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Biology subjects

Milazzo, M.

Publications and source records attributed to Milazzo, M..

5 recordsLinked to original sources

Biological and ecological insights from a rare underwater footage of the white shark (Carcharodon carcharias) in the Mediterranean Sea

The white shark Carcharodon carcharias (Linnaeus, 1758) is one of the most iconic and threatened marine predators globally and is listed as critically endangered by the IUCN in the Mediterranean Sea, where populations are primarily affected by fishing pressure and the degradation of critical habitats. Available information on Mediterranean white sharks mostly relies on fishing interactions and opportunistic surface records, thereby limiting evaluations on the species ecology. Here, we report an exceptionally rare underwater encounter with this species, documented by divers involved in an expedition aimed at removing ghost fishing gear from a World War II shipwreck in the Strait of Sicily (SoS), central Mediterranean. Given the exceptional nature of this observation, we analysed the video footage in detail with the aim of providing morphological information and novel insights into the species ecology. The footage analysis also allowed close observations on behavioural aspects and on interspecific and parasitic associations, thus providing information that is rarely achievable through surface sightings or from captured individuals, which historically represent the majority of records for this species in the region. To contextualize this observation within the SoS--an area suggested to function as a nursery and reproductive ground for the species--we also provide an updated compilation of records reported in the scientific literature over the last decade, adding 18 new records to existing datasets. This study highlights the value of shipwrecks as observation sites for rare and elusive species, and underscores the importance of non-invasive, video-based approaches in advancing knowledge of a species whose ecology in the Mediterranean remains poorly understood.

ecology↗

Modular metagenomic analysis of pan-domain symbioses with MAGUS

Metagenomic analysis of deeply sequenced, eukaryotic-dominant symbiotic communities can be difficult for many metagenomic workflows. Here, we present MAGUS, a bioinformatic toolkit that uses a suite of custom bioinformatic methods for iterative genome assembly and filtering of pan-domain communities, where eukaryotes, bacteria, viruses, and functionally annotated gene catalogs are resolved and analyzed over a series of interconnected, modular software components. We evaluated MAGUS using deeply sequenced (median depth: 579 million reads) ten samples of hard corals, soft corals, and hydrozoans, which comprise complex, eukaryote-dominated symbiotic communities. We successfully resolved phylogenetically comparable host (N = 10), algal (N = 6), bacterial (N = 55), and viral (N = 160,925) genomes, as well as a gene catalog comprising 15,369,684 non-redundant genes (7.6% functionally annotated). MAGUS is available on GitHub (https://github.com/two-frontiers-project/2FP_MAGUS/).

bioinformatics↗

The microbiology and geochemistry of the shallow-water hydrothermal vents of the Gulf of Naples, Italy

Shallow-water hydrothermal vents are dynamic ecosystems that occur below 200 m in tectonically active regions of the planet. While their geochemical composition has been investigated in several locations, knowledge about the microbial diversity they harbour remains scarce. Moreover, the relationships between hydrothermal fluid chemistry, geological settings and microbial community structure in shallow vents have not been explored in detail. Here, we investigate the interplay between fluid geochemistry and microbial diversity in two underwater volcanic regions in the Gulf of Naples, Italy, one under the influence of the Somma-Vesuvio volcano and the other located within the underwater portion of the Campi Flegrei caldera. By combining 16S rRNA amplicon sequencing with geochemical measurements, and by contextualizing it with previous geochemical measurements done in the region, we found that hydrothermal fluid chemistry, influenced by the geological setting where the vents are hosted, plays a key role in shaping microbial ecological niches, and imposes strong selective pressures on the resident microbial communities. We additionally describe two new shallow vent sites, contributing to the characterization of the hydrothermalism in the area and unveiling the biodiversity associated with shallow-water hydrothermalism in the region.

microbiology↗

Cyanobacteria newly isolated from marine volcanic seeps display rapid sinking and robust, high density growth

Cyanobacteria are photosynthetic organisms that play important roles in carbon cycling as well as promising bioproduction chassis. Here, we isolate two novel cyanobacteria, UTEX 3221 and UTEX 3222, from a unique marine environment with naturally elevated CO2. We describe complete genome sequences for both isolates and, focusing on UTEX 3222 due to its planktonic growth in liquid, characterize biotechnologically-relevant growth and biomass characteristics. UTEX 3222 outpaces other fast-growing model strains on solid medium. It can double every 2.35 hours in a liquid medium and grows to high density (>31g/L biomass dry weight) in batch culture, nearly double that of Synechococcus sp. PCC 11901, whose high-density growth was recently reported. In addition, UTEX 3222 sinks readily, settling more quickly than other fast-growing strains, suggesting improved de-watering of UTEX 3222 biomass. This settling behavior can be explained in part by larger cell volume. These traits may make UTEX 3222 a compelling choice for photosynthetic bioproduction from CO2. Overall, we find that bio-prospecting in environments with naturally elevated CO2 may uncover novel CO2-metabolizing organisms with unique characteristics.

microbiology↗

Complex sex-specific age-related changes in DNA methylation including variability, epimutations and entropy

In humans, females live longer than males but experience a worse longevity, as genome-wide autosomal DNA methylation differences between males and females have been reported. So far, few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes shows age-by-sex interaction. We experimentally validated 2 regions mapping in FIGN and PRR4 genes, and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and in entropy, we showed that the number of probes showing age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.

genomics↗