Search Results (5)

Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary–coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of high-throughput amplicon sequencing using the internal transcribed spacer (ITS) primers. Additionally, the FUNGuild database was employed to assess the potential functional traits of fungi. A total of 1242 ASV sequences, affiliated to 144 genera and five phyla, were identified. Ascomycota (68.97%) and Basidiomycota (6.41%) were the dominant fungal groups, together accounting for 75.38% of the total relative abundance of the fungal community. Significant differences were observed in the α-diversity indices (Shannon index and richness) and β-diversity of fungal communities across the three distinct salinity regions. The fungal molecular network exhibited primarily positive species interactions, with notable structural differences across salinity gradients. The low-salinity group had a large network with high modularity; the medium-salinity group a small, simple network with high centralization, and the high-salinity group a compact, moderately complex network. Symbiotrophs, saprotrophs, and pathotrophs, being the three trophic types with the highest proportions, were estimated based on ITS. A redundancy analysis (RDA) indicated that salinity was the primary factor influencing the distribution of Ascomycota communities, while the distributions of Basidiomycota, Chytridiomycota, Mucoromycota, and Rozellomycota were more strongly affected by environmental factors such as chlorophyll a, chemical oxygen demand (COD), pH, and temperature. Our work provides new scientific data on the diversity, composition, and distribution of fungal communities in Zhanjiang Bay, which helps to understand the biodiversity of fungi in the estuary–coast ecosystems. Full article

Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR. Full article

(1) Background: The widespread application of ChIP-seq technology requires annotation of cis-regulatory modules through the search of co-occurred motifs. (2) Methods: We present the web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single ChIP-seq dataset detects the composite elements (CEs) or overrepresented homo- and heterotypic pairs of motifs with spacers and overlaps, with any mutual orientations, uncovering various similarities to recognition models within pairs of motifs. The first (Anchor) motif in CEs respects the target transcription factor of the ChIP-seq experiment, while the second one (Partner) can be defined either by a user or a public library of Partner motifs being processed. (3) Results: Web-MCOT computes the significances of CEs without reference to motif conservation and those with more conserved Partner and Anchor motifs. Graphic results show histograms of CE abundance depending on orientations of motifs, overlap and spacer lengths; logos of the most common CE structural types with an overlap of motifs, and heatmaps depicting the abundance of CEs with one motif possessing higher conservation than another. (4) Conclusions: Novel capacities of Web-MCOT allow retrieving from a single ChIP-seq dataset with maximal information on the co-occurrence of motifs and potentiates planning of next ChIP-seq experiments. Full article

Cyanobacteria taxonomy is changing significantly, with many new genera and species having been uncovered from a variety of cultures over the last decade. The use of cultures allowed for genetic studies using molecular markers, e.g., 16S rRNA and 16S-23S internal transcribed spacer (ITS) rRNA, complementing the morphological and ecological information traditionally used in the description of new taxa. Presently, the culture collection BACA (Azorean Bank of Algae and Cyanobacteria) comprises more than 350 strains of cyanobacteria isolated from terrestrial, aquatic, and thermal habitats in the Azores. The phylogenetic study of more than 200 strains shows new phylogenetic clades and possibly many new genera and species. Strains belonging to possible new taxa were selected for further genetic studies by 16S rRNA and 16S-23S ITS rRNA gene amplification using the 27F and 23S30R primers and sequenced. The secondary structure of the ITS gene was predicted using the mFold web server, and the D1-D1’ helix, Box-B helix and V3 helix were compared. Transmission electron microscopy was performed on simple coccoid and filamentous strains to visualize the thylakoid position in the cell. The use of a polyphasic approach enabled the identification of several new cyanobacteria taxa, supported by the phylogenetic analysis and the identification of diacritical morphological characters. The description of these new taxa contributes to the knowledge of cyanobacteria biodiversity and a better understanding of their taxonomy, which is still very confusing and problematic, allowing a better clarification of species and genera distribution. Full article

The study aims at lowering the pressure drop and extending the service life at a given set of filter materials implementing a space between the filter layers. As design factors, the web-to-web space was implemented by inserting either a bulk air gap or porous spacer web between the filter webs. The effect of spacing, either by the air gap or by the spacer web, on the pressure drop reduction was apparent for 4-layer constructions, and the effect was greater at the higher face velocity. The use of spacer web was more effective than the air gap in reducing the pressure drop, because the porous, fluffy spacer web acted as an effective air flow channel between the compact filter layers. The loading capacity was also increased with the spacer web implementation, effectively delaying the clogging point and extending the service life. Employing both experimental investigation and numerical simulation, this study intended to provide a practical design solution to the important problem in the field of air filtration. The results of this study can be used as a practical design guide to reduce pressure drop via depth filtration. Full article