Classification Methods for 16S rRNA Based Functional Annotation

Microbial communities play an essential role in Earth’s ecosystems. The goal of this study was to investigate whether the functional potential of microorganisms forming these diverse communities can be directly identified using a 16S rRNA marker gene with supervised learning methods. The recently developed FAPROTAX database has been used along with the SILVA database to produce a training set where 16S rRNA sequences are linked to a number of metabolic functions. Since gene sequences cannot be explicitly used as feature vectors by most classification algorithms, the present research aimed to investigate possible feature engineering approaches for 16S rRNA. Techniques based on Multiple Sequence Alignment (MSA) and N-grams are proposed and tested. The results showed that the feature representation based on the Ngrams outperformed MSA, especially when implemented with large and diverse functional groups. This suggests that a clustering-like alignment procedure results in a biased feature representation of the marker gene. Since classifiers trained using Random Forest and Support Vector Machines techniques were able to accurately detect a range of functional groups it is concluded that the 16S rRNA gene provides substantial information for the direct identification of functional capabilities

Nanopatterning Gold by Templated Solid State Dewetting on the Silica Warp and Weft of Diatoms

The diatom, Nitzschia palea, exhibits complex silica shell (frustule) topography that resembles the warp and weft pattern of woven glass. The surface is perforated with a rhombic lattice of roughly oblong pores between periodically undulating transverse weft costae. Exfoliated frustules can be used to template gold nanoparticles by thermally induced dewetting of thin gold films. Acting as templates for the process, the frustules give rise to two coexisting hierarchies of particle sizes and patterned distributions of nanoparticles. By examining temperature dependent dewetting of 5, 10, and 15 nm Au films for various annealing times, we establish conditions for particle formation and patterning. The 5 nm film gives distributions of small particles randomly distributed over the surface and multiple particles at the rhombic lattice points in the pores. Thicker films yield larger faceted particles on the surface and particles that exhibit shapes that are roughly conformal with the shape of the pore container. The pores and costae are sources of curvature instabilities in the film that lead to mass transport of gold and selective accumulation in the weft valleys and pores. We suggest that, with respect to dewetting, the frustule comprises 2-dimensional sublattices of trapping sites. The pattern of dewetting is radically altered by interposing a self-assembled molecular adhesive of mercaptopropyltrimethoxysilane between the Au film overlayer and the frustule. By adjusting the interfacial energy in this manner, a fractal-like overlay of Au islands coexists with a periodic distribution of nanoparticles in the pores

Metabolic variation in natural populations of wild yeast

Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on a core diet of about 10 substrates, and most were also able to grow on a much larger ancillary diet comprising most of the 190 substrates we tested. There was substantial genetic variation within each population for some substrates. We found geographical variation of substrate use at continental, regional, and local scales. Isolates from Europe and North America could be distinguished on the basis of the pattern of yield across substrates. Two geographical races at the North American sites also differed in the pattern of substrate utilization. Substrate utilization patterns were also geographically correlated at local spatial scales. Pairwise genetic correlations between substrates were predominantly positive, reflecting overall variation in metabolic performance, but there was a consistent negative correlation between categories of substrates in two cases: between the core diet and the ancillary diet, and between pentose and hexose sugars. Such negative correlations in the utilization of substrate from different categories may indicate either intrinsic physiological trade‐offs for the uptake and utilization of substrates from different categories, or the accumulation of conditionally neutral mutations. Divergence in substrate use accompanies genetic divergence at all spatial scales in S. paradoxus and may contribute to race formation and speciation

Predictable ecological response to rising CO2 of a community of marine phytoplankton

Rising atmospheric CO2 and ocean acidification are fundamentally altering conditions for life of all marine organisms, including phytoplankton. Differences in CO2 related physiology between major phytoplankton taxa lead to differences in their ability to take up and utilize CO2. These differences may cause predictable shifts in the composition of marine phytoplankton communities in response to rising atmospheric CO2. We report an experiment in which seven species of marine phytoplankton, belonging to four major taxonomic groups (cyanobacteria, chlorophytes, diatoms, and coccolithophores), were grown at both ambient (500 ?atm) and future (1,000 ?atm) CO2 levels. These phytoplankton were grown as individual species, as cultures of pairs of species and as a community assemblage of all seven species in two culture regimes (high?nitrogen batch cultures and lower?nitrogen semicontinuous cultures, although not under nitrogen limitation). All phytoplankton species tested in this study increased their growth rates under elevated CO2 independent of the culture regime. We also find that, despite species?specific variation in growth response to high CO2, the identity of major taxonomic groups provides a good prediction of changes in population growth and competitive ability under high CO2. The CO2?induced growth response is a good predictor of CO2?induced changes in competition (R2 > .93) and community composition (R2 > .73). This study suggests that it may be possible to infer how marine phytoplankton communities respond to rising CO2 levels from the knowledge of the physiology of major taxonomic groups, but that these predictions may require further characterization of these traits across a diversity of growth conditions. These findings must be validated in the context of limitation by other nutrients. Also, in natural communities of phytoplankton, numerous other factors that may all respond to changes in CO2, including nitrogen fixation, grazing, and variation in the limiting resource will likely complicate this prediction

Comparison of thermal traits between non-toxic and potentially toxic marine phytoplankton: Implications to their responses to ocean warming

Understanding the effect of temperature on growth in marine phytoplankton is crucial in predicting the biogeography and phenology of algal blooms in the warming ocean. Here, we investigated the temperature dependence of the growth of non-toxic and potentially toxic marine phytoplankton. Using non-toxic strains (Prorocentrum sp. NRR 188, Prorocentrum micans CCAP 1136/15, and Alexandrium tamutum PARALEX 242) and potentially toxic strains (Prorocentrum minimum Poulet, Prorocentrum lima CCAP 1136/11, and Alexandrium minutum PARALEX 246) of dinoflagellates as test organisms, we measured their growth rates along a wide temperature gradient and estimated their maximum growth rates, thermal traits (e.g. thermal optima (Topt), critical thermal minima (CTmin), critical thermal maximum (CTmax), fundamental thermal niche (FTN), and skewness), thermal sensitivity, and warming vulnerability. To allow a comparison of these traits with an adequate number of observations, we independently analyzed datasets compiled from published laboratory experiments. Our experiments revealed that the temperature traits were independent of the toxicity of phytoplankton, except for Topt and CTmax. Also, the results of the analysis of the published datasets showed that maximum growth rates and thermal traits were comparable between non-toxic and potentially toxic phytoplankton. Our findings suggest that non-toxic and potentially toxic phytoplankton have generally comparable temperature traits that they can use to respond to climate change. However, depending on the climate scenario, non-toxic phytoplankton may be more vulnerable to warming than potentially toxic phytoplankton. Further studies are needed to improve our understanding of the response of marine phytoplankton to temperature, which can advance our ability to predict algal blooms in response to ongoing climate change

Data from: Long-term culture at elevated atmospheric CO2 fails to evoke specific adaptation in seven freshwater phytoplankton species

The concentration of CO2 in the atmosphere is expected to double by the end of the century. Experiments have shown that this will have important effects on the physiology and ecology of photosynthetic organisms, but it is still unclear if elevated CO2 will elicit an evolutionary response in primary producers that causes changes in physiological and ecological attributes. In this study, we cultured lines of seven species of freshwater phytoplankton from three major groups at current (approx. 380 ppm CO2) and predicted future conditions (1000 ppm CO2) for over 750 generations. We grew the phytoplankton under three culture regimes: nutrient-replete liquid medium, nutrient-poor liquid medium and solid agar medium. We then performed reciprocal transplant assays to test for specific adaptation to elevated CO2 in these lines. We found no evidence for evolutionary change. We conclude that the physiology of carbon utilization may be conserved in natural freshwater phytoplankton communities experiencing rising atmospheric CO2 levels, without substantial evolutionary change

Surface litter decomposition, soil respiration as a function of Taxonomic diversity, functional diversity and functional identity

No.Sp – number of species CO2 – rates of soil respiration in µmolCO2m-2s-1 K – decomposition rate of home litter in d-1 ComsubK – decomposition rate of common substrate (“Common litter experiment”) Pred.CO2 – soil respiration rates predicted from those in monospecific plots Pred.K – decomposition rates of home litter predicated from those in monospecific plots Pred.ComsubK – decomposition rates of the common substrate predicted from the same common substrate decomposition in monoculture plots Dev.pred – (observed – predicted) CWM – community-weighted mean FD- functional Diversity Traits maxH – max height GR – growth rate LS – leaf size WD – wood density WDR – wood decay resistence Sem – seed mass RoH – root habut AM - Arbuscular mycorrhizas (Endomycorrhiza ) EM - Ectomycorrhizas Rdiam – root diameter Llo – lead longevity Lma – leaf mass per area Nleaf – leaf nitrogen content C – litter carbon content N – litter carbon content LDMC – leaf dry matter content SLA – specific leaf are