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Xiao Z, Duan C, Li S, Chen J, Peng C, Che R, Liu C, Huang Y, Mei R, Xu L, Luo P, Yu Y. The microbial mechanisms by which long-term heavy metal contamination affects soil organic carbon levels. CHEMOSPHERE 2023; 340:139770. [PMID: 37562505 DOI: 10.1016/j.chemosphere.2023.139770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Globally, reducing carbon emissions and mitigating soil heavy metal pollution pose pressing challenges. We evaluated the effects of lead (Pb) and cadmium (Cd) contamination in the field over 20 years. The five treatment groups featured Pb concentrations of 40 and 250 mg/kg, Cd concentrations of 10 and 60 mg/kg, and a combination of Pb and Cd (60 and 20 mg/kg, respectively); we also included a pollution-free control group. After 20 years, soil pH decreased notably in all treatments, particularly by 1.02 in Cd10-treated soil. In addition to the increase of SOC in Cd10 and unchanged in Pb40 treatment, the SOC was reduced by 9.62%-12.98% under the other treatments. The α diversities of bacteria and fungi were significantly changed by Cd10 pollution (both p < 0.05) and the microbial community structure changed significantly. However, there were no significant changes in bacterial and fungal communities under other treatments. Cd10 pollution reduced the numbers of Ascomycota and Basidiomycota fungi, and enhanced SOC accumulation. Compared to the control, long-term heavy Cd, Pb, and Pb-Cd composite pollution caused SOC loss by increasing Basidiomycota which promoting carbon degradation, and decreasing Proteobacteria which promoting carbon fixation via the Krebs cycle. Our findings demonstrate that heavy metal pollution mediates Carbon-cycling microorganisms and genes, impacting SOC storage.
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Affiliation(s)
- Zhineng Xiao
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Changqun Duan
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Shiyu Li
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China; Hangzhou Carbon Peaking and Carbon Neutrality Research Center, Business School, Zhejiang University City College, Hangzhou, 310015, China.
| | - Ji Chen
- Department of Agroecology & Aarhus University Centre for Circular Bioeconomy, Aarhus University, 8830, Tjele, Denmark
| | - Changhui Peng
- Institute of Environment Sciences, Department of Biology Sciences, University of Quebec at Montreal, Case Postale 8888, Succ. Centre-Ville, Montreal, H3C 3P8, Canada
| | - Rongxiao Che
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Chang'e Liu
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Yin Huang
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Runran Mei
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Liangliang Xu
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Pengfei Luo
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
| | - Yadong Yu
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan University, Kunming, 650091, China
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Liu H, Hu Z, Zhou M, Zhang H, Zhang X, Yue Y, Yao X, Wang J, Xi C, Zheng P, Xu X, Hu B. PM 2.5 drives bacterial functions for carbon, nitrogen, and sulfur cycles in the atmosphere. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118715. [PMID: 34933062 DOI: 10.1016/j.envpol.2021.118715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Airborne bacteria may absorb the substance from the atmospheric particles and play a role in biogeochemical cycling. However, these studies focused on a few culturable bacteria and the samples were usually collected from one site. The metabolic potential of a majority of airborne bacteria on a regional scale and their driving factors remain unknown. In this study, we collected particulates with aerodynamic diameter ≤2.5 μm (PM2.5) from 8 cities that represent different regions across China and analyzed the samples via high-throughput sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) analysis, and functional database prediction. Based on the FAPROTAX database, 326 (80.69%), 191 (47.28%) and 45 (11.14%) bacterial genera are possible to conduct the pathways of carbon, nitrogen, and sulfur cycles, respectively. The pathway analysis indicated that airborne bacteria may lead to the decrease in organic carbon while the increase in ammonium and sulfate in PM2.5 samples, all of which are the important components of PM2.5. Among the 19 environmental factors studied including air pollutants, meteorological factors, and geographical conditions, PM2.5 concentration manifested the strongest correlations with the functional genes for the transformation of ammonium and sulfate. Moreover, the PM2.5 concentration rather than the sampling site will drive the distribution of functional genera. Thus, a bi-directional relationship between PM2.5 and bacterial metabolism is suggested. Our findings shed light on the potential bacterial pathway for the biogeochemical cycling in the atmosphere and the important role of PM2.5, offering a new perspective for atmospheric ecology and pollution control.
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Affiliation(s)
- Huan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; School of Civil Engineering, Chongqing University, Chongqing, 400044, China
| | - Zhichao Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Ping Zheng
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Xu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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Datta A, Gujre N, Gupta D, Agnihotri R, Mitra S. Application of enzymes as a diagnostic tool for soils as affected by municipal solid wastes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 286:112169. [PMID: 33621849 DOI: 10.1016/j.jenvman.2021.112169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/01/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Assessing the relationship between soil enzyme activities (SEAs) and heavy metals (HMs) without any amendment has rarely been conducted in soils contaminated with municipal solid wastes (MSW). Five soil enzymes [dehydrogenase (DHA), alkaline phosphatase (ALP), acid phosphatase (ACP), urease (UR), and nitrate reductase (NR)] have been assessed for HMs bioremediation using Zea mays L. grown in unamended soils that were contaminated with different types of MSW. Pot experiment was conducted for two seasons with soils collected from seven different locations within the MSW site. Experimental soil samples included a control (CA), contaminated by brick kiln wastes (SA1), kitchen and household wastes (SA2), medical wastes (SA3), mixed wastes (SA4), glass wastes (SA5), and metal scrap wastes (SA6). Rhizospheric soils were collected after the harvest of each season to investigate the impact of HMs on SEAs and physicochemical properties of soil. The results revealed an increase in DHA, ALP, and NR activities by 89.30%, 58.03% and 21.98% in SA1. Likewise, enhanced activities for UR (28.26%) and ACP (19.6%) were observed in SA3 and SA5 respectively. Insignificant increase in the macronutrients and organic carbon (OC) were also noted. The increased microbial count and the relatively higher amount of organic matter (OM) in the rhizosphere indicated the role of OM in HMs immobilization. Principal component analysis (PCA) indicated that DHA and NR are the important soil enzymes, underscored by their active involvement in the C and N turnover in the soil. Likewise, correlation analysis showed that DHA and NR activities were positively correlated with copper (Cu) (0.90, p < 0.01; 0.88, p < 0.01), suggesting its participation as a cofactor in enzymatic activities. In contrast, DHA was negatively correlated with cadmium (Cd) (-0.48, p < 0 0.05). Finally, these results indicated that in the absence of exogenous nutrient amendment, the SEAs were governed by OC, available nitrogen (Avl. N), Cu and Cd respectively. The study also highlighted the need for extensive research on SEAs for its utilization as a bioindicator in various soil bioremediation and quality management practices.
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Affiliation(s)
- Ankita Datta
- Agro-ecotechnology Laboratory, Centre for Rural Technology, Indian Institute of Technology Guwahati (IITG), North Guwahati, Assam, 781039, India
| | - Nihal Gujre
- Agro-ecotechnology Laboratory, Centre for Rural Technology, Indian Institute of Technology Guwahati (IITG), North Guwahati, Assam, 781039, India
| | - Debaditya Gupta
- Agro-ecotechnology Laboratory, Centre for Rural Technology, Indian Institute of Technology Guwahati (IITG), North Guwahati, Assam, 781039, India
| | - Richa Agnihotri
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, 452001, India
| | - Sudip Mitra
- Agro-ecotechnology Laboratory, Centre for Rural Technology, Indian Institute of Technology Guwahati (IITG), North Guwahati, Assam, 781039, India.
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Shahbaz U. Chitin, Characteristic, Sources, and Biomedical Application. Curr Pharm Biotechnol 2020; 21:1433-1443. [PMID: 32503407 DOI: 10.2174/1389201021666200605104939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/22/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Chitin stands at second, after cellulose, as the most abundant polysaccharide in the world. Chitin is found naturally in marine environments as it is a crucial structural component of various marine organisms. METHODS Different amounts of waste chitin and chitosan can be discovered in the environment. Chitinase producing microbes help to hydrolyze chitin waste to play an essential function for the removal of chitin pollution in the Marine Atmosphere. Chitin can be converted by using chemical and biological methods into prominent derivate chitosan. Numerous bacteria naturally have chitin degrading ability. RESULTS Chitin shows promise in terms of biocompatibility, low toxicity, complete biodegradability, nontoxicity, and film-forming capability. The application of these polymers in the different sectors of biomedical, food, agriculture, cosmetics, pharmaceuticals could be lucrative. Moreover, the most recent achievement in nanotechnology is based on chitin and chitosan-based materials. CONCLUSION In this review, we examine chitin in terms of its natural sources and different extraction methods, chitinase producing microbes and chitin, chitosan together with its derivatives for use in biomedical and agricultural applications.
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Affiliation(s)
- Umar Shahbaz
- Jiangnan University, School of Biotechnology, Jiangnan University Wuxi, Jiansu, China
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Hui C, Jiang H, Liu B, Wei R, Zhang Y, Zhang Q, Liang Y, Zhao Y. Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:136003. [PMID: 31846813 DOI: 10.1016/j.scitotenv.2019.136003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/20/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Chitin amendment is a promising agricultural management strategy to control fungal and nematodal plant diseases and to improve crop yield. Chitin degradation in the soil contributes significantly to carbon and nitrogen cycling in terrestrial ecosystems. However, little is known about chitin degradation and bacterial chitinolytic communities in agricultural soil under different fertilization regimes. Thus, in the present study, a 42-day soil incubation experiment was conducted, in which soil under four fertilization regimes (i.e., no fertilization (CK), chemical fertilizer (CF), pig manure plus 50% chemical fertilizer (PMCF), and rice straw plus 100% chemical fertilizer (SRCF)) were amended or not with chitin or its monomer, N-acetylglucosamine (NAG). Different nitrogen forms and CO2 and N2O emission were measured to evaluate chitin degradation and its environmental implications. SRCF soil had the highest CO2 emission, chitin N mineralization, and fungal abundance. NAG and chitin were enriched to exploit the chitin degraders. High-throughput sequencing analyses reveled that Streptomycetaceae, Oxalobacteraceae, Gemmatimonadaceae, and Acidobacteria were generally increased upon chitin amendment in CK, CF, and PMCF soil, whereas Streptomycetaceae dominated chitin-amended SRCF soil. Herpetosiphonaceae was enriched only in chitin-amended CK soil. LEfSe and network analysis were used to predict chitinolytic and opportunistic species, and revealed that most previously reported chitinolytic bacteria were detected in the present study and new potential chitin degraders, including unidentified_Solibacterales, Gemmatimonadaceae, and Herpetosiphonaceae, were identified. Some members of Firmicutes, Actinobacteria, and Proteobacteria, including Bacillus, and Kitasatospora, were speculated to be opportunistic species. The findings improve our understanding of the effects of chitin degradation on carbon and nitrogen cycling in agricultural soil under different fertilization regimes and help to identify chitinolytic bacteria.
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Affiliation(s)
- Cai Hui
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hui Jiang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bing Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ran Wei
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yiping Zhang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qichun Zhang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Regulation of Streptomyces Chitinases by Two-Component Signal Transduction Systems and their Post Translational Modifications: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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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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Identification of Chitin Degrading Bacterial Strains Isolated from Bulk and Rhizospheric Soil. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.1.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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9
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Veliz EA, Martínez-Hidalgo P, Hirsch AM. Chitinase-producing bacteria and their role in biocontrol. AIMS Microbiol 2017; 3:689-705. [PMID: 31294182 PMCID: PMC6604996 DOI: 10.3934/microbiol.2017.3.689] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 11/30/2022] Open
Abstract
Chitin is an important component of the exteriors of insects and fungi. Upon degradation of chitin by a number of organisms, severe damage and even death may occur in pathogens and pests whose external surfaces contain this polymer. Currently, chemical fungicides and insecticides are the major means of controlling these disease-causing agents. However, due to the potential harm that these chemicals cause to the environment and to human and animal health, new strategies are being developed to replace or reduce the use of fungal- and pest-killing compounds in agriculture. In this context, chitinolytic microorganisms are likely to play an important role as biocontrol agents and pathogen antagonists and may also function in the control of postharvest rot. In this review, we discuss the literature concerning chitin and the basic knowledge of chitin-degrading enzymes, and also describe the biocontrol effects of chitinolytic microorganisms and their potential use as more sustainable pesticides and fungicides in the field.
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Affiliation(s)
- Esteban A Veliz
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
| | | | - Ann M Hirsch
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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Gupta R, Singh A, Srivastava M, Singh V, Gupta MM, Pandey R. Microbial modulation of bacoside A biosynthetic pathway and systemic defense mechanism in Bacopa monnieri under Meloidogyne incognita stress. Sci Rep 2017; 7:41867. [PMID: 28157221 PMCID: PMC5291102 DOI: 10.1038/srep41867] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/29/2016] [Indexed: 01/17/2023] Open
Abstract
Plant-associated beneficial microbes have been explored to fulfill the imperative function for plant health. However, their impact on the host secondary metabolite production and nematode disease management remains elusive. Our present work has shown that chitinolytic microbes viz., Chitiniphilus sp. MTN22 and Streptomyces sp. MTN14 singly as well as in combination modulated the biosynthetic pathway of bacoside A and systemic defense mechanism against Meloidogyne incognita in Bacopa monnieri. Interestingly, expression of bacoside biosynthetic pathway genes (3-Hydroxy-3-methylglutaryl coenzyme A reductase, mevalonate diphosphate decarboxylase, and squalene synthase) were upregulated in plants treated with the microbial combination in the presence as well as in absence of M. incognita stress. These microbes not only augmented bacoside A production (1.5 fold) but also strengthened host resistance via enhancement in chlorophyll a, defense enzymes and phenolic compounds like gallic acid, syringic acid, ferulic acid and cinnamic acid. Furthermore, elevated lignification and callose deposition in the microbial combination treated plants corroborate well with the above findings. Overall, the results provide novel insights into the underlying mechanisms of priming by beneficial microbes and underscore their capacity to trigger bacoside A production in B. monnieri under biotic stress.
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Affiliation(s)
- Rupali Gupta
- Department of Microbial Technology and Nematology, CSIR- Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
- Academy of Scientific and Innovative Research, CSIR- Central Institute of Medicinal and Aromatic Plants Campus, Lucknow 226015, Uttar Pradesh, India
| | - Akanksha Singh
- Department of Microbial Technology and Nematology, CSIR- Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
| | - Madhumita Srivastava
- Department of Analytical Chemistry, CSIR- Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
| | - Vivek Singh
- Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi, 221005, India
| | - M. M. Gupta
- Department of Analytical Chemistry, CSIR- Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
| | - Rakesh Pandey
- Department of Microbial Technology and Nematology, CSIR- Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India
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Campos M, Perruchon C, Karas PA, Karavasilis D, Diez MC, Karpouzas DG. Bioaugmentation and rhizosphere-assisted biodegradation as strategies for optimization of the dissipation capacity of biobeds. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 187:103-110. [PMID: 27886583 DOI: 10.1016/j.jenvman.2016.11.031] [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: 07/12/2016] [Revised: 10/12/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Biobeds are on-farm biodepuration systems whose efficiency rely on their high pesticide biodegradation capacity. We evaluated two optimization strategies, bioaugmentation and/or rhizosphere-assisted biodegradation, to maximize the dissipation capacity of biobeds. Iprodione was used as a model pesticide. Its dissipation and metabolism was determined in a biobed packing material inoculated with an iprodione-degrading Arthrobacter strain C1 (bioaugmentation, treatments B+C1) and/or seeded with ryegrass (rhizosphere-assisted biodegradation, treatments B+P). The impact of those strategies on the activity and composition of the microbial community was determined. Bioaugmentation accelerated the dissipation of iprodione which was further enhanced in the bioaugmented, rhizosphere-assisted treatment (treatment B+P+C1, Half-life (DT50) = 3.4 d), compared to the non-bioaugmented, non rhizosphere-assisted control (DT50 = 9.5 d, treatment B). Bioaugmentation resulted in the earlier formation of intermediate formation of metabolites I (3,5-dichlorophenyl-carboxamide), II (3,5-dichlorophenylurea acetate) and 3,5-dichloroaniline (3,5-DCA). The latter was further dissipated by the indigenous microbial community. Acid phosphatase (AP) and β-glucosidase (GLU) were temporarily stimulated in rhizosphere-assisted treatments, whereas a stimulation of the fluorescein diacetate (FDA) hydrolytic activity in the bioaugmented treatments coincided with the hydrolysis of iprodione. q-PCR showed that changes in the abundance of alpha-proteobacteria and firmicutes was driven by the presence of rhizosphere while bioaugmentation had no significant effect.
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Affiliation(s)
- M Campos
- Biotechnological Research Center Applied to the Environment (CIBAMA), Universidad de La Frontera, Temuco, Chile
| | - C Perruchon
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - P A Karas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - D Karavasilis
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - M C Diez
- Chemical Engineering Department, Universidad de La Frontera, Chile
| | - D G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece.
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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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14
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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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15
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Francioli D, Schulz E, Lentendu G, Wubet T, Buscot F, Reitz T. Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies. Front Microbiol 2016; 7:1446. [PMID: 27683576 PMCID: PMC5022044 DOI: 10.3389/fmicb.2016.01446] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/30/2016] [Indexed: 02/02/2023] Open
Abstract
Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
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Affiliation(s)
- Davide Francioli
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Elke Schulz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern Kaiserslautern, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
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16
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A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure. BIOMED RESEARCH INTERNATIONAL 2015; 2015:857639. [PMID: 26273652 PMCID: PMC4529920 DOI: 10.1155/2015/857639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/31/2015] [Accepted: 04/15/2015] [Indexed: 11/26/2022]
Abstract
Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering.
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17
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Srinivasiah S, Lovett J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE. Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation. FEMS Microbiol Ecol 2015; 91:fiv063. [PMID: 26149131 DOI: 10.1093/femsec/fiv063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2015] [Indexed: 11/14/2022] Open
Abstract
Viruses are highly abundant in soils with their numbers exceeding those of cooccurring bacterial cells by 10- to over 1000-fold. Water and organic matter content influence the magnitude of the viral-to-bacterial ratio in soils; thus, ecosystem type and land use shape interactions between viral and host microbial communities in soils. Less understood are the shorter term interactions between viral and host communities that ultimately maintain the large viral standing stock within soils. This study examined short-term dynamics of viral and bacterial communities in soils to determine whether the growth of soil bacterial communities results in the production of soil viruses, and if viral community responses occur within specific populations. In microcosms amended with different carbon sources, increases in viral abundance (VA) accompanied increases in bacterial abundance (BA) and bacterial respiration rate (BRR). The timing and intensity of increases in BA, VA and BRR were different across C sources suggesting differences in the predominant mode of viral replication within growth-stimulated bacterial populations. Moreover, compositional changes occurred in soil bacterial and viral communities indicating that new viral production arose from a subset of host populations. To our knowledge, these are the first observations of soil viral populations responding to short-term changes in soil bacterial communities.
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Affiliation(s)
- Sharath Srinivasiah
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Jacqueline Lovett
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Dhritiman Ghosh
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - Krishnakali Roy
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mark Radosevich
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
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18
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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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19
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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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20
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Viens P, Dubeau MP, Kimura A, Desaki Y, Shinya T, Shibuya N, Saito A, Brzezinski R. Uptake of chitosan-derived D-glucosamine oligosaccharides in Streptomyces coelicolor A3(2). FEMS Microbiol Lett 2015; 362:fnv048. [DOI: 10.1093/femsle/fnv048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2015] [Indexed: 12/23/2022] Open
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21
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Hjort K, Presti I, Elväng A, Marinelli F, Sjöling S. Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics. Appl Microbiol Biotechnol 2014; 98:2819-28. [PMID: 24121932 PMCID: PMC3936118 DOI: 10.1007/s00253-013-5287-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/08/2013] [Accepted: 09/12/2013] [Indexed: 12/16/2022]
Abstract
Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F175DGIDIDWE183, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes.
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Affiliation(s)
- Karin Hjort
- School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ilaria Presti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, 21100 Italy
| | - Annelie Elväng
- School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, 21100 Italy
- The Protein Factory Research Center, Politecnico of Milano, ICRM CNR and University of Insubria, Varese, 21100 Italy
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden
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22
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Johnson-Rollings AS, Wright H, Masciandaro G, Macci C, Doni S, Calvo-Bado LA, Slade SE, Vallin Plou C, Wellington EMH. Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics. THE ISME JOURNAL 2014; 8:2148-50. [PMID: 25036924 PMCID: PMC4184004 DOI: 10.1038/ismej.2014.130] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
Functionally important proteins at the interface of cell and soil are of potentially low abundance when compared with commonly recovered intracellular proteins. A novel approach was developed and used to extract the metaexoproteome, the subset of proteins found outside the cell, in the context of a soil enriched with the nitrogen-containing recalcitrant polymer chitin. The majority of proteins recovered was of bacterial origin and localized to the outer membrane or extracellular milieu. A wide variety of transporter proteins were identified, particularly those associated with amino-acid and phosphate uptake. The metaexoproteome extract retained chitinolytic activity and we were successful in detecting Nocardiopsis-like chitinases that correlated with the glycoside hydrolase family 18 (GH18) chi gene data and metataxonomic analysis. Nocardiopsis-like chitinases appeared to be solely responsible for chitinolytic activity in soil. This is the first study to detect and sequence bacterial exoenzymes with proven activity in the soil enzyme pool.
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Affiliation(s)
| | - Helena Wright
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Cristina Macci
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | - Serena Doni
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | | | - Susan E Slade
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Carlos Vallin Plou
- Grupo de Biotecnología, CEIEB, IFAL, Universidad de La Habana, Havana, Cuba
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23
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Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W. Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 2014; 18:38-49. [DOI: 10.1111/1462-2920.12545] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Yani Bai
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Aas Norway
| | - Anna M. Kielak
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Institute of Biology; Faculty of Science; Leiden University; Leiden The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Soil Quality Group; Wageningen University; P.O. Box 9101 Wageningen 6700 HB The Netherlands
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24
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Wang J, Dong H, Wang W, Gu JD. Reverse-transcriptional gene expression of anammox and ammonia-oxidizing archaea and bacteria in soybean and rice paddy soils of Northeast China. Appl Microbiol Biotechnol 2014; 98:2675-86. [PMID: 24077726 DOI: 10.1007/s00253-013-5242-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
The relative gene expression of hydrazine oxidoreductase encoding gene (hzo) for anaerobic ammonium oxidizing bacteria (anammox) and ammonia monooxygenase encoding gene (amoA) for both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in Sanjiang Plain soybean and rice paddy soils of Northeast China was investigated by using real-time reverse-transcriptional quantitative PCR. Metabolically active populations of anammox, AOA, and AOB in rice paddy soils were evident by the presence and successful quantification of hzo mRNA and amoA mRNA genes. The expression ratio of amoA gene for both AOA and AOB varied between soybean soils and different rice paddy soils while the expression of hzo gene for anammox was detectable only in rice paddy soils by showing a diverse relative expression ratio in each soil sample. Gene expression of both archaeal and bacterial amoA genes in rice paddy soils differed among the three sampling depths, but that of hzo was not. Both archaeal and bacterial amoA genes showed an increase trend of expression level with continuation of rice paddy cultivation, but the low expression ratio of hzo gene indicated a relatively small contribution of anammox in overall removal of inorganic nitrogen through N2 even under anoxic and high nitrogen input in agriculture. Bacterial amoA gene from two soybean fields and three rice paddy fields were also analyzed for community composition by denaturing gradient gel electrophoresis fingerprint. Community shift was observed between soybean and paddy fields and within each of them. The consistent occurrence of three bands 5, 6, and 7 in all samples showed their high adaptability for both arid cultivation and continuous rice paddy cultivation. Our data suggest that AOA and AOB are playing a more important role in nitrogen transformation in agricultural soils in oxic or anoxic environment and anammox bacteria may also contribute but in a less extent to N transformation in these agricultural soils under anoxic condition.
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25
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Jacquiod S, Franqueville L, Cécillon S, M. Vogel T, Simonet P. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach. PLoS One 2013; 8:e79699. [PMID: 24278158 PMCID: PMC3835784 DOI: 10.1371/journal.pone.0079699] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- Microbial Molecular Ecology Group, Section of Microbiology, København Universitat, København, Denmark
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- * E-mail:
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Fang C, Xu T, Ye C, Huang L, Wang Q, Lin W. Method for RNA extraction and cDNA library construction from microbes in crop rhizosphere soil. World J Microbiol Biotechnol 2013; 30:783-9. [PMID: 24078111 DOI: 10.1007/s11274-013-1504-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/20/2013] [Indexed: 10/26/2022]
Abstract
Techniques to analyze the transcriptome of the soil rhizosphere are essential to reveal the interactions and communications between plants and microorganisms in the soil ecosystem. In this study, different volumes of Al₂(SO₄)₃ were added to rhizosphere soil samples to precipitate humic substances, which interfere with most procedures of RNA and DNA analyses. After humic substances were precipitated, cells of soil microorganisms were broken by vortexing with glass beads, and then DNA and RNA were recovered using Tris-HCl buffer with LiCl, SDS, and EDTA. The crude extract was precipitated and dissolved in RNAse-free water, and then separated by agarose gel electrophoresis. We determined the optimum volume of Al₂(SO₄)₃ for treating rhizosphere soil of rice, tobacco, sugarcane, Rehmannia glutinosa, and Pseudostellaria heterophylla. The crude nucleic acids extract from rice soil was treated with DNase I and then RNA was purified using a gel filtration column. The purified RNA was reverse-transcribed into single-strand cDNA and then ligated with an adaptor at each end before amplifying ds cDNA. The ds cDNA was sub-cloned for subsequent gene sequence analysis. We conducted qPCR to amplify 16S ribosomal DNA and observed highly efficient amplification. These results show that the extraction method can be optimized to isolate and obtain high-quality nucleic acids from microbes in different rhizosphere soils, suitable for genomic and post-genomic analyses.
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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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Du H, Lu H, Xu Y, Du X. Community of environmental streptomyces related to geosmin development in Chinese liquors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:1343-1348. [PMID: 23373536 DOI: 10.1021/jf3040513] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Diverse Streptomyces species act as geosmin producers in the Chinese liquor-making process. In this paper, the ecology of these Streptomyces species was analyzed using denaturing gradient gel electrophoresis (DGGE) of amplified Actinobacteria -specified rDNA. The result showed that Streptomyces were widely distributed during Daqu incubation, and multiple processing, geographic, and climate factors can affect their distribution and diversity. The genes associated with geosmin production were characterized in four geosmin-producing Streptomyces strains, all of which were isolated from geosmin-contaminated Daqu. On the basis of this information, a real-time PCR method was developed, enabling the detection of traces of Streptomyces in complex solid-state matrices. The primer was targeted at the gene coding for geosmin synthase (geoA). The real-time PCR method was found to be specific for geosmin-producing Streptomyces and did not show any cross-reactivity with geosmin-negative isolates, which are frequently present in the Chinese liquor-brewing process. Quantification of geoA in the Chinese liquor-making process could permit the monitoring of the level of geosmin producers prior to the occurrence of geosmin production. Comparison of the qPCR results based on the gene encoding geosmin synthase and Actinobacteria-specified rDNA showed that about 1-10% of the Actinobacteria carry the geosmin synthesis gene.
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Affiliation(s)
- Hai Du
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, China 214122
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Kielak AM, Cretoiu MS, Semenov AV, Sørensen SJ, van Elsas JD. Bacterial chitinolytic communities respond to chitin and pH alteration in soil. Appl Environ Microbiol 2013; 79:263-72. [PMID: 23104407 PMCID: PMC3536121 DOI: 10.1128/aem.02546-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/21/2012] [Indexed: 01/21/2023] Open
Abstract
Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.
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Affiliation(s)
- Anna M. Kielak
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Mariana Silvia Cretoiu
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Alexander V. Semenov
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
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Hamid R, Khan MA, Ahmad M, Ahmad MM, Abdin MZ, Musarrat J, Javed S. Chitinases: An update. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2013; 5:21-9. [PMID: 23559820 PMCID: PMC3612335 DOI: 10.4103/0975-7406.106559] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 03/16/2012] [Accepted: 05/21/2012] [Indexed: 11/04/2022] Open
Abstract
Chitin, the second most abundant polysaccharide in nature after cellulose, is found in the exoskeleton of insects, fungi, yeast, and algae, and in the internal structures of other vertebrates. Chitinases are enzymes that degrade chitin. Chitinases contribute to the generation of carbon and nitrogen in the ecosystem. Chitin and chitinolytic enzymes are gaining importance for their biotechnological applications, especially the chitinases exploited in agriculture fields to control pathogens. Chitinases have a use in human health care, especially in human diseases like asthma. Chitinases have wide-ranging applications including the preparation of pharmaceutically important chitooligosaccharides and N-acetyl D glucosamine, preparation of single-cell protein, isolation of protoplasts from fungi and yeast, control of pathogenic fungi, treatment of chitinous waste, mosquito control and morphogenesis, etc. In this review, the various types of chitinases and the chitinases found in different organisms such as bacteria, plants, fungi, and mammals are discussed.
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Affiliation(s)
- Rifat Hamid
- Department of Biochemistry, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Minhaj A. Khan
- Department of Biochemistry, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Mahboob Ahmad
- Department of Biochemistry, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Malik Mobeen Ahmad
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Malik Zainul Abdin
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, India
| | - Javed Musarrat
- Department of Microbiology, Faculty of Agricultural Sciences, AMU, Aligarh, India
| | - Saleem Javed
- Department of Biochemistry, Faculty of Science, Jamia Hamdard, New Delhi, India
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Chitin-induced gene expression in secondary metabolic pathways of Streptomyces coelicolor A3(2) grown in soil. Appl Environ Microbiol 2012; 79:707-13. [PMID: 23124229 DOI: 10.1128/aem.02217-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microarray analyses revealed that the expression of genes for secondary metabolism together with that of primary metabolic genes was induced by chitin in autoclaved soil cultures of Streptomyces coelicolor A3(2). The data also indicated that DasR was involved in the regulation of gene expression for chitin catabolism, secondary metabolism, and stress responses.
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Cretoiu MS, Kielak AM, Abu Al-Soud W, Sørensen SJ, van Elsas JD. Mining of unexplored habitats for novel chitinases--chiA as a helper gene proxy in metagenomics. Appl Microbiol Biotechnol 2012; 94:1347-58. [PMID: 22526805 PMCID: PMC3353111 DOI: 10.1007/s00253-012-4057-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/26/2012] [Accepted: 03/27/2012] [Indexed: 11/29/2022]
Abstract
The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encompassed (1) classical overall enzymatic assays, (2) chiA gene abundance measurement by qPCR, (3) chiA gene pyrosequencing, and (4) chiA gene-based PCR-DGGE was used. The chiA gene pyrosequencing is unprecedented, as it is the first massive parallel sequencing of this gene. The data obtained showed the existence across habitats of core bacterial communities responsible for chitin assimilation irrespective of ecosystem origin. Conversely, there were habitat-specific differences. In addition, a suite of sequences were obtained that are as yet unregistered in the chitinase database. In terms of chiA gene abundance and diversity, typical low-abundance/diversity versus high-abundance/diversity habitats was distinguished. From the combined data, we selected chitin-amended agricultural soil, the rhizosphere of the Arctic plant Oxyria digyna and the freshwater sponge Ephydatia fluviatilis as the most promising habitats for subsequent bioexploration. Thus, the screening strategy used is proposed as a guide for further metagenomics-based exploration of the selected habitats.
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Diversity analysis of streptomycetes and associated phosphotranspherase genes in soil. PLoS One 2012; 7:e35756. [PMID: 22540003 PMCID: PMC3335164 DOI: 10.1371/journal.pone.0035756] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/26/2012] [Indexed: 11/23/2022] Open
Abstract
An attempt was made to verify the observation that Streptomyces griseus was prevalent in soil based on isolation work. A genus-specific PCR was developed for Streptomyces based on the housekeeping gene atpD and used to investigate species diversity within selected soils. The presence of S. griseus was investigated to determine coexistence of resistance-only streptomycin phosphotransferase (strA) in the same soil as streptomycin producers. Two additional PCR-based assays were developed; one specific for strA in association with production, the other for more diverse strA and other related phosphotranferases. Both the S. griseus atpD and strA genes were below the PCR detection limit in all soils examined. A number of more diverse phosphotransferase genes were amplified, a minority of which may be associated with streptomycin production. We conclude that neither streptomycin producers nor S. griseus are prevalent in the fresh or chitin and starch-amended soils examined (less than 0.1% of soil actinobacteria). One of the soil sites had received plantomycin (active ingredient: streptomycin) and diversity studies suggested that this altered the streptomycete populations present in the soil.
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35
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Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems. Res Microbiol 2011; 162:820-31. [DOI: 10.1016/j.resmic.2011.01.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/11/2011] [Indexed: 11/15/2022]
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Souza CP, Almeida BC, Colwell RR, Rivera ING. The importance of chitin in the marine environment. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:823-830. [PMID: 21607543 DOI: 10.1007/s10126-011-9388-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 02/15/2011] [Indexed: 05/30/2023]
Abstract
Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.
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Affiliation(s)
- Claudiana P Souza
- Instituto de Ciências Biomédicas, Universidade de São Paulo, 1374, Prof. Lineu Prestes Av., 05508-000, São Paulo, Brazil
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Bhuiyan FA, Nagata S, Ohnishi K. Novel chitinase genes from metagenomic DNA prepared from marine sediments in southwest Japan. Pak J Biol Sci 2011; 14:204-11. [PMID: 21870643 DOI: 10.3923/pjbs.2011.204.211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Chitinase degrades chitin which comprises an important source of carbon and nitrogen in the marine environment. The aim of this study was to evaluate the population of chitinases in the marine sediments in southwest Japan. We collected marine sediments from eutrophic inner bay and offshore. Chitin-degrading bacteria were enriched from both sediments. Metagenomic DNA was isolated from the enriched chitin-degrading bacterial cell culture. At the same time, 25 chitin-degrading bacteria were isolated from the enriched culture. Partial fragments of chitinase genes were successfully amplified with degenerate primers designed for the glycoside hydrolase 18 family. We analyzed chitinase gene sequences of about 500 clones from metagenomic DNA prepared from chitin-degrading bacteria. Based on translated amino acid sequences, chitinases were grouped into five groups. Chitinases in groups II and III was most abundant and close to chitinase genes of several species of proteobacteria. On the other hand, chitinases in groups I, IV and V were unique and distinct from the known chitinases. These results indicate that the marine sediments used in this study contain diversity of chitinase genes.
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Affiliation(s)
- F A Bhuiyan
- Department of Applied Bioresource Science, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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Nazari B, Saito A, Kobayashi M, Miyashita K, Wang Y, Fujii T. High expression levels of chitinase genes in Streptomyces coelicolor A3(2) grown in soil. FEMS Microbiol Ecol 2011; 77:623-35. [PMID: 21631548 DOI: 10.1111/j.1574-6941.2011.01143.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although Streptomyces species are major chitin-degraders in soil ecosystems, the expression of the diverse chitinase genes within Streptomyces coelicolor grown in soil has not been assessed. As a first step, the induction pattern of nine chitinase genes in S. coelicolor growing in autoclaved soil was compared with those in liquid cultures. The relative expression levels of nine chitinase genes were measured using real-time reverse transcription PCR. The expression of all chitinase genes was induced by chitin in both autoclaved soil and liquid cultures, but to different levels. The expression levels of five chitinase genes in autoclaved soil were significantly higher than those in the liquid cultures. In particular, a putative chitinase gene, chitinase H, showed the highest induction in autoclaved soil. The same induction pattern was confirmed in nonautoclaved soil, indicating that soil contains some factors affecting the expression of chitinase genes. The chiH gene product, ChiH, cloned in Streptomycetes lividans was secreted and exhibited chitin degradation activity that was stable within a wide range of acidic pHs. The disruption of dasR, a transcriptional regulator for the uptake of N-acetylglucosamine, abolished the expression of chiH, demonstrating that DasR is required for the regulation of ChiH expression.
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Affiliation(s)
- Behnam Nazari
- Institute of Applied Biochemistry, Graduate School of Life and Environmental Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
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Abstract
Phylogeny-based analysis of chitinase and 16S rRNA genes from metagenomic data suggests that salinity is a major driver for the distribution of both chitinolytic and total bacterial communities in aquatic systems. Additionally, more acidic chitinase proteins were observed with increasing salinity. Congruent habitat separation was further observed for both genes according to latitude and proximity to the coastline. However, comparison of chitinase and 16S rRNA genes extracted from different geographic locations showed little congruence in distribution. There was no indication that dispersal limited the global distribution of either gene.
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Hjort K, Bergström M, Adesina MF, Jansson JK, Smalla K, Sjöling S. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil. FEMS Microbiol Ecol 2009; 71:197-207. [PMID: 19922433 DOI: 10.1111/j.1574-6941.2009.00801.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF(103) of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.
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Affiliation(s)
- Karin Hjort
- Södertörn University, School of Life Sciences, Huddinge, Sweden
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O'Neill B, Grossman J, Tsai MT, Gomes JE, Lehmann J, Peterson J, Neves E, Thies JE. Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification. MICROBIAL ECOLOGY 2009; 58:23-35. [PMID: 19381712 DOI: 10.1007/s00248-009-9515-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 03/18/2009] [Indexed: 05/09/2023]
Abstract
Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.
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Affiliation(s)
- B O'Neill
- Department of Crop and Soil Sciences, Cornell University, 235 Emerson Hall, Ithaca, NY 14853, USA
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Islam SMA, Hong SJ, Cho KM, Math RK, Heo JY, Lee YH, Lee KS, Yun HD. Bacterial diversity and structural changes of oyster shell during 1-year storage. MICROBIAL ECOLOGY 2009; 57:221-228. [PMID: 18762853 DOI: 10.1007/s00248-008-9439-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 08/04/2008] [Indexed: 05/26/2023]
Abstract
We examined the biodiversity of bacteria associated with oyster-shell waste during a 1-year storage period using 16S ribosomal DNA analysis. Temperature variation and structural changes of oyster shell were observed during storage. Initial and final temperatures were at 16-17 degrees C, but a high temperature of about 60 degrees C was recorded after approximately 6 months of storage. The crystal structure and nanograin of the oyster shell surface were sharp and large in size initially and became gradually blunter and smaller over time. Phylogenetic analysis revealed that Firmicutes were dominant in the oyster-shell waste initially, during the high-temperature stage, and after 1 year of storage (making up >65% of the biodiversity at all three sampling times). Bacillus licheniformis was presumed as the predominate Firmicutes present. These bacteria are likely to have important roles in the biodegradation of oyster shell.
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Affiliation(s)
- Shah Md Asraful Islam
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Chinju, 660-701, Republic of Korea
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Recent Advances in Functional Genomics and Proteomics of Plant Associated Microbes. SOIL BIOLOGY 2008. [DOI: 10.1007/978-3-540-75575-3_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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LeCleir GR, Buchan A, Maurer J, Moran MA, Hollibaugh JT. Comparison of chitinolytic enzymes from an alkaline, hypersaline lake and an estuary. Environ Microbiol 2007; 9:197-205. [PMID: 17227424 DOI: 10.1111/j.1462-2920.2006.01128.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We examined the genetic and physiological characteristics of chitin degrading enzymes expressed by fosmids cloned from two strains of chitinolytic gammaproteobacteria isolated from alkaline, hypersaline Mono Lake, California; and from a metagenomic library derived from an estuarine bacterial community (Dean Creek, Sapelo Island, GA, USA). The Mono Lake chitinolytic enzymes presented unique adaptations in terms of halo- and alkalitolerance. The sequence from one of the Mono Lake isolates (strain 12A) was a conventional family 18 glycosyl hydrolase; however, the expressed protein had a novel secondary activity peak at pH 10. We obtained a novel family 20 glycosyl hydrolase sequence from Mono Lake strain AI21. The activity of the expressed protein had a pH optimum of 10, several pH units higher than any other enzyme currently assigned to this family, and the enzyme retained 80% of its activity at pH 11. The enzyme was also halotolerant, retaining activity in salt solutions of up to 225 g l(-1). Sequence analysis indicated a molecular weight of approximately 90 kDa for the protein, and that it contained two active sites. Culture supernatant contained two chitinolytic proteins, 45 and 31 kDa, suggesting possible post-expression modification of the gene product. In contrast, the sequence found in the estuarine metagenomic library and the functional characteristics of the protein expressed from it were those of a conventional family 18 glycosyl hydrolase.
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Affiliation(s)
- Gary R LeCleir
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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Hjort K, Lembke A, Speksnijder A, Smalla K, Jansson JK. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. MICROBIAL ECOLOGY 2007; 53:399-413. [PMID: 16944345 DOI: 10.1007/s00248-006-9120-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/01/2006] [Indexed: 05/11/2023]
Abstract
The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia, Kitasatospora, and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas-specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil.
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Affiliation(s)
- Karin Hjort
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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Poulain AJ, Ní Chadhain SM, Ariya PA, Amyot M, Garcia E, Campbell PGC, Zylstra GJ, Barkay T. Potential for mercury reduction by microbes in the high arctic. Appl Environ Microbiol 2007; 73:2230-8. [PMID: 17293515 PMCID: PMC1855672 DOI: 10.1128/aem.02701-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions.
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Affiliation(s)
- Alexandre J Poulain
- Groupe de Recherche Inter-universitaire en Limnologie (GRIL), Département des Sciences Biologiques, Université de Montréal, C. P. 6128, Succursale Centre-Ville, Pavillon Marie-Victorin, Montréal, Québec, Canada H3C 3J7
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Lian M, Lin S, Zeng R. Chitinase gene diversity at a deep sea station of the east Pacific nodule province. Extremophiles 2007; 11:463-7. [PMID: 17225927 DOI: 10.1007/s00792-006-0057-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 12/06/2006] [Indexed: 11/30/2022]
Abstract
The Pacific nodule province covered about 4.5 million km(2) in the east tropical Pacific with an abundance of polymetallic nodules at the seafloor. In view of the environmental protection and resource preservation, the survey of biodiversity was important during the reconnaissance and exploitation in this area. As one of the important component of the deep sea ecosystem, the microbial community in the Pacific nodule province was still largely unknown. The chitinolytic bacteria diversity in deep-sea sediment of a station within the Pacific nodule province was examined by molecular technology. A total of 18 chitinase genes were detected by a set of degenerate PCR primer specific for chiA gene fragment of family 18 chitinase. Most of them belonged to the Serratia-like chitinase. Eight genes had different amino acid sequences in the conserved motif, encompassing the catalytic site among the ChiA protein of family 18 glycosyl hydrolases, and clustered in an independent clade on the phylygenetic tree.
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Affiliation(s)
- Mingzhu Lian
- Key Lab of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, Daxue road, No. 178, Xiamen, 361005, China
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Ikeda S, Ytow N, Ezura H, Minamisawa K, Miyashita K, Fujimura T. Analysis of Molecular Diversity of Bacterial Chitinase Genes in the Maize Rhizosphere Using Culture-Independent Methods. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.71] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Xiao X, Yin X, Lin J, Sun L, You Z, Wang P, Wang F. Chitinase genes in lake sediments of Ardley Island, Antarctica. Appl Environ Microbiol 2006; 71:7904-9. [PMID: 16332766 PMCID: PMC1317360 DOI: 10.1128/aem.71.12.7904-7909.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of gamma-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.
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Affiliation(s)
- Xiang Xiao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
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