Publications

4358

AbstractBackgroundCandidate Phyla Radiation (CPR) is a large monophyletic group thought to cover about 25% of bacterial diversity. Due to peculiar characteristics and unusual 16S rRNA gene structure, they are often under-represented or lost in 16S rRNA-based microbiota surveys. Among CPR, “CandidatusSaccharibacteria” is a phylum experimentally found to modulate the immune response and enriched in the oral microbiota of subjects suffering from several immune-mediated disorders, e.g. food allergies, as reported by us in a previous work. Due to the growing evidence of “Ca. Saccharibacteria”’s role in clinical settings and in order to unravel its role in host physiology and pathology, it is crucial to have a reliable method to detect and quantify this lineage.Methods and ResultsFour qPCR protocols for quantifying “Ca.Saccharibacteria” (one targeting the 23S rRNA gene and three the 16S) were selected from the literature among the few available. Efficiency and coverage of primer pairs used in these protocols were preliminary evaluated viain silicoanalyses on the “Ca.Saccharibacteria” known taxonomic variability, and then testedin vitroon the salivary DNA previously investigated by 16S metagenomics in the food allergy study.In silicoanalyses evidenced that the 23S qPCR protocol covered more “Ca. Saccharibacteria” variability compared to the 16S-based ones, and that the 16S metagenomics primers were the most comprehensive. qPCR experiments confirmed that 16S-based protocols strongly underestimated “Ca. Saccharibacteria” while the 23S protocol was the only one to yield results comparable to 16S metagenomics both in terms of correlation and absolute quantification. However, only 16S metagenomics evidenced an expansion of “Ca. Saccharibacteria” in allergic subjects compared to controls, while none of the four qPCR protocols detected it.ConclusionThese results underline the current limits in experimentally approaching “Ca. Saccharibacteria”. To obtain a more realistic picture of their abundance within bacterial communities, and to enable more efficient taxonomic resolution, it is essential to find novel experimental strategies. This is a necessary premise for more targeted and systematic functional studies to clarify the role of “Ca. Saccharibacteria” and, generally, CPR bacteria, in maintaining the health of the host.

Abstract Syndrome ‘basses richesses’ (SBR) disease in sugar beet caused by two phloem-limited pathogens, 'Candidatus Arsenophonus phytopathogenicus' and 'Candidatus Phytoplasma solani' is a fastspreading disease in Central Europe. The planthopper vector, Pentastiridius leporinus (Cixiidae), has recently expanded its host range to potato in Germany. However, the genetic diversity of 'Ca P. solani' in potato and possible association to SBR phytoplasma is unknown. In this study we charachterized ‘Ca. P. solani’ infecting sugar beet and potato plants in close distance fields in Southern Germany. Initially, the pathogen was detected in the potato tubers (18.7%) and sugar beet roots (60%) using TaqMan Real-Time PCR. Then, the sequences of 16S rRNA and other informative genes (stamp, vmp1, tuf and secY) were analysed in a number of infected potato and sugar beet plants. The phytoplasma strain infecting sugar beet in Southern Germany was classified into 16SrXII-P subgroup, a novel subgroup recently reported from sugar beet in Eastern Germany. While, the potato related strains were close to 16SrXII-A, which is a common subgroup for potato stolbur reported in Europe. The multilocus sequence analysis (MLSA) of non-ribosomal genes of the phytoplasma strains showed that the potato strain is clearly different from the sugar beet associated strain in this region. The presence and prevalence of 16SrXII-P in sugar beet in Southern and Eastern Germany suggests that this subgroup is dominant in sugar beet in Germany. In addition, this study elucidates for the first time, the genetic diversity of ‘Ca. P. solani’ strains in potato in Germany with a possible different source rather than sugar beet. Further investigation is required to investigate genetic variation of ‘Ca. P. solani’ in all sugar beet and potato-growing regions including weeds host in Central Europe to better understand the epidemiology of both sugar beet SBR and potato stolbur disease.

Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus , including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.

AbstractZinnia peruviana (Asteraceae) is an annual flowering plant cultivated in various gardens of Mysore, the south of Karnataka state, India. During 2021, phytoplasma‐like symptoms such as virescence and phyllody were observed on Zinnia in Mysore local gardens. A total of 10 symptomatic and five asymptomatic samples were collected, and the DNA was amplified by PCR using primers specific to 16S RNA and secA genes. The nucleotide sequence analysis showed that the 16S RNA and SecA gene sequences were most similar to those of ‘Ca. P. aurantifolia’, with identities greater than 99%. The phytoplasma sequence from this study shared a common clade with ‘Ca. P. aurantifolia’ when phylogenetic analysis was done. Similarly, the reference sequences for the 16S rRNA and SecA region confirmed the identity of the phytoplasma associated with the leaves of Zinnia. This is the new host record for ‘Ca. P. aurantifolia’ (16SrII‐D) phytoplasma associated with Z. peruviana from India.

Huanglongbing (HLB) is a major disease of citrus associated with phloem-limited bacteria in the genus Candidatus Liberibacter that affects all known citrus species and relatives, with many commercial cultivars being greatly damaged. Testing cultivar tolerance to HLB in field conditions is difficult because of the erratic spread of the bacteria, scion and rootstock interactions, and influence of many biotic and abiotic factors on the tree response to the disease. This study aimed to validate the effect of CLas infection on different citrus species and hybrids thought to have different levels of tolerance to the disease using CLas graft inoculation under controlled greenhouse conditions. Young potted seedlings from 12 different citrus germplasm selections were graft-inoculated with CLas or mock-inoculated. Plants were monitored periodically during 18 months for canopy growth, HLB and nutritional leaf symptoms, and leaf CLas titers. The leaf nutrient content was measured at the end of the experiment. Roots were also assessed at 18 months after inoculation (mai) for CLas titers and biomass distribution. There were significant differences in most analyzed variables of healthy and infected plants. Some plants of all cultivars were successfully infected; however, overall, the CLas transmission rate was low and inconsistent. Ct values of roots were generally higher than those in leaves at 18 mai. HLB symptoms were not observed on seedlings until 1 year after inoculation; at 18 mai, infected trees of all cultivars were HLB symptomatic. Significant shoot and root biomass reductions (44%–75%) in infected ‘Cleopatra’, ‘Duncan’, ‘Olinda Valencia’, ‘Sunburst’, and ‘Valencia 1-14-19’, considered susceptible to HLB, were measured. These cultivars also showed more severe HLB symptoms than the presumed tolerant cultivars such as Microcitrus inodora, Rich 16-6 trifoliate orange, and US-897. This study provides new knowledge of the efficacy and value of greenhouse screening of citrus germplasm for response to HLB to support the development of new cultivars with improved HLB tolerance or resistance.