Correlation Between Microbial Community and Hatching Failure in Loggerhead Sea Turtle Caretta caretta

Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability. Caretta caretta is the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests of C. caretta featuring different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (Pseudomonadaceae and Brucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests' active role in modulating the sand's bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures

Initial pH Conditions Shape the Microbial Community Structure of Sewage Sludge in Batch Fermentations for the Improvement of Volatile Fatty Acid Production

Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that can be precursors of polyhydroxyalkanoate thermoplastic polyesters. The role of various operating parameters in VFA production has yet to be elucidated. This study aimed to correlate the levels of VFA yields with prokaryotic microbiota structures of sewage sludge in two sets of batch fermentations with an initial pH of 8 and 10. The sewage sludge used to inoculate the batch fermentations was collected from a Sicilian WWTP located in Marineo (Italy) as a case study. Gas chromatography analysis revealed that initial pH 10 stimulated chemical oxygen demands (sCOD) and VFA yields (2020 mg COD/L) in comparison with initial pH 8. Characterization of the sewage sludge prokaryotic community structures-analyzed by next-generation sequencing of 16S rRNA gene amplicons-demonstrated that the improved yield of VFA paralleled the increased abundance of fermenting bacteria belonging to Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes phyla and, conversely, the reduced abundance of VFA-degrading strains, such as archaeal methanogens

Enhancing volatile fatty acid production in batch test reactors by modulating microbial communities with potassium permanganate

The shift from conventional wastewater treatment plants to biorefineries is one of the most environmentally and economically sustainable pathways for extracting valuable compounds from waste. Besides chemical-physical processes, microorganisms within sewage sludge utilize organic and inorganic pollutants in the wastewater as nutrients, leading to effective water purification. However, the remaining solid sludge residue, typically destined for specific landfills or incineration, could undergo microbial fermentation to produce volatile fatty acids (VFA), metabolic precursors for biopolymers. Increasing attention has been directed towards optimizing operational parameters to enhance VFA production during sewage sludge fermentation. This study examined the impact of potassium permanganate (PP) on microbial communities during the sewage sludge’s acidogenic fermentation. The results highlighted the positive effect of PP treatment, which increased COD production and VFA yield up to 1263.5 mg/L and 664.2 mg COD/L, respectively. The presence of PP significantly enhances VFA yield promoting bacteria positively linked to VFA production

Modulation of sewage sludge microbiota for enhancing the transition from wastewater treatment plants into biorefineries in the circular economy era

Transitioning traditional wastewater treatment plants into biorefineries offers an environmentally and economically sustainable solution. Indeed, valuable compounds can still be extracted from waste. Utilizing sewage sludge (SS) with its microbial component, materials such as volatile fatty acids (VFAs) and polyhydroxyalkanoates (PHAs) within specially designed WWTP reactors can be obtained. VFAs serve as precursors to PHAs, which provide an eco-friendly alternative to petroleum-based plastics. Understanding the impact of various operating conditions on microbial components is crucial for driving microbial metabolism toward the biosynthesis of these molecules. This innovative study, part of the European project “Achieving wider uptake of water-smart solutions”, focused on evaluating the effects of two operating conditions—the headspace volume in the fermenter and the organic loading rate (ORL) in the selective-sequence batch reactor (S-SBR)—on VFA and PHA production. The wastewater from the Palermo University campus was used to inoculate a pilot plant to simulate a real urban WWTP. Our approach is based on comparing the microbial community before and after the incubation process through metagenomic DNA extraction and 16S rDNA sequencing and on quantifying PHA and VFA yields by gas chromatography analysis. This analysis revealed that 40% of headspace volume in a 225L fermenter and an ORL of 1.3 g COD L−1d−1 in S-SBR maximized VFA and PHA production. The metataxonomic analysis showed significant changes in the SS microbiota structure, promoting the growth of bacteria like Proteobacteria, Firmicutes, and Actinobacteria while reducing Verrucomicrobia. These findings enhance our understanding of bacterial modulation under various operational conditions and highlight the potential for exploiting the resources in SS within a circular economy framework

Enhancing volatile fatty acid production from sewage sludge in batch fermentation tests

Volatile fatty acids (VFA) from sewage sludge represent an excellent recovered resource from wastewater treatment. This study investigated four sludge pre-treatments (namely, potassium permanganate - KMnO4, initial pH = 10, initial pH = 2.5 and low-temperature thermal hydrolysis) by operating batch reactors under acidogenic fermentation conditions. Results revealed that 0.1 g KMnO4/g of total suspended solids represents the best pre-treatment obtaining up to 2713 mgCOD L-1 and 452 mgCOD/g of volatile suspended solids. These results also paralleled metataxonomic analysis highlighting changes in prokaryotic microbial structures of sewage sludge of the batch fermentations subjected to the different pre-treatments

Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure

The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-tobacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH

Extending the clinical spectrum of X-linked Tonne-Kalscheuer syndrome (TOKAS):new insights from the fetal perspective

INTRODUCTION: Tonne-Kalscheuer syndrome (TOKAS) is a recessive X-linked multiple congenital anomaly disorder caused by RLIM variations. Of the 41 patients reported, only 7 antenatal cases were described.METHOD: After the antenatal diagnosis of TOKAS by exome analysis in a family followed for over 35 years because of multiple congenital anomalies in five male fetuses, a call for collaboration was made, resulting in a cohort of 11 previously unpublished cases.RESULTS: We present a TOKAS antenatal cohort, describing 11 new cases in 6 French families. We report a high frequency of diaphragmatic hernia (9 of 11), differences in sex development (10 of 11) and various visceral malformations. We report some recurrent dysmorphic features, but also pontocerebellar hypoplasia, pre-auricular skin tags and olfactory bulb abnormalities previously unreported in the literature. Although no clear genotype-phenotype correlation has yet emerged, we show that a recurrent p.(Arg611Cys) variant accounts for 66% of fetal TOKAS cases. We also report two new likely pathogenic variants in RLIM, outside of the two previously known mutational hotspots.CONCLUSION: Overall, we present the first fetal cohort of TOKAS, describe the clinical features that made it a recognisable syndrome at fetopathological examination, and extend the phenotypical spectrum and the known genotype of this rare disorder.</p

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Characterization of microorganisms and by-products beneficial to human and environmental health: A perspective from a local dairy to industrial use

Microbial communities are crucial in several ecosystems and pivotal in helping various human, animal, and environmental health aspects. Microbial cells act as mini-biofactories, synthesizing economically and ecologically essential compounds that benefit and improve several fields. In a world seeking biological, sustainable, and safe methods, microbial communities and their by-products offer a green, low-cost alternative to chemical and polluting industrial processes. These bacterial communities help several industrial sectors by providing eco-friendly and secure solutions for biotechnologies processes. This PhD project, funded by the European project PON 2014 -2020 and the Fondo per lo Sviluppo e la Coesione (FSC), aims to reinforce the innovation capacity of regional production systems. Developed in collaboration with Tenuta Manchi, an organic dairy farm in Caccamo (Palermo, Italy), the project seeks to contribute to the challenge of food safety issues and enhance the products of an inland area of Sicily. Organic farms provide excellent sources of microbial biodiversity for biotechnological applications. This thesis aims to characterize bacteria from soil and acid curd (derived from goat milk) to produce various by-products, such as bacteriocins, antibiofilm compounds, antibiotics, and enzymes, to improve agricultural products' organoleptic and sensory properties while promoting local community development. In this context, the results of this PhD project advance the exploitation of environmental microbial biodiversity in an uncontaminated Sicilian environment and highlight the potential of microbial resources for industrial improvement and biotechnological applications