Microbiology, Agricultural and Biological Sciences, Ecology
13
Scopus Publications
223
Scholar Citations
7
Scholar h-index
6
Scholar i10-index
Scopus Publications
Bacillus altitudinis GG-22: A novel plant growth-promoting bacterium with beneficial agronomic properties Ana Falcón-Piñeiro, Alberto Baños, Eva M. Molin, Elías González-Gragera, Annalisa Giampetruzzi, Raied Abou Kubaa, Livio Antonielli, Adrian Wallner, Günter Brader, Satish K. Verma, Antonio M. Martin-Platero, Manuel Martínez-Bueno, Stéphane Compant, Pasquale Saldarelli Biotechnology Reports, 2026 • Whole-genome sequencing confirmed GG-22 as Bacillus altitudinis . • Genome shows genes for siderophores, pumilacidin, pumilarin and VOCs. • GG-22 inhibited V. dahliae, Pythium sp. and F. oxysporum mycelial growth in vitro. • Treated olive trees showed early SAR activation and auxin pathway changes. • Transcriptome showed defense activation, but GG-22 did not reduce Xylella symptoms. Bacillus altitudinis GG-22, isolated from the phyllosphere of agricultural crops, has been identified as a promising biocontrol agent and plant growth-promoting bacterium with substantial potential in sustainable agriculture. In this study, whole-genome sequencing using Illumina technology, combined with ANI analysis, confirmed the strain's classification as B. altitudinis . The genome revealed a rich set of genes involved in biocontrol mechanisms, including the capacity of synthesis of siderophores (schizokinen and bacillibactin-like compounds), the lipopeptide pumilacidin, the bacteriocin pumilarin, alkylpyrones and Bacillus volatiles. In vitro antagonism assays demonstrated significant inhibitory effects against phytopathogenic fungi and oomycetes, such as Verticillium dahliae and Pythium sp., and B. altitudinis GG-22 also showed limited efficacy against bacterial phytopathogens, including Xylella fastidiosa . Transcriptomic profiling of olive trees treated with GG-22 indicated early activation of auxin transport and systemic acquired resistance (SAR) pathways, alongside substantial downregulation of cell wall remodelling genes. These findings suggest that B. altitudinis GG-22 primes plant defence responses and modulates hormonal pathways critical for growth and stress resilience. Future research should prioritize optimizing application strategies and exploring synergies with other microbial agents to fully harness the biocontrol and growth-promoting potential of B. altitudinis GG-22. This strain holds promise for sustainable agricultural practices, particularly in controlling fungal diseases and improving plant performance under stress conditions.
Endofungal bacteria: Emerging paradigms and future directions Adrian Wallner, Utkarsh Talukdar, Aurélie Deveau, Julia Buchner, Deepak Kumar, Pooja Shukla, Stéphane Compant, Satish K. Verma Microbiological Research, 2026 The colonization of fungal hyphae and spores by bacteria represents a widespread phenomenon with significant ecological and biotechnological implications across all surveyed fungal phyla. First thought to be restricted to Mollicutes and Burkholderiaceae -Related Endobacteria, these endofungal associations exhibit remarkable diversity, from simple uniform populations to complex communities, contradicting earlier assumptions of uniform populations. Acquisition dynamics demonstrate both ancient co-evolutionary relationships and recent horizontal transfer events, with environmental factors driving strain-level variation in symbiont presence even within the same fungal species. Fungi can harbor either uniform or diverse bacterial communities, sometimes within specialized structures, and exhibit varying degrees of dependence on their symbionts. These interactions can be mutualistic, commensal, or parasitic, influencing fungal physiology, metabolism, and ecological function. Yet the underlying mechanisms have been thoroughly characterized in only a few model systems in which endofungal bacteria have been shown to affect nutrient acquisition, stress tolerance, secondary metabolite production, and even fungal pathogenicity. In return, fungi offer a protective niche and promote dispersion. These concepts collectively illustrate the evolutionary flexibility and ecological importance of fungi-bacteria partnerships across terrestrial ecosystems. This review synthesizes emerging paradigms in endofungal bacteria research, integrating recent discoveries that challenge traditional assumptions about these symbioses. We examine host specificity patterns, acquisition mechanisms, and functional impacts while identifying critical knowledge gaps requiring investigation. A deeper understanding of these associations is essential to establish standardized frameworks for their applications in agriculture, medicine, and environmental sustainability. • Endofungal bacteria are widespread, diverse, and occur as obligate or transient symbionts across fungal phyla. • EFB communities range from simple host-specific partnerships to complex multi-phylum consortia. • Endofungal symbiosis is shaped by evolution and environment. • EFB have potential applications in agriculture, biotechnology, and medicine. • Knowledge gaps remain for many fungal lineages and for understanding how fungal holobionts assemble and affect host biology.
Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola Morgane Duret, Adrian Wallner, Ludovic Besaury, Aziz Aziz Environmental Microbiome, 2025 BACKGROUND: Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated. RESULTS: Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants. CONCLUSIONS: This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.
Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota David Labarga, Andreu Mairata, Miguel Puelles, Adrian Wallner, Aziz Aziz, Pou Alícia Microbiological Research, 2025 The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.
Genomic and metabolomic insights into the modes-of-action of bacterial strains to control the grapevine wood pathogen, Fomitiporia mediterranea Ouiza Mesguida, Stéphane Compant, Adrian Wallner, Livio Antonielli, Ryszard Lobinski, Simon Godin, Mickaël Le Bechec, Maxence Terrasse, Ahmed Taibi, Assia Dreux-Zigha, Jean-Yves Berthon, Rémy Guyoneaud, Patrice Rey, Eléonore Attard Microbiological Research, 2025 Grapevine trunk diseases (GTDs), particularly Esca, represent a major challenge for viticulture worldwide, leading to substantial economic losses. With no effective control treatments available, developing new methods such as biocontrol is crucial for managing GTDs. Our aim was to select biocontrol bacteria effective against the white-rot fungal pathogen Fomitiporia mediterranea (Fmed) and to investigate their mechanisms of action. A stepwise screening of 58 bacterial strains was conducted in vitro to assess their ability to inhibit Fmed growth through volatile and diffusible metabolites production. The screening was also done on wood sawdust from seven different grapevine cultivars. Out of 58 tested strains, 49 inhibited Fmed growth by over 50 % through their volatile organic compounds, only eight achieving this through their agar-diffusible metabolites. Pseudomonas lactis SV9, Pseudomonas paracarnis S45, and Paenibacillus polymyxa SV13 exhibited a strong efficacy in inhibiting Fmed on wood sawdust in a cultivar-dependent manner. We selected these strains for whole genome analysis and metabolomic profiling via LC-MS/MS for diffusible compounds and SPME GC-MS for volatile compounds. P. polymyxa SV13 inhibited Fmed primarily through diffusible metabolites, producing mainly fusaricidin-type compounds. Conversely, Pseudomonas strains acted mainly via their volatile metabolites, producing mainly the antifungal compound dimethyl disulfide. Genome analysis of the three bacterial strains revealed gene clusters responsible for regulating both direct and indirect mechanisms in biocontrol agents (BCAs). Our findings highlight the importance of comprehensive studies that combine in vitro experiments mimicking field conditions, with detailed investigations into modes of action to improve BCAs efficacy. • P. paracarnis S45 and P. lactis SV9 strongly inhabited F. mediterranea through their volatile organic compound. • P. polymyxa SV13 strongly inhibited F. mediterranea growth by producing diffusible metabolites. • The effectiveness of a bacterial strain in grapevine wood sawdust microcosms was cultivar-dependent. • Genomic analysis revealed that the genomes of the three strains harbor gene clusters encoding biocontrol functions. • Pseudomonas strains mainly produce dimethyl disulfide, while P. polymyxa SV13 produce fusaricidin. - P. paracarnis S45, P. lactis SV9 and P. polymyxa SV13 may impair the structural integrity of F. mediterranea .
Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability Adrian Wallner, Livio Antonielli, Ouiza Mesguida, Patrice Rey, Stéphane Compant BMC Genomics, 2024 Background Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses. Results Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients. Conclusions Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.
Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health Morgane Duret, Adrian Wallner, Marc Buée, Aziz Aziz Microbiological Research, 2024 Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.
Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia s.l. endophytes Eoghan King, Adrian Wallner, Ludivine Guigard, Isabelle Rimbault, Hugues Parrinello, Agnieszka Klonowska, Lionel Moulin, Pierre Czernic Scientific Reports, 2023 The plant microbiome has recently emerged as a reservoir for the development of sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes emerges as a critical issue to understand the molecular basis of plant-microbiota interactions. In this study, we combined root colonization, phenotypic and transcriptomic analyses to unravel the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these results indicate that a rice-non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while eliciting a markedly different response compared to rice-native Burkholderia s.l. strains. This demonstrates the variability of plant response to microbes from different hosts of origin. The most striking finding of the investigation was that a much more conserved response to the three endophytes used in this study is elicited in leaves compared to roots. In addition, transcriptional regulation of genes related to secondary metabolism, immunity, and phytohormones appear to be markers of strain-specific responses. Future studies need to investigate whether these findings can be extrapolated to other plant models and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.
Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species Adrian Wallner, Agnieszka Klonowska, Ludivine Guigard, Eoghan King, Isabelle Rimbault, Eddy Ngonkeu, Phuong Nguyen, Gilles Béna, Lionel Moulin Peer Community Journal, 2023 Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.
Bacillus altitudinis GG-22: A novel plant growth-promoting bacterium with beneficial agronomic properties A Falcón-Piñeiro, A Baños, EM Molin, E González-Gragera, ... Biotechnology Reports, e00945 , 2026 2026
Endofungal bacteria: Emerging paradigms and future directions A Wallner, U Talukdar, A Deveau, J Buchner, D Kumar, P Shukla, ... Microbiological Research, 128361 , 2025 2025 Citations: 2
Genomic and metabolomic insights into the modes-of-action of bacterial strains to control the grapevine wood pathogen, Fomitiporia mediterranea O Mesguida, S Compant, A Wallner, L Antonielli, R Lobinski, S Godin, ... Microbiological Research 293, 128085 , 2025 2025 Citations: 3
Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota D Labarga, A Mairata, M Puelles, A Wallner, A Aziz, P Alícia Microbiological Research 293, 128073 , 2025 2025 Citations: 6
Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola M Duret, A Wallner, L Besaury, A Aziz Environmental Microbiome 20 (1), 30 , 2025 2025 Citations: 5
Bajo la viña, una comunidad oculta lucha contra la sequía DL Varona, A Mairata, MPR de Gopegui, A Wallner, A Aziz, AP Mir Tierras: Agricultura, 62-65 , 2025 2025
Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health M Duret, A Wallner, M Buée, A Aziz Microbiological Research 287, 127860 , 2024 2024 Citations: 36
Genomic diversity in Paenibacillus polymyxa : unveiling distinct species groups and functional variability A Wallner, L Antonielli, O Mesguida, P Rey, S Compant BMC genomics 25 (1), 720 , 2024 2024 Citations: 7
Bacteria-fungi interactions and impacts on plant growth and health A Wallner, T Kiss, A del Barrio Duque, L Antonielli, A Sessitsch, ... XX International Plant Protection Congress–healthy Plants Support Human Welfare , 2024 2024
Root-associated microbiomes are influenced by grapevine genotype, disease expression and cultivation practices. M Duret, A Wallner, A Aziz 2023
Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia sl endophytes E King, A Wallner, L Guigard, I Rimbault, H Parrinello, A Klonowska, ... Scientific reports 13 (1), 10696 , 2023 2023 Citations: 13
Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species A Wallner, A Klonowska, L Guigard, E King, I Rimbault, E Ngonkeu, ... Peer Community Journal 3 , 2023 2023 Citations: 9
Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp. japonica and O. sativa subsp. indica … A Wallner, N Busset, J Lachat, L Guigard, E King, I Rimbault, P Mergaert, ... Applied and Environmental Microbiology 88 (14) , 2022 2022 Citations: 28
Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation A Wallner, L Moulin, N Busset, I Rimbault, G Béna Frontiers in microbiology 12, 761215 , 2021 2021 Citations: 14
Frontiers in the adaptation of rice-interacting burkholderia species: genetic and functional approaches A Wallner Université de Montpellier , 2020 2020
Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans A Wallner, E King, ELM Ngonkeu, L Moulin, G Béna BMC genomics 20 (1), 803 , 2019 2019 Citations: 67
Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic … E King, A Wallner, I Rimbault, C Barrachina, A Klonowska, L Moulin, ... Frontiers in plant science 10, 1141 , 2019 2019 Citations: 33
MOST CITED SCHOLAR PUBLICATIONS
Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans A Wallner, E King, ELM Ngonkeu, L Moulin, G Béna BMC genomics 20 (1), 803 , 2019 2019 Citations: 67
Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health M Duret, A Wallner, M Buée, A Aziz Microbiological Research 287, 127860 , 2024 2024 Citations: 36
Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic … E King, A Wallner, I Rimbault, C Barrachina, A Klonowska, L Moulin, ... Frontiers in plant science 10, 1141 , 2019 2019 Citations: 33
Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp. japonica and O. sativa subsp. indica … A Wallner, N Busset, J Lachat, L Guigard, E King, I Rimbault, P Mergaert, ... Applied and Environmental Microbiology 88 (14) , 2022 2022 Citations: 28
Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation A Wallner, L Moulin, N Busset, I Rimbault, G Béna Frontiers in microbiology 12, 761215 , 2021 2021 Citations: 14
Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia sl endophytes E King, A Wallner, L Guigard, I Rimbault, H Parrinello, A Klonowska, ... Scientific reports 13 (1), 10696 , 2023 2023 Citations: 13
Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species A Wallner, A Klonowska, L Guigard, E King, I Rimbault, E Ngonkeu, ... Peer Community Journal 3 , 2023 2023 Citations: 9
Genomic diversity in Paenibacillus polymyxa : unveiling distinct species groups and functional variability A Wallner, L Antonielli, O Mesguida, P Rey, S Compant BMC genomics 25 (1), 720 , 2024 2024 Citations: 7
Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota D Labarga, A Mairata, M Puelles, A Wallner, A Aziz, P Alícia Microbiological Research 293, 128073 , 2025 2025 Citations: 6
Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola M Duret, A Wallner, L Besaury, A Aziz Environmental Microbiome 20 (1), 30 , 2025 2025 Citations: 5
Genomic and metabolomic insights into the modes-of-action of bacterial strains to control the grapevine wood pathogen, Fomitiporia mediterranea O Mesguida, S Compant, A Wallner, L Antonielli, R Lobinski, S Godin, ... Microbiological Research 293, 128085 , 2025 2025 Citations: 3
Endofungal bacteria: Emerging paradigms and future directions A Wallner, U Talukdar, A Deveau, J Buchner, D Kumar, P Shukla, ... Microbiological Research, 128361 , 2025 2025 Citations: 2
Bacillus altitudinis GG-22: A novel plant growth-promoting bacterium with beneficial agronomic properties A Falcón-Piñeiro, A Baños, EM Molin, E González-Gragera, ... Biotechnology Reports, e00945 , 2026 2026
Bajo la viña, una comunidad oculta lucha contra la sequía DL Varona, A Mairata, MPR de Gopegui, A Wallner, A Aziz, AP Mir Tierras: Agricultura, 62-65 , 2025 2025
Bacteria-fungi interactions and impacts on plant growth and health A Wallner, T Kiss, A del Barrio Duque, L Antonielli, A Sessitsch, ... XX International Plant Protection Congress–healthy Plants Support Human Welfare , 2024 2024
Root-associated microbiomes are influenced by grapevine genotype, disease expression and cultivation practices. M Duret, A Wallner, A Aziz 2023
Frontiers in the adaptation of rice-interacting burkholderia species: genetic and functional approaches A Wallner Université de Montpellier , 2020 2020
