Pseudomonassyringae pv. actinidiae (Psa) is a gram-negative bacterium responsible for the bacterial canker in Actinidia chinensis var. deliciosa and A. chinensis var. chinensis, a quarantine organism threatening the kiwifruit industry sustainability. The present study aimed to determine the genetic structure of the endophytic and epiphytic populations of Psa isolated from four different Portuguese orchards with distinct abiotic conditions in two consecutive seasons. The results identified several coexisting and highly heterogeneous Psa populations. Moreover, evident changes in population structure occurred between the epiphytic and endophytic populations, and between seasons with a notable decrease in Psa diversity in autumn. This work provided solid evidence that the initial clonal expansion of Psa in Europe was followed by a wide genomic diversification. This perspective is important for the understanding of kiwifruit bacterial canker disease occurrence and Psa evolution, namely when adopting strategies for management of epidemics.

Pseudomonas syringae pv. actinidiae is a quarantine bacterium affecting all the Portuguese main areas of kiwifruit production. We report the draft genome of six P. syringae pv. actinidiae strains isolated from symptomatic leaves of Actinidia chinensis var. deliciosa in a study that determined the genetic population structure of the endophytic and epiphytic populations in two consecutive seasons. Average nucleotide identity values were above 99% similarity with reference strains from P. syringae pv. actinidiae biovar 3. The genomic differences found between these strains confirm the genetic diversity described for P. syringae pv. actinidiae population in Portugal. Furthermore, data provide evidence that the initial clonal expansion of P. syringae pv. actinidiae in Europe was followed by a genomic diversification constituting a valuable resource for epidemiological and evolutionary studies, namely when adopting strategies for epidemics management.

Bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to global kiwifruit production. Copper-based bactericides remain widely used, but increasing resistance highlights the urgency of developing sustainable alternatives. Understanding the functional capabilities of phyllosphere bacteria under copper pressure is critical for designing microbiome-informed management strategies. This study provides a culture-based functional inventory of bacteria associated with Actinidia chinensis var. deliciosa leaves from Portuguese orchards under long-term copper management, aiming to identify native taxa with traits relevant to plant health and resilience. A total of 1058 isolates were recovered and grouped into 261 Random Amplification of Polymorphic DNA (RAPD) clusters, representing 58 species across 29 genera. Representative strains were screened for Plant Growth-Promoting (PGP) traits (Indole-3-acetic acid (IAA), siderophore production, phosphate solubilization, ammonia production), copper tolerance, and in vitro antagonism against Psa. Copper resistance was widespread (53.3% of isolates with MIC ≥ 0.8 mM), including the first evidence of a highly copper-resistant PSA strain in Portuguese kiwifruit orchards and an exceptionally resistant non-pathogenic strain closely related to Erwinia iniecta (MIC 2.8 mM). A subset of 25 isolates combined all four PGP traits, and several also exhibited antagonism against Psa in vitro, among them Bacillus pumilus consistently supressed pathogen growth. Notably, antagonistic and multifunctional traits co-occurred in some isolates, highlighting promising candidates for integrated biocontrol strategies. Overall, the findings reveal a functionally diverse and copper-resilient collection of cultured bacteria, offering both challenges and opportunities for microbiome-based disease management. This work establishes a robust functional basis for subsequent in planta validation and the development of sustainable, microbiome-informed approaches for Psa control.

Bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to global kiwifruit production. Copper-based bactericides remain widely used, but increasing resistance underscores the need for alternative strategies. Understanding the functional capabilities of phyllosphere bacteria under copper pressure is critical for designing sustainable alternatives. This study provides a culture-based functional inventory of bacteria associated with Actinidia chinensis var. deliciosa leaves from Portuguese orchards under long-term copper management, aiming to identify native taxa with traits relevant to plant health and resilience. A total of 1,058 isolates were recovered and grouped into 261 RAPD clusters, representing 58 species across 29 genera. Representative strains were screened for plant growth-promoting (PGP) traits (IAA, siderophore production, phosphate solubilization, ammonia production), copper tolerance, and in vitro antagonism against Psa. Copper resistance was widespread (53.3% of isolates with MIC ≥0.8 mM), including the first evidence of a highly copper-resistant PSA in Portuguese kiwifruit orchards and an exceptionally resistant non-pathogenic strain ( Erwinia iniecta , MIC 2.8 mM). A subset of 25 isolates combined all PGP traits. In parallel, several isolates exhibited antagonism against Psa, including Bacillus pumilus , which consistently inhibited pathogen growth. Notably, some antagonistic isolates overlapped with the multifunctional PGP subset, highlighting promising candidates for integrated biocontrol strategies. These findings reveal the kiwifruit phyllosphere as a reservoir of functionally diverse and copper-resilient bacteria, highlighting both ecological risks and opportunities for microbiome-based biocontrol innovation. This work establishes a functional baseline for future in planta validation and microbiome-informed disease management strategies.

Cities concentrate most of the world’s population and human activities, generating pollution that threatens ecosystem functioning and human well-being. Yet, the relative importance of different drivers shaping urban pollution and the spatial distribution of multiple contaminants across cities remain poorly understood. Here, we conducted a standardized survey across 51 cities in the Iberian Peninsula to quantify metals, pesticides, macrolitter and microplastics. We sampled four urban greenspace types (parks, golf courses, urban farms, roundabouts) and nearby natural areas to link contaminants with soil microbiome structure and functioning.Urban parks, roundabouts and urban farms accumulated the highest metal levels, sometimes exceeding regulatory thresholds, whereas golf courses showed lower contamination levels. Pesticide concentrations were higher in urban soils than in nearby natural areas, especially in parks and golf courses, consistent with intensive chemical inputs. In contrast, microplastic concentrations peaked in natural ecosystems, indicating that regional transport and deposition processes can decouple their accumulation from local urban sources. Macrolitter was most abundant in parks and roundabouts, while golf courses exhibited the lowest densities, highlighting the influence of local management and access control. Contamination indices predicted microbial diversity, community composition and key soil functions. Pesticides reduced bacterial diversity and, together with macrolitter impaired carbon and phosphorus cycling. Metals were linked to tolerant microbial communities with maintained or enhanced biogeochemical ecosystem functions such as respiration and enzymatic activity. This study highlights that land use and management drive soil contamination and microbiome functioning, and that mitigation actions are needed to support EU Soil Strategy implementation in cities.

Fungal community dynamics play a fundamental role in plant health, influencing resilience, disease progression, and ecosystem stability. Monilinia fructicola, a quarantine pathogen affecting Prunus persica, is hypothesized to drive fungal dysbiosis by altering microbial diversity, ecological interactions, and functional roles. In this study, the impact on fungal community composition, trophic dynamics, and network structure was investigated using internal transcribed spacer metabarcoding based on high-throughput sequencing of flowers and branches from infected and noninfected P. persica trees. The results showed a pathogen-induced shift, most pronounced in flowers, in which M. fructicola increased richness (Chao1), diversity (Shannon), and dominance (Simpson). In wood samples, increased dominance suggested pathogen-associated ecological filtering. Network analysis demonstrated that M. fructicola disrupts fungal connectivity, leading to fragmentation of microbial interactions, reduced network complexity, and increased modularity, indicative of weakened ecological cohesion. Shifts in fungal primary lifestyles further suggested that M. fructicola accelerates tissue decomposition and induces an imbalance in functional guilds, potentially facilitating secondary infections. Taxonomic restructuring was marked by the decline of dominant genera and the emergence of stress-adapted or pathogen-associated taxa. The isolation of Epicoccum nigrum, a known biocontrol agent, highlights its potential as a nature-based solution for disease management. Overall, these findings identify M. fructicola as a driver of fungal dysbiosis in P. persica, with cascading effects on microbial function, network resilience, and plant health. Understanding these pathogen-induced shifts is essential to inform sustainable microbiome-based approaches to disease management.