaerobic biodegradation of diesel components (e.g., naphthyl-2-methyl-succinate synthase, naphthalene carboxylase, alkylsuccinate synthase, and benzoyl coenzyme A reductase) were measured to be 2-3 orders of magnitude greater than unimpacted, background samples. Intrinsic bioremediation mechanisms were determined to be sufficient to achieve groundwater remediation objectives. Nonetheless, the framework was further utilized to assess that an enhanced bioremediation could be a successful remedial alternative or complement to source area treatment. While bioremediation of chlorinated solvents, PHCs, and other contaminants has been demonstrated to successfully reduce environmental risk and reach site goals, the application of field-scale MBT data in combination with contaminant and geochemical data analyses to design, implement, and monitor a site-specific bioremediation approach can result in more consistent remedy effectiveness.
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Affiliation(s)
- Andrew S. Madison
- Golder Associates USA Inc., (Currently WSP USA Inc.), Marlton, NJ, United States,*Correspondence: Andrew S. Madison, ✉
| | - Skyler J. Sorsby
- Golder Associates USA Inc., (Currently WSP USA Inc.), Marlton, NJ, United States
| | | | - Trent A. Key
- ExxonMobil Environmental and Property Solutions Company, Spring, TX, United States
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14
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Wei F, Xu R, Rao Q, Zhang S, Ma Z, Ma Y. Biodegradation of asphaltenes by an indigenous bioemulsifier-producing Pseudomonas stutzeri YWX-1 from shale oil in the Ordos Basin: Biochemical characterization and complete genome analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114551. [PMID: 36669280 DOI: 10.1016/j.ecoenv.2023.114551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Crude oil pollution is environmentally ubiquitous and has become a global public concern about its impact on human health. Asphaltenes are the key components of heavy crude oil (HCO) that are underutilized due to their high viscosity and density, and yet, the associated information about biodegradation is extremely limited in the literature. In the present study, an indigenous bacterium with effective asphaltene-degrading activity was isolated from oil shale and identified as Pseudomonas stutzeri by a polyphasic taxonomic approach, named YWX-1. Supplemented with 75 g L-1 heavy crude oil as the sole carbon source for growth in basic mineral salts liquid medium (MSM), strain YWX-1 was able to remove 49% of asphaletene fractions within 14 days, when it was cultivated with an initial inoculation size of 1%. During the degradation process, the bioemulsifier produced by strain YWX-1 could emulsify HCO obviously into particles, as well as it had the ability to solubilize asphaletenes. The bioemulsifier was identified to be a mixture of polysaccharide and protein through Fourier transform infrared spectroscopy (FT-IR). The genome of strain YWX-1 contains one circular chromosome of 4488441 bp with 63.98% GC content and 4145 protein coding genes without any plasmid. Further genome annotation indicated that strain YWX-1 possesses a serial of genes involved in bio-emulsification and asphaltenes biodegradation. This work suggested that P. stutzeri YWX-1 could be a promising species for bioremediation of HCO and its genome analysis provided insight into the molecular basis of asphaltene biodegradation and bioemulsifier production.
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Affiliation(s)
- Fengdan Wei
- College of Life Science, Northwest University, Xi´an, China
| | - Rui Xu
- College of Life Science, Northwest University, Xi´an, China
| | - Qingyan Rao
- College of Life Science, Northwest University, Xi´an, China
| | - Shuqi Zhang
- College of Life Science, Northwest University, Xi´an, China
| | - Zhiwei Ma
- College of Life Science, Northwest University, Xi´an, China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi´an, Shaanxi 710069, China; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi´an, Shaanxi 710069, China.
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15
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Wu Z, Liu G, Ji Y, Li P, Yu X, Qiao W, Wang B, Shi K, Liu W, Liang B, Wang D, Yanuka-Golub K, Freilich S, Jiang J. Electron acceptors determine the BTEX degradation capacity of anaerobic microbiota via regulating the microbial community. ENVIRONMENTAL RESEARCH 2022; 215:114420. [PMID: 36167116 DOI: 10.1016/j.envres.2022.114420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Anaerobic degradation is the major pathway for microbial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) under electron acceptor lacking conditions. However, how exogenous electron acceptors modulate BTEX degradation through shaping the microbial community structure remains poorly understood. Here, we investigated the effect of various exogenous electron acceptors on BTEX degradation as well as methane production in anaerobic microbiota, which were enriched from the same contaminated soil. It was found that the BTEX degradation capacities of the anaerobic microbiota gradually increased along with the increasing redox potentials of the exogenous electron acceptors supplemented (WE: Without exogenous electron acceptors < SS: Sulfate supplement < FS: Ferric iron supplement < NS: Nitrate supplement), while the complexity of the co-occurring networks (e.g., avgK and links) of the microbiota gradually decreased, showing that microbiota supplemented with higher redox potential electron acceptors were less dependent on the formation of complex microbial interactions to perform BTEX degradation. Microbiota NS showed the highest degrading capacity and the broadest substrate-spectrum for BTEX, and it could metabolize BTEX through multiple modules which not only contained fewer species but also different key microbial taxa (eg. Petrimonas, Achromobacter and Comamonas). Microbiota WE and FS, with the highest methanogenic capacities, shared common core species such as Sedimentibacter, Acetobacterium, Methanobacterium and Smithella/Syntrophus, which cooperated with Geobacter (microbiota WE) or Desulfoprunum (microbiota FS) to perform BTEX degradation and methane production. This study demonstrates that electron acceptors may alter microbial function by reshaping microbial community structure and regulating microbial interactions and provides guidelines for electron acceptor selection for bioremediation of aromatic pollutant-contaminated anaerobic sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Guiping Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanhan Ji
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Xin Yu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Wenzhong Liu
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Dong Wang
- Jiangsu Academy of Environmental Science and Technology Co., Ltd, Nanjing, 210095, China
| | - Keren Yanuka-Golub
- The Galilee Society Institute of Applied Research, Shefa-Amr, 20200, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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16
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Gou Y, Song Y, Yang S, Yang Y, Cheng Y, Li J, Zhang T, Cheng Y, Wang H. Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120023. [PMID: 36030953 DOI: 10.1016/j.envpol.2022.120023] [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: 05/11/2022] [Revised: 07/21/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO2 as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO3 (CO2) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO2 addition (EC2000) promoted PAH degradation compared to soil without added CO2 (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 108 g-1 soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO2 application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.
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Affiliation(s)
- Yaling Gou
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China; Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Yun Song
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Sucai Yang
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Yan Yang
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Yanan Cheng
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Jiabin Li
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Tengfei Zhang
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Yanjun Cheng
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Hongqi Wang
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
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17
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Viggi CC, Tucci M, Resitano M, Matturro B, Crognale S, Feigl V, Molnár M, Rossetti S, Aulenta F. Passive electrobioremediation approaches for enhancing hydrocarbons biodegradation in contaminated soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157325. [PMID: 35839884 DOI: 10.1016/j.scitotenv.2022.157325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/10/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Electrobioremediation technologies hold considerable potential for the treatment of soils contaminated by petroleum hydrocarbons (PH), since they allow stimulating biodegradation processes with no need for subsurface chemicals injection and with little to no energy consumption. Here, a microbial electrochemical snorkel (MES) was applied for the treatment of a soil contaminated by hydrocarbons. The MES consists of direct coupling of a microbial anode with a cathode, being a single conductive, non-polarized material positioned suitably to create an electrochemical connection between the anoxic zone (the contaminated soil) and the oxic zone (the overlying oxygenated water). Soil was also supplemented with electrically conductive particles of biochar as a strategy to construct a conductive network with microbes in the soil matrix, thus extending the radius of influence of the snorkel. The results of a comprehensive suite of chemical, microbiological and ecotoxicological analyses evidenced that biochar addition, rather than the presence of a snorkel, was the determining factor in accelerating PH removal from contaminated soils, possibly accelerating syntrophic and/or cooperative metabolisms involved in the degradation of PH. The enhancement of biodegradation was mirrored by an increased abundance of anaerobic and aerobic microorganisms known to be involved in the degradation of PH and related functional genes. Plant ecotoxicity assays confirmed a reduction of soils toxicity in treatments receiving electrically conductive biochar.
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Affiliation(s)
- Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy.
| | - Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Viktória Feigl
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Mónika Molnár
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
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18
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Castro AR, Martins G, Salvador AF, Cavaleiro AJ. Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review. Microorganisms 2022; 10:2142. [PMID: 36363734 PMCID: PMC9695802 DOI: 10.3390/microorganisms10112142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 09/22/2023] Open
Abstract
Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.
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Affiliation(s)
- Ana R. Castro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Andreia F. Salvador
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Ana J. Cavaleiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
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19
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Zhang W, Wang Z, Guo H, Li L, Zhang M, Zhang W, Sun X, Sun S, Kou C, Zhao W. Biochemical Process and Microbial Evolution in the Conversion of Corn Straw Combined with Coal to Biogas. ACS OMEGA 2022; 7:31138-31148. [PMID: 36092578 PMCID: PMC9453931 DOI: 10.1021/acsomega.2c03331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The combined anaerobic fermentation of coal and straw can increase the production of biogas. To explore the mechanism of adding corn straw to increase methane production, coal with different metamorphic degrees and corn straw were collected for biogas production simulation experiments under different substrate ratios. The changes in liquid products, the structure of lignocellulose in corn straw, and microbial evolution were monitored. The results showed that the combined fermentation of bituminous coal A with corn straw and bituminous coal C with corn straw at a mass ratio of 2:1 each ((AC-2) and (CC-2)) and that of bituminous coal B and corn straw at a mass ratio of 3:1 (BC-3) had the best gas production, and methane yields reached 17.28, 12.51, and 14.88 mL/g, respectively. The fermentation liquid had organic matter with more types and higher contents during the early and peak stages of gas production, and fewer types of organic matter were detected in the terminal stage. The degradation of lignocelluloses in the corn straw of AC-2 was higher. With the increase in fermentation time, the carbohydrates in the fermentation system increased and the degradation rate of cellulose decreased gradually. The abundance of genes related to nitrate reduction gradually increased, while that of sulfate reduction was on the contrary. Bacteria in the cofermentation system mainly metabolized carbohydrates. During cofermentation with high metamorphic coal, corn straw would be preferentially degraded. The structure of the archaea community changed from Methanosarcina and Methanothrix to Methanobacterium.
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Affiliation(s)
- Wei Zhang
- China
University of Mining and Technology, Xuzhou 221018, China
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Zebin Wang
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Hongyu Guo
- School
of Energy Science and Engineering, Henan
Polytechnic University, Jiaozuo 454000, China
| | - Libo Li
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Minglu Zhang
- School
of Energy Science and Engineering, Henan
Polytechnic University, Jiaozuo 454000, China
| | - Wen Zhang
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Xiaoguang Sun
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Shixuan Sun
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Congliang Kou
- PetroChina
Coalbed Methane Company Limited, Beijing 100028, China
| | - Weizhong Zhao
- Department
of Environmental Engineering, Technical
University of Denmark, DK-2800 Lyngby, Denmark
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20
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Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions. SUSTAINABILITY 2022. [DOI: 10.3390/su14127027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.
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21
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Chen X, Sheng Y, Wang G, Guo L, Zhang H, Zhang F, Yang T, Huang D, Han X, Zhou L. Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water. WATER RESEARCH 2022; 215:118277. [PMID: 35305487 DOI: 10.1016/j.watres.2022.118277] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO42-/rCl-), coefficient of sodium and chloride (rNa+/rCl-), and coefficient of magnesium and chloride (rMg2+/rCl-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO3-, Fe3+, and SO42-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.
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Affiliation(s)
- Xianglong Chen
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China; Department of Geology and Environmental Earth Science, Miami University, OH 45056, USA.
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China.
| | - Liang Guo
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an 710054, PR China
| | - Hongyu Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Fan Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Tao Yang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Dandan Huang
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang 330013, PR China
| | - Xu Han
- Geology Institute of China Chemical Geology and Mine Bureau, Beijing, PR China
| | - Ling Zhou
- Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
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22
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Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps. Sci Rep 2022; 12:7245. [PMID: 35508504 PMCID: PMC9068923 DOI: 10.1038/s41598-022-10850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.
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23
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Massot F, Bernard N, Alvarez LMM, Martorell MM, Mac Cormack WP, Ruberto LAM. Microbial associations for bioremediation. What does "microbial consortia" mean? Appl Microbiol Biotechnol 2022; 106:2283-2297. [PMID: 35294589 DOI: 10.1007/s00253-022-11864-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/02/2022]
Abstract
Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.
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Affiliation(s)
- Francisco Massot
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Nathalie Bernard
- Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Lucas M Martinez Alvarez
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - María M Martorell
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Walter P Mac Cormack
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina
| | - Lucas A M Ruberto
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina. .,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. .,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina.
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24
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Péquin B, Cai Q, Lee K, Greer CW. Natural attenuation of oil in marine environments: A review. MARINE POLLUTION BULLETIN 2022; 176:113464. [PMID: 35231783 DOI: 10.1016/j.marpolbul.2022.113464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/31/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Natural attenuation is an important process for oil spill management in marine environments. Natural attenuation affects the fate of oil by physical, chemical, and biological processes, which include evaporation, dispersion, dissolution, photo-oxidation, emulsification, oil particle aggregation, and biodegradation. This review examines the cumulative knowledge regarding these natural attenuation processes as well as their simulation and prediction using modelling approaches. An in-depth discussion is provided on how oil type, microbial community and environmental factors contribute to the biodegradation process. It describes how our understanding of the structure and function of indigenous oil degrading microbial communities in the marine environment has been advanced by the application of next generation sequencing tools. The synergetic and/or antagonist effects of oil spill countermeasures such as the application of chemical dispersants, in-situ burning and nutrient enrichment on natural attenuation were explored. Several knowledge gaps were identified regarding the synergetic and/or antagonistic effects of active response countermeasures on the natural attenuation/biodegradation process. This review highlighted the need for field data on both the effectiveness and potential detrimental effects of oil spill response options to support modelling and decision-making on their selection and application.
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Affiliation(s)
- Bérangère Péquin
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, Quebec, Canada.
| | - Qinhong Cai
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada, Ottawa, Ontario, Canada
| | - Charles W Greer
- McGill University, Department of Natural Resource Sciences, Ste-Anne-de-Bellevue, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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25
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Voskuhl L, Brusilova D, Brauer VS, Meckenstock RU. Inhibition of sulfate-reducing bacteria with formate. FEMS Microbiol Ecol 2022; 98:6510814. [PMID: 35040992 PMCID: PMC8831227 DOI: 10.1093/femsec/fiac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8 or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Concerning D. multivorans, increasing formate concentrations delayed the onsets of growth and sulfate reduction, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
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Affiliation(s)
- L Voskuhl
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - D Brusilova
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - V S Brauer
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - R U Meckenstock
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
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26
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Vandermaesen J, Du S, Daly AJ, Baetens JM, Horemans B, De Baets B, Boon N, Springael D. Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1352-1364. [PMID: 34982540 DOI: 10.1021/acs.est.1c06653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.
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Affiliation(s)
- Johanna Vandermaesen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Siyao Du
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Aisling J Daly
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Jan M Baetens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
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27
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Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature 2022; 601:257-262. [PMID: 34937940 DOI: 10.1038/s41586-021-04235-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1-3. However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.
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28
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Mandal A, Dutta A, Das R, Mukherjee J. Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review. MARINE POLLUTION BULLETIN 2021; 170:112626. [PMID: 34153859 DOI: 10.1016/j.marpolbul.2021.112626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 05/16/2023]
Abstract
Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm-2y-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.
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Affiliation(s)
- Abhishek Mandal
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Ahana Dutta
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Reshmi Das
- School of Environmental Studies, Jadavpur University, 700032, India.
| | - Joydeep Mukherjee
- School of Environmental Studies, Jadavpur University, 700032, India.
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Pal S, Dutta A, Sarkar J, Roy A, Sar P, Kazy SK. Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50074-50093. [PMID: 33945094 DOI: 10.1007/s11356-021-13744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.
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Affiliation(s)
- Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
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30
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Singh A, Moestedt J, Berg A, Schnürer A. Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community. Front Microbiol 2021; 12:700256. [PMID: 34484143 PMCID: PMC8415747 DOI: 10.3389/fmicb.2021.700256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/21/2021] [Indexed: 11/15/2022] Open
Abstract
Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Moestedt
- Tekniska Verken i Linköping AB, Department R&D, Linköping, Sweden
| | | | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Deng S, Wang B, Zhang W, Su S, Dong H, Banat IM, Sun S, Guo J, Liu W, Wang L, She Y, Zhang F. Elucidate microbial characteristics in a full-scale treatment plant for offshore oil produced wastewater. PLoS One 2021; 16:e0255836. [PMID: 34383807 PMCID: PMC8360554 DOI: 10.1371/journal.pone.0255836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/24/2021] [Indexed: 11/19/2022] Open
Abstract
Oil-produced wastewater treatment plants, especially those involving biological treatment processes, harbor rich and diverse microbes. However, knowledge of microbial ecology and microbial interactions determining the efficiency of plants for oil-produced wastewater is limited. Here, we performed 16S rDNA amplicon sequencing to elucidate the microbial composition and potential microbial functions in a full-scale well-worked offshore oil-produced wastewater treatment plant. Results showed that microbes that inhabited the plant were diverse and originated from oil and marine associated environments. The upstream physical and chemical treatments resulted in low microbial diversity. Organic pollutants were digested in the anaerobic baffled reactor (ABR) dominantly through fermentation combined with sulfur compounds respiration. Three aerobic parallel reactors (APRs) harbored different microbial groups that performed similar potential functions, such as hydrocarbon degradation, acidogenesis, photosynthetic assimilation, and nitrogen removal. Microbial characteristics were important to the performance of oil-produced wastewater treatment plants with biological processes.
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Affiliation(s)
- Shuyuan Deng
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Bo Wang
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Wenda Zhang
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Sanbao Su
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Hao Dong
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Ibrahim M. Banat
- Faculty of Life and Health Sciences, University of Ulster, Coleraine, N. Ireland, United Kingdom
| | - Shanshan Sun
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Jianping Guo
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Weiming Liu
- Sinopec Shengli Oilfield, Dongying, Shangdong, China
| | - Linhai Wang
- CNOOC Energy Development Co. Ltd. Technology Branch, Beijing, China
| | - Yuehui She
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Fan Zhang
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
- * E-mail:
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Zhao JY, Hu B, Dolfing J, Li Y, Tang YQ, Jiang Y, Chi CQ, Xing J, Nie Y, Wu XL. Thermodynamically favorable reactions shape the archaeal community affecting bacterial community assembly in oil reservoirs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146506. [PMID: 33794455 DOI: 10.1016/j.scitotenv.2021.146506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet rarely investigated in the context of deep terrestrial ecology. Here, the microbial communities in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined and analyzed by proportional distribution analysis and null model analysis. A 'core' microbiota consisting of three bacterial genera, including Arcobacter, Pseudomonas and Acinetobacter, and eight archaeal genera, including Archaeoglobus, Methanobacterium, Methanothermobacter, unclassified Methanobacteriaceae, Methanomethylovorans, Methanoculleus, Methanosaeta and Methanolinea, was found to be present in all production water samples. Canonical correlation analysis reflected that the core archaea were significantly influenced by temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Thermodynamic calculations indicate that bioenergetic constraints are the driving force that governs the enrichment of two core archaeal guilds, aceticlastic methanogens versus hydrogenotrophic methanogens, in low- and high-temperature oil reservoirs, respectively. Collectively, our study indicates that microbial community structures in wells of oil reservoirs are structured by the thermodynamic window of opportunity, through which the core archaeal communities are accommodated directly followed by the deterministic recruiting of core bacterial genera, and then the stochastic selection of some other microbial members from local environments. Our study enhances the understanding of the microbial assembly mechanism in deep terrestrial habitats. Meanwhile, our findings will support the development of functional microbiota used for bioremediation and bioaugmentation in microbial enhanced oil recovery.
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Affiliation(s)
- Jie-Yu Zhao
- College of Engineering, Peking University, Beijing, China
| | - Bing Hu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology of China; Institute of Biochemical Engineering, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Jan Dolfing
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, United Kingdom
| | - Yan Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München/Technical University of Munich, Munich, Germany
| | - Chang-Qiao Chi
- College of Engineering, Peking University, Beijing, China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, China; Institute of Ocean Research, Peking University, Beijing, China.
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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.
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Affiliation(s)
- Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Pune, 411004, India
| | - Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
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34
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Silva-Castro GA, Rodríguez-Calvo A, Robledo-Mahón T, Aranda E, González-López J, Calvo C. Design of Bio-Absorbent Systems for the Removal of Hydrocarbons from Industrial Wastewater: Pilot-Plant Scale. TOXICS 2021; 9:toxics9070162. [PMID: 34357905 PMCID: PMC8309889 DOI: 10.3390/toxics9070162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
The objective of this study was the development and design of a treatment system at a pilot-plant scale for the remediation of hydrocarbons in industrial wastewater. The treatment consists of a combined approach of absorption and biodegradation to obtain treated water with sufficient quality to be reused in fire defense systems (FDSs). The plant consists of four vertical flow columns (bioreactors) made of stainless steel (ATEX Standard) with dimensions of 1.65 × 0.5 m and water volumes of 192.4 L. Each bioreactor includes a holder to contain the absorbent material (Pad Sentec polypropylene). The effectiveness of the treatment system has been studied in wastewater with high and low pollutant loads (concentrations higher than 60,000 mg L−1 of total petroleum hydrocarbons (TPH) and lower than 500 mg L−1 of TPHs, respectively). The pilot-plant design can function at two different flow rates, Q1 (180 L h−1) and Q2 (780 L h−1), with or without additional aeration. The results obtained for strongly polluted wastewaters showed that, at low flow rates, additional aeration enhanced hydrocarbon removal, while aeration was unnecessary at high flow rates. For wastewater with a low pollutant load, we selected a flow rate of 780 L h−1 without aeration. Different recirculation times were also tested along with the application of a post-treatment lasting 7 days inside the bioreactor without recirculation. The microbial diversity studies showed similar populations of bacteria and fungi in the inlet and outlet wastewater. Likewise, high similarity indices were observed between the adhered and suspended biomass within the bioreactors. The results showed that the setup and optimization of the reactor represent a step forward in the application of bioremediation processes at an industrial/large scale.
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Affiliation(s)
- Gloria Andrea Silva-Castro
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
| | - Alfonso Rodríguez-Calvo
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
| | - Tatiana Robledo-Mahón
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, University of Granada, 18071 Granada, Spain
| | - Elisabet Aranda
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, University of Granada, 18071 Granada, Spain
| | - Jesús González-López
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, University of Granada, 18071 Granada, Spain
| | - Concepción Calvo
- Institute of Water Research, University of Granada, 18071 Granada, Spain; (G.A.S.-C.); (A.R.-C.); (T.R.-M.); (E.A.); (J.G.-L.)
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, University of Granada, 18071 Granada, Spain
- Correspondence: ; Tel.: +34-958-248021
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35
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Pannekens M, Voskuhl L, Mohammadian S, Köster D, Meier A, Köhne JM, Kulbatzki M, Akbari A, Haque S, Meckenstock RU. Microbial Degradation Rates of Natural Bitumen. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8700-8708. [PMID: 34169718 PMCID: PMC8264945 DOI: 10.1021/acs.est.1c00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms are present in nearly every oil or bitumen sample originating from temperate reservoirs. Nevertheless, it is very difficult to obtain reliable estimates about microbial processes taking place in deep reservoirs, since metabolic rates are rather low and differ strongly during artificially cultivation. Here, we demonstrate the importance and impact of microorganisms entrapped in microscale water droplets for the overall biodegradation process in bitumen. To this end, we measured degradation rates of heavily biodegraded bitumen from the Pitch Lake (Trinidad and Tobago) using the novel technique of reverse stable isotope labeling, allowing precise measurements of comparatively low mineralization rates in the ng range in microcosms under close to natural conditions. Freshly taken bitumen samples were overlain with artificial brackish water and incubated for 945 days. Additionally, three-dimensional distribution of water droplets in bitumen was studied with computed tomography, revealing a water bitumen interface of 1134 cm2 per liter bitumen, resulting in an average mineralization rate of 9.4-38.6 mmol CO2 per liter bitumen and year. Furthermore, a stable and biofilm-forming microbial community established on the bitumen itself, mainly composed of fermenting and sulfate-reducing bacteria. Our results suggest that small water inclusions inside the bitumen substantially increase the bitumen-water interface and might have a major impact on the overall oil degradation process.
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Affiliation(s)
- Mark Pannekens
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - Lisa Voskuhl
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - Sadjad Mohammadian
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - Daniel Köster
- Instrumental
Analytical Chemistry, University of Duisburg—Essen, 45141 Essen, Germany
| | - Arne Meier
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - John M. Köhne
- Department
of Soil System Science, Helmholtz Centre
for Environmental Research, 06120 Halle, Germany
| | - Michelle Kulbatzki
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - Ali Akbari
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
| | - Shirin Haque
- Department
of Physics, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Rainer U. Meckenstock
- Environmental
Microbiology and Biotechnology, Aquatic Microbiology, University of Duisburg—Essen, 45141 Essen, Germany
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36
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do Nascimento JGDS, Silva EVA, Dos Santos AB, da Silva MER, Firmino PIM. Microaeration improves the removal/biotransformation of organic micropollutants in anaerobic wastewater treatment systems. ENVIRONMENTAL RESEARCH 2021; 198:111313. [PMID: 33991572 DOI: 10.1016/j.envres.2021.111313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/18/2020] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
This work assessed the effect of increasing microaeration flow rates (1-6 mL min-1 at 28 °C and 1 atm, equivalent to 0.025-0.152 L O2 L-1 feed) on the removal/biotransformation of seven organic micropollutants (OMPs) (three hormones, one xenoestrogen, and three pharmaceuticals), at 200 μg L-1 each, in a lab-scale upflow anaerobic sludge blanket reactor operated at a hydraulic retention time (HRT) of 7.4 h. Additionally, the operational stability of the system and the evolution of its microbial community under microaerobic conditions were evaluated. Microaeration was demonstrated to be an effective strategy to improve the limited removal/biotransformation of the evaluated OMPs in short-HRT anaerobic wastewater treatment systems. The rise in the airflow rate considerably increased the removal efficiencies of all OMPs. However, there seems to be a saturation limit for the biochemical reactions. Then, the best results were obtained with 4 mL air min-1 (0.101 L O2 L-1 feed) (~90%) because, above this flow rate, the efficiency increase was negligible. The long-term exposure to microaerobic conditions (249 days) led the microbiota to a gradual evolution. Consequently, there was some enrichment with species potentially associated with the biotransformation of OMPs, which may explain the better performance at the end of the microaerobic term even with the lowest airflow rate tested.
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Affiliation(s)
| | - Ester Viana Alencar Silva
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Paulo Igor Milen Firmino
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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37
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Kozlowski MT, Silverman BR, Johnstone CP, Tirrell DA. Genetically Programmable Microbial Assembly. ACS Synth Biol 2021; 10:1351-1359. [PMID: 34009951 DOI: 10.1021/acssynbio.0c00616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Engineered microbial communities show promise in a wide range of applications, including environmental remediation, microbiome engineering, and synthesis of fine chemicals. Here we present methods by which bacterial aggregates can be directed into several distinct architectures by inducible surface expression of heteroassociative protein domains (SpyTag/SpyCatcher and SynZip17/18). Programmed aggregation can be used to activate a quorum-sensing circuit, and aggregate size can be tuned via control of the amount of the associative protein displayed on the cell surface. We further demonstrate reversibility of SynZip-mediated assembly by addition of soluble competitor peptide. Genetically programmable bacterial assembly provides a starting point for the development of new applications of engineered microbial communities in environmental technology, agriculture, human health, and bioreactor design.
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Affiliation(s)
- Mark T. Kozlowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Bradley R. Silverman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Christopher P. Johnstone
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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38
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Ramdass AC, Rampersad SN. Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad. Microorganisms 2021; 9:1167. [PMID: 34071489 PMCID: PMC8230346 DOI: 10.3390/microorganisms9061167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/29/2022] Open
Abstract
Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.
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Affiliation(s)
| | - Sephra N. Rampersad
- Biochemistry Research Laboratory (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, Trinidad and Tobago, West Indies;
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39
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Grandel NE, Reyes Gamas K, Bennett MR. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol 2021; 29:1095-1105. [PMID: 33966922 DOI: 10.1016/j.tim.2021.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.
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Affiliation(s)
- Nicolas E Grandel
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA.
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40
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Gao Y, Du J, Bahar MM, Wang H, Subashchandrabose S, Duan L, Yang X, Megharaj M, Zhao Q, Zhang W, Liu Y, Wang J, Naidu R. Metagenomics analysis identifies nitrogen metabolic pathway in bioremediation of diesel contaminated soil. CHEMOSPHERE 2021; 271:129566. [PMID: 33460896 DOI: 10.1016/j.chemosphere.2021.129566] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/11/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen amendment is known to effectively enhance the bioremediation of hydrocarbon-contaminated soil, but the nitrogen metabolism in this process is not well understood. To unravel the nitrogen metabolic pathway(s) of diesel contaminated soil, six types of nitrogen sources were added to the diesel contaminated soil. Changes in microbial community and soil enzyme genes were investigated by metagenomics analysis and chemical analysis through a 30-day incubation study. The results showed that ammonium based nitrogen sources significantly accelerated the degradation of total petroleum hydrocarbon (TPH) (79-81%) compared to the control treatment (38%) and other non-ammonium based nitrogen amendments (43-57%). Different types of nitrogen sources could dramatically change the microbial community structure and soil enzyme gene abundance. Proteobacteria and Actinobacteria were identified as the two dominant phyla in the remediation of diesel contaminated soil. Metagenomics analysis revealed that the preferred metabolic pathway of nitrogen was from ammonium to glutamate via glutamine, and the enzymes governing this transformation were glutamine synthetase and glutamate synthetase; while in nitrate based amendment, the conversion from nitrite to ammonium was restrained by the low abundance of nitrite reductase enzyme and therefore retarded the TPH degradation rate. It is concluded that during the process of nitrogen enhanced bioremediation, the most efficient nitrogen cycling direction was from ammonium to glutamine, then to glutamate, and finally joined with carbon metabolism after transforming to 2-oxoglutarate.
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Affiliation(s)
- Yongchao Gao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China; Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - Jianhua Du
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Md Mezbaul Bahar
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Hui Wang
- School of Resources and Environment, University of Jinan, Jinan, 250022, China
| | - Suresh Subashchandrabose
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Luchun Duan
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo, 315211, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wen Zhang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Yanju Liu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Jianing Wang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Ravi Naidu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Australia.
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41
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Zhang C, Meckenstock RU, Weng S, Wei G, Hubert CRJ, Wang JH, Dong X. Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition. FEMS Microbiol Ecol 2021; 97:6171024. [PMID: 33720296 DOI: 10.1093/femsec/fiab045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology, University Duisburg-Essen, Universitätsstrasse 5, Essen 45141, Germany
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Siming District, Xiamen 361005, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N1N4, Canada
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 2 Daxue Road, XiangZhou District, Zhuhai 519000, China
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42
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Bhatt P, Verma A, Gangola S, Bhandari G, Chen S. Microbial glycoconjugates in organic pollutant bioremediation: recent advances and applications. Microb Cell Fact 2021; 20:72. [PMID: 33736647 PMCID: PMC7977309 DOI: 10.1186/s12934-021-01556-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 02/27/2021] [Indexed: 02/06/2023] Open
Abstract
The large-scale application of organic pollutants (OPs) has contaminated the air, soil, and water. Persistent OPs enter the food supply chain and create several hazardous effects on living systems. Thus, there is a need to manage the environmental levels of these toxicants. Microbial glycoconjugates pave the way for the enhanced degradation of these toxic pollutants from the environment. Microbial glycoconjugates increase the bioavailability of these OPs by reducing surface tension and creating a solvent interface. To date, very little emphasis has been given to the scope of glycoconjugates in the biodegradation of OPs. Glycoconjugates create a bridge between microbes and OPs, which helps to accelerate degradation through microbial metabolism. This review provides an in-depth overview of glycoconjugates, their role in biofilm formation, and their applications in the bioremediation of OP-contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Amit Verma
- Department of Biochemistry, College of Basic Science and Humanities, SD Agricultural University, Gujarat, 385506, India
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, Dehradun, Uttarakhand, 248002, India
| | - Geeta Bhandari
- Department of Biotechnology, Sardar Bhagwan Singh University, Dehradun, Uttarakhand, 248161, India
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China.
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43
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Hamdan HZ, Salam DA. Ferric iron stimulation in marine SMFCs: Impact on the microbial structure evolution in contaminated sediments with low and high molecular weight PAHs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 280:111636. [PMID: 33218829 DOI: 10.1016/j.jenvman.2020.111636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/10/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
The impact of ferric iron stimulation on the evolution of microbial structure in marine sediment microbial fuel cells (SMFCs), operated for the bioremediation of a complex mixture of low and high molecular weight PAHs (naphthalene, fluorene, pyrene and benzo(a)pyrene), was assessed. Microbial evolution profiles showed high relative abundances of exoelectrogenic iron-reducing bacteria throughout the biodegradation, namely Geoalkalibacter, under ferric iron stimulation and anode reducing conditions, irrespective of sulfate reducing bacteria (SRB) inhibition. Highest PAHs removal was measured in the absence of anode reduction, under Fe stimulation and SRB inhibition, reaching 40.85% for benzo(a)pyrene, the most persistent PAH used in this study. Results suggest that amendment of contaminated sediment with ferric iron could constitute a better bioremediation strategy than using SMFCs. This becomes significant when considering the well-established and dominant indigenous SRB population in marine sediments that usually limits the performance of the anode as a terminal electron acceptor in marine SMFCs.
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Affiliation(s)
- Hamdan Z Hamdan
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
| | - Darine A Salam
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
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44
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Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure. Microorganisms 2021; 9:microorganisms9020356. [PMID: 33670234 PMCID: PMC7916938 DOI: 10.3390/microorganisms9020356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/02/2022] Open
Abstract
Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments.
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45
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Cai G, Zhao L, Wang T, Lv N, Li J, Ning J, Pan X, Zhu G. Variation of volatile fatty acid oxidation and methane production during the bioaugmentation of anaerobic digestion system: Microbial community analysis revealing the influence of microbial interactions on metabolic pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142425. [PMID: 33254934 DOI: 10.1016/j.scitotenv.2020.142425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) is widely used on waste treatment for its great capability of organic degradation and energy recovery. Accumulation of volatile fatty acids (VFAs) caused by impact loadings often leads to the acidification and failure of AD systems. Bioaugmentation is a promising way to accelerate VFA degradation but the succession of microbial communities usually caused unpredictable consequences. In this study, we used the sludge previously acclimated with VFAs for the bioaugmentation of an acidified anaerobic digestion system and increased the methane yield by 8.03-9.59 times. To see how the succession of microbial communities affected bioaugmentation, dual-chamber devices separated by membrane filters were used to control the interactions between the acidified and acclimated sludges. The experimental group with separated sludges showed significant advantages of VFA consumption (5.5 times less final VFA residue than the control), while the group with mixed sludge produced more methane (4.0 times higher final methane yield than the control). Microbial community analysis further highlighted the great influences of microbial interaction on the differentiation of metabolic pathways. Acetoclastic methanogens from the acclimated sludge acted as the main contributors to pH neutralization and methane production during the early phase of bioaugmentation, and maintained active in the mixed sludge but degenerated in the separated sludges where interactions between sludge microbiotas were limited. Instead, syntrophic butyrate and acetate oxidation coupled with nitrate and sulfate reduction was enriched in the separated sludges, which lowered the methane conversion rate and would cause the failure of bioaugmentation. Our study revealed the importance of microbial interactions and the functionality of enriched microbes, as well as the potential strategies to optimize the durability and efficiency of bioaugmentation.
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Affiliation(s)
- Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, China
| | - Tao Wang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Li
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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46
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Aulenta F, Tucci M, Cruz Viggi C, Dolfing J, Head IM, Rotaru A. An underappreciated DIET for anaerobic petroleum hydrocarbon-degrading microbial communities. Microb Biotechnol 2021; 14:2-7. [PMID: 32864850 PMCID: PMC7888475 DOI: 10.1111/1751-7915.13654] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/24/2022] Open
Abstract
Direct interspecies electron transfer (DIET) via electrically conductive minerals can play a role in the anaerobic oxidation of petroleum hydrocarbons in contaminated sites and can be exploited for the development of new, more effective bioremediation approaches.
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Affiliation(s)
- Federico Aulenta
- Water Research Institute (IRSA)National Research Council (CNR)MonterotondoRMItaly
| | - Matteo Tucci
- Water Research Institute (IRSA)National Research Council (CNR)MonterotondoRMItaly
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA)National Research Council (CNR)MonterotondoRMItaly
| | - Jan Dolfing
- School of EngineeringNewcastle UniversityNewcastle upon TyneUK
| | - Ian M. Head
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
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47
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Taylor NM, Toth CRA, Collins V, Mussone P, Gieg LM. The Effect of an Adsorbent Matrix on Recovery of Microorganisms from Hydrocarbon-Contaminated Groundwater. Microorganisms 2021; 9:microorganisms9010090. [PMID: 33401442 PMCID: PMC7823327 DOI: 10.3390/microorganisms9010090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/24/2020] [Indexed: 01/04/2023] Open
Abstract
The microbial degradation of recalcitrant hydrocarbons is an important process that can contribute to the remediation of oil and gas-contaminated environments. Due to the complex structure of subsurface terrestrial environments, it is important to identify the microbial communities that may be contributing to biodegradation processes, along with their abilities to metabolize different hydrocarbons in situ. In this study, a variety of adsorbent materials were assessed for their ability to trap both hydrocarbons and microorganisms in contaminated groundwater. Of the materials tested, a porous polymer resin (Tenax-TA) recovered the highest diversity of microbial taxa in preliminary experiments and was selected for additional (microcosm-based) testing. Oxic and anoxic experiments were prepared with groundwater collected from a contaminated aquifer to assess the ability of Tenax-TA to adsorb two environmental hydrocarbon contaminants of interest (toluene and benzene) while simultaneously providing a surface for microbial growth and hydrocarbon biodegradation. Microorganisms in oxic microcosms completely degraded both targets within 14 days of incubation, while anoxically-incubated microorganisms metabolized toluene but not benzene in less than 80 days. Community analysis of Tenax-TA-associated microorganisms revealed taxa highly enriched in sessile hydrocarbon-degrading treatments, including Saprospiraceae, Azoarcus, and Desulfoprunum, which may facilitate hydrocarbon degradation. This study showed that Tenax-TA can be used as a matrix to effectively trap both microorganisms and hydrocarbons in contaminated environmental systems for assessing and studying hydrocarbon-degrading microorganisms of interest.
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Affiliation(s)
- Nicole M. Taylor
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
| | - Courtney R. A. Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada;
| | - Victoria Collins
- Applied BioNanotechnology Industrial Research Chair Program, Northern Alberta Institute of Technology, 11762-106 Street, Edmonton, AB T5G 2R1, Canada; (V.C.); (P.M.)
| | - Paolo Mussone
- Applied BioNanotechnology Industrial Research Chair Program, Northern Alberta Institute of Technology, 11762-106 Street, Edmonton, AB T5G 2R1, Canada; (V.C.); (P.M.)
| | - Lisa M. Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
- Correspondence:
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48
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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.
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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
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49
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Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N, Kamagata Y, Tamaki H. Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes. Syst Appl Microbiol 2020; 44:126154. [PMID: 33227632 DOI: 10.1016/j.syapm.2020.126154] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022]
Abstract
An anaerobic thermophilic, rod-shaped bacterium possessing a unique non-lipid sheathed-like structure enveloping a single-membraned cell, designated strain NRmbB1T was isolated from at the deep subsurface oil field located in Yamagata Prefecture, Japan. Growth occurred with 40-60°C (optimum, 55°C), 0-2% (2%), NaCl and pH 6.0-8.5 (8.0). Fermentative growth with various sugars was observed. Glucose-grown cells generated acetate, hydrogen, pyruvate and lactate as the main end products. Syntrophic growth occurred with glucose, pyruvate and 3,4,5-trimethoxybenzoate in the presence of an H2-scavenging partner, and growth on 3,4,5-trimethoxybenzoate was only observed under syntrophic condition. The predominant cellular fatty acids were C16:0, iso-C16:0, anteiso-C15:0, and iso-C14:0. Respiratory quinone was not detected. The genomic G+C content was 40.8mol%. Based on 16S rRNA gene phylogeny, strain NRmbB1T belongs to a distinct order-level clade in the class Clostridia of the phylum Firmicutes, sharing low similarity with other isolated organisms (i.e., 87.5% for top hit Moorella thermoacetica DSM 2955T). In total, chemotaxonomic, phylogenetic and genomic characterization revealed that strain NRmbB1T (=KCTC 25035T, =JCM 39120T) represents a novel species of a new genus. In addition, we also propose the associated family and order as Koleobacteraceae fam. nov and Koleobacterales ord. nov., respectively.
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Affiliation(s)
- Sachiko Sakamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Satoshi Tamazawa
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Northern Advancement Center for Science & Technology, H-RISE, 5-3 Sakae-machi, Horonobe-cho, Teshio-gun, BPRI, Hokkaido 098-3221, Japan
| | - Hiroyuki Kusada
- JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideharu Yonebayashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Hiroki Iwama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Masayuki Ikarashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Tatsuki Wakayama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Haruo Maeda
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan; Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideyuki Tamaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
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Lv X, Ma B, Lee K, Ulrich A. Potential syntrophic associations in anaerobic naphthenic acids biodegrading consortia inferred with microbial interactome networks. JOURNAL OF HAZARDOUS MATERIALS 2020; 397:122678. [PMID: 32497975 DOI: 10.1016/j.jhazmat.2020.122678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Naphthenic acids (NAs) can be syntrophically metabolized by indigenous microbial communities in pristine sediments beneath oil sands tailings ponds. Syntrophy is an essential determinant of the microbial interactome, however, the interactome network in anaerobic NAs-degrading consortia has not been previously addressed due to complexity and resistance of NAs. To evaluate the impact of electron acceptors on topology of interactome networks, we inferred two microbial interactome networks for anaerobic NAs-degrading consortia under nitrate- and sulfate-reducing conditions. The complexity of the network was higher under sulfate-reducing conditions than nitrate-reducing conditions. Differences in the taxonomic composition between the two modules implies that different potential syntrophic interactions exist in each network. We inferred the presence of the same syntrophic microorganisms, from genera Bellilinea, Longilinea, and Litorilinea, initiating the metabolism in both networks, but within each network, we predicted unique syntrophic associations that have not been reported. Electron acceptor has a large effect on the interactome networks for anaerobic NAs-degrading consortia, offers insight into an unrecognized dimension of these consortia. These results provide a novel approach for exploring potential syntrophic relationships in biodegrading processes to help cost-effectively remove NAs in oil sands tailings ponds.
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Affiliation(s)
- Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
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