The aim of the present work is to assess mortality associated to extreme meteorological and hydrological events (storms, floods, landslides, avalanches) for the period 2003–2020 in Italy. These extreme events are particularly worrying phenomena due to their increasing frequency and intensity connected to climate change. The considerable rise of extreme meteorological events in Italy has been having a dramatic impact on the environment and territories, particularly on intrinsically fragile ones, and on resident populations. More than 90% of Italian municipalities are at risk for extreme events, with more than 8 million inhabitants exposed. Number of deaths and SMRates due to such extreme events (X International Classification of Diseases: X36, X37 and X38) in Italy were calculated from regional to municipal level by ENEA mortality database (data source ISTAT). Geographic maps were elaborated by QGIS software (QGIS, RRID:SCR_018507) version 3.28. In the selected period, 378 overall deaths were detected: 321 deaths due to landslides and avalanches, 28 to cataclysmic storm, and 29 to floods. The regions with the highest mortality levels and/or number of municipalities involved and the municipalities at highest risk were identified. In consideration of the forecasted increase of such extreme events in Italy, the knowledge of Italian areas at highest risk can be used in the decision-making processes to assess priorities, allocate financial resources, define warning measures, and undertake preventive or mitigation actions. Moreover, the attributable mortality levels can be a useful basis for further risk assessment research aimed at estimating the cost in terms of human lives’ loss associated to such events in future climatic scenarios.

Heat and cold temperatures associated with exposure to poor air quality lead to increased mortality. Using a generalized linear model with Poisson regression for overdispersion, this study quantifies the natural-caused mortality burden attributable to heat/cold temperatures and PM10 and O3 air pollutants in Rome and Milan, the two most populated Italian cities. We calculate local-specific mortality relative risks (RRs) for the period 2004-2015 considering the overall population and the most vulnerable age category (≥85 years). Combining a regional climate model with a chemistry-transport model under future climate and air pollution scenarios (RCP2.6 and RCP8.5), we then project mortality to 2050. Results show that for historical mortality the burden is much larger for cold than for warm temperatures. RR peaks during wintertime in Milan and summertime in Rome, highlighting the relevance of accounting for the effects of air pollution besides that of climate, in particular PM10 for Milan and O3 for Rome. Overall, Milan reports higher RRs while, in both cities, the elderly appear more susceptible to heat/cold and air pollution events than the average population. Two counterbalancing effects shape mortality in the future: an increase associated with higher and more frequent warmer daily temperatures - especially in the case of climate inaction - and a decrease due to declining cold-mortality burden. The outcomes highlight the urgent need to adopt more stringent and integrated climate and air quality policies to reduce the temperature and air pollution combined effects on health.

Climate change is expected to raise the threats to human health. The effects of temperatures on excess of mortality, for exposed populations, can be amplified by the simultaneous presence of air pollution. Using Distributed Lag Nonlinear Models with delayed effects, we assess the combined short-term impact of temperature and air pollution (PM10, O3) for Milan and Rome, the latter located at the center of the Mediterranean basin. Relative mortality risks (RRs) are estimated for the city population as a whole and the most vulnerable group of people (over the age of 85), for the historical decade 2004-2015 and for the future (2050), assuming climate and air pollution scenarios consistent with the representative concentration pathways RCP2.6 and RCP8.5. The daily mean temperature (T) and the daily apparent mean temperature (AT) exposure variables are used to proxy the effects of climate change; the MDA8 (maximum daily 8-hour average concentration) indicator for O3 and the daily mean of PM10 characterize, instead, past and future air pollution effects. The minimum mortality temperature (Tmm), which is city specific due to human adaptability to the local climate, is defined and inferred for both cities and age groups, together with exposure-response functions for each exposure variable. Results on past mortality show lower RRs for Rome along the whole year and a larger influence of temperature rather than air pollutant on short-term mortality. Specifically, attributable deaths are mainly associated with low temperature conditions (Tmm) and increase when considering the older age group. As regard of air pollutants, their combined influence sum up to those of temperature with a seasonal connotation: while PM10 affects the risk values mainly in association with low temperatures, O3 exerts its greatest effect especially in conjunction with high temperatures. RRs projections to 2050 confirm that Rome is the least affected city with a smaller fraction of total deaths attributable to climate change and air pollution. The effects of global warming is captured by a double-sided effect: a decrease in the cold-related mortality burden and a rise in the attributable mortality due to increasing temperatures. However, the latter effect partially offsets the relief in the health burden achieved from the former one. This substitution effect between cold- and warm-related mortality is more evident in the RCP8.5 scenario and for the 85+ age group. Concluding, the results suggest that a more rigorous and internationally coordinated climate action, implying more stringency in related policies, can lead to significant co-benefits: in addition to reducing the future health burden, containing the air pollution implications, and achieving climate objectives, health costs and loss of life can be also reduced. Indeed, when the effects of climate change and air pollution are contained with climate policy action (RCP2.6) the number of fatalities could decrease by 8 times in Rome and 1.4 in Milan, compared to historical values.

This study presents an approach developed to derive a Delayed-Multivariate Exposure-Response Model (D-MERF) useful to assess the short-term influence of temperature on mortality, accounting also for the effect of air pollution (O3 and PM10). By using Distributed, lag non-linear models (DLNM) we explain how city-specific exposure-response functions are derived for the municipality of Rome, which is taken as an example. The steps illustrated can be replicated to other cities while the statistical model presented here can be further extended to other exposure variables. We derive the mortality relative-risk (RR) curve averaged over the period 2004-2015, which accounts for city-specific climate and pollution conditions. Key aspects of customization are as follows: This study reports the steps followed to derive a combined, multivariate exposure-response model aimed at translating climatic and air pollution effects into mortality risk. Integration of climate and air pollution parameters to derive RR values. A specific interest is devoted to the investigation of delayed effects on mortality in the presence of different exposure factors.

The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347T (99.31 % similarity) and Actinomadura mexicana DSM 44485T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H6), with minor amounts of MK-9(H8) and MK-9(H4). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C18:1ω9c, C16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521T(=LMG 31258T=DSM 109019T).

BACKGROUND:Burkholderia contaminans is one of the 20 closely related bacterial of the Burkholderia cepacia complex, a group of bacteria that are ubiquitous in the environment and capable of infecting people with cystic fibrosis (CF). This species is an emerging pathogen and it has been widely isolated from CF patients in Argentina, Spain, Portugal, Australia, Canada, USA with a low prevalence in Ireland, France, Russia, Switzerland, Czech Republic, and Italy. This is the first report of B. contaminans affecting two Italian CF patients attending the same CF Centre. We correlate B. contaminans colonisation with lung function decline and co-infection with other clinically relevant CF pathogens.CASE PRESENTATION:B. contaminans was identified by Multi Locus Sequence Typing in routine sputum analysis of two Caucasian CF women homozygous for Phe508del CFTR mutation. Sequence Type 102 was detected in both strains. It is known that B. contaminans ST102 was isolated both from CF and non-CF patients, with an intercontinental spread across the world. Random Amplified Polymorphic DNA analysis revealed the genetic relatedness between the two strains. We examined their susceptibility to antimicrobial agents, comparing the latter with that recorded for other B. contaminans isolated from different countries. We also described key virulence factors possibly linked with a clinical outcome. Specifically, we attempted to correlate colonization with the incidence of acute exacerbation of symptoms and lung function decline.CONCLUSIONS:This case presentation suggests that acquisition of B. contaminans ST102 is not directly associated with a lung function decline. We retain that the presence of other CF pathogens (i.e. MRSA and Trichosporon) along with B. contaminans ST102 might have contributed to the worsening of clinical conditions in our CF patients. The circumstances leading to the establishment of B. contaminans ST102 infections are still unknown. We highlight the importance to proper detect and typing bacteria implicated in CF infection by using molecular techniques.

We describe here one way to achieve hybrid DNA-inorganic nanostructures on rigid flat insulating substrates. We report methods to prepare rectangular DNA origami and incubate them onto arrays of anchoring gold nanodots either in a static solution or in a microfluidic system. We give details on the design and lithographic methods employed to pattern usable arrays of gold nanoanchors on naturally oxidized silicon wafer chips. Scanning electron and atomic force microscopy methodological details are also given for obtaining the relevant characterizations of the immobilized and ordered DNA origami.

BACKGROUND:Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage.RESULTS:An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed.CONCLUSION:The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry.

Strain ATCC 33076, which produces the antibiotic ramoplanin, was isolated from a soil sample collected in India, and it was classified as a member of the genus Actinoplanes on the basis of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain forms a distinct clade within the genus Actinoplanes, and it is most closely related to Actinoplanes deccanensis IFO 13994T (98.71 % similarity) and Actinoplanes atraurantiacus Y16T (98.33 %). The strain forms an extensively branched substrate mycelium; the sporangia are formed very scantily and are globose with irregular surface. Spores are oval and motile. The cell wall contains meso-diaminopimelic acid and the diagnostic sugars are xylose and arabinose. The predominant menaquinone is MK-9(H6), with minor amounts of MK-9(H4) and MK-9(H2). Mycolic acids are absent. The diagnostic phospholipids are phosphatidylethanolamine, hydroxyphosphatidylethanolamine and phosphatidylglycerol. The major cellular fatty acids are anteiso-C17 : 0 and iso-C16 : 0, followed by iso-C15 : 0 and moderate amounts of anteiso-C15 : 0, iso-C17 : 0 and C18 : 1ω9c. The genomic DNA G+C content is 71.4 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA-DNA relatedness between strain ATCC 33076 and closely related type strains, clearly demonstrated that strain ATCC 33076 represents a novel species of the genus Actinoplanes, for which the name Actinoplanes ramoplaninifer sp. nov. is proposed. The type strain is ATCC 33076T (=DSM 105064T=NRRL B-65484T).

Soil is a complex and dynamic ecosystem whose functionality is related to the equilibrium existing among chemical, physical and biological parameters and the resident microbial communities. Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling, and have direct and indirect effects on both crop growth and quality, as well as on the sustainability of soil productivity. In addition, soil microorganisms substantially contribute to the resistance and resilience of agro-ecosystems to abiotic disturbance and stress. Therefore, changes in microbial communities may directly affect soil ecosystem function since microbes can respond rapidly to environmental changes because of the vastness of microbial biomass and diversity. An increasing number of studies have shown how environmental impacts that cause modifications in microbial community structure and diversity ultimately affect soil biological processes. Agricultural land management is one of most significant anthropogenic activities that substantially alter soil characteristics, including physical, chemical, and biological properties. The present chapter gives a picture of the effect of different agricultural management practices on soil microbial community structure and function. A case study on the effects of tillage and nitrogen fertilization on soil bacterial community structure is also reported.

[This corrects the article DOI: 10.1371/journal.pone.0156807.].

Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.

With the growing demand of fresh-cut vegetables, a variety of packaging films are produced specifically to improve safety and quality of the fresh vegetables over the storage period. The aim of our work was to evaluate the influence of different packaging films on the quality of fresh-cut lettuce analyzing changes in bacterial community composition and modifications at the proteome level, by means of culture-dependent/culture-independent methods and differential gel electrophoresis combined with mass spectrometry analysis. Total viable counts indicated the presence of a highly variable and complex microbial flora, around a mean value of 6.26 log10 CFU g(-1). Analysis of terminal-restriction fragment length polymorphism data indicated that bacterial communities changed with packaging films and time, showing differences in community composition and diversity indices between the commercially available package (F) and the new packages (A and C), in the first days after packaging. Also proteomic analysis revealed significant changes, involving proteins related to energy metabolism, photosynthesis, plant defense and oxidative stress processes, between F and A/C packages. In conclusion, microbiological and proteomic analysis have proved to be powerful tools to provide new insights into both the composition of leaf-associated bacterial communities and protein content of fresh-cut lettuce during the shelf-life storage process.

Strain ATCC 39727, which produces the antibiotic A40926 (the natural precursor of the antibiotic dalbavancin), was isolated from a soil sample collected in India, and it was originally classified as a member of the genus Actinomadura on the base of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicates that the strain forms a distinct clade within the genus Nonomuraea, and it is most closely related to Nonomuraea angiospora DSM 43173T (98.72 % similarity) and Nonomuraea jabiensis A4036T (98.69 %). The strain forms an extensively branched substrate mycelium and aerial hyphae that form spiral chains of spores with ridged surfaces. The cell wall contains meso-diaminopimelic acid and the whole-cell sugars are glucose, ribose, galactose, mannose and madurose (madurose as the diagnostic sugar). The N-acyl type of muramic acid is acetyl. The predominant menaquinone is MK-9(H4), with minor amounts of MK-9(H2), MK-9(H6) and MK-9(H0). The polar-lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylinositol and a series of uncharacterized phospholipids, glycolipids and phosphoglycolipids. The major cellular fatty acids are iso-C16 : 0 and 10-methyl C17 : 0. The genomic DNA G+C content is 71.2 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA-DNA relatedness between strain ATCC 39727 and closely related type strains, clearly demonstrated that strain ATCC 39727 represents a novel species of the genus Nonomuraea, for which the name Nonomuraea gerenzanensis sp. nov. is proposed. The type strain is ATCC 39727T ( = DSM 100948T).

Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the development of predictive biomarkers of substantial decline in lung function.

In this work the analysis of the plasmid presence on soil aerobic cultivable heterotrophic bacterial communities was carried out checking a panel of 1,200 isolates, in order to establish the frequency of plasmid presence as well as the degree of plasmid flow between strains affiliated to the same or different taxon. Bacterial communities were isolated from two different sites of a 13-year experimental field with a clay-silt texture. Plasmid molecules were detected at low frequency (27 isolates, 2%) with a size ranging between 2 Kb and 40 Kb. The RAPD analysis performed on the plasmid-harboring isolates and the phylogenetic analysis of the whole community using the 16S rRNA gene sequences revealed the existence of transfer of the same plasmids between strains belonging to the same species and, in some cases, to different species of the same genus. As it might be expected, even though the viable cells title did not differ significantly between the two samplings, the overall data disclosed an uneven distribution of both species and plasmid-harboring strains.

Rectangular DNA origami functionalized with thiols in each of the four corners immobilizes by self-assembly between lithographically patterned gold nanodots on a silicon oxide surface.

Objectives: To gain insight into the underlying causes of severe lung diseases, we compared the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD).Methods: Fifty-two patients belonging to three FEV1 groups (normal/mild, FEV1 >70%; moderate, 40 < FEV1 < 69%; severe, FEV1 < 40%) were enrolled in the study.After DNA extraction from sputum samples, 16S rRNA metagenomic analysis was performed using the Roche 454 platform and the ecological issues (biological diversity, taxa composition, interaction among taxa) were investigated.Results: A sharp difference in the structure and composition of airway microbiota between S and SD patients was found, especially in patients with severe lung disease, where Pseudomonas represented the most abundant genus.A cooccurrence network analysis showed that microbial communities were less complex in SD patients than in S ones.Moreover, an inverse relationship between bacterial community diversity and disease severity was found.Indeed, the analysis of the main biodiversity indices on microbiota data has shown a significant drop passing from normal/mild FEV1 group to moderate lung disease FEV1 group suggesting that the patients with intermediate FEV1 values are experiencing changes in the airway assembly of taxa. Conclusion:We can claim that bacterial lung microbiota is modified along with substantial decline in lung function.Higher levels of pulmonary deficiency can lead to a drastic decrement of bacterial community complexity leaving the way clear for the proliferation of opportunistic pathogens.