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Song R, Zhu WZ, Li H, Wang H. Impact of wine-grape continuous cropping on soil enzyme activity and the composition and function of the soil microbial community in arid areas. Front Microbiol 2024; 15:1348259. [PMID: 38414771 PMCID: PMC10896694 DOI: 10.3389/fmicb.2024.1348259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Abstract
Introduction Continuous cropping affected the stability of soil enzyme activity and the structural characteristics of microbial community. Owing to challenges in the study of complex rhizosphere microbial communities, the composition and function of these microbial communities in farmland ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere of wine grapes with different years of continuous cropping and investigated their relationships with soil enzyme activity. Methods Metagenomic sequencing was conducted on the rhizosphere soils from one uncultivated wasteland and four vineyards with varying durations of continuous cropping. Results The predominant microbial were bacteria (98.39%), followed by archaea (1.15%) and eukaryotes (0.45%). Continuous cropping caused a significant increase in the relative abundance of Rhizobiales and Micrococcales but a marked decrease in Solirubrobacterales. At the genus level, 75, 88, 65, 132, and 128 microbial genera were unique to uncultivated wasteland, 5, 10, 15, and 20 years of continuous cropping, respectively. The relative abundance of genes with signal transduction function was the highest. The activity of all enzymes measured in this study peaked at 5 years of continuous cropping, and then decreased with 10 to 15 year of continuous cropping, but increased at 20 years again. In addition, soil enzyme activity, especially of alkaline phosphatase was significantly correlated with the diversity of the dominant microorganisms at the genus level. Moreover, the coupled enzyme activities had a greater impact on the diversity of the microbial community than that of individual enzymes. Conclusion Our findings reveal the composition and function of the soil microbial communities and enzymes activity in response to changes in cropping years, which has important implications for overcoming continuous cropping obstacles and optimizing land use.
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Affiliation(s)
- Rui Song
- College of Enology, Northwest A&F University, Yangling, Shanxi, China
| | - Wen Zong Zhu
- College of Enology, Northwest A&F University, Yangling, Shanxi, China
| | - Hua Li
- College of Enology, Northwest A&F University, Yangling, Shanxi, China
- China Wine Industry Technology Institute, Yinchuan, Ningxia, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Yangling, Shanxi, China
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Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. BIOLOGY 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
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Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
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Díaz-García L, Chuvochina M, Feuerriegel G, Bunk B, Spröer C, Streit WR, Rodriguez-R LM, Overmann J, Jiménez DJ. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes. Syst Appl Microbiol 2024; 47:126485. [PMID: 38211536 DOI: 10.1016/j.syapm.2023.126485] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
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Affiliation(s)
- Laura Díaz-García
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia; Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Zhu YX, Zhang X, Yang WC, Li JF. Enhancement of Biomass Conservation and Bioethanol Production of Sweet Sorghum Silage by Constructing Synergistic Microbial Consortia. Microbiol Spectr 2023; 11:e0365922. [PMID: 36645314 PMCID: PMC9927380 DOI: 10.1128/spectrum.03659-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/20/2022] [Indexed: 01/17/2023] Open
Abstract
The efficient storage of materials before bioethanol production could be key to improving pretreatment protocol and facilitating biodegradation, in turn improving the cost-effectiveness of biomass utilization. Biological inoculants were investigated for their effects on ensiling performance, biodegradability of silage materials, and final bioethanol yield from sweet sorghum. Two cellulolytic microbial consortia (CF and PY) were used to inoculate silages of sweet sorghum, with and without combined lactic acid bacteria (Xa), for up to 60 days of ensiling. We found that the consortia notably decreased pH and ammonia nitrogen content while increasing lactic acid/acetic acid ratios. The microbes also functioned in synergy with Xa, significantly reducing lignocellulose content and improving biomass preservation. First-order exponential decay models captured the kinetics of nonstructural carbohydrates and suggested high water-soluble carbohydrate (grams per kilogram dry matter [DM]) preservation potential in PY-Xa (33.48), followed by CF-Xa (30.51). Combined addition efficiently improved enzymatic hydrolysis and enhanced bioethanol yield, and sweet sorghum treated with PY-Xa had the highest ethanol yield (28.42 g L-1). Thus, combined bioaugmentation of synergistic microbes provides an effective method of improving biomass preservation and bioethanol production from sweet sorghum silages. IMPORTANCE Ensiling is an effective storage approach to ensure stable year-round supply for downstream biofuel production; it offers combined facilities of storage and pretreatment. There are challenges in ensiling sweet sorghum due to its coarse structure and high fiber content. This study provides a meaningful evaluation of the effects of adding microbial consortia, with and without lactic acid bacteria, on changes in key properties of sweet sorghum. This study highlighted the bioaugmented ensiling using cellulolytic synergistic microbes to outline a cost-effective strategy to store and pretreat sweet sorghum for bioethanol production.
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Affiliation(s)
- Yu-Xi Zhu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Xu Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Nanjing, China
| | - Wen-Chao Yang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Jun-Feng Li
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
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Zhou T, Liu S, Jiang A. Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia ( Leiothrix argentauris) living in mining area. Front Microbiol 2023; 14:1076523. [PMID: 36760498 PMCID: PMC9904241 DOI: 10.3389/fmicb.2023.1076523] [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: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
The complex gut bacterial communities have a major impact on organismal health. However, knowledge of the effects of habitat change on the gut microbiota of wild birds is limited. In this study, we characterized the gut microbiota of two different subspecies of the Silver-eared Mesia (Leiothrix argentauris), the native subspecies (L. a. rubrogularis) and immigrant subspecies (L. a. vernayi), using 16S rRNA gene high-throughput sequencing. These two subspecies live in a trace metal-contaminated area, and L. a. vernayi was trafficked. They are an excellent system for studying how the gut microbiome of wild animal changes when they move to new habitats. We hypothesized that the immigrant subspecies would develop the same adaptations as the native subspecies in response to habitat changes. The results showed that there were no significant differences in the composition, diversity, or functional metabolism of gut microbiota between native and immigrant subspecies under the combined action of similar influencing factors (the p values of all analyses of variance >0.05). In addition, the composition and functional metabolism of gut microbiota in two subspecies showed adaptation against trace metal damage. Linear discriminant analysis effect size (LEfSe) analysis revealed that Massilia in the intestinal microbiota of immigrant subspecies was significantly higher than that of native subspecies, suggesting that immigrant subspecies suffered habitat change. Finally, we found that these two subspecies living in the mining area had an extremely high proportion of pathogenic bacteria in their gut microbiota (about 90%), much higher than in other species (about 50%) living in wild environment. Our results revealed the adaptation of intestinal microbiota of immigrant Silver-eared Mesias under heavy metals stress, which would provide guidance for biodiversity conservation and pollution management in mining area.
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Zhang X, Borjigin Q, Gao JL, Yu XF, Hu SP, Zhang BZ, Han SC. Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature. Sci Rep 2022; 12:20163. [PMID: 36424390 PMCID: PMC9691720 DOI: 10.1038/s41598-022-23507-z] [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: 12/22/2021] [Accepted: 11/01/2022] [Indexed: 11/26/2022] Open
Abstract
To systematically explore and analyze the microbial composition and function of microbial consortium M44 with straw degradation in the process of subculture at low temperature. In this study, straw degradation characteristics of samples in different culture stages were determined. MiSeq high-throughput sequencing technology was used to analyze the evolution of community structure and its relationship with degradation characteristics of microbial consortium in different culture periods, and the PICRUSt function prediction analysis was performed. The results showed that straw degradation rate, endoglucanase activity, and filter paper enzyme activity of M44 generally decreased with increasing culture algebra. The activities of xylanase, laccase, and lignin peroxidase, as well as VFA content, showing a single-peak curve change with first an increase and then decrease. In the process of subculture, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in different culture stages. Pseudomonas, Flavobacterium, Devosia, Brevundimonas, Trichococcus, Acinetobacter, Dysgonomonas, and Rhizobium were functional bacteria in different culture stages. It was found by PICRUSt function prediction that the functions were concentrated in amino acid transport and metabolism, carbohydrate transship and metabolism related genes, which may contain a large number of fibers and lignin degrading enzyme genes. In this study, the microbial community succession and the gene function in different culture periods were clarified and provide a theoretical basis for screening and rational utilization of microbial consortia.
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Affiliation(s)
- Xin Zhang
- grid.411638.90000 0004 1756 9607Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019 China ,grid.443600.50000 0001 1797 5099Life Sciences College, TongHua Normal University, No. 950, YuCai Road, Tonghua, 314002 China
| | - Qinggeer Borjigin
- grid.411638.90000 0004 1756 9607Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019 China ,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019 China
| | - Ju-Lin Gao
- grid.411638.90000 0004 1756 9607Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019 China ,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019 China
| | - Xiao-Fang Yu
- grid.411638.90000 0004 1756 9607Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019 China ,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019 China
| | - Shu-Ping Hu
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019 China ,grid.411638.90000 0004 1756 9607Vocational and Technical College, Inner Mongolia Agricultural University, Altan Street, Baotou, 014109 China
| | - Bi-Zhou Zhang
- grid.496716.b0000 0004 1777 7895Special Crops Institute, Inner Mongolia Academy of Agricultural Animal Husbandry Sciences, No. 22, ZhaoJun Road, Hohhot, 010031 China
| | - Sheng-Cai Han
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019 China ,grid.411638.90000 0004 1756 9607Hortlculture and Plant Protection College, Inner Mongolia Agricultural University, No. 29, Eerduosi East Street, Hohhot, 010019 China
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Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME COMMUNICATIONS 2022; 2:89. [PMID: 37938754 PMCID: PMC9723784 DOI: 10.1038/s43705-022-00176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2023]
Abstract
The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.
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Affiliation(s)
- Carlos Andrés Díaz Rodríguez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katherine Herrera
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Hua Z, Liu T, Han P, Zhou J, Zhao Y, Huang L, Yuan Y. Isolation, genomic characterization, and mushroom growth-promoting effect of the first fungus-derived Rhizobium. Front Microbiol 2022; 13:947687. [PMID: 35935222 PMCID: PMC9354803 DOI: 10.3389/fmicb.2022.947687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
Polyporus umbellatus is a well-known edible and medicinal mushroom, and some bacteria isolated from mushroom sclerotia may have beneficial effects on their host. These mushroom growth-promoting bacteria (MGPBs) are of great significance in the mushroom production. In this work, we aimed to isolate and identify MGPBs from P. umbellatus sclerotia. Using the agar plate dilution method, strain CACMS001 was isolated from P. umbellatus sclerotia. The genome of CACMS001 was sequenced using PacBio platform, and the phylogenomic analysis indicated that CACMS001 could not be assigned to known Rhizobium species. In co-culture experiments, CACMS001 increased the mycelial growth of P. umbellatus and Armillaria gallica and increased xylanase activity in A. gallica. Comparative genomic analysis showed that CACMS001 lost almost all nitrogen fixation genes but specially acquired one redox cofactor cluster with pqqE, pqqD, pqqC, and pqqB involved in the synthesis of pyrroloquinoline quinone, a peptide-derived redox participating in phosphate solubilization activity. Strain CACMS001 has the capacity to solubilize phosphate using Pikovskaya medium, and phnA and phoU involved in this process in CACMS001 were revealed by quantitative real-time PCR. CACMS001 is a new potential Rhizobium species and is the first identified MGPB belonging to Rhizobium. This novel bacterium would play a vital part in P. umbellatus, A. gallica, and other mushroom cultivation.
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Affiliation(s)
- Zhongyi Hua
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianrui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengjie Han
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Yuan Yuan,
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Enrichment of Anaerobic Microbial Communities from Midgut and Hindgut of Sun Beetle Larvae (Pachnoda marginata) on Wheat Straw: Effect of Inoculum Preparation. Microorganisms 2022; 10:microorganisms10040761. [PMID: 35456811 PMCID: PMC9024811 DOI: 10.3390/microorganisms10040761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/05/2022] Open
Abstract
The Pachnoda marginata larva have complex gut microbiota capable of the effective conversion of lignocellulosic biomass. Biotechnological utilization of these microorganisms in an engineered system can be achieved by establishing enrichment cultures using a lignocellulosic substrate. We established enrichment cultures from contents of the midgut and hindgut of the beetle larva using wheat straw in an alkaline medium at mesophilic conditions. Two different inoculation preparations were used: procedure 1 (P1) was performed in a sterile bench under oxic conditions using 0.4% inoculum and small gauge needles. Procedure 2 (P2) was carried out under anoxic conditions using more inoculum (4%) and bigger gauge needles. Higher methane production was achieved with P2, while the highest acetic acid concentrations were observed with P1. In the enrichment cultures, the most abundant bacterial families were Dysgonomonadaceae, Heliobacteriaceae, Ruminococcaceae, and Marinilabiliaceae. Further, the most abundant methanogenic genera were Methanobrevibacter, Methanoculleus, and Methanosarcina. Our observations suggest that in samples processed with P1, the volatile fatty acids were not completely converted to methane. This is supported by the finding that enrichment cultures obtained with P2 included acetoclastic methanogens, which might have prevented the accumulation of acetic acid. We conclude that differences in the inoculum preparation may have a major influence on the outcome of enrichment cultures from the P. marginata larvae gut.
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Besaury L, Rémond C. Culturable and metagenomic approaches of wheat bran and wheat straw phyllosphere's highlight new lignocellulolytic microorganisms. Lett Appl Microbiol 2022; 74:840-850. [PMID: 35158407 DOI: 10.1111/lam.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/09/2021] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Abstract
The phyllosphere, defined as the aerial parts of plants, is one of the most prevalent microbial habitats on earth. The microorganisms present on the phyllosphere can have several interactions with the plant. The phyllosphere represents then a unique niche where microorganisms have evolved through time in that stressful environment and may have acquired the ability to degrade lignocellulosic plant cell walls in order to survive to oligotrophic conditions. The dynamic lignocellulolytic potential of two phyllospheric microbial consortia (wheat straw and wheat bran) has been studied. The microbial diversity rapidly changed between the native phyllospheres and the final degrading microbial consortia after 48 hours of culture. Indeed, the initial microbial consortia was dominated by the Ralstonia (35.8%) and Micrococcus (75.2%) genera for the wheat bran and wheat straw whereas they were dominated by Candidatus phytoplasma (59%) and Acinetobacter (31.8%) in the final degrading microbial consortia respectively. Culturable experiments leading to the isolation of several new lignocellulolytic isolates (belonging to Moraxella and Atlantibacter genera) and metagenomic reconstruction of the microbial consortia highlighted the existence of an unpredicted microbial diversity involved in lignocellulose fractionation but also the existence of new pathways in known genera (presence of CE2 for Acinetobacter,several AAs for Pseudomonas and several GHs for Bacillus in different Metagenomes Assembled Genomes). The phyllosphere from agricultural co-products represents then a new niche as a lignocellulolytic degrading ecosystem.
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Affiliation(s)
- Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
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Figueiredo G, Gomes M, Covas C, Mendo S, Caetano T. The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study. MICROBIAL ECOLOGY 2022; 83:470-481. [PMID: 33987687 DOI: 10.1007/s00248-021-01762-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.
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Affiliation(s)
- Gonçalo Figueiredo
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Margarida Gomes
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Claúdia Covas
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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Unveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses. Braz J Microbiol 2022; 53:99-130. [PMID: 35088248 PMCID: PMC8882562 DOI: 10.1007/s42770-021-00660-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/19/2021] [Indexed: 01/30/2023] Open
Abstract
Klebsiella variicola is generally known as endophyte as well as lignocellulose-degrading strain. However, their roles in goat omasum along with lignocellulolytic genetic repertoire are not yet explored. In this study, five different pectin-degrading bacteria were isolated from a healthy goat omasum. Among them, a new Klebsiella variicola strain HSTU-AAM51 was identified to degrade lignocellulose. The genome of the HSTU-AAM51 strain comprised 5,564,045 bp with a GC content of 57.2% and 5312 coding sequences. The comparison of housekeeping genes (16S rRNA, TonB, gyrase B, RecA) and whole-genome sequence (ANI, pangenome, synteny, DNA-DNA hybridization) revealed that the strain HSTU-AAM51 was clustered with Klebsiella variicola strains, but the HSTU-AAM51 strain was markedly deviated. It consisted of seventeen cellulases (GH1, GH3, GH4, GH5, GH13), fourteen beta-glucosidase (2GH3, 7GH4, 4GH1), two glucosidase, and one pullulanase genes. The strain secreted cellulase, pectinase, and xylanase, lignin peroxidase approximately 76-78 U/mL and 57-60 U/mL, respectively, when it was cultured on banana pseudostem for 96 h. The catalytically important residues of extracellular cellulase, xylanase, mannanase, pectinase, chitinase, and tannase proteins (validated 3D model) were bound to their specific ligands. Besides, genes involved in the benzoate and phenylacetate catabolic pathways as well as laccase and DiP-type peroxidase were annotated, which indicated the strain lignin-degrading potentiality. This study revealed a new K. variicola bacterium from goat omasum which harbored lignin and cellulolytic enzymes that could be utilized for the production of bioethanol from lignocelluloses.
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Díaz-García L, Chaparro D, Jiménez H, Gómez-Ramírez LF, Bernal AJ, Burbano-Erazo E, Jiménez DJ. Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere. Front Microbiol 2022; 12:744075. [PMID: 35035382 PMCID: PMC8753987 DOI: 10.3389/fmicb.2021.744075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1–T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4–5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Dayanne Chaparro
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jiménez
- Colombian Corporation for Agricultural Research (Agrosavia), Mosquera, Colombia
| | | | - Adriana J Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts. Arch Microbiol 2021; 204:2. [PMID: 34870719 DOI: 10.1007/s00203-021-02600-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.
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Wang D, Zheng Q, Lv Q, Cai Y, Zheng Y, Chen H, Zhang W. Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture. Orthop Surg 2021; 14:139-148. [PMID: 34816606 PMCID: PMC8755877 DOI: 10.1111/os.13060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/09/2021] [Accepted: 05/06/2021] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques. METHODS Seawater samples and physicochemical factors were collected from the coastal zone of Changle city on 8 September 2019. Nineteen filter membranes were obtained after using a suction filtration system. We randomly selected eight samples for total seawater bacteria (SWDNA group) sequencing and three samples for active seawater bacteria (SWRNA group) sequencing by Illumina MiSeq. The remaining eight samples were used for bacterial culture and identification. Alpha diversity including species coverage (Coverage), species diversity (Shannon-Wiener and Simpson index), richness estimators (Chao1), and abundance-based richness estimation (ACE) were calculated to assess biodiversity of seawater bacterioplankton. Beta diversity was used to evaluate the differences between samples. The species abundance differences were determined using the Wilcoxon rank-sum test. Statistical analyses were performed in R environment. RESULTS The Alpha diversity in the SWDNA group in each index was ACE 3206.99, Chao1 2615.12, Shannon 4.64, Simpson 0.05, and coverage 0.97; the corresponding index was ACE 1199.55, Chao1 934.75, Shannon 3.49, Simpson 0.09, and coverage 0.99. The sequencing results of seawater bacterial genes in the coastal waters of Changle city showed that the phyla of high-abundance bacteria of both the SWDNA and SWRNA groups included Cyanobacteria, Proteobacteria, and Bacteroidetes. The main classes included Oxyphotobacteria, Alphaproteobacteria, and Gammaproteobacteria. The main genera included Synechococcus CC9902, Chloroplast, and Cyanobium_PCC-6307. Beta diversity analysis showed a significant difference between the SWDNA and SWRNA groups (P < 0.05). The species abundance differences between SWDNA and SWRNA groups after Wilcoxon rank-sum test showed that, at the phylum level, Actinomycetes was more abundant in SWDNA group (9.17 vs 1.02%, P < 0.05); at the class level, Actinomycetes (δ- Proteus) was more abundant in SWDNA group (9.47% vs 1.01%, P < 0.05); and at the genus level, Chloroplast was more abundant in SWRNA group (13.07% vs 44.57%, P < 0.05). Nine species and 53 colonies were found by bacterial culture: 20 strains of Vibrio (37.74%), 22 strains of Enterobacter (41.51%), and 11 strains of non-fermentative bacteria (20.75%). CONCLUSION Illumi MiSeq sequencing of seawater bacteria revealed that the total bacterial community groups and the active bacterial community groups mainly comprised Cyanobacteria, Proteobacteria, and Bacteroides at the phylum level; Oxyphotobacteria, α-Proteobacteria, and γ-Proteobacteria at the class level; with Synechococcus_CC9902, Chloroplast, and Cyanobium_PCC-6307 comprising the predominant genera. Exploring the composition and differences of seawater bacteria assists understanding regarding the biodiversity and the infections related to seawater bacteria along the coast of the Changle, provides information that will aid in the diagnosis and treatment of such infections.
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Affiliation(s)
- Du Wang
- Department of Joint Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qingcong Zheng
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Qi Lv
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Yuanqing Cai
- Department of Joint Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yun Zheng
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Huidong Chen
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Wenming Zhang
- Department of Joint Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Paixão DAA, Tomazetto G, Sodré VR, Gonçalves TA, Uchima CA, Büchli F, Alvarez TM, Persinoti GF, da Silva MJ, Bragatto J, Liberato MV, Franco Cairo JPL, Leme AFP, Squina FM. Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties. Enzyme Microb Technol 2021; 148:109820. [PMID: 34116762 DOI: 10.1016/j.enzmictec.2021.109820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022]
Abstract
Although lignocellulose is the most abundant and renewable natural resource for biofuel production, its use remains under exploration because of its highly recalcitrant structure. Its deconstruction into sugar monomers is mainly driven by carbohydrate-active enzymes (CAZymes). To develop highly efficient and fast strategies to discover biomass-degrading enzymes for biorefinery applications, an enrichment process combined with integrative omics approaches was used to identify new CAZymes. The lignocellulolytic-enriched mangrove microbial community (LignoManG) established on sugarcane bagasse (SB) was enriched with lignocellulolytic bacteria and fungi such as Proteobacteria, Bacteroidetes, Basidiomycota, and Ascomycota. These microbial communities were able to degrade up to 55 % of the total SB, indicating the production of lignocellulolytic enzymes. Metagenomic analysis revealed that the LignoManG harbors 18.042 CAZyme sequences such as of cellulases, hemicellulases, carbohydrate esterases, and lytic polysaccharide monooxygenase. Similarly, our metaproteomic analysis depicted several enzymes from distinct families of different CAZy families. Based on the LignoManG data, a xylanase (coldXynZ) was selected, amplified, cloned, expressed, and biochemically characterized. The enzyme displayed psicrofilic properties, with the highest activity at 15 °C, retaining 77 % of its activity when incubated at 0 °C. Moreover, molecular modeling in silico indicated that coldXynZ is composed of a TIM barrel, which is a typical folding found in the GH10 family, and displayed similar structural features related to cold-adapted enzymes. Collectively, the data generated in this study represent a valuable resource for lignocellulolytic enzymes with potential biotechnological applications.
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Affiliation(s)
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200, Aarhus, Denmark
| | - Victoria Ramos Sodré
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Thiago A Gonçalves
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fernanda Büchli
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Thabata Maria Alvarez
- Graduate Programme in Industrial Biotechnology, Universidade Positivo, Curitiba, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Márcio José da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliano Bragatto
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - João Paulo L Franco Cairo
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.
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Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium. Appl Environ Microbiol 2021; 87:AEM.02427-20. [PMID: 33127812 PMCID: PMC7783344 DOI: 10.1128/aem.02427-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems. The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.
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18
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Fernandez-Bayo JD, Simmons CW, VanderGheynst JS. Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes. ACTA ACUST UNITED AC 2020; 47:1031-1044. [DOI: 10.1007/s10295-020-02326-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Abstract
Abstract
The properties of digestates generated through anaerobic digestion are influenced by interactions between the digester microbial communities, feedstock properties and digester operating conditions. This study investigated the effect of varying initial feedstock carbon to nitrogen (C/N) ratios on digestate microbiota and predicted abundance of genes encoding lignocellulolytic activity. The C/N ratio had a significant impact on the digestate microbiome. Feedstocks with intermediate C/N ratio (20–27) (where higher biomethane potential was observed) showed higher relative abundance of archaea compared to feedstocks with C/N ratios at 17 and 34. Within microbial networks, four microbial clusters and eight connector microorganisms changed significantly with the C/N ratio (P < 0.05). Feedstocks with C/N < 23 were richer in organisms from the family Thermotogaceae and genus Caldicoprobacter and enhanced potential for degradation of maltose, galactomannans, melobiose and lactose. This study provides new insights into how anaerobic digestion conditions relate to the structure and functional potential of digester microbial communities, which may be relevant to both digester performance and subsequent utilization of digestates for composting or amending soil.
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Affiliation(s)
- Jesus D Fernandez-Bayo
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Christopher W Simmons
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Jean S VanderGheynst
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.266686.a 0000000102217463 Department of Bioengineering University of Massachusetts Dartmouth MA USA
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19
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Jiménez DJ, Wang Y, Chaib de Mares M, Cortes-Tolalpa L, Mertens JA, Hector RE, Lin J, Johnson J, Lipzen A, Barry K, Mondo SJ, Grigoriev IV, Nichols NN, van Elsas JD. Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium. FEMS Microbiol Ecol 2020; 96:5643886. [PMID: 31769802 DOI: 10.1093/femsec/fiz186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.
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Affiliation(s)
- Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Maryam Chaib de Mares
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Jeffrey A Mertens
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Ronald E Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Junyan Lin
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, Colorado 80521, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720-3102, USA
| | - Nancy N Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
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Cortes-Tolalpa L, Wang Y, Salles JF, van Elsas JD. Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15. Front Microbiol 2020; 11:248. [PMID: 32194522 PMCID: PMC7065263 DOI: 10.3389/fmicb.2020.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 02/03/2020] [Indexed: 01/19/2023] Open
Abstract
Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcao Salles
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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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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22
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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23
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Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
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Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
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24
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Mondo SJ, Jiménez DJ, Hector RE, Lipzen A, Yan M, LaButti K, Barry K, van Elsas JD, Grigoriev IV, Nichols NN. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:229. [PMID: 31572496 PMCID: PMC6757388 DOI: 10.1186/s13068-019-1569-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). RESULTS The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. CONCLUSIONS We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.
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Affiliation(s)
- Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO 80521 USA
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102 USA
| | - Nancy N. Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
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25
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Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA, Henske JK, Theodorou MK, Valentine DL, O’Malley MA. Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. ACS Synth Biol 2019; 8:2174-2185. [PMID: 31461261 DOI: 10.1021/acssynbio.9b00271] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.
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Affiliation(s)
- Sean P. Gilmore
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - St. Elmo Wilken
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jennifer L. Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - John K. Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael K. Theodorou
- Harper Adams University, Agriculture Centre for Sustainable Energy Systems, Newport, Shropshire TF10 8NB, United Kingdom
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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26
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Assessment of soil potential to natural attenuation and autochthonous bioaugmentation using microarray and functional predictions from metagenome profiling. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01486-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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27
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Carrillo-Barragan P, Bowler B, Dolfing J, Sallis P, Gray ND. Enrichment and Characterisation of a Mixed-Source Ethanologenic Community Degrading the Organic Fraction of Municipal Solid Waste Under Minimal Environmental Control. Front Microbiol 2019; 10:722. [PMID: 31024500 PMCID: PMC6465759 DOI: 10.3389/fmicb.2019.00722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/21/2019] [Indexed: 01/08/2023] Open
Abstract
The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.
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Affiliation(s)
| | - Bernard Bowler
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul Sallis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Neil Duncan Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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28
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Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA. Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems. MICROBIAL ECOLOGY 2019; 77:713-725. [PMID: 30209585 DOI: 10.1007/s00248-018-1251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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Affiliation(s)
- Aicha Asma Houfani
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Oscar U Navarrete
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
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29
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Fernández-Bayo JD, Hestmark KV, Claypool JT, Harrold DR, Randall TE, Achmon Y, Stapleton JJ, Simmons CW, VanderGheynst JS. The initial soil microbiota impacts the potential for lignocellulose degradation during soil solarization. J Appl Microbiol 2019; 126:1729-1741. [PMID: 30895681 DOI: 10.1111/jam.14258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 02/02/2023]
Abstract
AIMS Soil biosolarization (SBS) is a pest control technology that includes the incorporation of organic matter into soil prior to solarization. The objective of this study was to measure the impact of the initial soil microbiome on the temporal evolution of genes encoding lignocellulose-degrading enzymes during SBS. METHODS AND RESULTS Soil biosolarization field experiments were completed using green waste (GW) as a soil amendment and in the presence and absence of compost activating inoculum. Samples were collected over time and at two different soil depths for measurement of the microbial community and the predicted lignocellulosic-degrading microbiome. Compost inoculum had a significant positive effect on several predicted genes encoding enzymes involved in cellulose, hemicellulose and lignin degradation. These included beta-glucosidase, endo-1,3(4)-beta-glucanase, alpha-galactosidase and laccase. CONCLUSION Amendment of micro-organisms found in compost to soil prior to SBS enhanced the degradation potential of cellulose, hemicellulose and lignin found in GW. SIGNIFICANCE AND IMPACT OF THE STUDY The type of organic matter amended and its biotransformation by soil micro-organisms impact the efficacy of SBS. The results suggest that co-amending highly recalcitrant biomass with micro-organisms found in compost improves biomass conversion during SBS.
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Affiliation(s)
- J D Fernández-Bayo
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - K V Hestmark
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - J T Claypool
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - D R Harrold
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - T E Randall
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - Y Achmon
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA.,Department of Biotechnology and Food Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - J J Stapleton
- Statewide Integrated Pest Management Program, University of California, Kearney Agricultural Research and Extension Center, Parlier, CA, USA
| | - C W Simmons
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - J S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Bioengineering, University of Massachusetts, Dartmouth, MA, USA
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Lv Y, Wan C, Lee DJ, Liu X, Zhang Y, Tay JH. Dehydrated and recovered aerobic granules: Identifying acetone-dehydration resistant strains. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2018.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Vieira F, Pecchia J, Segato F, Polikarpov I. Exploring oyster mushroom (Pleurotus ostreatus
) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields. J Appl Microbiol 2018; 126:931-944. [DOI: 10.1111/jam.14168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 11/27/2022]
Affiliation(s)
- F.R. Vieira
- Departamento de Engenharia Rural; Universidade Estadual Paulista ‘Júlio de Mesquita Filho’; Botucatu São Paulo Brazil
- Department of Plant Pathology and Environmental Microbiology; The Pennsylvania State University; University Park PA USA
| | - J.A. Pecchia
- Department of Plant Pathology and Environmental Microbiology; The Pennsylvania State University; University Park PA USA
| | - F. Segato
- Departmento de Biotecnologia; Escola de Engenharia de Lorena; Universidade de São Paulo; Lorena São Paulo Brazil
| | - I. Polikarpov
- Departamento de Física e Ciências Interdiciplinares; Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos São Paulo Brazil
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Lazuka A, Auer L, O’Donohue M, Hernandez-Raquet G. Anaerobic lignocellulolytic microbial consortium derived from termite gut: enrichment, lignocellulose degradation and community dynamics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:284. [PMID: 30356893 PMCID: PMC6191919 DOI: 10.1186/s13068-018-1282-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/06/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant renewable carbon resource that can be used for biofuels and commodity chemicals production. The ability of complex microbial communities present in natural environments that are specialized in biomass deconstruction can be exploited to develop lignocellulose bioconversion processes. Termites are among the most abundant insects on earth and play an important role in lignocellulose decomposition. Although their digestive microbiome is recognized as a potential reservoir of microorganisms producing lignocellulolytic enzymes, the potential to enrich and maintain the lignocellulolytic activity of microbial consortia derived from termite gut useful for lignocellulose biorefinery has not been assessed. Here, we assessed the possibility of enriching a microbial consortium from termite gut and maintaining its lignocellulose degradation ability in controlled anaerobic bioreactors. RESULTS We enriched a termite gut-derived consortium able to transform lignocellulose into carboxylates under anaerobic conditions. To assess the impact of substrate natural microbiome on the enrichment and the maintenance of termite gut microbiome, the enrichment process was performed using both sterilized and non-sterilized straw. The enrichment process was carried out in bioreactors operating under industrially relevant aseptic conditions. Two termite gut-derived microbial consortia were obtained from Nasutitermes ephratae by sequential batch culture on raw wheat straw as the sole carbon source. Analysis of substrate loss, carboxylate production and microbial diversity showed that regardless of the substrate sterility, the diversity of communities selected by the enrichment process strongly changed compared to that observed in the termite gut. Nevertheless, the community obtained on sterile straw displayed higher lignocellulose degradation capacity; it showed a high xylanase activity and an initial preference for hemicellulose. CONCLUSIONS This study demonstrates that it is possible to enrich and maintain a microbial consortium derived from termite gut microbiome in controlled anaerobic bioreactors, producing useful carboxylates from raw biomass. Our results suggest that the microbial community is shaped both by the substrate and the conditions that prevail during enrichment. However, when aseptic conditions are applied, it is also affected by the biotic pressure exerted by microorganisms naturally present in the substrate and in the surrounding environment. Besides the efficient lignocellulolytic consortium enriched in this study, our results revealed high levels of xylanase activity that can now be further explored for enzyme identification and overexpression for biorefinery purposes.
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Affiliation(s)
- Adèle Lazuka
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Lucas Auer
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Michael O’Donohue
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Guillermina Hernandez-Raquet
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
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Guo H, Wang XD, Lee DJ. Proteomic researches for lignocellulose-degrading enzymes: A mini-review. BIORESOURCE TECHNOLOGY 2018; 265:532-541. [PMID: 29884341 DOI: 10.1016/j.biortech.2018.05.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 05/14/2023]
Abstract
Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Xiao-Dong Wang
- Research Center of Engineering Thermophysics, North China Electric Power University, Beijing 102206, China; School of Energy Power and Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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Kong X, Du J, Ye X, Xi Y, Jin H, Zhang M, Guo D. Enhanced methane production from wheat straw with the assistance of lignocellulolytic microbial consortium TC-5. BIORESOURCE TECHNOLOGY 2018; 263:33-39. [PMID: 29729539 DOI: 10.1016/j.biortech.2018.04.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
The major obstacle of methane production from lignocellulose lies in the inefficient deconstruction of biomass. In this study, an anaerobic microbial consortium TC-5 was enriched with high lignocellulose-degradation capacity to enhance methane production from wheat straw. High degradation ratio of 45.7% of un-pretreated wheat straw was achieved due to a multi-species lignocellulolytic enzyme presented in the crude culture supernatant. The specific activity of xylanase, xylan esterase and β-xylosidase reached the highest level of 4.23, 0.15 and 0.48 U/mg, while cellobiohydrolase, endoglucanase and β-glucosidase showed the highest specific activity of 0.36, 0.22 and 0.41 U/mg during 9 days' degradation. Inoculation of TC-5 in digestion sludge during anaerobic digestion of wheat straw resulted in remarkable enhancement of 22.2% and 36.6% in methane yield under mesophilic and thermophilic conditions, respectively. This work demonstrates the potential of TC-5 for enhancing the production of biogas and other chemicals through biomass based biorefinery.
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Affiliation(s)
- Xiangping Kong
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China
| | - Jing Du
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China
| | - Xiaomei Ye
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China.
| | - Yonglan Xi
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China
| | - Hongmei Jin
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China
| | - Min Zhang
- East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture, Biomass Conversion Laboratory, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, People's Republic of China
| | - Dong Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing 211816, People's Republic of China
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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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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Mohammed WS, Ziganshina EE, Shagimardanova EI, Gogoleva NE, Ziganshin AM. Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae). Sci Rep 2018; 8:10073. [PMID: 29968731 PMCID: PMC6030058 DOI: 10.1038/s41598-018-27342-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.
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Affiliation(s)
- Waleed S Mohammed
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Elvira E Ziganshina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Natalia E Gogoleva
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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Hu Y, Xia Y, Sun Q, Liu K, Chen X, Ge T, Zhu B, Zhu Z, Zhang Z, Su Y. Effects of long-term fertilization on phoD-harboring bacterial community in Karst soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:53-63. [PMID: 29428860 DOI: 10.1016/j.scitotenv.2018.01.314] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/24/2018] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Phosphorus (P) acquisition by plants from soil organic P mainly relies on microorganisms. Examining the community of functional microbes that encode phosphatases (e.g. PhoD) under different fertilization managements may provide valuable information for promoting soil organic P availability. Here, we investigated how the abundance and community diversity of phoD-harboring bacteria responded to long-term fertilization in Karst soils. Six fertilization treatments were designed as follows: non-fertilized control (CK), inorganic fertilization only (NPK), and inorganic fertilization combined with low- and high amounts of straw (LSNPK and HSNPK), or cattle manure (LMNPK and HMNPK). We found that soil available phosphorus (AP) content and the activity of alkaline phosphatase (ALP) were significantly higher in all combined inorganic/organic fertilization treatments, while the abundance of the phoD gene was only higher in the HMPNK treatment, compared to NPK. The combination of inorganic/organic fertilizations had no effect on the diversity of phoD genes compared to NPK alone, but the phoD gene richness was greater in these treatments as compared to the control. Only organic fertilization combinations with high amounts of organic matter (both HSNPK and HMNPK) significantly affected the phoD community structure. A structure equation model demonstrated that soil organic carbon (SOC), rather than P, greatly affected the phoD community structure, suggesting that organic P mineralization in soils is decoupled from C mineralization. Our results suggested that optimized combinations of inorganic/organic fertilizations could promote P availability via regulating soil phoD-harboring bacteria community diversity and ALP activity.
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Affiliation(s)
- Yajun Hu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, PR China
| | - Yinhang Xia
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qi Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kunping Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China
| | - Xiangbi Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, PR China
| | - Tida Ge
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China
| | - Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz-Zentrum Muenchen, Germany
| | - Zhenke Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China
| | - Zhenhua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, PR China
| | - Yirong Su
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, PR China.
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Jiménez DJ, Chaib De Mares M, Salles JF. Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse. Front Microbiol 2018. [PMID: 29535687 PMCID: PMC5834485 DOI: 10.3389/fmicb.2018.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and α-arabinosidases/β-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular β-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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Su X, Zhao W, Xia D. The diversity of hydrogen-producing bacteria and methanogens within an in situ coal seam. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:245. [PMID: 30202440 PMCID: PMC6128992 DOI: 10.1186/s13068-018-1237-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/27/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Biogenic and biogenic-thermogenic coalbed methane (CBM) are important energy reserves for unconventional natural gas. Thus, to investigate biogenic gas formation mechanisms, a series of fresh coal samples from several representative areas of China were analyzed to detect hydrogen-producing bacteria and methanogens in an in situ coal seam. Complete microbial DNA sequences were extracted from enrichment cultures grown on coal using the Miseq high-throughput sequencing technique to study the diversity of microbial communities. The species present and differences between the dominant hydrogen-producing bacteria and methanogens in the coal seam are then considered based on environmental factors. RESULTS Sequences in the Archaea domain were classified into four phyla and included members from Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Pacearchaeota. The Bacteria domain included members of the phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi, and Nitrospirae. The hydrogen-producing bacteria was dominated by the genera: Clostridium, Enterobacter, Klebsiella, Citrobacter, and Bacillus; the methanogens included the genera: Methanorix, Methanosarcina, Methanoculleus, Methanobrevibacter, Methanobacterium, Methanofollis, and Methanomassiliicoccus. CONCLUSION Traces of hydrogen-producing bacteria and methanogens were detected in both biogenic and non-biogenic CBM areas. The diversity and abundance of bacteria in the biogenic CBM areas are relatively higher than in the areas without biogenic CBM. The community structure and distribution characteristics depend on coal rank, trace metal elements, temperature, depth and groundwater dynamic conditions. Biogenic gas was mainly composed of hydrogen and methane, the difference and diversity were caused by microbe-specific fermentation of substrates; as well as by the environmental conditions. This discovery is a significant contribution to extreme microbiology, and thus lays the foundation for research on biogenic CBM.
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Affiliation(s)
- Xianbo Su
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000 China
- Collaborative Innovation Center of Coalbed Methane and Shale Gas for Central Plains Economic Region, Jiaozuo, 454000 Henan Province China
| | - Weizhong Zhao
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Daping Xia
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000 China
- Collaborative Innovation Center of Coalbed Methane and Shale Gas for Central Plains Economic Region, Jiaozuo, 454000 Henan Province China
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends Microbiol 2017. [PMID: 28648267 DOI: 10.1016/j.tim.2017.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003-9298, USA
| | - Steven W Singer
- Joint BioEnergy Institute,5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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Maruthamuthu M, Jiménez DJ, van Elsas JD. Characterization of a furan aldehyde-tolerant β-xylosidase/α-arabinosidase obtained through a synthetic metagenomics approach. J Appl Microbiol 2017; 123:145-158. [PMID: 28489302 DOI: 10.1111/jam.13484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/16/2022]
Abstract
AIMS The aim of the study was to characterize 10 hemicellulolytic enzymes obtained from a wheat straw-degrading microbial consortium. METHODS AND RESULTS Based on previous metagenomics analyses, 10 glycosyl hydrolases were selected, codon-optimized, synthetized, cloned and expressed in Escherichia coli. Nine of the overexpressed recombinant proteins accumulated in cellular inclusion bodies, whereas one, a 37·5-kDa protein encoded by gene xylM1989, was found in the soluble fractions. The resulting protein, denoted XylM1989, showed β-xylosidase and α-arabinosidase activities. It fell in the GH43 family and resembled a Sphingobacterium sp. protein. The XylM1989 showed optimum activity at 20°C and pH 8·0. Interestingly, it kept approximately 80% of its β-xylosidase activity in the presence of 0·5% (w/v) furfural and 0·1% (w/v) 5-hydroxymethylfurfural. Additionally, the presence of Ca2+ , Mg2+ and Mn2+ ions increased the enzymatic activity and conferred complete tolerance to 500 mmol l-1 of xylose. Protein XylM1989 is also able to release sugars from complex polysaccharides. CONCLUSION We report the characterization of a novel bifunctional hemicellulolytic enzyme obtained through a targeted synthetic metagenomics approach. SIGNIFICANCE AND IMPACT OF THE STUDY The properties of XylM1989 turn this protein into a promising enzyme that could be useful for the efficient saccharification of plant biomass.
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Affiliation(s)
- M Maruthamuthu
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - D J Jiménez
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - J D van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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43
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Selection and characterization of an anaerobic microbial consortium with high adaptation to crude glycerol for 1,3-propanediol production. Appl Microbiol Biotechnol 2017; 101:5985-5996. [DOI: 10.1007/s00253-017-8311-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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44
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Ma S, Huang Y, Wang C, Fan H, Dai L, Zhou Z, Liu X, Deng Y. Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw. Int J Syst Evol Microbiol 2017; 67:1607-1612. [PMID: 27902335 PMCID: PMC5817277 DOI: 10.1099/ijsem.0.001664] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6-1×2.5-8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40-60 °C, 6.5-8.0 and 0-15.0 g l-1, with optimum growth noted at 50-55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to Defluviitalea saccharophila DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus Defluviitalea, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).
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Affiliation(s)
- Shichun Ma
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Present address: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nan Road, Chengdu 610041, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yan Huang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Cong Wang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, Sichuan, P.R. China.,Present address: College of Light Industry, Textile and Food Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, Sichuan, P.R. China
| | - Hui Fan
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Lirong Dai
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Zheng Zhou
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Xing Liu
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yu Deng
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
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45
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Predicting the biotechnological potential of bacteria isolated from Antarctic soils, including the rhizosphere of vascular plants. Polar Biol 2017. [DOI: 10.1007/s00300-016-2065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol 2017; 122:940-952. [PMID: 28092137 DOI: 10.1111/jam.13401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.
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Affiliation(s)
- C A Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M Prabhakaran
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - K D Ramachandriya
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, Stillwater, OK, USA
| | - P Canaan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - B Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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47
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Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, de Oliveira JCF, Pascon RC, Cruz JBD, da Silva AM, Setubal JC. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci Rep 2016; 6:38915. [PMID: 27941956 PMCID: PMC5150989 DOI: 10.1038/srep38915] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
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Affiliation(s)
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Andrew Maltez Thomas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Deibs Barbosa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Leandro Nascimento Lemos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Gianluca Major Machado Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - George Willian Condomitti Epamino
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Karen Cristina Lombardi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ronaldo Bento Quaggio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
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48
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Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures. PLoS One 2016; 11:e0167216. [PMID: 27936240 PMCID: PMC5147896 DOI: 10.1371/journal.pone.0167216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/10/2016] [Indexed: 12/16/2022] Open
Abstract
Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.
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49
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Yu C, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Appl Microbiol Biotechnol 2016; 100:10237-10249. [PMID: 27838839 DOI: 10.1007/s00253-016-7955-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
Abstract
Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.
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Affiliation(s)
- Chaowei Yu
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biosciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Jean S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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50
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Wang J, Du X, Zhang Y, Li T, Liao X. Effect of Substrate on Identification of Microbial Communities in Poultry Carcass Composting and Microorganisms Associated with Poultry Carcass Decomposition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:6838-6847. [PMID: 27548371 DOI: 10.1021/acs.jafc.6b02442] [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] [Indexed: 06/06/2023]
Abstract
Three composting systems, which consisted of different ratios of chicken manure, sawdust, and poultry carcasses, were used to investigate the effect of substrate on the identification of microbial communities and microorganisms associated with poultry carcass decomposition by characterizing the microbial communities and physicochemical parameters. The physicochemical and Miseq Illumina sequencing results showed the composition of substrate had a significant effect on the identification and metabolic capabilities of microbial communities in decomposting process. Poultry carcasses might be the potential driver for the identification of bacterial communities in poultry carcass composting, whereas the initial C/N ratio may mainly contribute to the diversity of fungal communities and the similar dominant microbial communities in treatments. Poultry carcasses and initial C/N ratio could respectively affect the composition and abundance of microorganisms associated with the decomposition of poultry carcasses. Understanding the potential composting driver could allow development of an efficient carcass degradation system.
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Affiliation(s)
- Jie Wang
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Xueqing Du
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Yitao Zhang
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Ting Li
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Xindi Liao
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
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