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Author(s): Daniele Daffonchio (corresponding author) [1]; Sara Borin [1]; Tullio Brusa [1]; Lorenzo Brusetti [1]; Paul W. J. J. van der Wielen [2]; Henk Bolhuis [2]; Michail M. Yakimov [3]; [...]

Summary: Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite‐entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory‐grown halite over 21 weeks, using high‐throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite‐entombed communities. These results show that halite‐entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long‐term successional dynamics in this environment. [ABSTRACT FROM AUTHOR]

Summary: In cold marine environments, the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8, which utilizes aliphatic alkanes almost exclusively as substrates, dominates microbial communities following oil spills. In this study, LC–MS/MS shotgun proteomics was used to identify changes in the proteome induced during growth on n‐alkanes and in cold temperatures. Specifically, proteins with significantly higher relative abundance during growth on tetradecane (n‐C14) at 16°C and 4°C have been quantified. During growth on n‐C14, O. antarctica expressed a complete pathway for the terminal oxidation of n‐alkanes including two alkane monooxygenases, two alcohol dehydrogenases, two aldehyde dehydrogenases, a fatty‐acid‐CoA ligase, a fatty acid desaturase and associated oxidoreductases. Increased biosynthesis of these proteins ranged from 3‐ to 21‐fold compared with growth on a non‐hydrocarbon control. This study also highlights mechanisms O. antarctica may utilize to provide it with ecological competitiveness at low temperatures. This was evidenced by an increase in spectral counts for proteins involved in flagella structure/output to overcome higher viscosity, flagella rotation to accumulate cells and proline metabolism to counteract oxidative stress, during growth at 4°C compared with 16°C. Such species‐specific understanding of the physiology during hydrocarbon degradation can be important for parameterizing models that predict the fate of marine oil spills. [ABSTRACT FROM AUTHOR]

Summary: Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates. [ABSTRACT FROM AUTHOR]

Pesticides can have strong deleterious impacts in fresh waters, but understanding how these effects cascade through natural ecosystems, from microbes to apex predators, is limited because research that spans multiple levels of biological organisation is rare., We report how an accidental insecticide spill altered the structure and functioning of a river across levels ranging from genes to ecosystems. We quantified the impacts on assemblages of microbes, diatoms, macroinvertebrates and fish and measured leaf-litter decomposition rates and microbial functional potential at upstream control and downstream impacted sites 2 months after the spill., Both direct and indirect impacts were evident across multiple levels of organisation and taxa, from the base of the food web to higher trophic levels. At the molecular level, differences in functional gene abundance within the impacted sites reflected a combination of direct and indirect effects of the pesticide, via elevated abundances of microbial populations capable of using chlorpyrifos as a resource (i.e. direct effect) and oxidising ammonia released by decaying macroinvertebrate carcasses (i.e. indirect effect)., At the base of the food chains, diatom taxa found only in the impacted sites were an order-of-magnitude larger in cell size than the largest comparable taxa in control communities, following the near extirpation of their consumers. Population biomass of the key detritivore Gammarus pulex was markedly lower, as was the rate of litter decomposition in the impacted sites. This was partially compensated for, however, by elevated microbial breakdown, suggesting another indirect food-web effect of the toxic spill., Although many species exhibited population crashes or local extirpation, total macroinvertebrate biomass and abundance were largely unaffected due to a compensatory elevation in small tolerant taxa such as oligochaetes, and/or taxa which were in their adult aerial life stage at the time of the spill (e.g. chironomids) and thus avoided contact with the polluted waters and were able to repopulate the river quickly. Mass-abundance scaling of trophic links between consumers and resources revealed extensive restructuring within the food web., This case study shows that pesticides can affect food-web structure and ecosystem functioning, both directly and indirectly across levels of biological organisation. It also demonstrates how an integrated assessment approach, as adopted here, can elucidate links between microbiota, macroinvertebrates and fish, for instance, thus improving our understanding of the range of biological consequences of chemical contamination in natural ecosystems. [ABSTRACT FROM AUTHOR]