Publications

4463

Abstract Background ‘Candidatus Phytoplasma ulmi’ is the agent associated with elm yellows and has been categorised in the European Union as a quarantine pathogen. For central and northern European countries, information on the occurrence and distribution of the pathogen and its impact on elms is scarce, so a survey of native elm trees has been conducted in Germany. Results About 6500 samples from Ulmus minor, Ulmus laevis and Ulmus glabra, were collected nationwide. Phytoplasma detection was performed by applying a universal 16Sr DNA-based quantitative PCR (qPCR) assay and a novel ‘Ca. P. ulmi’ specific qPCR assay targeting the 16S–23S spacer region. Both assays revealed that 28% of the samples were infected by ‘Ca. P. ulmi’, but infection rates of the elm species and regional incidences differed. The phytoplasma presence in the trees was not correlated to disease-specific symptoms. The survey identified a regional disparity of infection which was high in east, south and central Germany, whereas only a few infected sites were found in the western and northern parts of the country. Monitoring the seasonal titre of ‘Ca. P. ulmi’ in an infected tree by qPCR revealed a high colonisation in all parts of the tree throughout the year. Conclusions ‘Ca. P. ulmi’ is widely present in elms in Germany. The rare occurrence of symptoms indicates either a high degree of tolerance in elm populations or a low virulence of pathogen strains enabling high infection rates in a long-living host.

Abstract Objectives In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of “Candidatus Afipia apatlaquensis” strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity. Data description Here, we report the first draft genome sequence of “Candidatus Afipia apatlaquensis” sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.

Abstract Background Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

Specific scopeThis Standard describes a national regulatory control system for the bacterial pathogen ‘Candidatus Liberibacter solanacearum’ and its vector Bactericera cockerelli when regulated as quarantine pests. It also covers measures to reduce the risk of ‘Ca. L. solanacearum’ spreading to potato production systems when listed as a regulated nonquarantine pest (RNQP) on seed potatoFor the EPPO A1 listed pests recommended for regulation as quarantine pests B. cockerelli and ‘Ca. L. solanacearum’ (Solanaceae haplotypes, i.e. non‐European haplotypes, such as haplotypes A and B), the Standard describes measures to achieve: Exclusion from the EPPO region of B. cockerelli, which is an efficient vector of ‘Ca. L. solanacearum’ within solanaceous crops (e.g. potato, tomato) Eradication of incursions of B. cockerelli Exclusion from the EPPO region of non‐European haplotypes of ‘Ca. L. solanacearum’ Eradication of incursions of non‐European haplotypes of ‘Ca. L. solanacearum’. Although reference will only be made to the non‐European haplotypes A and B, the Standard would also apply to new non‐European haplotypes of ‘Ca. L. solanacearum’ which may have different host ranges or which may be vectored more efficiently by psyllids which are widespread in the region.For the haplotypes which are not recommended for regulation as quarantine pests but are recommended for regulation as RNQPs on seed potato (i.e. European haplotypes, such as C, D and E), the Standard describes measures (specified in Appendix 4) to reduce the risk of spread to potato production systems to achieve: Exclusion of European haplotypes of ‘Ca. L. solanacearum’ from the potato production system Suppression of European haplotypes of ‘Ca. L. solanacearum’ in potato production systems where they are present. Although reference will only be made to haplotypes C, D and E, Appendix 4 would also apply to new European haplotypes of ‘Ca. L. solanacearum’.SpecificapprovalFirst approved in 2017‐09. Revised in 2020‐09.