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The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

We investigated the antibiotic effects of extracts of freeze-dried biomass and culture supernatants from the mixotrophic chrysophyte species Ochromonas danica, Poterioochromonas sp. strain DS, and Poterioochromonas malhamensis on bacterial strains isolated from lake water. Methanolic biomass extracts inhibited the growth of all tested strains, albeit to a different extent, whereas aqueous biomass extracts only affected bacteria of the genus Flectobacillus. The antibiotic action of supernatants from flagellate cultures could be mostly attributed to lipophilic substances, but the growth of bacteria affiliated with Flectobacillus and Sphingobium was also affected by hydrophilic compounds. A comparison of biomass extracts from light- and dark-adapted cultures of Poterioochromonas sp. strain DS showed that the growth-inhibiting factor was unrelated to chlorophyll derivatives. Supernatants from a dark-adapted, phagotrophically grown flagellate culture had stronger antibiotic effects and affected more bacterial strains than the supernatant from a light-adapted culture. Significant growth reduction of a Flectobacillus isolate was already induced by extremely low concentrations of lipophilic extracts from these supernatants. Our results show that metabolites of the studied flagellates - either released actively or during cell lysis - may selectively affect the growth of some aquatic bacteria even in very small doses and thus potentially affect microbial community composition. Moreover, the antibiotic potential of mixotrophic chrysophytes may change with their nutritional mode.

Flagellates are very important predators on bacteria in soil. Because of their high growth rates, flagellate populations respond rapidly to changes in bacterial numbers. Previous results indicate that actinobacteria are generally less suitable than proteobacteria as food for flagellates. In this study, we investigated the growth of the flagellate Cercomonas sp. (ATCC 50334) on each of the two bacteria Sphingopyxis witflariensis (Alphaproteobacteria) and Rhodococcus fascians (actinobacteria) separately and in combination. The growth rate of the flagellate was lower and the lag phase was longer when fed with R. fascians than when fed with S. witflariensis. This supports our initial hypothesis that the actinobacterium is less suitable as food than the alphaproteobacterium. However, after longer periods of growth the peak abundance of flagellates was higher on R. fascians, indicating that the food quality of bacterial prey depends on the time perspective of the flagellate-bacterial interaction. There was no evidence that the flagellates selected against the actinobacterium when feeding in mixed cultures of the two bacteria. Experiments where flagellates were fed with washed bacterial cells or with bacteria growing with different substrate concentrations suggested that the low food quality of R. fascians is related both to the intrinsic cell properties and to the extracellular metabolites.

Aerobic anoxygenic phototrophs were recently found to constitute a significant portion of the marine microbial community. These bacteria use bacteriochlorophyll-containing reaction centers to perform photoheterotrophic metabolism. A new instrument for routine measurements of both chlorophyll a and bacteriochlorophyll a was used for monitoring anoxygenic phototrophs in the Baltic Sea in late summer 2003. Bacteriochlorophyll a concentration ranged from 8 to 50 ngl(-1), with an average bacteriochlorophyll/chlorophyll ratio of 4.2 x 10(-3). Moreover, diel trends in bacteriochlorophyll a signals were observed, with a distinct decline occurring during daylight hours. Based on laboratory measurements this phenomenon was ascribed to the complete inhibition of bacteriochlorophyll synthesis by light, which, in combination with a concurrent turnover of the cells, resulted in a pigment decline. Following this explanation, we postulate that bacteriochlorophyll a can serve as a natural 'pulse-and-chase' marker, allowing estimation of the mortality rates of anoxygenic phototrophs from the rates of pigment decline. Based on this assumption, we suggest that the Baltic photoheterotrophic community was characterized by high turnover rates, in a range of 0.7-2 d(-1).