Mycobacterium ulcerans persistence at a village water source of Buruli ulcer patients

Buruli ulcer (BU), a neglected tropical disease of the skin and subcutaneous tissue, is caused by Mycobacterium ulcerans and is the third most common mycobacterial disease after tuberculosis and leprosy. While there is a strong association of the occurrence of the disease with stagnant or slow flowing water bodies, the exact mode of transmission of BU is not clear. M. ulcerans has emerged from the environmental fish pathogen M. marinum by acquisition of a virulence plasmid encoding the enzymes required for the production of the cytotoxic macrolide toxin mycolactone, which is a key factor in the pathogenesis of BU. Comparative genomic studies have further shown extensive pseudogene formation and downsizing of the M. ulcerans genome, indicative for an adaptation to a more stable ecological niche. This has raised the question whether this pathogen is still present in water-associated environmental reservoirs. Here we show persistence of M. ulcerans specific DNA sequences over a period of more than two years at a water contact location of BU patients in an endemic village of Cameroon. At defined positions in a shallow water hole used by the villagers for washing and bathing, detritus remained consistently positive for M. ulcerans DNA. The observed mean real-time PCR Ct difference of 1.45 between the insertion sequences IS2606 and IS2404 indicated that lineage 3 M. ulcerans, which cause human disease, persisted in this environment after successful treatment of all local patients. Underwater decaying organic matter may therefore represent a reservoir of M. ulcerans for direct infection of skin lesions or vector-associated transmission.

Lake surface water temperatures of European Alpine lakes (1989–2013) based on the Advanced Very High Resolution Radiometer (AVHRR) 1 km data set

Lake water temperature (LWT) is an important driver of lake ecosystems and it has been identified as an indicator of climate change. Consequently, the Global Climate Observing System (GCOS) lists LWT as an essential climate variable. Although for some European lakes long in situ time series of LWT do exist, many lakes are not observed or only on a non-regular basis making these observations insufficient for climate monitoring. Satellite data can provide the information needed. However, only few satellite sensors offer the possibility to analyse time series which cover 25 years or more. The Advanced Very High Resolution Radiometer (AVHRR) is among these and has been flown as a heritage instrument for almost 35 years. It will be carried on for at least ten more years, offering a unique opportunity for satellite-based climate studies. Herein we present a satellite-based lake surface water temperature (LSWT) data set for European water bodies in or near the Alps based on the extensive AVHRR 1 km data record (1989–2013) of the Remote Sensing Research Group at the University of Bern. It has been compiled out of AVHRR/2 (NOAA-07, -09, -11, -14) and AVHRR/3 (NOAA-16, -17, -18, -19 and MetOp-A) data. The high accuracy needed for climate related studies requires careful pre-processing and consideration of the atmospheric state. The LSWT retrieval is based on a simulation-based scheme making use of the Radiative Transfer for TOVS (RTTOV) Version 10 together with ERA-interim reanalysis data from the European Centre for Medium-range Weather Forecasts. The resulting LSWTs were extensively compared with in situ measurements from lakes with various sizes between 14 and 580 km2 and the resulting biases and RMSEs were found to be within the range of −0.5 to 0.6 K and 1.0 to 1.6 K, respectively. The upper limits of the reported errors could be rather attributed to uncertainties in the data comparison between in situ and satellite observations than inaccuracies of the satellite retrieval. An inter-comparison with the standard Moderate-resolution Imaging Spectroradiometer (MODIS) Land Surface Temperature product exhibits RMSEs and biases in the range of 0.6 to 0.9 and −0.5 to 0.2 K, respectively. The cross-platform consistency of the retrieval was found to be within ~ 0.3 K. For one lake, the satellite-derived trend was compared with the trend of in situ measurements and both were found to be similar. Thus, orbital drift is not causing artificial temperature trends in the data set. A comparison with LSWT derived through global sea surface temperature (SST) algorithms shows lower RMSEs and biases for the simulation-based approach. A running project will apply the developed method to retrieve LSWT for all of Europe to derive the climate signal of the last 30 years. The data are available at doi:10.1594/PANGAEA.831007.

Physical oceanography during UPAT cruise to the Amvrakikos Gulf, August 2009

Oceanographic research in the Amvrakikos Gulf in Western Greece, a semi-enclosed embayment isolated from the Ionian Sea by a narrow, shallow sill, has shown that it is characterised by a fjord-like oceanographic regime. The Gulf is characterised by a well-stratified two layer structure in the water column made up of a surface layer and a bottom layer that are separated by a strong pycnocline. At the entrance over the sill, there is a brackish water outflow in the surface water and a saline water inflow in the near-bed region. This morphology and water circulation pattern makes the Amvrakikos Gulf the only Mediterranean Sea fjord. The investigations have also shown that the surface layer is well oxygenated, whereas in the pycnocline, the dissolved oxygen (DO) declines sharply and finally attains a value of zero, thus dividing the water column into oxic, dysoxic and anoxic environments. At the dysoxic/anoxic interface, at a depth of approximately 35 m, a sharp redox cline develops with Eh values between 0 and 120 mV occurring above and values between 0 and -250 mV occurring below, where oxic and anoxic biochemical processes prevail, respectively. On the seafloor underneath the anoxic waters, a black silt layer and a white mat cover resembling Beggiatoa-like cells are formed. The dysoxic/anoxic conditions appeared during the last 20 to 30 years and have been caused by the excessive use of fertilisers, the increase in animal stocks, intensive fish farming and domestic effluents. The inflicted dysoxia/anoxia has resulted in habitat loss on the seafloor over an area that makes up just over 50% of the total Gulf area and approximately 28% of the total water volume. Furthermore, anoxia is also considered to have been responsible for the sudden fish mortality which occurred in aquaculture rafts in the Gulf in February 2008. Therefore, anoxic conditions can be considered to be a potential hazard to the ecosystem and to the present thriving fishing and mariculture industry in the Gulf.

Wetland maps including open water extent dynamics based on ENVISAT ASAR WS for Siberia, 2007 and 2008, links to GeoTIFFs

Wetlands store large amounts of carbon, and depending on their status and type, they release specific amounts of methane gas to the atmosphere. The connection between wetland type and methane emission has been investigated in various studies and utilized in climate change monitoring and modelling. For improved estimation of methane emissions, land surface models require information such as the wetland fraction and its dynamics over large areas. Existing datasets of wetland dynamics present the total amount of wetland (fraction) for each model grid cell, but do not discriminate the different wetland types like permanent lakes, periodically inundated areas or peatlands. Wetland types differently influence methane fluxes and thus their contribution to the total wetland fraction should be quantified. Especially wetlands of permafrost regions are expected to have a strong impact on future climate due to soil thawing. In this study ENIVSAT ASAR Wide Swath data was tested for operational monitoring of the distribution of areas with a long-term SW near 1 (hSW) in northern Russia (SW = degree of saturation with water, 1 = saturated), which is a specific characteristic of peatlands. For the whole northern Russia, areas with hSW were delineated and discriminated from dynamic and open water bodies for the years 2007 and 2008. The area identified with this method amounts to approximately 300,000 km**2 in northern Siberia in 2007. It overlaps with zones of high carbon storage. Comparison with a range of related datasets (static and dynamic) showed that hSW represents not only peatlands but also temporary wetlands associated with post-forest fire conditions in permafrost regions. Annual long-term monitoring of change in boreal and tundra environments is possible with the presented approach. Sentinel-1, the successor of ENVISAT ASAR, will provide data that may allow continuous monitoring of these wetland dynamics in the future complementing global observations of wetland fraction.

(Table 3) Air temperatures, and snow and ice characteristics of fresh and brackish water lakes in the Northwest Territories, Canada

The algorithms designed to estimate snow water equivalent (SWE) using passive microwave measurements falter in lake-rich high-latitude environments due to the emission properties of ice covered lakes on low frequency measurements. Microwave emission models have been used to simulate brightness temperatures (Tbs) for snowpack characteristics in terrestrial environments but cannot be applied to snow on lakes because of the differing subsurface emissivities and scattering matrices present in ice. This paper examines the performance of a modified version of the Helsinki University of Technology (HUT) snow emission model that incorporates microwave emission from lake ice and sub-ice water. Inputs to the HUT model include measurements collected over brackish and freshwater lakes north of Inuvik, Northwest Territories, Canada in April 2008, consisting of snowpack (depth, density, and snow water equivalent) and lake ice (thickness and ice type). Coincident airborne radiometer measurements at a resolution of 80x100 m were used as ground-truth to evaluate the simulations. The results indicate that subsurface media are simulated best when utilizing a modeled effective grain size and a 1 mm RMS surface roughness at the ice/water interface compared to using measured grain size and a flat Fresnel reflective surface as input. Simulations at 37 GHz (vertical polarization) produce the best results compared to airborne Tbs, with a Root Mean Square Error (RMSE) of 6.2 K and 7.9 K, as well as Mean Bias Errors (MBEs) of -8.4 K and -8.8 K for brackish and freshwater sites respectively. Freshwater simulations at 6.9 and 19 GHz H exhibited low RMSE (10.53 and 6.15 K respectively) and MBE (-5.37 and 8.36 K respectively) but did not accurately simulate Tb variability (R= -0.15 and 0.01 respectively). Over brackish water, 6.9 GHz simulations had poor agreement with airborne Tbs, while 19 GHz V exhibited a low RMSE (6.15 K), MBE (-4.52 K) and improved relative agreement to airborne measurements (R = 0.47). Salinity considerations reduced 6.9 GHz errors substantially, with a drop in RMSE from 51.48 K and 57.18 K for H and V polarizations respectively, to 26.2 K and 31.6 K, although Tb variability was not well simulated. With best results at 37 GHz, HUT simulations exhibit the potential to track Tb evolution, and therefore SWE through the winter season.

Properties of water masses, taxa abundance, and isotopic ratios of samples obtained around Svalbard archipelago

The feeding strategies of Calanus hyperboreus, C. glacialis, and C. finmarchicus were investigated in the high-Arctic Svalbard region (77-81 °N) in May, August, and December, including seasons with algal blooms, late- to post-bloom situations, and unproductive winter periods. Stable isotope and fatty acid trophic marker (FATM) techniques were employed together to assess trophic level (TL), carbon sources (phytoplankton vs. ice algae), and diet of the three Calanus species. In addition, population development, distribution, and nutritional state (i.e. storage lipids) were examined to estimate their population status at the time of sampling. In May and August, the vertical distribution of the three Calanus species usually coincided with the maximum algal biomass. Their stable isotope and fatty acid (FA) composition indicated that they all were essentially herbivores in May, when the algal biomass was highest. Their FA composition, however, revealed different food preferences. C. hyperboreus had high proportions of 18:4n3, suggesting that it fed mainly on Phaeocystis, whereas C. glacialis and C. finmarchicus had high proportions of 16:4n1, 16:1n7, and 20:5n3, suggesting diatoms as their major food source. Carbon sources (i.e. phytoplankton vs. ice algae) were not possible to determine solely from FATM techniques since ice-diatoms and pelagic-diatoms were characterised by the same FA. However, the enriched d13C values of C. glacialis and C. finmarchicus in May indicated that they fed both on pelagic- and ice-diatoms. Patterns in absolute FA and fatty alcohol composition revealed that diatoms were the most important food for C. hyperboreus and C. glacialis, followed by Phaeocystis, whereas diatoms, Phaeocystis and other small autotrophic flagellates were equally important food for C. finmarchicus. During periods of lower algal biomass, only C. glacialis exhibited evidence of significant dietary switch, with a TL indicative of omnivory (mean TL=2.4). Large spatial variability was observed in population development, distribution, and lipid store sizes in August. At the northernmost station at the southern margin of the Arctic Ocean, the three Calanus species had similarly low lipid stores as they had in May, suggesting that they ascended later in the year. In December, relatively lipid-rich specimens had TL similar to those during the peak productive season (TL~2.0), suggesting that they were hibernating and not feeding on the available refractory material available at that time of the year. In contrast, lipid-poor specimens in December had substantially high TL (TL=2.5), suggesting that they were active and possibly were feeding.