Biology subjects

Squartini, A.

Publications and source records attributed to Squartini, A..

5 recordsLinked to original sources

bioRxiv2026

DNA Traces on the Shroud of Turin: Metagenomics of the 1978 Official Sample Collection

This research provides original insights into the diversity of DNA extracted from samples collected in 1978 from the Turin Shroud, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. Several human mitochondrial DNA (mtDNA) lineages were identified, including K1a1b1a, which matches the 1978 official collectors mitogenome, H2a2 (i.e. the lineage of the mtDNA reference sequence rRCS), H1b, which is common in Western Eurasia, and H33, which is prevalent in the Near East and frequent among the Druze. Moreover, the reconstructed microbiome of the Shroud reveals a rich tapestry of multiple microbes commonly found on the human epidermis, as well as archaeal communities adapted to high salinity, and fungi including molds. This is indicative of the Shrouds preservation conditions over the centuries. Additionally, the presence of abundant Mediterranean endemic red coral, various cultivated plants (e.g. carrot, wheat, corn, bananas, and peanuts) and domesticated animals (e.g. cattle, pigs, chickens, dogs, and cats) provide a fascinating glimpse into the diverse biological sources of the contaminants that have accumulated on the Turin Shroud over time. Finally, radiocarbon dating of two distinct threads collected from the reliquary provides evidence of their use to repair the Shroud in the years 1534 and 1694 of the Common Era (CE). Significance statementAn in-depth metagenomic analysis was conducted on several linen strands collected from different areas of the body image of the Man of the Shroud during the official sampling in 1978. Our analyses revealed several human mtDNA lineages, including one common in Western Eurasia and another prevalent in the Near East. Additionally, the diversity of animal and plant species identified details the significant environmental contamination of the Shroud that likely occurred in recent centuries, particularly following the voyages of Marco Polo and Christopher Columbus. Radiocarbon dating of two distinct textile residuals from the Shrouds reliquary indicated a time range between 1451 and 1800 CE, overlapping with the period of its repair interventions.

genomics↗

bioRxiv2025

What can the current global bacterial taxonomy knowledge reveal about the actual (past and present) ecological success of each lineage?

Our up-to-date sources of the man-known microbiology are publicly available, and include, as the most complete repository, the Genome Taxonomy Database GTDB https://gtdb.ecogenomic.org/, encompassing, on one end, 196 phyla, across which, at the other end, 107,235 bacterial species have been currently defined. The intermediate ranks feature 541 classes, 1,863 orders, 4,896 families, and 23,112 genera. Such a dataset is hereby used, not as a source of DNA sequences but rather as the handiest and presently most exhaustive checklist matrix of our current taxonomical notions. In the mathematical zero assumption of an equal opportunity chance for each taxon throughout a parallel evolution, a perfectly even community featuring those values would display today, within each of the 196 phyla, the mean values that would result by dividing the actual observed ones by the number of phyla. Such a virtual assemblage would therefore have the following numbers per phylum in each of them: 2.76 classes, 9.51 orders, 24.98 families, 117.92 genera, and 547.12 species. The deltas between these set-point null hypothesis values and the truly observed and described numbers for each lineage member featured by the database (numbers of species per genus, genera per family, families per order, orders per class, and classes per phylum) can reveal how much, and in which lineages, their evolution differed from each of those mere ranks means. The comparison among the actual data also allows one to answer a series of questions: 1) What is the actually occurred uneven dynamics of evolutionary differentiation across each lineage?; 2) Which taxa are, at present, the winners of the evolutionary race?, And, have they always led the run, or when did they overtake their formerly faster competitors? 3) Are there chronological bottlenecks that violate the assumption of either a constant or of a progressive speed of evolution (i.e. is speciation to each deeper, and more modern rank, consistently faster than its former step, or is there evidence of evolutionary congestion jams?); 4) which past step turns out to have been the most determinant to shape the modern assemblages? Which ones, among the taxa dominating todays diversity, have risen up just recently (e.g. by a massive radiation from genera), and which ones had instead started or accomplished the critical expansion that still keeps them as leaders, in remote times (e.g. by class or order radiations?; 5) Which patterns characterize in this respect the lineages of the most relevant bacterial agents in food, soil, industrial, clinical and environmental microbiology? Corresponding queries are addressed for the 5,869 species of Archaea. The methods and the results of this database-mined in silico analysis are hereby presented and discussed. The dataset provided as supplementary material allows the reader to address the above aspects for any taxon of interest within the 107,235 species covered by this analysis.

microbiology↗

bioRxiv2024

Modulatory effect of plasma-activated water on arbuscular mycorrhizal symbiosis in Lotus japonicus

Plasma-activated water (PAW) is a recently developed cutting-edge technology that is increasingly gaining interest for its applications in medicine, food industry and agriculture. In plant biology, PAW has been shown to promote seed germination, plant growth, and plant resistance to biotic and abiotic stresses. Despite increasing knowledge of the beneficial effects exerted by PAW on plants, little information is currently available about how this emerging technology may affect the mutualistic plant-microbe interactions in the rhizosphere. In this work we have investigated the impact of irrigation with PAW, generated by a plasma torch, on arbuscular mycorrhizal (AM) symbiosis between the model legume Lotus japonicus and the AM fungus Rhizophagus irregularis. Since PAW sensing by plants has recently been demonstrated to occur through calcium-mediated signalling, we monitored early cellular responses to different doses of PAW in L. japonicus roots expressing the Ca2+-sensitive photoprotein aequorin targeted to either the cytosol or nucleus. Quantitative analyses of AM fungal accommodation in host roots along with phosphate accumulation in leaves, as well as chemical analysis of N, C, S in shoots, showed that treatments with PAW play a modulatory role on plant AM symbiotic performance, in a manner dependent on the time interval of water exposure to the plasma and on the duration of plant irrigation treatment with PAW. Establishing a solid scientific ground for plasma-related technology may provide key elements to develop tools and treatments aimed to increase crop plant yield in a sustainable manner.

plant biology↗

bioRxiv2024

Plant phenotypic differentiation outweighs genetic variation in shaping the lettuce leaf microbiota

Lettuce is a widely consumed raw vegetable, making it crucial to understand and predict its leaf-associated microbial communities for the benefit of both plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated the impact of three key plant factors -genetic distance, morphology and leaf micro- and macronutrient content- on the composition and diversity of lettuce leaf bacterial communities. Using 131 fully-sequenced Lactuca sativa genotypes, we analyzed their leaf-associated bacterial communities via 16S rRNA amplicon sequencing. Our findings revealed that morphological classification, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with shoot traits they explained 13.9% of the observed bacterial diversity. Further analysis of 10 specific leaf morphological traits showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. The strong association between leaf morphology and bacterial community structure suggests that phenotypic traits play a disproportionately large, yet understudied, role in leaf microbiota establishment offering new potential for manipulation by breeders.

plant biology↗

bioRxiv2020

The distribution of functional N-cycle related genes and nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Nitrogen (N) fertilizers applied to agricultural soils result in the release of nitrogen, mainly nitrate (NO3-) in addition to nitrous oxide (N2O) and ammonia (NH3), into the environment. Nitrogen transformation in soil is a complex process and the soil microbial population can regulate the potential for N mineralization, nitrification and denitrification. Here we show that agricultural soils under standard agricultural N-management are consistently characterized by a high presence of gene copies for some of the key biological activities related to the N-cycle. This led to a strong NO3- reduction (75%) passing from the soil surface (15.38 {+/-} 11.36 g N-NO3 kg-1 on average) to 1 m deep layer (3.92 {+/-} 4.42 g N-NO3 kg-1 on average), and ensured low nitrate presence in the deepest layer. Under these circumstances the other soil properties play a minor role in reducing soil nitrate presence in soil. However, with excessive N fertilization, the abundance of bacterial gene copies is not sufficient to explain N leaching in soil and other factors, i.e. soil texture and rainfall, become more important in controlling these aspects.

ecology↗