Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software

RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains.Results: In order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role.Conclusions: By comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis

A global gene evolution analysis on Vibrionaceae family using phylogenetic profile

<p>Abstract</p> <p>Background</p> <p><it>Vibrionaceae </it>represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens.</p> <p>In this work we propose an improved phylogenetic profile analysis on 14 <it>Vibrionaceae </it>genomes, to study the evolution of this family on the basis of gene content.</p> <p>The phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently present or absent within different genomes. This allows the prediction of hypothetical functions on the basis of a shared phylogenetic profiles. Moreover this approach is useful to identify putative laterally transferred elements on the basis of their presence on distantly phylogenetically related bacteria.</p> <p>Results</p> <p><it>Vibrionaceae </it>ORFs were aligned against all the available bacterial proteomes. Phylogenetic profile is defined as an array of distances, based on aminoacid substitution matrixes, from single genes to all their orthologues. Final phylogenetic profiles, derived from non-redundant list of all ORFs, was defined as the median of all the profiles belonging to the cluster. The resulting phylogenetic profiles matrix contains gene clusters on the rows and organisms on the columns.</p> <p>Cluster analysis identified groups of "core genes" with a widespread high similarity across all the organisms and several clusters that contain genes homologous only to a limited set of organisms. On each of these clusters, COG class enrichment has been calculated. The analysis reveals that clusters of core genes have the highest number of enriched classes, while the others are enriched just for few of them like DNA replication, recombination and repair.</p> <p>Conclusion</p> <p>We found that mobile elements have heterogeneous profiles not only across the entire set of organisms, but also within <it>Vibrionaceae</it>; this confirms their great influence on bacteria evolution even inside the same family. Furthermore, several hypothetical proteins highly correlate with mobile elements profiles suggesting a possible horizontal transfer mechanism for the evolution of these genes. Finally, we suggested the putative role of some ORFs having an unknown function on the basis of their phylogenetic profile similarity to well characterized genes.</p

Guidelines for the monitoring of Rosalia alpina

Rosalia alpina (Linnaeus, 1758) is a large longhorn beetle (Coleoptera: Cerambycidae) which is protected by the Habitats Directive and which typically inhabits beech forests characterised by the presence of mature, dead (or moribund) and sun-exposed trees. A revision of the current knowledge on systematics, ecology and conservation of R. alpina is reported. The research was carried out as part of the LIFE MIPP project which aims to find a standard monitoring method for saproxylic beetles protected in Europe. For monitoring this species, different methods were tested and compared in two areas of the Apennines, utilising wild trees, logs and tripods (artificially built with beech woods), all potentially suitable for the reproduction of the species. Even if all methods succeeded in the survey of the target species, these results showed that the use of wild trees outperformed other methods. Indeed, the use of wild trees allowed more adults to be observed and required less intensive labour. However, monitoring the rosalia longicorn on wild trees has the main disadvantage that they can hardly be considered “standard sampling units”, as each tree may be differently attractive to adults. Our results demonstrated that the most important factors influencing the attraction of single trunks were wood volume, sun-exposure and decay stage. Based on the results obtained during the project LIFE MIPP, as well as on a literature review, a standard monitoring method for R. alpina was developed

Updated distribution of Osmoderma eremita in Abruzzo (Italy) and agro-pastoral practices affecting its conservation (Coleoptera: Scarabaeidae)

New records of Osmoderma eremita (Scopoli, 1763) (Coleoptera: Scarabaeidae: Cetoniinae) are reported for Abruzzo (Italy), together with a review of its distribution in this region. O. eremita is a saproxylic beetle dependent on the presence of hollow deciduous trees with abundant wood mould in their cavities. The major threats for the species are habitat loss and fragmentation. EU Habitats Directive requests to the member States its protection and the monitoring of its conservation status. Detection of its occurrence is the first step to protect the species. The surveys have been carried out in ten sites of Abruzzo by using black cross-windows traps baited with specific pheromone. The species has been recorded for the first time in the Sant'Antonio forest and its presence is confirmed in the Peligna Valley, after a decade. The populations seem to be confined to small patches of suitable habitats. At local level, the abandonment of the pollarding practice (willow and beech forests) and the use of pollarded trees as biomass for fuel are the major threats for this species. Indeed some key actions, such as the protection of old hollow trees and the continuation of pollarding practice in rural landscape, could be key factors for the conservation strategies of the species in the study area

Scientists’ attitudes about citizen science at Long-Term Ecological Research (LTER) sites

A profound transformation, in recent decades, is promoting shifts in the ways ecological science is produced and shared; as such, ecologists are increasingly encouraged to engage in dialogues with multiple stakeholders and in transdisciplinary research. Among the different forms of public engagement, citizen science (CS) has significant potential to support science-society interactions with mutual benefits. While many studies have focused on the experience and motivations of CS volunteers, scarce literature investigating the perspectives of researchers is available. The main purpose of this paper is to better understand scientists’ attitudes about CS in the context of its potential to support outcomes that extent beyond more traditional ones focused on promoting science knowledge and interest. We surveyed the scientific community belonging to the International Long-Term Ecological Research (ILTER) network because ILTER is of interest to multiple stakeholders and occurs over long time scales. Via an online questionnaire, we asked ILTER scientists about their willingness to participate in different types of public engagement, their reasons for participating in CS, the associated barriers, and any impacts of these efforts on them. Our findings show that many ILTER scientists are open to participating in CS for a wide range of reasons; the dominant ones involve deeper public engagement and collaboration. The barriers of greatest concern of these respondents were the lack of institutional support to start and run a CS project and the difficulty of establishing long-term stable relationships with the public. They reported impacts of CS activities on how they pursue their work and acknowledged the benefit of opportunities to learn from the public. The emerging picture from this research is of a community willing and actively involved in many CS projects for both traditional reasons, such as data gathering and public education, and expanded reasons that activate a real two-way cooperation with the public. In the ILTER community, CS may thus become an opportunity to promote and develop partnerships with citizens, helping to advance the science-society interface and to rediscover and enhance the human and social dimension of the scientific work

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

BACKGROUND: 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 adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

BackgroundThe anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.ResultsThe primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.ConclusionsThis study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization

EPURAEA DEUBELI REITTER, 1898, A CONFIRMED SAPROXYLIC SAP BEETLE FOR THE ITALIAN FAUNA (Coleoptera, Nitidulidae)

During ecological investigations on saproxylic beetle communities at Monte Baldo (Veneto, Verona province), two specimens of Epuraea deubeli Reitter, 1898 (Coleoptera, Nitidulidae) were recently collected. It is the first known sure record of this species in Italy (previously known from Northern, Eastern, and Central Europe, southwards to Austria, and from Western Siberia)

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

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 not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies