7 research outputs found
The wheat microbiome and its associated Pseudomonas
No full textIn the quest for sustainable agriculture, this thesis examines the role of biological control agents (BCAs), focusing on beneficial Pseudomonas within the cereal phytobiome. Our research began with the isolation and in vitro characterization of various Pseudomonas strains, revealing an unexpected abundance of P. sivasensis across all tested field locations and plant compartments. This led to the discovery of a new species closely related to P. sivasensis, designated P. arvensis sp. nov. P. sivasensis strain CF10PS3 stood out for its biocontrol potential and plant colonization capabilities. A novel qPCR probe protocol was developed to specifically detect and quantify the CF10PS3 strain, distinguishing it from naturally occurring counterparts. Strain CF10PS3 was sprayed onto wheat leaves in the field to monitor its persistence in the phyllosphere and assess its impact on existing microbial communities through a newly developed bioinformatic pipeline for species-level metagenomic evaluation. The study explored the ecological effects of introducing CF10PS3, evaluating its colonization efficiency, impact on native microbiota, and its role in modifying microbial community structures crucial for plant health. Our findings indicate that the strain CF10PS3 dynamically affects the phyllospheric microbial landscape, initially causing detriment to many species before shifting to a more balanced interaction, eventually promoting several species. These results underscore the capability of BCAs like strain CF10PS3 to act as precise microbiome modifiers, selectively enhancing beneficial microbial interactions without broadly altering overall community structure. This study advances our understanding of microbial dynamics in the phyllosphere and highlights the importance of integrating microbial management strategies into sustainable crop cultivation practices.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 202
Monitoring the Persistence of Pseudomonas sivasensis Strain CF10PS3 in Cereal Fields
No full textABSTRACT The persistence and efficacy of biocontrol agents in agricultural fields are crucial for sustainable crop production. In this study, we investigated the persistence of the introduced bacterial strain Pseudomonas sivasensis CF10PS3 in the wheat phyllosphere using a novel qPCR probe protocol. The CF10PS3 strain, known for its in vitro biocontrol properties against wheat pathogens, was applied through foliar spray, and its persistence was monitored over 7 weeks. Our qPCR assays, designed to specifically detect CF10PS3, distinguished it from naturally occurring P. sivasensis strains, providing precise insights into its dynamics in the field. The experimental results indicated that CF10PS3 was already present on the wheat leaves before its application, suggesting its natural adaptation to the foliar environment. Following initial application, a significant increase in CF10PS3 was observed, though subsequent environmental factors such as rain and wind might have caused notable fluctuations in its population. Despite these variations, the introduced strain showed considerable persistence, with population levels significantly higher than those in untreated plots by the end of the study period. This research underscores the importance of understanding bacteria dynamics in the field, highlighting the influence of environmental conditions on their efficacy. The use of specific qPCR probes proved effective in monitoring introduced strains, offering valuable insights for optimizing biocontrol agent application strategies. Our findings contribute to the development of robust biocontrol methods, promoting sustainable agricultural practices and enhancing crop protection
Plant Microbiota Beyond Farming Practices: A Review
No full textPlants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspectiv
PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences
Get PDFBackgroundThe study of sample taxonomic composition has evolved from direct observations and labor-intensive morphological studies to different DNA sequencing methodologies. Most of these studies leverage the metabarcoding approach, which involves the amplification of a small taxonomically-informative portion of the genome and its subsequent high-throughput sequencing. Recent advances in sequencing technology brought by Oxford Nanopore Technologies have revolutionized the field, enabling portability, affordable cost and long-read sequencing, therefore leading to a significant increase in taxonomic resolution. However, Nanopore sequencing data exhibit a particular profile, with a higher error rate compared with Illumina sequencing, and existing bioinformatics pipelines for the analysis of such data are scarce and often insufficient, requiring specialized tools to accurately process long-read sequences.ResultsWe present PRONAME (PROcessing NAnopore MEtabarcoding data), an open-source, user-friendly pipeline optimized for processing raw Nanopore sequencing data. PRONAME includes precompiled databases for complete 16S sequences (Silva138 and Greengenes2) and a newly developed and curated database dedicated to bacterial 16S-ITS-23S operon sequences. The user can also provide a custom database if desired, therefore enabling the analysis of metabarcoding data for any domain of life. The pipeline significantly improves sequence accuracy, implementing innovative error-correction strategies and taking advantage of the new sequencing chemistry to produce high-quality duplex reads. Evaluations using a mock community have shown that PRONAME delivers consensus sequences demonstrating at least 99.5% accuracy with standard settings (and up to 99.7%), making it a robust tool for genomic analysis of complex multi-species communities.ConclusionPRONAME meets the challenges of long-read Nanopore data processing, offering greater accuracy and versatility than existing pipelines. By integrating Nanopore-specific quality filtering, clustering and error correction, PRONAME produces high-precision consensus sequences. This brings the accuracy of Nanopore sequencing close to that of Illumina sequencing, while taking advantage of the benefits of long-read technologies
Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.
No full textThe role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management
