Modeling carbon dynamics in two adjacent spruce forests with different soil conditions in Russia

International audienceNet ecosystem carbon exchange (NEE) were measured with eddy covariance method for two adjacent forests located at the southern boundary of European taiga in Russia in 1999?2004. The two spruce forests shared similar vegetation composition but differed in soil conditions. The wet spruce forest (WSF) possessed a thick peat layer (60 cm) with a high water table seasonally close to or above the soil surface. The dry spruce forest (DSF) had a relatively thin organic layer (5 cm) with a deep water table (>60 cm). The measured NEE fluxes (2000 and ?1440 kg C ha?1 yr?1 for WSF and DSF, respectively) indicated that WSF was a source while DSF a sink of atmospheric carbon dioxide during the experimental years. A process-based model, Forest-DNDC, was employed in the study to interpret the observations. The modeled NEE fluxes were 1800 and ?2200 kg C ha?1 yr?1 for WSF and DSF, respectively, which were comparable with the observations. The modeled data indicated that WSF and DSF had similar rates of photosynthesis and plant autotrophic respiration but differed in soil heterotrophic respiration. The simulations resulted in a hypothesis that the water table fluctuation at WSF could play a key role in determining the negative C balance in the ecosystem. A sensitivity test was conducted by running Forest-DNDC with varied water table scenarios for WSF. The results proved that the NEE fluxes from WSF were highly sensitive to the water table depth. When the water table dropped, the length of flooding season became shorter and more organic matter in the soil profile suffered from rapid decomposition that converted the ecosystem into a source atmospheric C. The conclusion from this modeling study could be applicable for a wide range of wetland and forest ecosystems that have accumulated soil organic C while face hydrological changes under certain climatic or land-use change scenarios

Editorial: Remembering Natalya Nikolaevna Vygodskaya

As the Guest Editor I want to dedicate this Special Issue in memory of my university professor Natalya Nikolaevna Vygodskaya (Figure 1) [...

A System for Information Management in BioMedical Studies—SIMBioMS

Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented

partitioning of ecosystem respiration in a paludified shallow peat spruce forest in the southern taiga of european russia

Soil, tree stems, and ecosystem carbon dioxide fluxes were measured by chambers and eddy covariance methods in a paludified shallow-peat spruce forest in the southern taiga of European Russia (Tver region, 56 N 33 E) during the growing seasons of 2002‐2012. The site was established in 1998 as part of the EUROSIBERIAN CARBONFLUX project, an international field experiment examining atmosphere‐biosphere interaction in Siberia and European Russia. In all years the observed annual cumulative net ecosystem flux was positive (the forest was a source of carbon to the atmosphere). Soil and tree stem respiration was a significant part of the total ecosystem respiration (ER) in this paludified shallow-peat spruce forest. On average, 49% of the ER came from soil respiration. We found that the soil fluxes exhibited high seasonal variability, ranging from 0.7 to 10 mol m 2 s 1 . Generally, the soil respiration depended on the soil temperature and ground water level. In drought conditions, the soil respiration was low and did not depend on temperature. The stem respiration of spruces grew intensively in May, had permanently high values from June to the end of September, and in October it dramatically decreased. The tree stem respiration in midsummer was about 3‐5 mol m 2 s 1 for dominant trees and about 1‐2 mol m 2 s 1 for subdominant trees. The respiration of living tree stems was about 10‐20% of the ER

Drug Susceptibility Patterns in MDR-TB Patients:Challenges for Future Regimen Design. A Cross-Sectional Study

Globally, there is substantial concern regarding the challenges of treating complex drug resistance patterns in multidrug resistant tuberculosis cases. Utilising data from three different settings (Estonia, Latvia, Romania) we sought to contrast drug susceptibility profiles for multidrug resistant tuberculosis cases, highlight the difficulties in designing universal regimen, and inform future regimen selection. Demographic and microbiological surveillance data for multidrug resistant tuberculosis cases from 2004-13 were analysed. High levels of additional resistance to currently recommended second line drugs were seen in all settings, with extensive variability between countries. Accurate drug susceptibility testing and drug susceptibility testing data are vital to inform the development of comprehensive, flexible, multidrug resistant tuberculosis guidance

PEAT-CLSM : A Specific Treatment of Peatland Hydrology in the NASA Catchment Land Surface Model

Peatlands are poorly represented in global Earth system modeling frameworks. Here we add a peatland-specific land surface hydrology module (PEAT-CLSM) to the Catchment Land Surface Model (CLSM) of the NASA Goddard Earth Observing System (GEOS) framework. The amended TOPMODEL approach of the original CLSM that uses topography characteristics to model catchment processes is discarded, and a peatland-specific model concept is realized in its place. To facilitate its utilization in operational GEOS efforts, PEAT-CLSM uses the basic structure of CLSM and the same global input data. Parameters used in PEAT-CLSM are based on literature data. A suite of CLSM and PEAT-CLSM simulations for peatland areas between 40 degrees N and 75 degrees N is presented and evaluated against a newly compiled data set of groundwater table depth and eddy covariance observations of latent and sensible heat fluxes in natural and seminatural peatlands. CLSM's simulated groundwater tables are too deep and variable, whereas PEAT-CLSM simulates a mean groundwater table depth of -0.20 m (snow-free unfrozen period) with moderate temporal fluctuations (standard deviation of 0.10 m), in significantly better agreement with in situ observations. Relative to an operational CLSM version that simply includes peat as a soil class, the temporal correlation coefficient is increased on average by 0.16 and reaches 0.64 for bogs and 0.66 for fens when driven with global atmospheric forcing data. In PEAT-CLSM, runoff is increased on average by 38% and evapotranspiration is reduced by 19%. The evapotranspiration reduction constitutes a significant improvement relative to eddy covariance measurements.Peer reviewe

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

<p>Abstract</p> <p>Background</p> <p>Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.</p> <p>Results</p> <p>OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.</p> <p>Conclusions</p> <p>OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.</p> <p>Availability</p> <p><url>http://www.ontocat.org</url></p

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy