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De la Cruz-Barrón M, Cruz-Mendoza A, Navarro-Noya YE, Ruiz-Valdiviezo VM, Ortíz-Gutiérrez D, Ramírez-Villanueva DA, Luna-Guido M, Thierfelder C, Wall PC, Verhulst N, Govaerts B, Dendooven L. The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices. MICROBIAL ECOLOGY 2017; 73:135-152. [PMID: 27538875 DOI: 10.1007/s00248-016-0807-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.
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Affiliation(s)
| | | | - Yendi E Navarro-Noya
- Cátedras CONACYT-Universidad Autónoma de Tlaxcala, Av. Universidad 1, C.P., 90062, Tlaxcala, Mexico
| | | | | | | | - Marco Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico
| | - Cristian Thierfelder
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Patrick C Wall
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico.
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252
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McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proc Natl Acad Sci U S A 2016; 113:14324-14329. [PMID: 27911781 PMCID: PMC5167157 DOI: 10.1073/pnas.1608917113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures, dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reacts with substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds.
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Affiliation(s)
- Ryan P McAndrew
- Joint BioEnergy Institute, Emeryville, CA 94608;
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Noppadon Sathitsuksanoh
- Joint BioEnergy Institute, Emeryville, CA 94608
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40292
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, KY 40292
| | - Michael M Mbughuni
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706
| | - Richard A Heins
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Jose H Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Anthe George
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Kenneth L Sale
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Brian G Fox
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA 94608;
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
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253
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Opportunities and challenges in biological lignin valorization. Curr Opin Biotechnol 2016; 42:40-53. [DOI: 10.1016/j.copbio.2016.02.030] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/24/2016] [Indexed: 02/08/2023]
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254
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Behbahani M, Mohabatkar H, Nosrati M. Analysis and comparison of lignin peroxidases between fungi and bacteria using three different modes of Chou’s general pseudo amino acid composition. J Theor Biol 2016; 411:1-5. [DOI: 10.1016/j.jtbi.2016.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/27/2016] [Accepted: 09/01/2016] [Indexed: 02/02/2023]
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255
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Pathak P, Kaur P, Bhardwaj NK. Chapter 6 Microbial Enzymes for Pulp and Paper Industry. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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256
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Weselowski B, Nathoo N, Eastman AW, MacDonald J, Yuan ZC. Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production. BMC Microbiol 2016; 16:244. [PMID: 27756215 PMCID: PMC5069919 DOI: 10.1186/s12866-016-0860-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paenibacillus polymyxa is a plant-growth promoting rhizobacterium that could be exploited as an environmentally friendlier alternative to chemical fertilizers and pesticides. Various strains have been isolated that can benefit agriculture through antimicrobial activity, nitrogen fixation, phosphate solubilization, plant hormone production, or lignocellulose degradation. However, no single strain has yet been identified in which all of these advantageous traits have been confirmed. RESULTS P. polymyxa CR1 was isolated from degrading corn roots from southern Ontario, Canada. It was shown to possess in vitro antagonistic activities against the common plant pathogens Phytophthora sojae P6497 (oomycete), Rhizoctonia solani 1809 (basidiomycete fungus), Cylindrocarpon destructans 2062 (ascomycete fungus), Pseudomonas syringae DC3000 (bacterium), and Xanthomonas campestris 93-1 (bacterium), as well as Bacillus cereus (bacterium), an agent of food-borne illness. P. polymyxa CR1 enhanced growth of maize, potato, cucumber, Arabidopsis, and tomato plants; utilized atmospheric nitrogen and insoluble phosphorus; produced the phytohormone indole-3-acetic acid (IAA); and degraded and utilized the major components of lignocellulose (lignin, cellulose, and hemicellulose). CONCLUSIONS P. polymyxa CR1 has multiple beneficial traits that are relevant to sustainable agriculture and the bio-economy. This strain could be developed for field application in order to control pathogens, promote plant growth, and degrade crop residues after harvest.
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Affiliation(s)
- Brian Weselowski
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Naeem Nathoo
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Biology, Biological and Geological Sciences Building, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Alexander William Eastman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
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257
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Carrillo D, Cruz LF, Kendra PE, Narvaez TI, Montgomery WS, Monterroso A, De Grave C, Cooperband MF. Distribution, Pest Status and Fungal Associates of Euwallacea nr. fornicatus in Florida Avocado Groves. INSECTS 2016; 7:E55. [PMID: 27754408 PMCID: PMC5198203 DOI: 10.3390/insects7040055] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/26/2016] [Accepted: 10/05/2016] [Indexed: 01/03/2023]
Abstract
Members of a complex of cryptic species, that correspond morphologically to the ambrosia beetle Euwallacea fornicatus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae), were recently found attacking avocado (Persea americana Mill.) in Israel and California. In early 2016, an outbreak of another member of this species complex was detected infesting approximately 1500 avocado trees in an avocado orchard at Homestead, Florida. An area-wide survey was conducted in commercial avocado groves of Miami-Dade County, Florida to determine the distribution and abundance of E. nr. fornicatus, to identify different populations of E. nr. fornicatus and their fungal associates, and to assess the extent of damage to avocado trees. Ewallacea nr. fornicatus were captured in 31 of the 33 sampled sites. A sample of 35 beetles from six different locations was identified as E. nr. fornicatus sp. #2, which is genetically distinct from the species causing damage in California and Israel. Eleven fungal associates were identified: an unknown Fusarium sp., AF-8, AF-6, Graphium euwallaceae, Acremonium sp. Acremonium morum, Acremonium masseei, Elaphocordyceps sp. and three yeast species. The unknown Fusarium isolates were the most abundant and frequently found fungus species associated with adult beetles and lesions surrounding the beetle galleries. In addition to fungal associates, three bacteria species were found associated with adult E. nr. fornicatus. Visual inspections detected significant damage in only two orchards. A large number of beetles were captured in locations with no apparent damage on the avocado trees suggesting that E. nr. fornicatus are associated with other host(s) outside the groves or with dead trees or branches inside the groves. More research is needed to determine the potential threat E. nr. fornicatus and its fungal associates pose to the avocado industry and agricultural and natural ecosystems in Florida.
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Affiliation(s)
- Daniel Carrillo
- IFAS-Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Luisa F Cruz
- IFAS-Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Paul E Kendra
- Subtropical Horticulture Research Station, Agricultural Research Service, United States Department of Agriculture, Miami, FL 33158, USA.
| | - Teresa I Narvaez
- IFAS-Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Wayne S Montgomery
- Subtropical Horticulture Research Station, Agricultural Research Service, United States Department of Agriculture, Miami, FL 33158, USA.
| | | | - Charlotte De Grave
- IFAS-Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
- Gembloux Agro-Bio Tech, University of Liège, Gembloux B-5030, Belgium.
| | - Miriam F Cooperband
- Otis Laboratory, Plant Protection and Quarantine's Science and Technology, Animal and Plant Health Inspection Service, United States Department of Agriculture, Buzzards Bay, MA 02542, USA.
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258
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Recovery and Utilization of Lignin Monomers as Part of the Biorefinery Approach. ENERGIES 2016. [DOI: 10.3390/en9100808] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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259
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Chen C, Li T. Bacterial dye-decolorizing peroxidases: Biochemical properties and biotechnological opportunities. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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260
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Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 2016; 113:E5802-E5811. [PMID: 27634497 DOI: 10.1073/pnas.1606043113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.
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261
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Machado LFM, Dixon N. Development and substrate specificity screening of an in vivo biosensor for the detection of biomass derived aromatic chemical building blocks. Chem Commun (Camb) 2016; 52:11402-11405. [PMID: 27722239 PMCID: PMC5048394 DOI: 10.1039/c6cc04559f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/24/2016] [Indexed: 12/01/2022]
Abstract
Measuring substrate and/or product concentration can create a major bottleneck for synthetic and biosynthetic processes. Here we report the development and substrate screening of a whole cell biosensor to detect biomass-derived aromatic chemical building blocks, supporting the use of sustainable feedstocks in the bulk and fine chemical industries.
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Affiliation(s)
- Leopoldo F M Machado
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Neil Dixon
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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262
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Wang L, Nie Y, Tang YQ, Song XM, Cao K, Sun LZ, Wang ZJ, Wu XL. Diverse Bacteria with Lignin Degrading Potentials Isolated from Two Ranks of Coal. Front Microbiol 2016; 7:1428. [PMID: 27667989 PMCID: PMC5016517 DOI: 10.3389/fmicb.2016.01428] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/29/2016] [Indexed: 11/13/2022] Open
Abstract
Taking natural coal as a “seed bank” of bacterial strains able to degrade lignin that is with molecular structure similar to coal components, we isolated 393 and 483 bacterial strains from a meager lean coal sample from Hancheng coalbed and a brown coal sample from Bayannaoer coalbed, respectively, by using different media. Statistical analysis showed that isolates were significantly more site-specific than medium-specific. Of the 876 strains belonging to 27 genera in Actinobacteria, Firmicutes, and Proteobacteria, 612 were positive for lignin degradation function, including 218 strains belonging to 35 species in Hancheng and 394 strains belonging to 19 species in Zhongqi. Among them, the dominant lignin-degrading strains were Thauera (Hancheng), Arthrobacter (Zhongqi) and Rhizobium (both). The genes encoding the laccases- or laccase-like multicopper oxidases, key enzymes in lignin production and degradation, were detected in three genera including Massila for the first time, which was in high expression by real time PCR (qRT-PCR) detection, confirming coal as a good seed bank.
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Affiliation(s)
- Lu Wang
- School of Earth and Space Sciences, Peking UniversityBeijing, China; College of Engineering, Peking UniversityBeijing, China
| | - Yong Nie
- College of Engineering, Peking University Beijing, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University Chengdu, China
| | - Xin-Min Song
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development Beijing, China
| | - Kun Cao
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Li-Zhu Sun
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Zhi-Jian Wang
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Xiao-Lei Wu
- College of Engineering, Peking University Beijing, China
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263
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Zhao D, Liu P, Pan C, Du R, Ping W, Ge J. Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02. Sci Rep 2016; 6:31812. [PMID: 27585559 PMCID: PMC5009381 DOI: 10.1038/srep31812] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/26/2016] [Indexed: 12/02/2022] Open
Abstract
High-throughput sequencing and GC-MS (gas chromatography-mass spectrometry) were jointly used to reveal the bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting. The inoculation of Bacillus cereus HDYM-02 decreased bacterial richness and diversity. This inoculum led to the replacement of Enterobacteriaceae by Bacillaceae. The level of aerobic Pseudomonadaceae (mainly Azotobacter) and anaerobic Clostridiaceae_1 gradually increased and decreased, respectively. Following the addition of B. cereus HDYM-02, the dominant groups were all degumming enzyme producers or have been proven to be involved in microbial retting throughout the entire retting period. These results could be verified by the metabolite changes, either degumming enzymes or their catalytic products galacturonic acid and reducing sugars. The GC-MS data showed a clear separation between flax retting with and without B. cereus HDYM-02, particularly within the first 72 h. These findings reveal the important bacterial groups that are involved in fiber retting and will facilitate improvements in the retting process.
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Affiliation(s)
- Dan Zhao
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
| | - Pengfei Liu
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Chao Pan
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Renpeng Du
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Wenxiang Ping
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
| | - Jingping Ge
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
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264
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Lopez Pinar A, Rauhut D, Ruehl E, Buettner A. Effects of Botrytis cinerea and Erysiphe necator fungi on the aroma character of grape must: A comparative approach. Food Chem 2016; 207:251-60. [DOI: 10.1016/j.foodchem.2016.03.110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 03/19/2016] [Accepted: 03/29/2016] [Indexed: 11/24/2022]
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265
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Pandit PD, Gulhane MK, Khardenavis AA, Purohit HJ. Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community. BIORESOURCE TECHNOLOGY 2016; 216:923-930. [PMID: 27323244 DOI: 10.1016/j.biortech.2016.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Study creates a scenario for enrichment and selection of ligno-hemicellulose degrading genotypes with anaerobic bioreactor as a model using rice straw, vegetable waste and food waste as substrates. Relative discrimination analysis showed that the hydrolytic pathways and associated microbial communities for ligno-hemicellulose degradation were dominatingly colonized with rice straw as substrate. The dominating bacteria were Caldicellulosiruptor, Fervidobacterium, Cytophaga, Ruminococcus, Thermotoga associated with hemicellulose degradation and Burkholderia, Pandorea, Sphingomonas, Spirochaeta, Pseudomonas for lignocellulose hydrolysis. This was further supported by the abundance of anaerobic aromatic compound degrading genes along with genes for xylanase and xylosidase in rice straw enriched community. The metagenome analysis data was validated by evaluation of the biochemical methane potential for these substrates. Food waste being most amenable substrate yielded 1410mL of biogas/gVS added whereas, biogas yield of 1160mL/gVS and 1080mL/gVS was observed in presence of vegetable waste and rice straw respectively.
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Affiliation(s)
- Prabhakar D Pandit
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India; CSIR-NEERI, Nagpur, India
| | | | | | - Hemant J Purohit
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India; CSIR-NEERI, Nagpur, India.
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266
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Palazzolo MA, Kurina-Sanz M. Microbial utilization of lignin: available biotechnologies for its degradation and valorization. World J Microbiol Biotechnol 2016; 32:173. [PMID: 27565783 DOI: 10.1007/s11274-016-2128-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
Abstract
Lignocellulosic biomasses, either from non-edible plants or from agricultural residues, stock biomacromolecules that can be processed to produce both energy and bioproducts. Therefore, they become major candidates to replace petroleum as the main source of energy. However, to shift the fossil-based economy to a bio-based one, it is imperative to develop robust biotechnologies to efficiently convert lignocellulosic streams in power and platform chemicals. Although most of the biomass processing facilities use celluloses and hemicelluloses to produce bioethanol and paper, there is no consolidated bioprocess to produce valuable compounds out of lignin at industrial scale available currently. Usually, lignin is burned to provide heat or it remains as a by-product in different streams, thus arising environmental concerns. In this way, the biorefinery concept is not extended to completion. Due to Nature offers an arsenal of biotechnological tools through microorganisms to accomplish lignin valorization or degradation, an increasing number of projects dealing with these tasks have been described recently. In this review, outstanding reports over the last 6 years are described, comprising the microbial utilization of lignin to produce a variety of valuable compounds as well as to diminish its ecological impact. Furthermore, perspectives on these topics are given.
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Affiliation(s)
- Martín A Palazzolo
- Instituto de Investigaciones en Tecnología Química, Universidad Nacional de San Luis, CONICET, Area de Química Orgánica, FQByF, 5700, San Luis, Argentina.
| | - Marcela Kurina-Sanz
- Instituto de Investigaciones en Tecnología Química, Universidad Nacional de San Luis, CONICET, Area de Química Orgánica, FQByF, 5700, San Luis, Argentina
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267
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Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 2016; 92:fiw179. [PMID: 27559028 DOI: 10.1093/femsec/fiw179] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/02/2023] Open
Abstract
The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.
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Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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268
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Makhlynets OV, Gosavi PM, Korendovych IV. Short Self-Assembling Peptides Are Able to Bind to Copper and Activate Oxygen. Angew Chem Int Ed Engl 2016; 55:9017-20. [PMID: 27276534 PMCID: PMC5064842 DOI: 10.1002/anie.201602480] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/21/2016] [Indexed: 11/07/2022]
Abstract
We have shown that de novo designed peptides self-assemble in the presence of copper to create supramolecular assemblies capable of carrying out the oxidation of dimethoxyphenol in the presence of dioxygen. Formation of the supramolecular assembly, which is akin to a protein fold, is critical for productive catalysis since peptides possessing the same functional groups but lacking the ability to self-assemble do not catalyze substrate oxidation. The ease with which we have discovered robust and productive oxygen activation catalysts suggests that these prion-like assemblies might have served as intermediates in the evolution of enzymatic function and opens the path for the development of new catalyst nanomaterials.
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.
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269
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Su L, Yang L, Huang S, Li Y, Su X, Wang F, Bo C, Wang ET, Song A. Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets. Appl Biochem Biotechnol 2016; 181:32-47. [PMID: 27457759 DOI: 10.1007/s12010-016-2197-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/13/2016] [Indexed: 11/29/2022]
Abstract
Termites are well recognized for their thriving on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling microbiota; however, the effects of diet changes on termite gut microbiota are poorly understood, especially for the lower termites. In this study, we employed high-throughput 454 pyrosequencing of 16S V1-V3 amplicons to compare gut microbiotas of Tsaitermes ampliceps fed with lignin-rich and lignin-poor cellulose diets after a 2-week-feeding period. As a result, the majority of bacterial taxa were shared across the treatments with different diets, but their relative abundances were modified. In particular, the relative abundance was reduced for Spirochaetes and it was increased for Proteobacteria and Bacteroides by feeding the lignin-poor diet. The evenness of gut microbiota exhibited a significant difference in response to the diet type (filter paper diets < corn stover diets < wood diets), while their richness was constant, which may be related to the lower recalcitrance of this biomass to degradation. These results have important implications for sampling and analysis strategies to probe the lignocellulose degradation features of termite gut microbiota and suggest that the dietary lignocellulose composition could cause shifting rapidly in the termite gut microbiota.
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Affiliation(s)
- Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Lele Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Xiaoquan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Fengqin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China
| | - Cunpei Bo
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México D.F., Mexico.
| | - Andong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China.
- , No. 93, Nongye Road, Zhengzhou, Henan Province, China.
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270
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Rosnow JJ, Anderson LN, Nair RN, Baker ES, Wright AT. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Crit Rev Biotechnol 2016; 37:626-640. [PMID: 27439855 DOI: 10.1080/07388551.2016.1209158] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.
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Affiliation(s)
- Joshua J Rosnow
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Lindsey N Anderson
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Reji N Nair
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Erin S Baker
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Aaron T Wright
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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271
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Rinaldi R, Jastrzebski R, Clough MT, Ralph J, Kennema M, Bruijnincx PCA, Weckhuysen BM. Paving the Way for Lignin Valorisation: Recent Advances in Bioengineering, Biorefining and Catalysis. Angew Chem Int Ed Engl 2016; 55:8164-215. [PMID: 27311348 PMCID: PMC6680216 DOI: 10.1002/anie.201510351] [Citation(s) in RCA: 776] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/28/2016] [Indexed: 12/23/2022]
Abstract
Lignin is an abundant biopolymer with a high carbon content and high aromaticity. Despite its potential as a raw material for the fuel and chemical industries, lignin remains the most poorly utilised of the lignocellulosic biopolymers. Effective valorisation of lignin requires careful fine-tuning of multiple "upstream" (i.e., lignin bioengineering, lignin isolation and "early-stage catalytic conversion of lignin") and "downstream" (i.e., lignin depolymerisation and upgrading) process stages, demanding input and understanding from a broad array of scientific disciplines. This review provides a "beginning-to-end" analysis of the recent advances reported in lignin valorisation. Particular emphasis is placed on the improved understanding of lignin's biosynthesis and structure, differences in structure and chemical bonding between native and technical lignins, emerging catalytic valorisation strategies, and the relationships between lignin structure and catalyst performance.
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Affiliation(s)
- Roberto Rinaldi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| | - Robin Jastrzebski
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands
| | - Matthew T Clough
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - John Ralph
- Department of Energy's Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, and Department of Biochemistry, University of Wisconsin, Madison, WI, 53726, USA.
| | - Marco Kennema
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Pieter C A Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands.
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands.
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272
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Rinaldi R, Jastrzebski R, Clough MT, Ralph J, Kennema M, Bruijnincx PCA, Weckhuysen BM. Wege zur Verwertung von Lignin: Fortschritte in der Biotechnik, der Bioraffination und der Katalyse. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510351] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Roberto Rinaldi
- Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ Großbritannien
| | - Robin Jastrzebski
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Universiteitsweg 99 3584 CG Utrecht Niederlande
| | - Matthew T. Clough
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - John Ralph
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, and Department of Biochemistry University of Wisconsin Madison WI 53726 USA
| | - Marco Kennema
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Pieter C. A. Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Universiteitsweg 99 3584 CG Utrecht Niederlande
| | - Bert M. Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Universiteitsweg 99 3584 CG Utrecht Niederlande
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273
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Lambertz C, Ece S, Fischer R, Commandeur U. Progress and obstacles in the production and application of recombinant lignin-degrading peroxidases. Bioengineered 2016; 7:145-54. [PMID: 27295524 DOI: 10.1080/21655979.2016.1191705] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Lignin is 1 of the 3 major components of lignocellulose. Its polymeric structure includes aromatic subunits that can be converted into high-value-added products, but this potential cannot yet been fully exploited because lignin is highly recalcitrant to degradation. Different approaches for the depolymerization of lignin have been tested, including pyrolysis, chemical oxidation, and hydrolysis under supercritical conditions. An additional strategy is the use of lignin-degrading enzymes, which imitates the natural degradation process. A versatile set of enzymes for lignin degradation has been identified, and research has focused on the production of recombinant enzymes in sufficient amounts to characterize their structure and reaction mechanisms. Enzymes have been analyzed individually and in combinations using artificial substrates, lignin model compounds, lignin and lignocellulose. Here we consider progress in the production of recombinant lignin-degrading peroxidases, the advantages and disadvantages of different expression hosts, and obstacles that must be overcome before such enzymes can be characterized and used for the industrial processing of lignin.
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Affiliation(s)
- Camilla Lambertz
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
| | - Selin Ece
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
| | - Rainer Fischer
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany.,b Fraunhofer Institute for Molecular Biology and Applied Ecology , Aachen , Germany
| | - Ulrich Commandeur
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
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274
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Makhlynets OV, Gosavi PM, Korendovych IV. Short Self‐Assembling Peptides Are Able to Bind to Copper and Activate Oxygen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602480] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Olga V. Makhlynets
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
| | - Pallavi M. Gosavi
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
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275
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Xie S, Ragauskas AJ, Yuan JS. Lignin Conversion: Opportunities and Challenges for the Integrated Biorefinery. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2016.0007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shangxian Xie
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Texas A&M University, College Station, TX
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX
| | - Arthur J. Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Joshua S. Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Texas A&M University, College Station, TX
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX
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276
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Huo Y, Zeng H, Zhang Y. Integrating Metabolic Engineering and Heterogeneous Chemocatalysis: New Opportunities for Biomass to Chemicals. CHEMSUSCHEM 2016; 9:1078-1080. [PMID: 27151374 DOI: 10.1002/cssc.201600254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 06/05/2023]
Abstract
Creating breakthroughs: Integrating metabolic engineering process and chemocatalysis system creates tremendous opportunities in biomass transformation. Recently, a breakthrough in the field of applying integrated metabolic process and chemocatalysis systems in biomass transformation has been achieved by combining biocatalysis with electrochemical processes in one pot.
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Affiliation(s)
- Yanping Huo
- Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong, 510006, PR China
| | - Huaqiang Zeng
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore.
| | - Yugen Zhang
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore.
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277
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Akita H, Kimura ZI, Mohd Yusoff MZ, Nakashima N, Hoshino T. Isolation and characterization of Burkholderia sp. strain CCA53 exhibiting ligninolytic potential. SPRINGERPLUS 2016; 5:596. [PMID: 27247892 PMCID: PMC4864794 DOI: 10.1186/s40064-016-2237-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/26/2016] [Indexed: 12/04/2022]
Abstract
Microbial degradation of lignin releases fermentable sugars, effective utilization of which could support biofuel production from lignocellulosic biomass. In the present study, a lignin-degrading bacterium was isolated from leaf soil and identified as Burkholderia sp. based on 16S rRNA gene sequencing. This strain was named CCA53, and its lignin-degrading capability was assessed by observing its growth on medium containing alkali lignin or lignin-associated aromatic monomers as the sole carbon source. Alkali lignin and at least eight lignin-associated aromatic monomers supported growth of this strain, and the most effective utilization was observed for p-hydroxybenzene monomers. These findings indicate that Burkholderia sp. strain CCA53 has fragmentary activity for lignin degradation.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506 Japan
| | - Mohd Zulkhairi Mohd Yusoff
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan ; Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan ; Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
| | - Tamotsu Hoshino
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan ; Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
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278
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Wu SG, Shimizu K, Tang JKH, Tang YJ. Facilitate Collaborations among Synthetic Biology, Metabolic Engineering and Machine Learning. CHEMBIOENG REVIEWS 2016. [DOI: 10.1002/cben.201500024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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279
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Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem 2016; 291:10228-38. [PMID: 26940872 PMCID: PMC4858972 DOI: 10.1074/jbc.m115.700427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 12/23/2022] Open
Abstract
There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
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Affiliation(s)
- Jose Henrique Pereira
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Richard A Heins
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Ryan P McAndrew
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kai Deng
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Paul D Adams
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720
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280
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Structure of Thermobifida fusca DyP-type peroxidase and activity towards Kraft lignin and lignin model compounds. Arch Biochem Biophys 2016; 594:54-60. [DOI: 10.1016/j.abb.2016.02.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/20/2022]
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281
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Kielak AM, Scheublin TR, Mendes LW, van Veen JA, Kuramae EE. Bacterial Community Succession in Pine-Wood Decomposition. Front Microbiol 2016; 7:231. [PMID: 26973611 PMCID: PMC4771932 DOI: 10.3389/fmicb.2016.00231] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Tanja R Scheublin
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Lucas W Mendes
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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282
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Nelsen MP, DiMichele WA, Peters SE, Boyce CK. Delayed fungal evolution did not cause the Paleozoic peak in coal production. Proc Natl Acad Sci U S A 2016; 113:2442-7. [PMID: 26787881 PMCID: PMC4780611 DOI: 10.1073/pnas.1517943113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organic carbon burial plays a critical role in Earth systems, influencing atmospheric O2 and CO2 concentrations and, thereby, climate. The Carboniferous Period of the Paleozoic is so named for massive, widespread coal deposits. A widely accepted explanation for this peak in coal production is a temporal lag between the evolution of abundant lignin production in woody plants and the subsequent evolution of lignin-degrading Agaricomycetes fungi, resulting in a period when vast amounts of lignin-rich plant material accumulated. Here, we reject this evolutionary lag hypothesis, based on assessment of phylogenomic, geochemical, paleontological, and stratigraphic evidence. Lignin-degrading Agaricomycetes may have been present before the Carboniferous, and lignin degradation was likely never restricted to them and their class II peroxidases, because lignin modification is known to occur via other enzymatic mechanisms in other fungal and bacterial lineages. Furthermore, a large proportion of Carboniferous coal horizons are dominated by unlignified lycopsid periderm with equivalent coal accumulation rates continuing through several transitions between floral dominance by lignin-poor lycopsids and lignin-rich tree ferns and seed plants. Thus, biochemical composition had little relevance to coal accumulation. Throughout the fossil record, evidence of decay is pervasive in all organic matter exposed subaerially during deposition, and high coal accumulation rates have continued to the present wherever environmental conditions permit. Rather than a consequence of a temporal decoupling of evolutionary innovations between fungi and plants, Paleozoic coal abundance was likely the result of a unique combination of everwet tropical conditions and extensive depositional systems during the assembly of Pangea.
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Affiliation(s)
| | - William A DiMichele
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Shanan E Peters
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706
| | - C Kevin Boyce
- Geological Sciences, Stanford University, Stanford, CA 94305;
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283
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Hervé V, Ketter E, Pierrat JC, Gelhaye E, Frey-Klett P. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood. PLoS One 2016; 11:e0147100. [PMID: 26824755 PMCID: PMC4732817 DOI: 10.1371/journal.pone.0147100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.
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Affiliation(s)
- Vincent Hervé
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
- * E-mail:
| | - Elodie Ketter
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
| | - Jean-Claude Pierrat
- INRA, UMR 1092 LERFOB, F-54280 Champenoux, France
- AgroParisTech, UMR 1092 LERFOB, F-54000 Nancy, France
| | - Eric Gelhaye
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
| | - Pascale Frey-Klett
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
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284
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Lignin Biodegradation with Fungi, Bacteria and Enzymes for Producing Chemicals and Increasing Process Efficiency. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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285
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Ma J, Zhang K, Liao H, Hector SB, Shi X, Li J, Liu B, Xu T, Tong C, Liu X, Zhu Y. Genomic and secretomic insight into lignocellulolytic system of an endophytic bacterium Pantoea ananatis Sd-1. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:25. [PMID: 26839588 PMCID: PMC4736469 DOI: 10.1186/s13068-016-0439-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 01/14/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Exploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production. The rice endophytic bacterium Pantoea ananatis Sd-1 with strong lignocellulose degradation capacity has been reported in our previous study. However, a comprehensive analysis of its corresponding degradative system has not yet been conducted. The aim of this work is to identify and characterize the lignocellulolytic enzymes of the bacterium to understand its mechanism of lignocellulose degradation and facilitate its application in sustainable energy production. RESULTS The genomic analysis revealed that there are 154 genes encoding putative carbohydrate-active enzymes (CAZy) in P. ananatis Sd-1. This number is higher than that of compared cellulolytic and ligninolytic bacteria as well as other eight P. ananatis strains. The CAZy in P. ananatis Sd-1 contains a complete repertoire of enzymes required for cellulose and hemicellulose degradation. In addition, P. ananatis Sd-1 also possesses plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Quantitative real-time PCR analysis of parts of genes encoding lignocellulolytic enzymes revealed that they were significantly up-regulated (at least P < 0.05) in presence of rice straw. Further identification of secretome of P. ananatis Sd-1 by nano liquid chromatography-tandem mass spectrometry confirmed that considerable amounts of proteins involved in lignocellulose degradation were only detected in rice straw cultures. Rice straw saccharification levels by the secretome of P. ananatis Sd-1 reached 129.11 ± 2.7 mg/gds. Correspondingly, the assay of several lignocellulolytic enzymes including endoglucanase, exoglucanase, β-glucosidase, xylanase-like, lignin peroxidase-like, and laccase-like activities showed that these enzymes were more active in rice straw relative to glucose substrates. The high enzymes activities were not attributed to bacterial cell densities but to the difference of secreted protein contents. CONCLUSION Our results indicate that P. ananatis Sd-1 can produce considerable lignocellulolytic enzymes including cellulases, hemicellulases, and ligninolytic relevant enzymes. The high activities of those enzymes could be efficiently induced by lignocellulosic biomass. This identified degradative system is valuable for the lignocellulosic bioenergy industry.
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Affiliation(s)
- Jiangshan Ma
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Keke Zhang
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Hongdong Liao
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Stanton B. Hector
- />Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602 South Africa
- />DNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602 South Africa
| | - Xiaowei Shi
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Jianglin Li
- />State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Bin Liu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Ting Xu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Chunyi Tong
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Xuanming Liu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Yonghua Zhu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
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286
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Joshua CJ, Simmons BA, Singer SW. Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties. RSC Adv 2016. [DOI: 10.1039/c6ra04443c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A simple and reproducible ferricyanide-based technique for routine qualitative and semi-quantitative comparative analysis of aqueous lignin extracts.
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Affiliation(s)
- C. J. Joshua
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Systems Engineering Division
- Lawrence Berkeley National Laboratory
| | - B. A. Simmons
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Systems Engineering Division
- Lawrence Berkeley National Laboratory
| | - S. W. Singer
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Systems Engineering Division
- Lawrence Berkeley National Laboratory
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287
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Kameshwar AKS, Qin W. Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms. Int J Biol Sci 2016; 12:156-71. [PMID: 26884714 PMCID: PMC4737673 DOI: 10.7150/ijbs.13537] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/03/2015] [Indexed: 01/23/2023] Open
Abstract
Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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288
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Bacterial Enzymes for Lignin Oxidation and Conversion to Renewable Chemicals. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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289
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Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:22. [PMID: 26834834 PMCID: PMC4731972 DOI: 10.1186/s13068-016-0440-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/14/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. RESULTS Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. CONCLUSION These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.
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Affiliation(s)
- Cheng Wang
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Da Dong
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
- />Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin’an, Hangzhou, 311300 China
| | - Haoshu Wang
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Karin Müller
- />Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Private Bag 3123, Hamilton, New Zealand
| | - Yong Qin
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Hailong Wang
- />Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin’an, Hangzhou, 311300 China
| | - Weixiang Wu
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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290
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Su L, Yang L, Huang S, Su X, Li Y, Wang F, Wang E, Kang N, Xu J, Song A. Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew081. [PMID: 27638955 PMCID: PMC5026480 DOI: 10.1093/jisesa/iew081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 07/30/2016] [Indexed: 05/12/2023]
Abstract
Aiming at learning the association between the gut microbiota and termites with different diet habits and phylogenetic positions, the gut bacteria of three populations for each of the two higher termites (wood-feeding Mironasutitermes shangchengensis and fungus-feeding Odontotermes formosanus) and two wood-feeding lower termites (Tsaitermes ampliceps and Reticulitermes flaviceps) were analyzed by high-throughput 454 pyrosequencing of 16S V1-V3 amplicons. As results, 132 bacterial genera and some unidentified operational taxonomic units within 29 phyla in the gut bacteria were detected, with Spirochaetes (11-55%), Firmicutes (7-18%), Bacteroidetes (7-31%), and Proteobacteria (8-14%) as the main phyla, and Treponema, TG5, Dysgonomonas, Tannerella, za29, Lactococcus, Pseudomonas, and SJA-88 as the common genera in all the four termites. The diversity of gut bacterial communities in the higher termite guts was significantly greater than that in the lower termites; while the gut microbiota in M. shangchengensis (wood-feeding higher termite) was more similar to those of the wood-feeding lower termites rather than that of O. formosanus (fungus-feeding higher termite), and phylum Spirochaetes and nitrogen-fixing bacteria were super-dominant in the wood-feeding termites, despite of their phylogenetic relations. This study reported for the first time the gut bacterial communities for the termites of M. shangchengensis and T. ampliceps and the comparative analyses showed that the gut microbial communities varied according to the phylogeny and the diet habits of termites.
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Affiliation(s)
- LiJuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - LeLe Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - XiaoQuan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - FengQin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
| | - EnTao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, DF 11340, México
| | - Ning Kang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - AnDong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
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291
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Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J Biol Chem 2015; 291:5234-46. [PMID: 26637355 PMCID: PMC4777856 DOI: 10.1074/jbc.m115.694307] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.
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Affiliation(s)
- Kate E Helmich
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Jose Henrique Pereira
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Richard A Heins
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Ryan P McAndrew
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Craig Bingman
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Deng
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Bacteriology, University of Wisconsin, Madison, Wisconsin 53706,
| | - Paul D Adams
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720, and
| | - George N Phillips
- the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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292
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Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments. PLoS One 2015; 10:e0143917. [PMID: 26633175 PMCID: PMC4669084 DOI: 10.1371/journal.pone.0143917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/23/2022] Open
Abstract
More than 50% of terrestrially-derived organic carbon (terrOC) flux from the continents to the ocean is remineralised in the coastal zone despite its perceived high refractivity. The efficient degradation of terrOC in the marine environment could be fuelled by labile marine-derived material, a phenomenon known as “priming effect”, but experimental data to confirm this mechanism are lacking. We tested this hypothesis by treating coastal sediments with 13C-lignocellulose, as a proxy for terrOC, with and without addition of unlabelled diatom detritus that served as the priming inducer. The occurrence of priming was assessed by the difference in lignocellulose mineralisation between diatom-amended treatments and controls in aerobic sediment slurries. Priming of lignocellulose degradation was observed only at the initial stages of the experiment (day 7) and coincided with overall high microbial activity as exemplified by total CO2 production. Lignocellulose mineralisation did not differ consistently between diatom treatments and control for the remaining experimental time (days 14–28). Based on this pattern, we hypothesize that the faster initiation of lignocellulose mineralisation in diatom-amended treatments is attributed to the decomposition of accessible polysaccharide components within the lignocellulose complex by activated diatom degraders. The fact that diatom-degraders contributed to lignocellulose degradation was also supported by the different patterns in 13C-enrichment of phospholipid fatty acids between treatments. Although we did not observe differences between treatments in the total quantity of respired lignocellulose at the end of the experiment, differences in timing could be important in natural ecosystems where the amount of time that a certain compound is subject to aerobic degradation before burial to deeper anoxic sediments may be limited.
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293
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Biocatalysts for biomass deconstruction from environmental genomics. Curr Opin Chem Biol 2015; 29:18-25. [DOI: 10.1016/j.cbpa.2015.06.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023]
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294
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Kupryashina MA, Petrov SV, Ponomareva EG, Nikitina VE. Ligninolytic activity of bacteria of the genera Azospirillum and Niveispirillum. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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295
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Duan J, Huo X, Du W, Liang J, Wang D, Yang S. Biodegradation of kraft lignin by a newly isolated anaerobic bacterial strain, Acetoanaerobium
sp. WJDL-Y2. Lett Appl Microbiol 2015; 62:55-62. [DOI: 10.1111/lam.12508] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 11/30/2022]
Affiliation(s)
- J. Duan
- Department of Environmental Engineering; Xi'an Jiaotong University; Xi'an China
| | - X. Huo
- Department of Environmental Engineering; Xi'an Jiaotong University; Xi'an China
| | - W.J. Du
- Department of Environmental Engineering; Xi'an Jiaotong University; Xi'an China
| | - J.D. Liang
- Department of Environmental Engineering; Xi'an Jiaotong University; Xi'an China
- State Key Laboratory of Frozen Soil Engineering; Cold and Arid Regions Environmental and Engineering Research Institute; Chinese Academy of Science; Lanzhou China
| | - D.Q. Wang
- State Key Laboratory Base of Eco-Hydraulic Engineering in Arid Area; Xi'an University of Technology; Xi'an China
| | - S.C. Yang
- Department of Environmental Engineering; Xi'an Jiaotong University; Xi'an China
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296
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Billings AF, Fortney JL, Hazen TC, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, DeAngelis KM. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci 2015; 10:106. [PMID: 26594307 PMCID: PMC4653933 DOI: 10.1186/s40793-015-0100-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023] Open
Abstract
Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. By characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.
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Affiliation(s)
- Andrew F Billings
- Microbiology Department, University of Massachusetts, Amherst, MA USA
| | - Julian L Fortney
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN USA
| | - Terry C Hazen
- Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN USA ; Department of Microbiology, The University of Tennessee, Knoxville, TN USA ; Department of Earth & Planetary Sciences, The University of Tennessee, Knoxville, TN USA
| | - Blake Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA USA ; Sandia National Lab, Livermore, CA USA
| | | | | | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
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297
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Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes. Appl Environ Microbiol 2015; 82:528-37. [PMID: 26546427 DOI: 10.1128/aem.02838-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/01/2015] [Indexed: 01/31/2023] Open
Abstract
The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications.
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298
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Hudson CM, Kirton E, Hutchinson MI, Redfern JL, Simmons B, Ackerman E, Singh S, Williams KP, Natvig DO, Powell AJ. Lignin‐modifying processes in the rhizosphere of arid land grasses. Environ Microbiol 2015; 17:4965-78. [DOI: 10.1111/1462-2920.13020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 01/23/2023]
Affiliation(s)
| | | | | | | | - Blake Simmons
- Sandia National Laboratories Livermore CA USA
- Joint BioEnergy Institute Emeryville CA USA
| | - Eric Ackerman
- Computational Simulation Sandia National Laboratories Albuquerque NM USA
| | - Seema Singh
- Sandia National Laboratories Livermore CA USA
- Joint BioEnergy Institute Emeryville CA USA
| | | | - Donald O. Natvig
- Department of Biology University of New Mexico Albuquerque NM USA
| | - Amy J. Powell
- Computational Simulation Sandia National Laboratories Albuquerque NM USA
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299
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Rashid GMM, Taylor CR, Liu Y, Zhang X, Rea D, Fülöp V, Bugg TDH. Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation. ACS Chem Biol 2015. [PMID: 26198187 DOI: 10.1021/acschembio.5b00298] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valorization of aromatic heteropolymer lignin is an important unsolved problem in the development of a biomass-based biorefinery, for which novel high-activity biocatalysts are needed. Sequencing of the genomic DNA of lignin-degrading bacterial strain Sphingobacterium sp. T2 revealed no matches to known lignin-degrading genes. Proteomic matches for two manganese superoxide dismutase proteins were found in partially purified extracellular fractions. Recombinant MnSOD1 and MnSOD2 were both found to show high activity for oxidation of Organosolv and Kraft lignin, and lignin model compounds, generating multiple oxidation products. Structure determination revealed that the products result from aryl-Cα and Cα-Cβ bond oxidative cleavage and O-demethylation. The crystal structure of MnSOD1 was determined to 1.35 Å resolution, revealing a typical MnSOD homodimer harboring a five-coordinate trigonal bipyramidal Mn(II) center ligated by three His, one Asp, and a water/hydroxide in each active site. We propose that the lignin oxidation reactivity of these enzymes is due to the production of a hydroxyl radical, a highly reactive oxidant. This is the first demonstration that MnSOD is a microbial lignin-oxidizing enzyme.
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Affiliation(s)
- Goran M. M. Rashid
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Charles R. Taylor
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yangqingxue Liu
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Xiaoyang Zhang
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dean Rea
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vilmos Fülöp
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Timothy D. H. Bugg
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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300
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Kumar M, Singh J, Singh MK, Singhal A, Thakur IS. Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15690-702. [PMID: 26018290 DOI: 10.1007/s11356-015-4771-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/22/2015] [Indexed: 05/07/2023]
Abstract
The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant Pandoraea sp. ISTKB utilizing KL as sole carbon source. The results displayed 50.2 % reduction in chemical oxygen demand (COD) and 41.1 % decolorization after bacterial treatment. The maximum lignin peroxidase (LiP) and manganese peroxidase (MnP) activity detected was 2.73 and 4.33 U ml(-1), respectively, on day 3. The maximum extracellular and intracellular laccase activities observed were 1.32 U ml(-1) on day 5 and 4.53 U ml(-1) on day 4, respectively. The decolorization and degradation was maximum on day 2. Further, it registered an increase with the production of extracellular laccase. This unusual trend of decolorization and degradation was studied using various aromatic compounds and dyes. SEM and FTIR results indicated significant change in surface morphology and functional group composition during the course of degradation. Gas chromatography and mass spectroscopy (GC-MS) analysis confirmed KL degradation by emergence of new peaks and the identification of low molecular weight aromatic intermediates in treated sample. The degradation of KL progressed through the generation of phenolic intermediates. The identified intermediates implied the degradation of hydroxyphenyl, ferulic acid, guaiacyl, syringyl, phenylcoumarane, and pinoresinol components commonly found in lignin. The degradation, decolorization, and GC-MS analysis indicated potential application of the isolate Pandoraea sp. ISTKB in treatment of lignin-containing pollutants and KL valorization.
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Affiliation(s)
- Madan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Jyoti Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Manoj Kumar Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Anjali Singhal
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India.
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