Comparative metagenomics and microbial dynamics of jute retting environment
International Microbiology - Trang 1-14 - 2023
Tóm tắt
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.
Tài liệu tham khảo
Ahmed Z, Akhter F (2001) Jute retting: An overview. Online J Biol Sci 1:685–688
Ahmed Z, Nizam SA (2008) Jute-microbiological and biochemical research. Plant Tissue Cult Biotech 18:197–220
Akin DE, Condon B, Sohn M, Foulk JA, Dodd RB, Rigsby LL (2007) Optimization for enzyme-retting of flax with pectate lyase. Ind Crops Prod 25:136–146
Banik S, Basak MK, Sil SC (2007) Effect of inoculation of pectinolytic mixed bacterial culture on improvement of ribbon retting of jute and kenaf. J Nat Fibers 4:33–50
Bankevich A, Nurk S, Antipov D (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
Barinova SA (1946) On the decomposition of pectin by microbial ferments. Mikrobiologiya
Bren A, Eisenbach M (2001) How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. J Bacteriol 182:6865–6873. https://doi.org/10.1128/JB.182.24.6865-6873.2000
Chin KJ, Hahn D, Hengstmann U, Liesack W, Janssen PH (1999) Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65:5042–5049
Chin KJ, Rainey FA, Janssen PH, Conrad R (1998) Methanogenic degradation of polysaccharides and characterization of polysaccharolytic Clostridia from anoxic rice field soil. Syst Appl Microbiol 21:185–200
Das B, Chakraborty A, Majumder B, Chakraborti A (2010) Studies on physic-chemical and microbial parameters of jute growing soil, retting water and jute fiber quality. Bangladesh J Agric Environ 6:1–13
Debsharma, GD. 1946. Biochemical investigations on jute retting. Indian J. Agric. Sci., 16: 453-58.
DeSantis TZ, Hugenholtz P, Larsen N (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072. https://doi.org/10.1128/AEM.03006-05
Dinghua L, Chi-Man L, Ruibang L, Kunihiko S, Tak-Wah L (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31(10):1674–1676. https://doi.org/10.1093/bioinformatics/btv033
Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Sébastien G (2020) Targeted metagenomics of retting in flax: the beginning of the quest to harness the secret powers of the microbiota. Front Genet 11:1246. https://doi.org/10.3389/fgene.2020.581664. https://www.frontiersin.org/articles/10.3389/fgene.2020.581664/full. Accessed 15 May 2023
Donaghy JA, Levette PN, Haylock RW (1990) Changes in microbial populations during anaerobic flax retting. J Appl Bacterio l69:634–641
Erwin S, Sabine H (1998) ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains. FEMS Microbiol Rev 22(1):1–20. https://doi.org/10.1111/j.1574-6976.1998.tb00358.x
Gomes I, Saha RK, Mohiuddin G, Hoq MM (1992) Isolation and characterization of a cellulase-free pectinolytic and hemicellulolytic thermophilic fungus. World J Microbiol Biotechnol 8:589–592
Harkasalmi T, Mauala P, Galkin S, Atakka A, Nykter M (2009) Method for retting, smoothening lignin of plant origin. (United States WO 2009/092865A1). WIPO (PCT). https://patents.google.com/patent/WO2009092865A1/en#patentCitations
Hasan R, Aktar N, Kabir SMT et al (2020) Pectinolytic bacterial consortia reduce jute retting period and improve fibre quality. Sci Rep 10:5174. https://doi.org/10.1038/s41598-020-61898-z
Husain F (2011) Introducing new and improved jute retting technique across in Bangladesh.31 Katalyst
Ibba M, Söll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69:617–650. https://doi.org/10.1146/annurev.biochem.69.1.617
Islam MS, Saito JA Alam M et al (2017) Comparative genomics of two jute species and insight into fibre biogenesis. Nature Plants 3:16223
Islam MM, Rahman MM (2013) Advances in Jute and Allied fibres post-harvest processing technologies in Bangladesh: adoption constraints, Prospect and Future Thrust. Res Web Pub 1:20–30
Jarman CG (1985) The retting of jute. FAO Agriculture Organization of the United Nations, Via delle Terme di Caracalla, Rome, Italy, pp 1–54
Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. In: Martin F., Uroz S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3369-3_13
Kersters K, De Vos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006) Introduction to the Proteobacteria. The Prokaryotes 3–37. https://doi.org/10.1007/0-387-30745-1_1
Kievit TD (2011) Comprehensive biotechnology, 2nd edn. Academic Press, Amsterdam, pp 547–558. https://doi.org/10.1016/B978-0-08-088504-9.00064-7
Law AD, McNees CR, Moe LA (2020) The microbiology of hemp retting in a controlled environment: steering the hemp microbiome towards more consistent fiber production. Agronomy 10:492. https://doi.org/10.3390/agronomy10040492
Lechevalier HA, Lechevalier MP (1965) Classification des actinomycètes aérobies basée sur leur morphologie et leur composition chimique. Ann Inst Pasteur 108:662–673 (In French)
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma 9:386. https://doi.org/10.1186/1471-2105-9-386
Munshi TK, Chattoo BB (2008) Bacterial population structure of the jute-retting environment. Microb Ecol 56:270–282
Page F, Altabe S, Hugouvieux-Cotte-Pattat N, Lacroix JM, Robert-Baudouy J, Bohin J-P (2001) Osmo regulated periplasmic glucan synthesis is required for Erwinia chrysanthemi pathogenicity. J Bacteriol 183:3134–3141
Peng Y, Leung HCM, Yiu SM, Chin FYL (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11):1420–1428. https://doi.org/10.1093/bioinformatics/bts174
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35:7188–7196
Rana S, Pichandi S, Parveen S and Fangueiro R (2014) Natural plant bres: production, processing, properties and their sustainability parameters. Roadmap to Sustainable Textiles and Clothing, pp 1–35. Textile Science and Clothing Technology, Springer Verlag, Singapore
Ray DP, Ghosh RK, Saha B, Sarkar A, Singha A, Mridha N, Das I, Sardar G, Mondal J, Manjunatha BS, Shakyawar DB (2022) Accelerated retting technology for the extraction of golden fibre from the Indian Tossa jute (Corchorus sp.). J Cleaner Prod 380(Part 2):135063. https://doi.org/10.1016/j.jclepro.2022.135063. (ISSN 0959-6526)
Sandin G, Peters GM (2018) Environmental impact of textile reuse and recycling – a review. J Cleaner Prod 184:353–365. https://doi.org/10.1016/j.jclepro.2018.02.266. (ISSN 0959-6526)
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6):863–864. https://doi.org/10.1093/bioinformatics/btr026
Soriano M, Diaz P, Pastor FIJ (2005) Pectinolytic systems of two aerobic sporogenous bacterial strains with high activity on pectin. Curr Microbiol 50:114–118
Tamburini E, Gordillo LA, Perito B, Mastromei G (2003) Characterization of bacterial pectinolytic strains involved in the water retting process. Environ Microbio L5:730–736
Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G (2011) Environmental and gut bacteroidetes: the food connection. Front Microbiol 2:93. DOI=10.3389/fmicb.2011.00093. ISSN=1664-302X. https://www.frontiersin.org/articles/10.3389/fmicb.2011.00093/full. Accessed 15 May 2023
Zhang J, Henriksson G, Johansson G (2000) Polygalacturonase is the key component in enzymatic retting of flax. J Biotechnol 81:85–89
Zhao D, Liu P, Pan C (2016) Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02. Sci Rep 6:31812. https://doi.org/10.1038/srep31812
Zimmerman W (1980) Degradation of lignin by bacteria. J Biotechnol 13:199–130