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

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

The effects of elevated atmospheric CO₂ on freshwater periphyton in a temperate stream

This study examines the effects of elevated CO 2 on the benthic biology of a temperate freshwater stream. We tested the hypotheses that elevated CO 2 would increase periphyton biomass, alter elemental composition, and change community composition by increasing the frequency of algal taxa most limited by CO 2 availability. Carbon dioxide was bubbled into reservoirs of stream water, increasing the ambient pCO 2 by approximately 1100 ppm. The CO 2 -enriched water then flowed into artificial stream channels. Ceramic tiles were placed into the channels to allow for periphyton colonization. Dissolved inorganic carbon increased and pH decreased with added CO 2 . Measurements of biological parameters including periphyton biomass, algal C:N:P ratios, and community composition suggest that the periphyton were unaffected by the changes in stream water chemistry. We infer that rising atmospheric CO 2 will impact stream water chemistry but that periphyton may not be the first to respond to these changes. Impacts to alkaline freshwater streams from elevated CO 2 initially may be due to changes to terrestrial inputs that affect microbial decomposition and grazer activity, rather than through increases in periphyton carbon fixation. However, environmental characteristics of freshwater systems vary considerably, and additional studies are needed for accurate predictive modeling and monitoring of the effects of increasing atmospheric CO 2 on freshwater streams