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Su H, Lai H, Gao F, Zhang R, Wu S, Ge F, Li Y, Yao H. The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:25688-25705. [PMID: 38483720 DOI: 10.1007/s11356-024-32851-8] [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: 10/21/2023] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.
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Affiliation(s)
- Hao Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiling Lai
- Lianhe Equator Environmental Impact Assessment Co., Ltd, Tianjin, 300042, China
| | - Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruipeng Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sixuan Wu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Furong Ge
- Beilun District Agriculture and Rural Bureau, Ningbo, 315800, Zhejiang Province, China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China.
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China.
| | - Huaiying Yao
- Wuhan Institute of Technology, Wuhan, 430074, China
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2
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Weiland-Bräuer N, Saleh L, Schmitz RA. Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds. Methods Mol Biol 2023; 2555:23-49. [PMID: 36306077 DOI: 10.1007/978-1-0716-2795-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Livía Saleh
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany.
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3
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Singh RV, Sambyal K, Negi A, Sonwani S, Mahajan R. Chitinases production: A robust enzyme and its industrial applications. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1883004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Krishika Sambyal
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Anjali Negi
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Shubham Sonwani
- Department of Biosciences, Christian Eminent College, Indore, India
| | - Ritika Mahajan
- Department of Microbiology, School of Sciences, JAIN (Deemed-to-be University), Bengaluru, India
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4
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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5
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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6
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Aktuganov GE, Melentiev AI, Varlamov VP. Biotechnological Aspects of the Enzymatic Preparation of Bioactive Chitooligosaccharides (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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7
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Microbial and viral chitinases: Attractive biopesticides for integrated pest management. Biotechnol Adv 2018; 36:818-838. [DOI: 10.1016/j.biotechadv.2018.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 02/01/2023]
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8
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Zhang M, Wang W, Wang J, Teng Y, Xu Z. Dynamics of biochemical properties associated with soil nitrogen mineralization following nitrification inhibitor and fungicide applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:11340-11348. [PMID: 28303541 DOI: 10.1007/s11356-017-8762-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
Agrochemical applications may have side effects on soil biochemical properties related to soil nitrogen (N) mineralization and thus affect N cycling. The present study aimed to evaluate the effects of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) and fungicide iprodione on soil neutral protease (NPR), alkaline protease (APR), chitinase (CHI), and their functional genes (nprA, aprA, and chiA) related to soil N mineralization. The following four treatments were included: blank control (CK), single DMPP application (DAA), weekly iprodione applications (IPR), and the combined applications of DMPP and iprodione (DI). Compared with the CK treatment, DMPP application significantly inhibited the CHI activity in the first 14 days of incubation, and iprodione applications, particularly when applied alone, decreased the NPR, APR, and CHI activities. Relative to the IPR treatment, extra DMPP application had the potential to alleviate the inhibitory effects of iprodione on the activities of these enzymes. DMPP application significantly increased aprA gene abundances after 14 days of incubation. However, repeated iprodione applications, alone or with the DMPP, decreased nprA and chiA gene abundances. Relative to the CK treatment, DMPP application generated negligible effects on the positive/negative correlations between soil enzyme activities and the corresponding functional gene abundances. However, the positive correlation between the CHI activity and chiA gene abundance was changed to negative correlation by repeated iprodione applications, alone or together with the DMPP. Our results demonstrated that agrochemical applications, particularly repeated fungicide applications, can have inadvertent effects on enzyme activities and functional gene abundances associated with soil N mineralization.
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Affiliation(s)
- Manyun Zhang
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Weijin Wang
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia
- Department of Science, Information Technology and Innovation, Dutton Park, QLD, 4102, Australia
| | - Jun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Chongqing Research Academy of Environmental Sciences, Chongqing, 401147, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
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9
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Teplyuk AV, Samarov NI, Korzhenkov AA, Ul’yanova MO, Goeva MA, Kublanov IV, Kanapatskii TA, Pimenov NV, Toshchakov SV. Analysis of chitinase diversity in the Baltic Sea bottom sediments. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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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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Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM, Pedrosa FO. A broad pH range and processive chitinase from a metagenome library. ACTA ACUST UNITED AC 2017; 50:e5658. [PMID: 28076454 PMCID: PMC5264535 DOI: 10.1590/1414-431x20165658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 01/14/2023]
Abstract
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine
linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and
fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil
was functionally screened for chitinase activity leading to the isolation and
identification of a chitinase gene named metachi18A. The
metachi18A gene was subcloned and overexpressed in
Escherichia coli BL21 and the MetaChi18A chitinase was purified
by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is
a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family
18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50°C.
Moreover, the enzyme retained at least 80% of its activity in the pH range from 4 to
9 and 98% at 600 mM NaCl. Thin layer chromatography analyses identified chitobiose as
the main product of MetaChi18A on chitin polymers as substrate. Kinetic analysis
showed inhibition of MetaChi18A activity at high concentrations of colloidal chitin
and 4-methylumbelliferyl N,N′-diacetylchitobiose and sigmoid kinetics at low
concentrations of colloidal chitin, indicating a possible conformational change to
lead the chitin chain from the chitin-binding to the catalytic domain. The observed
stability and activity of MetaChi18A over a wide range of conditions suggest that
this chitinase, now characterized, may be suitable for application in the industrial
processing of chitin.
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Affiliation(s)
- S S Thimoteo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A Glogauer
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Agência de Inovação, Instituto de Tecnologia do Paraná - Tecpar, Curitiba, PR, Brasil
| | - H Faoro
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brasil
| | - E M de Souza
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L F Huergo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - B M Moerschbacher
- Institute for Biology and Biotechnology of Plants, WWU Münster University, Münster, Germany
| | - F O Pedrosa
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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12
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Gandolfi I, Canedoli C, Imperato V, Tagliaferri I, Gkorezis P, Vangronsveld J, Padoa Schioppa E, Papacchini M, Bestetti G, Franzetti A. Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:650-658. [PMID: 27745913 DOI: 10.1016/j.envpol.2016.10.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 06/06/2023]
Abstract
Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas.
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Affiliation(s)
- Isabella Gandolfi
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy.
| | - Claudia Canedoli
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Valeria Imperato
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Ilario Tagliaferri
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | | | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Emilio Padoa Schioppa
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Maddalena Papacchini
- INAIL, Dipartimento Innovazioni Tecnologiche e Sicurezza degli Impianti, Prodotti ed Insediamenti Antropici, Rome, Italy
| | - Giuseppina Bestetti
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Andrea Franzetti
- Dept. of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
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13
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Weiland-Bräuer N, Langfeldt D, Schmitz RA. Construction and Screening of Marine Metagenomic Large Insert Libraries. Methods Mol Biol 2017; 1539:23-42. [PMID: 27900682 DOI: 10.1007/978-1-4939-6691-2_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Daniela Langfeldt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
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Gaikwad S, Shouche YS, Gade WN. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity. AMB Express 2016; 6:40. [PMID: 27299740 PMCID: PMC4908081 DOI: 10.1186/s13568-016-0211-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/03/2016] [Indexed: 11/10/2022] Open
Abstract
Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities.
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Cortes-Tolalpa L, Jiménez DJ, de Lima Brossi MJ, Salles JF, van Elsas JD. Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity. Appl Microbiol Biotechnol 2016; 100:7713-25. [PMID: 27170322 PMCID: PMC4980425 DOI: 10.1007/s00253-016-7516-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 11/25/2022]
Abstract
Despite multiple research efforts, the current strategies for exploitation of lignocellulosic plant matter are still far from optimal, being hampered mostly by the difficulty of degrading the recalcitrant parts. An interesting approach is to use lignocellulose-degrading microbial communities by using different environmental sources of microbial inocula. However, it remains unclear whether the inoculum source matters for the degradation process. Here, we addressed this question by verifying the lignocellulose degradation potential of wheat (Triticum aestivum) straw by microbial consortia generated from three different microbial inoculum sources, i.e., forest soil, canal sediment and decaying wood. We selected these consortia through ten sequential-batch enrichments by dilution-to-stimulation using wheat straw as the sole carbon source. We monitored the changes in microbial composition and abundance, as well as their associated degradation capacity and enzymatic activities. Overall, the microbial consortia developed well on the substrate, with progressively-decreasing net average generation times. Each final consortium encompassed bacterial/fungal communities that were distinct in composition but functionally similar, as they all revealed high substrate degradation activities. However, we did find significant differences in the metabolic diversities per consortium: in wood-derived consortia cellobiohydrolases prevailed, in soil-derived ones β-glucosidases, and in sediment-derived ones several activities. Isolates recovered from the consortia showed considerable metabolic diversities across the consortia. This confirmed that, although the overall lignocellulose degradation was similar, each consortium had a unique enzyme activity pattern. Clearly, inoculum source was the key determinant of the composition of the final microbial degrader consortia, yet with varying enzyme activities. Hence, in accord with Beyerinck's, "everything is everywhere, the environment selects" the source determines consortium composition.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
| | - Diego Javier Jiménez
- Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Maria Julia de Lima Brossi
- Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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16
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Berini F, Caccia S, Franzetti E, Congiu T, Marinelli F, Casartelli M, Tettamanti G. Effects of Trichoderma viride chitinases on the peritrophic matrix of Lepidoptera. PEST MANAGEMENT SCIENCE 2016; 72:980-989. [PMID: 26179981 DOI: 10.1002/ps.4078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The peritrophic matrix (PM) is formed by a network of chitin fibrils associated with proteins, glycoproteins and proteoglycans that lines the insect midgut. It is a physical barrier involved in digestion processes, and protects the midgut epithelium from food abrasion, pathogen infections and toxic materials. Given its fundamental role in insect physiology, the PM represents an excellent target for pest control strategies. Although a number of viral, bacterial and insect chitinolytic enzymes affecting PM integrity have already been tested, exploitation of fungal chitinases has been almost neglected. Fungal chitinases, already in use as fungal phytopathogen biocontrol agents, are known to attack the insect cuticle, but their action on the insect gut needs to be better investigated. RESULTS In the present paper, we performed a biochemical characterisation of a commercial mixture of chitinolytic enzymes derived from Trichoderma viride and analysed its in vitro and in vivo effects on the PM of the silkworm Bombyx mori, a model system among Lepidoptera. We found that these enzymes have significant in vitro effects on the structure and permeability of the PM of this insect. A bioassay supported these results and showed that the oral administration of the mixture causes PM alterations, leading to adverse consequences on larval growth and development, negatively affecting pupal weight and even inducing mortality. CONCLUSIONS This study provides an integrated experimental approach to evaluate the effects of fungal chitinases on Lepidoptera. The encouraging results obtained herein make us confident about the possible use of fungal chitinases to control lepidopteran pests.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Centre, Politecnico di Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Silvia Caccia
- Department of Biosciences, University of Milano, Milano, Italy
- Department of Agriculture, University of Napoli Federico II, Portici, Napoli, Italy
| | - Eleonora Franzetti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Terenzio Congiu
- Department of Surgical and Morphological Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Centre, Politecnico di Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | | | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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Cretoiu MS, Berini F, Kielak AM, Marinelli F, van Elsas JD. A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil. Appl Microbiol Biotechnol 2015; 99:8199-215. [PMID: 26040993 PMCID: PMC4561078 DOI: 10.1007/s00253-015-6639-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022]
Abstract
Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.
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Affiliation(s)
- Mariana Silvia Cretoiu
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
- />Department of Marine Microbiology, Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Francesca Berini
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Anna Maria Kielak
- />Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO), Wageningen, The Netherlands
| | - Flavia Marinelli
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Jan Dirk van Elsas
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
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18
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Stöveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer F, Pühler A, Schlüter A, Moerschbacher B. Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. J Biotechnol 2015; 201:60-8. [DOI: 10.1016/j.jbiotec.2014.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 12/20/2022]
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Heterologous expression, purification and biochemical characterization of endochitinase ChiA74 from Bacillus thuringiensis. Protein Expr Purif 2014; 109:99-105. [PMID: 25478931 DOI: 10.1016/j.pep.2014.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/12/2014] [Accepted: 11/21/2014] [Indexed: 01/30/2023]
Abstract
ChiA74 is a secreted endochitinase produced by Bacillus thuringiensis. Previously we have partially characterized the physical parameters that affect enzymatic activity of ChiA74 in crude preparations of bacterial secretomes. In the present study, we cloned the chiA74 open reading frame (ORF) lacking the 5' sequence coding for its secretion signal peptide (chiA74Δsp) into a cold shock expression vector (pColdI) for production of the enzyme in Escherichia coli BL21-Rosetta 2. As a result, the N-terminal end of ChiA74Δsp ORF was fused to an artificial sequence of 28 amino acid, including a 6× histidine tag for purification of recombinant 6×His tagged-ChiA74Δsp (rChiA74, ∼74kDa). Along with a protein of ∼74kDa, we co-purified its ∼55kDa processed form which was confirmed by Western blot analysis. Optimal endochitinase activity of purified rChiA74 occurred at pH 7 and 40°C. Most divalent cations (e.g. Ba(+2), Ca(+2), Mn(+2), Mg(+2), Zn(+2) and Cu(+2)) at concentration of 10mM reduced chitinase activity by ∼30%, and Hg(+2) (10mM) drastically inhibited ChiA74 activity by ∼75-100%. The Vmax, Km and kcat for rChiA74 were 0.11±0.01nmol/min, 2.15μM±0.45 and 3.81s(-1), respectively, using 4-MU-GlcNAc3 as substrate. Using purified rChiA74 and colloidal chitin as substrate, chitin-derived oligosaccharides with degree of polymerization of 2 and 1 were detected.
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20
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Knief C. Analysis of plant microbe interactions in the era of next generation sequencing technologies. FRONTIERS IN PLANT SCIENCE 2014; 5:216. [PMID: 24904612 PMCID: PMC4033234 DOI: 10.3389/fpls.2014.00216] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/30/2014] [Indexed: 05/18/2023]
Abstract
Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation—Molecular Biology of the Rhizosphere, Faculty of Agriculture, University of BonnBonn, Germany
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21
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Jacquiod S, Demanèche S, Franqueville L, Ausec L, Xu Z, Delmont TO, Dunon V, Cagnon C, Mandic-Mulec I, Vogel TM, Simonet P. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J Biotechnol 2014; 190:18-29. [PMID: 24721211 DOI: 10.1016/j.jbiotec.2014.03.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/24/2014] [Accepted: 03/28/2014] [Indexed: 11/27/2022]
Abstract
A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
| | - Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Luka Ausec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zhuofei Xu
- Molecular Microbial Ecology Group, Section of Microbiology, København Universitet, København, Denmark
| | - Tom O Delmont
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Vincent Dunon
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, University of Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Christine Cagnon
- Équipe Environnement et Microbiologie, IBEAS - UFR Sciences et Techniques, Université de Pau et des Pays de l'Adour, 64013 Pau, France
| | - Ines Mandic-Mulec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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22
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Bioremediation of Southern Mediterranean oil polluted sites comes of age. N Biotechnol 2013; 30:743-8. [DOI: 10.1016/j.nbt.2013.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 04/21/2013] [Accepted: 05/10/2013] [Indexed: 11/21/2022]
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Cretoiu MS, Korthals GW, Visser JHM, van Elsas JD. Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field. Appl Environ Microbiol 2013; 79:5291-301. [PMID: 23811512 PMCID: PMC3753968 DOI: 10.1128/aem.01361-13] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/22/2013] [Indexed: 11/20/2022] Open
Abstract
A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.
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Affiliation(s)
- Mariana Silvia Cretoiu
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Gerard W. Korthals
- Applied Plant Research Institute, Wageningen University, Lelystad, The Netherlands
| | - Johnny H. M. Visser
- Applied Plant Research Institute, Wageningen University, Lelystad, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
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Beier S, Bertilsson S. Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol 2013; 4:149. [PMID: 23785358 PMCID: PMC3682446 DOI: 10.3389/fmicb.2013.00149] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/28/2013] [Indexed: 11/13/2022] Open
Abstract
Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.
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Affiliation(s)
- Sara Beier
- Department of Ecology and Genetics, Limnology, Uppsala University Uppsala, Sweden ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, UPMC Paris 06, UMR 7621 Banyuls sur mer, France ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique Centre National de la Recherche Scientifique, UMR 7621 Banyuls sur mer, France
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