Project description:Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive developmental windows of fish, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used adult European sea bass as a model to study the effects of a marine heatwave during development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.

2020-12-06 | GSE152444 | GEO

Marine environment

Project description:Marine environment Genome sequencing and assembly

| PRJNA1092564 | ENA

Transcriptomic responses to iron bioavailability from virus-mediated lysates in marine prokaryotes

Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.

2021-11-01 | GSE166618 | GEO

Metabolomic investigations on Nesterenkonia flava from different origins revealed significant intraspecies differences between marine and terrestrial actinomycetes

Project description:Marine is one of the most important resources of microorganisms, including bacteria, actinomycetes, and fungi. As marine and terrestrial environments differ a lot in many aspects it is not surprising that the species and characteristics of microorganisms living there are very different. Interestingly, many marine microorganisms can find their congeners of the same species from terrestrial resources. The aim of this work is to evaluate the intraspecies differences between marine and terrestrial actinomycetes on metabolic level and to uncover the mechanism responsible for the differences. To address this, we carried out comparative metabolomics study on Nesterenkonia flava strains isolated from marine and terrestrial environments. The results showed that marine strains were clearly distinguished from their terrestrial congeners on the principal components analysis (PCA) scores plot of intracellular metabolites. The markers responsible for the discrimination of marine and terrestrial strains were figured out using loading plot from partial least squares discrimination analysis (PLS-DA). Pathway analysis based on PLS-DA, univariate analysis, and correlation analysis of metabolites showed that the major differential metabolites between the terrestrial N. flava and the marine ones were involved in osmotic regulation, redox balancing, and energy metabolism. Together, these insights provide clues as to how the previous living environment of microbes affect their current metabolic performances under laboratory cultivation conditions.

2017-08-12 | ST000875 | MetabolomicsWorkbench

Warming-induced shifts in Antarctic soil microorganisms disrupt soil functioning

Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning.

2010-12-30 | GSE22825 | GEO

microorganisms

Project description:Microorganisms Genome sequencing

| PRJNA863464 | ENA