Diverse Arrangement of Photosynthetic Gene Clusters in Aerobic Anoxygenic Phototrophic Bacteria

BACKGROUND: Aerobic anoxygenic photototrophic (AAP) bacteria represent an important group of marine microorganisms inhabiting the euphotic zone of the ocean. They harvest light using bacteriochlorophyll (BChl) a and are thought to be important players in carbon cycling in the ocean. METHODOLOGY/PRINCIPAL FINDINGS: Aerobic anoxygenic phototrophic (AAP) bacteria represent an important part of marine microbial communities. Their photosynthetic apparatus is encoded by a number of genes organized in a so-called photosynthetic gene cluster (PGC). In this study, the organization of PGCs was analyzed in ten AAP species belonging to the orders Rhodobacterales, Sphingomonadales and the NOR5/OM60 clade. Sphingomonadales contained comparatively smaller PGCs with an approximately size of 39 kb whereas the average size of PGCs in Rhodobacterales and NOR5/OM60 clade was about 45 kb. The distribution of four arrangements, based on the permutation and combination of the two conserved regions bchFNBHLM-LhaA-puhABC and crtF-bchCXYZ, does not correspond to the phylogenetic affiliation of individual AAP bacterial species. While PGCs of all analyzed species contained the same set of genes for bacteriochlorophyll synthesis and assembly of photosynthetic centers, they differed largely in the carotenoid biosynthetic genes. Spheroidenone, spirilloxanthin, and zeaxanthin biosynthetic pathways were found in each clade respectively. All of the carotenoid biosynthetic genes were found in the PGCs of Rhodobacterales, however Sphingomonadales and NOR5/OM60 strains contained some of the carotenoid biosynthetic pathway genes outside of the PGC. CONCLUSIONS/SIGNIFICANCE: Our investigations shed light on the evolution and functional implications in PGCs of marine aerobic anoxygenic phototrophs, and support the notion that AAP are a heterogenous physiological group phylogenetically scattered among Proteobacteria

Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair

The error-free and efficient repair of DNA double-stranded breaks (DSBs) is extremely important for cell survival. RNA has been implicated in the resolution of DNA damage but the mechanism remains poorly understood. Here, we show that miRNA biogenesis enzymes, Drosha and Dicer, control the recruitment of repair factors from multiple pathways to sites of damage. Depletion of Drosha significantly reduces DNA repair by both homologous recombination (HR) and non-homologous end joining (NHEJ). Drosha is required within minutes of break induction, suggesting a central and early role for RNA processing in DNA repair. Sequencing of DNA:RNA hybrids reveals RNA invasion around DNA break sites in a Drosha-dependent manner. Removal of the RNA component of these structures results in impaired repair. These results show how RNA can be a direct and critical mediator of DNA damage repair in human cells

Coastal vulnerability assessment based on video wave run-up observations at a mesotidal, steep-sloped beach

Coastal imagery obtained from a coastal video monitoring station installed at Faro Beach, S. Portugal, was combined with topographic data from 40 surveys to generate a total of 456 timestack images. The timestack images were processed in an open-access, freely available graphical user interface (GUI) software, developed to extract and process time series of the cross-shore position of the swash extrema. The generated dataset of 2% wave run-up exceedence values R 2 was used to form empirical formulas, using as input typical hydrodynamic and coastal morphological parameters, generating a best-fit case RMS error of 0.39 m. The R 2 prediction capacity was improved when the shore-normal wind speed component and/or the tidal elevation η tide were included in the parameterizations, further reducing the RMS errors to 0.364 m. Introducing the tidal level appeared to allow a more accurate representation of the increased wave energy dissipation during low tides, while the negative trend between R 2 and the shore-normal wind speed component is probably related to the wind effect on wave breaking. The ratio of the infragravity-to-incident frequency energy contributions to the total swash spectra was in general lower than the ones reported in the literature E infra/E inci > 0.8, since low-frequency contributions at the steep, reflective Faro Beach become more significant mainly during storm conditions. An additional parameterization for the total run-up elevation was derived considering only 222 measurements for which η total,2 exceeded 2 m above MSL and the best-fit case resulted in RMS error of 0.41 m. The equation was applied to predict overwash along Faro Beach for four extreme storm scenarios and the predicted overwash beach sections, corresponded to a percentage of the total length ranging from 36% to 75%.info:eu-repo/semantics/publishedVersio

The origin and composition of carbonatite-derived carbonate-bearing fluorapatite deposits

Carbonate-bearing fluorapatite rocks occur at over 30 globally distributed carbonatite complexes and represent a substantial potential supply of phosphorus for the fertiliser industry. However, the process(es) involved in forming carbonate-bearing fluorapatite at some carbonatites remain equivocal, with both hydrothermal and weathering mechanisms inferred. In this contribution, we compare the paragenesis and trace element contents of carbonate-bearing fluorapatite rocks from the Kovdor, Sokli, Bukusu, Catalão I and Glenover carbonatites in order to further understand their origin, as well as to comment upon the concentration of elements that may be deleterious to fertiliser production. The paragenesis of apatite from each deposit is broadly equivalent, comprising residual magmatic grains overgrown by several different stages of carbonate-bearing fluorapatite. The first forms epitactic overgrowths on residual magmatic grains, followed by the formation of massive apatite which, in turn, is cross-cut by late euhedral and colloform apatite generations. Compositionally, the paragenetic sequence corresponds to a substantial decrease in the concentration of rare earth elements (REE), Sr, Na and Th, with an increase in U and Cd. The carbonate-bearing fluorapatite exhibits a negative Ce anomaly, attributed to oxic conditions in a surficial environment and, in combination with the textural and compositional commonality, supports a weathering origin for these rocks. Carbonate-bearing fluorapatite has Th contents which are several orders of magnitude lower than magmatic apatite grains, potentially making such apatite a more environmentally attractive feedstock for the fertiliser industry. Uranium and cadmium contents are higher in carbonate-bearing fluorapatite than magmatic carbonatite apatite, but are much lower than most marine phosphorites

Interdependency of tropical marine ecosystems in response to climate change

Ecosystems are linked within landscapes by the physical and biological processes they mediate. In such connected landscapes, the response of one ecosystem to climate change could have profound consequences for neighbouring systems. Here, we report the first quantitative predictions of interdependencies between ecosystems in response to climate change. In shallow tropical marine ecosystems, coral reefs shelter lagoons from incoming waves, allowing seagrass meadows to thrive. Deepening water over coral reefs from sea-level rise results in larger, more energetic waves traversing the reef into the lagoon1, 2, potentially generating hostile conditions for seagrass. However, growth of coral reef such that the relative water depth is maintained could mitigate negative effects of sea-level rise on seagrass. Parameterizing physical and biological models for Lizard Island, Great Barrier Reef, Australia, we find negative effects of sea-level rise on seagrass before the middle of this century given reasonable rates of reef growth. Rates of vertical carbonate accretion typical of modern reef flats (up to 3 mm yr−1) will probably be insufficient to maintain suitable conditions for reef lagoon seagrass under moderate to high greenhouse gas emissions scenarios by 2100. Accounting for interdependencies in ecosystem responses to climate change is challenging, but failure to do so results in inaccurate predictions of habitat extent in the future