scholarly journals Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

2019 ◽  
Author(s):  
Marie Simonin ◽  
Cindy Dasilva ◽  
Valeria Terzi ◽  
Eddy L. M. Ngonkeu ◽  
Diégane Diouf ◽  
...  

AbstractHere, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.Graphical Abstract

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Marie Simonin ◽  
Cindy Dasilva ◽  
Valeria Terzi ◽  
Eddy L M Ngonkeu ◽  
Diégane Diouf ◽  
...  

ABSTRACT Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.


Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.


2021 ◽  
Vol 18 (23) ◽  
pp. 6133-6146
Author(s):  
Hao Tang ◽  
Susanne Liebner ◽  
Svenja Reents ◽  
Stefanie Nolte ◽  
Kai Jensen ◽  
...  

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.


2010 ◽  
Vol 10 (8) ◽  
pp. 1510-1516 ◽  
Author(s):  
Xin Chen ◽  
Li-Mei Zhang ◽  
Ju-Pei Shen ◽  
Zhihong Xu ◽  
Ji-Zheng He

2004 ◽  
Vol 84 (3) ◽  
pp. 295-305 ◽  
Author(s):  
A. R. Michaud ◽  
M. R. Laverdière

A simulated rainfall study was conducted on an array of 36 runoff plots (6 m2 each) deployed on three benchmark soil series of the Missisquoi region in southwestern Québec. The split-plot experimental design tested the effects and interactions of pig slurry treatment as main plots (check vs. 59 kg P ha-1) and cropping (tilled vs. hay) as subplots, on runoff volume and concentrations in total suspended sediment (TSS), tot al phosphorus (TP), dissolved reactive soluble P (DRP), particulate P (PP) and bioavailable P (BioP). TP concentration in runoff ranged from a low of 1.17 mg L-1 average on non-amended Bedford hay, to a peak concentration average of 9.55 mg L-1 on manured and tilled Saint-Sébastien plots. Variance analysis indicated significant contributions of treatments in explaining TP concentration in runoff as follows: Soil type effect > Cropping effect > Soil × Cropping interaction > Manure effect. Erosion and sediment transport processes were identified as prime vectors of TP export . Manure effect alone accounted for 35% of overall DRP variability, while soil type alone accounted for 70% of variability in particulate P bioavaibility (BioP/PP). Among practical implications of this study is the importance of assessing PP bioavaibility to adequately predict the adverse impact of runoff on aquatic ecosystems. The high level of interaction among cropping and manure treatment and the site- specific influence of soil physical and chemical properties also calls for a holistic approach to nonpoint P risk assessment and management, that focusses on timely manure P management, control of soil P build-up and agricultural practices minimizing surface runoff. Key words: Phosphorus, P-index, rainfall simulation, runoff, erosion, bioavailability, sediment


2018 ◽  
Author(s):  
Charley J. Hubbard ◽  
Baohua Li ◽  
Robby McMinn ◽  
Marcus T. Brock ◽  
Lois Maignien ◽  
...  

SummaryRhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense remains unclear.In Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites.Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae, and the population with lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.) attack; no effect was observed of GLS on damage by a second herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (intact vs. disrupted) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted rhizosphere microbiome treatment, and distinct (as estimated from 16s rRNA amplicon sequencing) intact native microbiomes also differed in their effects on herbivore damage. These differences may be attributable to shifts in primary metabolic pathways.The findings suggest that rhizosphere microbes can play a greater role than plant genotype in defense against insect herbivores, and act through mechanisms independent of plant genotype.


2014 ◽  
Author(s):  
Rosana V Sandler ◽  
Liliana B Falco ◽  
César A Di Ciocco ◽  
Ricardo Castro-Huerta ◽  
Carlos E Coviella

Edaphic fauna play a crucial role in soil processes such as organic matter incorporation and cycling, nutrient content, soil structure, and stability. Collembolans in particular, play a very significant role in nutrient cycling and soil structure. The structure and functioning of the soil fauna can in turn be affected by soil use, leading to changes in soil characteristics and its sustainability. Therefore, the responses of soil fauna to different soil management practices, can be used as ecological indicators. Three different soil uses were researched: agricultural fields (AG) with 50 years of continuous farming, pastures entering the agricultural cycle (CG), and naturalized grasslands (NG). For each soil use, three fields were selected. Each sampling consisted of three soil samples per replicate. Collembolans were extracted from the samples and identified to family level. Five families were found: Hypogastruridae, Onychiuridae, Isotomidae, Entomobryidae, and Katiannidae. Soils were also characterized by means of physical and chemical analyses. The index of degree of change of diversity, was calculated. The results show that the biological index of degree of change can detect soil use effects on the collembolan community. Somewhat surprisingly the index showed that the diversity of collembolans is higher in the high anthropic impact site AG, followed by CG and being lower in lower impact sites, NG. The results also show that collembolan families respond differently to soil use. The families Hypogastruridae, Onychiuridae, and Isotomidae presented differences between systems. Therefore collembolan community structure can be a useful tool to assess agricultural practices´ impacts on soil.


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