Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions. 相似文献
RNA can function as a pathogen-associated molecular pattern (PAMP) whose recognition by the innate immune system alerts the body to an impending microbial infection. The recognition of tRNA as either self or nonself RNA by TLR7 depends on its modification patterns. In particular, it is known that the presence of a ribose methylated guanosine at position 18, which is overrepresented in self-RNA, antagonizes an immune response. Here, we report that recognition extends to the next downstream nucleotide and the effectively recognized molecular detail is actually a methylated dinucleotide. The most efficient nucleobases combination of this motif includes two purines, while pyrimidines diminish the effect of ribose methylation. The constraints of this motif stay intact when transposed to other parts of the tRNA. The results argue against a fixed orientation of the tRNA during interaction with TLR7 and, rather, suggest a processive type of inspection. 相似文献
Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics. 相似文献
Ge/Si ratios of plant phytoliths have been widely used to trace biogeochemical cycling of Si. However, until recently, information on how much of the Ge and Si transferred from soil to plants is actually stored in phytoliths was lacking. The aim of the present study is to (i) compare the uptake of Si and Ge in three grass species, (ii) localize Ge and Si stored in above-ground plant parts and (iii) evaluate the amounts of Ge and Si sequestrated in phytoliths and plant tissues. Mays (Zea mays), oat (Avena sativa) and reed canary grass (Phalaris arundinacea) were cultivated in the greenhouse on soil and sand to control element supply. Leaf phytoliths were extracted by dry ashing. Total elemental composition of leaves, phytoliths, stems and roots were measured by ICP-MS. For the localization of phytoliths and the determination of Ge and Si within leaf tissues and phytoliths scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX) and laser ablation inductively coupled mass spectrometry (LA-ICP-MS) was used. The amounts of Si and Ge taken up by the species corresponded with biomass formation and decreased in the order Z. mays > P. arundinacea, A. sativa. Results from LA-ICP-MS revealed that Si was mostly localized in phytoliths, while Ge was disorderly distributed within the leaf tissue. In fact, from the total amounts of Ge accumulated in leaves only 10% was present in phytoliths highlighting the role of organic matter on biogeochemical cycling of Ge and the necessity for using bulk Ge/Si instead of Ge/Si in phytoliths to trace biogeochemical cycling of Si.
Nickel is harmful to humans, being both carcinogenic and allergenic. However, the mechanisms of this toxicity are still unresolved. We propose that Ni(II) ions disintegrate proteins by hydrolysis of peptide bonds preceding the Ser/Thr‐Xaa‐His sequences. Such sequences occur in nuclear localization signals (NLSs) of human phospholipid scramblase 1, Sam68‐like mammalian protein 2, and CLK3 kinase. We performed spectroscopic experiments showing that model nonapeptides derived from these NLSs bind Ni(II) at physiological pH. We also proved that these sequences are prone to Ni(II) hydrolysis. Thus, the aforementioned NLSs may be targets for nickel toxicity. This implies that Ni(II) ions disrupt the transport of some proteins from cytoplasm to cell nucleus. 相似文献
Limnology - Green microalgae are of the utmost importance to aquatic ecosystems globally, as they are primary producers and major food sources for many organisms. Microalgae of the genus... 相似文献
Quantifying sublethal effects of plastics ingestion on marine wildlife is difficult, but key to understanding the ontogeny and population dynamics of affected species. We developed a method that overcomes the difficulties by modelling individual ontogeny under reduced energy intake and expenditure caused by debris ingestion. The predicted ontogeny is combined with a population dynamics model to identify ecological breakpoints: cessation of reproduction or negative population growth. Exemplifying this approach on loggerhead turtles, we find that between 3% and 25% of plastics in digestive contents causes a 2.5–20% reduction in perceived food abundance and total available energy, resulting in a 10–15% lower condition index and 10% to 88% lower total seasonal reproductive output compared to unaffected turtles. The reported plastics ingestion is insufficient to impede sexual maturation, but population declines are possible. The method is readily applicable to other species impacted by debris ingestion. 相似文献