The adoption of sewage sludge as an agricultural management strategy to improve soil properties and crop production is attracting great interest. Despite many positive effects on soil inorganic and organic components reported for different soil types, little information is available on sewage sludge application on Mediterranean soils, as well as on its use at different dose rates. The objectives of the present research was to evaluate, through an integrated approach, the effects of sewage sludge compost from urban wastewater on physicochemical, hydrological, biochemical parameters, and microbiota composition in soil pots under a three-year crop rotation system. Four different doses of sewage sludge compost (C3, C6, C9, C12) from municipal wastewater and a dose of them in combination with mineral fertilizer (C6N) were used. We have used 3-6-9-12 Mg/ha of sewage sludge compost for the treatments C3, C6, C9 and C12, respectively, and 6 Mg/ha of sewage sludge compost in combination with 60 kg/ha of ammonium nitrate for the treatment C6N.The effects were compared to non-fertilized (C0) and mineral fertilized (Min) sets of controls. The electrical conductivity, soil pH, stability of soil aggregates, percent of moisture of the dry soil both at the field capacity and at the wilting point, available P, and exchangeable K were all positively affected by increasing the amounts of composted sludge. The organic carbon and total N increased up to 66% and 39%, respectively. Increased enzymatic activities and microbial biomass were also observed in soil after the application of sewage sludge compost when compared to un-amended control. A higher richness and evenness among the soil plots amended with sewage sludge compost was observed, with no significant differences among the application dose rates, when compared to the un-amended soil control and soil treated with a mineral fertilizer. A three-year amendment was able to separate soil plots amended with high doses of sewage sludge compost from the low dose amended and control samples. Among the microbial groups responsible for such marked separation, bacteria belonging to Actinobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes contribute the most, with a shift from oligotrophic to copiotrophic taxa. Significant changes in bacterial composition and taxonomic structure should be considered in order to properly balance agronomic and economic advantages with environmental concerns. After all, our results have evidenced the effects of sewage sludge amendment on different soil properties, microbial activity, and composition already after a short period of application. The findings are particularly relevant in semiarid soils, where an immediate restoration of soil fertility by short-term compost application is needed.

Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species Staphylococcus arlettae (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two “outgroup” species, Bacillus subtilis (BS) and Macrococcus caseoliticus (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant mec, van, and cls genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic Staphylococcus species, such as Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, ica, nuc, and ssp), which are commonly found in the genomes of pathogenic staphylococci such as Staphylococcus haemolyticus (SH) and Staphylococcus saprophyticus (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.

Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans, whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large-scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites.

Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.

The greater amberjack Seriola dumerili is a promising aquaculture species in the Mediterranean Sea. However, first generation (F1) hatchery-produced individuals exhibit reproductive dysfunctions when reared in tanks or in cages. As part of a broader investigation into the impacts of captivity, we compared the pituitary transcriptomes of wild and F1 greater amberjack during spermatogenesis. Wild males (WILD group, n = 4) displayed normal testicular development; among F1 males, some had normal testicular development (NormalF, n = 4), while others showed spermatogenesis impairment (DysF, n = 2). Transcriptomic analysis revealed 301 differentially expressed genes (DEGs) in the DysF vs. WILD comparison and 376 DEGs in the NormalF vs. WILD comparison, while no DEGs were detected between DysF and NormalF. Protein-protein interaction (PPI) analysis identified regulatory networks involving 246 proteins across eleven functional categories in DysF vs. WILD, and 382 proteins across 10 categories in NormalF vs. WILD. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed DEGs enriched in 62 (DysF vs. WILD) and 84 (NormalF vs. WILD) pathways. Notably, several dysregulated pathways common to all F1 males are associated with reproductive functions, as well as nucleotide metabolism, calcium signaling, MAPK and mTOR signaling, neuroactive ligand-receptor interaction, Gonadotropin Releasing Hormone (GnRH) and ErbB signaling pathways. Among the DEGs, some genes were linked to GnRH neuron migration, panhypopituitarism and hypogonadotropic hypogonadism. These findings suggest that reproductive dysfunctions in F1 male greater amberjack may involve a suppression of pituitary activity mediated by dysregulation of the opioid, endocannabinoid and dopaminergic systems.