Alessandro Vezzi

University of Padua | UNIPD · Department of Biology

Introduction: Grey mullets comprise different species that represent the most ubiquitous teleost families in the planet’s coastal waters. They are an important proportion of the Mediterranean lagoon’s production and have been recently considered cultivated marine fish. This study aimed to explore the intestinal microbial communities of grey mullets...

Grey mullets comprise different species which represent the most ubiquitous teleost families in the planet coastal waters. They represent an important proportion of the Mediterranean lagoons production and have been recently considered a cultivated marine fish. This study aimed to explore the intestinal bacterial communities of 34 wild-caught grey...

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 Explor...

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 t...

The surface of seaweed serves as an interactive face between the seaweed and the surrounding environment. Microorganisms associated with seaweed modulate diverse functions, including morphological development, consumption of organic matter, and defence. These microbial communities experience changes in response to environmental perturbations and se...

The objective of this study was to explore the diversity of gut microbial communities from 34 wild mullets inhabiting a brackishwater ecosystem (Santa Giusta Lagoon, Sardinia, Italy,) along four different seasons, using next generation sequencing (NGS). Amplicon sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene was performed, yield...

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 negati...

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the...

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 s...

Background 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. ResultsHere we describe QueryOR, a web platform suitable for searching among known candidate genes as wel...

The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would n...

Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compar...

Pairwise alignment of region 1 (see Figure 2) of metal resistance fGI and pAM1A3. The large gap in the alignment refers to a mobile element which is present in the fGI but absent in the pAM1A3 sequence. The alignment was conducted using Geneious aligner with default parameters.

Abundance of the 100 most abundant functional SEED subsystems representation in different assembly methods compared to the final genome and plasmid. Asterisk marked columns showed significant difference (p = 0.05, Fishers Exact Test with Benjamini-Hochberg False Discovery Rate).

Sequence comparison using BLAST ring image generator (Alikhan et al., 2011), of pAM1A3 to four isolated A. macleodii plasmids and pGLAAG01 isolated from Glaciecola sp. 4H-3-7 + YE-5 (outer rings, colored according to the legend) to pAM1A3 (inner black thin ring). The regions in the figure represent at least 70% identity and an e-value ≤ 0.00001.

Phylogeny of selected genes on the pAM1A3 plasmid. The gray rectangles refer to genes placed within the metal resistance fGI. The phylogenetic trees were built using the Neighbor–Joining method, with bootstrap representation of >80% in all of the branches in all of the trees. The numbers in round brackets refer to the position of the gene in the pl...

Validation of the presence of plasmid pAM1A3 using PFGE. (A) Schematic illustration of the plasmid ring with the restriction digest sites; the table within the ring refers to the expected band sizes using each one of the enzymes. Two regions with higher sequencing coverage, which might be duplicated (see below), are shown. (B) PFGE gel of the plasm...

Phylogenetic analysis of Alteromonas strains. Maximum Likelihood tree of all Alteromonas strains for which a whole genome sequence is available. The numbers on the branches represent bootstraps percentage. (A) According to 16S rDNA sequences. (B) According to concatenated alignment of the following housekeeping genes: adenylylsulfate kinase, DNA ad...

BlastN results of draft A. macleodii MIT1002 genome search against the sequence of pAM1A3 plasmid (e-value ≤10e-1). Regions 1 and 2 refer to the mutual regions of the pAM1A3 plasmid and metal resistance fGI (see Figure 2).

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a singl...

Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae.Here we report a high quality genomic assembly of Nannochloropsis gaditana, consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of chromosomes. We identified 10,646 complete genes and charact...

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2...

Next generation sequencing technology has considerably improved over the past few years, making easier and more affordable the shotgun sequencing approach. Short reads are particularly popular as they are very easy and cheap to produce. On the other hand, their assembly results in the generation of a vast number of relatively short contigs that wou...

The plastome sequence of the European cultivated potato, Solanum tuberosum subsp. tuberosum (tbr, GenBank accession no. DQ386163), was compared with that of S. bulbocastanum, a wild potato relative (blb, GenBank accession no. DQ347958), in order to characterize the degree and type of variability in different genomic regions, and develop molecular m...

The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative...

Microorganisms adapted to piezopsychrophilic growth dominate the majority of the biosphere that is at relatively constant low temperatures and high pressures, but the genetic bases for the adaptations are largely unknown. Here we report the use of transposon mutagenesis with the deep-sea bacterium Photobacterium profundum strain SS9 to isolate doze...

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would requir...

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modula...

Multiple alignment of the 192 Mob-domain containing proteins. The label number refers the fourth column in Table 1S of the supplementary materials and corresponds to the gene code.

The ?rst column reports the organism name, the second one the gene code whereas the third column the Mob class. Finally the fourth column shows the code number used in the multiple alignment in Figure 1S.

The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the...

Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In this work we propose an improved phylogenetic profile analysis on 14 Vibrionaceae genomes, to study the evolution of this family on the basis of gene content. The phylogeneti...

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology...

List of Gene Ontology categories of differentially expressed genes. In this table differentially expressed genes reported in Additional file 3 are categorized in Gene Ontology classes using GoMiner software. Only highly significant GO classes are reported. Table columns show: (1) the Gene Ontology ID, (2) the total number of P. profundum SS9 genes...

Codon bias relative to average gene versus third position GC content in eight variable regions of the Photobacterium profundum SS9 genome. In these graphs are represented only ORFs longer than 200 codons. Eight variable regions of the SS9 genome are considered, one for each graph. In red are highlighted ORFs located in regions that were found absen...

Detection of the 80 kbp plasmid in two different P. profundum strains. Comparison of strain TW30 (lanes A, B) with parental strain DB110 (lanes C, D) with plasmid specific primers. Lane E: no DNA control for PCR. Lane F: 2-log ladder marker (New England Biolabs).

List of differentially expressed genes obtained in microarray experiments. This table reports only the ORFs identified univocally by the microarray clones and only those having log2 ratio ≥|0.7| and "d score" obtained from SAM analysis = |2.3| (indicated with "1" in columns 7–12). Table columns report respectively: (1, 2, 3) ORFs differentially exp...

List of ORFs absent only in 3TCK strain. Data obtained from genomic comparison experiments between 3TCK (the pressure sensitive strain) and SS9 strain. In this table are reported ORFs that were found absent only in 3TCK and not in DSJ4 strain. In order to obtain a more reliable result, clones obtained from SAM analysis of 3TCK strain were filtered...

Deep-sea life requires adaptation to high pressure, an extreme yet common condition given that oceans cover 70% of Earth's surface and have an average depth of 3800 meters. Survival at such depths requires specific adaptation but, compared with other extreme conditions, high pressure has received little attention. Recently, Photobacterium profundum...

Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure ada...

Arabidopsis thaliana is an important model system for plant biologists1. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis2 and in 1999 the sequence of the first two chromosomes was reported3, 4. The sequence of the last three chromosomes and an analysis of the whole ge...

In this work, we describe the disruption of nine ORFs of S. cerevisiae (YNL123w, YNL119w, YNL115c, YNL108c, YNL110c, YNL124w, YNL233w, YNL232w and YNL231c) in two genetic backgrounds: FY1679 and CEN.PK2. For the construction of the deletant strains, we used the strategy of short flanking homology (SFH) PCR. The SFH-deletion cassette was made by PCR...