Response of Growth and Grazing Rate of Nanoflagellates on Synechococcus spp. to Experimental Nutrient Enrichment

As important bacterivores in planktonic food webs, mixotrophic nanoflagellates cancause mortality in marine Synechococcus spp. Our previous study found that the pigmented nanoflagellate (PNF) has a significant grazing impact on Synechococcus spp. In the current study, we applied the dilution approach to test the growth and grazing rates of nanoflagellates on Synechococcus spp. We then compared the differences between experimental nutrient additions and in situ conditions in the coastal waters of the East China Sea during the summer season from July to September. The growth rates of Synechococcus spp. in the ambient environment were between 0.54 and 0.62 day−1, which were slightly higher than the 0.56 and 0.66 day−1 with nutrient enrichment in summer. In contrast, our nutrient enrichment experiments produced a marked decline approximately from 21% to 58%in the nanoflagellate grazing rate on Synechococcus spp. The reason was that the mixotrophic PNFs directly used the added nutrients and reduced their supply of nutrients from prey during the incubation experiments.

Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits

Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompass our considerations and guidelines for bait design to benefit researchers and practitioners. The supeRbaits R package is user‐friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10x coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

Elevated CO2 has concurrent effects on leaf and grain metabolism but minimal effects on yield in wheat

While the general effect of CO2 enrichment on photosynthesis, stomatal conductance, N content, and yield has been documented, there is still some uncertainty as to whether there are interactive effects between CO2 enrichment and other factors, such as temperature, geographical location, water availability, and cultivar. In addition, the metabolic coordination between leaves and grains, which is crucial for crop responsiveness to elevated CO2, has never been examined closely. Here, we address these two aspects by multi-level analyses of data from several free-air CO2 enrichment experiments conducted in five different countries. There was little effect of elevated CO2 on yield (except in the USA), likely due to photosynthetic capacity acclimation, as reflected by protein profiles. In addition, there was a significant decrease in leaf amino acids (threonine) and macroelements (e.g. K) at elevated CO2, while other elements, such as Mg or S, increased. Despite the non-significant effect of CO2 enrichment on yield, grains appeared to be significantly depleted in N (as expected), but also in threonine, the S-containing amino acid methionine, and Mg. Overall, our results suggest a strong detrimental effect of CO2 enrichment on nutrient availability and remobilization from leaves to grains.

Ammonium is the preferred source of nitrogen for planktonic foraminifer and their dinoflagellate symbionts

The symbiotic planktonic foraminifera Orbulina universa inhabits open ocean oligotrophic ecosystems where dissolved nutrients are scarce and often limit biological productivity. It has previously been proposed that O. universa meets its nitrogen (N) requirements by preying on zooplankton, and that its symbiotic dinoflagellates recycle metabolic ‘waste ammonium’ for their N pool. However, these conclusions were derived from bulk 15 N-enrichment experiments and model calculations, and our understanding of N assimilation and exchange between the foraminifer host cell and its symbiotic dinoflagellates remains poorly constrained. Here, we present data from pulse-chase experiments with 13 C-enriched inorganic carbon, 15 N-nitrate, and 15 N-ammonium, as well as a 13 C- and 15 N- enriched heterotrophic food source, followed by TEM (transmission electron microscopy) coupled to NanoSIMS (nanoscale secondary ion mass spectrometry) isotopic imaging to visualize and quantify C and N assimilation and translocation in the symbiotic system. High levels of 15 N-labelling were observed in the dinoflagellates and in foraminiferal organelles and cytoplasm after incubation with 15 N-ammonium, indicating efficient ammonium assimilation. Only weak 15 N-assimilation was observed after incubation with 15 N-nitrate. Feeding foraminifers with 13 C- and 15 N-labelled food resulted in dinoflagellates that were labelled with 15 N, thereby confirming the transfer of 15 N-compounds from the digestive vacuoles of the foraminifer to the symbiotic dinoflagellates, likely through recycling of ammonium. These observations are important for N isotope-based palaeoceanographic reconstructions, as they show that δ 15 N values recorded in the organic matrix in symbiotic species likely reflect ammonium recycling rather than alternative N sources, such as nitrates.

Phytoplankton growth and consumption by microzooplankton stimulated by turbulent nitrate flux suggest rapid trophic transfer in the oligotrophic Kuroshio

The Kuroshio Current has been thought to be biologically unproductive because of its oligotrophic conditions and low plankton standing stocks. Even though vulnerable life stages of major foraging fishes risk being entrapped by frontal eddies and meanders and encountering low food availability, they have life cycle strategies that include growing and recruiting around the Kuroshio Current. Here we report that phytoplankton growth and consumption by microzooplankton are stimulated by turbulent nitrate flux amplified by the Kuroshio Current. Oceanographic observations demonstrate that the Kuroshio Current topographically enhances significant turbulent mixing and nitrate influx to the euphotic zone. Graduated nutrient enrichment experiments show that growth rates of phytoplankton and microheterotroph communities were stimulated within the range of the turbulent nitrate flux. Results of dilution experiments imply significant microzooplankton grazing on phytoplankton. We propose that these rapid and systematic trophodynamics enhance biological productivity in the Kuroshio.

Measurement of Air Drag as Physics Experiment Enrichment at Senior High School Laboratory Using the Air Track Apparatus

Linear air track is often used in physics learning for linear motion experiments because it can reduce friction between objects with trajectories. However, the use of air tracks for motion experiments in schools often does not care about aspects of air drag, so the purpose of this study is to calculate the air friction contained in the air track and as an offer of enrichment experiments at senior high school. The research method used is an experimental method that uses a set of air track experimental devices consisting of trajectors, carts, blower, and time counters with light sensors. Cart objects with a mass of 120.02 gram is given the initial velocity variation 12.272 cm/s, 16.286 cm/s and 24.599 cm/s. Then the time recorded when the cart crosses the distance of 10 cm to 110 cm at intervals of 10 cm. This experiment is conducted in the Integrated Science Laboratory, Faculty of Mathematics and Natural Sciences, Universitas Negeri Semarang. The second Newton law has been derived to obtain a special exponential function, so the relation between distance and time is obtained. The non-linear relation between distance and time shows the effect of air drag. Then, fitting the graph of the distance and time relation so that the air drag constants obtained are (10.6 ± 0.1) gram/s, (10.6 ± 0.2) gram/s, and (11.1 ± 0.2) gram/s. The results of the air drag constants obtained can be additional data as a factor affecting experiments using linear air track and can be enrichment experiments at senior high school laboratory.

Varying Biological Activity and Wind Stress Affect the DMS Response during the SAGE Iron Enrichment Experiment

Surface dissolved dimethylsulfide (DMS) and depth-integrated dimethylsulfoniopropionate (DMSP) measurements were made from March to April 2004 during the SOLAS Air–Sea Gas Exchange Experiment (SAGE), a multiple iron enrichment experiment in subantarctic waters SE of New Zealand. During the first two iron enrichments, chl a and DMS production were constrained, but during the third enrichment, large pulses of DMS occurred in the fertilised IN patch, compared with the unfertilised OUT patch. During the third and fourth iron infusions, total chl a concentrations doubled from 0.52 to 1.02 µg/L. Hapto8s and prasinophytes accounted for 50%, and 20%, respectively, of total chl a. The large pulses of DMS during the third iron enrichment occurred during high dissolved DMSP concentrations and wind strength; changes in dinoflagellate, haptophyte, and cyanobacteria biomass; and increased microzooplankton grazing that exerted a top down control on phytoplankton production. A further fourth iron enrichment did cause surface waters to increase in DMS, but the effect was not as great as that recorded in the third enrichment. Differences in the biological response between SAGE and several other iron enrichment experiments were concluded to reflect microzooplankton grazing activities and the microbial loop dominance, resulting from mixing of the MLD during storm activity and high winds during iron enrichment.