Laurent Philippot

• PhD
• Research Director at French National Institute for Agriculture, Food, and Environment (INRAE)

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...

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...

Nitrogen is the major nutrient limiting plant growth in terrestrial ecosystems, and the transformation of inert nitrogen to forms that can be assimilated by plants is mediated by soil micro‐organisms. The last decade has witnessed many significant advances in our understanding of plant–microbe interactions with evidence that plants have evolved mul...

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...

Highly diverse and abundant organisms coexist in soils. However, the contribution of biotic interactions between soil organisms to microbial community assembly remains to be explored. Here, we assess the extent to which soil fauna can shape microbial community assembly using an exclusion experiment in a grassland field to sort soil biota based on b...

Coalescence events, which consist in the mixing of previously separated communities, are frequent in nature or as a result of human activities. Despite recently gaining attention as a tool to test ecological theories and engineer microbial communities, little is known about the factors that influence the outcome of such coalescence events. Here, we...

Denitrification, a major source of gaseous nitrogen (N) emissions from agricultural soils, is influenced by management. Practices promoting belowground diversity are suggested to support sustainable agriculture, but their ability to modulate gaseous N-losses via denitrification remains inconclusive. To fill this knowledge gap, we sampled 106 cereal...

This paper assesses the effect of long-term contrasting tillage practices on topsoil structural characteristics critical for nitrous oxide (N 2 O) emissions and carbon sequestration across a pedoclimatic gradient. The hypotheses tested are that: (i) aeration is greater in the topsoil of ploughed (to 0.20-0.30 m depth) than in no-till soils and (ii)...

Introduction Improving soil health while maintaining crop yield is a key challenge for farmers. So far, only a few studies assessed the effects of compost and solid digestate application on soil health and plant yield under practical on‐farm conditions across both organic and conventional cropping systems. Materials and Methods This study examined...

Introduction Increasing soil organic carbon (SOC) in croplands is a natural climate mitigation effort that can also enhance crop yields. However, there is a lack of comprehensive field studies examining the impact of SOC on crop yields across wide climatic, soil, and farming gradients. Furthermore, it is largely unknown how water retention, soil mi...

Despite the rapid development of microbial inoculants use, their effectiveness still lacks robustness, partly due to our limited understanding of the factors influencing their establishment in soil. Recurrent inoculation can temporarily increase their abundance, but the effect of this inoculation strategy on plant growth and on the resident microbi...

Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulat...

Interactions between plants and microorganisms are pivotal for plant growth and productivity. Several plant molecular mechanisms that shape these microbial communities have been identified. However, the importance of nitric oxide (NO) produced by plants for the associated microbiota remains elusive. Using Arabidopsis thaliana isogenic mutants overp...

Nitric oxide (NO) is a key substance in atmospheric chemistry, influencing the formation and destruction of tropospheric ozone and the atmosphere's oxidizing capacity. It also affects the physiological functions of organisms. NO is produced, consumed, and emitted by soils, the effects of soil NO concentrations on microbial C and N cycling and assoc...

The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarit...

Protists, a crucial part of the soil food web, are increasingly acknowledged as significant influencers of nutrient cycling and plant performance in farmlands. While topographical and climatic factors are often considered to drive microbial communities on a continental scale, higher trophic levels like heterotrophic protists also rely on their food...

Background Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil coloniza...

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasin...

Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. F...

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil...

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil...

Environmental factors (e.g., climate and edaphic factors) indirectly regulate residue decomposition via microbial communities. Microbial ecological clusters (eco-clusters) structured by specific environmental factors have consequences for ecosystem functions. However, less is known about how microbial eco-clusters affect residue decomposition, espe...

Organic carbon and aggregate stability are key features of soil quality and important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here we...

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...

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...

Tetracyclines are the most widely used antibiotics worldwide. Their presence in soils could affect nutrient cycling, but our knowledge regarding how they affect soil microbial communities involved in greenhouse gas emissions is limited. The objective of the current study was to evaluate how tetracycline is affecting N2O emissions and the abundance...

NIs could improve N use efficiency and decelerate N cycling. Still, we know little about their activity on the distinct AOM groups and about their effects on off-target soil microorganisms.

Microbiomes are important for crop performance. However, a deeper knowledge of crop-associated microbial communities is needed to harness beneficial host-microbe interactions. Here, by assessing the assembly and functions of maize microbiomes across soil types, climate zones, and genotypes, we found that the stem xylem selectively recruits highly c...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation...

Large-scale information regarding nitrous oxide (N2O) emissions is needed as an evidence base to underpin land use policy and mitigation approaches. However, the highly variable rates of denitrification make the prediction of N2O emission demanding. Here, we evaluated the role of abiotic and biotic factors on the potential denitrification of Irish...

Relative microbiome profiling (RMP) using new sequencing approaches has limited capacity to detect shifts in microbial abundances. The growing need for absolute abundances has led to advances in absolute microbiome profiling (AMP). However, the performance and universal applicability of these various AMP methods remain unclear. Here, the two most p...

Soil compaction caused by highly mechanized agriculture can constrain soil microbial diversity and functioning. Physical pressure on the soil decreases macropores and thereby limits oxygen diffusion. The associated shift from aerobic to anaerobic conditions can reduce nitrification and promote denitrification processes, leading to nitrogen (N) loss...

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...

Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia‐oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of enviro...

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...

The implementation of the new Water Reuse regulation in the European Union brings to the forefront the need to evaluate the risks of using wastewater for crop irrigation. Here, a two-tier ecotoxicological risk assessment was performed to evaluate the fate of wastewater-borne micropollutants in soil and their ecotoxicological impact on plants and so...

Although studied for more than a century, the spatial distribution of microorganisms in a root system still remains partly understood. In a repeated greenhouse experiment using the model plant Brachypodium distachyon, we investigated the composition and distribution of rhizosphere bacteria and their response to inoculation with artificially selecte...

Plant roots are shaping microbial communities that are distinct from the surrounding soil. These root-associated microbial communities can have both positive and negative effects on the host nutrient acquisition and thereby growth, yet how loss of soil microbial diversity will constrain the plant microbiome selection is relatively unknown. In this...

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...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovatio...

Shifts in the frequency and magnitude of rain events (precipitation patterns) associated with climate change may impact ecosystem nitrogen and carbon cycling through effects on plant physiology and soil microbial activity. Here, we determined how the combination of temporal irrigation distribution and N supply affects plant-microbial C and N dynami...

Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil micr...

Background: Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effec...

The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition...

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...

Plant functional traits affect soil nutrient cycling in many ecosystems, but high levels of diversity make it challenging to identify their influence in tropical rainforests. Here, we used a litter manipulation experiment to demonstrate that differences in litter chemistry alone are sufficient to drive changes in soil nitrogen (N) cycling within a...

The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the c...

Nitrification inhibitors have often been found to reduce nitrous oxide (N2O) emissions from agricultural soils, but N2O mitigation is variable and may depend on soil and climate variables. This study investigated how key abiotic factors modified the effect of Vizura®, a new formulation with the nitrification inhibitor 3,4-dimethylpyrazole phosphate...

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...

Minimizing nitrogen (N) losses and increasing plant N uptake in agroecosystems is a major global challenge. Ecological concepts from (semi)natural grasslands suggest that manipulating plant community composition using plant species with different traits may represent a promising opportunity to face this challenge. Here, we translate these trait‐bas...

In recent years there has been an upsurge of studies on ecosystem multifunctionality (EMF), or the ability of ecosystems to simultaneously provide multiple functions and/or services. The concept of EMF itself, the analytical approaches used to calculate it, and its implications depending on the spatial scale and field of study have been discussed i...

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...

Nitric Oxide (NO) is essential for plant growth and development, as well as interactions with abiotic and biotic environments. Its importance for multiple functions in plants means that tight regulation of NO concentrations are required. This is of particular significance in roots, where NO signalling is involved in processes, such as root growth,...

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...

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...

Intensive agriculture is dominated by monocultures of high‐yielding plants that receive large applications of nitrogen (N) fertilizers to boost plant productivity. However, these systems have low N use efficiency (NUE) as fertilized plants generally take up less than half of the N applied. A large fraction of the remainder N is susceptible to be lo...

Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide...

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...

Introduction. Shifts in the frequency and magnitude of rain events (precipitation regime) associated with climate change may affect plant morphological and physiological strategies as well as soil microbial activity. Objectives. The objective of this study was to determine i) how precipitation history shapes the response dynamics of soil bacterial...

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...

Though tropical forest ecosystems are among the largest natural sources of the potent greenhouse gas nitrous oxide (N2O), the spatial distribution of emissions across landscapes is often poorly resolved. Leaf cutter ants (LCA; Atta and Acromyrmex, Myrmicinae) are dominant herbivores throughout Central and SouthAmerica, and influencemultiple aspects...

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...

Tropical forests exhibit significant heterogeneity in plant functional and chemical traits that may contribute to spatial patterns of key soil biogeochemical processes, such as carbon storage and greenhouse gas emissions. Although tropical forests are the largest ecosystem source of nitrous oxide (N2O), drivers of spatial patterns within forests ar...

Tropical forests exhibit significant heterogeneity in plant functional and chemical traits that may contribute to spatial patterns of key soil biogeochemical processes, such as carbon storage and greenhouse gas emissions. Although tropical forests are the largest ecosystem source of nitrous oxide (N2O), drivers of spatial patterns within forests ar...

Tropical forests exhibit significant heterogeneity in plant functional and chemical traits that may contribute to spatial patterns of key soil biogeochemical processes, such as carbon storage and greenhouse gas emissions. Although tropical forests are the largest ecosystem source of nitrous oxide (N2O), drivers of spatial patterns within forests ar...

Climate change causes droughts, which in turn cause significant physiological stress for soil microorganisms. In this study, we investigated how the abundance of total bacterial, crenarchaeal and fungal communities and the abundance of N-cycling microbial guilds responded to a severe agricultural drought event in a long-term experiment of minimum t...

Microorganisms withthecapacitytoreducethegreenhousegasnitrousoxide (N2O) toharmlessdinitrogengasarereceivingincreasedattentiondueto increasing N2O emissions(andourneedtomitigateclimatechange)andto recent discoveriesofnovelN2O-reducing bacteriaandarchaea.Thediversityof denitrifying andnondenitrifyingmicroorganismswithcapacityforN2O reduc- tion wasre...

The relative contribution of fungi, bacteria, nirS and nirK denirifiers to nitrous oxide (N2O) emission with unknown isotopic signature from dairy manure compost was examined by selective inhibition (SI) technique. Chloramphenicol (CHP), cycloheximide (CYH), diethyldithiocarbamate (DDTC) were used to suppress the activity of bacteria, fungi and nir...

How plant species associations affect the rhizosphere microbiota, in comparison to each plant species, has been overlooked. Here we investigated how bi-species plant associations affect total bacterial and N-cycling microbial communities (nitrate reducers and ammonia-oxidizers), as an example of functional communities, at low and high soil N levels...

Spatial and temporal variations related to hydric seasonality in abundance and diversity of denitrifier communities were examined in sediments taken from two sites differing in nitrate concentration along a stream Doñana National Park during a 3-year study. We found a positive relationship between the relative abundance of denitrifiers, determined...

Ni-hyperaccumulators are ideal candidates for agromining on ultramafic Ni-rich soils where other technologies for metal recovery are economically unviable. However, agronomic practices can be optimised in order to fully develop agromining at a large scale. Nitrogen (N) supply is a relevant factor, since it is generally a limiting nutrient, and espe...

We assessed the impact of intercropping on the microbial communities in the rhizosphere of wheat (Triticum turgidum L. ssp durum) and pea (Pisum sativum L.). Using a RNA based approach coupled with bacterial phylum specific real time PCR, we found that the active bacterial communities in the wheat-pea association were distinct from those in the rhi...

Metagenomics continues to be one of the most dynamic scientific fields due largely to the development of new and cheaper sequencing technologies. The diversity of habitats explored with metagenomics and other meta-omics techniques has increased exponentially in recent years. The resulting cascade of data has led to a new range of methodological pro...