Microbiota and Microsatellite genotypes of Pacific oysters stemming from three oyster bed in the Northern Wadden Sea

Background: Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host. Results: While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains. Conclusion: The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Contemporary genetic, historical genetic and morphological data sets for the Yellow-tufted Honeyeater Lichenostomus melanops

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55 years. Using a combination of morphometric, genetic and modelling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modelling historical distribution supported the lack of vicariance and suggested a possibility of gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighbouring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops + meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, thus managed gene flow from gippslandicus is recommended for its recovery.

Flow separation and roughness lengths over large bedforms in a tidal environment

This study characterises the shape of the flow separation zone (FSZ) and wake region over large asymmetric bedforms under tidal flow conditions. High resolution bathymetry, flow velocity and turbulence data were measured along two parallel transects in a tidal channel covered with bedforms. The field data are used to verify the applicability of a numerical model for a systematic study using the Delft3D modelling system and test the model sensitivity to roughness length. Three experiments are then conducted to investigate how the FSZ size and wake extent vary depending on tidally-varying flow conditions, water levels and bathymetry. During the ebb, a large FSZ occurs over the steep lee side of each bedform. During the flood, no flow separation develops over the bedforms having a flat crest; however, a small FSZ is observed over the steepest part of the crest of some bedforms, where the slope is locally up to 15°. Over a given bedform morphology and constant water levels, no FSZ occurs for velocity magnitudes smaller than 0.1 m s**-1; as the flow accelerates, the FSZ reaches a stable size for velocity magnitudes greater than 0.4 m s**-1. The shape of the FSZ is not influenced by changes in water levels. On the other hand, variations in bed morphology, as recorded from the high-resolution bathymetry collected during the tidal cycle, influence the size and position of the FSZ: a FSZ develops only when the maximum lee side slope over a horizontal distance of 5 m is greater than 10°. The height and length of the wake region are related to the length of the FSZ. The total roughness along the transect lines is an order of magnitude larger during the ebb than during the flood due to flow direction in relation to bedform asymmetry: during the ebb, roughness is created by the large bedforms because a FSZ and wake develops over the steep lee side. The results add to the understanding of hydrodynamics of natural bedforms in a tidal environment and may be used to better parameterise small-scale processes in large-scale studies.

Stable isotopic ratios, shell lengths and organochlorine compounds in four bivalve species collected in July 2009 around Svalbard

Organochlorine compounds (OC) were determined in Arctic bivalves (Mya truncata, Serripes groenlan-dicus, Hiatella arctica and Chlamys islandica) from Svalbard with regard to differences in geographic location, species and variations related to their size and age. Higher chlorinated polychlorinated biphenyls (PCB 101-PCB 194), chlordanes and alpha-hexachlorocyclohexane (alpha-HCH) were consistently detected in the bivalves and PCBs dominated the OC load in the organisms. OC concentrations were highest in Mya truncata and the lowest in Serripes groenlandicus. Species-specific OC levels were likely related to differences in the species' food source, as indicated by the d13C results, rather than size and age. Higher OC concentrations were observed in bivalves from Kongsfjorden compared to the northern sampling locations Liefdefjorden and Sjuoyane. The spatial differences might be related to different water masses influencing Kongsfjorden (Atlantic) and the northern locations (Arctic), with differing phytoplankton bloom situations.

Table I: Schedule of the drilling operation and lengths of the recovered core material for the boreholes on Vernagtferner in 1979

In 1979 a core drilling project was carried out on Vernagtferner in the Oetztal Alps (Austria). This report describes the field work of the drilling project, the recovered core material and the occurrence of water in the boreholes and compiles the succeding investigation program.

Estimatin of roughness lengths with a ship-mounted ADCP from Knudedyb, Denmark in October 2009

The hydraulic effect of asymmetric compound bedforms on tidal currents was assessed from field measurements of flow velocity in the Knudedyb tidal inlet, Denmark. Large asymmetric bedforms with smaller superimposed ones are a common feature of sandy shallow water environments and are known to act as hydraulic roughness elements in dependence with flow direction. The presence of a flow separation zone on the bedform lee was estimated through analysis of the measured velocity directions and the calculation of the flow separation line. The Law of the Wall was used to calculate roughness lengths and shear velocities from log-linear segments sought on transect-averaged and single-location velocity profiles. During the ebb tide a permanent flow separation zone was established over the steep (10-20°) lee sides of the ebb-oriented primary bedforms, which generated a consequent drag on the flow. During the flood, no flow separation was induced by the gentle (2°) lee side of the primary bedforms except over the steepest (10°) part of the lee side where a small separation zone was sometimes observed. As a result, hydraulic roughness was only due to the superimposed bedforms. The parameterized flow separation line was found to underestimate the length of the flow separation zone of the primary bedforms. A better estimation of the presence and shape of the flow separation zone over complex bedforms in a tidal environment still needs to be determined; in particular the relationship between flow separation zone and bedform geometry (asymmetry, relative height or slope of the lee side) is unclear. This would improve the prediction of complex bedform roughness in tidal flows.

(Appendix) Recent surface areas and historical lengths of glaciers from Patagonia and Tierra del Fuego, South America

Fluctuations in the length of 72 glaciers in the Northern and Southern Patagonia Icefield (NPI and SPI, respectively) and the Cordillera Darwin Icefield (CDI) were estimated between 1945 and 2005. The information obtained from historical maps based on 1945 aerial photographs was compared to ASTER and Landsat satellite images and to information found in the literature. The majority of glaciers have retreated considerably, with maximum values of 12.2 km for Marinelli Glacier in the CDI, 11.6 km for O'Higgins Glacier in the SPI and 5.7 km for San Rafael Glacier in the NPI. Among the 20 glaciers that have retreated the most relative to their size, small (less than 50 km**2) and medium (between 50 and 200 km**2) glaciers are the most affected. However, no direct relation between glacier retreat and size was found for the 72 glaciers studied. The highest percentage retreat in the CDI was by the CDI-03 Glacier (37.9%) and Marinelli Glacier (37.6%). In the SPI, relative retreats were heterogeneous and fluctuated between 27.2% (Amelia Glacier) and 0.4% (Viedma Glacier). In the NPI, relative retreat was very high for Strindberg and Cachet glaciers (35.9% and 27.6%, respectively) but for the remaining glaciers in this icefield it ranged between 11.8% (Piscis Glacier) and 3.6% (San Quintin Glacier). In addition to surface area, the surface slope (calculated on the basis of the DEM SRTM) was also related to the relative retreat and no straightforward relation was found. From a global point of view, we suggest that glacier retreat in the region is controlled firstly by atmospheric warming, as it has been reported in this area. Besides the general increase in temperature observed, no signal of a geographical pattern for the fluctuations in glacier length was found. Consequently, glaciers appear to initially react to local conditions most probably induced by their exposition, geometry and hypsometry. The heterogeneity of rates of retreat suggests that differences in basin geometry, glacier dynamics and response time are key features to explain fluctuations of each glacier.

(Table 1) Number of alleles per locus and heterozygosity of Arctic charr (Salvelinus alpinus) populations in Iceland

The ecological theory of adaptive radiation predicts that the evolution of phenotypic diversity within species is generated by divergent natural selection arising from different environments and competition between species. Genetic connectivity among populations is likely also to have an important role in both the origin and maintenance of adaptive genetic diversity. Our goal was to evaluate the potential roles of genetic connectivity and natural selection in the maintenance of adaptive phenotypic differences among morphs of Arctic charr, Salvelinus alpinus, in Iceland. At a large spatial scale, we tested the predictive power of geographic structure and phenotypic variation for patterns of neutral genetic variation among populations throughout Iceland. At a smaller scale, we evaluated the genetic differentiation between two morphs in Lake Thingvallavatn relative to historically explicit, coalescent-based null models of the evolutionary history of these lineages. At the large spatial scale, populations are highly differentiated, but weakly structured, both geographically and with respect to patterns of phenotypic variation. At the intralacustrine scale, we observe modest genetic differentiation between two morphs, but this level of differentiation is nonetheless consistent with strong reproductive isolation throughout the Holocene. Rather than a result of the homogenizing effect of gene flow in a system at migration-drift equilibrium, the modest level of genetic differentiation could equally be a result of slow neutral divergence by drift in large populations. We conclude that contemporary and recent patterns of restricted gene flow have been highly conducive to the evolution and maintenance of adaptive genetic variation in Icelandic Arctic charr.