Population genetic structure in <i>Sabatieria</i> (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea

BackgroundThere is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic.ResultsIndividuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1–8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow.ConclusionsThe presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria

Detection of a Subset of Posttranscriptional Transfer RNA Modifications in Vivo with a Restriction Fragment Length Polymorphism-Based Method

Transfer RNAs (tRNAs) are among the most heavily modified RNA species. Posttranscriptional tRNA modifications (ptRMs) play fundamental roles in modulating tRNA structure and function and are being increasingly linked to human physiology and disease. Detection of ptRMs is often challenging, expensive, and laborious. Restriction fragment length polymorphism (RFLP) analyses study the patterns of DNA cleavage after restriction enzyme treatment and have been used for the qualitative detection of modified bases on mRNAs. It is known that some ptRMs induce specific and reproducible base “mutations” when tRNAs are reverse transcribed. For example, inosine, which derives from the deamination of adenosine, is detected as a guanosine when an inosine-containing tRNA is reverse transcribed, amplified via polymerase chain reaction (PCR), and sequenced. ptRM-dependent base changes on reverse transcription PCR amplicons generated as a consequence of the reverse transcription reaction might create or abolish endonuclease restriction sites. The suitability of RFLP for the detection and/or quantification of ptRMs has not been studied thus far. Here we show that different ptRMs can be detected at specific sites of different tRNA types by RFLP. For the examples studied, we show that this approach can reliably estimate the modification status of the sample, a feature that can be useful in the study of the regulatory role of tRNA modifications in gene expression

Electrochemical transfer at p-type silicon(1 1 1)-alkyl monolayer hybrid electrodes in acetonitrile medium

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Different oceanographic regimes in the vicinity of the Antarctic Peninsula reflected in benthic nematode communities

Marine free-living nematode communities were studied at similar depths (~500 m) at two sides of the Antarctic Peninsula, characterised by different environmental and oceanographic conditions. At the Weddell Sea side, benthic communities are influenced by cold deep-water formation and seasonal sea-ice conditions, whereas the Drake Passage side experiences milder oceanic conditions and strong dynamics of the Antarctic Circumpolar Current. This resulted in different surface primary productivity, which contrasted with observed benthic pigment patterns and varied according to the area studied: chlorophyll a concentrations (as a proxy for primary production) were high in the Weddell Sea sediments, but low in the surface waters above; this pattern was reversed in the Drake Passage. Differences between areas were largely mirrored by the nematode communities: nematode densities peaked in Weddell stations and showed deeper vertical occurrence in the sediment, associated with deeper penetration of chlorophyll a and indicative of a strong bentho-pelagic coupling. Generic composition showed some similarities across both areas, though differences in the relative contribution of certain genera were noted, together with distinct community shifts with depth in the sediment at all locations

Meiofaunal communities in the Clarion-Clipperton Zone: geographic distribution and link with environmental conditions

Polymetallic nodule mining in the abyss is a nascent industry hoping to meet the growing worldwide demand for metallic minerals. Given that prospective mining is likely to have a profound impact on deep seafloor communities, knowledge on their wider geographic distribution is pivotal in order to provide sound guidelines for environmentally sustainable mining practices. We therefore studied benthic meiofaunal communities spread along four prospective mining areas and one non-mining Area of Particular Environmental Interest in the Clarion-Clipperton Zone (CCZ) of the east Pacific Ocean. Meiobenthic abundance in the upper sediment layer followed an eastward increase in particulate organic matter input, indicating their dependence upon water-column processes. Additionally, standing stock was clearly correlated with the degree of nodule coverage at the different prospective mining areas, with high nodule coverage leading to less sediment volume and thus lower numbers. Future nodule removal through mining activities might therefore lead to an increase in numbers for smaller-sized benthic taxa.In terms of community composition, nematodes were the most abundant meiobenthic taxon, yet showed no pronounced variation in diversity or genus composition between the different mining and non-mining areas. Assemblages were typically dominated by a few genera accounting for the majority of community totals, as well as a large number of rare genera contributing only little to overall abundances. Dominant genera were widely spread within the CCZ and shared among all sampled areas, whereas rare genera were usually limited to one area. The same trend was present when looking at the level of morphospecies, implying that it might be mainly those taxa with a more limited spatial distribution that will be affected by changes in their habitat and/or reduced connectivity between different areas

BIANZO II: Biodiversity of three representative groups of the Antarctic Zoobenthos - Coping with Change

BIANZO I