Biology subjects

Junco, L. M. F.

Publications and source records attributed to Junco, L. M. F..

3 recordsLinked to original sources

bioRxiv2026

Danish profile of soft rot Pectobacteriaceae; A three-year field sampling study proving several clonal clades of soft rot isolates across diverse locations implicating a common origin

Soft rot Pectobacteriaceae (SRP) are among the most economically important plant pathogenic bacteria and are especially known to be problematic in potato production. The epidemiology of disease transmission has been investigated for almost a century, and several aspects have been highlighted as plausible infection routes. However, it is generally accepted that the major source of disease is the latently infected mother tuber, but several parameters are still influencing disease prevalence including contaminated equipment, soil water status as well as temperature. Management of the disease is limited to hygiene practices, dry storage and seed certification systems but several studies have also proven biocontrol agents such as bacteriophages (phages) as promising tools. Despite the severity of SRP on potato production, little is known about the genetic diversity of SRPs in Denmark, and since only few isolates are available, the possibility to design a broadly effective phage cocktail is limited. Here we describe a three-year field study utilizing an agri-citizen science approach where Danish farmers provided symptomatic potato plants or tubers, together with metadata such as date, location, potato variety and origin. By using whole genome sequencing (Illumina and Nanopore) together with metadata we were able to investigate and monitor the epidemiological disease spread across the country using 103 complete genomes, sampled across all three years. In this study we provide epidemiological evidence of disease origins and a suite of phages that could be used as a biocontrol tool for early disease intervention. Our results revealed several clonal clades across diverse locations (SNPs < 20) which strongly indicate common origin. A total of 17 Pectobacterium phages were tested and did target > 80% of clonal clades. Based on the clonality across the soft rot isolates we propose the possibility to set in early on using phages targeting strains relevant for soft rot development, with the possibility of a surveillance program together with customizing the phage preference.

microbiology↗

bioRxiv2021

Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in envi-ronmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage communitys shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media corresponds to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum 2-fold change above 0 in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, was highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlights how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.

microbiology↗

bioRxiv2020

Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Phages drive bacterial diversity - profoundly influencing diverse microbial communities, from microbiomes to the drivers of global biogeochemical cycling. The vast genomic diversity of phages is gradually being uncovered as >8000 phage genomes have now been sequenced. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples (0.5 ml) and identified 136 phages of which 104 are unique phage species and 91 represent novel species, including several novel lineages. These phages are estimated to represent roughly a third of the true diversity of Escherichia phages in Danish wastewater. The novel phages are remarkably diverse and represent four different families Myoviridae, Siphoviridae, Podoviridae and Microviridae. They group into 14 distinct clusters and nine singletons without any substantial similarity to other phages in the dataset. Their genomes vary drastically in length from merely 5 342 bp to 170 817 kb, with an impressive span of GC contents ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, in the go-to source for phages, substantial diversity remains to be uncovered. These results expand and underlines the range of Escherichia phage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.

microbiology↗