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Jacquiod S, Olsen NMC, Blouin M, Røder HL, Burmølle M. Genotypic variations and interspecific interactions modify gene expression and biofilm formation of Xanthomonas retroflexus. Environ Microbiol 2023; 25:3225-3238. [PMID: 37740256 DOI: 10.1111/1462-2920.16503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/24/2023]
Abstract
Multispecies biofilms are important models for studying the evolution of microbial interactions. Co-cultivation of Xanthomonas retroflexus (XR) and Paenibacillus amylolyticus (PA) systemically leads to the appearance of an XR wrinkled mutant (XRW), increasing biofilm production. The nature of this new interaction and the role of each partner remain unclear. We tested the involvement of secreted molecular cues in this interaction by exposing XR and XRW to PA or its supernatant and analysing the response using RNA-seq, colony-forming unit (CFU) estimates, biofilm quantification, and microscopy. Compared to wild type, the mutations in XRW altered its gene expression and increased its CFU number. These changes matched the reported effects for one of the mutated genes: a response regulator part of a two-component system involved in environmental sensing. When XRW was co-cultured with PA or its supernatant, the mutations effects on XRW gene expression were masked, except for genes involved in sedentary lifestyle, being consistent with the higher biofilm production. It appears that the higher biofilm production was the result of the interaction between the genetic context (mutations) and the biotic environment (PA signals). Regulatory genes involved in environmental sensing need to be considered to shed further light on microbial interactions.
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Affiliation(s)
- Samuel Jacquiod
- Agroécologie, INRAE, Institut Agro Dijon, Université de Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Nanna Mee Coops Olsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Blouin
- Agroécologie, INRAE, Institut Agro Dijon, Université de Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Henriette Lyng Røder
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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2
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Azhar U, Ahmad H, Shafqat H, Babar M, Shahzad Munir HM, Sagir M, Arif M, Hassan A, Rachmadona N, Rajendran S, Mubashir M, Khoo KS. Remediation techniques for elimination of heavy metal pollutants from soil: A review. ENVIRONMENTAL RESEARCH 2022; 214:113918. [PMID: 35926577 DOI: 10.1016/j.envres.2022.113918] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 05/27/2023]
Abstract
Contaminated soil containing toxic metals and metalloids is found everywhere globally. As a consequence of adsorption and precipitation reactions, metals are comparatively immobile in subsurface systems. Hence remediation techniques in such contaminated sites have targeted the solid phase sources of metals such as sludges, debris, contaminated soils, or wastes. Over the last three decades, the accumulation of these toxic substances inside the soil has increased dramatically, putting the ecosystem and human health at risk. Pollution of heavy metal have posed severe impacts on human, and it affects the environment in different ways, resulting in industrial anger in many countries. Various procedures, including chemical, biological, physical, and integrated approaches, have been adopted to get rid of this type of pollution. Expenditure, timekeeping, planning challenges, and state-of-the-art gadget involvement are some drawbacks that need to be properly handled. Recently in situ metal immobilization, plant restoration, and biological methods have changed the dynamics and are considered the best solution for removing metals from soil. This review paper critically evaluates and analyzes the numerous approaches for preparing heavy metal-free soil by adopting different soil remediation methods.
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Affiliation(s)
- Umair Azhar
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Huma Ahmad
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hafsa Shafqat
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Muhammad Babar
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hafiz Muhammad Shahzad Munir
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Muhammad Sagir
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Muhammad Arif
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan.
| | - Afaq Hassan
- Department of Chemical Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan.
| | - Nova Rachmadona
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan; Research Collaboration Center for Biomass and Biorefinery between BRIN and Universitas Padjadjaran, West Java, Indonesia
| | - Saravanan Rajendran
- Faculty of Engineering, Department of Mechanical Engineering, University of Tarapacá, Avda. General Velasquez, 1775, Arica, Chile
| | - Muhammad Mubashir
- Department of Petroleum Engineering, School of Engineering, Asia Pacific University of Technology and Innovation, 57000, Kuala Lumpur, Malaysia
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan.
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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Gonzalo M, Espersen R, Al‐Soud WA, Cristiano Falco F, Hägglund P, Sørensen SJ, Svensson B, Jacquiod S. Azo dying of α-keratin material improves microbial keratinase screening and standardization. Microb Biotechnol 2020; 13:984-996. [PMID: 32110845 PMCID: PMC7264887 DOI: 10.1111/1751-7915.13541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/30/2022] Open
Abstract
Microbial conversion through enzymatic reactions has received a lot of attention as a cost-effective and environmentally friendly way to recover amino acids and short peptides from keratin materials. However, accurate assessment of microbial keratinase activity is not straightforward, and current available methods lack sensitivity and standardization. Here, we suggest an optimized Azokeratin assay, with substrate generated directly from azo-dyed raw keratin material. We introduced supernatant filtration in the protocol for optimal stopping of keratinase reactions instead of the widely used trichloroacetic acid (TCA), as it generated biases and impacted the sensitivity. We furthermore suggest a method for standardization of keratinase activity signals using proteinase K, a well-known keratinase, as a reference enabling reproducibility between studies. Lastly, we evaluated our developed method with several bacterial isolates through benchmarking against a commercial assay (Keratin Azure). Under different setups, the Azokeratin method was more sensitive than commonly used Keratin Azure-based assays (3-fold). We argue that this method could be applied with any type of keratin substrate, enabling more robust and sensitive results which can be used for further comparison with other studies, thus representing an important progress within the field of microbial keratin degradation.
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Affiliation(s)
- Milena Gonzalo
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
- Present address:
Interactions Arbres/Micro‐organismesINRA/Univ. de LorraineChampenouxFrance
| | - Roall Espersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Waleed A. Al‐Soud
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Francesco Cristiano Falco
- Department of Chemical and Biochemical EngineeringTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Per Hägglund
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
- Present address:
Department of Biomedical SciencesPanum Institute 12.6University of CopenhagenCopenhagenDenmark
| | - Søren J. Sørensen
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Birte Svensson
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Samuel Jacquiod
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
- Present address:
AgroécologieAgroSup DijonINRAEUniv. BourgogneUniv. Bourgogne Franche‐ComtéF‐21000DijonFrance
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles. Appl Environ Microbiol 2019; 85:AEM.01369-19. [PMID: 31420342 DOI: 10.1128/aem.01369-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.
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Dandare SU, Young JM, Kelleher BP, Allen CCR. The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:19-27. [PMID: 30927724 DOI: 10.1016/j.scitotenv.2019.03.250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 03/12/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential 'public good' proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.
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Affiliation(s)
| | | | | | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, UK; Institute for Global Food Security, Queen's University Belfast, UK.
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8
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Alvarez-Silva MC, Álvarez-Yela AC, Gómez-Cano F, Zambrano MM, Husserl J, Danies G, Restrepo S, González-Barrios AF. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PLoS One 2017; 12:e0181826. [PMID: 28767679 PMCID: PMC5540551 DOI: 10.1371/journal.pone.0181826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/09/2017] [Indexed: 01/02/2023] Open
Abstract
Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.
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Affiliation(s)
- María Camila Alvarez-Silva
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Astrid Catalina Álvarez-Yela
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Fabio Gómez-Cano
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - María Mercedes Zambrano
- Center for Genomics and Bioinformatics of Extreme Environments (Gebix), Bogotá, Colombia
- Corporación Corpogen Research Center, Bogotá, Colombia
| | - Johana Husserl
- Centro de Investigaciones en Ingeniería Ambiental, Department of Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Giovanna Danies
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Andrés Fernando González-Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
- * E-mail:
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Jacquiod S, Brejnrod A, Morberg SM, Abu Al-Soud W, Sørensen SJ, Riber L. Deciphering conjugative plasmid permissiveness in wastewater microbiomes. Mol Ecol 2017; 26:3556-3571. [DOI: 10.1111/mec.14138] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Asker Brejnrod
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Stefan M. Morberg
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Søren J. Sørensen
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Leise Riber
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
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10
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Berini F, Presti I, Beltrametti F, Pedroli M, Vårum KM, Pollegioni L, Sjöling S, Marinelli F. Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome. Microb Cell Fact 2017; 16:16. [PMID: 28137256 PMCID: PMC5282697 DOI: 10.1186/s12934-017-0634-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/20/2017] [Indexed: 01/20/2023] Open
Abstract
Background Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase—named Chi18H8 and belonging to family 18 glycosyl hydrolases—was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential. Results We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca2+-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate. Conclusions Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0634-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy. .,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.
| | - Ilaria Presti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.,Chemo Biosynthesis, Corana, Pavia, Italy
| | | | | | - Kjell M Vårum
- NOBIPOL, Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
| | - Sara Sjöling
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
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11
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Bouhajja E, Agathos SN, George IF. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnol Adv 2016; 34:1413-1426. [PMID: 27825829 DOI: 10.1016/j.biotechadv.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 12/23/2022]
Abstract
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
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Affiliation(s)
- Emna Bouhajja
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium
| | - Spiros N Agathos
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador
| | - Isabelle F George
- Université Libre de Bruxelles, Laboratoire d'Ecologie des Systèmes Aquatiques, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
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12
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Bouhajja E, McGuire M, Liles MR, Bataille G, Agathos SN, George IF. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries. Appl Microbiol Biotechnol 2016; 101:797-808. [PMID: 27785541 DOI: 10.1007/s00253-016-7934-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/25/2022]
Abstract
The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.
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Affiliation(s)
- E Bouhajja
- Earth and Life Institute, Laboratoire de Génie Biologique, Université catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348, Louvain-la-Neuve, Belgium
| | - M McGuire
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, Alabama, 36849, USA
| | - M R Liles
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, Alabama, 36849, USA
| | - G Bataille
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, Place Croix du Sud 4-5, Bte L.7.07.04, 1348, Louvain-la-Neuve, Belgium
| | - S N Agathos
- Earth and Life Institute, Laboratoire de Génie Biologique, Université catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348, Louvain-la-Neuve, Belgium.,School of Life Sciences and Biotechnology, Yachay Tech University, San Miguel de Urcuquí, Ecuador
| | - I F George
- Laboratoire d'Ecologie des Systèmes Aquatiques, Université libre de Bruxelles, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050, Brussels, Belgium.
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13
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Baweja M, Nain L, Kawarabayasi Y, Shukla P. Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 2016; 7:965. [PMID: 27379087 PMCID: PMC4909775 DOI: 10.3389/fmicb.2016.00965] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.
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Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi India
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology, Tsukuba Japan
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
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14
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Jacquiod S, Stenbæk J, Santos SS, Winding A, Sørensen SJ, Priemé A. Metagenomes provide valuable comparative information on soil microeukaryotes. Res Microbiol 2016; 167:436-50. [DOI: 10.1016/j.resmic.2016.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/16/2016] [Accepted: 03/20/2016] [Indexed: 02/02/2023]
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15
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RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis. Biotechniques 2015; 59:347, 349-52, 354-6 passim. [PMID: 26651514 DOI: 10.2144/000114363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/28/2015] [Indexed: 11/23/2022] Open
Abstract
Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.
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16
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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