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

BathyBot - a Deep-sea Crawler to See the Unseen in the NW Mediterranean Sea

Ocean Sciences Meeting (OSM), 16-21 February 2020, San Diego, CA, USA.- 1 page, 3 figuresThe deep sea remains one of the less known environment on Earth and is characterized by high pressure, low availability of organic matter and absence of light. While there are still numerous discoveries concerning the diversity and adaptations of deep-sea organisms to their environement, this ecosystem is under an increasing anthropogenic pressure such as climate-related stressors (warming, acidification and deoxygenation), deep-sea fishing, human pollution (microplastics, POP), oil and gas extraction and could face new threats from emerging industries (e.g. mineral mining). How these changes will affect biodiversity and ecosystem functioning is one question of major importance for the future. In the darkness of the oceans, several organisms have the capability to emit light: called bioluminescence. Recent studies quantified that as much as 75% of pelagic and about 40% of benthic organisms are known to be bioluminescent. In this framework, we present a new deep-sea crawler, BathyBot, to be dedicated to the long-term exploration of deep-sea ecosystems allowing biological and-geochemical surveys. BathyBot will be deployed in 2020 in the Mediterranean Sea, at the MEUST-NUMerEnv/KM3NeT site, to strength the ecological-based monitoring capability of the European Multidisciplinary Seafloor and water column Observatory (EMSO ERIC) network. BathyBot will be able to explore an area of about 15 000 m2 at a depth of 2500m and will be devoted to 1) observe and monitor the dynamics of deep-sea pelagic and benthic organisms, 2) better define the occurrence and functions of bioluminescence in situ (increasing the dataset of bioluminescence records), 3) explore relationships between deep-sea organisms, biogeochemical (carbon content, oxygen concentrations) and environmental variables (temperature, salinity, current) in the context of global changes and their effects on the deep ocean, and 4) investigate benthic biogeochemical processes through the use of oxygen microprofiling in sediment porewatersThis work is funded by UE FEDER NUMerEnv project (number: 1166-39417, 2017), CNRS-INSU Moyens Mi-Lourd 2019 and VICAT-Tangram-MIO projectPeer reviewe

Probe design strategies for oligonucleotide microarrays

Chapter 6Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters