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Aktar N, Mannan E, Kabir SMT, Hasan R, Hossain MS, Ahmed R, Ahmed B, Islam MS. Comparative metagenomics and microbial dynamics of jute retting environment. Int Microbiol 2024; 27:113-126. [PMID: 37204507 DOI: 10.1007/s10123-023-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.
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Affiliation(s)
- Nasima Aktar
- Basic and Applied Research on Jute, Dhaka, Bangladesh.
| | | | | | - Rajnee Hasan
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md Shahidul Islam
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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Bou Orm E, Sauvagère S, Rocher J, Benezet JC, Bayle S, Siatka C, Bergeret A, Malhautier L. Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12582-5. [PMID: 37227475 DOI: 10.1007/s00253-023-12582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.
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Affiliation(s)
- Eliane Bou Orm
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Stéphane Sauvagère
- École de l'ADN, Université de Nîmes, 19 Grand Rue BP 81295, 30015, Nîmes cedex 1, France
| | - Janick Rocher
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Jean-Charles Benezet
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Sandrine Bayle
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Christian Siatka
- UPR CHROME, Université de Nîmes, Place Gabriel Péri, 30000, Nîmes cedex 1, France
| | - Anne Bergeret
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Luc Malhautier
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France.
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Zhang C, Cai B, Sun Y, Kang J, Pei F, Ge J. Microbial communities that drive the degradation of flax pectin and hemicellulose during dew retting with Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 addition. BIORESOURCE TECHNOLOGY 2023; 371:128516. [PMID: 36563865 DOI: 10.1016/j.biortech.2022.128516] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
In this study, the combined addition of Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 to flax degradation increased the degradation rates of pectin (74.7 %) and pectinic acid (59.3 %) and increased the maximum activities of pectinase (610.66 ± 7.03 U/mL) and mannanase (656.97 ± 13.16 U/mL). 16S rRNA sequencing showed that the added bacterial agent (Bacillus) was the dominant bacterium, and its addition increased the relative abundance (RA) of Firmicutes and decreased the RA of Bacteroidetes. The core bacterial community linked to degradation (Firmicutes) was determined by RDA. Network analysis showed that the number of bacteria related to pectin and hemicellulose degradation increased with the addition of the bacteria combination. SEM analysis showed that Bacillus was positively correlated with the degradation of pectic substances. These results provide new ideas for improving the utilization of agricultural waste resources and promoting sustainable development in modern agriculture.
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Affiliation(s)
- Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Yangcun Sun
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Fangyi Pei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China.
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Xu H, Zhang L, Feng X, Yang Q, Zheng K, Duan S, Cheng L. Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast. BMC PLANT BIOLOGY 2022; 22:516. [PMID: 36333799 PMCID: PMC9636830 DOI: 10.1186/s12870-022-03890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Data on the microbial community and functional proteins associated with degumming in kenaf remains scant. Here, we analyzed the microbial communities associated with kenaf (Hibiscus cannabinus) bast fibers during retting to identify potential candidate degumming bacteria. Retting liquids were collected and analyzed at 0 days, 10 days, and 34 days and then evaluated the yield and quality of kenaf fiber at the different retting times. Besides, the microbial communities were characterized using metagenomic and proteomic analysis by LC-MS/MS technology. RESULTS The data showed that increase in the retting time significantly improves the softness, dispersion, and fiber whiteness of the kenaf fiber. The relative abundance of Acinetobacter increased from 2.88% at the baseline to 6.64% at the 34th retting. On the other hand, some members of Clostridium were reduced from 3% at the baseline to 2% at the 34th retting. Analysis of carbohydrate active enzymes showed constant changes in the utilization of carbohydrates. Besides, benzoquinone reductase, cellobiose dehydrogenase, glucose 1-oxidase, aryl alcohol oxidase and alcohol oxidase were the top five most abundant enzymes in the retting liquids. This present results demonstrated that the expressions of B7GYR8, Q6RYW5 and Q6FFK2 proteins were suppressed in Acinetobacter with the retting time. On the contrary, P05149 was upregulated with the retting time. In Clostridium, P37698, P52040 and P54937 proteins were upregulated with the retting time. CONCLUSION In addition, bacteria Acinetobacter and Clostridium might be playing important roles in the kenaf degumming process. Similarly, up-regulation of P37698, P52040 and P54937 proteins is an important manifestation and mediates important roles in the degumming process.
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Affiliation(s)
- Huan Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Lixia Zhang
- Xinyang City Academy of Agricultural Sciences, 20 Minquan South Street, Shihe District, Xinyang, Henan, China
| | - Xiangyuan Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Qi Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Ke Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Shengwen Duan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China.
| | - Lifeng Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China.
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Yuan H, Ren G, Liu K, Zhao Z. Effect of Incorporating Polyvinyl Alcohol Fiber on the Mechanical Properties of EICP-Treated Sand. MATERIALS 2021; 14:ma14112765. [PMID: 34071150 PMCID: PMC8197091 DOI: 10.3390/ma14112765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 01/27/2023]
Abstract
Enzyme-induced calcium carbonate precipitation (EICP) technology can improve the strength of treated soil. But it also leads to remarkable brittleness of the soil. This study used polyvinyl alcohol (PVA) fiber combined with EICP to solidify sand. Through the unconfined compressive strength (UCS) test, the effect of PVA fiber incorporation on the mechanical properties of EICP-solidified sand was investigated; the distribution of CaCO3 in the sample and the microstructure of fiber-reinforced EICP-treated sand were explored through the calcium carbonate content (CCC) test and microscopic experiment. Compared with the sand treated by EICP, the strength and stiffness of the sand reinforced by the fiber combined with EICP were greatly improved, and the ductility was also improved to a certain extent. However, the increase of CCC was extremely weak, and the inhomogeneity of CaCO3 distribution was enlarged; the influence of fiber length on the UCS and CCC of the treated sand was greater than that of the fiber content. The improvement of EICP-solidified sand by PVA fiber was mainly due to the formation of a "fiber-CaCO3-sand" spatial structure system through fiber bridging, not the increase of CCC.
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Affiliation(s)
- Hua Yuan
- School of Civil Engineering and Architecture, Henan University, Kaifeng 475004, China; (H.Y.); (G.R.); (K.L.)
- Henan Rail Transit Intelligent Construction Engineering Research Center, Kaifeng 475004, China
| | - Guanzhou Ren
- School of Civil Engineering and Architecture, Henan University, Kaifeng 475004, China; (H.Y.); (G.R.); (K.L.)
| | - Kang Liu
- School of Civil Engineering and Architecture, Henan University, Kaifeng 475004, China; (H.Y.); (G.R.); (K.L.)
| | - Zhiliang Zhao
- Central Plains Development Research Institute, Henan University, Kaifeng 475004, China
- Correspondence:
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Imran MA, Gowthaman S, Nakashima K, Kawasaki S. The Influence of the Addition of Plant-Based Natural Fibers (Jute) on Biocemented Sand Using MICP Method. MATERIALS 2020; 13:ma13184198. [PMID: 32967316 PMCID: PMC7560478 DOI: 10.3390/ma13184198] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022]
Abstract
The microbial-induced carbonate precipitation (MICP) method has gained intense attention in recent years as a safe and sustainable alternative for soil improvement and for use in construction materials. In this study, the effects of the addition of plant-based natural jute fibers to MICP-treated sand and the corresponding microstructures were measured to investigate their subsequent impacts on the MICP-treated biocemented sand. The fibers used were at 0%, 0.5%, 1.5%, 3%, 5%, 10%, and 20% by weight of the sand, while the fiber lengths were 5, 15, and 25 mm. The microbial interactions with the fibers, the CaCO3 precipitation trend, and the biocemented specimen (microstructure) were also evaluated based on the unconfined compressive strength (UCS) values, scanning electron microscopy (SEM), and fluorescence microscopy. The results of this study showed that the added jute fibers improved the engineering properties (ductility, toughness, and brittleness behavior) of the biocemented sand using MICP method. Furthermore, the fiber content more significantly affected the engineering properties of the MICP-treated sand than the fiber length. In this study, the optimal fiber content was 3%, whereas the optimal fiber length was s 15 mm. The SEM results indicated that the fiber facilitated the MICP process by bridging the pores in the calcareous sand, reduced the brittleness of the treated samples, and increased the mechanical properties of the biocemented sand. The results of this study could significantly contribute to further improvement of fiber-reinforced biocemented sand in geotechnical engineering field applications.
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Affiliation(s)
- Md Al Imran
- Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan;
- Correspondence: ; Tel.: +81-8011-706-6318
| | - Sivakumar Gowthaman
- Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan;
| | - Kazunori Nakashima
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan; (K.N.); (S.K.)
| | - Satoru Kawasaki
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan; (K.N.); (S.K.)
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Pectinolytic Bacterial Consortia Reduce Jute Retting Period and Improve Fibre Quality. Sci Rep 2020; 10:5174. [PMID: 32198430 PMCID: PMC7083874 DOI: 10.1038/s41598-020-61898-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/28/2020] [Indexed: 11/29/2022] Open
Abstract
Jute fibre is the second most important fibre next to cotton. It is obtained from the bark of plant through microbial retting process. Here we report optimized microbial retting protocol that can lower retting period and produce high fibre quality. A total of 451 bacterial colonies have been isolated from five jute retting water samples in Bangladesh. Higher pectinolytic bacterial isolates were predominant in the later stage of jute retting. Out of these, 168 isolates have been screened by both semi-quantitative and quantitative pectinase, xylanase and cellulase enzyme assay. Among them, 144 isolates have been selected on the basis of extra cellular enzyme activity of these three enzymes. 16 s ribosomal gene sequencing analysis identified 2 phyla- Firmicutis (80.55%) and Proteobacteria (19.45%). To check the synergistic and antagonistic effect 10 selected isolates were tested in 167 different combinations. Three best combinations were identified that lowered retting period from 18–21 days to 10 days producing high quality fibre in both laboratory and field trial. This improved retting technology can be adopted in industrial scale for the production of quality jute fibre in a controlled condition in reduced water quantity without polluting the environment.
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Liu M, Ale MT, Kołaczkowski B, Fernando D, Daniel G, Meyer AS, Thygesen A. Comparison of traditional field retting and Phlebia radiata Cel 26 retting of hemp fibres for fibre-reinforced composites. AMB Express 2017; 7:58. [PMID: 28275995 PMCID: PMC5342995 DOI: 10.1186/s13568-017-0355-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022] Open
Abstract
Classical field retting and controlled fungal retting of hemp using Phlebia radiata Cel 26 (a mutant with low cellulose degrading ability) were compared with pure pectinase treatment with regard to mechanical properties of the produced fibre/epoxy composites. For field retting a classification of the microbial evolution (by gene sequencing) and enzyme profiles were conducted. By phylogenetic frequency mapping, different types of fungi, many belonging to the Ascomycota phylum were found on the fibres during the first 2 weeks of field retting, and thereafter, different types of bacteria, notably Proteobacteria, also proliferated on the field retted fibres. Extracts from field retted fibres exhibited high glucanase activities, while extracts from P. radiata Cel 26 retted fibres showed high polygalacturonase and laccase activities. As a result, fungal retting gave a significantly higher glucan content in the fibres than field retting (77 vs. 67%) and caused a higher removal of pectin as indicated by lower galacturonan content of fibres (1.6%) after fibres were retted for 20 days with P. radiata Cel 26 compared to a galacturonan content of 3.6% for field retted fibres. Effective fibre stiffness increased slightly after retting with P. radiata Cel 26 from 65 to 67 GPa, while it decreased after field retting to 52 GPa. Effective fibre strength could not be determined similarly due to variations in fibre fracture strain and fibre-matrix adhesion. A maximum composite strength with 50 vol% fibres of 307 MPa was obtained using P. radiata Cel 26 compared to 248 MPa with field retting.
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Affiliation(s)
- Ming Liu
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kongens Lyngby, Denmark
| | - Marcel T. Ale
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kongens Lyngby, Denmark
| | - Bartłomiej Kołaczkowski
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kongens Lyngby, Denmark
| | - Dinesh Fernando
- Department of Forest Products/Wood Science, Swedish University of Agricultural Sciences, Vallvägen 9D, 750-07 Uppsala, Sweden
| | - Geoffrey Daniel
- Department of Forest Products/Wood Science, Swedish University of Agricultural Sciences, Vallvägen 9D, 750-07 Uppsala, Sweden
| | - Anne S. Meyer
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kongens Lyngby, Denmark
| | - Anders Thygesen
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kongens Lyngby, Denmark
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Djemiel C, Grec S, Hawkins S. Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS) Metabarcoding during Flax Dew-Retting. Front Microbiol 2017; 8:2052. [PMID: 29104570 PMCID: PMC5655573 DOI: 10.3389/fmicb.2017.02052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/06/2017] [Indexed: 11/13/2022] Open
Abstract
Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS) DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq) on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples. Dominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes (bacteria) and Ascomycota, Basidiomycota, and Zygomycota (fungi) all of which have been previously associated with flax dew-retting except for Bacteroidetes and Basidiomycota that were identified for the first time. Rare phyla also identified for the first time in this process included Acidobacteria, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes, Nitrospirae and TM6 (bacteria), and Chytridiomycota (fungi). No differences in microbial communities and colonization dynamics were observed between early and standard flax harvests. In contrast, the common agricultural practice of swath turning affects both bacterial and fungal community membership and structure in straw samples and may contribute to a more uniform retting. Prediction of community function using PICRUSt indicated the presence of a large collection of potential bacterial enzymes capable of hydrolyzing backbones and side-chains of cell wall polysaccharides. Assignment of functional guild (functional group) using FUNGuild software highlighted a change from parasitic to saprophytic trophic modes in fungi during retting. This work provides the first exhaustive description of the microbial communities involved in flax dew-retting and will provide a valuable benchmark in future studies aiming to evaluate the effects of other parameters (e.g., year-to year and site variability etc.) on this complex process.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, Centre National de la Recherche Scientifique, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, Centre National de la Recherche Scientifique, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Simon Hawkins
- Univ. Lille, Centre National de la Recherche Scientifique, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Duan S, Feng X, Cheng L, Peng Y, Zheng K, Liu Z. Bio-degumming technology of jute bast by Pectobacterium sp. DCE-01. AMB Express 2016; 6:86. [PMID: 27699704 PMCID: PMC5047873 DOI: 10.1186/s13568-016-0255-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/21/2016] [Indexed: 11/10/2022] Open
Abstract
Among industrial fiber crops, jute is ranked second to cotton in terms of yield and planting area worldwide. The traditional water retting and chemical semi-degumming methods restrict the development of the jute industry. Jute fiber can be extracted from jute bast through mechanical rolling (preprocessing), culture of bacteria, soaking fermentation (liquor ratio = 10, inoculum size = 1 %, temperature = 35 °C, and time = 15 h), inactivation, washing, and drying. Pectobacterium sp. DCE-01 secretes key degumming enzymes: pectinase, mannase, and xylanase, which match well the main non-cellulosic components of jute bast. Compared with the traditional water retting degumming, the bio-degumming cycle is shortened from more than 10 days to 15 h. The proposed bio-degumming achieved higher efficiency and lower pollution than water retting and chemical semi-degumming.
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Zhao D, Liu P, Pan C, Du R, Ping W, Ge J. Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02. Sci Rep 2016; 6:31812. [PMID: 27585559 PMCID: PMC5009381 DOI: 10.1038/srep31812] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/26/2016] [Indexed: 12/02/2022] Open
Abstract
High-throughput sequencing and GC-MS (gas chromatography-mass spectrometry) were jointly used to reveal the bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting. The inoculation of Bacillus cereus HDYM-02 decreased bacterial richness and diversity. This inoculum led to the replacement of Enterobacteriaceae by Bacillaceae. The level of aerobic Pseudomonadaceae (mainly Azotobacter) and anaerobic Clostridiaceae_1 gradually increased and decreased, respectively. Following the addition of B. cereus HDYM-02, the dominant groups were all degumming enzyme producers or have been proven to be involved in microbial retting throughout the entire retting period. These results could be verified by the metabolite changes, either degumming enzymes or their catalytic products galacturonic acid and reducing sugars. The GC-MS data showed a clear separation between flax retting with and without B. cereus HDYM-02, particularly within the first 72 h. These findings reveal the important bacterial groups that are involved in fiber retting and will facilitate improvements in the retting process.
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Affiliation(s)
- Dan Zhao
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
| | - Pengfei Liu
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Chao Pan
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Renpeng Du
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
| | - Wenxiang Ping
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
| | - Jingping Ge
- Laboratory of Microbiology, College of Life Science, Heilongjiang University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
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Microbial diversity observed during hemp retting. Appl Microbiol Biotechnol 2015; 99:4471-84. [DOI: 10.1007/s00253-014-6356-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/22/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022]
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A diverse community of jute (Corchorus spp.) endophytes reveals mutualistic host–microbe interactions. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-1001-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Das B, Chakrabarti K, Ghosh S, Chakraborty A, Saha MN. Assessment of changes in community level physiological profile and molecular diversity of bacterial communities in different stages of jute retting. Pak J Biol Sci 2013; 16:1722-1729. [PMID: 24506039 DOI: 10.3923/pjbs.2013.1722.1729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Retting of jute is essentially microbiological and biochemical in nature. Community Level Physiological Profiles (CLPP) as well as genomic diversity of bacterial communities were assessed in water samples collected during pre-retting, after 1st and 2nd charges of retting. The water samples were collected from two widely cultivated jute growing locations, Sonatikari (22 degrees 41'27"N; 88 degrees 35'44"E) and Baduria (22 degrees 44'24"N; 88 degrees 47'24"E), West Bengal, India. The CLPP, expressed as net area under substrate utilization curve, was studied by carbon source utilization patterns in BIOLOG Ecoplates. Molecular diversity was studied by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) of total DNA from water samples. Both between locations and stages of retting, substrate utilizations pattern were carbohydrates > carboxylic acids > polymers > amino acids > amines/amides > phenolic compounds. Differential substrate utilization pattern as well as variation in banding pattern in DGGE profiles was observed between the two locations and at different stages of retting. The variations in CLPP in different stages of retting were due to the change in bacterial communities.
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Affiliation(s)
- Biswapriya Das
- Department of Agricultural Chemistry and Soil Science, Institute of Agricultural Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Kalyan Chakrabarti
- Department of Agricultural Chemistry and Soil Science, Institute of Agricultural Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Sagarmoy Ghosh
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Ashis Chakraborty
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, West Bengal 741252, India
| | - Manabendra Nath Saha
- Central Research Institute for Jute and Allied Fibres, Indian Council of Agricultural Research, Barrackpore, Kolkata 700120, West Bengal, India
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15
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Visi DK, D’Souza N, Ayre BG, Webber III CL, Allen MS. Investigation of the bacterial retting community of kenaf (Hibiscus cannabinus) under different conditions using next-generation semiconductor sequencing. ACTA ACUST UNITED AC 2013; 40:465-75. [DOI: 10.1007/s10295-013-1242-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/08/2013] [Indexed: 10/27/2022]
Abstract
Abstract
The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 h from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources and having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria established themselves and in addition their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.
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Affiliation(s)
- David K Visi
- grid.266871.c 0000000097656057 Department of Forensics and Investigative Genetics University of North Texas Health Science Center 76107 Ft. Worth TX USA
- grid.266869.5 000000011008957X Department of Biological Sciences University of North Texas 76203-3677 Denton TX USA
| | - Nandika D’Souza
- grid.266869.5 000000011008957X Department of Mechanical and Energy Engineering University of North Texas 76203-3677 Denton TX USA
| | - Brian G Ayre
- grid.266869.5 000000011008957X Department of Biological Sciences University of North Texas 76203-3677 Denton TX USA
| | - Charles L Webber III
- grid.463419.d 0000 0004 0404 0958 Sugarcane Research Unit USDA, ARS 70361 Houma LA USA
| | - Michael S Allen
- grid.266871.c 0000000097656057 Department of Forensics and Investigative Genetics University of North Texas Health Science Center 76107 Ft. Worth TX USA
- grid.266869.5 000000011008957X Department of Biological Sciences University of North Texas 76203-3677 Denton TX USA
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Fu J, Li X, Gao W, Wang H, Cavaco-Paulo A, Silva C. Bio-processing of bamboo fibres for textile applications: a mini review. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.650450] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Fu J, Mueller H, de Castro JV, Yu C, Cavaco-Paulo A, Guebitz GM, Nyanhongo GS. Changes in the bacterial community structure and diversity during bamboo retting. Biotechnol J 2011; 6:1262-71. [PMID: 21695788 DOI: 10.1002/biot.201100105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/23/2011] [Accepted: 04/15/2011] [Indexed: 11/11/2022]
Abstract
Microbial retting is a critical step in obtaining fiber bundles from bamboo culm using indigenous microorganisms. A cultivation-independent technique for monitoring the changes in bacteria community during bamboo retting was applied in this work. This technique involves genetic profiling of PCR-amplified small-subunit rRNA and the single-strand conformation polymorphism (SSCP) gel analysis of the PCR-amplified 16S rDNA fragments. The study revealed that both the structure and the diversity of investigated communities varied with the incubation periods and sample locations. The bacteria bands from SCCP gel profiles related to Bacillus sp. decreased in intensity, and Phaeospirillum sp. and Azospirillum brasilense completely disappeared during the 4(th) and 5(th) month of incubation, while the bands related to the Sphingomonas japonica, Alphaproteobacterium Ellin335 and Microbacterium sp. increased. The bands closely related to Sphingomonads, Brevundimonas brasilense, Pseudoclavibacter sp., Agrococcus jenensis and Oxalophagus oxalicus remained dominant during the whole incubation period. This study showed that the use of PCR assay targeting 16S rRNA and SCCP profiling provided valuable information on monitoring the bacteria dynamic changes occurring in the bacteria community during bamboo retting, which is crucial for controlling the quality of the retting process and improving the retting efficiency, and thus benefits for fiber recovery.
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Affiliation(s)
- Jiajia Fu
- Key Laboratory of Science and Technology of Eco-Textile, Ministry of Education (Donghua University), Shanghai, PR China
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de Oliveira LL, Costa RB, Okada DY, Vich DV, Duarte ICS, Silva EL, Varesche MBA. Anaerobic degradation of linear alkylbenzene sulfonate (LAS) in fluidized bed reactor by microbial consortia in different support materials. BIORESOURCE TECHNOLOGY 2010; 101:5112-5122. [PMID: 20189800 DOI: 10.1016/j.biortech.2010.01.141] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 01/15/2010] [Accepted: 01/19/2010] [Indexed: 05/28/2023]
Abstract
Four anaerobic fluidized bed reactors filled with activated carbon (R1), expanded clay (R2), glass beads (R3) and sand (R4) were tested for anaerobic degradation of LAS. All reactors were inoculated with sludge from a UASB reactor treating swine wastewater and were fed with a synthetic substrate supplemented with approximately 20 mg l(-1) of LAS, on average. To 560 mg l(-1) COD influent, the maximum COD and LAS removal efficiencies were mean values of 97+/-2% and 99+/-2%, respectively, to all reactors demonstrating the potential applicability of this reactor configuration for treating LAS. The reactors were kept at 30 degrees C and operated with a hydraulic retention time (HRT) of 18h. The use of glass beads and sand appear attractive because they favor the development of biofilms capable of supporting LAS degradation. Subsequent 16S rRNA gene sequencing and phylogenetic analysis of samples from reactors R3 and R4 revealed that these reactors gave rise to broad microbial diversity, with microorganisms belonging to the phyla Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria, indicating the role of microbial consortia in degrading the surfactant LAS.
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Affiliation(s)
- Lorena Lima de Oliveira
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av Trabalhador Sãocarlense 400, 13566-590 São Carlos, SP, Brazil.
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