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Microfluidic monitoring of the growth of individual hyphae in confined environments

Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass, and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared to measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behavior of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to adress its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.

Data from: Behavioural and fitness effects of translocation to a novel environment: whole-lake experiments in two aquatic top predators

Translocation into a novel environment through common fisheries-management practices, such as fish stocking, provides opportunities to study behavioural and fitness impacts of translocations at realistic ecological scales. The process of stocking, as well as the unfamiliarity with novel ecological conditions and the interactions with resident fish may affect translocated individuals, leading to alterations of behaviours and causing fitness impacts. Our objectives were to investigate how aquatic top-predators behaviourally establish themselves and compete with resident individuals following introduction in a novel lake environment and to investigate the resulting fitness consequences. Using high-resolution acoustic telemetry, we conducted whole-lake experiments and compared the activity, activity-space size and fate of translocated and resident individuals in two model top predators, northern pike (Esox lucius, n = 160) and European catfish (Silurus glanis, n = 33). Additionally, we compared the reproductive fitness of translocated and resident northern pike. The experiment was conducted with large (adult) individuals of different origins, resilient to predation, but subject to agonistic interactions and competition with resident fish. Over a period of several months, the translocated catfish exhibited consistently larger activity-space sizes than resident catfish, but did not differ from residents in activity and survival. The pike from one of the two translocated origins we tested also showed elevated space-use, and both translocated origins revealed higher mortality rates than their resident conspecifics, indicating maladjustment to their novel environment. When non-resident pike reproduced, they overwhelmingly produced hybrid offspring with resident fish, indicating that introductions fostered gene flow of non-native genes. Our study indicates that fish introductions result in behavioural and fitness impacts even in large-bodied top predators that experience low levels of natural predation risk.

Data from: Effect of pH regulation by microbes on corrosion behaviour of duplex stainless steel 2205 in acidic artificial seawater environment

Sulphate reducing bacteria (SRB) can regulate environmental pH because of their metabolism. Since local acidification results in pitting corrosion, the potential capacity of pH regulation by SRB would have important consequences for electrochemical aspects of the bio-corrosion process. This study focussed on identifying the effect of pH on the corrosion of duplex stainless steel (DSS) 2205 in a nutrient rich artificial seawater medium containing SRB species, Desulfovibrio vulgaris. DSS samples were exposed to the medium for 13 days at 37 0C at pH ranging from 4.0 to 7.4. The open circuit potential value (OCP), sulphide level, pH and number of bacteria in the medium were recorded daily. Electrochemical impedance spectroscopy (EIS) and potential dynamic polarization were used to study the properties of the films and corrosion behaviour of the material. Inductively coupled plasma mass spectrometry (ICPMS) was used to measure the concentration of cations Cr, Fe, Ni, Mo, Mn in the experimental solution after 13 days. Scanning electron microscopy (SEM) and Energy Dispersive X-Ray Spectroscopy (EDX) were used for surface analysis. The results showed the pH changed from acidic values set at the beginning of the experiment to approximately pH 7.5 after 5 days due to bacterial metabolism. After 13 days, the highest iron concentration was in the solution that was initially at pH 4 accompanied by pitting on the stainless steel. Sulphide was present on all specimens but with more sulphide corrosion products at pH 4. The results of this study suggest that the corrosion process for the first few days exposure at low pH was driven by pH in solution rather than by bacteria. The increasing pH during the course of the experiment slowed down the corrosion process of materials originally at low pH. The nature and mechanism of SRB attack on duplex stainless steel at different acidic environments are discussed.

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms) with climate and geography, among 140 wild accessions. RDA, SEM, and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.

opencc-by-4.0Aug 2020View details →

Task Bench Software Environment

This is the execution environment artifact for "Task Bench: A Parameterized Benchmark for Evaluating Parallel Runtime Performance", published in SC'20.

opencc-zeroDec 2017View details →

Data from: Feeding environment and other traits shape species' roles in marine food webs

Food webs and meso-scale motifs allow us to understand the structure of ecological communities and define species' roles within them. This species-level perspective on networks permits tests for relationships between species' traits and their patterns of direct and indirect interactions. Such relationships could allow us to predict food-web structure based on more easily-obtained trait information. Here we calculated the roles of species (as vectors of motif position frequencies) in six well-resolved marine food webs and identified the motif positions associated with the greatest variation in species' roles. We then tested whether the frequencies of these positions varied with species' traits. Despite the coarse-grained traits we used, our approach identified several strong associations between traits and motifs. Feeding environment was a key trait in our models and may shape species' roles by affecting encounter probabilities. Incorporating environment into future food web models may improve predictions of an unknown network structure.

opencc-zeroSep 2020View details →

Identifying the fitness consequences of sex in complex natural environments

In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale multi-site reciprocal transplant using multiple sexual and asexual genotypes of a native North American wildflower to show that sexual genotypes have reduced lifetime fitness, despite lower herbivory. We separated the effects of sex from those of hybridity, finding that over-winter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals more than non-hybrid asexual or sexual genotypes. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped not just by sex itself, but by complex natural environments, correlated traits, and the identity and availability of mates.

opencc-zeroOct 2020View details →

Phylogenetic restriction of plant invasion in drought-stressed environments: implications for insect-pollinated plant communities in water-limited ecosystems

Background: Plant-pollinator community diversity has been found to decrease under conditions of drought stress, however research into the temporal dimensions of this phenomenon remains limited. In this study, we investigated the effect of seasonal drought on the temporal niche dynamics of entomophilous flowering plants in a water-limited ecosystem. We hypothesized that closely related native and exotic plants would tend to share similar life history, and that peak flowering events would therefore coincide with phylogenetic clustering in plant communities based on expected phenological responses of plant functional types to limitations in soil moisture availability. Location: Galiano Island, British Columbia, Canada Methods: Combining methods from pollinator research and phylogenetic community ecology, we tested the influence of environmental filtering over plant community phenology across gradients of landscape disturbance and soil moisture. Floral resource availability and community structure were quantified by counts of flowering shoots. We constructed a robust phylogeny to analyze spatial and temporal variation in phylogenetic patterns across the landscape, testing the significance of the observed patterns against a randomly generated community phylogeny. Phylogenetic metrics were then regressed against factors of disturbance and soil moisture availability. Results: Critical seasonal fluctuations in floral resources coincided with significant phylogenetic clustering in plant communities, with decreasing plant diversity observed under conditions of increasing drought stress. Exotic plant species in the Asteraceae became increasingly pervasive across the landscape, occupying a late season temporal niche in drought-stressed environments. Main conclusion: Results suggest that environmental filtering is the dominant assembly process structuring the temporal niche of plant communities in this water-limited ecosystem. Based on these results, and trends seen elsewhere, the overall diversity of plant-pollinator communities may be expected to decline with the increasing drought stress predicted under future climate scenarios.

opencc-zeroOct 2020View details →

The effects of age on the demography of a perennial plant depend on interactions with size and environment

Age-dependence of the demographic rates survival, fecundity and individual growth is a fundamental aspect of population biological theory. Knowledge about plant ageing can also be important for conservation and agriculture as it will improve the accuracy of population viability assessments and long-term performance assessments in perennial crops. Recent studies show age effects on demographic rates for several plant species, yet much remains to be learned about the patterns and mechanisms of plant ageing, particularly about how age effects interact with the environment and with plant size. We collected age-and-size-based demographic data, as well as individual-based environmental data, for the perennial herb Plantago lanceolata in Denmark over three annual transitions (four years). We combined frequent field monitoring of carefully mapped individuals with the underused technique of root histology to determine age of herbaceous plants. We used generalized linear mixed effects models to assess how age, soil properties, and year influenced survival, growth, and reproduction. Our results show no strong evidence of consistent age declines, rather, we found mostly positive effects of age on vital rates. For all vital rates, i.e. survival, growth, flowering, and reproductive output, age effects also differed significantly among years. Additionally, we detected an interactive effect of age and size in the growth model. Size, and temporal and spatial environmental variation also affected vital rates independently of age. Synthesis: Our study shows that age-dependence of demographic rates can depend both on individual size and environmental variation. These results suggest that a consideration of potential age-interactions may improve the accuracy of comparative studies of ageing and population projections. Moreover, this study shows that much is still unknown about how plant ageing can be affected by the environment, and illustrates how age determination using herb chronology provides an opportunity to increase our knowledge about ageing in herbaceous plants.

opencc-by-4.0Oct 2020View details →

Southern Ocean Cloud and Aerosol data set: a compilation of measurements from the 2018 Southern Ocean Ross Sea Marine Ecosystems and Environment voyage

Due to its remote location and extreme weather conditions, atmospheric in situ measurements are rare in the Southern Ocean. As a result, aerosol-cloud interactions in this region are poorly understood and remain a major source of uncertainty in climate models. This, in turn, contributes substantially to persistent biases in climate model simulations, numerical weather prediction models and reanalyses. It has been shown in previous studies that in situ and ground-based remote sensing measurements across the Southern Ocean are critical for complementing satellite data sets due to the importance of boundary layer and low-level cloud processes. These processes are poorly sampled by satellite-based measurements which are typically obscured by near-continuous overlying cloud cover observed in this region. Here we provide a comprehensive set of ship-based aerosol and meteorological observations collected on the TAN1802 voyage of R/V Tangaroa across the Southern Ocean, from Wellington, New Zealand, to the Ross Sea, Antarctica. The voyage was carried out from 8 February to 21 March, 2018. The compiled data set provides here includes measurements from a range of instruments, such as (i) meteorological conditions at the sea surface and profile measurements; (ii) the size and concentration of particles; (iii) trace gases dissolved in the ocean surface such as dimethyl sulfide and carbonyl sulfide; (iv) and remotely sensed observations of low clouds. We encourage the scientific community to use these measurements for further analysis and model evaluation studies, in particular, for studies of Southern Ocean clouds, aerosol and their interaction.

opencc-zeroNov 2020View details →

Foraging behaviour alters with social environment in a juvenile songbird

Early independence from parents is a critical period where social information acquired vertically may become outdated, or conflict with new information. However, across natural populations it is unclear if newly-independent young persist in using information from parents, or if group-level effects of conformity override previous behaviours. Here we test if wild juvenile hihi (Notiomystis cincta, a New Zealand passerine) retain a foraging behaviour from parents, or if they change in response to the behaviour of peers. We provided feeding stations to parents during chick-rearing to seed alternative access routes, and then tracked their offspring's behaviour. Once independent, juveniles formed mixed-treatment social groups, where they did not retain preferences that we detected when with parents. Instead, juvenile groups converged over time to use one access route per group, and juveniles that moved between groups switched to copy the locally-favoured option. Juvenile hihi did not copy specific individuals, even if they were more familiar with the preceding bird. Our study shows that early social experiences with parents affect initial foraging decisions, but social environments encountered later on can update transmission of arbitrary behaviours. This suggests that conformity may be widespread in animal groups, with potential cultural, ecological, and evolutionary consequences.

opencc-zeroNov 2020View details →

Rethinking Gloger's Rule: climate, light environments and color in a large family of tropical birds (Furnariidae)

Ecogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts endothermic animals should have darker colors in warm and rainy climates. This rule also predicts animals should be redder in warm and dry climates, the so-called "complex Gloger's rule." Empirical studies frequently demonstrate that animals are darker in cool and wet rather than warm and wet climates. Further, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage brightness and redness in the large Neotropical passerine family Furnariidae. Birds in cooler and rainier climates had darker plumage, even after controlling for habitat type. Birds in darker habitats had darker plumage, even after controlling for climate. The effects of temperature and brightness interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be redder in warm and dry habitats but also, surprisingly, in cool and wet locales. We suggest Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence and resistance to feather abrasion.

opencc-zeroNov 2020View details →

Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments

Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.

opencc-by-4.0Aug 2020View details →

Build-in-Wood Regulation Analysis – Energy and Indoor Environment

This dataset contains an analysis of selected EU Member State building regulations covering energy and indoor environment in multi-storey wood buildings. The data has been collected as part of the Build-in-Wood project (<a href="https://www.build-in-wood.eu/)">https://www.build-in-wood.eu/)</a> which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 862820. Disclaimer: The presented data might be outdated, flawed, or otherwise incomplete. Users are responsible for checking the correctness of the presented data.

opencc-zeroDec 2020View details →

Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA

Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3– and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.

opencc-zeroDec 2020View details →

Increased sperm production linked to competition in the maternal social environment

Maternal or early life effects may prepare offspring for similar social conditions to those experienced by their mothers. For males, the ability to achieve mating and fertilisation success is a key social challenge. Competitive conditions may therefore favour increased body size or ejaculate production in male offspring. We tested this experimentally by comparing reproductive traits of adult male bank voles (Myodes glareolus), whose mothers had experienced contrasting encounter regimes with female conspecifics while breeding. We found that daily sperm production rates and epididymis mass were significantly higher when dams had experienced more frequent encounters with female conspecifics. This response to maternal and early life experience was specific to sperm production and storage, with no evidence for effects on male body mass or the size of testes and accessory reproductive glands. Our findings reveal a potentially adaptive effect of maternal and early-life experience on the development of sperm production, which is worthy of wider investigation.

opencc-by-4.0Nov 2020View details →

Supplementary Data for "Influence of First And Second Coordination Environment on Structural Fe(II) Sites in MIL-101 for C-H Bond Activation in Methane"

Cartesian coordinates for all the optimized geometries reported in "Influence of First And Second Coordination Environment on Structural Fe(II) Sites in MIL-101 for C-H Bond Activation in Methane" (acscatal.0c03906)

opencc-zeroJan 2021View details →

Data from: Evolution and disappearance of sympatric Coregonus albula in a changing environment - a case study of the only remaining population pair in Sweden

During the past 50 years Fennoscandian populations of spring-spawning Baltic cisco (Coregonus albula), sympatric to common autumn-spawners, have declined or disappeared; e.g., three out of four known spring-spawning populations in Sweden are regarded as extinct. Over the same period, climate has changed and populations have been subject to other anthropogenic stressors. We compared historic (1960s) and recent (1990-2000s) morphological data from the still existent sympatric cisco populations in Lake Fegen, Sweden. Phenotypic changes were found for spring-spawners making them more similar to the sympatric autumn-spawners (that had remained virtually unchanged). Based on results for other salmoniform fishes, a phenotypically plastic response to increased temperature during early development appears unlikely. The recent material was also analysed with microsatellite markers; long-term effective population size in spring-spawners was estimated to be about 20 times lower than autumn-spawners, with signs of long-term gene flow in both directions and a recent genetic bottleneck in spring-spawners. The change towards a less distinct phenotype in spring-spawners is suggested to reflect a recent increase in gene flow from autumn-spawners. Time since divergence was estimated to only c. 1 900 years (95% CI: 400 – 5 900), but still the Fegen populations represent the most morphologically and genetically distinct sympatric populations studied. Consequently, we hypothesise that less distinct population pairs can be even younger, and that spring-spawning may have repeatedly evolved and disappeared in several lakes since the end of the last glaciation, concurrent with changed environmental conditions.

opencc-by-4.0Dec 2020View details →

Uncertainties associated with microwave link rainfall estimates in an urban environment

These dataset were collected from a dedicated microwave link setup between Mt View Reservoir (T) and 33 Lakeside Burwood (R). There were two OTT1 disdrometers installed at both ends of the microwave link complemented by 3 tipping bucket rain gauges.