BioBits by Steve

The increasing prevalence of Ralstonia pseudosolanacearum phylotype I (phy I) in agricultural regions across Europe highlights the need for heightened awareness and preventive measures. Recent detections in multiple European countries span a range of agricultural systems, host plants, and natural aquatic environments. These findings have been linked either to infected plant material at import (interceptions) or to plants cultivated in specific European regions, often after importation of infected plant material. To investigate the genetic diversity of these emerging populations, we analysed whole-genome sequence (WGS) data from a collection of 62 R. pseudosolanacearum phy I isolates, including those recently obtained in various European countries, using average nucleotide analysis (ANI) and core genome multilocus sequence typing (cgMLST). ANI analysis revealed two distinct major clades: the r̈ose clade\", comprising isolates from rose, potato, surface water, and bittersweet, most closely matching with sequevar 33, and the m̈ajor ginger clade\", including isolates from members of the Zingiberaceae family, with the best match to sequevar 30. Additionally, several minor clades of Zingiberaceae isolates and a ẗomato clade\" (most closely related to sequevar 18) were identified. Pathogenicity assays with high inoculation titers were performed on tomato to assess the biological relevance of the observed genetic diversity. Our findings suggest multiple independent introduction events of virulent R. pseudosolanacearum phy I populations into Europe between 2015 and 2024. Given the genetic variability of the introduced bacterial isolates, the pathogen’s ability to systemically infect a broad range of host plants which can differ per isolate, and its persistence in diverse agricultural and environmental niches, the implementation of stringent import control measures for plant material entering the European Union is strongly recommended.

Despite the recognition of the complexity of soil ecosystem dynamics, most soil microbiome studies sample one field, take one sample per field, or use limited samples throughout the year. This limits our understanding of the spatiotemporal role of the soil microbiome in relation to management practices. To address these limitations, we conducted a year-long investigation of the soil microbiome in two agricultural fields, sampling multiple plots at different soil depths every 5 weeks. We examined spatial and temporal variabilities in response to the application of organic amendments (one-time biochar and annual compost application) on bacterial and fungal communities, studying both the microbial composition (metabarcoding, phospholipid fatty acids [PLFA], hot-water extractable-carbon) and activity (metatranscriptomics). Indicated by metabarcoding and PLFA, fungal communities were less affected over time per field, whereas bacteria exhibited more pronounced temporal trends. In contrast, fungi displayed clear spatial effects, while bacterial spatial differences within the field were predominantly observed in the deeper soil layer. Effects on functional roles and metabolic processes of the active microbial community were mainly related to temporal trends, especially in the topsoil. Organic amendments did not affect the microbial activity and affected fewer than 2 emphasizing the importance of field-specific factors, sampling depth, and community type. This ushers in the need for a well-considered experimental design and sampling strategy that accounts for spatiotemporal trends.IMPORTANCE This study addresses a critical gap in soil microbiome research by investigating spatiotemporal effects on soil bacterial and fungal composition and activity in relation to field management practices. Moving beyond single-field and limited sampling approaches, this research conducted monthly sampling events on two fields at various depths. By combining metabarcoding, phospholipid fatty acid analysis, and metatranscriptomics, the study examined bacterial and fungal community composition, biomass, and functionality. Key findings reveal distinct responses of bacterial and fungal communities to spatiotemporal variability and management practices. Functional categories were predominantly driven by temporal trends rather than compost amendments. Temporal changes were more pronounced in the topsoil. These insights into the complex interactions between soil microbial communities, management practices, and spatiotemporal dynamics contribute significantly to soil microbiome research and sampling strategies.