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A D, Zhang Y, Huang H, Pan Y, Di HJ, Yi Y, Zhang X, Yang J. Unraveling the mechanism of interaction: accelerated phenanthrene degradation and rhizosphere biofilm/iron plaque formation influenced by phenolic root exudates. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:35853-35863. [PMID: 38743334 DOI: 10.1007/s11356-024-33349-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
Phenolic root exudates (PREs) secreted by wetland plants facilitate the accumulation of iron in the rhizosphere, potentially providing the essential active iron required for the generation of enzymes that degrade polycyclic aromatic hydrocarbon, thereby enhancing their biodegradation. However, the underlying mechanisms involved are yet to be elucidated. This study focuses on phenanthrene (PHE), a typical polycyclic aromatic hydrocarbon pollutant, utilizing representative PREs from wetland plants, including p-hydroxybenzoic, p-coumaric, caffeic, and ferulic acids. Using hydroponic experiments, 16S rRNA sequencing, and multiple characterization techniques, we aimed to elucidate the interaction mechanism between the accelerated degradation of PHE and the formation of rhizosphere biofilm/iron plaque influenced by PREs. Although all four types of PREs altered the biofilm composition and promoted the formation of iron plaque on the root surface, only caffeic acid, possessing a similar structure to the intermediate metabolite of PHE (catechol), could accelerate the PHE degradation rate. Caffeic acid, notable for its catechol structure, plays a significant role in enhancing PHE degradation through two main mechanisms: (a) it directly boosts PHE co-metabolism by fostering the growth of PHE-degrading bacteria, specifically Burkholderiaceae, and by facilitating the production of the key metabolic enzyme catechol 1,2-dioxygenase (C12O) and (b) it indirectly supports PHE biodegradation by promoting iron plaque formation on root surfaces, thereby enriching free iron for efficient microbial synthesis of C12O, a crucial factor in PHE decomposition.
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Affiliation(s)
- Dan A
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Yifei Zhang
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Hanjie Huang
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yuan Pan
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Yunqiang Yi
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaomeng Zhang
- Department of Ecology, Jinan University, Guangzhou, 510632, China.
| | - Jiewen Yang
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
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Zou H, He J, Chu Y, Xu B, Li W, Huang S, Guan X, Liu F, Li H. Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133139. [PMID: 38056273 DOI: 10.1016/j.jhazmat.2023.133139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/31/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 μg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.
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Affiliation(s)
- Hua Zou
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Jiangtao He
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China.
| | - Yanjia Chu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Baoshi Xu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Wei Li
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Shiwen Huang
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Xiangyu Guan
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Haiyan Li
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Wang J, Zhang Y, Liu T, Shi Y, Ding Y, Zhang Y, Xu W, Zhang X, Wang Y, Li D. A biodegradable chitosan-based polymer for sustained nutrient release to stimulate groundwater hydrocarbon-degrading microflora. CHEMOSPHERE 2023; 344:140346. [PMID: 37832890 DOI: 10.1016/j.chemosphere.2023.140346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023]
Abstract
Petroleum hydrocarbon-contaminated groundwater often has a low indigenous microorganism population and lacks the necessary nutrient substrates for biodegradation reaction, resulting in a weak natural remediation ability within the groundwater ecosystem. In this paper, we utilized the principle of petroleum hydrocarbon degradation by microorganisms to identify effective nutrients (NaH2PO4, K2HPO4, NH4NO3, CaCl2, MgSO4·7H2O, FeSO4·7H2O, and VB12) and optimize nutrient substrate allocation through a combination of actual surveys of petroleum hydrocarbon-contaminated sites and microcosm experiments. Building on this, combining biostimulation and controlled-release technology, we developed a biodegradable chitosan-based encapsulated targeted biostimulant (i.e., YZ-1) characterized by easy uptake, good stability, controllable slow-release migration, and longevity to stimulate indigenous microflora in groundwater to efficiently degrade petroleum hydrocarbon. Results showed that YZ-1 extended the active duration of nutrient components by 5-6 times, with a sustainable release time exceeding 2 months. Under YZ-1 stimulation, microorganisms grew rapidly, increasing the degradation rate of petroleum hydrocarbon (10 mg L-1) by indigenous microorganisms from 43.03% to 79.80% within 7 d. YZ-1 can easily adapt to varying concentrations of petroleum hydrocarbon-contaminated groundwater. Specifically, in the range of 2-20 mg L-1 of petroleum hydrocarbon, the indigenous microflora was able to degrade 71.73-80.54% of the petroleum hydrocarbon within a mere 7 d. YZ-1 injection facilitated the delivery of nutrient components into the underground environment, improved the conversion ability of inorganic electron donors/receptors in the indigenous microbial community system, and strengthened the co-metabolism mechanism among microorganisms, achieving the goal of efficient petroleum hydrocarbon degradation.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China.
| | - Ting Liu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Yujia Shi
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China; Changchun Gold Research Institute Co., Ltd, Changchun 130021, China
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Xinying Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Yiliang Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
| | - Dong Li
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun 130021,China
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Kim J, Hwangbo M, Shih CH, Chu KH. Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation. WATER RESEARCH X 2023; 20:100187. [PMID: 37671037 PMCID: PMC10477051 DOI: 10.1016/j.wroa.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 09/07/2023]
Abstract
Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.
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Affiliation(s)
- Jinha Kim
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
- School of Earth, Environmental and Marine Sciences, The University of Texas – Rio Grande Valley, Brownsville, TX, USA
| | - Chih-Hsuan Shih
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
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Juárez K, Reza L, Bretón-Deval L, Morales-Guzmán D, Trejo-Hernández MR, García-Guevara F, Lara P. Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico. World J Microbiol Biotechnol 2023; 39:264. [PMID: 37515608 PMCID: PMC10386958 DOI: 10.1007/s11274-023-03703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023]
Abstract
Bacterial degradation of crude oil is a promising strategy for reducing the concentration of hydrocarbons in contaminated environments. In the first part of this study, we report the enrichment of two bacterial consortia from deep sediments of the Gulf of Mexico with crude oil as the sole carbon and energy source. We conducted a comparative analysis of the bacterial community in the original sediment, assessing its diversity, and compared it to the enrichment observed after exposure to crude oil in defined cultures. The consortium exhibiting the highest hydrocarbon degradation was predominantly enriched with Rhodococcus (75%). Bacterial community analysis revealed the presence of other hydrocarbonoclastic members in both consortia. In the second part, we report the isolation of the strain Rhodococcus sp. GOMB7 with crude oil as a unique carbon source under microaerobic conditions and its characterization. This strain demonstrated the ability to degrade long-chain alkanes, including eicosane, tetracosane, and octacosane. We named this new strain Rhodococcus qingshengii GOMB7. Genome analysis revealed the presence of several genes related to aromatic compound degradation, such as benA, benB, benC, catA, catB, and catC; and five alkB genes related to alkane degradation. Although members of the genus Rhodococcus are well known for their great metabolic versatility, including the aerobic degradation of recalcitrant organic compounds such as petroleum hydrocarbons, this is the first report of a novel strain of Rhodococcus capable of degrading long-chain alkanes under microaerobic conditions. The potential of R. qingshengii GOMB7 for applications in bioreactors or controlled systems with low oxygen levels offers an energy-efficient approach for treating crude oil-contaminated water and sediments.
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Affiliation(s)
- Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México.
| | - Lizeth Reza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
| | - Luz Bretón-Deval
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
- Consejo Nacional de Ciencia y Tecnología, Avenida Insurgentes Sur 1582, Crédito Constructor, Ciudad de México, México
| | - Daniel Morales-Guzmán
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001. Col. Chamilpa., Cuernavaca, Morelos, 62209, México
| | - María R Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001. Col. Chamilpa., Cuernavaca, Morelos, 62209, México
| | - Fernando García-Guevara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Paloma Lara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México.
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62210, México.
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6
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Barbosa FAS, Brait LAS, Coutinho FH, Ferreira CM, Moreira EF, de Queiroz Salles L, Meirelles PM. Ecological landscape explains aquifers microbial structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160822. [PMID: 36526191 DOI: 10.1016/j.scitotenv.2022.160822] [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: 09/05/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.
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Affiliation(s)
| | | | - Felipe Hernandes Coutinho
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Camilo M Ferreira
- Institute of Biology, Federal University of Bahia, Salvador, Brazil; National Institute of Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (IN-TREE), Brazil
| | | | | | - Pedro Milet Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Brazil; National Institute of Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (IN-TREE), Brazil.
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Akash S, Sivaprakash B, Rajamohan N, Selvankumar T. Biotransformation as a tool for remediation of polycyclic aromatic hydrocarbons from polluted environment - review on toxicity and treatment technologies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120923. [PMID: 36566676 DOI: 10.1016/j.envpol.2022.120923] [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: 08/11/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Polycyclic aromatic hydrocarbons, a prominent family of persistent organic molecules produced by both anthropogenic and natural processes, are widespread in terrestrial and aquatic environments owing to their hydrophobicity, electrochemical stability and low aqueous solubility. Phenanthrene and naphthalene belong to the group of polycyclic aromatic hydrocarbons whose occurrence are reported to be relatively higher. The bioremediation mode of removing the toxicities of these two compounds has been reported to be promising than other methods. Most of the microbial classes of bacterial, fungal and algal origin are reported to degrade the target pollutants into non-toxic compounds effectively. The review aims to give an overview on toxicological studies, identification and enrichment techniques of phenanthrene and naphthalene degrading microbes and the bioremediation technologies (microbial assisted reactors, microbial fuel cells and microbial assisted constructed wetlands) reported by various researchers. All the three modes of bioremediation techniques were proved to be promising on different perspectives. In the treatment of phenanthrene, a maximum recovery of 96% and 98% was achieved in an aerobic membrane reactor with Bacillus species and single chamber air cathode microbial fuel cell with Acidovorax and Aquamicrobium respectively were reported. With the constructed wetland configuration, 95.5% of removal was attained with manganese oxide based microbial constructed wetland. The maximum degradation efficiency reported for naphthalene are 99% in a reverse membrane bioreactor, 98.5% in a marine sediment microbial fuel cell and 92.8% with a low-cost sandy soil constructed wetland.
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Affiliation(s)
- S Akash
- Department of Chemical Engineering, Annamalai University, Annamalai Nagar, PC-608002, India
| | - Baskaran Sivaprakash
- Department of Chemical Engineering, Annamalai University, Annamalai Nagar, PC-608002, India
| | - Natarajan Rajamohan
- Chemical Engineering Section, Faculty of Engineering, Sohar University, Sohar, PC-311, Oman.
| | - Thangaswamy Selvankumar
- PG and Research Department of Biotechnology, Mahendra Arts and Science College, Kalipatti, Namakkal, Tamilnadu, India
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8
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Ibrar M, Khan S, Hasan F, Yang X. Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:24391-24410. [PMID: 35061186 DOI: 10.1007/s11356-022-18492-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Hydrocarbons are routinely detected at low concentrations, despite the degrading metabolic potential of ubiquitous microorganisms. The potential drivers of hydrocarbons persistence are lower bioavailability and mass transfer limitation. Recently, bioremediation strategies have developed rapidly, but still, the solution is not resilient. Biosurfactants, known to increase bioavailability and augment biodegradation, are tightly linked to bacterial surface motility and chemotaxis, while chemotaxis help bacteria to locate aromatic compounds and increase the mass transfer. Harassing the biosurfactant production and chemotaxis properties of degrading microorganisms could be a possible approach for the complete degradation of hydrocarbons. This review provides an overview of interplay between biosurfactants and chemotaxis in bioremediation. Besides, we discuss the chemical surfactants and biosurfactant-mediated biodegradation by microbial consortium.
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Affiliation(s)
- Muhammad Ibrar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, 430074, Hubei, People's Republic of China
| | - Salman Khan
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Fariha Hasan
- Department of Microbiology, Applied, Environmental and Geomicrobiology Laboratory, Quaid-I-Azam University, Islamabad, Pakistan
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China.
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9
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Eziuzor SC, Corrêa FB, Peng S, Schultz J, Kleinsteuber S, da Rocha UN, Adrian L, Vogt C. Structure and functional capacity of a benzene-mineralizing, nitrate-reducing microbial community. J Appl Microbiol 2022; 132:2795-2811. [PMID: 34995421 DOI: 10.1111/jam.15443] [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: 09/29/2021] [Revised: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 11/26/2022]
Abstract
AIMS How benzene is metabolized by microbes under anoxic conditions is not fully understood. Here, we studied the degradation pathways in a benzene-mineralizing, nitrate-reducing enrichment culture. METHODS AND RESULTS Benzene mineralization was dependent on the presence of nitrate and correlated to the enrichment of a Peptococcaceae phylotype only distantly related to known anaerobic benzene degraders of this family. Its relative abundance decreased after benzene mineralization had terminated, while other abundant taxa-Ignavibacteriaceae, Rhodanobacteraceae and Brocadiaceae-slightly increased. Generally, the microbial community remained diverse despite the amendment of benzene as single organic carbon source, suggesting complex trophic interactions between different functional groups. A subunit of the putative anaerobic benzene carboxylase previously detected in Peptococcaceae was identified by metaproteomic analysis suggesting that benzene was activated by carboxylation. Detection of proteins involved in anaerobic ammonium oxidation (anammox) indicates that benzene mineralization was accompanied by anammox, facilitated by nitrite accumulation and the presence of ammonium in the growth medium. CONCLUSIONS The results suggest that benzene was activated by carboxylation and further assimilated by a novel Peptococcaceae phylotype. SIGNIFICANCE AND IMPACT OF THE STUDY The results confirm the hypothesis that Peptococcaceae are important anaerobic benzene degraders.
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Affiliation(s)
- Samuel C Eziuzor
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Felipe B Corrêa
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Shuchan Peng
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Department of Environmental Science, Chongqing University, Chongqing, China
| | - Júnia Schultz
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulisses N da Rocha
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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10
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Urrutia A, Mitsi K, Foster R, Ross S, Carr M, Ward GM, van Aerle R, Marigomez I, Leger MM, Ruiz-Trillo I, Feist SW, Bass D. Txikispora philomaios n. sp., n. g., a Micro-Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea. J Eukaryot Microbiol 2021; 69:e12875. [PMID: 34726818 DOI: 10.1111/jeu.12875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study provides a morphological, ultrastructural, and phylogenetic characterization of a novel micro-eukaryotic parasite (2.3-2.6 µm) infecting amphipod genera Echinogammarus and Orchestia. Longitudinal studies across two years revealed that infection prevalence peaked in late April and May, reaching 64% in Echinogammarus sp. and 15% in Orchestia sp., but was seldom detected during the rest of the year. The parasite infected predominantly haemolymph, connective tissue, tegument, and gonad, although hepatopancreas and nervous tissue were affected in heavier infections, eliciting melanization and granuloma formation. Cell division occurred inside walled parasitic cysts, often within host haemocytes, resulting in haemolymph congestion. Small subunit (18S) rRNA gene phylogenies including related environmental sequences placed the novel parasite as a highly divergent lineage within Class Filasterea, which together with Choanoflagellatea represent the closest protistan relatives of Metazoa. We describe the new parasite as Txikispora philomaios n. sp. n. g., the first confirmed parasitic filasterean lineage, which otherwise comprises four free-living flagellates and a rarely observed endosymbiont of snails. Lineage-specific PCR probing of other hosts and surrounding environments only detected T. philomaios in the platyhelminth Procerodes sp. We expand the known diversity of Filasterea by targeted searches of metagenomic datasets, resulting in 13 previously unknown lineages from environmental samples.
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Affiliation(s)
- Ander Urrutia
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK.,Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology (Faculty of Science and Technology), Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Areatza Pasealekua z/g, Plentzia, 48620, Basque Country, Spain
| | - Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain
| | - Rachel Foster
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Stuart Ross
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - Martin Carr
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Georgia M Ward
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - Ionan Marigomez
- Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology (Faculty of Science and Technology), Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Areatza Pasealekua z/g, Plentzia, 48620, Basque Country, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain.,Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, 08028, Catalonia, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Stephen W Feist
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK.,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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11
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Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput Biol 2021; 17:e1008972. [PMID: 33961626 PMCID: PMC8172020 DOI: 10.1371/journal.pcbi.1008972] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/02/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.
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Affiliation(s)
- Lauren M. Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, CA, United States of America
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12
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Cui Y, Li B, Wang X, Tang R. Organism–Materials Integration: A Promising Strategy for Biomedical Applications. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202000044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yihao Cui
- Center for Biomaterials and Biopathways Department of Chemistry Zhejiang University No. 38 Zheda Road Hangzhou Zhejiang 310027 China
| | - Benke Li
- Center for Biomaterials and Biopathways Department of Chemistry Zhejiang University No. 38 Zheda Road Hangzhou Zhejiang 310027 China
| | - Xiaoyu Wang
- Qiushi Academy for Advanced Studies Zhejiang University No. 38 Zheda Road Hangzhou Zhejiang 310027 China
| | - Ruikang Tang
- Center for Biomaterials and Biopathways Department of Chemistry Zhejiang University No. 38 Zheda Road Hangzhou Zhejiang 310027 China
- Qiushi Academy for Advanced Studies Zhejiang University No. 38 Zheda Road Hangzhou Zhejiang 310027 China
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13
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BenIsrael M, Habtewold JZ, Khosla K, Wanner P, Aravena R, Parker BL, Haack EA, Tsao DT, Dunfield KE. Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:846-856. [PMID: 33397125 DOI: 10.1080/15226514.2020.1860901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.
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Affiliation(s)
- Michael BenIsrael
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | | | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Philipp Wanner
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
| | - Ramon Aravena
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada
| | - Beth L Parker
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
| | | | - David T Tsao
- BP Corporation North America, Inc, Naperville, IL, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Canada
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14
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Hidalgo KJ, Sierra-Garcia IN, Dellagnezze BM, de Oliveira VM. Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain. Front Microbiol 2020; 11:561506. [PMID: 33072021 PMCID: PMC7530279 DOI: 10.3389/fmicb.2020.561506] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 02/01/2023] Open
Abstract
Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.
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Affiliation(s)
- Kelly J. Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabel N. Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Biology Department & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bruna M. Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
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15
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Thorn CE, Bergesch C, Joyce A, Sambrano G, McDonnell K, Brennan F, Heyer R, Benndorf D, Abram F. A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures. Mol Ecol Resour 2019; 19:439-455. [PMID: 30565880 DOI: 10.1111/1755-0998.12979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022]
Abstract
The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.
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Affiliation(s)
- Camilla E Thorn
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christian Bergesch
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aoife Joyce
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Gustavo Sambrano
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Kevin McDonnell
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Fiona Brennan
- Department of Environment, Soils and Land-use, Teagasc, Wexford, Ireland
| | - Robert Heyer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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