Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapsho

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d’Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.

Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/ .

MOSE is a system of mobile gates engineered to temporarily isolate the Venice Lagoon from the Adriatic Sea and to protect the city from flooding during extreme high tides. Within the framework of the Venezia2021 program, we conducted two enclosure experiments in July 2019 (over 48 h) and October 2020 (over 28 h) by means of 18 mesocosms, in order to simulate the structural alterations that microphytobenthos (MPB) assemblages might encounter when the MOSE system is operational. The reduced hydrodynamics inside the mesocosms favored the deposition of organic matter and the sinking of cells from the water column towards the sediment. Consequently, MPB abundances increased over the course of both experiments and significant changes in the taxonomic composition of the community were recorded. Species richness increased in summer while it slightly decreased in autumn, this latter due to the increase in relative abundances of taxa favored by high organic loads and fine grain size. By coupling classical taxonomy with 18S rRNA gene metabarcoding we were able to obtain a comprehensive view of the whole community potential, highlighting the complementarity of these two approaches in ecological studies. Changes in the structure of MPB could affect sediment biostabilization, water turbidity and lagoon primary production.

Environmental DNA (eDNA) metabarcoding is widely used in biodiversity monitoring, and its popularity is also growing because of its potential to simultaneously detect multiple taxonomic groups, allowing holistic community assessments. When working with water samples, the choice of the filter type is one of the key methodological factors influencing community characterization, with 0.22 μm pore size filters typically used for microbial communities and larger filters for eDNA of larger organisms. However, as holistic community assessments are increasingly adopted, the use of a single filter pore size would help to optimize sampling and experimental efforts. Yet, it remains unclear whether filters with large pore sizes can effectively capture both microbial and macro‐organism eDNA. This study evaluates the use of 0.45 μm filters, commonly used for metazoan eDNA metabarcoding, in assessing microbial diversity across different coastal environments. Replicates of water samples from the Venice Lagoon and nearby waters were filtered independently using both 0.45 μm and the standard 0.22 μm pore size filters and analyzed through 16S rRNA gene metabarcoding. Both filters capture a shared core microbial community, but they also retain distinct taxa. Alpha diversity was significantly higher in samples collected with the 0.45 μm filters, which also showed a more effective recovery of particle‐associated microbes. Our work contributes to optimizing eDNA‐based methodologies for large‐scale multi‐taxa biodiversity monitoring, demonstrating that 0.45 μm filters can effectively capture microbial diversity and supporting their use in holistic studies in aquatic environments.