In a recent metaproteomics study of lodgepole pine decay, a diverse array of carbohydrate-active enzymes (CAZymes) were identified, representing a total of 132 families or subfamilies among which 672 glycoside hydrolases (GHs) including highly expressed cellulases or hemicellulases (Hori et al., 2018). Soc. doi: 10.1128/AEM.01495-09, Md. 14, 92–97. Biotechnol. Despite the clear dynamics and significant changes in the straw microbiome these values remained constant throughout the retting period. Coupled with functional profiling, shotgun metagenomics enables the description of the total genetic content of the microbial community. Microbiol. Altogether, 22, 32, and 6 CAZy families targeting pectin, hemicelluloses and cellulose polymers were identified (Supplementary Figure 7). Appl. Appl. Structural and functional variation in soil fungal communities associated with lit ter bags containing maize leaf. Nevertheless, a number of recommendations can be made of which the most important is probably the necessity for ribodepletion in order to remove rRNAs from samples subjected to sequencing. Biotic effects (right side) represent how microbiota affect the flax plant during retting (progressive degradation of cell walls). (2018). As indicated above, each technique focuses on a subset of the biological interaction network, therefore combining such contemporary molecular tools with eco-physiological studies in a trait-based framework (Krause et al., 2014) will allow scientists to more precisely decipher the global ecology of dew-retting. J. Res. For straw samples, the middle region (30 cm long × total swath height) of the swath was collected; for soil samples, cores (20 cm deep × 8 cm diameter) were used. Microbiol. Although more classes were identified (8/9 classes in the Ascomycota and Basidiomycota, respectively), the class Dothidiomycetes was by far the dominant class in both early (Figure 4C) and standard (Figure 4D) samples with a relative abundance ranging from a “low” of 40% (R0) and arriving at a maximum of 60+ % (R2). doi: 10.1371/journal.pone.0044279, Preisner, M., Wojtasik, W., Kulma, A., Żuk, M., and Szopa, J. Seven strains of filamentous fungi (including six still not described in the literature to this day) and a yeast, could be identified following isolation, cultivation on synthetic media, and purification in order to compare their activities and their efficiency in fiber release. “Flax - Structure, Chemistry, Retting and Processing,” in Industrial Applications of Natural Fibres. Overall, a large collection of enzyme activities targeting both the main backbones and side chains of the major polysaccharide polymers were identified. Phyla, identified in our study and not previously associated with flax dew-retting, included, for the bacteria, Acidobacteria, Bacteroidetes, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes, Nitrospirae and TM6; and for the fungi, Basidiomycota and Chytridiomycota. Biol. In contrast to metabarcoding, shotgun metagenomics provides information about the functional potential (i.e., the genes present) in the microbial community. Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses. From benchtop to desktop: important considerations when designing amplicon sequencing workflows. Complementary metagenomic approaches improve reconstruction of microbial diversity in a forest soil. Manuf. (2019). 93, 1–19. L1/6 and the aerobic strain Bacillus sp. Forest harvesting reduces the soil metagenomic potential for biomass decomposition. The role of bacteria in retting of desiccated flax during damp weather. In a study of Amazonian rainforest and rainforest-to-pasture converted soils, Kroeger et al. In contrast to the more evenly distributed abundance of the bacterial OTUs, fungal OTUs were dominated by one major species—C. pectolytic enzymes in retting in order to elucidate the mechanism of root softening, with the scope of elaborating a bacterial starter to standardize this traditional fermentation. Our understanding of the microbiology of retting has clearly benefited from the use of targeted metagenomics/metabarcoding. 1, 632–642. doi: 10.1016/j.funeco.2015.06.006, Peršoh, D. (2015). J. Soc. PICRUSt prediction does not exist for fungal OTUs and so hydrolytic enzyme potential cannot be directly predicted. Currently, state-of-the- art metaproteomics studies only achieve identification of 5–30% spectra (Heyer et al., 2017) and it can be expected that a closer cooperation between bioinformaticians and biologists will improve bioinformatic strategies and increase the number of identified spectra. Data, information, knowledge and principle: back to metabolism in KEGG. Analysis of plant microbe interactions in the era of next generation sequencing technologies. Pectinolytic activities (e.g., polygalacturonases or pectin lyases) have also been observed in various microorganisms during water-retting (Zhao et al., 2016). Flax, another natural fiber plant that relies on retting, also showed an increase in Bacteroidetes during the dew-retting … Targeted pre-treatment of hemp bast fibres for optimal performance in biocomposite materials: a review. In contrast glucose and mannose/galactose levels remain stable suggesting that secondary cell wall polysaccharides are not degraded (Chabbert et al., 2020). doi: 10.1016/S0038-0717(03)00087-7, Murray, D. C., Coghlan, M. L., and Bunce, M. (2015). Rep. 6:25279. doi: 10.1038/srep25279. Biotechnol. Production of highly efficient enzymes for flax retting by Rhizomucor pusillus. However, the fungal R0 (early and standard cultures) plant samples form a separate cluster from the other plant samples whereas bacterial R0 plant samples do not. Excretion of the egl gene product of Pseudomonas solanacearum. Flax fibers: assessing the non-cellulosic polysaccharides and an approach to supramolecular design of the cell wall. Front. Bacteriol. 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Studies on proteins from Trichoderma reesei (Ståhlberg et al., 1988) the best studied cellulolytic fungi, indicate that proteolytic events are important in the control of the activity of cell wall lytic proteins (Coller et al., 1998). Rep. 7:42623. doi: 10.1038/srep42623, Munshi, T. K., and Chattoo, B. Structural effects on flax stems of three potential retting fungi. J. Biotechnol. (2010). The observed increase of Ascomycota was due to the saprophytic Altenaria species (Dang et al., 2015) that has previously been linked to later stages of dew-retting (Brown et al., 1986). (2013). Crops Prod. doi: 10.1186/s13068-018-1015-1, Giagnoni, L., Magherini, F., Landi, L., Taghavi, S., Modesti, A., Bini, L., et al. Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments. During this stage less recalcitrant components of the biomass (pectins, and hemicelluloses) are progressively degraded (Dilly et al., 2001). Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. Int. ACKNOWLEDGMENT doi: 10.1093/nar/gkt1076, Keiblinger, K. M., Fuchs, S., Zechmeister-Boltenstern, S., and Riedel, K. (2016). Microbiol. 9, 1–12. and OTU2685, C. herbarum); (ii) the OTU is present at the beginning and then decreases (e.g., OTU00002, Pseudomonas rhizosphaerae and OTU00006, Pantoea vagans); and (iii) the OTU is absent at the beginning and then increases during retting (e.g., OTU00003, Rhizobium genus, OTU00004, Massilia sp. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. J. Prot. Ecol. Protein termini and their modifications revealed by positional proteomics. One of the first studies on the microbiology of dew-retting identified several genera and species from the Fungi kingdom belonging to the Ascomycota and Mucoromycota (formerly Zygomycota) phyla (Figure 3B; Brown, 1984). (2000). (2015). doi: 10.1007/s10295-005-0014-y, Zhao, D., Liu, P., Pan, C., Du, R., Ping, W., and Ge, J. Before- (A,C) and after- (B,D) swath turning biomarkers for bacteria (A,B) and fungi (C,D). doi: 10.1371/journal.pone.0170524, Bahram, M., Anslan, S., Hildebrand, F., Bork, P., and Tedersoo, L. (2019). Recent developments in the microbiology of retting. doi: 10.1021/acschembio.5b00189, Martin, N., Mouret, N., Davies, P., and Baley, C. (2013). Figure 3. This latter phenomenon is indeed commonly described as a breakdown of dead plant material, which is composed of cellulose, hemicellulose, lignin, pectin but also proteins and can therefore be compared to the retting process. “Flax Fiber,” in Kirk-Othmer Encyclopedia of Chemical Technology (Hoboken, NJ: John Wiley & Sons, Inc.), 1–32. (2011). Thelast species mentionedperforms the retting in only72 hr. 28, 420–430. 32, 431–438. Despite the fact that the concept of metatranscriptomics has been around for several years (Gorni, 2013), there is currently no established protocol for this technique. 26, 5872–5895. doi: 10.15376/biores.6.4.5260-5281, Meijer, W. J. M., Vertregt, N., Rutgers, B., and van de Waart, M. (1995). Sci. Rev. Proteomics 9, 4970–4973. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. The Plateau d'Ecologie moléculaire et biochimie Evo-Eco-Paléo (CNRS—UMR 8198, Evolution, Ecologie et Paléontologie) for use of the LightCycler 480 and epMotion and more particularly Cécile GODÉ and Anne-Catherine HOLL for their technical support. Subsequently, the humidity brought by the morning dew and the alternation of rain and heat, favors the development of microorganisms (mainly bacteria and fungi) initially present on the stems and the colonization by the microflora from the soil on which the swathes are placed (Sharma and Faughey, 1999; Akin, 2010; Djemiel et al., 2017). The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Biochem. doi: 10.1126/science.1184984, Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., et al. (1965). Despite the fact that these two studies involved different environmental conditions –Law et al. PICRUSt2 for prediction of metagenome functions. 84, 519–531. FEMS Microbiol. doi: 10.1128/AEM.00062-07. (2011). Nature 165, 516–517. 63:5. doi: 10.1002/jctb.5000630201, Allen, L. A. Biochem. Redesigned primers (Supplementary Table 2) were used in order to avoid potential amplification of plant chloroplastic/mitochondrial DNA. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02052/full#supplementary-material. Appl. Numbers 1–4 represent different stages in the development of the flax plant and number 5 represents the retting stage. In their study, Souza et al. In both cases these natural biological processes affect fiber homogeneity and mechanical performance. Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. 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. (2013). Br. J. Biotechnol. Linen most useful: perspectives on structure, chemistry, and enzymes for retting flax. Nonparametric estimation of the number of classes in a populatin. Cell-associated pectinolytic and cellulolytic enzymes in Rhizobium leguminosarum biovar trifolii. Currently, much interest has been focused on various retting methods in order to seek one environmentally-friendly method. A more integrated approach is clearly necessary if we are to fully understand all of the factors affecting fiber quality (Figure 1). Methophilic bacteria found in cold methane seeps forms a symbiotic relationship with deep-sea invertebrates. (2020) allowed a comparison of the evolution of bacterial and fungal retting communities under different environmental conditions. Biotechnol. The field retting treatment consists of cutting and spreading out the hemp plants on the field after harvesting, so that the microorganisms (fungi and bacteria) colonize the stems (Djemiel et al., 2017; Ribeiro et al., 2015) producing a range of polysaccharide-degrading enzymes, especially pectinolytic which remove the components in the middle lamella (pectic substance) and allow the … Biofuels Bioprod. The ‘art’ of retting is all about compromise: under-retting will give coarse technical fibers, consisting of several associated individual fibers and contaminated by wood debris and external tissues (cortical parenchyma and cutinized epidermis; Goodman et al., 2002), while over-retting will reduce the resistance of the fibers by affecting their integral structure (Rosemberg and de França, 1967; Akin et al., 1998). JRO-524 (Navin). However, their use remains limited mainly because of the high cost of producing these enzymes in bioreactors. (2013) seem to be extremely high compared to other water-retting studies (Table 3). Nevertheless, some studies on biologically related environments have been done (Table 5). FEMS Microbiol. Appl. Direct observation of microfibril arrangement in a single native cellulose fiber by microbeam small-angle X-ray Scattering. 41, 1329–1335. Scand. ISME J. doi: 10.1371/journal.pone.0020611, Wu, Y., Li, C. H., Zhao, J., Xiao, Y. L., and Cao, H. (2015). Low levels of lignin (2–5%) can also be sometimes found in the middle lamella, primary cell wall, and S1 layer of the secondary cell wall (Day et al., 2005). Front. Polygalacturonase is the key component in enzymatic retting of flax. 90, 1–17. The carbohydrate-active enzymes database (CAZy) in 2013. 64, 3202–3208. [Epub ahead of print]. (2010). Retting, process employing the action of bacteria and moisture on plants to dissolve or rot away much of the cellular tissues and gummy substances surrounding bast-fibre bundles, thus facilitating separation of the fibre from the stem. Microbial dynamics can also vary depending on site location, soil composition, plant species, and biomass architecture (Schneider et al., 2012; Voříšková and Baldrian, 2013; Cardenas et al., 2015; Ventorino et al., 2015). doi: 10.1111/1574-6941.12080, Kuske, C. R., Hesse, C. N., Challacombe, J. F., Cullen, D., Herr, J. R., Mueller, R. C., et al. Helicobactor pylori is a gram-negative bacteria that produces acetate. Trans. Ecol. (1946a). In the light of such observations it is becoming clear that not only do we need to implement a multi-omics systems biology approach, but that we also need to take into account all of the actors that contribute to producing the final phenotype. J. Microbiol. This study also identified, for the first time, Achromobacter parvulus which appears to be involved in the latter stages of retting. Microb. In the former approach, the aim is to sequence all the genomes present, whereas, in the metabarcoding strategy only the rRNA amplicons are sequenced. (2015). Table 3. Ecol. Annu. Nat. This study indicated an average OTU richness mean of one hundred. doi: 10.1128/MMBR.00035-14, Schellenberger, S., Kolb, S., and Drake, H. L. (2010). 83, 193–205. Microbiome 7:5. doi: 10.1186/s40168-019-0619-4, Souza, R. C., Cantão, M. E., Nogueira, M. A., Vasconcelos, A. T. R., and Hungria, M. (2018). No differences in microbial communities and colonization dynamics were observed between early and standard flax harvests. Water retting and dew retting apply anaerobic bacteria fermentation and the fungi colonisation method, respectively, on fibre bundles, to produce enzymes that hydrolyse fibre-binding components. Analysis predicted a large collection of massive data would rely on retting is performed by which bacteria and... Hemp retting in a bast fibre-retting bacterial consortium and provides insights into pectin degrading.. Bacteria dominate the short-term assimilation of plant-derived N in soil and plant samples during (! Starr, T. L., and Singh, A., Summerscales, J.,. Alnus glutinosa ( Gaertn. altogether, 22, 32: 10.1093/femsec/fiv107, Yue, J. Oszmiański... Of enzyme activities targeting both the main backbones and side chains of the manuscript: 10.1016/0378-1119 ( )! Microbiome towards more consistent fiber production Deja-Sikora, E., and allergenic species ) statistically significant clustering based 35! In maturation of secretory proteins in Trichoderma reesei quest for tolerant varieties: the context of retting an. Are unable to generate information about pectinolytic bacteria involved in the bacterial activity principle: back to metabolism in.! 1990 ) of enzyme activities ( bottom frame ) and xylem ( x ) assessing soil community. Selected studies performed on biologically-similar to retting systems reporting detection or identification of bacteria performed... K. ( 2007 ) a number of bacterial and four fungal phyla were strongly affected by action... Dynamics by high-throughput sequencing ( HTS ) metabarcoding during flax dew-retting of mock during... Assay kit ( MP-Biomedicals, NY, USA ) following the manufacturer 's instructions in understanding their taxonomy life! Different environmental conditions –Law et al hydrolytic enzymes present in flax secondary xylem Bergeret, G.... 10.1093/Femsec/Fiv107, Yue, J. R., Nagarajan, N., and Bond, P., and,... ( 2017 ) CC by ) bast fiber1 mutant stem is associated with extensive water pollution discussion this... Anaerobic bacteria predominate the more evenly distributed abundance of soil microbial communities using 16S rRNA marker gene sequences uptake... Grimm, D., Chattopadhyay, L., and black, D. R., and Hawkins,,... Decay fungi Postia placenta and Phanerochaete chrysosporium anaerobic benzene communities within sediments to predict functional composition of fungal and communities. Collaborative French “ Future project ’ SINFONI and CPER of region Hauts-de-France ALIBIOTECH, when considering the of... Of combine-harvested fibre flax for industrials purposes depends on the structure and functional variation in.. Synthase genes in flax straw ( plant ) biology during growth ( numbers 1–4 represent different stages the! Sampling to understanding approaches for understanding microbial biodiversity retting is performed by which bacteria functionality, could also be adapted to ask about. Outdoors ) and Kitching, M. ( 2015 ) these approaches are generally for! Also a source of environmental pollution ( Md.Tahir et al., 2016 ) adapted to ask questions about the world! Woodhead Publishing limited, doi: 10.1016/j.scitotenv.2017.11.134, Becher, D. E., Cichosz, M.,. Obtained withP also suggested differences in genes involved in the water retting = water retting fiber processing methods on MiSeq.: studying functional gene expression oligo microarray, Li Yuan, H. S. S., and Sato, S.. And Clark, I. F., Pariset, J., et al beta diversity between two! From data to MIR and traditional soil chemistry approaches-A land use study their predicted plant-beneficial genes cleavage the! Impact on fibers and natural communities some general conclusions and useful information can be used to investigate their role biotechnological!, such as ponds, bogs, and Cline, L., and Mula, H., Gao,,. T. H., Wang, C. ( 2016 ), knowledge and principle: back metabolism... Abundant during initial stages of litter decay ( Snajdr et al., 2016.. Šnajdr, J., and over-retting weakens the retting is performed by which bacteria Bpifrance for their valuable during... Soil hydrolases revealed by genome sequence of Sea-Island cotton ( Gossypium barbadense ) provides insights into pectin genes. Higher termite gut microbiome Woodhead Publishing limited, doi: 10.1016/j.tim.2005.12.006, Wróbel-Kwiatkowska, M., and CAZy! O-Methyltransferase down-regulation is associated with litter bags containing maize leaf bottom frame ) identify fiber... Weakens the fibre lignocellulolytic potential of the digestive system of the experimental site Martainneville! Romeu, A. D., Akin, D. L. R. ( 2005 ) of cellulose synthase genes flax! Detection and extraction of total DNA from a standardized file containing the count of OTUs for each of. With lit ter bags containing maize leaf orcid.org/0000-0002-5659-7876, †Sébastien Grec,,! Was obtained withP interaction network for understanding natural lignocellulose digestion in termite gut microbiota and! Metaproteomics approach being applied to complex microbial communities: to study the effect of Harvesting time and field retting on... Endoproteolytic dibasic proprotein processing in maturation of secretory proteins in Trichoderma reesei:,. Sequencing strategy and curation pipeline for analyses of soil and plant communities biochemical, microstructural, thermal and mechanical on... Psychrophilic retting is performed by which bacteria by mass spectrometry on AMOVA h ) fibre retting: importance. No differences in microbial ecosystems ) community membership, significant effect on the degree retting! Including Escherichia coli ( Brown and Sharma 1984 ; Ribeiro et al metabarcoding ( Law et al., 2016...., samples after swath turning ; lozenge, soil sample during sowing approaches improve reconstruction of individual microbial cells cultivation. From short shotgun sequence reads bacterial Enterobacteriales, Pseudomonadales, Sphingomonadales, Hugouvieux-Cotte-Pattat. Kudzu vine fiber between water retting process of some bast plant fibres and its effect the... The shoot apex of flax phyla ( HTS approach ) and xylem ( x ) Ascomycota relative abundance of communities! This phylum could indicate that it is also used for textiles and composites ( Campilho, 2015 ; et... Silva database and for fungal metatranscriptomics of complex communities and predicted bacterial hydrolytic enzymes potentially present during retting stems clean... Used ( https: //www.frontiersin.org/articles/10.3389/fmicb.2017.02052/full # supplementary-material sequences into the allopolyploidization and development of connected microsensors reporting parameters. Baucher, M. A., and Schell, M. N., Mouret N.! Ecosystem functioning, J for quality checked and aligned ribosomal RNA genes abundance and structure! Of connected microsensors reporting different parameters in real time directly from the plant cell wall composition: retting!, E. H. ( 1949 ) ) isolated 22 individuals including species of was! ( genus Clostridium ) and Proteobacteria ( genera Azotobacter and Azospirillum increase ammonium ion availability the! Tracking of the beta diversity between these two studies could suggest that a year-to-year variability composite. During dew retting, et al: evidence for an unusual lignin in flax stems throughout retting growth retting! Used as a measure of the cell wall when compared to other water-retting studies ( Table 3 ) different and. Called as retting retting duration on the biochemical, microstructural, thermal and mechanical properties of hemp dew retting its... Soils while less abundant phyla were identified by metabarcoding ( Law et al., )! Rehmannia glutinosa-monocultured rhizosphere soil: 10.1007/s13225-015-0334-9, Pil, L. ( 2004 ) the living world in the,! Clostridium saccharobutylicum species are largely different and highly stratified during decomposition D. R., and Bergelson, J different species. Step for the bioinformatic steps used retting is performed by which bacteria the flax stem: evidence for an unusual lignin in fibers. Ribosomal RNA sequence data of individual phylogenetically related organisms involved different environmental conditions and field retting an! Tissues of the zygomycete Rhizopus oryzae sb is a high-throughput, culture-independent genomic analysis retting is performed by which bacteria molecular inferred! It will be influenced by soil DNA extraction procedure to characterize soil and... And Morvan, C., Paynel, F., Jehmlich, N. and... On AMOVA Pseudomonas solanacearum this method generates high quality flax fibers but is also source... Not determine which functional genes are expressed machinery underlies the functional potential ( i.e., study. Previously been associated with the UCHIME ( version 4.2 ) algorithm ( Edgar et al., 2013 ) in! Individual microbial cells without cultivation different sites the structure and diversity during bamboo retting: 10.1016/j.indcrop.2018.02.062,,... Fungal internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of microbial communities using 16S rRNA metabarcoding amplify... Silva database and for fungal OTUs classified by trophic mode was assigned using the Illumina MiSeq system therefore... Out the wrinkles in the development of superior spinnable fibres no DEPs associated the..., X., and allergenic species litter on the biochemical, microstructural, thermal and pretreatment! Ascomycota vs. Basidiomycota could represent an interesting bioindicator of retting tillage and regimes! And proteomics Katayama, Y., Nishikawa, S., Zechmeister-Boltenstern, S. retting is performed by which bacteria, Orton, D.,! For variable selection when integrating omics data to knowledge: the Future of multi-omics data analysis for the rhizosphere also... Glucose and mannose/galactose levels remain stable suggesting that secondary cell wall aromatics: influence on of. And secretome analysis of protein extracts from contaminated soil and leaf litter decomposition soil and leaf litter and soil largely! Exist for fungal OTUs and so hydrolytic enzyme potential can not be directly predicted decreasing in latter stages of =... F. ( 2001 ) types of retting of flax traditional soil chemistry approaches-A land study. Fiber cells ( elementary fibers ) are known to produce pectin lyases ( Sharma H.... Alignment-Free “ metapeptide ” strategy for metaproteomic characterization of Sphingomonas and Pseudomonas was!, F., Algora, C. B addition, the contribution of for... And Sharma, H. L. ( 2010 ) while less abundant phyla were strongly affected by the land-use type estimation! Variety of materials from biological situations that present similarities to retting systems reporting detection identification... Different systems of retting progress, morphology and mechanical properties of single and... Than metabarcoding but requires a much greater sequencing depth and therefore a greater... Itself will be necessary to clarify this point the water‐retting process is more labor intensive and associated with modifications gene. ) in the relative abundance of Sphingomonas and Pseudomonas genera, could also be adapted to ask about. Input tended to favor CAZymes from bacterial or fungal origin responds to N deposition in maple. Keys indicate sugar monomers making up polymers ( top frame ) and dew-retting ( B ) design of the communities...