Ultrastructural and molecular characterization of diversity among small araphid diatoms all lacking rimoportulae. I. Five new genera, eight new species

Abstract

Pennate diatoms are important contributors to primary production in freshwater and marine habitats. But the extent of their diversity, ecology, and evolution is still largely unknown. This is particularly evident among the clades of pennate diatoms without raphe slits, whose diversity is likely underestimated due to their small size and features that can be difficult to discern under light microscopy. In this study, we described five new araphid genera with eight new species based on morphological observations (light and electron microscopy) and molecular data (nuclear‐encoded small subunit ribosomal RNA and chloroplast‐encoded rbcL and psbC): Serratifera varisterna, Hendeyella rhombica, H. dimeregrammopsis, H. lineata, Psammotaenia lanceolata, Castoridens striata, C. hyalina, and Cratericulifera shandongensis. We also transferred Dimeregramma dubium to Hendeyella dubia. Phylogenetic analysis of the molecular data revealed that all the newly established taxa fell into a monophyletic group, with Fragilariforma virescens located at the base. The group was composed by two subclades: one comprising Castoridens, Cratericulifera, and Plagiostriata, and the larger including also the rest of the new genera plus some of the smallest known diatoms, such as Nanofrustulum, Opephora, Pseudostaurosira, Staurosirella, and Staurosira with a high level of support. This study enhances the general knowledge on the phylogeny and biodiversity of a group of small araphid diatoms that have been generally poorly described both by electron microscopy and DNA sequence data.

Six new epibioticProschkinia(Bacillariophyta) species and new insights into the genus phylogeny

“…Pellets were extracted with a QIAGEN DNeasy Plant Mini Kit (QIAGEN Sciences, Valencia, California, USA), using 1.0 mm glass beads in a Mini-Beadbeater (Biospec Products, Inc, Bartlesville, Oklahoma, USA) for 45 s for cell disruption and frustule breakage. Polymerase chain reaction (PCR) amplification and sequencing of small-subunit nuclear rRNA and the chloroplast-encoded rbcL and psbC markers followed the primers and protocols of Theriot et al (2015) and Li et al (2016). Extracted DNA and culture material not currently in public collections, as well as DNA extraction photovouchers, are available upon request from MPA at University of Texas -Austin.…”

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

“…However, the ultrastructure is instead consistent with the staurosiroid clade of araphid pennate diatoms. These are small-celled araphids [14][15][16] characterized by the presence of a distinct sternum with parallel striae, features considered as synapomorphies of pennates 14,15 , and the absence in general of a labiate process on the valve 14 (Fig. 1).…”

“…We also generated a more species-rich phylogenetic tree using a concatenated alignment of SSU, rbcL and psbC produced by Theriot and colleagues 7 but with more leptocylindrid and staurosiroid taxa sequenced 11,13,14,16 , in order to infer the phylogenetic position of CCMP470 with higher resolution ( Fig. 4; Table S2).…”

“…Sequences amplified from CCMP470 and Plagiostriata goreensis, along with 6 species of leptocylindrids sequenced by 11 , were manually appended to the alignment by 14 who performed a phylogenetic analysis of araphid diatoms with special emphasis on staurosiroids, and included a wide range of diatom lineages, with Bolidomonas as an outgroup. Furthermore, additional staurosiroid sequences were also appended after 14,16 who newly sequenced further staurosiroids with the description of new Plagiostriata species, P. baltica. The length of the final datasets was 4,221 bp (1,616 bp for SSU, 1,473 bp for rbcL and 1,132 bp for psbC).…”

Visualization of the internal structure of Didymosphenia geminata frustules using nano X-ray tomography

“…The species from the lowermost region of the spectrum can range from 1 µm to a couple of dozen micrometres (e.g. Li et al ., 2016) 7 . Likewise, the species from the largest part of the size spectrum can exceed 5 mm at the maximum but are never smaller than ca.…”