scholarly journals Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1942
Author(s):  
Lisanne Smulders ◽  
Emilio Benítez ◽  
Beatriz Moreno ◽  
Álvaro López-García ◽  
María J. Pozo ◽  
...  
Keyword(s):  
Ecosystem Services ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Plant Domestication ◽  
Host Genotype ◽  
Tomato Root ◽  
Agronomic Practices ◽  
Evolutionarily Conserved ◽  
Poor Understanding ◽  
Functional Profiles

While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.

scholarly journals Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Stefanie P Glaeser ◽  
Iulian Gabur ◽  
Hossein Haghighi ◽  
Jens-Ole Bartz ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Quantitative Resistance ◽  
Bacterial Community Composition ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Host Genotype ◽  
Brassica Napus L ◽  
Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Genetic Diversity of Soil Bacteria

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 414
Author(s):  
Carmine Crecchio
Keyword(s):  
Genetic Diversity ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Agricultural Soils ◽  
Field Trials ◽  
Laboratory Scale ◽  
Special Issue ◽  
Soil Bacterial Communities ◽  
Review Articles ◽  
Different Types

The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management.

scholarly journals High functional diversity stimulates diversification in experimental microbial communities

2016 ◽  
Vol 2 (6) ◽  
pp. e1600124 ◽  
Author(s):  
Alexandre Jousset ◽  
Nico Eisenhauer ◽  
Monika Merker ◽  
Nicolas Mouquet ◽  
Stefan Scheu
Keyword(s):  
Ecosystem Services ◽  
Functional Diversity ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Bacterial Species ◽  
Focal Species ◽  
Evolutionary Diversification ◽  
The Impact ◽  
High Diversity

There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

scholarly journals Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses

2021 ◽  
Author(s):  
Yingnan Gao ◽  
Martin Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Copy Number ◽  
Rrna Gene ◽  
Prediction Uncertainty ◽  
Functional Profiles ◽  
Diversity Studies

Background: 16S rRNA gene has been widely used in microbial diversity studies to determine the community composition and structure. 16S rRNA gene copy number (16S GCN) varies among microbial species and this variation introduces biases to the relative cell abundance estimated using 16S rRNA read counts. To correct the biases, methods (e.g., PICRUST2) have been developed to predict 16S GCN. 16S GCN predictions come with inherent uncertainty, which is often ignored in the downstream analyses. However, a recent study suggests that the uncertainty can be so great that copy number correction is not justified in practice. Despite the significant implications in 16S rRNA based microbial diversity studies, the uncertainty associated with 16S GCN predictions has not been well characterized and its impact on microbial diversity studies needs to be investigated. Results: Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S rRNA GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms PICRUST2 in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, PERMANOVA and random forest test. Conclusion: We have developed a method to accurately account for uncertainty in 16S rRNA GCN predictions and the downstream analyses. For almost all 16S rRNA surveyed bacterial communities, correction of 16S GCN should improve the results when estimating their compositional and functional profiles. However, such correction is not necessary for beta-diversity analyses.

scholarly journals Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources

2020 ◽  
Author(s):  
Hugo R. Barajas ◽  
Shamayim Martínez-Sánchez ◽  
Miguel F. Romero ◽  
Cristóbal Hernández-Álvarez ◽  
Luis Servín-González ◽  
...  
Keyword(s):  
Plant Root ◽  
Plant Domestication ◽  
Tomato Root ◽  
Breeding Programs ◽  
Active Selection ◽  
Trade Offs ◽  
Step Model ◽  
Tomato Roots ◽  
Microbe Interactions

AbstractThe two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease towards roots. We collected in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. Tomato roots did follow the two-step model, while ruderal plants did not. Ruderal plants and their soils are closer than tomato and its soil, based on protein comparisons. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-microbe interactions.

scholarly journals Mechanism of Intermittent Deep Tillage and Different Depths Improving Crop Growth From the Perspective of Rhizosphere Soil Nutrients, Root System Architectures, Bacterial Communities, and Functional Profiles

2022 ◽  
Vol 12 ◽  
Author(s):  
Yabing Gu ◽  
Yongjun Liu ◽  
Jiaying Li ◽  
Mingfeng Cao ◽  
Zhenhua Wang ◽  
...  
Keyword(s):  
Root System ◽  
Soil Nutrients ◽  
Crop Yield ◽  
System Architecture ◽  
Bacterial Communities ◽  
Root System Architecture ◽  
Crop Growth ◽  
Deep Tillage ◽  
Tillage Practices ◽  
Functional Profiles

Long-term conventional shallow tillage reduced soil quality and limited the agriculture development. Intermittent deep tillage could effectively promote agricultural production, through optimizing soil structure, underground ecology system, and soil fertility. However, the microecological mechanism of intermittent deep tillage promoting agriculture production has never been reported, and the effect of tillage depth on crop growth has not been explored in detail. In this study, three levels of intermittent deep tillage (30, 40, and 50 cm) treatments were conducted in an experimental field site with over 10 years of conventional shallow tillage (20 cm). Our results indicated that intermittent deep tillage practices helped to improve plant physiological growth status, chlorophyll a, and resistance to diseases, and the crop yield and value of output were increased with the deeper tillage practices. Crop yield (18.59%) and value of output (37.03%) were highest in IDT-50. There were three mechanisms of intermittent deep tillage practices that improved crop growth: (1) Intermittent deep tillage practices increased soil nutrients and root system architecture traits, which improved the fertility and nutrient uptake of crop through root system. (2) Changing rhizosphere environments, especially for root length, root tips, pH, and available potassium contributed to dissimilarity of bacterial communities and enriched plant growth-promoting species. (3) Functions associated with stress tolerance, including signal transduction and biosynthesis of other secondary metabolites were increased significantly in intermittent deep tillage treatments. Moreover, IDT-30 only increased soil characters and root system architecture traits compared with CK, but deeper tillage could also change rhizosphere bacterial communities and functional profiles. Plant height and stem girth in IDT-40 and IDT-50 were higher compared with IDT-30, and infection rates of black shank and black root rot in IDT-50 were even lower in IDT-40. The study provided a comprehensive explanation into the effects of intermittent deep tillage in plant production and suggested an optimal depth.

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