What constitutes a stigma? A review of isolated pores in raphid diatoms (Bacillariophyceae) and the value of precise terminology.

Scanning electron microscopy has revealed variation in the ultrastructure of distinctive isolated pores in or near the central area of raphid diatoms, with different types of pores being restricted to phylogenetic groups. Thus, the widespread use of the term stigma for all such pores not only hides the structural diversity but also obscures the phylogenetic distribution of the different types. This paper provides images of the different types of isolated pores, particularly refining the discrimination of variants within the Cymbellales, and reveals some interesting ecological patterns.

, A Novel Cosmopolitan Species of Blue Diatoms.

Specimens of a new species of blue diatoms from the genus Simonsen were discovered in geographically distant sampling sites, first in the Canary Archipelago, then North Carolina, Gulf of Naples, the Croatian South Adriatic Sea, and Turkish coast of the Eastern Mediterranean Sea. An exhaustive characterization of these specimens, using a combined morphological and genomic approach led to the conclusion that they belong to a single new to science cosmopolitan species, sp. nov.

Post-mortem oxygen isotope exchange within cultured diatom silica.

Rationale: Potential post-mortem alteration to the oxygen isotope composition of biogenic silica is critical to the validity of palaeoclimate reconstructions based on oxygen isotope ratios (δ O values) from sedimentary silica. We calculate the degree of oxygen isotope alteration within freshly cultured diatom biogenic silica in response to heating and storing in the laboratory.

Methods: The experiments used freshly cultured diatom silica.

Diatoms can be an important exception to temperature-size rules at species and community levels of organization.

Climate warming has been linked to an apparent general decrease in body sizes of ectotherms, both across and within taxa, especially in aquatic systems. Smaller body size in warmer geographical regions has also been widely observed. Since body size is a fundamental determinant of many biological attributes, climate-warming-related changes in size could ripple across multiple levels of ecological organization.

Integrated simulation with experimentation is a powerful tool for understanding diatom valve morphogenesis.

We present a number of promising examples of computational studies, which improve our understanding of the morphogenesis process of diatom cell walls. Each example considers a different physical scenario whereby computational and mathematical models are used to evaluate hypotheses pertaining to diatom valve formation; considering the roles of cytoskeletal elements, interactions between cell components that might generate patterned structures from the submicron (nanoscale) to cell level, and the effect of environmental variables. We propose that the complex, multiscale phenomenon of diatom valve morphogenesis requires better integration of computational/mathematical and experimental procedures if we are to untangle all the contributing processes.

DIATOM COLONY FORMATION: A COMPUTATIONAL STUDY PREDICTS A SINGLE MECHANISM CAN PRODUCE BOTH LINKAGE AND SEPARATION VALVES DUE TO AN ENVIRONMENTAL SWITCH(1).

The morphological plasticity and adaptive behavior exhibited during diatom colony formation in Aulacoseira is explored through computer simulation to study how the interplay of mechanisms such as cytoskeletal-driven membrane protrusions, silica deposition, and environmental factors may contribute to the generation of two distinct spine morphologies on linkage and separation valves. A multiscale agent-based computational model was developed, which showed that a single cytoskeleton-driven, competitive growth mechanism could generate either of the two characteristic phenotypes, given only a single switch in the environment (as might be experienced by a change in light regime). Hypotheses are formulated from the model, and predictions made for potential follow-up experiments.

ONTOGENY, HOMOLOGY, AND TERMINOLOGY-WALL MORPHOGENESIS AS AN AID TO CHARACTER RECOGNITION AND CHARACTER STATE DEFINITION FOR PENNATE DIATOM SYSTEMATICS(1).

This article reviews current knowledge of wall morphogenesis in pennate diatoms in relation to the way characters are defined and described for taxonomic and systematic analyses. It argues that an understanding of ontogeny is essential for the accurate identification of character homologies, which in turn must underpin all phylogenetic and systematic analyses. Terminology should reflect character homology, but most diatom terminology fails to do this, with concomitant confusion and potential taxonomic mistakes.

A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia.

Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' diversification.

Nature's Batik: a computer evolution model of diatom valve morphogenesis.

This paper describes a novel computer simulation that uses evolution to design functioning raphid pennate diatom valves. The model of valve morphogenesis used is based on current theories that highlight the importance of cytoskeletal elements in valve development. An "organic" negative imprint is grown in a grid-based system, using both local and global rules to dictate grid cell states.