Biology subjects

Compant, S.

Publications and source records attributed to Compant, S..

7 recordsLinked to original sources

bioRxiv2026

Comparative genomics of Cadophora luteo-olivacea reveals a divergent lineage, conserved functional repertoires, and strain-level variation in pathogenicity

Cadophora luteo-olivacea is an ecologically versatile fungus associated with grapevine trunk diseases, yet the extent to which strains from different hosts and environments differ in genome composition, functional potential, and pathogenicity remains poorly understood. Here, we performed a comparative genomic analysis of 12 C. luteo-olivacea isolates recovered from grapevine, almond, apple, Crocus bulbs, soil, air, wastewater, and deep-sea sediment. Genome assemblies were highly complete (BUSCO >99%) and ranged from 46.94 to 50.70 Mbp. Pairwise average nucleotide identity (ANI) revealed a cohesive 11-strain group and one markedly divergent strain, CBS 266.93. Phylogenomic analysis based on 2,645 single-copy orthologs further showed that CBS 266.93 lies outside the main C. luteo-olivacea clade and forms a sister relationship with Cadophora malorum, indicating that its taxonomic placement warrants reassessment. Across the remaining strains, broad functional conservation was observed, including similar KOG profiles, extensive carbohydrate-active enzyme repertoires (798-849 genes per genome), and abundant biosynthetic gene clusters (26-35 per genome). Transposable element content varied substantially among strains (0.67-4.45% of genome), but this variation did not parallel overall functional profiles. All isolates colonized grapevine leaves in vitro, although lesion severity differed significantly among strains, indicating conserved plant-colonizing capacity with quantitative variation in aggressiveness. Small RNA profiling of inoculated grapevine leaves further revealed isolate-associated differences in host miRNA family expression, particularly for miR398, miR827, and miR156. Together, these results show that most C. luteo-olivacea strains share a conserved genomic framework compatible with plant colonization, while retaining lineage-and strain-level phenotypic and host-associated variation.

genomics↗

bioRxiv2024

Genomic diversity in Paenibacillus polymyxa: Unveiling distinct species groups and functional variability

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 was repeatedly suggested for this species, the available genomic data is now sufficient to confidently segregate strains affiliated to P. polymyxa into two major species groups. As these strains exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic affiliation to facilitate reliable and durable approval as active ingredients. 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.

microbiology↗

bioRxiv2023

Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization

Trichoderma harzianum is a filamentous ascomycete frequently applied as biocontrol agent in agriculture. While mycoparasitism and antagonism of Trichoderma spp. against fungal pathogens are well known, early fungal responses to the presence of a plant await broader investigation. Analyzing early stages of plant-fungus communication we show that T. harzianum B97 chemotropically responds to a plant extract and that both plant and fungus alter secondary metabolite secretion upon recognition. We developed a strategy for omics-analysis simulating conditions of early plant recognition eliciting a chemotropic response in the fungus and found 102 genes to be differentially regulated, including nitrate and nitrite reductases. Additionally, the previously uncharacterized Plant Communication Associated (PCA) gene cluster was strongly induced upon recognition of the plant, comprises a palindromic DNA motif and was essential for plant colonization. The PCA-cluster is only present in the Harzianum clade of Trichoderma and closely related to a homologous cluster in Metarhizium spp. Horizontal gene transfer (HGT) was detected for PCA-cluster genes by plants, while the cluster in T. harzianum is likely under balancing or positive selection. Hence, the PCA-cluster mediates early fungus-plant chemical communication and may be responsible for the high potential of T. harzianum and closely related species for biocontrol applications. Plain language summaryInteractions of plants with fungi - beneficial or pathogenic - are crucial for the ecological function of both partners. Yet, the chemical "language" they use and how or when they use it is still insufficiently known. We describe discovery of a novel gene cluster, which is strongly induced upon plant recognition and essential for plant-fungal interkingdom interaction in the biocontrol-agent Trichoderma harzianum.

microbiology↗

bioRxiv2022

Paenibacillus xylinteritus sp. nov., a novel bacterial species isolated from grapevine wood

Bacteria naturally colonize grapevine wood, and some populations interact synergistically with fungal pathogens to promote wood degradation. In this study, we characterized a bacterial strain, designated S150T, isolated from the wood of grapevine cultivar Sauvignon Blanc. The strain was previously known as promoting wood degradation caused by the causal agent of white-rot, Fomitiporia mediterranea. Phylogenetic analysis based on the full-length 16S rRNA gene sequence showed that the strain S150T belonged to the genus Paenibacillus. Based on 16S rRNA gene sequences, S150T shared low sequence similarity values (between 96.5 and 97.5%) with closed recognized members of the genus (P. jilunlii Be17, P. tepidiphilus SYSU G01001, P. tengchongensis SYSU-G-01003, P. sonchi X19-5, P. helianthi P26E). The cell wall peptidoglycan of S150 contains meso-diaminopimelate. MK6 and MK7 are the two respiratory quinones. The main cellular fatty acids are iso-C16:0 and anteiso-C15:0. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, three amino phospholipids, two phospholipids and three polar lipids. The whole-genome is 7.45 Mb, with a G+C content of 52.54%. The average nucleotide identity (ANI) value between S150T and the closely related Paenibacillus member (P. sonchi X19-5) was 85.06%. Biochemical and physiological analyses revealed that strain S150T has different characteristics from reference strains Paenibacillus spp.. Phenotypic, phylogenetic and chemotaxonomic analyses show strain S150T is a novel species of the genus Paenibacillus, for which the name Paenibacillus xylinteritus is proposed.

microbiology↗

bioRxiv2021

Integration of chemosensing and carbon catabolite repression impacts fungal enzyme regulation and plant associations

Fungal metabolism and enzyme production are regulated by nutrient availability and by interactions with the living environment. We investigated the mechanisms underpinning adaptation of the biotechnological fungus Trichoderma reesei to decaying plant biomass versus living plants. We found that concentration-gated response to glucose, the main molecule sensed from dead plant biomass, is mediated by a conserved signaling pathway downstream of G protein-coupled receptors (GPCRs), while the carbon catabolite repressor CRE1 is critical for glucose concentration gating. The GPCRs CSG1 and CSG2 are further required for root colonization and formation of appressorium like structures on plant surfaces. Acceleration of sexual development in the presence of plant roots and their interactions with fruiting bodies indicates preferential association with plants. Our results reveal a complex sensing network governing resource distribution, enzyme production and fungal development that explains previously observed phenomena in fermentations and opens new perspectives for industrial strain improvement and agriculture.

microbiology↗

bioRxiv2019

Maternal effects and environmental filtering shape seed fungal communities in oak trees

O_LITrees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have received little attention.\nC_LIO_LITo unravel these processes, we analyzed the microbial communities of seeds collected in populations of sessile oak (Quercus petraea) growing along elevation gradients. We focused on the fungal communities as this group includes seed pathogens. Ecological processes shaping the communities were quantified using joint species distribution models.\nC_LIO_LIFungi were present in all seed tissues, including the embryo. Fungal communities differed significantly among oak populations along the elevation gradients, and among mother trees within the same population. These maternal effects remained significant after seed fall, despite colonization by fungal species on the ground. Associations between tree pathogens and their antagonists were detected in the seeds.\nC_LIO_LIOur results demonstrate that both maternal effects and environmental filtering shape seed microbial communities of sessile oak. They provide a starting point for future research aimed at identifying the seed extended phenotypic traits that influence seed dispersal and germination, and seedling survival and growth across environments.\nC_LI

ecology↗

bioRxiv2019

Differences in resources use lead to coexistence of seed-transmitted microbial populations

Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.

plant biology↗