scholarly journals Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis

2019 ◽  
Author(s):  
Chol Gyu Lee ◽  
Yasunori Baba ◽  
Ryoki Asano ◽  
Yasuhiro Fukuda ◽  
Chika Tada ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Rumen Fluid ◽  
Waste Paper ◽  
Metagenomic Analysis ◽  
Fluid Systems ◽  
Genes Encoding ◽  
Identification Of Bacteria

AbstractPreviously, pretreatment of plant biomass using rumen fluid systems was developed to decompose cell wall. However, microbes which involved in plant cell wall decomposition in this system have not been identified, because the conditions of this system are different from the in situ rumen environment. We investigated the bacteria involved in the decomposition of cellulose and hemicellulose in a waste paper with the rumen pretreatment system using shotgun metagenomic analysis with next generation sequencing. After pretreatment of waste paper, about a half of the cellulose and hemicellulose content was decomposed. Genes encoding for cellulase and hemicellulase were mainly found to belonging to Ruminococcus, Clostridium, and Exiguobacterium. This study shows that Clostridium and Exiguobacterium, which have not been identified as predominant genus involved in cellulose and hemicellulose decomposition, might be categorized as the main fibrolytic bacteria in this system.

scholarly journals The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

2020 ◽  
Vol 117 (11) ◽  
pp. 6003-6013 ◽  
Author(s):  
Vincent W. Wu ◽  
Nils Thieme ◽  
Lori B. Huberman ◽  
Axel Dietschmann ◽  
David J. Kowbel ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Carbon Sources ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding

Filamentous fungi, such asNeurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling ofN. crassaon 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors inN. crassaand characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

scholarly journals Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Isaac Cann ◽  
Gabriel V. Pereira ◽  
Ahmed M. Abdel-Hamid ◽  
Heejin Kim ◽  
Daniel Wefers ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Animal Feed ◽  
Value Added ◽  
Building Blocks ◽  
Economic Feasibility ◽  
Renewable Fuels ◽  
Microbial Enzymes

ABSTRACT Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.

scholarly journals A comparative study of ruminal activity in Churra and Merino sheep offered alfalfa hay

1997 ◽  
Vol 65 (1) ◽  
pp. 121-128 ◽  
Author(s):  
M. J. Ranilla ◽  
M. D. Carro ◽  
C. Valdés ◽  
F. J. Giráldez ◽  
S. López
Keyword(s):  
Cell Wall ◽  
Rumen Fluid ◽  
Merino Sheep ◽  
Rumen Ph ◽  
Sheep Rumen ◽  
Fermentation Parameters ◽  
Micro Organisms ◽  
Kinetics Of

AbstractA study was carried out to compare the fermentation parameters and kinetics of digestion of a range of different foods in the rumen of two breeds of sheep (Churra and Merino). Ten mature sheep (five Churra and five Merino), each fitted with a rumen cannula, were used in this study. In situ rumen degradability of both dry matter (DM) and cell wall was greater in Churra than in Merino sheep, the breed differences being significant for most of the foods used in the study (P < 0·05). These differences were greater when the foods had a higher cell wall concentration and this could be related to differences in the ruminal environment. However, when the foods were incubated with rumen fluid their in vitro organic matter (OM) degradability was similar in both breeds. Rumen pH was higher (P < 0·05) and ammonia concentrations were lower (P < 0·05) in Churra than in Merino sheep. Rumen volatile fatty acid concentrations tended to be higher in Merino than in Churra sheep, though differences were only significant just before feeding (P < 0·05). The ratio acetate: propionate was higher in the Churra than Merino breed before and 12 h after feeding (P < 0·05). Protozoa numbers in rumen liquid were similar for both genotypes. The greater degradation of forages in the rumen of Churra sheep is discussed in relation to the possible higher activity of fibre-degrading micro-organisms and the greater buffering capacity of the rumen contents against fermentation acids, which could result in more favourable conditions for the microbial degradation of foods in the rumen.

scholarly journals Ruminal and total plant cell-wall digestibility estimated by a combinedin situmethod utilizing mathematical models

1997 ◽  
Vol 78 (4) ◽  
pp. 583-598 ◽  
Author(s):  
Pekka Huhtanen ◽  
Aila Vanhatalo
Keyword(s):  
Cell Wall ◽  
Incubation Period ◽  
Plant Cell Wall ◽  
Intestinal Cell ◽  
Cell Wall Digestibility ◽  
Stages Of Growth ◽  
Cell Wall Digestion ◽  
Intestinal Digestion ◽  
Ruminal Digestion

Three ruminally and duodenally cannulated non-lactating Finnish Ayrshire cows were used to investigate ruminal and intestinal digestion of cell-wall carbohydrates by a combinedin situmethod. Five grasses cut at 10 d intervals were incubated in the rumen for 0, 6, 12, 24, 48, 72 and 96 h, and the undegraded residues were exposed to intestinal digestion. With advancing maturity of grass both the rate and extent of cell-wall digestion decreased. At early stages of growth the decreases were faster for the rate of digestion and at late stages of growth for the extent of digestion. Applying a passage rate of 0.02/h in one compartmental rumen model resulted in digestibility values markedly lower than typically observedin vivo.However, applying a rumen model incorporating a selective retention of particles and time-dependent release of particles from the non-escapable pool resulted in much higher digestibility values. Recovery of lignin after 96 h ruminal incubation with a subsequent mobile-bag incubation was very low (from 244 to 460 mg/g). Intestinal disappearance of neutral-detergent fibre (NDF) and hemicellulose decreased with advancing maturity of grass and with increasing length of preceding ruminal incubation period, i.e. with decreasing potential digestibility of the material. Disappearance of hemicellulose was much greater than that of cellulose for intact grasses but the difference diminished with increasing length of preceding rumen incubation period. On average, 195 mg/g of potentially digestible NDF disappeared from the mobile bags in the intestines. The post-ruminal digestion as a proportion of the total NDF digestibility varied between 0.034 and 0.058. Despite methodological problems both in ruminalin situand intestinal mobile bag techniques, these methods can be used to investigate ruminal and intestinal cell-wall digestion and to partition cell-wall digestibility between ruminal and post-ruminal digestion providing that appropriate rumen models are used.

scholarly journals Direct Target Network of the Neurospora crassa Plant Cell Wall Deconstruction Regulators CLR-1, CLR-2, and XLR-1

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
James P. Craig ◽  
Samuel T. Coradetti ◽  
Trevor L. Starr ◽  
N. Louise Glass
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Transcription Factors ◽  
Neurospora Crassa ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Nutrient Sensing ◽  
Wall Material ◽  
Content Type ◽  
Genes Encoding

ABSTRACTFungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. InNeurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. WhenN. crassais exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog inSaccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex.IMPORTANCEUnderstanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

scholarly journals Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7220
Author(s):  
Yanhua Dou ◽  
Yan Yang ◽  
Nitesh Kumar Mund ◽  
Yanping Wei ◽  
Yisong Liu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Fungal Pathogens ◽  
Plant Cell Wall ◽  
Apple Tree ◽  
Plant Biomass ◽  
Genomic Analysis ◽  
Pathogenic Fungi ◽  
Cell Wall Degrading Enzymes ◽  
Enzyme Activity Assay

Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.

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