scholarly journals Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Simon Lewin ◽  
Davide Francioli ◽  
Andreas Ulrich ◽  
Steffen Kolb
Keyword(s):  
Oilseed Rape ◽  
Growth Stages ◽  
Plant Host ◽  
Crop Species ◽  
Differential Abundance ◽  
Core Microbiota ◽  
Network Analyses ◽  
Bacterial Microbiota ◽  
Species Effect ◽  
Occurrence Patterns

Abstract Background The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.

scholarly journals Crop Host Signatures Reflected by Co-association Patterns of Keystone Bacteria in the Rhizosphere Microbiota

2021 ◽  
Author(s):  
Simon Lewin ◽  
Davide Francioli ◽  
Andreas Ulrich ◽  
Steffen Kolb
Keyword(s):  
Oilseed Rape ◽  
Growth Stages ◽  
Plant Host ◽  
Crop Species ◽  
Differential Abundance ◽  
Core Microbiota ◽  
Network Analyses ◽  
Bacterial Microbiota ◽  
Species Effect ◽  
Occurrence Patterns

Abstract Background: The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results: Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extend of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions: Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiome for future agriculture and to develop effective bio-fertilizers.

scholarly journals Influence of plant host and organ, management strategy, and spore traits on microbiome composition

2020 ◽  
Author(s):  
Kristi Gdanetz ◽  
Zachary Noel ◽  
Frances Trail
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Life Histories ◽  
Management Strategies ◽  
Alpha Diversity ◽  
Fungal Spore ◽  
Organ Specificity ◽  
Growth Stages ◽  
Plant Host ◽  
Network Analyses

ABSTRACTMicrobiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

scholarly journals Influence of plant host and organ, management strategy, and spore traits on microbiome composition

2021 ◽  
Author(s):  
Kristi Gdanetz ◽  
Zachary Albert Noel ◽  
Frances Trail
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Life Histories ◽  
Management Strategies ◽  
Alpha Diversity ◽  
Fungal Spore ◽  
Organ Specificity ◽  
Growth Stages ◽  
Plant Host ◽  
Network Analyses

Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

Absorption, Distribution, and Translocation of Nitrogen at Growth Stages in Oilseed Rape Plant

2010 ◽  
Vol 36 (2) ◽  
pp. 321-326
Author(s):  
Zhen-Hua ZHANG ◽  
Hai-Xing SONG ◽  
Qiang LIU ◽  
Xiang-Min RONG ◽  
Gui-Xian XIE ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Growth Stages ◽  
Rape Plant

scholarly journals Osmotic Stress or Ionic Composition: Which Affects the Early Growth of Crop Species More?

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 435
Author(s):  
Agnieszka Ludwiczak ◽  
Monika Osiak ◽  
Stefany Cárdenas-Pérez ◽  
Sandra Lubińska-Mielińska ◽  
Agnieszka Piernik
Keyword(s):  
Osmotic Stress ◽  
Stress Responses ◽  
Ionic Composition ◽  
Degradation Process ◽  
Early Growth ◽  
Cultivated Plants ◽  
C3 Plants ◽  
Growth Stages ◽  
Crop Species ◽  
Ionic Salt

Salinization is a key soil degradation process. An estimated 20% of total cultivated lands and 33% of irrigated agricultural lands worldwide are affected by high salinity. Much research has investigated the influence of salt (mainly NaCl) on plants, but very little is known about how this is related to natural salinity and osmotic stress. Therefore, our study was conducted to determine the osmotic and ionic salt stress responses of selected C3 and C4 cultivated plants. We focused on the early growth stages as those critical for plant development. We applied natural brine to simulate natural salinity and to compare its effect to NaCl solution. We assessed traits related to germination ability, seedlings and plantlet morphology, growth indexes, and biomass and water accumulation. Our results demonstrate that the effects of salinity on growth are strongest among plantlets. Salinity most affected water absorption in C3 plants (28% of total traits variation), but plant length in C4 plants (17–27%). Compensatory effect of ions from brine were suggested by the higher model plants’ growth success of ca 5–7% under brine compared to the NaCl condition. However, trait differences indicated that osmotic stress was the main stress factor affecting the studied plants.

scholarly journals RNAi efficacy is enhanced by chronic dsRNA feeding in pollen beetle

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jonathan Willow ◽  
Liina Soonvald ◽  
Silva Sulg ◽  
Riina Kaasik ◽  
Ana Isabel Silva ◽  
...  
Keyword(s):  
Rna Interference ◽  
Pest Management ◽  
Oilseed Rape ◽  
Growth Stages ◽  
Short Term ◽  
Pollen Beetle ◽  
Brassicogethes Aeneus ◽  
Crop Growth Stages ◽  
Insecticidal Compounds ◽  
Significant Mortality

AbstractDouble-stranded RNAs (dsRNAs) represent a promising class of biosafe insecticidal compounds. We examined the ability to induce RNA interference (RNAi) in the pollen beetle Brassicogethes aeneus via anther feeding, and compared short-term (3 d) to chronic (17 d) feeding of various concentrations of dsRNA targeting αCOP (dsαCOP). In short-term dsαCOP feeding, only the highest concentration resulted in significant reductions in B. aeneus survival; whereas in chronic dsαCOP feeding, all three concentrations resulted in significant mortality. Chronic dsαCOP feeding also resulted in significantly greater mortality compared to short-term feeding of equivalent dsαCOP concentrations. Our results have implications for the economics and development of dsRNA spray approaches for managing crop pests, in that multiple lower-concentration dsRNA spray treatments across crop growth stages may result in greater pest management efficacy, compared to single treatments using higher dsRNA concentrations. Furthermore, our results highlight the need for research into the development of RNAi cultivars for oilseed rape protection, given the enhanced RNAi efficacy resulting from chronic, compared to short-term, dsRNA feeding in B. aeneus.

scholarly journals Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Siles ◽  
Kirsty L. Hassall ◽  
Cristina Sanchis Gritsch ◽  
Peter J. Eastmond ◽  
Smita Kurup
Keyword(s):  
Oilseed Rape ◽  
Seed Yield ◽  
Complex Trait ◽  
Growth Conditions ◽  
Phenotypic Traits ◽  
Oilseed Crop ◽  
Crop Species ◽  
Trade Offs ◽  
Whole Plant ◽  
Plant Level

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.

scholarly journals Meiosis in Polyploids and Implications for Genetic Mapping: A Review

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1517
Author(s):  
Nina Reis Soares ◽  
Marcelo Mollinari ◽  
Gleicy K. Oliveira ◽  
Guilherme S. Pereira ◽  
Maria Lucia Carneiro Vieira
Keyword(s):  
Oilseed Rape ◽  
Genetic Maps ◽  
Crop Species ◽  
Map Construction ◽  
Complex Process ◽  
New Gene ◽  
Specific Proteins ◽  
Bivalent Formation ◽  
Essential Knowledge

Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.

scholarly journals In-Field Observation of Root Growth and Nitrogen Uptake Efficiency of Winter Oilseed Rape

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 105
Author(s):  
Julien Louvieaux ◽  
Antoine Leclercq ◽  
Loïc Haelterman ◽  
Christian Hermans
Keyword(s):  
Root Growth ◽  
Oilseed Rape ◽  
Root Development ◽  
Nitrogen Uptake ◽  
Root Morphology ◽  
Growth Stages ◽  
Winter Oilseed Rape ◽  
Nitrogen Uptake Efficiency ◽  
Uptake Efficiency ◽  
N Concentration

Field trials were conducted with two nitrogen applications (0 or 240 kg N ha−1) and three modern cultivars of winter oilseed rape (Brassica napus L.) previously selected from a root morphology screen at a young developmental stage. The purpose is to examine the relationship between root morphology and Nitrogen Uptake Efficiency (NUpE) and to test the predictiveness of some canopy optical indices for seed quality and yield. A tube-rhizotron system was used to incorporate below-ground root growth information. Practically, clear tubes of one meter in length were installed in soil at an angle of 45°. The root development was followed with a camera at key growth stages in autumn (leaf development) and spring (stem elongation and flowering). Autumn was a critical time window to observe the root development, and exploration in deeper horizons (36–48 cm) was faster without any fertilization treatment. Analysis of the rhizotron images was challenging and it was not possible to clearly discriminate between cultivars. Canopy reflectance and leaf optical indices were measured with proximal sensors. The Normalized Difference Vegetation Index (NDVI) was a positive indicator of biomass and seed yield while the Nitrogen Balance Index (NBI) was a positive indicator of above-ground biomass N concentration at flowering and seed N concentration at harvest.

scholarly journals The Cpc1 Regulator of the Cross-Pathway Control of Amino Acid Biosynthesis Is Required for Pathogenicity of the Vascular Pathogen Verticillium longisporum

2013 ◽  
Vol 26 (11) ◽  
pp. 1312-1324 ◽  
Author(s):  
Christian Timpner ◽  
Susanna A. Braus-Stromeyer ◽  
Van Tuan Tran ◽  
Gerhard H. Braus
Keyword(s):  
Amino Acid ◽  
Oilseed Rape ◽  
Host Plants ◽  
Pathogenic Fungus ◽  
Amino Acid Biosynthesis ◽  
Amino Acid Starvation ◽  
Acid Biosynthesis ◽  
Plant Host ◽  
Verticillium Longisporum ◽  
The Cross

The plant-pathogenic fungus Verticillium longisporum is a causal agent of early senescence and ripening in cruciferous crops like Brassica napus. Verticillium wilts have become serious agricultural threats in recent decades. Verticillium species infect host plants through the roots and colonize xylem vessels of the host plant. The xylem fluid provides an environment with limited carbon sources and unbalanced amino acid supply, which requires V. longisporum to induce the cross-pathway control of amino acid biosynthesis. RNA-mediated gene silencing reduced the expression of the two CPC1 isogenes (VlCPC1-1 and VlCPC1-2) of the allodiploid V. longisporum up to 85%. VlCPC1 encodes the conserved transcription factor of the cross-pathway control. The silenced mutants were highly sensitive to amino-acid starvation, and the infected plants showed significantly fewer symptoms such as stunting or early senescence in oilseed rape plant infection assays. Consistently, deletion of single CPC1 of the haploid V. dahliae resulted in strains that are sensitive to amino-acid starvation and cause strongly reduced symptoms in the plant-host tomato (Solanum lycopersicum). The allodiploid V. longisporum and the haploid V. dahliae are the first phytopathogenic fungi that were shown to require CPC1 for infection and colonization of their respective host plants, oilseed rape and tomato.

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