Temporal dynamics of total and active prokaryotic communities in two Mediterranean orchard soils treated with solid anaerobic digestate or managed under no-tillage

AbstractA field experiment was carried out to investigate the impact of two improved tillage systems (conventional tillage combined with the incorporation of solid anaerobic digestate, no-tillage) on the prokaryotic community composition in two tree orchard (olive, citrus) soils with contrasting texture, carbonate content, and pH, located in Southern Italy. Soil samples were taken over a 5-month period to assess immediate (2 days) vs short-term (7 and 18 weeks) responses. Phylogenetic diversity and compositional shifts of both total and metabolically active soil prokaryotic communities were assessed by next-generation sequencing of 16S rRNA gene templates from soil-extracted DNA/RNA. In both digestate-treated soils, copiotrophic α-Proteobacteria and oligotrophic Acidobacteria, Gemmatimonadetes, and Verrucomicrobia showed an immediate (2 days) but short-lived (7 weeks) shift in their relative abundance similar in persistence but not in magnitude; whereas selective soil type-dependent responses were observed for Actinobacteria, Chloroflexi, Firmicutes, and Planctomycetes. The autochthonous soil microbiota demonstrated resilience to the addition of the anaerobic digestate, which was dominated by Firmicutes, Bacteroidetes, Deinococcus-Thermus, and Euryarchaeota (Methanomicrobia). Likewise, a temporary increase in the relative abundances of copiotrophic taxa (Firmicutes, Bacteroidetes, Thaumarchaeota) was observed under conventional tillage, especially in the sandy loam (citrus) soil. Conversely, no-tillage favored the establishment of oligotrophic Chloroflexi and Verrucomicrobia in both soils. The active and the total prokaryotic communities differed from each other only in physically disturbed soils. Soil management induced compositional shifts in the predominant microbial copiotrophic/oligotrophic community balance, whose persistence was linked to the tillage system, while magnitude depended on soil type

Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system

Background: Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms. These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra-and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. annosum, we investigated mechanisms of evolution of SSRs.Results: Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- and tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5' untranslated region (5'UTR). Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5'UTR were more conserved within species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions.Conclusions: Our work linked the variation and the type of SSRs with regions upstream 5'UTR, putatively harbouring regulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome. Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environment mediated by SSRs

SARS-CoV-2 Infection Incidence and Outcome Before and After Full Vaccination in Patients With Monoclonal Gammopathy of Undetermined Significance

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Essential oil chemical composition and antifungal effects on Sclerotium cepivorum of Thymus capitatus wild populations from Calabria, southern Italy

The paper reports the qualitative and quantitative composition and its antifungal activities of Thymus capitatus (L.) Hoffmanns. & Link, Lamiaceae, essential oils isolated by hydrodistillation from the aerial parts of plants collected in Calabria, Southern Italy. The essential oils of 22 samples were analysed by GC-Flame ionization detection and GC/MS. A total of sixty five compounds were identified. Phenols were present in highest percentage (average: 79,03%). Carvacrol was the main component (81,52%-78,40%) in all samples, confirming that T. capitatus is a carvacrol chemotype, according to literature data for this species. This essential oil was also characterized by high level of biogenetic precursor of the phenols: p-cimene (4,98%), γ-terpinene (3,13%) and by β-cariophyllene, were the most abundant sesquiterpene hydrocarbons. Antifungal activity against Sclerotium cepivorum Berk., a soil born fungus, was tested. At the concentration of 250 ppm there was no development of fungal mycelium. To our knowledge, studies have never been conducted on Calabria wild populations of T. capitatus essential oil nor were conducted studies on parasitic fungi of specific interest for crops such as Sclerotium cepivorum

Additional file 1: of Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system

SSRs markers used to determine the genetic variability of the five populations of H. irregulare and H. annosum . (DOCX 17 kb

Additional file 2: of Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system

Locus per locus fixation index (Fst) and gene flow (2Nm) among 2 distinct sampling populations of H. irregulare, both from Latium, and from 3 populations of H. annosum from various regions of Northern and central Italy, including Latium . (DOCX 14 kb

Additional file 4: of Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system

List of Heterobasidion genotypes analyzed . (DOCX 14 kb