Molecular and biochemical analyses of wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits

The physiological and molecular responses of ripe fruit to wounding were evaluated in two peach (Prunus persica) varieties ('Glohaven', GH, melting and 'BigTop', BT, slow melting nectarine) by comparing mesocarp samples from wedges (as in minimal processing) and whole fruit as the control. Slight differences between the two varieties were detected in terms of ethylene production, whereas total phenol and flavonoid concentrations, and PPO and POD enzyme activities showed a general increase in wounded GH but not in BT. This was associated with the better appearance of the BT wedges at the end of the experimental period (72 h). Microarray (genome-wide ?PEACH3.0) analysis revealed that a total number of 2218 genes were differentially expressed (p < 0.01, log2 fold change expression ratio >1 or <-1) in GH 24 h after wounding compared to the control. This number was much lower (1208) in BT. According to the enrichment analysis, cell wall, plasma membrane, response to stress, secondary metabolic processes, oxygen binding were the GO categories over-represented among the GH up-regulated genes, whereas plasma membrane and response to endogenous stimulus were the categories over-represented among the down-regulated genes. Only 32 genes showed a common expression trend in the two varieties 24 h after wounding, whereas a total of 512 genes (with highly represented transcription factors), displayed opposite behavior. Quantitative RT-PCR analysis confirmed the microarray data for 18 out of a total of 20 genes selected. Specific WRKY, AP2/ERF and HSP20 genes were markedly up-regulated in wounded GH, indicating the activation of regulatory and signaling mechanisms probably related to different hormone categories. Compared to BT, the expression of specific genes involved in phenylpropanoid and triterpenoid biosynthetic pathways showed a more pronounced induction in GH, highlighting the difference between the two peach varieties in terms of molecular responses to wounding in the mesocarp tissue.

Biogeochemistry and microbiology of groundwater during acetate and bicarbonate amendment to an alluvial aquifer

These data are from a field experiment conducted in a shallow alluvial aquifer along the Colorado River in Rifle, Colorado, USA. In this experiment, bicarbonate-promoted uranium desorption and acetate amendment were combined and compared to an acetate amendment-only experiment in the same experimental plot. Data include names and location data for boreholes, geochemical data for all the boreholes between June 1, 2010 and January 1, 2011, microarray data provided as signal to noise ratio (SNR) for individual microarray probes, microarray data provided as signal to noise ratio (SNR) by Genus.

Contextual classification of full waveform lidar data in the Wadden Sea

The classification of airborne lidar data is a relevant task in different disciplines. The information about the geometry and the full waveform can be used in order to classify the 3D point cloud. In Wadden Sea areas the classification of lidar data is of main interest for the scientific monitoring of coastal morphology and habitats, but it becomes a challenging task due to flat areas with hardly any discriminative objects. For the classification we combine a Conditional Random Fields framework with a Random Forests approach. By classifying in this way, we benefit from the consideration of context on the one hand and from the opportunity to utilise a high number of classification features on the other hand. We investigate the relevance of different features for the lidar points in coastal areas as well as for the interaction of neighbouring points.

The Lena River Delta - Land cover classification of tundra environments based on Landsat 7 ETM+ data and its application for upscaling of methane emissions

The Lena River Delta, situated in Northern Siberia (72.0 - 73.8° N, 122.0 - 129.5° E), is the largest Arctic delta and covers 29,000 km**2. Since natural deltas are characterised by complex geomorphological patterns and various types of ecosystems, high spatial resolution information on the distribution and extent of the delta environments is necessary for a spatial assessment and accurate quantification of biogeochemical processes as drivers for the emission of greenhouse gases from tundra soils. In this study, the first land cover classification for the entire Lena Delta based on Landsat 7 Enhanced Thematic Mapper (ETM+) images was conducted and used for the quantification of methane emissions from the delta ecosystems on the regional scale. The applied supervised minimum distance classification was very effective with the few ancillary data that were available for training site selection. Nine land cover classes of aquatic and terrestrial ecosystems in the wetland dominated (72%) Lena Delta could be defined by this classification approach. The mean daily methane emission of the entire Lena Delta was calculated with 10.35 mg CH4/m**2/d. Taking our multi-scale approach into account we find that the methane source strength of certain tundra wetland types is lower than calculated previously on coarser scales.

Habitat map of Danajon Bank, Philippines, derived from a high-spatial-resolution multi-spectral satellite image and georeferenced point intercept transect and spot-check survey field data, using an object-based image classification method

A mosaic of two WorldView-2 high resolution multispectral images (Acquisition dates: October 2010 and April 2012), in conjunction with field survey data, was used to create a habitat map of the Danajon Bank, Philippines (10°15'0'' N, 124°08'0'' E) using an object-based approach. To create the habitat map, we conducted benthic cover (seafloor) field surveys using two methods. Firstly, we undertook georeferenced point intercept transects (English et al., 1997). For ten sites we recorded habitat cover types at 1 m intervals on 10 m long transects (n= 2,070 points). Second, we conducted geo-referenced spot check surveys, by placing a viewing bucket in the water to estimate the percent cover benthic cover types (n = 2,357 points). Survey locations were chosen to cover a diverse and representative subset of habitats found in the Danajon Bank. The combination of methods was a compromise between the higher accuracy of point intercept transects and the larger sample area achievable through spot check surveys (Roelfsema and Phinn, 2008, doi:10.1117/12.804806). Object-based image analysis, using the field data as calibration data, was used to classify the image mosaic at each of the reef, geomorphic and benthic community levels. The benthic community level segregated the image into a total of 17 pure and mixed benthic classes.

SADA and DESYRE DSSs descriptive classification criteria (main issues related to DSS's)

Brownfield rehabilitation is an essential step for sustainable land-use planning and management in the European Union. In brownfield regeneration processes, the legacy contamination plays a significant role, firstly because of the persistent contaminants in soil or groundwater which extends the existing hazards and risks well into the future; and secondly, problems from historical contamination are often more difficult to manage than contamination caused by new activities. Due to the complexity associated with the management of brownfield site rehabilitation, Decision Support Systems (DSSs) have been developed to support problem holders and stakeholders in the decision-making process encompassing all phases of the rehabilitation. This paper presents a comparative study between two DSSs, namely SADA (Spatial Analysis and Decision Assistance) and DESYRE (Decision Support System for the Requalification of Contaminated Sites), with the main objective of showing the benefits of using DSSs to introduce and process data and then to disseminate results to different stakeholders involved in the decision-making process. For this purpose, a former car manufacturing plant located in the Brasov area, Central Romania, contaminated chiefly by heavy metals and total petroleum hydrocarbons, has been selected as a case study to apply the two examined DSSs. Major results presented here concern the analysis of the functionalities of the two DSSs in order to identify similarities, differences and complementarities and, thus, to provide an indication of the most suitable integration options.

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

Shape-invariant multibeam backscatter data of the eastern slope of the Porcupine Seabight (50 m grid size)

In this study multibeam angular backscatter data acquired in the eastern slope of the Porcupine Seabight are analysed. Processing of the angular backscatter data using the 'NRGCOR' software was made for 29 locations comprising different geological provinces like: carbonate mounds, buried mounds, seafloor channels, and inter-channel areas. A detailed methodology is developed to produce a map of angle-invariant (normalized) backscatter data by correcting the local angular backscatter values. The present paper involves detailed processing steps and related technical aspects of the normalization approach. The presented angle-invariant backscatter map possesses 12 dB dynamic range in terms of grey scale. A clear distinction is seen between the mound dominated northern area (Belgica province) and the Gollum channel seafloor at the southern end of the site. Qualitative analyses of the calculated mean backscatter values i.e., grey scale levels, utilizing angle-invariant backscatter data generally indicate backscatter values are highest (lighter grey scale) in the mound areas followed by buried mounds. The backscatter values are lowest in the inter-channel areas (lowest grey scale level). Moderate backscatter values (medium grey level) are observed from the Gollum and Kings channel data, and significant variability within the channel seafloor provinces. The segmentation of the channel seafloor provinces are made based on the computed grey scale levels for further analyses based on the angular backscatter strength. Three major parameters are utilized to classify four different seafloor provinces of the Porcupine Seabight by employing a semi-empirical method to analyse multibeam angular backscatter data. The predicted backscatter response which has been computed at 20° is the highest for the mound areas. The coefficient of variation (CV) of the mean backscatter response is also the highest for the mound areas. Interestingly, the slope value of the buried mound areas are found to be the highest. However, the channel seafloor of moderate backscatter response presents the lowest slope and CV values. A critical examination of the inter-channel areas indicates less variability within the estimated three parameters.

Potential of RapidEye image data for sediment monitoring of the German tidal flats

The Wadden Sea is located in the southeastern part of the North Sea forming an extended intertidal area along the Dutch, German and Danish coast. It is a highly dynamic and largely natural ecosystem influenced by climatic changes and anthropogenic use of the North Sea. Changes in the environment of the Wadden Sea, natural or anthropogenic origin, cannot be monitored by the standard measurement methods alone, because large-area surveys of the intertidal flats are often difficult due to tides, tidal channels and unstable underground. For this reason, remote sensing offers effective monitoring tools. In this study a multi-sensor concept for classification of intertidal areas in the Wadden Sea has been developed. Basis for this method is a combined analysis of RapidEye (RE) and TerraSAR-X (TSX) satellite data coupled with ancillary vector data about the distribution of vegetation, mussel beds and sediments. The classification of the vegetation and mussel beds is based on a decision tree and a set of hierarchically structured algorithms which use object and texture features. The sediments are classified by an algorithm which uses thresholds and a majority filter. Further improvements focus on radiometric enhancement and atmospheric correction. First results show that we are able to identify vegetation and mussel beds with the use of multi-sensor remote sensing. The classification of the sediments in the tidal flats is a challenge compared to vegetation and mussel beds. The results demonstrate that the sediments cannot be classified with high accuracy by their spectral properties alone due to their similarity which is predominately caused by their water content.

A geomorphological seabed classification for the Weddell Sea, Antarctica, with links to ArcGIS project files

Sea floor morphology plays an important role in many scientific disciplines such as ecology, hydrology and sedimentology since geomorphic features can act as physical controls for e.g. species distribution, oceanographically flow-path estimations or sedimentation processes. In this study, we provide a terrain analysis of the Weddell Sea based on the 500 m × 500 m resolution bathymetry data provided by the mapping project IBCSO. Seventeen seabed classes are recognized at the sea floor based on a fine and broad scale Benthic Positioning Index calculation highlighting the diversity of the glacially carved shelf. Beside the morphology, slope, aspect, terrain rugosity and hillshade were calculated. Applying zonal statistics to the geomorphic features identified unambiguously the shelf edge of the Weddell Sea with a width of 45-70 km and a mean depth of about 1200 m ranging from 270 m to 4300 m. A complex morphology of troughs, flat ridges, pinnacles, steep slopes, seamounts, outcrops, and narrow ridges, structures with approx. 5-7 km width, build an approx. 40-70 km long swath along the shelf edge. The study shows where scarps and depressions control the connection between shelf and abyssal and where high and low declination within the scarps e.g. occur. For evaluation purpose, 428 grain size samples were added to the seabed class map. The mean values of mud, sand and gravel of those samples falling into a single seabed class was calculated, respectively, and assigned to a sediment texture class according to a common sediment classification scheme.

Icebergs in the Amundsen Sea (Antarctica) determined from ENVISAT ASAR WSM data using object-based image analysis approach, link to ESRI GDB files

ENVISAT ASAR WSM images with pixel size 150 × 150 m, acquired in different meteorological, oceanographic and sea ice conditions were used to determined icebergs in the Amundsen Sea (Antarctica). An object-based method for automatic iceberg detection from SAR data has been developed and applied. The object identification is based on spectral and spatial parameters on 5 scale levels, and was verified with manual classification in four polygon areas, chosen to represent varying environmental conditions. The algorithm works comparatively well in freezing temperatures and strong wind conditions, prevailing in the Amundsen Sea during the year. The detection rate was 96% which corresponds to 94% of the area (counting icebergs larger than 0.03 km**2), for all seasons. The presented algorithm tends to generate errors in the form of false alarms, mainly caused by the presence of ice floes, rather than misses. This affects the reliability since false alarms were manually corrected post analysis.

Single beam survey data and links to sea-bottom video files off Helgoland

Kelp forests represent a major habitat type in coastal waters worldwide and their structure and distribution is predicted to change due to global warming. Despite their ecological and economical importance, there is still a lack of reliable spatial information on their abundance and distribution. In recent years, various hydroacoustic mapping techniques for sublittoral environments evolved. However, in turbid coastal waters, such as off the island of Helgoland (Germany, North Sea), the kelp vegetation is present in shallow water depths normally excluded from hydroacoustic surveys. In this study, single beam survey data consisting of the two seafloor parameters roughness and hardness were obtained with RoxAnn from water depth between 2 and 18 m. Our primary aim was to reliably detect the kelp forest habitat with different densities and distinguish it from other vegetated zones. Five habitat classes were identified using underwater-video and were applied for classification of acoustic signatures. Subsequently, spatial prediction maps were produced via two classification approaches: Linear discriminant analysis (LDA) and manual classification routine (MC). LDA was able to distinguish dense kelp forest from other habitats (i.e. mixed seaweed vegetation, sand, and barren bedrock), but no variances in kelp density. In contrast, MC also provided information on medium dense kelp distribution which is characterized by intermediate roughness and hardness values evoked by reduced kelp abundances. The prediction maps reach accordance levels of 62% (LDA) and 68% (MC). The presence of vegetation (kelp and mixed seaweed vegetation) was determined with higher prediction abilities of 75% (LDA) and 76% (MC). Since the different habitat classes reveal acoustic signatures that strongly overlap, the manual classification method was more appropriate for separating different kelp forest densities and low-lying vegetation. It became evident that the occurrence of kelp in this area is not simply linked to water depth. Moreover, this study shows that the two seafloor parameters collected with RoxAnn are suitable indicators for the discrimination of different densely vegetated seafloor habitats in shallow environments.