Genome sequence of Rhizobium sullae HCNT1 isolated from Hedysarum coronarium nodules and featuring peculiar denitrification phenotypes

The genome sequence of Rhizobium sullae strain HCNT1, isolated from root nodules of the legume Hedysarum coronarium growing in wild stands in Tuscany, Italy, is described here. Unlike other R. sullae strains, this isolate features a truncated denitrification pathway lacking NO/N2O reductase activity and displaying high sensitivity to nitrite under anaerobic conditions

Strain-resolved metagenomics approaches applied to biogas upgrading

Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count—two for both hydrogenotrophic archaea—and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process

Guidelines for the monitoring of Lucanus cervus

Lucanus cervus is one of the most charismatic saproxylic beetles, widely distributed in Europe. The species is typical of mature deciduous forests, especially oak woodlands. Loss and fragmentation of suitable habitats is one of the major threats for this species which is included in Annex II of the Habitats Directive. Despite several studies carried out in the last years for the monitoring methods of the species, an analytical comparison between them is still lacking. The aims of this paper are (i) to review the current knowledge about systematics, ecology and conservation practices on L. cervus and (ii) to present the research carried out during the Life MIPP project, in order to define a standard monitoring method with a suitable protocol to be used for addressing the obligations of the Habitats Directive. Overall, five methods were tested during three years in two different study areas. Based on these results, a suitable standard method for L. cervus is proposed in this paper and, in order to assess the conservation status of populations and to compare them over time, a simple method for the calculation of a reference value is provided

Valorization of sewage sludge for volatile fatty acids production and role of microbiome on acidogenic fermentation

This work explored the production of volatile fatty acids (VFA) through the anaerobic digestion of sewage sludge (SS). The first experiment took place at batch scale to evaluate the combined effect of using a thermal pre- treatment (120 \ub0C, 15 min) and different Substrate/Inoculum ratios (S/I) (1, 2, 4 and 6 g VS substrate/g VS inoculum) on the acidogenic potential of the SS. The results showed that the thermal pre-treatment influenced positively the degree of acidification of the SS at low S/I ratios, reaching maximum of 45%. Afterwards, a continuous lab-scale experiment, was set-up to study two ranges of organic loading rates (OLR): 1300\u20131600 mg COD L 121 d 121 and 2400\u20133500 mg COD L 121 d 121 . The highest degree of acidification (22%) was achieved at the lowest OLR. Analysis of the microbial community in the reactor revealed that OTUs most abundant present genes related with amino acids and carbohydrates fermentation being crucial for VFA production

The development and evaluation of exercises for meaningful responses in reading in grade two

Research chapter for this study will be found in Ash, Dorothea: "Development and evaluation of silent reading exercises in grade one" Thesis (M.A.)--Boston Universit

Genomic comparison of lactobacillus helveticusstrains highlights probiotic potential

Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-beta-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches