Aymé Spor

French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Agroécologie

Background Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of i...

Interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can both occur through an independent evolution of the species composing the community and the interactions among them. In this study, we investigated how important the evolution of interspecific interactions wa...

Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-Eur...

Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function. Working with communities instead of individuals as selection units brings in additional sources of variation in the considered function that can influence...

In previous two-tier experiments designed to test agronomical (treated wastewater) and worst-case scenario (wastewater spiked with a mixture of 14 pharmaceuticals and personal care products (PPCPs) at 10 and 100 μg/L), 14 different wastewater-borne PPCPs accumulated in soil, lettuce roots, and leaves leading to a significant ecotoxicological impact...

The interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can not only occur through an evolution of the species composing the community but also of the interactions among them. In this study, we investigated how widespread was the evolution of interspecific intera...

Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use...

Artificial selection of microbiota opens new avenues for improving plants. However, reported results lack consistency. We hypothesised that the success in artificial selection of microbiota depends on the stabilisation of community structure. In a ten‐generation experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium d...

PurposeThe effect of plant species and genotypic diversity on productivity has been well documented but little is known about the contribution of the interaction between species and genotypic diversity. Since the influence of soil microorganisms on the plant diversity-productivity relationship is increasingly recognized, we investigated potential i...

Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function (i.e. community phenotype). Working with communities instead of individuals as selection units brings in additional sources of variation in the considered...

Phosphorus (P) acquisition is key for global food production. Arbuscular mycorrhizal fungi (AMF) help plants acquire P and are considered key for the design of sustainable agroecosystems. However, how the functioning of AMF varies across agricultural soils and responds to management practices is still unknown. Here, we collected soils from 150 cere...

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach base...

The responses of rhizosphere bacterial communities of Streptomyces (SS14 and IT20 stains) treated-pepper plants following inoculation by Phytophthora capsici (PC) was investigated using Illumina MiSeq sequencing. Distinct modulation of the bacteriome composition was found for PC samples with the highest relative abundance (RA) of Chitinophaga (22 ±...

Research on artificial selection of microbial community has become popular due to perspectives in improving plant and animal health ¹⁻⁴ . However, reported results still lack consistency ⁵⁻⁸ . We hypothesized that artificial selection may provide desired outcomes provided that microbial community structure has stabilized along the selection process...

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion...

One of the major problems with pesticides is linked to the non-negligible proportion of the sprayed active ingredient that does not reach its intended target and contaminates environmental compartments. Here, we have implemented and provided new insights to the preventive bioremediation process based on the simultaneous application of the pesticide...

In natural ecosystems, positive effects of plant diversity on ecosystem functioning have been widely observed, yet whether this is true in cropping systems remains unclear. Here we assessed the impact of crop diversification on soil microbial diversity, soil multifunctionality (SMF) and crop yields in 155 cereal fields across a 3,000 km north–south...

Maize cultivators often use β-triketone herbicides to prevent the growth of weeds in their fields. These herbicides target the 4-HPPD enzyme of dicotyledons. This enzyme, encoded by the hppd gene, is widespread among all living organisms including soil bacteria, which are considered as "non-target organisms" by the legislation. Within the framework...

We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.

Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum tur...

Microbial communities are continuously exposed to the arrival of alien species. In complex environments such as soil, the success of invasion depends on the characteristics of the habitat, especially the diversity and structure of the residing bacterial communities. While most data available on microbial invasion relies on experiments run under con...

Bacteriophages are viruses that infect and kill bacteria as a way to control their host populations. Complex soil microbial communities can be better understood by studying interactions between phages and bacteria. In a new paper, researchers quantified the extent to which phages drive the assembly and functioning of soil bacterial communities. The...

Background: Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic environments, but the current understanding of the role of phages in terrestrial ecosystems remains limited. Here, our objective wa...

The core microbiota defines the fraction of microorganisms common to all individuals from the same host species regardless of the abiotic context, be they located inside (e.g. animal guts) or outside (e.g. plant rhizospheres). While the core microbiota of many host species have been documented, no study attempted to decipher how these core microbio...

Microbial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQ...

Selection at the group level is proposed to be an evolutionary process occurring in the context of multilevel selection in natura. In artificial selection experiments, selecting at the community level can allow to find multispecies assemblages that are more efficient than a single species at solving a given problem. In such procedures, the main dif...

Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures var...

Microbial communities exert a pivotal role in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypot...

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively (1). While effects of indiv...

In the article listed above, Béatrice Morio was inadvertently identified in the byline as Béatrice Morio-Liondor. The authors apologize for the error. The online version of the article (https://doi.org/10.2337/db17-1488) has been updated to correct this omission.

There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate c...

The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these t...

Pesticides are intentionally applied to agricultural fields for crop protection. They can harm non-target organisms such as soil microorganisms involved in important ecosystem functions with impacts at the global scale. Within the frame of the pesticide registration process, the ecotoxicological impact of pesticides on soil microorganisms is still...

Altering the gut microbiome may be beneficial to the host, and it recently arose as a promising strategy to manage obesity. Here, we investigated the relative contribution of ω3 polyunsaturated fatty acid (PUFA)-mediated alterations in the microbiota to metabolic parameter changes in mice. Four groups were compared: male fat-1 transgenic mice (with...

The rapid expansion of perennial crops is a major threat to biodiversity in Southeast Asia. The biodiversity losses related to the conversion of forest lands to oil palm or rubber plantations (RP) are well documented by recent studies. However, the impact of the conversion from intensively managed annual crops to perennial crops on soil biodiversit...

Full paper available at: http://rdcu.be/HFqJ Changes in frequency and amplitude of rain events, that is, precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used 18O stable isotope probing (SIP) to investigate bacterial and fungal communi...

Agriculture is the main source of terrestrial N2 O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N2 O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N...

FREE PDF at: http://rdcu.be/pJTX Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential...

We report here the 7,259,392-bp draft genome of [i]Pseudomonas[/i] sp. strain ADP. This is a bacterial strain that was first isolated in the 1990s from soil for its ability to mineralize the herbicide atrazine. It has extensively been studied as a model to understand the atrazine biodegradation pathway. This genome will be used as a reference and c...

Agriculture is the main source of terrestrial emissions of N2O, a potent greenhouse gas and the main cause of ozone layer depletion. The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only biological process known to eliminate this greenhouse gas. Recent studies showed that a previously unknown cl...

N 2 O is a powerful greenhouse gas contributing both to global warming and ozone depletion. While fungi have been identified as a putative source of N 2 O, little is known about their production of this greenhouse gas. Here we investigated the N 2 O-producing ability of a collection of 207 fungal isolates. Seventy strains producing N 2 O in pure cu...

Nitrous oxide (N2O) is the predominant ozone-depleting substance and contributes approximately 6% to overall global warming1,2. Terrestrial ecosystems account for nearly 70% of total global N2O atmospheric loading, of which at least 45% can be attributed to microbial cycling of nitrogen in agriculture3. The reduction of N2O to nitrogen gas by micro...

Purpose Soil contamination by pollutants is increasing, urging for remediation strategies but little is known about the functional sustainability of these strategies. Materials and methods We assessed the resistance and resistance of a microbial respiratory process, denitrification, to two different levels of heat-drought disturbances among (1) the...

Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrai...

Listeria monocytogenes is a food-borne pathogen responsible for the potentially fatal disease listeriosis and terrestrial ecosystems have been hypothesized to be its natural reservoir. Therefore, identifying the key edaphic factors that influence its survival in soil is critical. We measured the survival of L. monocytogenes in a set of 100 soil sam...

The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of ge...

http://www.nature.com/ismej/journal/v7/n8/full/ismej201334a.html Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution a...

Many of the immune and metabolic changes occurring during normal pregnancy also describe metabolic syndrome. Gut microbiota can cause symptoms of metabolic syndrome in nonpregnant hosts. Here, to explore their role in pregnancy, we characterized fecal bacteria of 91 pregnant women of varying prepregnancy BMIs and gestational diabetes status and the...

Maintenance of a reduced body weight is accompanied by a decrease in energy expenditure beyond that accounted for by reduced body mass and composition, as well as by an increased drive to eat. These effects appear to be due--in part--to reductions in circulating leptin concentrations due to loss of body fat. Gut microbiota have been implicated in t...

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known or...

To what extent do host genetics control the composition of the gut microbiome? Studies comparing the gut microbiota in human twins and across inbred mouse lines have yielded inconsistent answers to this question. However, candidate gene approaches, in which one gene is deleted or added to a model host organism, show that a single host gene can have...

The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-y case study of the assembly of the human infant gut microbiome, to relate life events to microbiome composition and function. Sixty fecal samples were coll...

Periodontal disease has been associated with atherosclerosis, suggesting that bacteria from the oral cavity may contribute to the development of atherosclerosis and cardiovascular disease. Furthermore , the gut microbiota may affect obesity, which is associated with atherosclerosis. Using qPCR, we show that bacterial DNA was present in the atherosc...

We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems i...

Adaptation is the process whereby a population or species becomes better fitted to its habitat through modifications of various life history traits which can be positively or negatively correlated. The molecular factors underlying these covariations remain to be elucidated. Using Saccharomyces cerevisiae as a model system, we have investigated the...

Periodontal disease has been associated with atherosclerosis, suggesting that bacteria from the oral cavity may contribute to the development of atherosclerosis and cardiovascular disease. Furthermore, the gut microbiota may affect obesity, which is associated with atherosclerosis. Using qPCR, we show that bacterial DNA was present in the atheroscl...

Hierarchical Bayesian Modelling is powerful however under-used to model and evaluate the risks associated with the development of pathogens in food industry, to predict exotic invasions, species extinctions and development of emerging diseases, or to assess chemical risks. Modelling population dynamics of Saccharomyces cerevisiae considering its bi...