Monitoring zoonoses in urban environments is of great relevance, where the incidence of certain pathogens may be higher and where population density makes the spread of any contagious disease more likely. In this study we applied a metabarcoding approach to study potentially zoonotic pathogens in faecal samples of 9 urban vertebrate species. We applied this methodology with two objectives. Firstly, to obtain information on potential pathogens present in the urban fauna of a large European city (Madrid, Spain) and to determine which are their main reservoirs. In addition, we tested for differences in the prevalence of these potential pathogens between urban and rural European rabbits, used as ubiquitous species. Additionally, based on the results obtained, we evaluated the effectiveness of metabarcoding as a tool for monitoring potential pathogen. Our results revealed the presence of potentially zoonotic bacterial genera in all studied host species, 10 of these genera with zoonotic species of mandatory monitoring in the European Union. Based on these results, urban birds (especially house sparrows and pigeons) and bats are the species posing the greatest potential risk, with Campylobacter and Listeria genera in birds and of Chlamydia and Vibrio cholerae in bats as most relevant pathogens. This information highlights the risk associated with fresh faeces from urban wildlife. In addition, we detected Campylobacter in >50 % of the urban rabbit samples, while we only detected it in 11 % of the rural rabbit samples. We found that urban rabbits have a higher prevalence of some pathogens relative to rural rabbits, which could indicate increased risk of pathogen transmission to humans. Finally, our results showed that metabarcoding can be an useful tool to quickly obtain a first screening of potentially zoonotic organisms, necessary information to target the monitoring efforts on the most relevant pathogens and host species.

Synanthropic birds might play an important role as reservoirs of many zoonotic endoparasites; however, little information is available on many parasites and their prevalence. Here, we use an approach based on targeted metagenomic detection through the use of DNA metabarcoding of faecal samples to screen for circulating parasites in alien parakeets (Myiopsitta monachus and Psittacula krameri) and urban landfill-feeding storks (Ciconia ciconia) and gulls (Larus fuscus). We focus especially on potentially zoonotic parasites, with the aim of better understanding the zoonotic risk that these birds’ faeces may pose. We detected a total of 23 genera of eukaryotic parasites: six fungi, three protists, five nematodes, two cestodes and seven trematodes. Among them, six stood out for their relevance to human health: Cryptococcus spp., Aspergillus spp. and Candida spp. (fungi); Cryptosporidium spp. (a protist); and Ascaris spp. and Halicephalobus spp. (nematodes). In parakeets, we detected Cryptococcus spp. and Ascaris spp., the latter being detected in 10–20% of the samples. In the White Stork and the Lesser Black-backed Gull, we found a high prevalence of Aspergillus spp. (in 15% and 50% of the samples, respectively) and Candida spp. (in 63% and 82% of the samples, respectively), and the presence of Cryptosporidium spp. in 10% of the samples. We detected Halicephalobus spp. in one gull sample (2%). Our results show that synanthropic birds may act as vectors and reservoirs of zoonotic parasites and their faeces could pose a risk to human health associated with the zoonotic parasites present in them. This should be taken into account when developing management plans for urban populations of these bird species.

Plant–microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity, and the outcome of these interactions can significantly affect plant productivity. A better understanding of the rhizosphere microbiome is, therefore, required to develop successful knowledge-based microbiome modification strategies that help improve plant productivity. Here, we investigated the community assembly process of the tomato rhizosphere microbiome and its potential composition–function relationships through the lens of a conceptual framework based on the phylogenetically constrained assembly of microbial communities. In this study, we grew tomato plantlets on different soil types with high replication and assessed community composition using high-throughput sequencing of the 16S rRNA bacterial marker gene and community function based on the predicted minimal metagenome of the microbial ecosystem. We also conducted additional computer simulations to examine the relationship between phylogenetic clustering and community function. We observed a systematic enrichment in the rhizosphere in terms of phylogeny and predicted functional content and were able to delimit the phylogenetic signal in the ecosystem owing to the presence of 12 functionally coherent phylogenetic core groups in all samples. These groups, which accounted for a large fraction of the total community, belonged to the Alpha, Beta, and Gammaproteobacteria, Actinobacteria, and Bacilli classes and presented exclusive functions related to important ecosystem services. Furthermore, our analyses indicated that these groups accounted for a large proportion of the ecosystem's predicted minimal metagenome. Overall, our study suggests that community assembly followed coupled phylo-functional selection, a phenomenon that likely occurs in other rhizosphere microbiomes. This knowledge not only advances our understanding of how community composition–phylogeny–function relationships drive the assembly process of the rhizosphere microbiome but also will help guide the design of synthetic rhizosphere microbiomes for both research and commercial purposes. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

In the present work, we present the draft genome sequence of a new putative Arthrobacter species associated with the tomato rhizosphere.

Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high‐throughput isolation of microbiome members thus represents a core resource in this field of research.

The isolation and characterization of additional phages is crucial for adding reliable viral sequences with relevant biological information to viral databases. In this study, we present the complete genomes of two Arthrobacter phages obtained from different soil samples.