Development of morbidity and mortality of SARS-CoV-2 in nursing homes for the elderly in Frankfurt am Main, Germany, 2020-2022: What protective measures are still required?

Introduction: Nursing-home residents are among the highest risk group in the SARS-CoV-2 pandemic. At the onset of the SARS-CoV-2 pandemic, the majority of all deaths from or with SARS-CoV-2 occurred in long-term care facilities (LTCFs), so that maximum protective measures were mandated for these facilities. This study analyzed the impact of the new virus variants and the vaccination campaign on disease severity and mortality among nursing home residents and staff through 2022 as a basis for determining which protective measures remain necessary and appropriate. Methods: In five homes in Frankfurt am Main, Germany, with a total capacity for 705 residents, all cases occurring in the facility among residents and staff were recorded and documented (date of birth and diagnosis, hospitalization and death, vaccination status) and were descriptively analyzed with SPSS. Results: By 31st August 2022, 496 residents tested positive for SARS-CoV-2, 93 in 2020, 136 in 2021, and 267 in 2022; 14 residents presented with a second SARS-CoV-2 infection in 2022, having previously experienced an infection in 2020 or 2021. The percentage of hospitalizations decreased from 24.7% (2020) and 17.6% (2021) to 7.5% (2022), and the percentage of deaths decreased from 20.4% and 19.1% to 1.5%. In 2021, 61.8% of those infected were vaccinated (at least 2x); in 2022, 86.2% of residents had been vaccinated twice, 84% of whom had already had a booster vaccination. Hospitalization and death rates were significantly higher among the unvaccinated than the vaccinated throughout all years (unvaccinated 21.5% and 18.0%; vaccinated 9.8% and 5.5%; KW test p=0.000). However, this difference was no longer significant under the prevalence of the Omicron variant in 2022 (unvaccinated 8.3% and 0%; p=0.561; vaccinated 7.4% and 1.7%; p=0.604). From 2020 to 2022, 400 employees were documented as infected, with 25 having second infections in 2022. Only one employee showed a second infection in 2021 following the first in 2020. Three employees were hospitalized; no deaths occurred. Discussion and conclusion: Severe COVID-19 courses occurred with the Wuhan Wild type in 2020, with a high death rate among nursing-home residents. In contrast, during the waves in 2022 with the relatively mildly pathogenic Omicron variant, many infections but few severe courses and deaths were observed among the now mostly vaccinated and boostered nursing-home residents. Given the high immunity of the population and the low pathogenicity of the circulating virus - even in nursing-home residents - protective measures in nursing homes that restrict people's right to self-determination and quality of life no longer seem justified. Instead, the general hygiene rules and the recommendations of the KRINKO (German Commission for Hospital Hygiene and Infection Prevention) on infection prevention should be followed, and the recommendations of the STIKO (German Standing Commission on Vaccination) on vaccination not only against SARS-CoV-2 but also against influenza and pneumococci should be observed.

Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings.

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris L. seedlings' biomass growth and allocation, transpiration and N uptake in response to additions of organic N (the amino acid arginine) or inorganic N (ammonium nitrate). We also monitored in situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings' nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.

Hexokinase 1 is required for glucose-induced repression of bZIP63, At5g22920, and BT2 in Arabidopsis.

Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

Functional dissection of sugar signals affecting gene expression in Arabidopsis thaliana.

BACKGROUND: Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. METHODOLOGY/PRINCIPAL FINDINGS: To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. Using functional genomics we have identified 290 sugar responsive genes, responding rapidly (within 1 h) and specifically to low concentration (1 mM) of glucose, fructose and/or sucrose. For selected genes, the true nature of the signaling sugar molecules and sites of sugar perception were further clarified using non-metabolizable sugar analogues. Using both transgenic and wild-type A. thaliana seedlings, it was shown that the expression of selected sugar-responsive genes was not restricted to a specific tissue or cell type and responded to photoperiod-related changes in sugar availability. This suggested that sugar-responsiveness of genes identified in the cell culture system was not biased toward heterotrophic background and resembled that in whole plants. CONCLUSIONS: Altogether, our research strategy, using a combination of cell culture and whole plants, has provided an unequivocal evidence for the identity of sugar-responsive genes and the identity of the sugar signaling molecules, independently from their inter-conversions or use for energy metabolism.

Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes.

Various rhizobacteria are known for their beneficial effects on plants, i. e. promotion of growth and induction of systemic resistance against pathogens. These bacteria are categorized as plant growth promoting rhizobacteria (PGPR) and are associated with plant roots. Knowledge of the underlying mechanisms of plant growth promotion in vivo is still very limited, but interference of bacteria with plant hormone metabolism is suggested to play a major role. To obtain new growth promoting bacteria, we started a quest for rhizobacteria that are naturally associated to Arabidopsis thaliana. A suite of native root-associated bacteria were isolated from surface-sterilized roots of the Arabidopsis ecotype Gol-1 derived from a field site near Golm (Berlin area, Germany). We found several Pseudomonas and a Microbacterium species and tested these for growth promotion effects on the Arabidopsis ecotypes Gol-1 and Col-0, and for growth-promotion associated traits, such as auxin production, ACC deaminase activity and phosphate solubilization capacity. We showed that two of the bacteria strains promote plant growth with respect to rosette diameter, stalk length and accelerate development and that the effects were greater when bacteria were applied to Col-0 compared with Gol-1. Furthermore, the capability of promoting growth was not explained by the tested metabolic properties of the bacteria, suggesting that further bacterial traits are required. The natural variation of growth effects, combined with the extensive transgenic approaches available for the model plant Arabidopsis, will build a valuable tool to augment our understanding of the molecular mechanisms involved in the natural Arabidopsis - PGPR association.

Microbacterium yannicii sp. nov., isolated from Arabidopsis thaliana roots.

Bacterial strain G72T was isolated from surface-sterilized roots of Arabidopsis thaliana growing in its natural habitat. This Gram-positive, rod-shaped, non-motile, microaerophilic and aerobically growing isolate was characterized by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, strain G72T belongs to the genus Microbacterium. However, reassociation values in a DNA-DNA hybridization analysis with closely related strains were between 45.1  and 15.9 %. The DNA G+C content was 70.1 mol%. Strain G72T possessed a peptidoglycan type based on B2ß with partial substitution of glutamic acid by 3-hydroxy glutamic acid (Glu/Hyg-Gly-D-Orn). The isolate contained MK-13, MK-12 and MK-11 as major respiratory quinones and anteiso-C15:0, anteiso-C17:0 and iso-C16:0 as predominant fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. Based on its physiological and biochemical traits, as well as genotypic results, strain G72T is considered to represent a novel species, for which the name Microbacterium yannicii sp. nov. is proposed. The type strain is G72T (=DSM 23203T=LMG 25521T).

A naturally associated rhizobacterium of Arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth.

Plant growth promotion by rhizobacteria is a known phenomenon but the underlying mechanisms are poorly understood. We searched for plant growth-promoting rhizobacteria that are naturally associated with Arabidopsis thaliana to investigate the molecular mechanisms that are involved in plant growth-promotion. We isolated a Pseudomonas bacterium (Pseudomonas sp. G62) from roots of field-grown Arabidopsis plants that has not been described previously and analyzed its effect on plant growth, gene expression and the level of sugars and amino acids in the host plant. Inoculation with Pseudomonas sp. G62 promoted plant growth under various growth conditions. Microarray analysis revealed rapid changes in transcript levels of genes annotated to energy-, sugar- and cell wall metabolism in plants 6 h after root inoculation with P. sp. G62. The expression of several of these genes remained stable over weeks, but appeared differentially regulated in roots and shoots. The global gene expression profile observed after inoculation with P. sp. G62 showed a striking resemblance with previously described carbohydrate starvation experiments, although plants were not depleted from soluble sugars, and even showed a slight increase of the sucrose level in roots 5 weeks after inoculation. We suggest that the starvation-like transcriptional phenotype - while steady state sucrose levels are not reduced - is induced by a yet unknown signal from the bacterium that simulates sugar starvation. We discuss the potential effects of the sugar starvation signal on plant growth promotion.

Transcriptome analysis of Arabidopsis clubroots indicate a key role for cytokinins in disease development.

The clubroot disease of the family Brassicaceae is caused by the obligate biotrophic protist Plasmodiophora brassicae. Infected roots undergo a developmental switch that results in the formation of aberrant roots (clubs). To investigate host gene expression during the development of the disease, we have used the Arabidopsis ATH1 genome array. Two timepoints were chosen, an early timepoint at which the pathogen has colonized the root but has induced only very limited change of host cell and root morphology and a later timepoint at which more than 60% of the host root cells were colonized and root morphology was drastically altered. At both timepoints, more than 1,000 genes were differentially expressed in infected versus control roots. These included genes associated with growth and cell cycle, sugar phosphate metabolism, and defense. The involvement of plant hormones in club development was further supported; genes involved in auxin homeostasis, such as nitrilases and members of the GH3 family, were upregulated, whereas genes involved in cytokinin homeostasis (cytokinin synthases and cytokinin oxidases/dehydrogenases) were already strongly downregulated at the early timepoint. Cytokinin oxidase/dehydrogenase overexpressing lines were disease resistant, clearly indicating the importance of cytokinin as a key factor in clubroot disease development.