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Mon ML, Romano N, Farace PD, Tortone CA, Oriani DS, Picariello G, Zumárraga MJ, Gioffré AK, Talia PM. Exploring the cellulolytic activity of environmental mycobacteria. Tuberculosis (Edinb) 2024; 147:102516. [PMID: 38735123 DOI: 10.1016/j.tube.2024.102516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Although studies on non-tuberculous mycobacteria have increased in recent years because they cause a considerable proportion of infections, their cellulolytic system is still poorly studied. This study presents a characterization of the cellulolytic activities of environmental mycobacterial isolates derived from soil and water samples from the central region of Argentina, aimed to evaluate the conservation of the mechanism for the degradation of cellulose in this group of bacteria. The molecular and genomic identification revealed identity with Mycolicibacterium septicum. The endoglucanase and total cellulase activities were assessed both qualitatively and quantitatively and the optimal enzymatic conditions were characterized. A specific protein of around 56 kDa with cellulolytic activity was detected in a zymogram. Protein sequences possibly arising from a cellulase were identified by mass spectrometry-based shotgun proteomics. Results showed that M. septicum encodes for cellulose- and hemicellulose-related degrading enzymes, including at least an active β-1,4 endoglucanase enzyme that could be useful to improve its survival in the environment. Given the important health issues related to mycobacteria, the results of the present study may contribute to the knowledge of their cellulolytic system, which could be important for their ability to survive in many different types of environments.
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Affiliation(s)
- María Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nelson Romano
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Pablo Daniel Farace
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Claudia A Tortone
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Delia S Oriani
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Gianluca Picariello
- Istituto di Scienze Dell'Alimentazione, Consiglio Nazionale Delle Ricerche, Via Roma 64, 83100, Avellino, Italy.
| | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Andrea Karina Gioffré
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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2
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Li J, Dong C, Sen B, Lai Q, Gong L, Wang G, Shao Z. Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158714. [PMID: 36113801 DOI: 10.1016/j.scitotenv.2022.158714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.
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Affiliation(s)
- Jianyang Li
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China.
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3
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Mon ML, Marrero Díaz de Villegas R, Campos E, Soria MA, Talia PM. Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome. BIORESOUR BIOPROCESS 2022; 9:84. [PMID: 38647897 PMCID: PMC10992782 DOI: 10.1186/s40643-022-00572-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.
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Affiliation(s)
- Maria Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Rubén Marrero Díaz de Villegas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Marcelo A Soria
- Facultad de Agronomía, Cátedra de Microbiología Agrícola, Universidad de Buenos Aires, INBA UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina.
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Lignocellulosic Waste Degradation Potential of Some Cellulolytic Fungal Strains Isolated from Putrid Fruits. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.4.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi are plentiful in nature and they are found growing on wastes of wood materials. These wastes are equally found in our environment with no usefulness. The aim of this study was to exploit the probability of the isolated fungi from fruits to produce cellulase from wastes of lignocellulosic materials. Cellulase- producing fungi were isolated from fruits (tomato, banana, plantain). The organisms were screened for cellulase production. Culture conditions were optimized with pH, temperature and carbon. Cellulase was produced using lignocellulosic wastes; sawdust, corn cob, sugarcane bagasse. Six cellulase producers were isolated, four of which were selected for synthesis and quantification of the cellulase. The fungi were identified as Saccharomyces cerevisiae4, Trichoderma species1 and Scopulariopsis brevicaulis1. Of all the tested substrates used in this study, pretreated sugarcane bagasse at 3% w/v concentration with Scopulariopsis brevicaulis gave highest cellulase production 18.18 U/mL at 40°C, 5day incubation time and pH 5, followed by Trichoderma with 12.39 U/mL. These fungi are good potentials cellulase producers that can be considered at industrial level.
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Puentes-Téllez PE, Salles JF. Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass. MICROBIAL ECOLOGY 2020; 79:312-325. [PMID: 31286170 PMCID: PMC7033055 DOI: 10.1007/s00248-019-01403-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 06/02/2023]
Abstract
Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Brusetti L, Ciccazzo S, Borruso L, Bellucci M, Zaccone C, Beneduce L. Metataxonomy and functionality of wood-tar degrading microbial consortia. JOURNAL OF HAZARDOUS MATERIALS 2018; 353:108-117. [PMID: 29655090 DOI: 10.1016/j.jhazmat.2018.03.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/24/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Wood-tar is a liquid material obtained by wood gasification process, and comprises several polycyclic aromatic hydrocarbons (PAH). Tar biodegradation is a very challenging task, due to its toxicity and to its complex chemistry. The 'microbial resource management' concerns the use of environmental microbial communities potentially able to provide us services. We applied this concept in tar biodegradation. Tar composed by several PAH (including phenanthrene, acenaphthylene and fluorene) was subjected to a biodegradation process in triplicate microcosms spiked with a microbial community collected from PAH-rich soils. In 20 days, 98.9% of tar was mineralized or adsorbed to floccules, while negative controls showed poor PAH reduction. The dynamics of fungal and bacterial communities was assessed through Automated Ribosomal Intergenic Spacer Analysis (ARISA), 454 pyrosequencing of the fungal ITS and of the bacterial 16S rRNA. Quantification of the degrading bacterial communities was performed via quantitative Real Time PCR of the 16S rRNA genes and of the cathecol 2,3-dioxygenase genes. Results showed the importance of fungal tar-degrading populations in the first period of incubation, followed by a complex bacterial dynamical growth ruled by co-feeding behaviors.
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Affiliation(s)
- Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, I-39100 Bozen/Bolzano, Italy.
| | - Sonia Ciccazzo
- Department of Agricultural Food and Environmental Science, University of Foggia, Via Napoli 25, I-71121 Foggia, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, I-39100 Bozen/Bolzano, Italy
| | - Micol Bellucci
- Department of Agricultural Food and Environmental Science, University of Foggia, Via Napoli 25, I-71121 Foggia, Italy; Department of Civil and Environmental Engineering (DICA) Sec. Environment, Polytechnic University of Milan, Piazza Leonardo da Vinci 32, I-20133 Milan, Italy
| | - Claudio Zaccone
- Department of Agricultural Food and Environmental Science, University of Foggia, Via Napoli 25, I-71121 Foggia, Italy
| | - Luciano Beneduce
- Department of Agricultural Food and Environmental Science, University of Foggia, Via Napoli 25, I-71121 Foggia, Italy
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Lepcha K, Ghosh S. Glycoside hydrolases from a thermophilic microbial consortium and their implication in the saccharification of agroresidues. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Ghio S, Insani EM, Piccinni FE, Talia PM, Grasso DH, Campos E. GH10 XynA is the main xylanase identified in the crude enzymatic extract of Paenibacillus sp. A59 when grown on xylan or lignocellulosic biomass. Microbiol Res 2016; 186-187:16-26. [DOI: 10.1016/j.micres.2016.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
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Manfredi AP, Perotti NI, Martínez MA. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina. J Basic Microbiol 2015; 55:1384-93. [DOI: 10.1002/jobm.201500269] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/02/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Adriana P. Manfredi
- PROIMI Planta Piloto de Procesos Industriales Microbiológicos; CONICET; Tucumán Argentina
- Facultad de Ciencias Exactas y Tecnología; Universidad Nacional de Tucumán; Tucumán Argentina
| | - Nora I. Perotti
- PROIMI Planta Piloto de Procesos Industriales Microbiológicos; CONICET; Tucumán Argentina
- Facultad de Ciencias Exactas y Tecnología; Universidad Nacional de Tucumán; Tucumán Argentina
| | - María A. Martínez
- PROIMI Planta Piloto de Procesos Industriales Microbiológicos; CONICET; Tucumán Argentina
- Facultad de Ciencias Exactas y Tecnología; Universidad Nacional de Tucumán; Tucumán Argentina
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Prospection and Evaluation of (Hemi) Cellulolytic Enzymes Using Untreated and Pretreated Biomasses in Two Argentinean Native Termites. PLoS One 2015; 10:e0136573. [PMID: 26313257 PMCID: PMC4552170 DOI: 10.1371/journal.pone.0136573] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/04/2015] [Indexed: 01/30/2023] Open
Abstract
Saccharum officinarum bagasse (common name: sugarcane bagasse) and Pennisetum purpureum (also known as Napier grass) are among the most promising feedstocks for bioethanol production in Argentina and Brazil. In this study, both biomasses were assessed before and after acid pretreatment and following hydrolysis with Nasutitermes aquilinus and Cortaritermes fulviceps termite gut digestome. The chemical composition analysis of the biomasses after diluted acid pretreatment showed that the hemicellulose fraction was partially removed. The (hemi) cellulolytic activities were evaluated in bacterial culture supernatants of termite gut homogenates grown in treated and untreated biomasses. In all cases, we detected significantly higher endoglucanase and xylanase activities using pretreated biomasses compared to untreated biomasses, carboxymethylcellulose and xylan. Several protein bands with (hemi) cellulolytic activity were detected in zymograms and two-dimensional gel electrophoresis. Some proteins of these bands or spots were identified as xylanolytic peptides by mass spectrometry. Finally, the diversity of cultured cellulolytic bacterial endosymbionts associated to both Argentinean native termite species was analyzed. This study describes, for the first time, bacterial endosymbionts and endogenous (hemi) cellulases of two Argentinean native termites as well as their potential application in degradation of lignocellulosic biomass for bioethanol production.
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Padilha IQM, Carvalho LCT, Dias PVS, Grisi TCSL, Silva FLHD, Santos SFM, Araújo DAM. PRODUCTION AND CHARACTERIZATION OF THERMOPHILIC CARBOXYMETHYL CELLULASE SYNTHESIZED BY Bacillus sp. GROWING ON SUGARCANE BAGASSE IN SUBMERGED FERMENTATION. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2015. [DOI: 10.1590/0104-6632.20150321s00003298] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gong Y, Tang G, Wang M, Li J, Xiao W, Lin J, Liu Z. Direct fermentation of amorphous cellulose to ethanol by engineered Saccharomyces cerevisiae coexpressing Trichoderma viride EG3 and BGL1. J GEN APPL MICROBIOL 2014; 60:198-206. [DOI: 10.2323/jgam.60.198] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Jiménez DJ, Dini-Andreote F, van Elsas JD. Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:92. [PMID: 24955113 PMCID: PMC4064818 DOI: 10.1186/1754-6834-7-92] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/23/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. RESULTS In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions. CONCLUSION In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
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Jiménez DJ, Korenblum E, van Elsas JD. Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion. Appl Microbiol Biotechnol 2013; 98:2789-803. [PMID: 24113822 DOI: 10.1007/s00253-013-5253-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/03/2013] [Accepted: 09/07/2013] [Indexed: 10/26/2022]
Abstract
To develop a targeted metagenomics approach for the analysis of novel multispecies microbial consortia involved in the bioconversion of lignocellulose and furanic compounds, we applied replicated sequential batch aerobic enrichment cultures with either pretreated or untreated wheat straw as the sources of carbon and energy. After each transfer, exponential growth of bacteria was detected using microscopic cell counts, indicating that the substrate was being utilized. In batch, the final bacterial abundances increased from an estimated 5 to 8.7-9.5 log 16S rRNA gene copy numbers/ml. The abundances of fungal propagules showed greater variation, i.e., between 5.4 and 8.0 log ITS1 copies/ml. Denaturing gradient gel electrophoresis analyses showed that the bacterial consortia in both treatments reached approximate structural stability after six transfers. Moreover, the structures of the fungal communities were strongly influenced by substrate treatment. A total of 124 bacterial strains were isolated from the two types of enrichment cultures. The most abundant strains were affiliated with the genera Raoultella/Klebsiella, Kluyvera, Citrobacter, Enterobacter, Pseudomonas, Acinetobacter, Flavobacterium and Arthrobacter. Totals of 43 and 11 strains obtained from the untreated and pretreated substrates, respectively, showed (hemi)cellulolytic activity (CMC-ase and xylanase), whereas 96 strains were capable of growth in 7.5 mM 5-hydroxymethylfurfural. About 50 % of the latter showed extracellular oxidoreductase activity as detected by a novel iodide oxidation method. Also, (hemi)cellulolytic fungal strains related to Coniochaeta, Plectosphaerella and Penicillium were isolated. One Trichosporon strain was isolated from pretreated wheat straw. The two novel bacterial-fungal consortia are starting points for lignocellulose degradation applications.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG, Groningen, The Netherlands,
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