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Tsers I, Marenina E, Meshcherov A, Petrova O, Gogoleva O, Tkachenko A, Gogoleva N, Gogolev Y, Potapenko E, Muraeva O, Ponomareva M, Korzun V, Gorshkov V. First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale. IMA Fungus 2023; 14:2. [PMID: 36627722 PMCID: PMC9830731 DOI: 10.1186/s43008-022-00107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.
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Affiliation(s)
- Ivan Tsers
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Ekaterina Marenina
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Azat Meshcherov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Petrova
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Alexander Tkachenko
- grid.35915.3b0000 0001 0413 4629Laboratory of Computer Technologies, ITMO University, Saint Petersburg, Russia 197101
| | - Natalia Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Yuri Gogolev
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Evgenii Potapenko
- grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, 3498838 Haifa, Israel ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
| | - Olga Muraeva
- grid.512700.1Bioinformatics Institute, Saint Petersburg, Russia 197342
| | - Mira Ponomareva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Viktor Korzun
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111 ,grid.425691.dKWS SAAT SE & Co. KGaA, 37555 Einbeck, Germany
| | - Vladimir Gorshkov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
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Gubiani JR, Bernardi DI, De Paula CCP, Seleghim MHR, Ferreira AG, Batista ANL, Batista JM, Oliveira LFP, Lira SP, Burdette JE, Berlinck RGS. Absolute configuration of cytotoxic anthraquinones from a Brazilian cave soil-derived fungus, Aspergillus sp. SDC28. Arch Pharm (Weinheim) 2022; 355:e2100441. [PMID: 35099085 PMCID: PMC8983557 DOI: 10.1002/ardp.202100441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 01/26/2023]
Abstract
Microbial strains isolated from extreme and understudied environments, such as caves, are still poorly investigated for the production of bioactive secondary metabolites. Investigation of the ethyl acetate extract from the growth medium produced by the soil-derived fungus Aspergillus sp. SDC28, isolated from a Brazilian cave, yielded two anthraquinones: versicolorin C (1) and versiconol (2). The complete assignment of nuclear magnetic resonance and mass spectroscopic data of 1 and 2 was performed for the first time. Moreover, the yet unreported absolute configuration of both compounds was unambiguously established by analysis of experimental and theoretical electronic circular dichroism data. Vibrational circular dichroism was also applied to confirm the absolute stereochemistry of 2. Compounds 1 and 2 showed cytotoxic activity against human ovarian cancer cells (OVCAR3).
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Affiliation(s)
- Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Caio C P De Paula
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, Brazil.,Biology Centre CAS, Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Mirna H R Seleghim
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Antonio G Ferreira
- Departamento de Química, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - João M Batista
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - Lucianne F P Oliveira
- Departamento de Ciências Exatas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Simone P Lira
- Departamento de Ciências Exatas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Joanna E Burdette
- Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Ashland, Oregon, USA
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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de Souza Falcão L, Santiago do Amaral T, Bittencourt Brasil G, Melchionna Albuquerque P. Improvement of endoglucanase production by Aspergillus brasiliensis in solid-state fermentation using cupuaçu (Theobroma grandiflorum) residue as substrate. J Appl Microbiol 2021; 132:2859-2869. [PMID: 34905274 DOI: 10.1111/jam.15412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/08/2021] [Accepted: 12/11/2021] [Indexed: 11/30/2022]
Abstract
AIMS Optimize the production of Aspergillus brasiliensis endoglucanase in a solid-phase bioprocess using cupuaçu shell as substrate. METHODS AND RESULTS The shells were supplemented with nitrogen and phosphorous and used as a substrate. The centesimal and inorganic composition of the residue was determined, and found to be rich in fibres, and possessed essential elements for fungal growth. In the initial cultivation of A. brasiliensis, endoglucanase activity of 7.35 U g-1 was obtained. A factorial experimental design was used to determine the most significant variables for the bioprocess. The interactions between moisture, temperature and nitrogen source were noteworthy (p < 0.05). From the rotational central composite design, the optimization of temperature and nitrogen supplementation was obtained, and this reached 40.50 U g-1 , which is an increase of more than five times the value obtained initially. The enzymatic extract was applied as the biocatalyst in the hydrolysis of cupuaçu shells and, after 48 h, it was possible to observe the production of reducing sugars. CONCLUSIONS Cupuaçu shell can be used as a substrate for endoglucanase production by A. brasiliensis. The process was optimized for the cultivation temperature and the nitrogen source. The enzymatic extract can be applied in the hydrolysis of lignocellulosic biomass. SIGNIFICANCE AND IMPACT OF THE STUDY Cupuaçu shells can be used to produce cellulases, a product of high added value that can generate economic and environmental benefits for communities and companies producing derivatives of the cupuaçu fruit.
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Affiliation(s)
- Lucas de Souza Falcão
- Programa Multicêntrico em Bioquímica e Biologia Molecular, Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil.,Laboratório de Química Aplicada à Tecnologia, Escola Superior de Tecnologia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Thaís Santiago do Amaral
- Laboratório de Química Aplicada à Tecnologia, Escola Superior de Tecnologia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Guilherme Bittencourt Brasil
- Laboratório de Química Aplicada à Tecnologia, Escola Superior de Tecnologia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Patrícia Melchionna Albuquerque
- Programa Multicêntrico em Bioquímica e Biologia Molecular, Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil.,Laboratório de Química Aplicada à Tecnologia, Escola Superior de Tecnologia, Universidade do Estado do Amazonas, Manaus, Brazil
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Kazeem MO, Uthman-Saheed L, Oke MA. Impact of pretreatment severity on fungal cellulase production on sugarcane bagasse substrate. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1981802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Muinat Olanike Kazeem
- Faculty of Life Sciences, Department of Microbiology, University of Ilorin, Ilorin, Nigeria
| | - Lateefah Uthman-Saheed
- Faculty of Life Sciences, Department of Microbiology, University of Ilorin, Ilorin, Nigeria
| | - Mushafau Adebayo Oke
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Diversity and Seasonal Dynamics of Airborne Fungi in Nerja Cave, Spain. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nerja Cave, Southern Spain, was revealed as an important biodiversity reservoir from which several novel species of Aspergillus were described. We carried out an aerobiological study in Nerja Cave to assess the origin of airborne fungi. This study quantified the fungi present in the air of ten representative halls covering the three sectors comprising the cave: Touristic Galleries, High Galleries, and New Galleries. Microclimatological monitoring allowed us to understand the dynamic of airborne fungi in two seasons of the year (winter and summer), corresponding to the strongest and the lowest cave ventilation, and to validate the influence that the transport of airborne fungi from outside may have on the cave itself. The data show that cold air enters in winter, as confirmed by the abundant presence of Aspergillus and Penicillium spores inside and outside the cave. In summer, the abundance of some fungi in the air of Nerja Cave, which are not detected outside, indicates a stagnation or low ventilation, and therefore, the concentration of fungal spores is maxima. The high occurrence of Cladosporium outside the cave and the scarce abundance inside support the cave stagnation in this season.
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Cunha AOB, Bezerra JDP, Oliveira TGL, Barbier E, Bernard E, Machado AR, Souza-Motta CM. Living in the dark: Bat caves as hotspots of fungal diversity. PLoS One 2020; 15:e0243494. [PMID: 33275627 PMCID: PMC7717564 DOI: 10.1371/journal.pone.0243494] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
Bat caves are very special roosts that harbour thousands of bats of one or more species. Such sites may hold an incredible “dark fungal diversity” which is still underestimated. We explored the culturable fungal richness in the air, on bats, and in the guano in a bat cave in Brazil’s Caatinga dry forest. Fungal abundance was 683 colony-forming units (CFU) in the guano, 673 CFU in the air, and 105 CFU on the bats. Based on morphological and phylogenetic analysis of ITS, LSU, and TUB2 sequences, fungal isolates of 59 taxa belonging to 37 genera in the phyla Ascomycota (28 genera, including Aspergillus, Penicillium, Cladosporium, and Talaromyces), Basidiomycota (eight genera, including Rhodotorula and Schizophyllum), and Mucoromycota (only Rhizopus) were identified. The fungal richness in the air was 23 taxa (especially Aspergillus taxa), mainly found at 15 m and 45 m from the cave entrance; on the bodies of bats it was 36 taxa (mainly Aspergillus taxa), especially on their wing membranes (21 taxa, nine of which were exclusively found in this microhabitat); and in guano 10 fungal taxa (especially Aspergillus and Penicillium) were found. The fungal richness associated with guano (fresh and non-fresh) was similar from bats with different eating habits (insectivorous, frugivorous, and haematophagous). Sampling effort was not sufficient to reveal the total fungal taxa richness estimated. Eight (21.6%) of the 37 genera and 17 (53.1%) of the 32 identified fungal species are reported for the first time in caves. Our results highlight bat caves in Brazil as hotspots of fungal diversity, emphasizing the need to protect such special roosts.
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Affiliation(s)
- Aline O B Cunha
- Departamento de Micologia Prof. Chaves Batista, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Jadson D P Bezerra
- Setor de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Thays G L Oliveira
- Departamento de Micologia Prof. Chaves Batista, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Eder Barbier
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Alexandre R Machado
- Departamento de Micologia Prof. Chaves Batista, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Cristina M Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
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Gorshkov V, Osipova E, Ponomareva M, Ponomarev S, Gogoleva N, Petrova O, Gogoleva O, Meshcherov A, Balkin A, Vetchinkina E, Potapov K, Gogolev Y, Korzun V. Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence. J Fungi (Basel) 2020; 6:E335. [PMID: 33287447 PMCID: PMC7761817 DOI: 10.3390/jof6040335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.
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Affiliation(s)
- Vladimir Gorshkov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Osipova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Mira Ponomareva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Sergey Ponomarev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Natalia Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Petrova
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Olga Gogoleva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Azat Meshcherov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Alexander Balkin
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Elena Vetchinkina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, 410049 Saratov, Russia;
| | - Kim Potapov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Yuri Gogolev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
| | - Viktor Korzun
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, ul. Lobachevskogo, 2/31, 420111 Kazan, Russia; (E.O.); (M.P.); (S.P.); (N.G.); (O.P.); (O.G.); (A.M.); (A.B.); (K.P.); (Y.G.); (V.K.)
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Naicker JE, Govinden R, Lekha P, Sithole B. Transformation of pulp and paper mill sludge (PPMS) into a glucose-rich hydrolysate using green chemistry: Assessing pretreatment methods for enhanced hydrolysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 270:110914. [PMID: 32721348 DOI: 10.1016/j.jenvman.2020.110914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/30/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Pulp and paper mill sludge is a waste stream derived from the pulp and paper making industry, comprised of organic and inorganic material in the form of cellulose, hemicellulose, lignin and ash. In South Africa, approximately fivefour hundred thousand wet tonnes are produced per annum and is currently disposed via landfilling or incineration. However, these disposal methods raise environmental and financial concerns. This waste stream is an attractive feedstock for fermentable sugars, mainly glucose, recovery and can be redirected for valorisation as a feedstock for microbial fermentation to produce value-added products. Sugar recovery by enzymatic hydrolysis, as opposed to acidic hydrolysis, is a promising approach but is hampered by the lignin and inorganic material found in pulp and paper mill sludge. Several treatment steps to reduce or remove these components prior to enzymatic hydrolysis are assessed in this review. Pretreatment improves hydrolysis of cellulosic fibres and ensures a substantial yield of sugars.
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Affiliation(s)
- Justin Emmanuel Naicker
- University of KwaZulu-Natal (Westville Campus), Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Sciences, University Road, Westville, Private Bag X 54001, Durban, 4000, South Africa.
| | - Roshini Govinden
- University of KwaZulu-Natal (Westville Campus), Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Sciences, University Road, Westville, Private Bag X 54001, Durban, 4000, South Africa
| | - Prabashni Lekha
- Council for Scientific and Industrial Research, Biorefinery Industry Development Facility, PO Box 59081, Umbilo, 4075, South Africa
| | - Bruce Sithole
- Council for Scientific and Industrial Research, Biorefinery Industry Development Facility, PO Box 59081, Umbilo, 4075, South Africa; University of KwaZulu-Natal (Howard Campus), Discipline of Chemical Engineering, College of Agriculture, Engineering and Sciences, Private Bag X 54001, Durban, 4000, South Africa
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Prayogo FA, Budiharjo A, Kusumaningrum HP, Wijanarka W, Suprihadi A, Nurhayati N. Metagenomic applications in exploration and development of novel enzymes from nature: a review. J Genet Eng Biotechnol 2020; 18:39. [PMID: 32749574 PMCID: PMC7403272 DOI: 10.1186/s43141-020-00043-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research. SHORT CONCLUSION Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.
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Affiliation(s)
- Fitra Adi Prayogo
- Department of Biology, Faculty of Science and Mathematics, Diponegoro University, Semarang City, 50275 Indonesia
| | - Anto Budiharjo
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
- Molecular and Applied Microbiology Laboratory, Center Central Laboratory of Research and Service - Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | | | - Wijanarka Wijanarka
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Agung Suprihadi
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Nurhayati Nurhayati
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
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