Alexandre Jousset

• Dr
• Professor (Assistant) at Utrecht University

Trophic interactions in micro‐food webs, such as those between nematodes and their bacterial prey, affect nitrogen cycling in soils, potentially changing nitrous oxide (N2O) production and consumption. However, how nematode‐mediated changes in soil bacterial community composition affect soil N2O emissions is largely unknown. Here, microcosm experim...

Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. S...

Abiotic and biotic soil properties are strong predictors of plant yield globally1-5, but they become unreliable over large areas when plant health is threatened by pathogen6-8. Here we present a novel approach to predict plant health based on spatiotemporal changes in soil chemical and biological properties. We first demonstrate that plant health a...

Predator–prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nemat...

Increasing drought events coupled with dwindling water reserves threaten global food production and security. This issue is exacerbated by the use of crops that overconsume water, undermining yield. We show here that microorganisms naturally associated with plant roots can undermine efficient water use, whereas modified bacteria can enhance it. We...

Understanding how microbiomes resist pathogen invasion remains a key challenge in natural ecosystems. Here, we combined genome-scale metabolic models with synthetic community experiments to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization prof...

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicte...

Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil pr...

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicte...

Plant growth-promoting rhizobacteria (PGPR) have been widely used for the promotion of plant performance. Predatory protists can influence the taxonomic and functional composition of rhizosphere bacteria. However, research on the impact of the interaction between protists and PGPR on plant performance remains at a very early stage. Here, we examine...

The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functional...

Anthropogenic activities such as long-term fertilizer application are known to lead to losses in above and belowground biodiversity, thereby negatively impacting ecosystem function. However, our understanding of the relative sensitivity of different soil organisms groups to increasing fertilizer application levels remains largely unknown. To addres...

The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt c...

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of synthesis enzymes can accurately be predicted....

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of synthesis enzymes can accurately be predicted....

Fusarium wilt disease of bananas, caused by the soil-borne pathogen Fusarium oxysporum, threatens banana production. Intercropping, cultivation of more than one crop simultaneously on the same field, has emerged as efficient and sustainable land management for suppressing Fusarium wilt disease. Although previous studies have proven the changes in s...

Overyielding, the high productivity of multispecies plant communities, is commonly seen as the result of plant genetic diversity. Here we demonstrate that biodiversity–ecosystem functioning relationships can emerge in clonal plant populations through interaction with microorganisms. Using a model clonal plant species, we found that exposure to vola...

Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90...

Unlocking the secrets of microbial interactions through genomics is pivotal for advancing microbial ecology. In most ecosystems, the scarcity of iron makes iron-mediated interactions a central theme in shaping microbial communities. Bacteria have evolved diverse strategies, including the production of siderophores, diverse secondary metabolites, to...

Microbial secondary metabolites have long been recognized as a rich source for pharmaceutical compound discovery and to have crucial ecological functions. However, the sequence-to-function mapping in microbial secondary metabolism pathways remains challenging because neither protein function nor substrate specificity can accurately be predicted fro...

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However , we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rh...

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transpos...

RIPENING-INHIBITOR (RIN) transcriptional factor is a central gene governing fruit ripening. While RIN also affects other physiological signals, its potential role in triggering interactions with rhizosphere microbiome and plant health is unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to rec...

Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve...

Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plan...

Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here we use Resource Availability (RA) as model parameter altering resistance...

Soil intrinsic heterogeneity affected the distribution of the microorganisms residing in it. Plants selectively recruit microorganisms for themselves from soil microbial reservoir. Currently, many studies looked into plant root associated microbial community as an entirety, assuming microorganisms uniformly distributing along the roots. However, th...

Microbiome transplants have the potential to disrupt agriculture and medicine by transferring the microbial genetic pool (and hence capabilities) from one host to another. Yet, for this technology to become reality, we need to understand the drivers shaping the success of microbiome transplant. We highlight here recent findings by Dr. Gaofei Jiang...

Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rh...

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance,...

Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth‐promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to...

Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However,...

While plant pathogens are traditionally controlled using synthetic agrochemicals the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant-growth-promoting bacteria (PGPBs) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to con...

Heterolobosea is one of the major protist groups in soils. While an increasing number of soil heterolobosean species has been described, we have likely only scratched the surface of heterolobosean diversity in soils. Here, we expand this knowledge by morphologically and molecularly classifying four novel strains. One was identified as Naegleria cla...

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between inoculated consortia members create conflicts for their survival and functioning. To circumvent this, we used transposon mutagenesis to incr...

Nutrient deficiencies are a major issue worldwide. Microorganisms can affect plant nutrition and may form the backbone of fortification strategies ensuring high nutritional values of grains and vegetables. However, to date it remains hard to harness this power. We surmise that this difficulty stems from the multiple different mechanisms involved in...

Protists are the most abundant and diverse eukaryotes that inhabit virtually all soils. They are active players in soil food webs as phototrophic algae, plant and animal parasites, and microbiome predators. As predators, protists lead to modification of their prey community composition typically promoting functions linked to (plant-)pathogen suppre...

Plant health largely depends on root-associated microorganisms that inhibit pathogens. Enriching the rhizosphere microbiome with beneficial bacteria has a high potential of supporting future sustainable food production. However, the introduced microorganisms often show low activity with a low survival rate. We propose to solve this limitation by co...

Mutation supply can influence evolutionary and thereby ecological dynamics in important ways which have received little attention. Mutation supply influences features of population genetics, such as the pool of adaptive mutations, evolutionary pathways and importance of processes, such as clonal interference. The resultant trait evolutionary dynami...

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant associated microbiome to deliver these functions is thus important for developing robust and sustainable crop production. However, it is y...

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hyp...

Plant rhizobiomes consist of microbes that are influenced by the physical, chemical, and biological properties of the plant root system. While plant-microbe interactions are generally thought to be local, accumulating evidence suggests that topologically disconnected bulk soil microbiomes could be linked with plants and their associated rhizospheri...

While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6...

Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics have led to the identification of...

The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links...

Mutation supply can influence eco-evolutionary dynamics in important ways which have received little attention. Mutation supply determines key features of population genetics, such as the pool of adaptive mutations, evolutionary pathways available, and importance of processes such as clonal interference. The resultant trait evolutionary dynamics, i...

There is a growing awareness that traits do not evolve individually but rather are organised as modular networks of co‐varying traits. While the importance of multi‐trait correlation has been linked to the ability to evolve in response to new environmental conditions, the evolvability of the network itself has to date rarely been assessed experimen...

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this e...

Even though beneficial plant-microbe interactions are commonly observed in nature, direct evidence for the evolution of bacterial mutualism in the rhizosphere remains elusive. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacterium evolves into mutualists in the rhizosphere of Arabidopsi...

Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics has led to the identification of...

Plant health is essential for food production, but plants are often affected by pathogens that can threaten plant performance including crop yield. Unfortunately, we can often only predict plant health when pathogens have infected plants and can no longer be controlled – and by then it is too late. To counteract pathogens, farmers often apply exten...

Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion p...

Microbes play an essential role in soil functioning including biogeochemical cycling and soil aggregate formation. Yet, a major challenge is to link microbes to higher trophic levels and assess consequences for soil functioning. Here, we aimed to assess how microbial consumers modify microbial community composition (PLFA markers), as well as C dyna...

Breeding better crops is a cornerstone of global food security. While efforts in plant genetic improvement show promise, it is increasingly becoming apparent that the plant phenotype should be treated as a function of the holobiont, in which plant and microbial traits are deeply intertwined. Using a minimal holobiont model, we track ethylene produc...

Plant pathogenic bacteria cause high crop and economic losses to human societies1-3. Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome4,5. This natural ecosystem is rarely studied experimentally at the microbiome-wide scale, and consequently we...

Plant‐derived low‐molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, most data are case‐specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low‐molecular weight co...

Psychrophilic bacteria are valuable biocatalysts to develop robust bioaugmentation formulations for enhanced wastewater treatment at low temperatures or fluctuating temperature conditions. Here, using different biodiversity indices [based on species richness (SR), phylogenetic diversity (PD) and functional diversity (FD)], we studied the effects of...

Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secr...

The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the...

Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between...

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent eff...

Background: Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key mic...

Abstract. The formation and stabilisation of soil macro-aggregates protects soils from erosion, a major worldwide threat on soils. While the role of bacteria and fungi in soil aggregation is well established, how predators feeding on microbes modify soil aggregation has hardly been tested. Here, we studied how predators modulate the effect of micro...

Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and poorly understood in natural rhizosphere microbiomes. We studied biocontrol efficacy of different phage combinations on Ralstonia solanacearum infection in tomato. Increasing the number of...

Plant-pathogen interactions are shaped by multiple environmental factors, making it difficult to predict disease dynamics even in relatively simple agricultural monocultures. Here, we explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. We found that the composition and functionin...

Growth-defense trade-offs are a major constraint on plant evolution. While the genetics of resource allocation is well established, the regulatory role of plant-associated microorganisms is still unclear. Here, we demonstrate that plant-associated microorganisms can reposition the plant phenotype along the same growth-defense tradeoff that determin...

Microorganisms drive several processes needed for robust plant growth and health.Harnessing microbial functions is thus key to productive and sustainable food production.Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a c...

Antibiosis and resource competition are major drivers shaping the assembly, diversity and functioning of microbial communities. While it is recognized that competition is sensitive to environmental conditions, it is unclear to what extent this mediated by the availability of different carbon resources. Here, we used a model laboratory system to dir...

The diversity-invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for...

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasio...

The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Her...

In natura, many organisms face multiple infections by pathogens. The ability of a pathogen to reinfect an already-infected host affects the genetic makeup of the pathogen population at the end of the infectious cycle. Despite the likely prevalence of this situation, the population dynamics of pathogens during multiple infections over time is still...

Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soi...

The concentration of atmospheric carbon dioxide (CO2) and polycyclic aromatic hydrocarbons (PAHs) contents in the environment have been rising due to human activities. Elevated CO2 (eCO2) levels have been shown to affect plant physiology and soil microbes, which may alter the degradation of organic pollutants. Here, we study the effect of eCO2 on P...

PAH contents and ANOVA analysis of seeds of rice grown under ambient and elevated CO2 conditions. aCO2, ambient CO2; eCO2, elevated CO2. NA, AP, AC, F, Phe, Ant, Fl, Pyr, BaA, Chr, BbF, BkF, BaP, IP, DBahA, BghiP represent Naphthalene, Acenaphthylene, Acenaphthene, Fluorene, Phenanthrene, Anthracene, Fluoranthene, Pyrene, Benzo(a)anthracene, Chryse...

Comparison of PAH contents in soils under ambient and elevated CO2 conditions in 2015 and 2016. aCO2, ambient CO2; eCO2, elevated CO2. NA, AP, AC, F, Phe, Ant, Fl, Pyr, BaA, Chr, BbF, BkF, BaP, IP, DBahA, BghiP represent Naphthalene, Acenaphthylene, Acenaphthene, Fluorene, Phenanthrene, Anthracene, Fluoranthene, Pyrene, Benzo(a)anthracene, Chrysene...

The concentrations of tropospheric CO2and O3have been rising due to human activities. These rising concentrations may have strong impacts on soil functions as changes in plant physiology may lead to altered plant-soil interactions. Here, the effects of eCO2and eO3on the removal of polycyclic aromatic hydrocarbon (PAH) pollutants in grassland soil w...

The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylen...

A number of rhizospheric bacterial strains (e.g. Bacillus spp., Pseudomonas spp.) have been identified for fostering plant health and are seen as potential candidates for biocontrol application. These candidates, however, often fail to efficiently support plant health under field conditions. The rhizosphere being a nutrient rich habitat in the soil...