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Yu KL, Shen S. Could intratumoural microbiota be key to unlocking treatment responses in hepatocellular carcinoma? Eur J Cancer 2025; 216:115195. [PMID: 39729679 DOI: 10.1016/j.ejca.2024.115195] [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: 09/29/2024] [Revised: 12/12/2024] [Accepted: 12/18/2024] [Indexed: 12/29/2024]
Abstract
Hepatocellular carcinoma (HCC) is the third cause of cancer-related mortality worldwide. Current treatments include surgery and immunotherapy with variable response. Despite aggressive treatment, disease progression remains the biggest contributor to mortality. Thus, there is an urgent unmet need to improve current treatments through a better understanding of HCC tumourigenesis. The gut microbiota has been intensively examined in the context of HCC, with evidence showing gut modulation has the potential to modulate tumourigenesis and prognosis. In addition, recent literature suggests the presence of an intratumoural microbiota that may exert significant impacts on the development of solid tumours including HCC. By drawing parallels between the gut and hepatic/tumoural microbiota, we explore in the present review how the hepatic microbiota is established, its impact on tumourigenesis, and how modulation of the gut and hepatic microbiota may be key to improving current treatments of HCC. In particular, we highlight key bacteria that have been discovered in HCC tumours, and how they may affect the tumour immune microenvironment and HCC tumourigenesis. We then explore current therapies that target the intratumoural microbiota. With a deeper understanding of how the intratumoural microbiota is established, how different bacteria may be involved in HCC tumourigenesis, and how they can be targeted, we hope to spark future research in validating intratumoural microbiota as an avenue for improving treatment responses in HCC.
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Affiliation(s)
- Kin Lam Yu
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, Australia
| | - Sj Shen
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Kogarah, NSW, Australia.
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2
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Bonilla-Espadas M, Zafrilla B, Lifante-Martínez I, Camacho M, Orgilés-Calpena E, Arán-Aís F, Bertazzo M, Bonete MJ. Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications. Microorganisms 2024; 12:1029. [PMID: 38792858 PMCID: PMC11124520 DOI: 10.3390/microorganisms12051029] [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: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.
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Affiliation(s)
- Manuela Bonilla-Espadas
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Basilio Zafrilla
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Irene Lifante-Martínez
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Mónica Camacho
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Elena Orgilés-Calpena
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Francisca Arán-Aís
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Marcelo Bertazzo
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - María-José Bonete
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
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3
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Liu Q, Wang Y, Sun S, Tang F, Chen H, Chen S, Zhao C, Li L. A novel chitosan-biochar immobilized microorganism strategy to enhance bioremediation of crude oil in soil. CHEMOSPHERE 2023; 313:137367. [PMID: 36427578 DOI: 10.1016/j.chemosphere.2022.137367] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
The chitosan-biochar composite is a clean and environmentally friendly immobilized microorganisms carrier. In this study, the chitosan-biochar composite as a carrier to immobilize a compound microbial agent contained Pseudomonas aeruginosa and Bacillus licheniformis, and investigated its role in the remediation of oil-contaminated soil. When using 1% (v/v) acetic acid, 3% (m/v) chitosan solution, 0.1% biochar, 4% (v/v) NaOH solution, freeze-drying 6 h, the optimal chitosan-biochar composite material could be obtained. The specific surfacearea of the material increased to 1.725 m2/g and the average pore size also increased from 130.2260 nm to 165.2980 nm after the addition of biochar through the analysis of specific surface area and pore size, which enlarged the contact area of microorganisms and crude oil with the material. SEM showed that the bacterial successfully adhered to the surface and internal of the material. Using FTIR, the results showed that the synthesis of composite carrier material was the covalent combination of -NH2 on chitosan and -COOH on biochar, forming a new chemical bond -NH-CO-. After 60 days of remediation of oil-contaminated soil, the removal rate of crude oil by chitosan-biochar composite immobilized microorganism method was 45.82%, which was 21.26% higher than that of natural remediation. Simultaneously, several oil-degrading bacteria increased at genus level, including Nocardioides (26.79%-33.09%), Bacillus (3.01%-4.10%), Dietzia (1.84%-5.56%), Pseudomonas (0-0.78%), among which Pseudomonas belongs to exogenous bacteria. The results indicated that the chitosan-biochar composite material has high application value in removing crude oil, and further provides a new strategy for bioremediation of oil-contaminated soil.
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Affiliation(s)
- Qiyou Liu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China.
| | - Yaru Wang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Shuo Sun
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Fang Tang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Hongxu Chen
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Shuiquan Chen
- College of Energy and Mining Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China
| | - Chaocheng Zhao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Lin Li
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China
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4
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Muthukumar B, Parthipan P, AlSalhi MS, Prabhu NS, Rao TN, Devanesan S, Maruthamuthu MK, Rajasekar A. Characterization of bacterial community in oil-contaminated soil and its biodegradation efficiency of high molecular weight (>C40) hydrocarbon. CHEMOSPHERE 2022; 289:133168. [PMID: 34890617 DOI: 10.1016/j.chemosphere.2021.133168] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
In this study, two biosurfactant producing Pseudomonas aeruginosa sp. were isolated from motor oil contaminated soil for crude oil, alkane and PAH degradation studies. Metagenomics analysis identified as proteobacteria phyla was the dominant. Isolated two bacterial species were well grown in mineral salt medium with 1% of crude oil, alkanes (dotriacontane and tetratetracontane) and PAH (pyrene, benzopyrene and anthracene) as sole carbon sources. Total biodegradation efficiency (BE) of strains PP3 and PP4 in Crude oil degradation evaluated by the analysis of gas chromatography and mass spectrometry was 50% and 86% respectively. BE of PP3, PP4 and mixed consortium in alkane biodegradation were 46%, 47% and 36%, respectively. BE of PP3, PP4 and mixed consortium in PAH biodegradation were 22%, 48% and 35%, respectively. Based on the results revealed that strain pp4 was more efficient bacteria to degrade the crude oil, alkane and PAH than pp3. This was due to the higher production of biosurfactant by PP4 than PP3 and also confirmed in the test of emulsification index (E24). FTIR results showed that the produced biosurfactant could partially solubilize the crude oil hydrocarbons, alkanes and PAH and confirmed as glycolipid (rhamnolipid) in nature. Thus, the obtained results from the GCMS showed that all hydrocarbons were utilized by bacteria as carbon source for biosurfactant production and utilize the high molecular weight hydrocarbons. Based on the present study we can suggest that identified potential biosurfactant producing bacteria are used for biodegradation of high molecular weight hydrocarbon (>C40).
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Affiliation(s)
- Balakrishnan Muthukumar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India
| | - Punniyakotti Parthipan
- Electro-Materials Research Laboratory, Centre for Nanoscience and Technology, Pondicherry University, Puducherry, 605014, India
| | - Mohamad S AlSalhi
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box-2455, Riyadh, 11451, Saudi Arabia
| | - Natarajan Srinivasa Prabhu
- Department of Biotechnology and Genetic Engineering, Bharathidasan University, Palkalaiperur, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - T Nageswara Rao
- Department of Chemistry, Krishna University, Machilipatnam, AP, 521001, India
| | - Sandhanasamy Devanesan
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box-2455, Riyadh, 11451, Saudi Arabia
| | - Murali Kannan Maruthamuthu
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, NC, United States
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India.
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Grewal J, Woła̧cewicz M, Pyter W, Joshi N, Drewniak L, Pranaw K. Colorful Treasure From Agro-Industrial Wastes: A Sustainable Chassis for Microbial Pigment Production. Front Microbiol 2022; 13:832918. [PMID: 35173704 PMCID: PMC8841802 DOI: 10.3389/fmicb.2022.832918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Colors with their attractive appeal have been an integral part of human lives and the easy cascade of chemical catalysis enables fast, bulk production of these synthetic colorants with low costs. However, the resulting hazardous impacts on the environment and human health has stimulated an interest in natural pigments as a safe and ecologically clean alternative. Amidst sources of natural producers, the microbes with their diversity, ease of all-season production and peculiar bioactivities are attractive entities for industrial production of these marketable natural colorants. Further, in line with circular bioeconomy and environmentally clean technologies, the use of agro-industrial wastes as feedstocks for carrying out the microbial transformations paves way for sustainable and cost-effective production of these valuable secondary metabolites with simultaneous waste management. The present review aims to comprehensively cover the current green workflow of microbial colorant production by encompassing the potency of waste feedstocks and fermentation technologies. The commercially important pigments viz. astaxanthin, prodigiosin, canthaxanthin, lycopene, and β-carotene produced by native and engineered bacterial, fungal, or yeast strains have been elaborately discussed with their versatile applications in food, pharmaceuticals, textiles, cosmetics, etc. The limitations and their economic viability to meet the future market demands have been envisaged. The most recent advances in various molecular approaches to develop engineered microbiological systems for enhanced pigment production have been included to provide new perspectives to this burgeoning field of research.
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Affiliation(s)
| | | | | | | | | | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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6
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Crippen TL, Singh B, Anderson RC, Sheffield CL. Adult Alphitobius diaperinus Microbial Community during Broiler Production and in Spent Litter after Stockpiling. Microorganisms 2022; 10:microorganisms10010175. [PMID: 35056628 PMCID: PMC8778262 DOI: 10.3390/microorganisms10010175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 12/10/2022] Open
Abstract
The facilities used to raise broiler chickens are often infested with litter beetles (lesser mealworm, Alphitobius diaperinus). These beetles have been studied for their carriage of pathogenic microbes; however, a more comprehensive microbiome study on these arthropods is lacking. This study investigated their microbial community in a longitudinal study throughout 2.5 years of poultry production and after the spent litter, containing the mealworms, was piled in pastureland for use as fertilizer. The mean most abundant phyla harbored by the beetles in house were the Proteobacteria (39.8%), then Firmicutes (30.8%), Actinobacteria (21.1%), Tenericutes (5.1%), and Bacteroidetes (1.6%). The community showed a modest decrease in Firmicutes and increase in Proteobacteria over successive flock rotations. The beetles were relocated within the spent litter to pastureland, where they were found at least 19 weeks later. Over time in the pastureland, their microbial profile underwent a large decrease in the percent of Firmicutes (20.5%). The lesser mealworm showed an ability to survive long-term in the open environment within the spent litter, where their microbiome should be further assessed to both reduce the risk of transferring harmful bacteria, as well as to enhance their contribution when the litter is used as a fertilizer.
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Affiliation(s)
- Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX 77845, USA; (R.C.A.); (C.L.S.)
- Correspondence:
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Robin C. Anderson
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX 77845, USA; (R.C.A.); (C.L.S.)
| | - Cynthia L. Sheffield
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX 77845, USA; (R.C.A.); (C.L.S.)
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Characterization of Dietzia maris AURCCBT01 from oil-contaminated soil for biodegradation of crude oil. 3 Biotech 2021; 11:291. [PMID: 34109094 DOI: 10.1007/s13205-021-02807-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
A bacterial strain was isolated from an oil-contaminated site and on its' further characterization, exhibited the potential of synthesising metabolites and the ability to degrade crude oil. Its' morphological, biochemical and 16S rRNA analysis suggested that the bacterium belongs to Dietzia maris AURCCBT01. This strain rapidly grew in the medium supplemented with n-alkanes C14, C18, C20, C28 and C32 utilizing them as a sole carbon source and produced a maximum canthaxanthin pigment of 971.37 µg/L in the n-C14 supplemented medium and produced the lowest pigment yield of 389.48 µg/L in the n-C-32 supplemented medium. Moreover, the strain effectively degraded 91.87% of crude oil in 7 days. The emulsification activity of the strain was 25% with the highest cell surface hydrophobicity (70.26%) and it showed a decrease in surface tension, indicating that the biosurfactant production lowers the surface tension. This is the first report on the characterization of the strain, Dietzia maris AURCCBT01 and its' novelty of alkane degradation and simultaneous production of canthaxanthin pigment. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02807-7.
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Hu B, Wang M, Geng S, Wen L, Wu M, Nie Y, Tang YQ, Wu XL. Metabolic Exchange with Non-Alkane-Consuming Pseudomonas stutzeri SLG510A3-8 Improves n-Alkane Biodegradation by the Alkane Degrader Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2020; 86:AEM.02931-19. [PMID: 32033953 PMCID: PMC7117941 DOI: 10.1128/aem.02931-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Biodegradation of alkanes by microbial communities is ubiquitous in nature. Interestingly, the microbial communities with high hydrocarbon-degrading performances are sometimes composed of not only hydrocarbon degraders but also nonconsumers, but the synergistic mechanisms remain unknown. Here, we found that two bacterial strains isolated from Chinese oil fields, Dietzia sp. strain DQ12-45-1b and Pseudomonas stutzeri SLG510A3-8, had a synergistic effect on hexadecane (C16 compound) biodegradation, even though P. stutzeri could not utilize C16 individually. To gain a better understanding of the roles of the alkane nonconsumer P. stutzeri in the C16-degrading consortium, we reconstructed a two-species stoichiometric metabolic model, iBH1908, and integrated in silico prediction with the following in vitro validation, a comparative proteomics analysis, and extracellular metabolomic detection. Metabolic interactions between P. stutzeri and Dietzia sp. were successfully revealed to have importance in efficient C16 degradation. In the process, P. stutzeri survived on C16 metabolic intermediates from Dietzia sp., including hexadecanoate, 3-hydroxybutanoate, and α-ketoglutarate. In return, P. stutzeri reorganized its metabolic flux distribution to fed back acetate and glutamate to Dietzia sp. to enhance its C16 degradation efficiency by improving Dietzia cell accumulation and by regulating the expression of Dietzia succinate dehydrogenase. By using the synergistic microbial consortium of Dietzia sp. and P. stutzeri with the addition of the in silico-predicted key exchanged metabolites, diesel oil was effectively disposed of in 15 days with a removal fraction of 85.54% ± 6.42%, leaving small amounts of C15 to C20 isomers. Our finding provides a novel microbial assembling mode for efficient bioremediation or chemical production in the future.IMPORTANCE Many natural and synthetic microbial communities are composed of not only species whose biological properties are consistent with their corresponding communities but also ones whose chemophysical characteristics do not directly contribute to the performance of their communities. Even though the latter species are often essential to the microbial communities, their roles are unclear. Here, by investigation of an artificial two-member microbial consortium in n-alkane biodegradation, we showed that the microbial member without the n-alkane-degrading capability had a cross-feeding interaction with and metabolic regulation to the leading member for the synergistic n-alkane biodegradation. Our study improves the current understanding of microbial interactions. Because "assistant" microbes showed importance in communities in addition to the functional microbes, our findings also suggest a useful "assistant-microbe" principle in the design of microbial communities for either bioremediation or chemical production.
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Affiliation(s)
- Bing Hu
- Institute for Synthetic Biosystems, Department of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, People's Republic of China
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Miaoxiao Wang
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Shuang Geng
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Liqun Wen
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Mengdi Wu
- School of Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yong Nie
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Yue-Qin Tang
- Department of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
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Schlatter DC, Paul NC, Shah DH, Schillinger WF, Bary AI, Sharratt B, Paulitz TC. Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat. MICROBIAL ECOLOGY 2019; 78:737-752. [PMID: 30796467 DOI: 10.1007/s00248-019-01339-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
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Affiliation(s)
- Daniel C Schlatter
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Narayan C Paul
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Andy I Bary
- Puyallup Research and Extension Center, Washington State University, Puyallup, WA, 98371, USA
| | - Brenton Sharratt
- Northwest Sustainable Agroecosystems Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Timothy C Paulitz
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA.
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10
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Rezaei Somee M, Shavandi M, Dastgheib SMM, Amoozegar MA. Bioremediation of oil-based drill cuttings by a halophilic consortium isolated from oil-contaminated saline soil. 3 Biotech 2018; 8:229. [PMID: 29719771 PMCID: PMC5924431 DOI: 10.1007/s13205-018-1261-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 04/24/2018] [Indexed: 10/17/2022] Open
Abstract
Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter, and Halomonas. DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter, and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus, and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.
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Affiliation(s)
- Maryam Rezaei Somee
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - Mahmoud Shavandi
- Biotechnology Research Center, Research Institute of Petroleum Industry, Tehran, Iran
| | | | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
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Gurav R, Lyu H, Ma J, Tang J, Liu Q, Zhang H. Degradation of n-alkanes and PAHs from the heavy crude oil using salt-tolerant bacterial consortia and analysis of their catabolic genes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:11392-11403. [PMID: 28315056 DOI: 10.1007/s11356-017-8446-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
In the present study, salt-tolerant strains, Dietzia sp. HRJ2, Corynebacterium variabile HRJ4, Dietzia cinnamea HRJ5 and Bacillus tequilensis HRJ6 were isolated from the Dagang oil field, China. These strains degraded n-alkanes and polycyclic aromatic hydrocarbons (PAHs) aerobically from heavy crude oil (HCO) in an experiment at 37 °C and 140 rpm. The GC/MS investigation for degradation of different chain lengths of n-alkanes (C8-C40) by individual strains showed the highest degradation of C8-C19 (HRJ5), C20-C30 (HRJ4) and C31-C40 (HRJ5), respectively. Moreover, degradation of 16 PAHs with individual strains demonstrated that the bicyclic and pentacyclic aromatic hydrocarbons (AHs) were mostly degraded by HRJ5, tricyclic and tetracyclic AHs by HRJ6 and hexacyclic AHs by HRJ2. However, the highest degradation of total petroleum hydrocarbons (TPHs), total saturated hydrocarbons (TSH), total aromatic hydrocarbons (TAH), n-alkanes (C8-C40) and 16 PAHs was achieved by a four-membered consortium (HRJ2 + 4 + 5 + 6) within 12 days, with the predominance of HRJ4 and HRJ6 strains which was confirmed by denaturing gradient gel electrophoresis. The abundance of alkB and nah genes responsible for catabolism of n-alkanes and PAHs was quantified using the qPCR. Maximum copy numbers of genes were observed in HRJ2 + 4 + 5 + 6 consortium (gene copies l-1) 2.53 × 104 (alkB) and 3.47 × 103 (nah) at 12 days, which corresponded to higher degradation rates of petroleum hydrocarbons. The superoxide dismutase (SOD) (total SOD (T-SOD), Cu2+Zn2+-SOD), catalase (CAT) and ascorbate peroxidase (APX) activities in Allium sativum and Triticum aestivum were lower in the HRJ2 + 4 + 5 + 6-treated HCO as compared to the plantlets exposed directly to HCO. The present results revealed the effective degradation of HCO-contaminated saline medium using the microbial consortium having greater metabolic diversity.
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Affiliation(s)
- Ranjit Gurav
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Centre of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Honghong Lyu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Centre of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Jianli Ma
- Tianjin Academy of Environmental Sciences, Tianjin, 300191, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Centre of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Qinglong Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Centre of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Hairong Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Centre of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
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Kavynifard A, Ebrahimipour G, Ghasempour A. Optimization of crude oil degradation by Dietzia cinnamea KA1, capable of biosurfactant production. J Basic Microbiol 2015; 56:566-75. [PMID: 26615815 DOI: 10.1002/jobm.201500386] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/11/2015] [Indexed: 11/07/2022]
Abstract
The aim of this study was isolation and characterization of a crude oil degrader and biosurfactant-producing bacterium, along with optimization of conditions for crude oil degradation. Among 11 isolates, 5 were able to emulsify crude oil in Minimal Salt Medium (MSM) among which one isolate, named KA1, showed the highest potency for growth rate and biodegradation. The isolate was identified as Dietzia cinnamea KA1 using morphological and biochemical characteristics and 16S rRNA gene sequencing. The optimal conditions were 510 mM NaCl, pH 9.0, 35 °C, and minimal requirement of 46.5 mM NH4 Cl and 2.10 mM NaH2 PO4 . Gravimetric test and Gas chromatography-Mass spectroscopy technique (GC-MS) showed that Dietzia cinnamea KA1 was able to utilize and degrade 95.7% of the crude oil after 5 days, under the optimal conditions. The isolate was able to grow and produce biosurfactant when cultured in MSM supplemented with crude oil, glycerol or whey as the sole carbon sources, but bacterial growth was occurred using molasses with no biosurfactant production. This is the first report of biosurfactant production by D. cinnamea using crude oil, glycerol and whey and the first study to report a species of Dietzia degrading a wide range of hydrocarbons in a short time.
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Affiliation(s)
- Amirarsalan Kavynifard
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | | | - Alireza Ghasempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
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Gharibzahedi S, Razavi S, Mousavi M. Optimisation and kinetic studies on the production of intracellular canthaxanthin in fed-batch cultures of Dietzia natronolimnaea HS-1. QUALITY ASSURANCE AND SAFETY OF CROPS & FOODS 2015. [DOI: 10.3920/qas2014.0503] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- S.M.T. Gharibzahedi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
| | - S.H. Razavi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
| | - M. Mousavi
- Center of Excellence for Application of Modern Technologies for Producing Functional Foods and Drinks and Bioprocess Engineering Laboratory (BPEL), Department of Food Science, Engineering & Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, P.O. Box 4111, Karaj 31587-77871, Iran
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Gao X, Gao W, Cui Z, Han B, Yang P, Sun C, Zheng L. Biodiversity and degradation potential of oil-degrading bacteria isolated from deep-sea sediments of South Mid-Atlantic Ridge. MARINE POLLUTION BULLETIN 2015; 97:373-380. [PMID: 26077158 DOI: 10.1016/j.marpolbul.2015.05.065] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 06/04/2023]
Abstract
The indigenous oil-degrading bacterial consortia MARA and MARB were enriched from the deep-sea sediments of South Mid-Atlantic Ridge (MAR) with crude oil as sole carbon and energy sources. Biodiversity and community analyses showed that members of α-Proteobacteria were the key players in consortium MARA, whereas those of γ-Proteobacteria were the key players in consortium MARB, which were studied by MiSeq sequencing method. Gravimetric method estimated the oil degradation rates of MARA and MARB to be 63.4% and 85.8%, respectively, after 20d. Eleven cultivable oil degraders with different morphologies were isolated. These strains were identified as Alcanivorax, Bacillus, Dietzia, Erythrobacter, Marinobacter, Nitratireductor, and Oceanicola based on 16S rRNA gene sequences. Three strains belonging to Dietzia exhibited the highest oil degradation capability. Results indicated that the intrinsic biodegradation capacity of oil contaminants by indigenous microbial communities exists in South MAR sediments.
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Affiliation(s)
- Xiangxing Gao
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China
| | - Wei Gao
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China; College of Marine life, Ocean University of China, Qingdao, China
| | - Zhisong Cui
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China
| | - Bin Han
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China
| | - Peihua Yang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chengjun Sun
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China
| | - Li Zheng
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, China.
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