CellBioNewsFeb 8, 2025

Scientists elucidate #molecular mechanisms behind #dinoflagellate #cyst #dormancy.

#cDNA #DinoSL #genomics #metatranscriptome #hormones #ABA #GA #metabolomics

https://phys.org/news/2025-02-scientists-elucidate-molecular-mechanisms-dinoflagellate.html

Scientists elucidate molecular mechanisms behind dinoflagellate cyst dormancy

Dinoflagellates play crucial roles in aquatic ecosystems, particularly as major contributors to harmful algal blooms. They can enter a dormant stage, known as the resting cyst stage, that allows them to survive for extended periods—up to 150 years—in marine sediments. This dormancy is essential for their annual population dynamics, blooming cycles, and geographic expansion.

Phys.org
CellBioNewsSep 16, 2023

Lack of maternal care found to affect development, #microbiome and #health of wild #bees.

#transcriptome #metatranscriptome

https://phys.org/news/2023-09-lack-maternal-affect-microbiome-health.html

Lack of maternal care found to affect development, microbiome and health of wild bees

Most wild bees are solitary, but one tiny species of carpenter bees fastidiously cares for and raises their offspring, an act that translates into huge benefits to the developing bee's microbiome, development and health, found York University researchers.

Phys.org
NIOO-KNAWAug 18, 2023
New NIOO publication: Impact of the fungal #pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root #microbiome. #rhizosphere #endosphere #metagenome #metatranscriptome
https://doi.org/10.1186/s40793-023-00524-7
Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome - Environmental Microbiome

Background Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. Results Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. Conclusion Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

BioMed Central
genomeresearchApr 3, 2023
The new issue of @genomeresearch is now live. Follow the link to new research on m6A RNA methylation following #SARSCoV2 infection, spatial #metatranscriptome and strand-specific RNA sequencing, and more! http://ow.ly/mKv050Nzeu8
Table of Contents — March 2023, 33 (3)

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Harald now @ treehouse.systemsNov 21, 2022

Open #Bioinformatics Research Associate position (m/f/d) in the field of #metatranscriptome analysis in #leukemia always post #job offers

For more details, see
https://www.denbi.de/de-nbi-jobs-portal/1504-research-associate-m-f-d-in-the-field-of-metatranscriptome-analysis-in-leukemia

Research Associate (m/f/d) in the field of metatranscriptome analysis in leukemia

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

cyanoneyNov 7, 2022

Cool paper on presence and distribution of viral auxilliary metabolic genes in environmental metaviromes and viral metatranscriptomes. Some interesting new putative metabolic genes in there that were not previously described in viral contigs
#phage #metavirome #metatranscriptome

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01384-y

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts - Microbiome

Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. Results Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. Conclusions Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract

BioMed Central