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    Ecological memory of prior nutrient exposure in the human gut microbiome

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    Development of microbial communities in biofilm and activated sludge in a hybrid reactor

    Bacterial community compositionIn order to study the microbial structure of the biofilm and activated sludge that were developing in the IFAS-MBSBBR reactor, a total of 15 samples were taken at intervals during an experiment lasting 573 days. The microbiome of both environments was described at the phylum and genus levels. A total of 26 bacterial phyla and 783 bacterial genera were identified. The most numerous phyla and genera in the biofim and activated sludge samples are presented in in Figs. 1 and 2. Both in the biofilm and the activated sludge, the most numerous phyla were Proteobacteria, with respective mean abundances of 39.3% ± 9.0 and 40.8% ± 8.2, and Bacteroidota, with respective mean abundances of 14.2% ± 4.9 and 26.1% ± 13.7. Additionally, the phylum Chloroflexi was rather abundant in the biofilm (with a mean abundance of 13.9 ± 8.1), while Actinobacteriota and Patescibacteria were relatively abundant in the activated sludge (with mean abundances of 9.0% ± 9.6 and 7.5% ± 8.1, respectively). STAMP analysis identified significant overrepresentations of Chloroflexi, Acidobacteriota, and Nitrospirota in biofilm and of Firmicutes in activated sludge.Figure 1Relative abundance (%) of the most prevalent phyla in the biofilm and activated sludge samples in general, as the mean values of relative abundance from all biofilm and activated sludge samples (A), and in each individual sample (B). The graph shows only phyla which contributed more than 0.5% to the total bacterial community in at least one sample. The abundance of the remaining phyla was summed and labelled as “other”.Full size imageFigure 2Relative abundance (%) of the most prevalent genera in the biofilm and activated sludge samples in general, as the mean values of relative abundance from all biofilm and activated sludge samples (A), and in each individual sample (B). The graph shows only genera which contributed more than 1.5% to the total bacterial community in at least one sample. The abundance of the remaining genera was summed and labelled as “other”.Full size imageIn both environments, the abundances of various groups of bacteria changed over time. In the biofilm, the abundance of Proteobacteria and Actinobacteria gradually decreased, while that of Chloroflexi increased. In the activated sludge, the changes in abundance were larger and more rapid, and the abundance of Bacteroidota changed to the largest extent, ranging from 12.7% after 42 days of reactor operation to 52.3% after 110 days, when it was the predominant phylum. The abundance of Patescibacteria also changed substantially: its abundance was highest on the 78th, 205th and 447th days of the process, reaching values of 20.1%, 11.0%, and 7.2%, respectively. Similar changes took place in the abundance of Armatimonadota, which reached 11.4% and 7.6% on the 547th and 573th day, but did not exceed 0.1% in the samples taken at other times.At the genus level, the less abundant genera (each  More

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    Phycobilisome light-harvesting efficiency in natural populations of the marine cyanobacteria Synechococcus increases with depth

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