scholarly journals Enhanced Yield of Pepper Plants Promoted by Soil Application of Volatiles From Cell-Free Fungal Culture Filtrates Is Associated With Activation of the Beneficial Soil Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Edurne Baroja-Fernández ◽  
Goizeder Almagro ◽  
Ángela María Sánchez-López ◽  
Abdellatif Bahaji ◽  
Samuel Gámez-Arcas ◽  
...  

Plants communicate with microorganisms by exchanging chemical signals throughout the phytosphere. Such interactions are important not only for plant productivity and fitness, but also for terrestrial ecosystem functioning. It is known that beneficial microorganisms emit diffusible substances including volatile organic compounds (VOCs) that promote growth. Consistently, soil application of cell-free culture filtrates (CF) of beneficial soil and plant-associated microorganisms enhances plant growth and yield. However, how this treatment acts in plants and whether it alters the resident soil microbiota, are largely unknown. In this work we characterized the responses of pepper (Capsicum annuum L.) plants cultured under both greenhouse and open field conditions and of soil microbiota to soil application of CFs of beneficial and phytopathogenic fungi. To evaluate the contribution of VOCs occurring in the CFs to these responses, we characterized the responses of plants and of soil microbiota to application of distillates (DE) of the fungal CFs. CFs and their respective DEs contained the same potentially biogenic VOCs, and application of these extracts enhanced root growth and fruit yield, and altered the nutritional characteristics of fruits. High-throughput amplicon sequencing of bacterial 16S and fungal ITS rRNA genes of the soil microbiota revealed that the CF and DE treatments altered the microbial community compositions, and led to strong enrichment of the populations of the same beneficial bacterial and fungal taxa. Our findings show that CFs of both beneficial and phytopathogenic fungi can be used as biostimulants, and provide evidence that VOCs occurring in the fungal CFs act as mediators of the plants’ responses to soil application of fungal CFs through stimulation of the beneficial soil microbiota.

Nature Plants ◽  
2021 ◽  
Author(s):  
Ka-Wai Ma ◽  
Yulong Niu ◽  
Yong Jia ◽  
Jana Ordon ◽  
Charles Copeland ◽  
...  

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.


Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Caitlin M. Singleton ◽  
Francesca Petriglieri ◽  
Jannie M. Kristensen ◽  
Rasmus H. Kirkegaard ◽  
Thomas Y. Michaelsen ◽  
...  

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.


Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.


Author(s):  
L A Gabbarini ◽  
E Figuerola ◽  
J P Frene ◽  
N B Robledo ◽  
F M Ibarbalz ◽  
...  

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.


2019 ◽  
Vol 38 (4) ◽  
Author(s):  
R.S. Anjana ◽  
K.R. Sheela

A field experiment was conducted during the summer, 2014 at College of Agriculture, Vellayani, Kerala to evaluate the influence of irrigation levels, nitrogen stress and method of application of fertilizers on growth and yield of yard long bean. The experiment consisted of four levels of irrigation, two levels of nitrogen and two methods of application. The results indicated that daily irrigation at 10 mm depth and recommended dose of nitrogen (30 kg ha-1) recorded superior values for growth parameters viz., functional leaves per plant and leaf area index The major yield attributes like number of pods per plant and pod yield per plant and total pod yield were not influenced by levels of irrigation and nitrogen indicating that irrigation once in three days at 20 mm depth and nitrogen level of 22.5 kg ha-1 is sufficient for yard long bean. Soil and foliar application of nitrogen and potassium recorded superior growth characters, however, the yield was superior when the recommended dose of nutrients were supplied as soil application. Increasing irrigation interval to three days and imparting N stress did not result in any reduction in gross income and net income while, a higher benefit: cost ratio was noted in irrigation at wider intervals. Soil application of nutrients recorded higher gross income, net income and BCR compared to soil + foliar application.


2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Doreen Babin ◽  
Loreen Sommermann ◽  
Soumitra Paul Chowdhury ◽  
Jan H Behr ◽  
Martin Sandmann ◽  
...  

ABSTRACT A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.


Agronomy ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 343 ◽  
Author(s):  
Muhammad Zafar-ul-Hye ◽  
Subhan Danish ◽  
Mazhar Abbas ◽  
Maqshoof Ahmad ◽  
Tariq Muhammad Munir

Drought stress retards wheat plant’s vegetative growth and physiological processes and results in low productivity. A stressed plant synthesizes ethylene which inhibits root elongation; however, the enzyme 1-Aminocyclopropane-1-Carboxylate (ACC) deaminase catabolizes ethylene produced under water stress. Therefore, the ACC deaminase producing plant growth promoting rhizobacteria (PGPR) can be used to enhance crop productivity under drought stress. Biochar (BC) is an organically active and potentially nutrient-rich amendment that, when applied to the soil, can increase pore volume, cation exchange capacity and nutrient retention and bioavailability. We conducted a field experiment to study the effect of drought tolerant, ACC deaminase producing PGPR (with and without timber waste BC) on plant growth and yield parameters under drought stress. Two PGPR strains, Agrobacterium fabrum or Bacillus amyloliquefaciens were applied individually and in combination with 30 Mg ha−1 BC under three levels of irrigation, i.e., recommended four irrigations (4I), three irrigations (3I) and two irrigations (2I). Combined application of B. amyloliquefaciens and 30 Mg ha−1 BC under 3I, significantly increased growth and yield traits of wheat: grain yield (36%), straw yield (50%), biological yield (40%). The same soil application under 2I resulted in greater increases in several of the growth and yield traits: grain yield (77%), straw yield (75%), above- and below-ground biomasses (77%), as compared to control; however, no significant increases in chlorophyll a, b or total, and photosynthetic rate and stomatal conductance in response to individual inoculation of a PGPR strain (without BC) were observed. Therefore, we suggest that the combined soil application of B. amyloliquefaciens and BC more effectively mitigates drought stress and improves wheat productivity as compared to any of the individual soil applications tested in this study.


2015 ◽  
Vol 4 (1) ◽  
pp. 73
Author(s):  
Ogundare S. K. ◽  
Mohammed S. A. ◽  
Owolabi J. F.

Experiments were carried out at the student’s experimental field, Kabba College of Agriculture, Horticulture section to examine the effect of soil application of cow dung combined with foliar application of boost extra on growth and yield of okra in an ultisol, Nigeria. The land was ploughed each year and harrowed with the aid of tractor mounted implements. The experiment was laid out in a randomized complete block design (RCBD). The treatments consisted of A = 3t/ha cow dung, B = 1.0 L/ha foliar + 2.5t/ha cow dung, C =1.5L/ha foliar + 2t/ha cow dung, D    = 2 L/ha foliar      + 1.5 t/ha cow dung, E = 2.5L/ha foliar + 1.0t/ha cow dung, F = 3t/ha foliar. Each year experiment was conducted using a single field having dimension of 35 by 14m which was laid out into three blocks with 1m guard row between blocks. Each block consists of six plots (5 by 4m) and 1m guard row between plots. Cow dung manure was applied a week before planting. Okra variety Lady’s finger was used. Three seeds per hole were planted on April 4th in both years on the flat with a spacing of 60cm x 25cm between and within the rows and later thinned to one plant per stand. Data taken included plant height at 50 % flowering, number of branches per plant, leaf area, pod length, pod diameter, number of pods per plant; and pod weight and yield (t/ha). The data were subjected to Analysis of Variance (ANOVA) while the Least Significant Difference (LSD) was used to separate treatment means. The result shows that plot treated with 2.0L/ha foliar + 1.5 t/ha cow dung had the best performance in yield and yield components in this study. It is therefore recommended that okra farmers should integrated foliar fertilizer (boost extra) at the rate of 2L per hectare with cow dung at rate of 1.5t per hectare be used for okra production in the study area.


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