Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences.

Background: Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods: rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results: A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion: The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.

Sound properties produced by white-edged rockfish (Sebastes taczanowskii) in relation to body and swim bladder size.

The sound properties produced by the white-edged rockfish (Sebastes taczanowskii Steindachner, 1880) were compared with the body size. We conducted a tank experiment to compare the sound properties with body length, which ranged from 12.4 to 19.8 cm. Sound production was composed of pulses with a duration of 0.010-0.022 s and a peak frequency of 400-1000 Hz. Peak frequency decreased with fish and swim bladder size and pulse duration. The relationship between sound properties and body size may be useful for estimating the body length of the target species by using passive acoustic monitoring.

Evaluation of static differential capacitance at the [C4mim+][TFSA-]/electrode interface using molecular dynamics simulation combined with electrochemical surface plasmon resonance measurements.

Molecular dynamic (MD) simulations have been performed for 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([C4mim+][TFSA-]), an ionic liquid (IL), on a charged graphene electrode to achieve the quantitative analysis of the static differential capacitance using the electrochemical surface plasmon resonance (ESPR). The MD simulations have provided the surface charge density on the electrode and ionic distributions in the electric double layer, both of which are indispensable for the evaluation of static differential capacitance using ESPR but are difficult to be measured by experimental techniques. This approach has allowed the quantitative analysis and explanation of the SPR angle shift in ESPR. The major contribution to the SPR angle shift is found to be the change in ionic concentrations of the first ionic layer on the electrode, owing to higher polarizabilities of ions in the first ionic layer than those in the overlayers. Moreover, the ionic orientation on the electrode and ionic multilayer structure have also been investigated in detail. The butyl group of C4mim+ in the first ionic layer is found to provide extra room for C4mim+ in the second ionic layer but exclude TFSA-, which affects the interval and regularity of ionic multilayers.

Evolution and Reversible Polarity of Multilayering at the Ionic Liquid/Water Interface.

Highly correlated positioning of ions underlies Coulomb interactions between ions and electrified interfaces within dense ionic fluids such as biological cells and ionic liquids. Recent work has shown that highly correlated ionic systems behave differently than dilute electrolyte solutions, and interest is focused upon characterizing the electrical and structural properties of the dense electrical double layers (EDLs) formed at internal interfaces. It has been a challenge for experiments to characterize the progressive development of the EDL on the nanoscale as the interfacial electric potential is varied over a range of positive and negative values. Here we address this challenge by measuring X-ray reflectivity from the interface between an ionic liquid (IL) and a dilute aqueous electrolyte solution over a range of interfacial potentials from -450 to 350 mV. The growth of alternately charged cation-rich and anion-rich layers was observed along with a polarity reversal of the layers as the potential changed sign. These data show that the structural development of an ionic multilayer-like EDL with increasing potential is similar to that suggested by phenomenological theories and MD simulations, although our data also reveal that the excess charge beyond the first ionic layer decays more rapidly than predicted.

An electric double layer structure and differential capacitance at the electrode interface of tributylmethylammonium bis(trifluoromethanesulfonyl)amide studied using a molecular dynamics simulation.

A molecular dynamics simulation at the electrode interface of a quaternary ammonium ionic liquid, tributylmethylammonium bis(trifluoromethanesulfonyl)amide ([N1444+][TFSA-]), has been performed. Unlike the commonly used cations, such as 1-alkyl-3-methylimidazolium and 1,1-alkylmethylpyrrolidinium cations, N1444+ has multiple long-alkyl groups (three butyl groups). The behavior of ions at the electrode interface, especially these butyl groups, has been investigated. N1444+ at the first layer mainly has two types of orientations, lying and standing. The lying orientation is dominant at moderately negative potentials. However, the standing one becomes dominant at the more negative potentials. Due to this orientational change, the number of N1444+ increases at the first layer as the potential becomes negative even at the potentials where the anions are completely depleted there. The change in orientation results in the upward deviation of the differential capacitance from the theoretical prediction at the negative potentials. The results suggest that the orientational preference caused by the steric constraint between alkyl groups plays an important role in the behavior of the electric double layer of the ionic liquids.

Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach, seasonality and environmental drivers.

During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.

A relationship between the force curve measured by atomic force microscopy in an ionic liquid and its density distribution on a substrate.

An ionic liquid forms a characteristic solvation structure on a substrate. For example, when the surface of the substrate is negatively or positively charged, cation and anion layers are alternately aligned on the surface. Such a solvation structure is closely related to slow diffusion, high electric capacity, and chemical reactions at the interface. To analyze the periodicity of the solvation structure, atomic force microscopy is often used. The measured force curve is generally oscillatory and its characteristic oscillation length corresponds not to the ionic diameter, but to the ion-pair diameter. However, the force curve is not the solvation structure. Hence, it is necessary to know the relationship between the force curve and the solvation structure. To find physical essence in the relationship, we have used statistical mechanics of a simple ionic liquid. We found that the basic relationship can be expressed by a simple equation and the reason why the oscillation length corresponds to the ion-pair diameter. Moreover, it is also found that Derjaguin approximation is applicable to the ionic liquid system.

Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community.

The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.