No observed developmental effects in early life stages of capelin (Mallotus villosus) exposed to a water-soluble fraction of crude oil during embryonic development.

The rise in offshore oil and gas operations, maritime shipping, and tourism in northern latitudes enhances the risk of oil spills to sub-Arctic and Arctic coastal environments. Therefore, there is a need to understand the potential adverse effects of petroleum on key species in these areas. Here, we investigated the effects of oil exposure on the early life stages of capelin (Mallotus villosus), an ecologically and commercially important Barents Sea forage fish species that spawns along the coast of Northern Norway. Capelin embryos were exposed to five different concentrations (corresponding to 0.5-19 µg/L total PAHs) of water-soluble fraction (WSF) of crude oil from 6 days post fertilization (dpf) until hatch (25 dpf), and development of larvae in clean seawater was monitored until 52 dpf. None of the investigated endpoints (embryo development, larval length, heart rate, arrhythmia, and larval mortality) showed any effects. Our results suggest that the early life stages of capelin may be more robust to crude oil exposure than similar life stages of other fish species.

Fast reactivation of photosynthesis in arctic phytoplankton during the polar night1.

Arctic microalgae experience long periods of continuous darkness during the polar night, when they are unable to photosynthesize. Despite numerous studies on overwintering strategies, such as utilization of stored energy products, formation of resting stages, reduction of metabolic rates and heterotrophic lifestyles, there have been few attempts to assess the in situ physiological state and restoration of the photosynthetic apparatus upon re-illumination. In this study, we found diverse and active marine phytoplankton communities during the polar night at 78°N. Furthermore, we observed rapid changes (≤20 min) in the efficiency of photosynthetic electron transport upon re-illumination. High photosynthetic capacity and net primary production were established after 24 h of re-illumination. Our results suggest that some Arctic autotrophs maintain fully functional photosystem II and downstream electron acceptors during the polar night even though the low in situ net primary production levels measured in January prove that light was not sufficient to support any measurable primary production. Due to low temperatures resulting in low respiratory rates as well as the absence of photodamage during the polar night, maintenance of basic photosynthetic machinery may actually pose relatively low metabolic costs for algal cells. This could allow Arctic microalgae to endure the polar night without the formation of dormant stages, enabling them to recover and take advantage of light immediately upon the suns return during the winter-spring transition.

Ordination with any dissimilarity measure: a weighted Euclidean solution.

The classical approach to ordination is to use variants of the Euclidean distance to measure differences between samples (e.g., sites in a community study) based on their observation vectors (e.g., abundance counts for a set of species). Examples include Euclidean distance on standardized or log-transformed data, on which principal component analysis and redundancy analysis are based; chi-square distance, on which (canonical) correspondence analysis is based; and Hellinger distance, using square roots of relative values in each multivariate vector. Advantages of the Euclidean approach include the neat decomposition of variance and the ordination's optimal biplot display. To extend this approach to any non-Euclidean or nonmetric dissimilarity, a simple solution is proposed, consisting of the estimation of a weighted Euclidean distance that optimally approximates the dissimilarities. This preliminary step preserves the good properties of the classical approach while giving two additional benefits as by-products. Firstly, the estimated species weights, quantifying each species' contribution to the dissimilarities, can be interpreted, and weights equal or close to zero can assist in variable selection. Secondly, the dimensionality remains that of the number of species, not the dimensionality inherent in the dissimilarities, which depends on the number of samples and can be considerably higher.

The contributions of rare objects in correspondence analysis.

Correspondence analysis, when used to understand relationships in a table of counts (for example, abundance data in ecology), has been criticized as being too sensitive to objects (for example, species) that occur with very low frequency or in very few samples. Here I show that this criticism is generally unfounded. This is demonstrated in several data sets by calculating the actual contributions of rare objects to the results of correspondence analysis and canonical correspondence analysis, both to the determination of the ordination axes and to the chi-square distance. It is a fact that rare objects are often positioned as outliers in correspondence analysis ordinations, which gives the impression that they are highly influential, but their low weight offsets their distant positions and reduces their effect on the results. An alternative scaling of the correspondence analysis solution, the contribution biplot, is proposed as a way of displaying the results in order to avoid the problem of outlying and low contributing rare objects. In this new scaling of the biplot (or triplot in canonical correspondence analysis), species points have coordinates that are directly related to their contributions to the solution.

Fuzzy coding in constrained ordinations.

Canonical correspondence analysis and redundancy analysis are two methods of constrained ordination regularly used in the analysis of ecological data when ordinations based on several response variables (for example, species abundances) are related linearly to several explanatory variables (for example, environmental variables, spatial positions of samples). In this report I demonstrate the advantages of the fuzzy coding of explanatory variables: first, nonlinear relationships can be diagnosed; second, more variance in the responses can be explained; and third, in the presence of categorical explanatory variables (for example, years, regions) the interpretation of the resulting triplot ordination is unified because all explanatory variables are measured at a categorical level.

Three approaches to supervised learning for compositional data with pairwise logratios.

Logratios between pairs of compositional parts (pairwise logratios) are the easiest to interpret in compositional data analysis, and include the well-known additive logratios as particular cases. When the number of parts is large (sometimes even larger than the number of cases), some form of logratio selection is needed. In this article, we present three alternative stepwise supervised learning methods to select the pairwise logratios that best explain a dependent variable in a generalized linear model, each geared for a specific problem. The first method features unrestricted search, where any pairwise logratio can be selected. This method has a complex interpretation if some pairs of parts in the logratios overlap, but it leads to the most accurate predictions. The second method restricts parts to occur only once, which makes the corresponding logratios intuitively interpretable. The third method uses additive logratios, so that K-1 selected logratios involve a K-part subcomposition. Our approach allows logratios or non-compositional covariates to be forced into the models based on theoretical knowledge, and various stopping criteria are available based on information measures or statistical significance with the Bonferroni correction. We present an application on a dataset from a study predicting Crohn's disease.

Light modulates the lipidome of the photosynthetic sea slug Elysia timida.

Long-term kleptoplasty, the capability to retain functional stolen chloroplasts (kleptoplasts) for several weeks to months, has been shown in a handful of Sacoglossa sea slugs. One of these sea slugs is Elysia timida, endemic to the Mediterranean, which retains functional chloroplasts of the macroalga Acetabularia acetabulum. To understand how light modulates the lipidome of E. timida, sea slug specimens were subjected to two different 4-week light treatments: regular light and quasi-dark conditions. Lipidomic analyses were performed by HILIC-HR-ESI-MS and MS/MS. Quasi-dark conditions caused a reduction in the amount of essential lipids for photosynthetic membranes, such as glycolipids, indicating high level of kleptoplast degradation under sub-optimal light conditions. However, maximum photosynthetic capacities (Fv/Fm) were identical in both light treatments (≈0.75), showing similar kleptoplast functionality and suggesting that older kleptoplasts were targeted for degradation. Although more stable, the phospholipidome showed differences between light treatments: the amount of certain lipid species of phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidylglycerol (PG) decreased under quasi-dark conditions, while other lipid species of phosphatidylcholine (PC), PE and lyso-PE (LPE) increased. Quasi-dark conditions promoted a decrease in the relative abundance of polyunsaturated fatty acids. These results suggest a light-driven remodelling of the lipidome according to the functions of the different lipids and highlight the plasticity of polar lipids in the photosynthetic sea slug E. timida.

Agta hunter-gatherer oral microbiomes are shaped by contact network structure.

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

The making of the oral microbiome in Agta hunter-gatherers.

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter-gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

Fatty acid ratio analysis identifies changes in competent meroplanktonic larvae sampled over different supply events.

Planktonic communities are a cornerstone of ocean food webs. Early benthic performance of meroplanktonic organisms is shaped by their life stages in planktonic communities. Fatty acid profiles of marine invertebrates are a good indicator of their nutritional state and allow inferring how dietary regimes experienced during larval pelagic life may drive their pre- and post-metamorphosis performance. Fatty acid profiles of Carcinus maenas megalopae were analysed during four larval supply events in two consecutive years to better understand the variability in their nutritional state at settlement. The logratio analysis of fatty acids showed differences between the four larval supply events, with five ratios explaining 83.1% of the variance. The ratios that contributed to separate larval supply events presented a combination of essential, de novo synthetized and diet origin fatty acids (e.g., phytanate/20:4 n-6, 16:0/18:2 n-4). The high fatty acid signature dispersion found within the same supply event suggests that larvae settling at Ria de Aveiro (Portugal) developed through different planktonic feeding zones and experienced contrasting feeding regimes. The fatty acid profile of megalopae demonstrated a high contribution of diatoms, flagellates and bacteria in the larval diet of C. maenas. The present study demonstrated differences between supply events, although a high variability of larval phenotypes was recorded within the same supply event.

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation.

Microbiome and omics datasets are, by their intrinsic biological nature, of high dimensionality, characterized by counts of large numbers of components (microbial genes, operational taxonomic units, RNA transcripts, etc.). These data are generally regarded as compositional since the total number of counts identified within a sample is irrelevant. The central concept in compositional data analysis is the logratio transformation, the simplest being the additive logratios with respect to a fixed reference component. A full set of additive logratios is not isometric, that is they do not reproduce the geometry of all pairwise logratios exactly, but their lack of isometry can be measured by the Procrustes correlation. The reference component can be chosen to maximize the Procrustes correlation between the additive logratio geometry and the exact logratio geometry, and for high-dimensional data there are many potential references. As a secondary criterion, minimizing the variance of the reference component's log-transformed relative abundance values makes the subsequent interpretation of the logratios even easier. On each of three high-dimensional omics datasets the additive logratio transformation was performed, using references that were identified according to the abovementioned criteria. For each dataset the compositional data structure was successfully reproduced, that is the additive logratios were very close to being isometric. The Procrustes correlations achieved for these datasets were 0.9991, 0.9974, and 0.9902, respectively. We thus demonstrate, for high-dimensional compositional data, that additive logratios can provide a valid choice as transformed variables, which (a) are subcompositionally coherent, (b) explain 100% of the total logratio variance and (c) come measurably very close to being isometric. The interpretation of additive logratios is much simpler than the complex isometric alternatives and, when the variance of the log-transformed reference is very low, it is even simpler since each additive logratio can be identified with a corresponding compositional component.

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment.

Our study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from -0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.

Correspondence analysis of raw data.

Correspondence analysis has found extensive use in ecology, archaeology, linguistics, and the social sciences as a method for visualizing the patterns of association in a table of frequencies or nonnegative ratio-scale data. Inherent to the method is the expression of the data in each row or each column relative to their respective totals, and it is these sets of relative values (called profiles) that are visualized. This "relativization" of the data makes perfect sense when the margins of the table represent samples from subpopulations of inherently different sizes. But in some ecological applications sampling is performed on equal areas or equal volumes so that the absolute levels of the observed occurrences may be of relevance, in which case relativization may not be required. In this paper, I define the correspondence analysis of the raw "unrelativized" data and discuss its properties, comparing this new method to regular correspondence analysis and to a related variant of nonsymmetric correspondence analysis.

Functional roles and redundancy of demersal Barents Sea fish: Ecological implications of environmental change.

When facing environmental change and intensified anthropogenic impact on marine ecosystems, extensive knowledge of how these systems are functioning is required in order to manage them properly. However, in high-latitude ecosystems, where climate change is expected to have substantial ecological impact, the ecosystem functions of biological species have received little attention, partly due to the limited biological knowledge of Arctic species. Functional traits address the ecosystem functions of member species, allowing the functionality of communities to be characterised and the degree of functional redundancy to be assessed. Ecosystems with higher functional redundancy are expected to be less affected by species loss, and therefore less sensitive to disturbance. Here we highlight and compare typical functional characteristics of Arctic and boreal fish in the Barents Sea and address the consequences of a community-wide reorganization driven by climate warming on functional redundancy and characterization. Based on trait and fish community composition data, we assessed functional redundancy of the Barents Sea fish community for the period 2004-2012, a period during which this northern region was characterized by rapidly warming water masses and declining sea ice coverage. We identified six functional groups, with distinct spatial distributions, that collectively provide a functional characterization of Barents Sea fish. The functional groups displayed different prevalence in boreal and Arctic water masses. Some functional groups displayed a spatial expansion towards the northeast during the study period, whereas other groups showed a general decline in functional redundancy. Presently, the observed patterns of functional redundancy would seem to provide sufficient scope for buffering against local loss in functional diversity only for the more speciose functional groups. Furthermore, the observed functional reconfiguration may affect future ecosystem functioning in the area. In a period of rapid environmental change, monitoring programs integrating functional traits will help inform management on ecosystem functioning and vulnerability.

Temporal changes in benthic macrofauna on the west coast of Norway resulting from human activities.

Quantitative analyses of soft bottom invertebrate fauna from four Norwegian sill fjords show increased macrofaunal abundance, species richness, and a considerably changed benthic deep water macrofaunal composition in the inner parts of the fjord system. In retrospect, the analyses show significantly altered benthic macrofaunal community structure that was not reflected by the changes in the Shannon-Wiener diversity indices during regular monitoring. The observed changes are mainly due to an increased abundance of opportunistic species, especially of the polychaete Polydora sp. during the last 10-15 years which is correlated significantly to declining dissolved oxygen, rising temperature in the bottom water and increasing total organic matter in the sediment. Possible anthropogenic and climatic impact factors related to the observed macrofaunal changes and environmental consequences of the changes are discussed.

Change in fish community structure in the Barents Sea.

Change in oceanographic conditions causes structural alterations in marine fish communities, but this effect may go undetected as most monitoring programs until recently mainly have focused on oceanography and commercial species rather than on whole ecosystems. In this paper, the objective is to describe the spatial and temporal changes in the Barents Sea fish community in the period 1992-2004 while taking into consideration the observed abundance and biodiversity patterns for all 82 observed fish species. We found that the spatial structure of the Barents Sea fish community was determined by abiotic factors such as temperature and depth. The observed species clustered into a deep assemblage, a warm water southern assemblage, both associated with Atlantic water, and a cold water north-eastern assemblage associated with mixed water. The latitude of the cold water NE and warm water S assemblages varied from year to year, but no obvious northward migration was observed over time. In the period 1996-1999 we observed a significant reduction in total fish biomass, abundance, mean fish weight, and a change in community structure including an increase in the pelagic/demersal ratio. This change in community structure is probably due to extremely cold conditions in 1996 impacting on a fish community exposed to historically high fishing rates. After 1999 the fish community variables such as biomass, abundance, mean weight, P/D ratio as well as community composition did not return to levels of the early 90s, although fishing pressure and climatic conditions returned to earlier levels.