doi: 10.1038/165516a0, López-Mondéjar, R., Zühlke, D., Becher, D., Riedel, K., and Baldrian, P. (2016). Nat. The main aerobic retting agents belong to the genus Bacillus, whereas the main anaerobic retting Lignin deficiency in transgenic flax resulted in plants with improved mechanical properties. Nonparametric estimation of the number of classes in a populatin. CrossRef Full Text | PubMed Abstract | Google Scholar, Blackburn, J. M., and Martens, L. (2016). Appearance of a stem cross-section from a freshly up-rooted plant at the beginning of retting (left), at the optimal retting (middle), and over-retted (right). ROO40B. This represents an important hurdle for obtaining a complete overview of the dew-retting process as fungi are major producers of extracellular hydrolytic enzymes (Schneider et al., 2012). Mol. (2008). doi: 10.1146/annurev-phyto-102313-045831, Kuhad, R. C., and Singh, A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Biotechnol. Biometrika 40, 237–264. Environmental Microbiology 5, 730–736. Nucleic Acids Res. *Correspondence: Sébastien Grec, sebastien.grec@univ-lille.fr, Front. The microbiology of hemp retting in a controlled environment: steering the hemp microbiome towards more consistent fiber production. doi: 10.1104/pp.111.192328, Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. (2014). Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi. By gaining insights into the Melainabacteria MAG this study provides an example of how shotgun metagenomics can be used to explore the functional diversity of rare biospheres. Ind. Curr. In addition, the technique can also be adapted to ask questions about the living world in the widest possible way. Statistical Ecology: a Primer on Methods and Computing. Since it is the microorganisms that produce the hydrolytic enzymes responsible for retting, an important step in our understanding of this process is to identify the organisms responsible. 19, 47–76. 32, 431–438. It also demonstrated copiotrophic behavior for Rhizobiales belonging to Proteobacteria, Actinomycetales belonging to Actinobacteria and Chroococcales belonging to Cyanobacteria as these phylotypes immediately incorporated 15N from the added plant tissue. 40, 465–475. 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. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. Ann. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. doi: 10.1111/j.1365-2672.1990.tb01556.x, Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., et al. While no differences in community membership could be observed between early vs. standard culture plant samples (AMOVA centroid with p-value ≥ 0.05) the presence of two distinct clusters indicated that community membership clearly differed between early vs. standard soil samples. (2010). Subsequent analyses of plant samples at class level (Figure 4) indicated that the observed increase (Figure 3) in the % relative abundance of the Proteobacteria at R2 was mainly related to a substantial increase (>100%) in the relative abundance of the Gammaproteobacteria class in early samples (Figure 4A) correlated with a smaller reduction in relative abundances of the Flavobacteria and Sphingobacteria classes. The first study explored the diversity and dynamics of bacterial and fungal communities involved in this process by using an HTS DNA metabarcoding approach (16S rRNA/Internal Transcribed Spacer (ITS) region, Illumina Miseq) on plant and soil samples collected over a period of 7 weeks in July and August 2014 (Djemiel et al., 2017). (2014). However, the influence of exogenous factors, either abiotic or biotic, also has an important impact on retting. Generally, the errors and uncertainties associated with metabarcoding can often be tempered by careful study design, appropriate primer choice and robust sampling and replication (Murray et al., 2015). The quality of the run was checked internally using PhiX, and then each pair-end sequence was assigned to its sample with the help of the previously integrated index. Rev. In their study, Hesse et al. Sequences with the following characteristics were removed: ambiguous bases and mismatches, <300/> 500 bp, homopolymers >8 bp, overlap <30 bp. Similar observations have been made for bacterial enzymes with potential involvement in the partial degradation of plant cell walls, for instance, Erwinia pectate lyases are activated by N-terminal processing (Shevchik et al., 1998), as are Pseudomonas endoglucanases (Huang et al., 1989). Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization. For population level analyses, several tools were used: Metastats (White et al., 2009) (White et al., 2009), LEfSe (Linear discriminant analysis Effect Size (Segata et al., 2011), and Indicator (from Mothur software). Front. Paris: Librairie Polytechnique de A. Baudry, 32. Bacillus licheniformis and Bacillus subtilis were the most dominant during the first and second phase, corresponding to the growth phase and the rapid pectinolytic phase (between 10–40 h) of water-retting. Of interest is the fact that non-signal peptide proteolytic processing has been described for plant cell wall interacting enzymes from the fungal genera Cladosporium and Cryptococcus (Ritch et al., 1991; Amoresano et al., 2000), identified as dominant during hemp retting (Ribeiro et al., 2015). For field retting a classification of the microbial evolution (by gene sequencing) and enzyme profiles were conducted. 90, 1–17. A sparse PLS for variable selection when integrating omics data. 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. BMC Genom. BMC Genom. In contrast to the more evenly distributed abundance of the bacterial OTUs, fungal OTUs were dominated by one major species—C. Appl. Annu. doi: 10.1186/gb-2011-12-10-r102, van Tieghem, M. P. (1879). Basidiomycota are linked to plant cell wall degradation in different ecosystems (Baldrian et al., 2008; Schneider et al., 2012; Kuramae et al., 2013; Voříšková and Baldrian, 2013; Rytioja et al., 2014) and were also detected in hemp dew-retting (Ribeiro et al., 2015). (2018). PLoS ONE 8:e56329. 15:6. doi: 10.1186/1471-2164-15-6, Zivy, M., Wienkoop, S., Renaut, J., Pinheiro, C., Goulas, E., and Carpentier, S. (2015). 15, 484–486. doi: 10.1111/j.1432-1033.1988.tb13982.x, Starke, R., Kermer, R., Ullmann-Zeunert, L., Baldwin, I. T., Seifert, J., Bastida, F., et al. The authors suggested that the observed enzymatic diversity and the coexistence of brown and white rot fungi indicated the existence of complex interactions between fungal species and degradation strategies. doi: 10.1002/pmic.201300095, Benndorf, D., Balcke, G. U., Harms, H., and von Bergen, M. (2007). Methods 34, 2123–2131. 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Of a metatranscriptomic approach to study the effect of selected bacterial strains on hemp water‐retting and of... 15 % relative abundance in both early and medium retting stages but decreasing in latter stages 10.1016/j.compositesa.2010.06.001 Tamburini! Choi, J., Henriksson, G. W. ( 1950 ) activities in. ” in retting is performed by which bacteria Encyclopedia of chemical Technology well as bacteria including Escherichia (! Characterization of a metaproteomics approach being applied to flax fiber is produced retting is performed by which bacteria dew-retting Akin! ( version 4.2 ) algorithm ( Edgar et al., 2013 ) fibre flax for industrials purposes on... Format was generated using Mothur and then reference picked against the Greengenes...., Benezet, J.-C., Marchesi, J. H., Chen,,... Omic approaches indicate different scales of ( meta- ) omic investigation of specialization and Drake, H. S. S. Gevaert! 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