Existing sediment management guidelines: an overview

At the inaugural conference of SedNet WG 4 in April 2002 in Venice it was decided that a survey of existing sediment management guidelines was an important pre-requisite to elaborate on the opportunities for river basin planning of sediment management. This article discusses the existing programmes, decision support system, and conventions and concludes that there is presently no comprehensive river basin sediment management guideline at an international (European) or national level. Management guidelines which are of high relevance for sediment management exist mostly for the purpose of environmentally sound handling for navigation. For the maintenance of waterways and harbours sediments have to be handled in an environmentally sound and economical way. There are some special international and national regulations for dredged material which have different legal and technical backgrounds, purposes and limited competence. The way to find the appropriate regulation within legislation is to ask the question: What will happen with the sediment/dredged material?     

Bodennutzung und Nitrat-Stickstoff in der Dränzone von Lößdecken der südlichen Niederrheinischen Bucht

Land use and nitrate-nitrogen in the vadose zone of loess deposits in the southern part of the Lower Rhenish Embayment Mean annual nitrogen-leaching was studied at seven experimental sites with grain-sugar beet crop rotation. Soil water simulation models and determination of the nitrogen content in the vadose zone below the rooting zone were combined to quantify the annual leaching rates. Leaching amounts to 11–18 kg NO₃^? N/ha · a at sites where only mineral fertilizer was applied, whereas sites with additional organic fertilizers show higher leaching rates of 30–36 kg NO₃^? N/ha · a.     

Estimating the age–diameter relationship of oak species in Switzerland using nonlinear mixed-effects models

Tree growth plays a key role in forest dynamics, yet little attention has been paid to quantifying tree age–diameter relationships. Predicting diameter growth of oaks is especially important due to their role in nature conservation and adaptive forest management under climate change. Thus, we (1) identified environmental variables that shape age–diameter relationships of oaks and (2) quantified the accuracy of predictions based on these variables. We determined the age–diameter relationship of 243 oaks (Quercus spp.) growing in Switzerland by using tree-ring samples. Nonlinear mixed-effects models based on a modified Chapman-Richards equation were fitted with environmental variables included as covariates. The fixed effects elevation, slope and water-holding capacity were most important in shaping the age–diameter relationships. Lower elevations, steeper slopes, north-facing aspects, higher water-holding capacities and moister summers resulted in larger maximum diameters. For 75 % of the oaks, age–diameter relationships predicted by the fixed effects matched fairly well the observations (root mean square error between predictions and observations <6 cm); the inclusion of random effects reduced root mean square errors for 86 % of the trees. These results suggest that water runoff plays a key role for the age–diameter relationships, accompanied by limiting temperature effects at higher elevations. The fixed effects covered variability in site quality, whereas the random effects included tree-specific deviations from expected age–diameter relationships, potentially due to neighbourhood effects such as stand density and competition.     

Impacts of changing climate and land use on vegetation dynamics in a Mediterranean ecosystem: insights from paleoecology and dynamic modeling

Forests near the Mediterranean coast have been shaped by millennia of human disturbance. Consequently, ecological studies relying on modern observations or historical records may have difficulty assessing natural vegetation dynamics under current and future climate. We combined a sedimentary pollen record from Lago di Massacciucoli, Tuscany, Italy with simulations from the LandClim dynamic vegetation model to determine what vegetation preceded intense human disturbance, how past changes in vegetation relate to fire and browsing, and the potential of an extinct vegetation type under present climate. We simulated vegetation dynamics near Lago di Massaciucoli for the last 7,000 years using a local chironomid-inferred temperature reconstruction with combinations of three fire regimes (small infrequent, large infrequent, small frequent) and three browsing intensities (no browsing, light browsing, and moderate browsing), and compared model output to pollen data. Simulations with low disturbance support pollen-inferred evidence for a mixed forest dominated by Quercus ilex (a Mediterranean species) and Abies alba (a montane species). Whereas pollen data record the collapse of A. alba after 6000 cal yr bp, simulated populations expanded with declining summer temperatures during the late Holocene. Simulations with increased fire and browsing are consistent with evidence for expansion by deciduous species after A. alba collapsed. According to our combined paleo-environmental and modeling evidence, mixed Q. ilex and A. alba forests remain possible with current climate and limited disturbance, and provide a viable management objective for ecosystems near the Mediterranean coast and in regions that are expected to experience a mediterranean-type climate in the future.     

Soil organic carbon in the rocky desert of northern Negev (Israel)

Purpose

So far, the soil organic carbon (SOC) literature is dominated by studies in the humid environments with huge stocks of vulnerable carbon. Limited attention has been given to dryland ecosystems despite being often considered to be highly sensitive to environmental change. Thus, there is insufficient research about the spatial patterns of SOC stocks and the interaction between soil depth, ecohydrology, geomorphic processes, and SOC stocks. This study aimed at identifying the relationship between surface characteristics, vegetation coverage, SOC, and SOC stocks in the arid northern Negev in Israel.

Materials and methods

The study site Sede Boker is ideally suited because of well-researched but variable ecohydrology. For this purpose, we sampled five slope sections with different ecohydrologic characteristics (e.g., soil and vegetation) and calculate SOC stocks. To identify controlling factors of SOC stocks on rocky desert slopes, we compared soil properties, vegetation coverage, SOC concentration, and stocks between the five ecohydrologic units.

Results and discussion

The results show that in Sede Boker, rocky desert slopes represent a significant SOC pool with a mean SOC stock of 0.58?kg?C?m^?2 averaged over the entire study area. The spatial variability of the soil coverage represents a strong control on SOC stocks, which varies between zero in uncovered areas and 1.54?kg?C?m^?2 on average in the soil-covered areas. Aspect-driven changes of solar radiation and thus of water availability are the dominant control of vegetation coverage and SOC stock in the study area.

Conclusions

The data indicate that dryland soils contain a significant amount of SOC. The SOC varies between the ecohydrologic units, which reflect (1) aspect-driven differences, (2) microscale topography, (3) soil formation, and (4) vegetation coverage, which are of greatest importance for estimating SOC stocks in drylands.     

Detection of expressed fungal Type I polyketide synthase genes in a forest soil

Secondary metabolites synthesized via the polyketide pathway are thought to mediate interference competition between soil microorganisms as well as cell-to-cell signaling. Although their synthesis has been documented in laboratory culture, it remains uncertain whether these compounds are actually produced under field conditions. Here, we report the presence and expression of fungal Type I polyketide synthase (PKS) genes in the organic horizon of a forest soil. If these expressed PKS genes produce compounds that elicit antagonistic interactions among soil microorganisms, then it could be a factor structuring microbial communities in soil.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Soil organic C as affected by silvicultural and exploitative interventions in Nothofagus pumilio forests of the Chilean Patagonia

This study evaluates the effect of silvicultural and exploitative interventions on soil organic carbon (SOC) in Chilean Lenga (Nothofagus pumilio (Poepp et Endl.) Krasser) forests in south Patagonia. We analyzed SOC and the organic soil horizons in five stands at different stages of development: intact native forest (NI); a 3-year-old shelterwood stand (S3); an 8-year-old shelterwood stand (S8); a 14-year-old stand that was initially treated with shelterwood and subsequently final cut (10 years after the first intervention) (S14), and a 25-year-old stand subject to a exploitative intervention (E25). The SOC under the forest stands, down to a depth of 50 cm (including the Oi horizon), was 60, 55, 71, 85, and 67 Mg ha⁻¹ for the NI, S3, S8, S14, and E25 forest stands, respectively. A significant decrease in SOC occurred 3 years after an intensive shelterwood cut (S3), particularly in the first 5 cm of the mineral soil. Slightly higher carbon contents were observed in the upper horizons of the mineral soil in both the S8 and S14 stands. Consequently, the applied shelterwood system appears to generate only short-term losses of SOC in the Lenga forest. Soil organic carbon increased over the medium term but decreased to the level observed in intact native forests over the long term. Regeneration, which influences stand microclimate (a factor in SOC storage) and provides an important source of organic soil material, was identified as one of the most important factors influencing SOC.