Impact of oil on bacterial community structure in bioturbated sediments

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions - with tidal cycles and natural seawater - was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g21 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities

Ediacaran skeletal Metazoans: affinities, ecology and the role of oxygenation

The evolution of the Metazoa is among the greatest success stories in Earth history. From modest origins, probably in the Cryogenian (~720 - 635 Ma), metazoans had acquired hard parts, and a vast range of life strategies and body plans by the middle Cambrian (around 520 Ma). This leaves a long delay between the origin of the Metazoa and their rise to ecological dominance. A popular explanatory hypothesis for this delay is that atmospheric oxygen levels, low in the Proterozoic (< 0.001 % PAL), began to rise towards modern levels towards the end of the Neoproterozoic. Among the earliest known putative metazoans are Namacalathus, Namapoikia and Cloudina, calcified marine invertebrates abundant in the latest Ediacaran (~ 548-541 Ma) Nama Group, Namibia. Although they were pioneers of metazoan biomineralisation, little is known of their affinities or palaeocology. The Nama Group, a well-characterised, relatively undeformed mixed carbonate and siliciclastic succession, provides a rare opportunity to investigate the palaeoecology of these important organisms in their environmental context. New geochemical data from the Nama Group confirm the heterogeneity of Ediacaran redox conditions. These contextualise in situ fossil assemblages which reveal diverse ecological strategies among the calcified metazoans of the Nama Group, and offer constraints on their affinities. Based on its large size (< 1 m), modular body plan and internal structure of interlinked tubules, Namapoikia was a long-lived specialist and possible Poriferan. I show that Namapoikia colonised both lithified and living microbial substrates in oxic, mid-ramp reef crypts. By contrast, size and occurrence data show that Namacalathus was an environmental generalist, forming large, thick aggregations in persistently oxic, mid-ramp reef environments but opportunistically exploiting the transiently oxic, inner ramp setting. Bilaterally symmetrical, asexual budding and a microlamellar skeletal ultrastructure suggest that Namacalathus may have been an early lophophorate, and had flexible growth depending on environmental setting, showing a cup diameter of 2 – 35 mm, and size distributions varying with substrate type, redox and water depth. In oxic mid-ramp reefs, Cloudina constructed large (> 20 m) reefs showing mutual attachment and consistent orientation in life position, making it the earliest known reef-building metazoan and suggesting that it was a passive suspension feeder. I further present food webs based on fossil assemblages from Ediacaran to Cambrian Stage 4 carbonate successions and evaluate their usefulness in tracking metazoan trophic diversification in the early Cambrian. Ediacaran redox conditions were a major control on the ecologies of the earliest metazoans. A requirement for oxygen made persistently oxic conditions a prerequisite for complex and long-lived ecologies, while highly flexible life strategies were used to exploit changeable environments. Ediacaran metazoans represent a phylogenetic and ecological foreshadowing of the complexity of the Phanerozoic, but it was not until much later that the Metazoa would attain their evolutionary potential

Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana

Understanding molecular factors determining local adaptation is a key challenge, particularly relevant for plants, which are sessile organisms coping with a continuously fluctuating environment. Here we introduce a rigorous network-based approach for investigating the relation between geographic location of accessions and heterogeneous molecular phenotypes. We demonstrate for Arabidopsis accessions that not only genotypic variability but also flowering and metabolic phenotypes show a robust pattern of isolation-by-distance. Our approach opens new avenues to investigate relations between geographic origin and heterogeneous molecular phenotypes, like metabolite profiles, which can easily be obtained in species where genome data is not yet available