Spatial and seasonal determinants of Lyme borreliosis incidence in France, 2016 to 2021.

BackgroundLyme borreliosis (LB) is the most widespread hard tick-borne zoonosis in the northern hemisphere. Existing studies in Europe have focused mainly on acarological risk assessment, with few investigations exploring human LB occurrence.AimWe explored the determinants of spatial and seasonal LB variations in France from 2016 to 2021 by integrating environmental, animal, meteorological and anthropogenic factors, and then mapped seasonal LB risk predictions.MethodsWe fitted 2016-19 LB national surveillance data to a two-part spatio-temporal statistical model. Spatial and temporal random effects were specified using a Besag-York-Mollie model and a seasonal model, respectively. Coefficients were estimated in a Bayesian framework using integrated nested Laplace approximation. Data from 2020-21 were used for model validation.ResultsA high vegetation index (≥ 0.6) was positively associated with seasonal LB presence, while the index of deer presence (> 60%), mild soil temperature (15-22 °C), moderate air saturation deficit (1.5-5 mmHg) and higher tick bite frequency were associated with increased incidence. Prediction maps show a higher risk of LB in spring and summer (April-September), with higher incidence in parts of eastern, midwestern and south-western France.ConclusionWe present a national level spatial assessment of seasonal LB occurrence in Europe, disentangling factors associated with the presence and increased incidence of LB. Our findings yield quantitative evidence for national public health agencies to plan targeted prevention campaigns to reduce LB burden, enhance surveillance and identify further data needs. This approach can be tested in other LB endemic areas.

Design theory to better target public health priorities: An application to Lyme disease in France.

In the context of complex public health challenges led by interdependent changes such as climate change, biodiversity loss, and resistance to treatment, it is important to mobilize methods that guide us to generate innovative interventions in a context of uncertainty and unknown. Here, we mobilized the concept-knowledge (CK) design theory to identify innovative, cross-sectoral, and cross-disciplinary research and design programs that address the challenges posed by tick-borne Lyme disease in France, which is of growing importance in the French public health and healthcare systems. Within the CK methodological framework, we developed an iterative approach based on literature analysis, expert interviews, analysis of active French research projects, and work with CK experts to contribute to design "an action plan against Lyme disease." We produced a CK diagram that highlights innovative concepts that could be addressed in research projects. The outcome is discussed within four areas: (i) effectiveness; (ii) environmental sustainability in prevention actions; (iii) the promotion of constructive involvement of citizens in Lyme challenges; and (iv) the development of care protocols for chronic conditions with an unknown diagnosis. Altogether, our analysis questioned the health targets ranging from population to ecosystem, the citizen involvement, and the patient consideration. This means integrating social and ecological science, as well as the multidisciplinary medical patient journey, from the start. CK theory is a promising framework to assist public health professionals in designing programs for complex yet urgent contexts, where research and data collection are still not sufficient to provide clear guidance.

Exploring convolutional neural networks with transfer learning for diagnosing Lyme disease from skin lesion images.

BACKGROUND AND OBJECTIVE: Lyme disease which is one of the most common infectious vector-borne diseases manifests itself in most cases with erythema migrans (EM) skin lesions. Recent studies show that convolutional neural networks (CNNs) perform well to identify skin lesions from images. Lightweight CNN based pre-scanner applications for resource-constrained mobile devices can help users with early diagnosis of Lyme disease and prevent the transition to a severe late form thanks to appropriate antibiotic therapy. Also, resource-intensive CNN based robust computer applications can assist non-expert practitioners with an accurate diagnosis. The main objective of this study is to extensively analyze the effectiveness of CNNs for diagnosing Lyme disease from images and to find out the best CNN architectures considering resource constraints. METHODS: First, we created an EM dataset with the help of expert dermatologists from Clermont-Ferrand University Hospital Center of France. Second, we benchmarked this dataset for twenty-three CNN architectures customized from VGG, ResNet, DenseNet, MobileNet, Xception, NASNet, and EfficientNet architectures in terms of predictive performance, computational complexity, and statistical significance. Third, to improve the performance of the CNNs, we used custom transfer learning from ImageNet pre-trained models as well as pre-trained the CNNs with the skin lesion dataset HAM10000. Fourth, for model explainability, we utilized Gradient-weighted Class Activation Mapping to visualize the regions of input that are significant to the CNNs for making predictions. Fifth, we provided guidelines for model selection based on predictive performance and computational complexity. RESULTS: Customized ResNet50 architecture gave the best classification accuracy of 84.42% ±1.36, AUC of 0.9189±0.0115, precision of 83.1%±2.49, sensitivity of 87.93%±1.47, and specificity of 80.65%±3.59. A lightweight model customized from EfficientNetB0 also performed well with an accuracy of 83.13%±1.2, AUC of 0.9094±0.0129, precision of 82.83%±1.75, sensitivity of 85.21% ±3.91, and specificity of 80.89%±2.95. All the trained models are publicly available at https://dappem.limos.fr/download.html, which can be used by others for transfer learning and building pre-scanners for Lyme disease. CONCLUSION: Our study confirmed the effectiveness of even some lightweight CNNs for building Lyme disease pre-scanner mobile applications to assist people with an initial self-assessment and referring them to expert dermatologist for further diagnosis.

Are Orienteers Protected Enough against Tick Bites? Estimating Human Exposure to Tick Bites through a Participative Science Survey during an Orienteering Competition.

Mass-participation events in temperate forests are now well-established features of outdoor activities and represent high-risk activities regarding human exposition to tick bites. In this study we used a citizen science approach to quantify the space-time frequency of tick bites and undetected tick bites among orienteers that participated in a 6-day orienteering competition that took place in July 2018 in the forests of Eastern France, and we looked at the use and efficacy of different preventive behaviors. Our study confirms that orienteers are a high-risk population for tick bites, with 62.4% of orienteers bitten at least once during the competition, and 2.4 to 12.1 orienteers per 100 orienteers were bitten by ticks when walking 1 km. In addition, 16.7% of orienteers bitten by ticks had engorged ticks, meaning that they did not detect and remove their ticks immediately after the run. Further, only 8.5% of orienteers systematically used a repellent, and the use of repellent only partially reduced the probability of being bitten by ticks. These results represent the first attempt to quantify the risk of not immediately detecting a tick bite and provide rare quantitative data on the frequency of tick bites for orienteers according to walking distance and time spent in the forest. The results also provide information on the use of repellent, which will be very helpful for modeling risk assessment. The study also shows that prevention should be increased for orienteers in France.

[The open labs Tous Chercheurs]. / Les laboratoires ouverts Tous Chercheurs.

TITLE: Les laboratoires ouverts Tous Chercheurs. ABSTRACT: L'enjeu d'une culture scientifique pour tous est d'importance face à la difficulté des citoyens à critiquer les données de la science avec des arguments rationnels, notamment en ce qui concerne la biologie et la santé (vaccination, procréation médicalement assistée, etc.), car le grand public ne veut plus croire sur parole ce que disent les experts. Dans ce contexte, rapprocher les citoyens de la recherche scientifique représente un réel défi pour l'avenir, que les laboratoires ouverts Tous Chercheurs1 ont voulu relever.

Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica.

Yeasts play a crucial role in cheese ripening. They contribute to the curd deacidification, the establishment of acid-sensitive bacterial communities, and flavour compounds production via proteolysis and catabolism of amino acids (AA). Negative yeast-yeast interaction was observed between the yeast Yarrowia lipolytica 1E07 (YL1E07) and the yeast Debaryomyces hansenii 1L25 (DH1L25) in a model cheese but need elucidation. YL1E07 and DH1L25 were cultivated in mono and co-cultures in a liquid synthetic medium (SM) mimicking the cheese environment and the growth inhibition of DH1L25 in the presence of YL1E07 was reproduced. We carried out microbiological, biochemical (lactose, lactate, AA consumption and ammonia production) and transcriptomic analyses by microarray technology to highlight the interaction mechanisms. We showed that the DH1L25 growth inhibition in the presence of YL1E07 was neither due to the ammonia production nor to the nutritional competition for the medium carbon sources between the two yeasts. The transcriptomic study was the key toward the comprehension of yeast-yeast interaction, and revealed that the inhibition of DH1L25 in co-culture is due to a decrease of the mitochondrial respiratory chain functioning.

Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development.

Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities.

Soil is composed of a mosaic of different rocks and minerals, usually considered as an inert substrata for microbial colonization. However, recent findings suggest that minerals, in soils and elsewhere, favour the development of specific microbial communities according to their mineralogy, nutritive content, and weatherability. Based upon recent studies, we highlight how bacterial communities are distributed on the surface of, and in close proximity to, minerals. We also consider the potential role of the mineral-associated bacterial communities in mineral weathering and nutrient cycling in soils, with a specific focus on nutrient-poor and acidic forest ecosystems. We propose to define this microbial habitat as the mineralosphere, where key drivers of the microbial communities are the physicochemical properties of the minerals.

Pseudomonas fluorescens pirates both ferrioxamine and ferricoelichelin siderophores from Streptomyces ambofaciens.

Iron is essential in many biological processes. However, its bioavailability is reduced in aerobic environments, such as soil. To overcome this limitation, microorganisms have developed different strategies, such as iron chelation by siderophores. Some bacteria have even gained the ability to detect and utilize xenosiderophores, i.e., siderophores produced by other organisms. We illustrate an example of such an interaction between two soil bacteria, Pseudomonas fluorescens strain BBc6R8 and Streptomyces ambofaciens ATCC 23877, which produce the siderophores pyoverdine and enantiopyochelin and the siderophores desferrioxamines B and E and coelichelin, respectively. During pairwise cultures on iron-limiting agar medium, no induction of siderophore synthesis by P. fluorescens BBc6R8 was observed in the presence of S. ambofaciens ATCC 23877. Cocultures with a Streptomyces mutant strain that produced either coelichelin or desferrioxamines, as well as culture in a medium supplemented with desferrioxamine B, resulted in the absence of pyoverdine production; however, culture with a double mutant deficient in desferrioxamines and coelichelin production did not. This strongly suggests that P. fluorescens BBbc6R8 utilizes the ferrioxamines and ferricoelichelin produced by S. ambofaciens as xenosiderophores and therefore no longer activates the production of its own siderophores. A screening of a library of P. fluorescens BBc6R8 mutants highlighted the involvement of the TonB-dependent receptor FoxA in this process: the expression of foxA and genes involved in the regulation of its biosynthesis was induced in the presence of S. ambofaciens. In a competitive environment, such as soil, siderophore piracy could well be one of the driving forces that determine the outcome of microbial competition.

Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus Laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria.

Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell-cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.

Bacteria associated with truffle-fruiting bodies contribute to truffle aroma.

Truffles, symbiotic fungi renown for the captivating aroma of their fruiting bodies, are colonized by a complex bacterial community of unknown function. We characterized the bacterial community of the white truffle Tuber borchii and tested the involvement of its microbiome in the production of sulphur-containing volatiles. We found that sulphur-containing volatiles such as thiophene derivatives, characteristic of T. borchii fruiting bodies, resulted from the biotransformation of non-volatile precursor(s) into volatile compounds by bacteria. The bacterial community of T. borchii was dominated by α- and ß-Proteobacteria. Interestingly, all bacteria phyla/classes tested in this study were able to produce thiophene volatiles from T. borchii fruiting body extract, irrespective of their isolation source (truffle or other sources). This indicates that the ability to produce thiophene volatiles might be widespread among bacteria and possibly linked to primary metabolism. Treatment of fruiting bodies with antibacterial agents fully suppressed the production of thiophene volatiles while fungicides had no inhibitory effect. This suggests that during the sexual stage of truffles, thiophene volatiles are exclusively synthesized by bacteria and not by the truffle. At this stage, the origin of thiophenes precursor in T. borchii remains elusive and the involvement of yeasts or other bacteria cannot be excluded.

Gluconic acid-producing Pseudomonas sp. prevent γ-actinorhodin biosynthesis by Streptomyces coelicolor A3(2).

Streptomyces are ubiquitous soil bacteria well known for their ability to produce a wide range of secondary metabolites including antibiotics. In their natural environments, they co-exist and interact with complex microbial communities and their natural products are assumed to play a major role in mediating these interactions. Reciprocally, their secondary metabolism can be influenced by the surrounding microbial communities. Little is known about these complex interactions and the underlying molecular mechanisms. During pairwise co-culture experiments, a fluorescent Pseudomonas, Pseudomonas fluorescens BBc6R8, was shown to prevent the production of the diffusible blue pigment antibiotic γ-actinorhodin by Streptomyces coelicolor A3(2) M145 without altering the biosynthesis of the intracellular actinorhodin. A mutant of the BBc6R8 strain defective in the production of gluconic acid from glucose and consequently unable to acidify the culture medium did not show any effect on the γ-actinorhodin biosynthesis in contrast to the wild-type strain and the mutant complemented with the wild-type allele. In addition, when glucose was substituted by mannitol in the culture medium, P. fluorescens BBc6R8 was unable to acidify the medium and to prevent the biosynthesis of the antibiotic. All together, the results show that P. fluorescens BBc6R8 impairs the biosynthesis of the lactone form of actinorhodin in S. coelicolor by acidifying the medium through the production of gluconic acid. Other fluorescent Pseudomonas and the opportunistic pathogen Pseudomonas aeruginosa PAO1 also prevented the γ-actinorhodin production in a similar way. We propose some hypotheses on the ecological significance of such interaction.

Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles.

Although truffles are cultivated since decades, their life cycle and the conditions stimulating ascocarp formation still remain mysterious. A role for bacteria in the development of several truffle species has been suggested but few is known regarding the natural bacterial communities of Périgord Black truffle. Thus, the aim of this study was to decipher the structure and the functional potential of the bacterial communities associated to the Black truffle in the course of its life cycle and along truffle maturation. A polyphasic approach combining 454-pyrosequencing of 16S rRNA gene, TTGE, in situ hybridization and functional GeoChip 3.0 revealed that Black truffle ascocarps provide a habitat to complex bacterial communities that are clearly differentiated from those of the surrounding soil and the ectomycorrhizosphere. The composition of these communities is dynamic and evolves during the maturation of the ascocarps with an enrichment of specific taxa and a differentiation of the gleba and peridium-associated bacterial communities. Genes related to nitrogen and sulphur cycling were enriched in the ascocarps. Together, these data paint a new picture of the interactions existing between truffle and bacteria and of the potential role of these bacteria in truffle maturation.

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay.

Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere.

Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems.

Unlike farmland, forests growing on acidic soils are among the terrestrial ecosystems that are the least influenced or amended by man. Forests which developed on acidic soils are characterized by an important stock of inorganic nutrients entrapped in poorly weatherable soil minerals. In this context, the mineral-weathering process is of great importance, since such minerals are not easily accessible to tree roots. To date, several bacterial genera have been noted for their ability to weather minerals and, in the case of some of them, to improve tree nutrition. Nevertheless, few studies have focused their analyses on mineral-weathering bacterial communities in relation to geochemical cycles and soil characteristics, their ecological origin, associated tree species and forest management practices. Here we discuss the heterogeneity of the mineral-weathering process in forest soils and present what is known concerning the taxonomic and functional characteristics of mineral-weathering bacteria, as well as the different locations where they have been isolated in forest soils. We also discuss the biotic and abiotic factors that may influence the distribution of these bacteria, such as the effect of tree species or forest management practices.

Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis.

The Mycorrhiza Helper Bacterium (MHB) Pseudomonas fluorescens BBc6R8 promotes the ectomycorrhizal symbiosis between Douglas fir roots and Laccaria bicolor. In this study, we identified a non-flagellar type III secretion system (T3SS) in the draft genome of BBc6R8 similar to that described in the biocontrol strain P. fluorescens SBW25. We examined whether this T3SS plays a role in the BBc6R8 mycorrhizal helper effect by creating a deletion in the rscRST genes encoding the central channel of the injectisome. The in vitro effect of BBc6R8 T3SS mutants on the radial growth rate of L. bicolor was unchanged compared with the parental strain. In contrast, T3SS mutants were unable to promote mycorrhization, suggesting that type III secretion plays an important role in the mycorrhizal helper effect of P. fluorescens BBc6R8 independent of the promotion of hyphal growth that BBc6R8 exhibits in vitro.

Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere.

In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil.

Several reports have highlighted that forest soil samples are more phylum-rich than agricultural soil samples. However, little is known about the structure and richness of the bacterial communities in forest soil. Using high-throughput next generation 454 pyrosequencing, we deeply investigated the diversity of bacterial communities colonizing the oak rhizosphere niche and the surrounding soil. From three spatially independent soil samples, we obtained over 300 000 partial 16S rRNA gene sequences. The most abundant bacterial groups were the Acidobacteria, Proteobacteria and unclassified bacteria. Multifactorial analysis of the relative proportions of the different phyla revealed a net differentiation of the bacterial communities present in the rhizosphere and soil environments, suggesting an oak rhizosphere effect. Significantly more ß-, γ- and unclassified Proteobacteria inhabited the rhizosphere when compared with the surrounding soil. Conversely, significantly more unclassified bacteria were detected in the bulk soil than in the rhizosphere, demonstrating that the soil remains a challenging reservoir of complexity. This work increases our understanding of the niche effect on bacterial diversity and on the rare phylogenetic groups inhabiting the soil.

Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp.

Traits contributing to the competence of biocontrol bacteria to colonize plant roots are often induced in the rhizosphere in response to plant components. These interactions have been studied using the two partners in gnotobiotic systems. However, in nature, beneficial or pathogenic fungi often colonize roots. Influence of these plant-fungus interactions on bacterial behavior remains to be investigated. Here, we have examined the influence of colonization of wheat roots by the take-all fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Bacteria were inoculated onto healthy, early G. graminis var. tritici-colonized and necrotic roots and transcriptomes were compared by shotgun DNA microarray. Pf29Arp decreased disease severity when inoculated before the onset of necrosis. Necrotic roots exerted a broader effect on gene expression compared with early G. graminis var. tritici-colonized and healthy roots. A gene encoding a putative type VI secretion system effector was only induced in necrotic conditions. A common pool of Pf29Arp genes differentially expressed on G. graminis var. tritici-colonized roots was related to carbon metabolism and oxidative stress, with a highest fold-change with necrosis. Overall, the data showed that the association of the pathogenic fungus with the roots strongly altered Pf29Arp adaptation with differences between early and late G. graminis var. tritici infection steps.