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

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Marie Simonin ◽  
Cindy Dasilva ◽  
Valeria Terzi ◽  
Eddy L M Ngonkeu ◽  
Diégane Diouf ◽  
...  
Keyword(s):  
Community Structure ◽  
Agricultural Practices ◽  
Plant Genotype ◽  
Wheat Genotype ◽  
Limited Effect ◽  
Data Set ◽  
Core Microbiome ◽  
Taxa Richness ◽  
Wheat Rhizosphere ◽  
Rhizosphere Microbiome

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.

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 ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Type ◽  
Agricultural Practices ◽  
Plant Genotype ◽  
Wheat Genotype ◽  
Limited Effect ◽  
Core Microbiome ◽  
Taxa Richness ◽  
Wheat Rhizosphere ◽  
Rhizosphere Microbiome

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

scholarly journals Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

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.

scholarly journals Plant genotype controls wetland soil microbial functioning in response to sea-level rise

2021 ◽  
Vol 18 (23) ◽  
pp. 6133-6146
Author(s):  
Hao Tang ◽  
Susanne Liebner ◽  
Svenja Reents ◽  
Stefanie Nolte ◽  
Kai Jensen ◽  
...  
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Microbial Community ◽  
Sea Level Rise ◽  
Sea Level ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
Litter Breakdown ◽  
Plant Genotype ◽  
Soil Microbial

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.

scholarly journals Agro-hydrology and multi-temporal high-resolution remote sensing: toward an explicit spatial processes calibration

2014 ◽  
Vol 18 (12) ◽  
pp. 5219-5237 ◽  
Author(s):  
S. Ferrant ◽  
S. Gascoin ◽  
A. Veloso ◽  
J. Salmon-Monviola ◽  
M. Claverie ◽  
...  
Keyword(s):  
High Resolution ◽  
Hydrological Model ◽  
A Priori ◽  
Agricultural Practices ◽  
Crop Growth ◽  
Data Set ◽  
Area Index ◽  
Field Level ◽  
Seeding Date ◽  
Crop Field

Abstract. The growing availability of high-resolution satellite image series offers new opportunities in agro-hydrological research and modeling. We investigated the possibilities offered for improving crop-growth dynamic simulation with the distributed agro-hydrological model: topography-based nitrogen transfer and transformation (TNT2). We used a leaf area index (LAI) map series derived from 105 Formosat-2 (F2) images covering the period 2006–2010. The TNT2 model (Beaujouan et al., 2002), calibrated against discharge and in-stream nitrate fluxes for the period 1985–2001, was tested on the 2005–2010 data set (climate, land use, agricultural practices, and discharge and nitrate fluxes at the outlet). Data from the first year (2005) were used to initialize the hydrological model. A priori agricultural practices obtained from an extensive field survey, such as seeding date, crop cultivar, and amount of fertilizer, were used as input variables. Continuous values of LAI as a function of cumulative daily temperature were obtained at the crop-field level by fitting a double logistic equation against discrete satellite-derived LAI. Model predictions of LAI dynamics using the a priori input parameters displayed temporal shifts from those observed LAI profiles that are irregularly distributed in space (between field crops) and time (between years). By resetting the seeding date at the crop-field level, we have developed an optimization method designed to efficiently minimize this temporal shift and better fit the crop growth against both the spatial observations and crop production. This optimization of simulated LAI has a negligible impact on water budgets at the catchment scale (1 mm yr−1 on average) but a noticeable impact on in-stream nitrogen fluxes (around 12%), which is of interest when considering nitrate stream contamination issues and the objectives of TNT2 modeling. This study demonstrates the potential contribution of the forthcoming high spatial and temporal resolution products from the Sentinel-2 satellite mission for improving agro-hydrological modeling by constraining the spatial representation of crop productivity.

scholarly journals Rhizosphere microbes and host plant genotype influence the plant metabolome and reduce insect herbivory

2018 ◽  
Author(s):  
Charley J. Hubbard ◽  
Baohua Li ◽  
Robby McMinn ◽  
Marcus T. Brock ◽  
Lois Maignien ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Flea Beetle ◽  
Insect Herbivory ◽  
Amplicon Sequencing ◽  
Plant Performance ◽  
Insect Herbivores ◽  
List Type ◽  
Plant Genotype ◽  
Herbivore Resistance ◽  
Rhizosphere Microbiome

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.

scholarly journals Dynamism of Landscape Transformation in Ibiono-Ibom, Akwa-Ibom State, Nigeria

2021 ◽  
Vol 14 (1) ◽  
pp. 19-38
Author(s):  
Orimoogunje Oluwagbenga O. Isaac ◽  
Adeleke Benjamin Olufemi ◽  
Dada Emmanuel ◽  
Shote Adebola Adekunle ◽  
Eudoxie-Okafor Aniefiok Nene ◽  
...  
Keyword(s):  
Agricultural Land ◽  
Arable Land ◽  
Agricultural Practices ◽  
Household Survey ◽  
Biodiversity Loss ◽  
Remotely Sensed ◽  
Structured Interviews ◽  
Remotely Sensed Data ◽  
Data Set ◽  
Landscape Transformation

Abstract Studies have shown that information on landscape transformation is an important benchmark data set because of its value as an environmental change indicator. Therefore, dynamism of landscape transformation over a 34-year period are analysed for a case study in Ibiono-Ibom, Akwa-Ibom State, Nigeria. The study adopted a mixed method consisting of remote sensing and GIS-based analysis, and semi-structured interviews covering 400 households while factors contributing to landscape structures and changes are studied. The results point out three main driving factors responsible for the landscape transformation in the study area: agricultural practices which lead to intensification of forest resources, riparian vegetation, vegetated wetlands and non-vegetated wetlands; urbanization which modifies the structure and morphology of the landscape, and finally, population growth directly related to massive infrastructural development which encroached on all other land spaces. GIS-based analysis of remotely-sensed data showed that built-up area had increased by 7535.2 ha between 1986 and 2020; shrub and arable land by 1343.9 ha and light forest decreased by 4998.3 ha. While bare-land reduced by 1522.1 ha; vegetated wetland reduced by 1092 ha; water body coverage reduced by 168 ha and non-vegetated wetland size also reduced by 2029.4 ha. Analysis of household survey results revealed that the perceptions of respondents validate the observed patterns during the remotely-sensed data analysis phase of the research, with 54 % (n=400) of respondents reporting a decline in agricultural land use, and 19.3 % (n=400) observing a decline in forest areas in the study area. Furthermore, agricultural intensification, urban development, timber exploitation, firewood collection and increase in settlements were identified as the proximate drivers of these observed landscape transformation dynamics in the study area. The study concluded that the variation in landscape transformation of the study area are clear indication of the extent of biodiversity loss and ecosystem degradation in the study area.

scholarly journals The degree of change of collembolan community structure related to anthropic soil disturbance

2014 ◽  
Author(s):  
Rosana V Sandler ◽  
Liliana B Falco ◽  
César A Di Ciocco ◽  
Ricardo Castro-Huerta ◽  
Carlos E Coviella
Keyword(s):  
Community Structure ◽  
Soil Structure ◽  
Management Practices ◽  
Soil Fauna ◽  
Agricultural Practices ◽  
Nutrient Content ◽  
Soil Disturbance ◽  
Biological Index ◽  
Collembolan Community ◽  
Physical And Chemical

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.

scholarly journals Diversity Patterns and Community Structure of the Ground-Associated Macrofauna along the Beach-Inland Transition Zone of Small Tropical Islands

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 377
Author(s):  
Sebastian Steibl ◽  
Robert Sigl ◽  
Paul E. Bräumer ◽  
Victoria Clauß ◽  
Simon Goddemeier ◽  
...  
Keyword(s):  
Community Structure ◽  
Transition Zone ◽  
Environmental Parameters ◽  
Gradual Change ◽  
Small Islands ◽  
Tropical Islands ◽  
Diversity Patterns ◽  
Transition Zones ◽  
Taxa Richness ◽  
Insular Ecosystems

Biodiversity follows distinct and observable patterns. Where two systems meet, biodiversity is often increased, due to overlapping occurrence ranges and the presence of specialized species that can tolerate the dynamic conditions of the transition zone. One of the most pronounced transition zones occurs at shores, where oceans and terrestrial habitat collide, forming the shore–inland transition zone. The relevance of this transition zone in shaping a system’s community structure is particularly pronounced on small islands due to their high shore-to-inland-area ratio. However, the community structure of insular faunas along this transition zone is unknown. Here, we investigated the diversity patterns along the beach–inland transition zone of small islands and tested the hypothesis that species diversity increases toward the transition zone where beach and interior habitat meet. By measuring environmental parameters, resource availability, and ground-associated macrofauna diversity along transects running across the beach–inland transition zone, we show that a gradual change in species composition from beach to the inland exists, but neither taxa richness, diversity, nor overall abundance changed significantly. These findings offer important insights into insular community structure at the transition zone from sea to land that are relevant to better understand the dynamic and unique characteristics of insular ecosystems.

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