Assessing Comparative Microbiome Performance in Plant Cell Wall Deconstruction Using Multi-omics-Informed Network Analysis

Plant cell walls are interwoven structures recalcitrant to degradation. Both native and adapted microbiomes are particularly effective at plant cell wall deconstruction. Studying these deconstructive microbiomes provides an opportunity to assess microbiome performance and relate it to specific microbial populations and enzymes. To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from time-dependent gene expression identified key deconstructive groups within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmanimonadetes populations. Functional analysis of gene expression demonstrated that the microbiomes proceeded through successional stages that are linked to enzymes that deconstruct plant cell wall polymers. This combination of network and functional analysis highlighted the importance of cellulose-active Actinobacteria in differentiating the performance of these microbiomes.

Cell wall composition determines handedness reversal in helicoidal cellulose architectures of Pollia condensata fruits

Chiral asymmetry is important in a wide variety of disciplines and occurs across length scales. While several natural chiral biomolecules exist only with single handedness, they can produce complex hierarchical structures with opposite chiralities. Understanding how the handedness is transferred from molecular to the macroscopic scales is far from trivial. An intriguing example is the transfer of the handedness of helicoidal organizations of cellulose microfibrils in plant cell walls. These cellulose helicoids produce structural colors if their dimension is comparable to the wavelength of visible light. All previously reported examples of a helicoidal structure in plants are left-handed except, remarkably, in the Pollia condensata fruit; both left- and right-handed helicoidal cell walls are found in neighboring cells of the same tissue. By simultaneously studying optical and mechanical responses of cells with different handednesses, we propose that the chirality of helicoids results from differences in cell wall composition. In detail, here we showed statistical substantiation of three different observations: 1) light reflected from right-handed cells is red shifted compared to light reflected from left-handed cells, 2) right-handed cells occur more rarely than left-handed ones, and 3) right-handed cells are located mainly in regions corresponding to interlocular divisions. Finally, 4) right-handed cells have an average lower elastic modulus compared to left-handed cells of the same color. Our findings, combined with mechanical simulation, suggest that the different chiralities of helicoids in the cell wall may result from different chemical composition, which strengthens previous hypotheses that hemicellulose might mediate the rotations of cellulose microfibrils.

Pectin self-assembly and its disruption by water: Insights into plant cell wall mechanics

Plant cell walls undergo multiple cycles of dehydration and rehydration during their life. Calcium crosslinked low methoxy pectin is a major constituent of plant cell walls. Understanding the dehydration-rehydration behavior of pectin gels may shed light on the water transport and mechanics of plant cells. In this work, we report the contributions of microstructure to the mechanics of pectin-Ca gels subjected to different extents of dehydration and subsequent rehydration. This is investigated using a pectin gel composition that forms ‘egg-box bundles’, a characteristic feature of the microstructure of low methoxy pectin-Ca gels. Large Amplitude Oscillatory Shear (LAOS) rheology along with Small Angle Neutron Scattering and Near Infrared (NIR) spectroscopy on pectin gels are used to elucidate the mechanical and microstructural changes during dehydration-rehydration cycles. As the extent of dehydration increase, the reswelling ability, strain-stiffening behavior and the yield strain decreases. These effects are more prominent at faster rates of dehydration and are not completely reversible upon rehydration to the initial undried state. Microstructural changes due to the aggregation of egg-box bundles and single chains and the associated changes in the water configurations lead to these irreversible changes.

Down-regulation of OsMYB103L distinctively alters beta-1,4-glucan polymerization and cellulose microfibers assembly for enhanced biomass enzymatic saccharification in rice

Background As a major component of plant cell walls, cellulose provides the most abundant biomass resource convertible for biofuels. Since cellulose crystallinity and polymerization have been characterized as two major features accounting for lignocellulose recalcitrance against biomass enzymatic saccharification, genetic engineering of cellulose biosynthesis is increasingly considered as a promising solution in bioenergy crops. Although several transcription factors have been identified to regulate cellulose biosynthesis and plant cell wall formation, much remains unknown about its potential roles for genetic improvement of lignocellulose recalcitrance. Results In this study, we identified a novel rice mutant (Osfc9/myb103) encoded a R2R3-MYB transcription factor, and meanwhile generated OsMYB103L-RNAi-silenced transgenic lines. We determined significantly reduced cellulose levels with other major wall polymers (hemicellulose, lignin) slightly altered in mature rice straws of the myb103 mutant and RNAi line, compared to their wild type (NPB). Notably, the rice mutant and RNAi line were of significantly reduced cellulose features (crystalline index/CrI, degree of polymerization/DP) and distinct cellulose nanofibers assembly. These alterations consequently improved lignocellulose recalcitrance for significantly enhanced biomass enzymatic saccharification by 10–28% at p < 0.01 levels (n = 3) after liquid hot water and chemical (1% H2SO4, 1% NaOH) pretreatments with mature rice straws. In addition, integrated RNA sequencing with DNA affinity purification sequencing (DAP-seq) analyses revealed that the OsMYB103L might specifically mediate cellulose biosynthesis and deposition by regulating OsCesAs and other genes associated with microfibril assembly. Conclusions This study has demonstrated that down-regulation of OsMYB103L could specifically improve cellulose features and cellulose nanofibers assembly to significantly enhance biomass enzymatic saccharification under green-like and mild chemical pretreatments in rice. It has not only indicated a powerful strategy for genetic modification of plant cell walls in bioenergy crops, but also provided insights into transcriptional regulation of cellulose biosynthesis in plants.

Uptake and Accumulation of Nano/Microplastics in Plants: A Critical Review

The ubiquitous presence of microplastics (MPs) and nanoplastics (NPs) in the environment is an undeniable and serious concern due to their higher persistence and extensive use in agricultural production. This review highlights the sources and fate of MPs and NPs in soil and their uptake, translocation, and physiological effects in the plant system. We provide the current snapshot of the latest reported studies with the majority of literature spanning the last five years. We draw attention to the potential risk of MPs and NPs in modern agriculture and their effects on plant growth and development. We also highlight their uptake and transport pathways in roots and leaves via different exposure methods in plants. Conclusively, agricultural practices, climate changes (wet weather and heavy rainfall), and soil organisms play a major role in transporting MPs and NPs in soil. NPs are more prone to enter plant cell walls as compared to MPs. Furthermore, transpiration pull is the dominant factor in the plant uptake and translocation of plastic particles. MPs have negligible negative effects on plant physiological and biochemical indicators. Overall, there is a dire need to establish long-term studies for a better understanding of their fate and associated risks mechanisms in realistic environment scenarios for safe agricultural functions.

Water-accessibility of interfibrillar spaces in spruce wood cell walls

Water interactions and accessibility of the nanoscale components of plant cell walls influence their properties and processability in relation to many applications. We investigated the water-accessibility of nanoscale pores within the fibrillar structures of unmodified Norway spruce cell walls by small-angle neutron scattering (SANS) and Fourier-transform infra-red (FTIR) spectroscopy. The different sensitivity of SANS to hydrogenated ($$\hbox {H}_2\hbox {O}$$ H 2 O ) and deuterated water ($$\hbox {D}_2\hbox {O}$$ D 2 O ) was utilized to follow the exchange kinetics of water among cellulose microfibrils. FTIR spectroscopy was used to study the time-dependent re-exchange of OD groups to OH in wood samples transferred from liquid $$\hbox {D}_2\hbox {O}$$ D 2 O to $$\hbox {H}_2\hbox {O}$$ H 2 O . In addition, the effects of drying on the nanoscale structure and its water-accessibility were addressed by comparing SANS results and the kinetics of water exchange between never-dried and dried/rewetted wood samples. The results of the kinetic analyses allowed to identify two processes with different timescales. The diffusion-driven exchange of water in the spaces between microfibrils, which was observed with both SANS and FTIR, takes place within minutes and rather homogeneously. The second, slower process appeared only in the OD/OH re-exchange followed by FTIR, and it still continued after several weeks of immersion in $$\hbox {H}_2\hbox {O}$$ H 2 O . SANS could not detect any significant difference between the never-dried and dried/rewetted samples, whereas FTIR revealed a small portion of OD groups that resisted the re-exchange and this portion became larger with drying. Graphic abstract

The ectomycorrhizal basidiomycete Laccaria bicolor releases a GH28 polygalacturonase that plays a key role in symbiosis establishment

In ectomycorrhiza, root penetration and colonization of the intercellular space by symbiotic hyphae is thought to rely on the mechanical force that results from hyphal tip growth, enhanced by the activity of secreted cell-wall-degrading enzymes. Here, we characterize the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A from the ectomycorrhizal fungus Laccaria bicolor. The transcriptional regulation of LbGH28A was measured by qPCR. The biological relevance of LbGH28A was confirmed by generating RNAi-silenced LbGH28A mutants. We localized the LbGH28A protein by immunofluorescence confocal and immunogold cytochemical microscopy in poplar ectomycorrhizal roots. qPCR confirmed the induced expression of LbGH28A during ectomycorrhiza formation. L. bicolor RNAi mutants have a lower ability to establish ectomycorrhiza confirming the key role of this enzyme in symbiosis. The purified recombinant LbGH28A has its highest activity towards pectin and polygalacturonic acid. In situ localization of LbGH28A indicates that this endopolygalacturonase is located in both fungal and plant cell walls at the symbiotic hyphal front. The present findings suggest that the symbiosis-induced pectinase LbGH28A is involved in the Hartig net formation and is an important determinant for successful symbiotic colonization.