Ken-Ichiro Ishii

Proposal of identification criteria for resting spores of Chaetoceros species (Bacillariophyceae) from a temperate coastal sea

Ishii K.-I., Iwataki M., Matsuoka K. and Imai I. 2011. Proposal of identification criteria for resting spores of Chaetoceros species (Bacillariophyceae) from a temperate coastal sea. Phycologia 50: 351–362. DOI: 10.2216/10-36.1 Chaetoceros is a large, ecologically important genus of marine planktonic diatoms. Many species of Chaetoceros form resting spores to survive environmental stress. Species identification based on morphological characteristics of resting spores is difficult. In the present study, we proposed a flow diagram for the identification of Chaetoceros species based on morphology. Resting spores of 18 Chaetoceros species were identified in water and sediment samples from southern Japan and the East China Sea based on morphological characteristics of resting spores and/or the vegetative cells containing them. A single ring of puncta was found to be the most important morphological feature of resting spores for species identification, by which the positions of primary and secondary valves were correctly determined. Other morphological characteristics such as features of the primary valve face, margins of the primary and secondary valve mantles, and secondary valve face are also useful for species identification. A combination of these morphological characteristics was used to construct a flow diagram for identification of the 18 Chaetoceros species found in our samples with light microscopy. This flow diagram is most applicable to Japanese waters, but the approach should be refined and improved to understand the biology and ecology of Chaetoceros species in any marine ecosystem.

Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes

Organisms with nonphotosynthetic plastids often retain genomes; their gene contents provide clues as to the functions of these organelles. Yet the functional roles of some retained genes-such as those coding for ATP synthase-remain mysterious. In this study, we report the complete plastid genome and transcriptome data of a nonphotosynthetic diatom and propose that its ATP synthase genes may function in ATP hydrolysis to maintain a proton gradient between thylakoids and stroma, required by the twin arginine translocator (Tat) system for translocation of particular proteins into thylakoids. Given the correlated retention of ATP synthase genes and genes for the Tat system in distantly related nonphotosynthetic plastids, we suggest that this Tat-related role for ATP synthase was a key constraint during parallel loss of photosynthesis in multiple independent lineages of algae/plants.

Algicidal and growth-inhibiting bacteria associated with seagrass and macroalgae beds in Puget Sound, WA, USA

The algicidal and growth-inhibiting bacteria associated with seagrasses and macroalgae were characterized during the summer of 2012 and 2013 throughout Puget Sound, WA, USA. In 2012, Heterosigma akashiwo-killing bacteria were observed in concentrations of 2.8×106CFUg-1 wet in the outer organic layer (biofilm) on the common eelgrass (Zostera marina) in north Padilla Bay. Bacteria that inhibited the growth of Alexandrium tamarense were detected within the biofilm formed on the eelgrass canopy at Dumas Bay and North Bay at densities of ∼108CFUg-1 wet weight. Additionally, up to 4100CFUmL-1 of algicidal and growth-inhibiting bacteria affecting both A. tamarense and H. akashiwo were detected in seawater adjacent to seven different eelgrass beds. In 2013, H. akashiwo-killing bacteria were found on Z. marina and Ulva lactuca with the highest densities of ∼108CFUg-1 wet weight at Shallow Bay, Sucia Island. Bacteria that inhibited the growth of H. akashiwo and A. tamarense were also detected on Z. marina and Z. japonica at central Padilla Bay. Heterosigma akashiwo cysts were detected at a concentration of 3400cystsg-1 wet weight in the sediment from Westcott Bay (northern San Juan Island), a location where eelgrass disappeared in 2002. These findings provide new insights on the ecology of algicidal and growth-inhibiting bacteria, and suggest that seagrass and macroalgae provide an environment that may influence the abundance of harmful algae in this region. This work highlights the importance of protection and restoration of native seagrasses and macroalgae in nearshore environments, in particular those regions where shellfish restoration initiatives are in place to satisfy a growing demand for seafood.

Diversity of Organellar Genomes in Non-photosynthetic Diatoms

We determined the complete sequences of the plastid and mitochondrial genomes of three non-photosynthetic Nitzschia spp., as well as those of a photosynthetic close relative, Nitzschia palea. All the plastid genomes and the three mitochondrial genomes determined were found to be circularly mapping, and the other mitochondrial genomes were predicted to be of a linear form with telomere-like structures at both ends. We found that all the non-photosynthetic plastid genomes are streamlined and lack a common gene set: two RNA genes, and 60 protein-coding genes, most of which are related to photosynthetic functions. Nevertheless, the non-photosynthetic plastid genomes commonly retain ATP synthase complex genes, although atpE is missing in Nitzschia sp. NIES-3581 and three other non-photosynthetic species lack atpF instead of atpE. This observation suggests an evolutionary constraint against the loss of ATP synthase complex genes. All the non-photosynthetic diatom plastid genomes lacked two genes, thiS and thiG, involved in thiamin biosynthesis. Consistent with this gene loss, non-photosynthetic Nitzschia spp. were incapable of thriving in vitamin B1-lacking media. This study clearly demonstrated not only the evolutionary trends of plastid genome reduction but also the linkage between plastid genome reduction and a biological change of nutrient requirements in Nitzschia.

A simple technique for establishing axenic cultures of centric diatoms from resting stage cells in bottom sediments

Abstract: We devised a simple and rapid technique for establishing axenic cultures of centric diatoms by sieving and washing resting stage cells. This technique is an effective means for establishing the axenic cultures of species that have endogenous resting spores. The primary advantage of this method is in the isolation of cells when the target species is absent from the water column.

Distribution of viable resting stage cells of diatoms in sediments and water columns of the Chukchi Sea, Arctic Ocean

Abstract: The distribution of resting stage cells of diatoms in the surface sediments and water samples collected in the Chukchi Sea was investigated using the most probable number (MPN) analysis to understand the mechanism underlying diatom blooms in the Arctic region. High densities (3.5 × 105 to 6.8 × 106 MPN cells cm−3 wet sediment) of viable resting stage cells of typical Arctic diatom species were found in the surface sediments of the Chukchi Sea. Resting stage cells of the sea-ice–related diatom genus Fragilariopsis were more abundant (2.6 × 106 MPN cells cm−3 wet sediment) than Chaetoceros (2.18 × 106 MPN cells cm−3 wet sediment) or Thalassiosira (1.76 × 106 MPN cells cm−3 wet sediment) in the southern Chukchi Sea. This reflected a previous bloom of Fragilariopsis ahead of typical planktonic blooms of Chaetoceros and Thalassiosira and suggests that sea-ice–related blooms are a substantial factor for primary production in this area. During the sampling period, diatom assemblages in the in situ water columns were dominated by Pseudo-nitzschia delicatissima, Cylindrotheca closterium, Proboscia alata, and Thalassionema spp. After storage of water samples for 6 months in the dark, viable diatom resting stage cells of typical Arctic species such as Attheya longicornis and Chaetoceros socialis were detected. These autochthonous species formed resting stage cells that remained viable in the dark for more than 6 months, while diatom species of Pacific origins could not survive under conditions of extremely limited light. The resting stage cells provide an advantage for autochthonous diatoms to endure the unfavourable light conditions of the Arctic winter. In the Chukchi Sea, resting stage cells of diatoms were supplied by current inflows from shallow sea areas. Densely distributed viable resting stages at the bottom are also a possible source for seeding the diatom cells into phytoplankton communities and ice assemblages in shallow marginal ice zones.

Chrysophyte plastid evolution dataset

This upload contains phylogenetic data, protein sequence libraries, and supporting tables pertaining to the comparative evolutionary analysis of plastid proteome content in photosynthetic and non-photosynthetic chrysophyte algae.