phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases.

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.

Electrolytic Hydrogen Release from Hydrogen Boride Sheets.

Solid-state hydrogen storage materials are safe and lightweight hydrogen carriers. Among the various solid-state hydrogen carriers, hydrogen boride (HB) sheets possess a high gravimetric hydrogen capacity (8.5 wt%). However, heating at high temperatures and/or strong ultraviolet illumination is required to release hydrogen (H2) from HB sheets. In this study, the electrochemical H2 release from HB sheets using a dispersion system in an organic solvent without other proton sources is investigated. H2 molecules are released from the HB sheets under the application of a cathodic potential. The Faradaic efficiency for H2 release from HB sheets reached >90%, and the onset potential for H2 release is -0.445 V versus Ag/Ag+, which is more positive than those from other proton sources, such as water or formic acid, under the same electrochemical conditions. The total electrochemically released H2 in a long-time experiment reached ≈100% of the hydrogen capacity of HB sheets. The H2 release from HB sheets is driven by a small bias; thus, they can be applied as safe and lightweight hydrogen carriers with economical hydrogen release properties.

Pathogenicity chromosome of Fusarium oxysporum f. sp. cepae.

Fusarium oxysporum f. sp. cepae (Foc) is the causative agent of Fusarium basal rot disease in onions, which leads to catastrophic global crop production losses. Therefore, the interaction of Foc with its host has been actively investigated, and the pathogen-specific (PS) regions of the British strain Foc_FUS2 have been identified. However, it has not been experimentally determined whether the identified PS region plays a role in pathogenicity. To identify the pathogenicity chromosome in the Japanese strain Foc_TA, we initially screened effector candidates, defined as small proteins with a signal peptide that contain two or more cysteines, from genome sequence data. Twenty-one candidate effectors were identified, five of which were expressed during infection. Of the expressed effector candidates, four were located on the 4-Mb-sized chromosome in Foc_TA. To clarify the relationship between pathogenicity and the 4-Mb-sized chromosome in Foc_TA, nine putative 4-Mb-sized chromosome loss strains were generated by treatment with benomyl (a mitotic inhibitor drug). A pathogenicity test with putative 4-Mb-sized chromosome loss strains showed that these strains were impaired in their pathogenicity toward onions. Genome analysis of three putative 4-Mb-sized chromosome loss strains revealed that two strains lost a 4-Mb-sized chromosome in common, and another strain maintained a 0.9-Mb region of the 4-Mb-sized chromosome. Our findings show that the 4-Mb-sized chromosome is the pathogenicity chromosome in Foc_TA, and the 3.1-Mb region within the 4-Mb-sized chromosome is required for full pathogenicity toward onion.

Steady nutrient upwelling around a biological hotspot of the confluence between the quasi-stationary jet and the Oyashio in the western North Pacific.

The quasi-stationary jet, a branch of the Kuroshio Extension, transports warm saline water in the mixed water region of the western North Pacific. Around the subarctic front between the quasi-stationary jet and Oyashio and its downstream area is a biologically productive area including small pelagic fishes. However, how nutrient is supplied to the euphotic zone in this region remains elusive, especially into the quasi-stationary jet. Using high-resolution hydrography sections across the jet, we showed that Oyashio water isopycnally intrudes under the jet around 26.5-26.8 σθ and forms nutrient-rich intermediate water. Upwelling associated with ageostrophic secondary circulation across the front, caused by confluence, uplifts the intermediate water. A local nitrate maximum was also identified inside the jet by the hydrographic observation. Upwelling has been suggested as a precondition for nutrient supply from nutrient-rich intermediate water to the jet through water mixing which potentially sustains high biological production in the downstream.

Mesoscale eddies exert inverse latitudinal effects on global industrial squid fisheries.

Squid species, as a burgeoning global food source, has garnered significant concerns due to expanding fisheries and little regulation. Elucidating the dynamics of squid fisheries and their biophysical coupling mechanisms is crucial for predicting spatiotemporal variations in squid fisheries and their sustainable management. Mesoscale eddies are discrete rotating oceanographic features that dominate local environmental variations and have been shown to modulate top predators. However, given controls of both predators and environmental factors, it remains unknown how eddies impact mid-trophic level species such as squids. Using satellite-based global squid fishery datasets, we showed an inverse latitudinal pattern of eddy-induced squid fisheries, where fishing activities are aggregated in (repelled from) cyclonic (anticyclonic) eddy cores in tropical waters and anticyclonic (cyclonic) eddy cores in temperate waters, and this pattern can be significantly enhanced with increasing eddy amplitude. Regarding solely the satellite-based global squid fisheries, eddy-induced environmental variations may generate a trade-off between food intake and energy expenditure, causing these oceanic squids to prefer cool cyclonic eddies in hot but food-limited waters, and warm anticyclonic eddies in nutritious but heat-limited waters. Given that eddy activity is projected to continuously enhance under global warming, our finding of eddy-driven bottom-up control for squid fisheries highlights an increasingly important hotspot for squid stock predictions and ecosystem-based ocean management in a changing climate.

Pathogenicity Differentiation of Fusarium spp. Causing Fusarium Basal Rot and Wilt Disease in Allium spp.

Here, 12 Fusarium strains, previously described as F. oxysporum f. sp. cepae (Foc), were examined via multi-locus sequencing of calmodulin (cmdA), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1), to verify the taxonomic position of Foc in the newly established epitype of F. oxysporum. The strains in this study were divided into two clades: F. nirenbergiae and Fusarium sp. To further determine the host specifications of the strains, inoculation tests were performed on onion bulbs and Welsh onion seedlings as potential hosts. Four strains (AC145, AP117, Ru-13, and TA) isolated from diseased onions commonly possessed the secreted in xylem (SIX)-3, 5, 7, 9, 10, 12, and 14 genes and were pathogenic and highly aggressive to onion bulbs, whereas all strains except for one strain (AF97) caused significant inhibition of Welsh onion growth. The inoculation test also revealed that the strains harboring the SIX9 gene were highly aggressive to both onion and Welsh onion and the gene was expressed during infection of both onions and Welsh onions, suggesting the important role of the SIX9 gene in pathogenicity. This study provides insights into the evolutionary pathogenicity differentiation of Fusarium strains causing Fusarium basal rot and wilt diseases in Allium species.

Effects of flusulfamide on spore germination of Plasmodiophora brassicae.

Flusulfamide inhibits germination of Plasmodiophora brassicae resting spores to suppress clubroot disease, but its mechanism of action on the germination of P. brassicae resting spores remains unclear. In this study, P. brassicae resting spores were treated with flusulfamide and visualized using transmission electron microscopy (TEM). The gene expression of P. brassicae resting spores was analyzed using RT-PCR, followed by immunoblotting analysis. TEM results revealed that flusulfamide suppressed the primary zoosporogenesis of P. brassicae resting spores during the early phase, and RT-PCR results revealed that flusulfamide affected the gene expression during the germination of the resting spores. Immunoblot and RT-qPCR analyses revealed that PbCyp3, an immunophilin (peptidyl-prolyl-isomerase) gene, was highly expressed, resulting in the unusual accumulation of PbCYP3 protein in P. brassicae resting spores immediately after treatment with flusulfamide. This suggests that flusulfamide may cause aberrant folding of proteins involved in primary zoosporogenesis, thereby inhibiting germination.

The SIX5 Protein in Fusarium oxysporum f. sp. cepae Acts as an Avirulence Effector toward Shallot (Allium cepa L. Aggregatum Group).

Fusarium oxysporum f. sp. cepae (Foc) causes basal rot disease in Allium species, including onions (Allium cepa L.) and shallots (A. cepa L. Aggregatum group). Among Allium species, shallots can be crossbred with onions and are relatively more resistant to Foc than onions. Thus, shallots are considered a potential disease-resistant resource for onions. However, the mechanisms underlying the molecular interactions between shallots and Foc remain unclear. This study demonstrated that SIX5, an effector derived from Foc (FocSIX5), acts as an avirulence effector in shallots. We achieved this by generating a FocSIX5 gene knockout mutant in Foc, for which experiments which revealed that it caused more severe wilt symptoms in Foc-resistant shallots than the wild-type Foc and FocSIX5 gene complementation mutants. Moreover, we demonstrated that a single amino acid substitution (R67K) in FocSIX5 was insufficient to overcome shallot resistance to Foc.