Biology subjects

Kuwata, A.

Publications and source records attributed to Kuwata, A..

3 recordsLinked to original sources

bioRxiv2026

Metatranscriptome data support the existence of two distinct morphotypes in a single parmalean species in natural environments

Parmales (Bolidophyceae), the closest relatives of diatoms, includes isolates exhibiting one of two distinct morphotypes: a silicified non-flagellated form (S-type) and a naked flagellated form (F-type). Although alternation of these two forms for a single isolate has not been formally established, previous studies hypothesized that these morphotypes represent alternating stages of a single parmalean. In this study, we investigated the global expression patterns of S- and F-type marker genes by integrating parmalean Metagenome-Assembled Genomes (MAGs) and the metatranscriptomic dataset from Tara Oceans. We detected the expression of both S- and F-type marker genes from individual environmental MAGs. This finding provides the first metatranscriptomic evidence that natural parmalean genomes possess the potential to manifest both morphotypes. Furthermore, our analysis revealed different geographical expression patterns between the two forms. The expression of F-type markers showed a broad distribution, whereas that of S-type markers was more restricted, suggesting distinct niches for the two morpho-phases. Moreover, S-type gene expression appears to require specific environmental triggers that lead to a higher population density, whereas F-type expression is rather constitutively maintained. Overall, our results support the hypothesis of a life cycle involving morphological switching and reconcile the long-standing discrepancy between the ubiquity of parmaleans in molecular surveys and the limited geographical range for the observation of silicified cells. Based on these patterns, we propose a threshold-based model in which F-type-dominated populations persist under conditions unfavorable for growth and a morphological switch to the S-type is triggered once environmental conditions exceed a critical threshold for growth.

microbiology↗

bioRxiv2023

Global distribution and diversity of marine Parmales

Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, that exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies of Parmales have been performed, but their global distribution remains under-investigated. Here, we compile over 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the analyzed samples. However, the relative abundance of parmaleans in the eukaryotic community is less than 0.2% on average, and the estimated true richness of parmalean ASVs is about 316 ASVs, confirming their low abundance and low diversity. Phylogenetic analysis clearly divides these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the pole and decreases toward the tropics, and individual clades/subclades show further distinctions in distributions. Overall, our results suggest their clade/subclade-specific adaptation to different ecological niches.

microbiology↗

bioRxiv2022

Genome analysis of Parmales, a sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

The order Parmales (Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compared the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans were predicted to be phago-mixotrophs. By contrast, diatoms have undergone loss of genes related to phagocytosis, indicating the ecological specialization from phago-mixotroph to photoautotroph in the early evolution of diatoms. Furthermore, diatoms showed significant enrichment in gene sets involved in silica metabolism, nutrient uptake capacity, carbon concentrating mechanisms, and iron uptake in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.

microbiology↗