Project description:Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

| S-EPMC5099912 | biostudies-literature

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (18S END-Seq)

Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.

2023-04-19 | GSE223167 | GEO

Functional Diversity and CO<sub>2</sub> Emission Characteristics of Soil Bacteria during the Succession of Halophyte Vegetation in the Yellow River Delta.

Project description:Carbon dioxide (CO2) is the most important greenhouse gas in the atmosphere, which is mainly derived from microbial respiration in soil. Soil bacteria are an important part of the soil ecosystem and play an important role in the process of plant growth, mineralization, and decomposition of organic matter. In this paper, we discuss a laboratory incubation experiment that we conducted to investigate the CO2 emissions and the underlying bacterial communities under the natural succession of halophyte vegetation in the Yellow River Delta by using high-throughput sequencing technology and PICRUSt functional prediction. The results showed that the bacterial abundance and diversity increased significantly along with the succession of halophyte vegetation. Metabolic function is the dominant function of soil bacteria in the study area. With the succession of halophyte vegetation, the rate of CO2 emissions gradually increased, and were significantly higher in soil covered with vegetation than that of the bare land without vegetation coverage. These results helped to better understand the relationships of soil bacterial communities under the background of halophyte vegetation succession, which can help to make efficient strategies to mitigate CO2 emissions and enhance carbon sequestration.

| S-EPMC9564505 | biostudies-literature

The integrated stress response regulates 18S nonfunctional rRNA decay in mammals

Project description:Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.

2024-12-09 | MSV000096620 | MassIVE

Soil Samples Along the Potomac River

Project description:Soil Samples Along the Potomac River

| PRJEB66296 | ENA

18S

Project description:18S metagenome

| PRJNA544742 | ENA