The Arctic Traits Database – a repository of Arctic benthic invertebrate traits

The recently increased interest in marine trait-based studies highlights one general demand – the access to standardized, reference-based trait information. This demand holds especially true for polar regions, where the gathering of ecological information is still challenging. The Arctic Traits Database is a freely accessible online repository (https://doi.org/10.25365/phaidra.49; https://www.univie.ac.at/arctictraits, last access: 20 February 2019) that fulfils these requests for one important component of polar marine life, the Arctic benthic macroinvertebrates. It accounts for (1) obligate traceability of information (every entry is linked to at least one source), (2) exchangeability among trait platforms (use of most common download formats), (3) standardization (use of most common terminology and coding scheme) and (4) user-friendliness (granted by an intuitive web interface and rapid and easy download options, for the first time including the option to download a fuzzy coded trait matrix). The combination of these aspects makes the Arctic Traits Database the currently most sophisticated online accessible trait platform in (not only) marine ecology and a role model for prospective databases of other marine compartments or other (also non-marine) ecosystems. At present the database covers 19 traits (80 trait categories) and holds altogether 14&thinsp;242 trait entries for 1911 macro- and megabenthic taxa. Thus, the Arctic Traits Database will foster and facilitate trait-based approaches in polar regions in the future and increase our ecological understanding of this rapidly changing system.</p

Long-term exposure to elevated pCO2 more than warming modifies juvenile shell growth patterns in a temperate gastropod

Co-occurring global change drivers, such as ocean warming and acidification, can have large impacts on the behaviour, physiology, and health of marine organisms. However, whilst early-life stages are thought to be most sensitive to these impacts, little is known about the individual level processes by which such impacts take place. Here, using mesocosm experiments simulating ocean warming (OW) and ocean acidification (OA) conditions expected for the NE Atlantic region by 2100 using a variety of treatments of elevated pCO2 and temperature. We investigated their impacts on bio-mineralization, microstructure, and ontogeny of Nucella lapillus (L.) juveniles, a common gastropod predator that exerts important top-down controls on biodiversity patterns in temperate rocky shores. The shell of juveniles hatched in mesocosms during a 14 month long experiment were analysed using micro-CT scanning, 3D geometric morphometrics, and scanning-electron microscopy. Elevated temperature and age determined shell density, length, width, thickness, elemental chemistry, shape, and shell surface damages. However, co-occurring elevated pCO2 modified the impacts of elevated temperature, in line with expected changes in carbonate chemistry driven by temperature. Young N. lapillus from acidified treatments had weaker shells and were therefore expected to be more vulnerable to predation and environmental pressures such as wave action. However, in some instances, the effects of both higher CO2 content and elevated temperature appeared to have reversed as the individuals aged. This study suggests that compensatory development may therefore occur, and that expected increases in juvenile mortality under OA and OW may be counteracted, to some degree, by high plasticity in shell formation in this species. This feature may prove advantageous for N. lapillus community dynamics in near-future conditions

Polytraits : a database on biological traits of marine polychaetes

The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

Background: Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information: In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data – Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pc-linux-gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https://portal.lifewatchgreece.eu

Методология компьютерного моделирования процесса алмазного выглаживания

Приведены результаты компьютерного динамического моделирования процесса алмазного выглаживания методом конечных элементов в программном пакете Third Wave AdvantEdge. Установлено влияние модуля упругости обрабатываемого материала, радиуса выглаживателя, глубины и скорости выглаживания на величину напряжений в зоне обработки.The results of the computer simulation of the process of diamond smoothing by the finite element method in the software package Third Wave AdvantEdge are presented. The effect of the modulus of elasticity of the processed material, the radius of the smoother, the depth and the speed of smoothing on the value of stresses in the treatment zone is established

ENVIRONMENTS and EOL : identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001]

Scaling up experimental ocean acidification and warming research: from individuals to the ecosystem

NERC UK Ocean Acidification Research Programme NE/HO1747X/1 The full text is under embargo until 17.08.1

Assessment of temporal and spatial evolution of bacterial communities in a biological sand filter mesocosm treating winery wastewater

AIMS: To assess the impact of winery wastewater (WW) on biological sand filter (BSF) bacterial community structures, and to evaluate whether BSFs can constitute alternative and valuable treatment-processes to remediate WW. METHODS AND RESULTS: During 112 days, WW was used to contaminate a BSF mesocosm (length 173 cm/width 106 cm/depth 30 cm). The effect of WW on bacterial communities of four BSF microenvironments (surface/deep, inlet/ outlet) was investigated using terminal-restriction fragment length polymorphism (T-RFLP). BSF achieved high Na (95·1%), complete Cl and almost complete chemical oxygen demand (COD) (98·0%) and phenolic (99·2%) removals. T-RFLP analysis combined with ANOSIM revealed that WW significantly modified the surface and deep BSF bacterial communities. CONCLUSIONS: BSF provided high COD, phenolic and salt removals throughout the experiment. WW-selected bacterial communities were thus able to tolerate and/or degrade WW, suggesting that community composition does not alter BSF performances. However, biomass increased significantly in the WW- impacted surface sediments, which could later lead to system clogging and should thus be monitored. SIGNIFICANCE AND IMPACT OF THE STUDY: BSFs constitute alternatives to constructed wetlands to treat agri effluents such as WW. To our knowledge, this study is the first unravelling the responses of BSF bacterial communities to contamination and suggests that WW-selected BSF communities maintained high removal performances.Web of Scienc

Selection of diazotrophic bacterial communities in biological sand filter mesocosms used for the treatment of phenolic-laden wastewater

Agri effluents such as winery or olive mill waste-waters are characterized by high phenolic concentrations. These compounds are highly toxic and generally refractory to biodegradation. Biological sand filters (BSFs) represent inexpensive, environmentally friendly, and sustainable wastewater treatment systems which rely vastly on microbial catabolic processes. Using denaturing gradient gel electrophoresis and terminal-restriction fragment length polymorphism, this study aimed to assess the impact of increasing concentrations of synthetic phenolic-rich wastewater, ranging from 96 mg L−1 gallic acid and138 mg L−1 vanillin (i.e., a total chemical oxygen demand (COD) of 234 mg L−1) to 2,400mg L−1 gallic acid and 3,442 mg L−1 vanillin (5,842 mg COD L−1), on bacterialcommunities and the specific functional diazotrophic community from BSF mesocosms. This amendment procedure instigated efficient BSF phenolic removal, significant modifications of the bacterial communities, and notably led to the selection of a phenolic-resistant and less diverse diazotrophic community. This suggests that bioavailable N is crucial in the functioning of biological treatment processes involving microbial communities, and thus that functional alterations in the bacterial communities in BSFs ensure provision of sufficient bioavailable nitrogen for the degradation of wastewater with a high C/N ratio.Web of Scienc

Table 3: List of excluded Tetramorium

With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography