scholarly journals Anatomical Boundaries in Plant Roots Form Important Barriers for Selection of the Soil Microbiome

2021 ◽  
Author(s):  
Yi Zhou ◽  
Yanli Wei ◽  
Zhongjuan Zhao ◽  
Jishun Li ◽  
Hongmei Li ◽  
...  
Keyword(s):  
Cell Wall ◽  
Lignin Content ◽  
Root Exudation ◽  
Minor Component ◽  
Bulk Soil ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Soil Rhizosphere ◽  
Selection Of

Abstract Background The microbiome in plant-soil systems has a significant influence in promoting plant growth. The extent of selectivity that the plant exerts on the microbiome in the continuum of internal plant tissues is not well understood. This study analysed the root microbiome of a legume, Melilotus officinalis (L.) Pall., sweet clover, and focused on dynamic shifts in the microbial community structure through the niches of bulk soil, rhizosphere, periderm, phloem and xylem, and further examined the effects of environmental factors, root exudates and root cell wall development on the microbiome assemblages in different root compartments.ResultsYoung and mature plants were sampled at 24 field sites and the microbial communities in different niches from bulk soil and rhizosphere through to root compartments were analysed by 16S rRNA gene sequencing. The microbiome composition changed from periderm to phloem to a greater extent than across other boundaries (0.95 vs 0.71 based Bray–Curtis distance). Variation in microbiome composition was associated with geographic distance and soil properties for the bulk soil, rhizosphere and periderm niches. The composition of root exudate compounds were correlated with the rhizosphere microbiome assemblages in mature and young plants. The endophyte communities that occupied the phloem and xylem were most conserved and were independent of growing environments and root exudation. Symbiotic rhizobia able to nodulate M. officinalis were prominent colonisers of the periderm (~15%) and xylem (~6.2%), but were only a minor component in other soil-related niches (0.1%-2.5%). In xylem tissues, endophyte diversity was correlated with the total cell wall and lignin content across the sampled sites (r=0.29-0.62). Conclusions Our results demonstrate that selection of microbiome constituents occurs at different boundaries through bulk soil, rhizosphere, periderm, phloem and xylem, and is especially strong across the periderm boundary. The conserved endophyte community in the innermost tissues (phloem and xylem) was identified, and will be advantageous to the development of specific beneficial microbial inoculants.

scholarly journals Longispora fulva sp. nov., isolated from a forest soil, and emended description of the genus Longispora

2011 ◽  
Vol 61 (4) ◽  
pp. 804-809 ◽  
Author(s):  
Hatsumi Shiratori-Takano ◽  
Koji Yamada ◽  
Teruhiko Beppu ◽  
Kenji Ueda
Keyword(s):  
Cell Wall ◽  
Forest Soil ◽  
Minor Component ◽  
Rrna Gene ◽  
Cell Wall Polysaccharides ◽  
Monophyletic Cluster ◽  
The Family ◽  
Actinomycete Strain ◽  
A Minor ◽  
The 16S Rrna Gene

A novel actinomycete, strain KZ0017T, was isolated from a forest soil collected in Ohnuma, Fukushima, Japan. Strain KZ0017T formed spore chains borne on top of short sporophores arising from vegetative hyphae. Spores were non-motile and cylindrical with smooth surfaces. Strain KZ0017T contained meso-diaminopimelic (A2pm) acid, 3-OH A2pm, d-glutamic acid, glycine and l-alanine in the cell-wall peptidoglycan, and xylose, mannose, galactose, rhamnose and ribose in cell-wall hydrolysates. The acyl type of the cell-wall polysaccharides was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and several unknown lipids and glycolipids. The major fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 70.7 mol%. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the single member of the genus Longispora in the family Micromonosporaceae. On the basis of morphological, chemotaxonomic and phylogenetic properties, strain KZ0017T represents a novel species of the genus Longispora, for which the name Longispora fulva sp. nov. is proposed; the type strain is KZ0017T ( = NBRC 105670T = DSM 45356T).

scholarly journals Variation in root exudate composition influences soil microbiome membership and function

2021 ◽  
Author(s):  
Valerie A Seitz ◽  
Bridget B McGivern ◽  
Mikayla A Borton ◽  
Jacqueline M. Chaparro ◽  
Rebecca A Daly ◽  
...  
Keyword(s):  
Plant Growth ◽  
Root Exudate ◽  
Root Exudation ◽  
Gene Profiling ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Soil Matrix ◽  
Soil Microbial ◽  
Plant Growth Promoting ◽  
Growth Promoting

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix. Previous research has shown that plant root exudate profiles vary between species and genotypes which can likely support different microbial associations. Here, utilizing distinct sorghum genotypes as a model system, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolisms. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments, a High Organic acid Treatment (HOT) and a High Sugar Treatment (HST). Root exudate treatments were added to laboratory soil reactors and 16S rRNA gene profiling illustrated distinct microbial membership in response to HST or HOT amendments. Alpha and beta diversity metrics were significantly different between treatments, (Shannon’s, p < 0.0001, mrpp = 0.01, respectively). Exometabolite production was highest in the HST, with increased production of key organic acids, non-proteinogenic amino acids, and three plant growth-promoting phytohormones (benzoic acid, salicylic acid, indole-3-acetic acid), suggesting plant-derived sugars fuel microbial carbon metabolism and contribute to phytohormone production. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified potential plant growth-promoting microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multi-omics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

Silicification of wood-cell walls

1994 ◽  
Vol 52 ◽  
pp. 428-429
Author(s):  
S. E. Keckler ◽  
D. M. Dabbs ◽  
N. Yao ◽  
I. A. Aksay
Keyword(s):  
Electron Microscopy ◽  
Cell Wall ◽  
Cell Walls ◽  
Lignin Content ◽  
Resin Composite ◽  
Middle Lamella ◽  
Cellulose Fibers ◽  
Complex Structures ◽  
Rich Region ◽  
Inorganic Precursors

Cellular organic structures such as wood can be used as scaffolds for the synthesis of complex structures of organic/ceramic nanocomposites. The wood cell is a fiber-reinforced resin composite of cellulose fibers in a lignin matrix. A single cell wall, containing several layers of different fiber orientations and lignin content, is separated from its neighboring wall by the middle lamella, a lignin-rich region. In order to achieve total mineralization, deposition on and in the cell wall must be achieved. Geological fossilization of wood occurs as permineralization (filling the void spaces with mineral) and petrifaction (mineralizing the cell wall as the organic component decays) through infiltration of wood with inorganics after growth. Conversely, living plants can incorporate inorganics into their cells and in some cases into the cell walls during growth. In a recent study, we mimicked geological fossilization by infiltrating inorganic precursors into wood cells in order to enhance the properties of wood. In the current work, we use electron microscopy to examine the structure of silica formed in the cell walls after infiltration of tetraethoxysilane (TEOS).

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

scholarly journals Evaluating polymer interplay after hot water pretreatment to investigate maize stem internode recalcitrance

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amandine Leroy ◽  
Xavier Falourd ◽  
Loïc Foucat ◽  
Valérie Méchin ◽  
Fabienne Guillon ◽  
...  
Keyword(s):  
Cell Wall ◽  
Negative Impact ◽  
Lignin Content ◽  
Structural Features ◽  
Hot Water ◽  
Condensed State ◽  
Structural Factors ◽  
Water Pretreatment ◽  
Hot Water Pretreatment ◽  
The Impact

Abstract Background Biomass recalcitrance is governed by various molecular and structural factors but the interplay between these multiscale factors remains unclear. In this study, hot water pretreatment (HWP) was applied to maize stem internodes to highlight the impact of the ultrastructure of the polymers and their interactions on the accessibility and recalcitrance of the lignocellulosic biomass. The impact of HWP was analysed at different scales, from the polymer ultrastructure or water mobility to the cell wall organisation by combining complementary compositional, spectral and NMR analyses. Results HWP increased the kinetics and yield of saccharification. Chemical characterisation showed that HWP altered cell wall composition with a loss of hemicelluloses (up to 45% in the 40-min HWP) and of ferulic acid cross-linking associated with lignin enrichment. The lignin structure was also altered (up to 35% reduction in β–O–4 bonds), associated with slight depolymerisation/repolymerisation depending on the length of treatment. The increase in $${T}_{1\rho }^{H}$$ T 1 ρ H , $${T}_{HH}$$ T HH and specific surface area (SSA) showed that the cellulose environment was looser after pretreatment. These changes were linked to the increased accessibility of more constrained water to the cellulose in the 5–15 nm pore size range. Conclusion The loss of hemicelluloses and changes in polymer structural features caused by HWP led to reorganisation of the lignocellulose matrix. These modifications increased the SSA and redistributed the water thereby increasing the accessibility of cellulases and enhancing hydrolysis. Interestingly, lignin content did not have a negative impact on enzymatic hydrolysis but a higher lignin condensed state appeared to promote saccharification. The environment and organisation of lignin is thus more important than its concentration in explaining cellulose accessibility. Elucidating the interactions between polymers is the key to understanding LB recalcitrance and to identifying the best severity conditions to optimise HWP in sustainable biorefineries.

scholarly journals Effect of Exogenously Applied 24-Epibrassinolide and Brassinazole on Xylogenesis and Microdistribution of Cell Wall Polymers in Leucaena leucocephala (Lam) De Wit

2021 ◽  
Author(s):  
S. Pramod ◽  
M. Anju ◽  
H. Rajesh ◽  
A. Thulaseedharan ◽  
Karumanchi S. Rao
Keyword(s):  
Electron Microscopy ◽  
Cell Wall ◽  
Leucaena Leucocephala ◽  
Higher Plants ◽  
Lignin Content ◽  
Wood Quality ◽  
Wall Structure ◽  
Vessel Element ◽  
Xylem Differentiation ◽  
Cell Wall Polymers

AbstractPlant growth regulators play a key role in cell wall structure and chemistry of woody plants. Understanding of these regulatory signals is important in advanced research on wood quality improvement in trees. The present study is aimed to investigate the influence of exogenous application of 24-epibrassinolide (EBR) and brassinosteroid inhibitor, brassinazole (BRZ) on wood formation and spatial distribution of cell wall polymers in the xylem tissue of Leucaena leucocephala using light and immuno electron microscopy methods. Brassinazole caused a decrease in cambial activity, xylem differentiation, length and width of fibres, vessel element width and radial extent of xylem suggesting brassinosteroid inhibition has a concomitant impact on cell elongation, expansion and secondary wall deposition. Histochemical studies of 24-epibrassinolide treated plants showed an increase in syringyl lignin content in the xylem cell walls. Fluorescence microscopy and transmission electron microscopy studies revealed the inhomogenous pattern of lignin distribution in the cell corners and middle lamellae region of BRZ treated plants. Immunolocalization studies using LM10 and LM 11 antibodies have shown a drastic change in the micro-distribution pattern of less substituted and highly substituted xylans in the xylem fibres of plants treated with EBR and BRZ. In conclusion, present study demonstrates an important role of brassinosteroid in plant development through regulating xylogenesis and cell wall chemistry in higher plants.

scholarly journals Isolation and Characterization of Lactic Acid Bacteria and Yeasts from Typical Bulgarian Sourdoughs

2021 ◽  
Vol 9 (7) ◽  
pp. 1346
Author(s):  
Mariana Petkova ◽  
Petya Stefanova ◽  
Velitchka Gotcheva ◽  
Angel Angelov
Keyword(s):  
Lactic Acid ◽  
Sequence Analysis ◽  
Lactic Acid Bacteria ◽  
Antimicrobial Properties ◽  
Matter Content ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Dry Matter Content ◽  
Isolation And Characterization ◽  
Selection Of

Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such cultures is based on geographical specificity and beneficial technological properties. In this connection, the aim of this study was to isolate, identify and characterize lactic acid bacteria (LAB) and yeasts from typical Bulgarian sourdoughs for the selection of strains for commercial sourdough starter cultures. Twelve samples of typical Bulgarian sourdoughs were collected from different geographical locations. All samples were analyzed for pH, total titratable acidity and dry matter content. Enumeration of LAB and yeast was also carried out. Molecular identification by 16S rDNA sequence analysis was performed for 167 LAB isolates, and 106 yeast strains were identified by ITS1-5.8S-ITS2 rRNA gene partial sequence analysis. The LAB strains were characterized according to their amylolytic and proteolytic activity and acidification capacity, and 11 strains were selected for further testing of their antimicrobial properties. The strains with the most pronounced antibacterial and antifungal activity are listed as recommended candidates for the development of starter cultures for sourdoughs or other food products.

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