1
|
Almutairi HH. Microbial communities in petroleum refinery effluents and their complex functions. Saudi J Biol Sci 2024; 31:104008. [PMID: 38766506 PMCID: PMC11097069 DOI: 10.1016/j.sjbs.2024.104008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Petroleum refinery effluents (PRE) are a significant cause of pollution. It contains toxic compounds such as total petroleum hydrocarbons (TPH), and polycyclic aromatic hydrocarbons (PAHs), as well as heavy metals. They show a huge threat facing the aquaculture habitats, human health, and the environment if they are not treated before discharging into the environment. Physical and chemical procedures are used to treat hydrocarbon pollution in PRE, but these techniques often result in the formation of hazardous by-products during the remediation process. However, PRE contains various microbial communities, including bacteria, yeast, microalgae, and fungi. The bioremediation and biodegradation of oil contaminants are the primary functions of these microbial communities. However, these microorganisms can perform various additional functions including but not limited to heavy metals removal, production of biosurfactants, and nitrogen fixation. This review contributes to the comprehension of natural microbial communities and their complex functions in petroleum refinery effluents. Understanding microbial communities would facilitate the advancement of innovative biotechnology aimed at treating PRE, improving bioremediation processes, and potentially transforming PRE into valuable bio-products. Moreover, it assists in determining the most effective bioaugmentation strategy to enhance biodegradation and bioremediation in PRE. The review highlights the potential for sustainable green approaches using microbial communities to replace toxic chemical therapies and expensive physical treatments in the future.
Collapse
Affiliation(s)
- Hayfa Habes Almutairi
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| |
Collapse
|
2
|
Bharali P, Gogoi B, Sorhie V, Acharjee SA, Walling B, Alemtoshi, Vishwakarma V, Shah MP. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments. Biodegradation 2024; 35:1-46. [PMID: 37436665 DOI: 10.1007/s10532-023-10042-5] [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: 03/16/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023]
Abstract
Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.
Collapse
Affiliation(s)
- Pranjal Bharali
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India.
| | - Bhagyudoy Gogoi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Viphrezolie Sorhie
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Shiva Aley Acharjee
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Bendangtula Walling
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Alemtoshi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Galgotias University, Greater Noida, NCR Delhi, India
| | - Maulin Pramod Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India
| |
Collapse
|
3
|
Singha NA, Neihsial R, Kipgen L, Lyngdoh WJ, Nongdhar J, Chettri B, Singh P, Singh AK. Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures. Curr Microbiol 2023; 81:22. [PMID: 38017305 DOI: 10.1007/s00284-023-03529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023]
Abstract
Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.
Collapse
Affiliation(s)
- Ningombam A Singha
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Roselin Neihsial
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Lhinglamkim Kipgen
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Waniabha J Lyngdoh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Jopthiaw Nongdhar
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Bobby Chettri
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Prabhakar Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
| | - Arvind K Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| |
Collapse
|
4
|
Qaria MA, Xu C, Hussain A, Nawaz MZ, Zhu D. Metagenomic investigations on antibiotic resistance and microbial virulence in oil-polluted soils from China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:110590-110599. [PMID: 37792198 DOI: 10.1007/s11356-023-30137-z] [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: 07/24/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil microbial communities. In this study, three samples were collected from oil-polluted soils (OPS), and one control soil (CS) from Taolin town, China, near the old engine's scrapes was used. The aims of this study were to conduct metagenomic sequencing and subsequently perform resistome and virulome analysis. We also aimed to validate anti-microbial resistance and virulence genes and anti-bacterial sensitivity profiles among the isolates from oil-polluted soils. The OPS microbial community was dominated by bacterial species compared to the control samples which were dominated by metazoans and other organisms. Secondly, the resistosome and virulome analysis showed that ARGs and virulence factors were higher among OPS microbial communities. Antibiotic susceptibility assay and qPCR analysis for ARGs and virulence factors showed that the oil-polluted soil samples had remarkably enhanced expression of these ARGs and some virulence genes. Our study suggests that oil pollution contributes to shifting microbial communities to more resilient types that could survive the toxicity of oil pollution and subsequently become more resilient in terms of higher resistance and virulence potential.
Collapse
Affiliation(s)
- Majjid A Qaria
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Chunyan Xu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | | | - Muhammad Zohaib Nawaz
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| |
Collapse
|
5
|
Zhu H, Fu Y, Yu J, Jing W, Zhou M. Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change. Enzyme Microb Technol 2023; 169:110285. [PMID: 37413912 DOI: 10.1016/j.enzmictec.2023.110285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Petroleum biodegradation is of importance for the mitigation of secondary pollutants from soil chemical remediation. Describing the gene abundance change of the petroleum degradation emerged as an important practice for success. In this study, an indigenous consortium with targeting-enzyme was utilized to develop a degradative system that was later subjected to metagenomic analysis on the soil microbial community. Centering on ko00625 pathway, abundance change of dehydrogenase gene was firstly found increasing from groups D, DS to DC in turn, just in an opposite direction with that of oxygenase. In addition, gene abundance of responsive mechanism went rising with degradative process as well. This finding sufficiently promoted that equal attention should be paid to both degradative and responsive processes. Hydrogen donor system was innovatively built on the consortium-used soil to satisfy the demand of dehydrogenase gene tendency and to sustain further petroleum degradation. Anaerobic pine-needle soil was supplemented to this system, bi-functionally serving as dehydrogenase substrate with nutrients and hydrogen donor. In doing so, two successive degradations optimally achieved the total removal rate 75.6-78.7% for petroleum hydrocarbon. The conception on the gene abundance changes and its corresponding supplement helps industries of concern to develop geno-tag guided framework.
Collapse
Affiliation(s)
- Hongfei Zhu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China.
| | - Yuting Fu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Jiashuai Yu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Wenjie Jing
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Mengting Zhou
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| |
Collapse
|
6
|
Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [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: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
Collapse
Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
7
|
García-García R, Bocanegra-García V, Vital-López L, García-Mena J, Zamora-Antuñano MA, Cruz-Hernández MA, Rodríguez-Reséndiz J, Mendoza-Herrera A. Assessment of the Microbial Communities in Soil Contaminated with Petroleum Using Next-Generation Sequencing Tools. APPLIED SCIENCES 2023; 13:6922. [DOI: 10.3390/app13126922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Microbial communities are known to play a principal role in petroleum degradation. This study tries to determine the composition of bacteria in selected crude oil-contaminated soil from Tabasco and Tamaulipas states, Mexico. We determined the microbial populations living under these conditions. We evaluated the structure and diversity of bacterial communities in the contaminated soil samples. The most abundant phylum is proteobacteria. Next Generation Sequencing (NGS) analysis of the sampled soils from both states revealed that this phylum has the most relative abundance among the identified bacteria phyla. The heatmap represented the relative percentage of each genus within each sample and clustered the four samples into two groups. Moreover, this allowed us to identify many genera in alkaline soil from Tamaulipas, such as Skermanella sp., Azospirillum sp. and Unclassified species from the Rhodospirillaceae family in higher abundance. Meanwhile, in acidic soil from Tabasco, we identified Thalassospira, Unclassified members of the Sphingomonadaceae family and Unclassified members of the Alphaproteobacteria class with higher abundance. Alpha diversity analysis showed a low diversity (Shannon and Simpson index); Chao observed species in both Regions. These results suggest that the bacteria identified in these genera may possess the ability to degrade petroleum, and further studies in the future should elucidate their role in petroleum degradation.
Collapse
Affiliation(s)
- Raul García-García
- Division of Chemistry and Renewable Energy, Universidad Tecnologica de San Juan del Rio (UTSJR), San Juan del Rio 76900, Queretaro, Mexico
| | - Virgilio Bocanegra-García
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
| | - Lourdes Vital-López
- Carrera de Mantenimiento Industrial, Universidad Tecnológica de Tamaulipas Norte, Reynosa 88680, Tamaulipas, Mexico
| | - Jaime García-Mena
- Department of Genetics and Molecular Biology, Cinvestav, Av. IPN# 2508, Col. Zacatenco, Mexico City 07360, Mexico
| | - Marco Antonio Zamora-Antuñano
- Engineering Area and Centro de Investigación, Innovación y Desarrollo Tecnológico de UVM (CIIDETEC-UVM), Universidad del Valle de Mexico (UVM), Santiago de Queretaro 76230, Queretaro, Mexico
| | - María Antonia Cruz-Hernández
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
| | | | - Alberto Mendoza-Herrera
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
| |
Collapse
|
8
|
Li YQ, Xin Y, Li C, Liu J, Huang T. Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil. Braz J Microbiol 2023:10.1007/s42770-023-01000-7. [PMID: 37162704 DOI: 10.1007/s42770-023-01000-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.
Collapse
Affiliation(s)
- Yong-Quan Li
- School of Medicine, Northwest Minzu University, Lanzhou, China.
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, State Ethnic Affairs Commission, Lanzhou, China.
| | - Ying Xin
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Caili Li
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Jin Liu
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Tao Huang
- School of Medicine, Northwest Minzu University, Lanzhou, China
| |
Collapse
|
9
|
Yang B, Zhou M, Meng Y, Chen K, Xu J, Huang X, Liu Y, Li L, Ma L, Chen M. Hydrocarbons removal and microbial community succession in petroleum-contaminated soil under hydrogen peroxide treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:27081-27091. [PMID: 36374389 DOI: 10.1007/s11356-022-23875-z] [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: 05/03/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Chemical oxidation as a pretreatment step coupled with bioremediation for petroleum-contaminated soil may pose serious impacts on indigenous microorganisms and the available nutrients. Petroleum-contaminated soil were treated by hydrogen peroxide (H2O2) at initial concentrations of 105 mM (HH), 21 mM (HL), and 105 mM in three equal amounts (HT) without adding any external catalyst. The contents of total petroleum hydrocarbons (TPH) and dissolved nutrients (total organic compounds, nitrogen, and phosphate), and the indigenous bacteria community succession (analyzed by high-throughput sequencing of 16S rDNA) were investigated over 50 days. Compared to the control treatment without H2O2 addition, H2O2 treatments for the petroleum-contaminated soil significantly promoted the TPH removal especially in the first 4 days and impacted the contents of dissolved nutrients. Both of chemical oxidation and nutrients contributed to microbial community structure changes in alpha diversity. Although the soil microbial community structure had undergone significant changes after different chemical oxidation pretreatments, Firmicutes, Proteobacteria, Gemmatimonadetes, and Actinobacteria were the main bacterial phyla. Compared with adding H2O2 at one time, H2O2 added in stepwise was beneficial to indigenous bacterial diversity recovery and TPH removal. H2O2 oxidation treatments showed a great influence on the microbial community structures in the start-up stage, while recovery time rather than the oxidation treatments presented greater effects on the composition of the microbial community structure with the incubation time extended. Therefore, adding H2O2 as pretreatment for petroleum-contaminated soil showed little effect on the structure of soil indigenous microbial community from a long-term scale, and was conducive to the continuous removal of TPH by indigenous microorganisms.
Collapse
Affiliation(s)
- Bing Yang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China.
- Institute of Industrial Hazardous Waste Disposal and Utilization, Southwest Petroleum University, Chengdu, 610500, Sichuan, China.
- Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Chengdu, 610500, Sichuan, China.
| | - Mi Zhou
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Yuan Meng
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Keming Chen
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Jie Xu
- Safety, Environment and Technology Supervision Research Institute of PetroChina Southwest Oil and Gas Field Company, Chengdu, 610056, Sichuan, China
| | - Xiangfu Huang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Yucheng Liu
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
- Institute of Industrial Hazardous Waste Disposal and Utilization, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Lingli Li
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Lili Ma
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| | - Mingyan Chen
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, Sichuan, China
| |
Collapse
|
10
|
Wu M, Liu Z, Gao H, Gao J, Xu Y, Ou Y. Assessment of bioremediation potential of petroleum-contaminated soils from the shanbei oilfield of China revealed by qPCR and high throughput sequencing. CHEMOSPHERE 2022; 308:136446. [PMID: 36113659 DOI: 10.1016/j.chemosphere.2022.136446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/28/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
With the crude oil exploration activities in the Shanbei oilfield of China, the risk of soil contamination with crude oil spills has become a major concern. This study aimed at assessing the bioremediation potential of the petroleum polluted soils by investigating the expression of key functional genes decoding alkane and aromatic component degradation using an array of primers and real-time quantitative PCR (qPCR), and the functional microbiomes were determined using a combination of substrate-induced metabolic responses and high throughput sequencing. The results showed that the species that were more inclined to degrade aliphatic fraction of crude oil included Acinetobacter, Stenotrophomonas, Neorhizobium and Olivebacter. And Pseudomonas genus was a highly specific keystone species with the potential to degrade PAH fraction. Both aliphatic and PAH-degrading genes were upregulated when the soil petroleum contents were less than 10,000 mg/kg but downregulated when the oil contents were over 10,000 mg/kg. Bioremediation potential could be feasible for medium pollution with petroleum contents of less than 10,000 mg/kg. Optimization of the niche of Acinetobacter, Stenotrophomonas, Pseudomonas, Neorhizobium and Olivebacter species was beneficial to the biodegradation of refractory hydrocarbon components in the Shanbei plateau oilfield.
Collapse
Affiliation(s)
- Manli Wu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
| | - Zeliang Liu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huan Gao
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Jinghua Gao
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Yinrui Xu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Yawen Ou
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; College of Environmental and Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| |
Collapse
|
11
|
Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
Collapse
Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| |
Collapse
|
12
|
Das N, Bhuyan B, Pandey P. Correlation of soil microbiome with crude oil contamination drives detection of hydrocarbon degrading genes which are independent to quantity and type of contaminants. ENVIRONMENTAL RESEARCH 2022; 215:114185. [PMID: 36049506 DOI: 10.1016/j.envres.2022.114185] [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: 03/24/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The impacts of crude oil contamination on soil microbial populations were explored in seven different polluted areas near oil and gas drilling sites and refineries of Assam, India. Using high-throughput sequencing techniques, the functional genes and metabolic pathways involved in the bioconversion of crude oil contaminants by the indigenous microbial community were explored. Total petroleum hydrocarbon (TPH) concentrations in soil samples ranged from 1109.47 to 75,725.33 mg/kg, while total polyaromatic hydrocarbon (PAH) concentrations ranged from 0.780 to 560.05 mg/kg. Pyrene, benzo[a]anthracene, naphthalene, phenanthrene, and anthracene had greater quantities than the maximum permitted limits, suggesting a greater ecological risk, in comparison to other polyaromatic hydrocarbons. According to the metagenomic data analysis, the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroides were the most prevalent among all polluted areas. The most prominent hydrocarbon degraders in the contaminated sites included Burkholderia, Mycobacterium, Polaromonas, and Pseudomonas. However, the kinds of pollutants and their concentrations did not correlate with the abundances of respective degrading genes for all polluted locations, as some of the sites with little to low PAH contamination had significant abundances of corresponding functional genes for degradation. Thus, the findings of this study imply that the microbiome of hydrocarbon-contaminated areas, which are biologically involved in the degradation process, has various genes, operons and catabolic pathways that are independent of the presence of a specific kind of contaminant.
Collapse
Affiliation(s)
- Nandita Das
- Soil and Environmental Microbiology Lab, Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | - Bhrigu Bhuyan
- Soil and Environmental Microbiology Lab, Department of Microbiology, Assam University, Silchar, 788011, Assam, India
| | - Piyush Pandey
- Soil and Environmental Microbiology Lab, Department of Microbiology, Assam University, Silchar, 788011, Assam, India.
| |
Collapse
|
13
|
Basim Y, Mohebali G, Jorfi S, Nabizadeh R, Moghadam MA, Ghadiri A, Haghighi Fard NJ. Bacterial strains diversity in contaminated soils and their potential for bioremediation of total petroleum hydrocarbons in south west of Iran. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2022; 20:601-608. [PMID: 36406594 PMCID: PMC9672257 DOI: 10.1007/s40201-020-00592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/08/2020] [Indexed: 06/16/2023]
Abstract
PURPOSE The main purpose of this research was investigating of bioremediation potential oily contaminated soils using native bacterial strains in an oil field. METHODS In this research, total bacterial consortium were identified in oily soils with sandy loam texture as case and non-contaminated soils as controls during six months. The dominant strains present on contaminated soil were identified by DNA extraction using 16S rDNA gene sequencing via NGS technique and compared with bacteria present in non-contaminated soil as control samples. Furthermore, quantitative variations of bacterial count along with total petroleum hydrocarbons (TPH) removal was performed in oily (case) samples to investigate the relation between TPH removal and changes in bacterial density. The TPH values were determined with gas chromatography equipped with a flame ionization detector (GC-FID). RESULTS The dominant identified bacteria in oily soil were as follows: Halomonas, Moraxellaceae, Thalassobacillus, Zhihengliuella and Enterobacteriaceae which varied significantly from those identified in control soil. The bacterial diversity was higher in contaminated soil and a TPH removal of 50.9% was observed over a period of six months monitoring. CONCLUSION Indigenous bacteria in oil-contaminated soils of an oilfield in south west of Iran were found to be able to degrade Total Petroleum Hydrocarbons. Our results showed that bioremediation of oil-contaminated soils can be implemented without need to amplification of heterogeneous bacteria. Considering sandy loam texture of soil samples, the identified strains of bacteria could be introduced as sufficient consortium for biodegradation of this soils with similar texture.
Collapse
Affiliation(s)
- Yalda Basim
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ghasemali Mohebali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Sahand Jorfi
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ramin Nabizadeh
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Ata Ghadiri
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | |
Collapse
|
14
|
Siles JA, Hendrickson AJ, Terry N. Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116132. [PMID: 36067666 DOI: 10.1016/j.jenvman.2022.116132] [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: 02/20/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.
Collapse
Affiliation(s)
- José A Siles
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
| | - Andrew J Hendrickson
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Norman Terry
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| |
Collapse
|
15
|
Gao Y, Yuan L, Du J, Wang H, Yang X, Duan L, Zheng L, Bahar MM, Zhao Q, Zhang W, Liu Y, Fu Z, Wang W, Naidu R. Bacterial community profile of the crude oil-contaminated saline soil in the Yellow River Delta Natural Reserve, China. CHEMOSPHERE 2022; 289:133207. [PMID: 34890619 DOI: 10.1016/j.chemosphere.2021.133207] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/13/2023]
Abstract
Crude oil contamination greatly influence soil bacterial community. Proliferative microbes in the crude oil-contaminated soil are closely related to the living conditions. Oil wells in the Yellow River Delta Natural Reserve (YRDNR) region is an ideal site for investigating the bacterial community of crude oil-contaminated saline soil. In the present study, 18 soil samples were collected from the depths of 0-20 cm and 20-40 cm around the oil wells in the YRDNR. The bacterial community profile was analyzed through high-throughput sequencing to trace the oil-degrading aerobic and anaerobic bacteria. The results indicated that C15-C28 and C29-C38 were the main fractions of total petroleum hydrocarbon (TPH) in the sampled soil. These TPH fractions had a significant negative effect on bacterial biodiversity (Shannon, Simpson, and Chao1 indices), which led to the proliferation of hydrocarbon-degrading bacteria. A comprehensive analysis between the environmental factors and soil microbial community structure showed that Streptococcus, Bacillus, Sphingomonas, and Arthrobacter were the aerobic hydrocarbon-degrading bacteria; unidentified Rhodobacteraceae and Porticoccus were considered to be the possible facultative anaerobic bacteria with hydrocarbon biodegradation ability; Acidithiobacillus, SAR324 clade, and Nitrosarchaeum were predicted to be the anaerobic hydrocarbon-degrading bacteria in the sub-surface soil. Furthermore, large amount of carbon sources derived from TPH was found to cause depletion of bioavailable nitrogen in the soil. The bacteria associated with nitrogen transformation, such as Solirubrobacter, Candidatus Udaeobacter, Lysinibacillus, Bradyrhizobium, Sphingomonas, Mycobacterium, and Acidithiobacillus, were highly abundant; these bacteria may possess the ability to increase nitrogen availability in the crude oil-contaminated soil. The bacterial community functions were significantly different between the surface and the sub-surface soil, and the dissolved oxygen concentration in soil was considered to be potential influencing factor. Our results could provide useful information for the bioremediation of crude oil-contaminated saline soil.
Collapse
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.
| | - Liyuan Yuan
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Jianhua Du
- 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
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo, 315211, China.
| | - Luchun Duan
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Liwen Zheng
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Md Mezbaul Bahar
- 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
| | - Zhaoyang Fu
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wei 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, Callaghan, NSW, 2308, Australia
| |
Collapse
|
16
|
Shelyakin PV, Semenkov IN, Tutukina MN, Nikolaeva DD, Sharapova AV, Sarana YV, Lednev SA, Smolenkov AD, Gelfand MS, Krechetov PP, Koroleva TV. The Influence of Kerosene on Microbiomes of Diverse Soils. Life (Basel) 2022; 12:221. [PMID: 35207510 PMCID: PMC8878009 DOI: 10.3390/life12020221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 01/04/2023] Open
Abstract
One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the composition of the topsoil microbiome in pot and field experiments with different loads of added kerosene (loads up to 100 g/kg; retention time up to 360 days). At four time points we measured kerosene concentration and sequenced variable regions of 16S ribosomal RNA in the microbial communities. Mainly alkaline Dystric Arenosols with low content of available phosphorus and soil organic matter had an increased fraction of Actinobacteriota, Firmicutes, Nitrospirota, Planctomycetota, and, to a lesser extent, Acidobacteriota and Verrucomicobacteriota. In contrast, in highly acidic Fibric Histosols, rich in soil organic matter and available phosphorus, the fraction of Acidobacteriota was higher, while the fraction of Actinobacteriota was lower. Albic Luvisols occupied an intermediate position in terms of both physicochemical properties and microbiome composition. The microbiomes of different soils show similar response to equal kerosene loads. In highly contaminated soils, the proportion of anaerobic bacteria-metabolizing hydrocarbons increased, whereas the proportion of aerobic bacteria decreased. During the field experiment, the soil microbiome recovered much faster than in the pot experiments, possibly due to migration of microorganisms from the polluted area. The microbial community of Fibric Histosols recovered in 6 months after kerosene had been loaded, while microbiomes of Dystric Arenosols and Albic Luvisols did not restore even after a year.
Collapse
Affiliation(s)
- Pavel V. Shelyakin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Department of Computational Biology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Ivan N. Semenkov
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | - Maria N. Tutukina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, 142290 Moscow, Russia
| | - Daria D. Nikolaeva
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Anna V. Sharapova
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | - Yulia V. Sarana
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Sergey A. Lednev
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | | | - Mikhail S. Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Pavel P. Krechetov
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | - Tatiana V. Koroleva
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| |
Collapse
|
17
|
Huang L, Ye J, Jiang K, Wang Y, Li Y. Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112740. [PMID: 34482066 DOI: 10.1016/j.ecoenv.2021.112740] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/12/2021] [Accepted: 08/30/2021] [Indexed: 05/16/2023]
Abstract
The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.
Collapse
Affiliation(s)
- Liping Huang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jiangyu Ye
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Kemei Jiang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yichao Wang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yunyi Li
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| |
Collapse
|
18
|
Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic. Sci Rep 2021; 11:19620. [PMID: 34608182 PMCID: PMC8490368 DOI: 10.1038/s41598-021-98680-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
The present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria-Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella-and fungi-Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Zhong X, Cui P, Jiang J, Ning C, Liang B, Zhou J, Tian L, Zhang Y, Lei T, Zuo T, Ye L, Huang J, Chen H. Streptococcus, the Predominant Bacterium to Predict the Severity of Liver Injury in Alcoholic Liver Disease. Front Cell Infect Microbiol 2021; 11:649060. [PMID: 33816353 PMCID: PMC8010180 DOI: 10.3389/fcimb.2021.649060] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/01/2021] [Indexed: 12/20/2022] Open
Abstract
Background New evidence implies that the imbalance of gut microbiota is associated with the progression of alcoholic liver disease (ALD) and that the composition of gut microbiota is altered in ALD patients. However, the predominant bacterium in patients involved in the progress of ALD has not been identified. The purpose of this study is to investigate the predominant bacterium in the early and end-stages of ALD as well as the relationship between the bacterium and the degree of liver injury. Methods We enrolled 21 alcoholic fatty liver (AFL) patients, 17 alcoholic liver cirrhosis (ALC) patients and 27 healthy controls, and sequenced the 16S rRNA gene of their fecal microbiota. The gut microbiota composition and its relationship with the indicators of clinical hepatic function were assessed using canonical correspondence analysis (CCA), spearman correlation heatmap and multivariate association with linear (MaAsLin) Models. Results The composition and structure of gut microbiota changed greatly in different stages of ALD, and the degree of disorder was aggravated with the progression of ALD, even in the early stage. Moreover, the relative abundance of Streptococcus was highly enriched only in patients with ALC (P <0.001), and positively correlated with AST level (P = 0.029). The abundance of Streptococcus distinguished the liver injury of ALC patients from the controls with an area under the receiver-operating characteristic curve (AUC) of 0.877 (P < 0.001). Conclusions These findings indicate that the imbalance of gut microbiota exists at the early and end-stages of ALD, and the degree of disorder is aggravated with the progression of ALD. Streptococcus, as the predominant bacterium, may be a microbiological marker to evaluate the severity of liver injury in ALD patients.
Collapse
Affiliation(s)
- Xiaodan Zhong
- Geriatrics Digestion Department of Internal Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Life Science Institute, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Nursing College, Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Li Tian
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Ting Lei
- Geriatrics Digestion Department of Internal Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Taiping Zuo
- Geriatrics Digestion Department of Internal Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Hui Chen
- Geriatrics Digestion Department of Internal Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| |
Collapse
|
21
|
Zhang X, Ji Z, Shao Y, Guo C, Zhou H, Liu L, Qu Y. Seasonal variations of soil bacterial communities in Suaeda wetland of Shuangtaizi River estuary, Northeast China. J Environ Sci (China) 2020; 97:45-53. [PMID: 32933739 DOI: 10.1016/j.jes.2020.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Estuarine wetland is the transitional interface linking terrestrial with marine ecosystems, and wetland microbes are crucial to the biogeochemical cycles of nutrients. The soil samples were collected in four seasons (spring, S1; summer, S2; autumn, S3; and winter, S4) from Suaeda wetland of Shuangtaizi River estuary, Northeast China, and the variations of bacterial community were evaluated by high-throughput sequencing. Soil properties presented a significant seasonal change, including pH, carbon (C) and total nitrogen (TN), and the microbial diversity, richness and structure also differed with seasons. Canonical correspondence analysis (CCA) and Mantel tests implied that soil pH, C and TN were the key factors structuring the microbial community. Gillisia (belonging to Bacteroidetes) and Woeseia (affiliating with Gammaproteobacteria) were the two primary components in the rhizosphere soils, displaying opposite variations with seasons. Based on PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) prediction, the xenobiotics biodegradation related genes exhibited a seasonal decline, while the majority of biomarker genes involved in nitrogen cycle showed an ascending trend. These findings could advance the understanding of rhizosphere microbiota of Suaeda in estuarine wetland.
Collapse
Affiliation(s)
- Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China.
| | - Zhe Ji
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Yating Shao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Chaochen Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Lifen Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
22
|
de Siqueira GMV, Silva-Rocha R, Guazzaroni ME. Turning the Screw: Engineering Extreme pH Resistance in Escherichia coli through Combinatorial Synthetic Operons. ACS Synth Biol 2020; 9:1254-1262. [PMID: 32438805 DOI: 10.1021/acssynbio.0c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh conditions, usually very distant from those in which these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different industrial appplications. In this work, synthetic biology approaches were used to engineer enhanced acidic resistance in Escherichia coli through the characterization of a collection of unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for resistance in synthetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.
Collapse
Affiliation(s)
- Guilherme M. V. de Siqueira
- Departamento de Bioquı́mica, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - Rafael Silva-Rocha
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP 14040-901, Brasil
| |
Collapse
|
23
|
Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
Collapse
|
24
|
Bhardwaj P, Singh KR, Jadeja NB, Phale PS, Kapley A. Atrazine Bioremediation and Its Influence on Soil Microbial Diversity by Metagenomics Analysis. Indian J Microbiol 2020; 60:388-391. [PMID: 32647398 DOI: 10.1007/s12088-020-00877-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/28/2020] [Indexed: 01/10/2023] Open
Abstract
Pesticide accumulation in agricultural soils is an environmental concern, often addressed through distinct bioremediation strategies. This study has tried to analyze various soil bioremediation options viz., biostimulation, bioaugmentation, and natural attenuation in terms of efficiency and the response of autochthonous microbial flora by using atrazine as a model contaminant. Soil mesocosms were established with 100 kg of soil simulating the field conditions. The soil previously exposed to the herbicide was used for the bioaugmentation strategy undertaken in this study. We have tried to analyze how the microbial community responds to a foreign compound, both in terms of taxonomic and functional capacities? To answer this, we have analyzed metagenome of the mesocosms at a time point when 90% atrazine was degraded. Bioaugmentation for bioremediation proved to be efficient with a DT90 value of 15.48 ± 0.79 days, in comparison to the natural attenuation where the DT90 value was observed to be 41.20 ± 1.95 days. Metagenomic analysis revealed the abundance of orders Erysipelotrichales, Selemonadales, Clostridiales, and Thermoanaerobacterales exclusively in SBS mesocosm. Besides Pseudomonas, bacterial genera such as Achromobacter, Xanthomonas, Stenotrophomonas, and Cupriavidus have emerged as the dominant members in various bioremediation strategies tested in this study. Inclusive results suggest that inherent microbial flora adjust their community and metabolic machinery upon exposure to the pollutant. The site under pollutant stress showed efficient microbial communities to bio-remediate the newly polluted terrestrial ecologies in relatively less time and by economic means.
Collapse
Affiliation(s)
- Pooja Bhardwaj
- Director's Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Kunvar Ravendra Singh
- Director's Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Niti B Jadeja
- Director's Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Prashant S Phale
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India
| | - Atya Kapley
- Director's Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| |
Collapse
|
25
|
Hidalgo KJ, Teramoto EH, Soriano AU, Valoni E, Baessa MP, Richnow HH, Vogt C, Chang HK, Oliveira VM. Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135152. [PMID: 31812384 DOI: 10.1016/j.scitotenv.2019.135152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.
Collapse
Affiliation(s)
- K J Hidalgo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, Campinas, SP. ZIP 13083-862, Brazil.
| | - E H Teramoto
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - A U Soriano
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - E Valoni
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - M P Baessa
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - H H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - C Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - H K Chang
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Paulínia, Brazil, Av. Alexandre Cazellato, 999, ZIP 13148-218, Brazil
| |
Collapse
|
26
|
Patel VR, Khan R, Bhatt N. Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils. CHEMOSPHERE 2020; 243:125253. [PMID: 31733540 DOI: 10.1016/j.chemosphere.2019.125253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Dyes & dyes intermediates are one of the important and critically polluted industrial sectors, generating a large environmental liability. Therefore characterization of microbial community structure and diversity of contaminated soils helps to optimize the bioremediation strategies and performance. This study investigated the roles of environmental variables and contamination levels in shaping microbial community structure at an abandoned aged. In total, 20 bacterial and 4 fungal phyla were identified across soils with different physiochemical properties and concentration of the contaminants. Taxonomic analysis revealed the Proteobacteria, Firmicutes, Ascomycota and Basidiomycota represented the lineages and accounted for 49.5%-51.2%, 5.1%-15.3%, 2.5%-3.8% and 1.6%-2.1% of the total population, respectively. Microbial community (site 1) achieved decolorization rate of 972 ± 1.21 mg dyes kgsoil-1d-1 after 15d and 692 ± 1.4 mg kg-soil-1d-1 COD removal rate after 30 day of the experiment. Microbial community mineralized intermediates, 4-amino benzenesulfonate, 6-amino naphthalene sulfonate and benzene/naphthalene sulfonate in TCA cycle and stimulate the growth of selected soil bacteria, primary nutrient as well as plant growth of contaminated soil.
Collapse
Affiliation(s)
- Vipul R Patel
- Department of Microbiology, Gujarat Vidyapeeth, SADRA, 382320, Dist: Gandhinagar, Gujarat, India.
| | - Razia Khan
- Girish Raval College of Science, Chiloda, Gujarat, 382355, India
| | - Nikhil Bhatt
- Department of Microbiology, Gujarat Vidyapeeth, SADRA, 382320, Dist: Gandhinagar, Gujarat, India
| |
Collapse
|
27
|
Wu M, Wu J, Zhang X, Ye X. Effect of bioaugmentation and biostimulation on hydrocarbon degradation and microbial community composition in petroleum-contaminated loessal soil. CHEMOSPHERE 2019; 237:124456. [PMID: 31376701 DOI: 10.1016/j.chemosphere.2019.124456] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/24/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
This study assessed the benefits of biostimulation with nitrogen and phosphorous (BS) versus bioaugmentation with native petroleum degrading flora (BA) in terms of petroleum hydrocarbon removal and microbial community structure shift in petroleum-polluted loessal soil. After 12 weeks of remediation, the TPH degradation efficiencies were 28.3% and 13.9% in BS and BA treated soils, respectively. Biostimulation was more effective than bioaugmentation for petroleum hydrocarbon degradation. Soil microbial community composition changed while microbial diversity decreased greatly by bioaugmentation treatment. The inoculum could survive, grow up quickly and become the predominant microorganisms after one week of inoculation. In the biostimulation treatment, microbial community composition is more evenness and richness than in the bioaugmented remediation. The strong positive correlations of the nitrogen and phosphorus with the petroleum hydrocarbon suggest the importance of nutrients for petroleum biodegradation in the contaminated loessal soil. The results indicate that the stabilization and variety of the microbial community structure are essential for the petroleum biodegradation performance. Further engineering is suggested to improve the evenness and richness of the soil microbial community since an abundance of nitrogen and phosphorus nutrients ensures the degraders' activity in the petroleum polluted soil.
Collapse
Affiliation(s)
- Manli Wu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
| | - Jialuo Wu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Xiaohui Zhang
- Exploration and Development Research Institute of Changqing Oilfield Company, PetroChina, Xi'an, 710018, People's Republic of China
| | - Xiqiong Ye
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| |
Collapse
|
28
|
Costessi A, van den Bogert B, May A, Ver Loren van Themaat E, Roubos JA, Kolkman MAB, Butler D, Pirovano W. Novel sequencing technologies to support industrial biotechnology. FEMS Microbiol Lett 2019; 365:4982775. [PMID: 30010862 DOI: 10.1093/femsle/fny103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/19/2018] [Indexed: 12/11/2022] Open
Abstract
Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and processing to bio-based chemicals, biofuels and pharmaceutical products. Next generation DNA sequencing technologies play an increasingly important role in improving and accelerating microbial strain development for existing and novel bio-products via screening, gene and pathway discovery, metabolic engineering and additional optimization and understanding of large-scale manufacturing. In this mini-review, we describe novel DNA sequencing and analysis technologies with a focus on applications to industrial strain development, enzyme discovery and microbial community analysis.
Collapse
Affiliation(s)
- Adalberto Costessi
- Next Generation Sequencing Department, BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, The Netherlands
| | | | - Ali May
- Bioinformatics Department, BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, The Netherlands
| | | | - Johannes A Roubos
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2600 MA, Delft, The Netherlands
| | - Marc A B Kolkman
- Division of Industrial Biosciences, DuPont, Archimedesweg 30, 2300 AE, Leiden, The Netherlands
| | - Derek Butler
- Bianomics Business Unit, BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, The Netherlands
| | - Walter Pirovano
- Bioinformatics Department, BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, The Netherlands
| |
Collapse
|
29
|
Comparative metagenomics and functional profiling of crude oil-polluted soils in Bodo West Community, Ogoni, with other sites of varying pollution history. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1438-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
30
|
Siles JA, Margesin R. Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site. Appl Microbiol Biotechnol 2018; 102:4409-4421. [PMID: 29594357 PMCID: PMC5932094 DOI: 10.1007/s00253-018-8932-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 11/26/2022]
Abstract
The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.
Collapse
Affiliation(s)
- José A Siles
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
| |
Collapse
|
31
|
Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A, Sharma VK. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Front Microbiol 2017; 7:2123. [PMID: 28105025 PMCID: PMC5214690 DOI: 10.3389/fmicb.2016.02123] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022] Open
Abstract
Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together, the results of this study reveal a novel consortium of microbes, genes, and pathways associated with the hot spring environment.
Collapse
Affiliation(s)
- Rituja Saxena
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Darshan B Dhakan
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Parul Mittal
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Prashant Waiker
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Anirban Chowdhury
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Arundhuti Ghatak
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| |
Collapse
|