Glossary terms starting with "s"

Secondary side

In raphid diatom ontogeny, the side of the valve formed by fusion of silica branches extending from the center and the poles of the raphe sternum. The secondary side forms after the primary side.

The secondary side can be identified by Voigt discontinuities and by the characteristic where both distal or both proximal raphe ends turn toward the same side of the valve, or are unilaterally deflected.


The acronym for scanning electron microscope. The SEM uses electrons to image specimens. It provides images of the surface of the silica cell wall, or frustule, while the light microscope (LM) provides images of the transparent features of the diatom.

Separation spines

In certain species of Aulacoseira, long spines formed by some valves which cause frustules within a chain to separate from each other. By contrast, short, linking spines join frustules together.


A silica sheet extending internally from the walls of a copula, or girdle band, occluding a portion of its length. By contrast, a septum is part of a copula, while a pseudoseptum is part of a valve. The septum is found in a number of genera such as Tabellaria. Plural form is septa.


A simple or robust extension of the diatom valve. The plural form is setae. Setae are more elongate than spines and are found in the genera Chaetoceros and Bacteriastrum. They join frustules together to form chains and maintain the buoyancy of colonies in a planktonic environment.


Having more or less the shape of the letter S.



The process by which a structure is formed from the deposition of silica


A pointed, silica extension of the valve, shorter than a seta. Spines and may be solid or hollow, very long or tiny, single or many, and they may arise from different points on the valve in different taxa.


A hyaline thickening of silica in the central area of a valve, found only in the genus Stauroneis.

Some references consider a fascia and a stauros to be equivalent structures, but recent work (Cox 1999, 2001, 2012) has shown that the stauros has a distinct pattern of development. During valve formation in Stauroneis, a transverse strip of silica develops from each side of the central nodule.


Having the shape of a star; having similar parts radiating from a common center. For example, cells of the genus Asterionella join into stellate colonies.


A longitudinal element of the valve of pennate diatoms. Usually thickened and hyaline. The sternum is usually positioned along the apical axis as in Navicula, but is sometimes positioned along the valve margin as in Eunotia. In many raphid diatoms, the sternum contains the raphe. Plural form is sterna.

The sternum is the ontogenic center of pennate valves, that is, it is the first silica deposited in valve formation following cell division.

Stigma - isolated punctum

An opening, or perforation, through the central area of the valve that is distinct in structure from the areolae composing the striae. The external opening is typically round, or nearly round, while the internal opening has the shape of a slit, or is complex. Plural form is stigmata.

A stigma is present in many genera, including Cymbella, Didymosphenia, Geissleria, Gomphoneis, Gomphonema, and Luticola, and may not be homologous across these taxa.


A row of areolae on the valve. In centric diatoms, usually oriented along radii; in pennate diatoms, usually oriented more or less perpendicular to the apical axis. Plural form is striae.

Features of the striae are important in diatom taxonomy and phylogeny, such as:

- density: number of striae that occur in 10 µm;
- orientation: radiate, parallel, or convergent;
- chambering: whether an alveolus or not;
- seriation: whether uni-, bi-, or multiseriate.

Stria density and count in centric diatoms

Stria density is based on the number of striae in an arc of circumference. The density = circumference * 10 / total number of striae on the valve. In Figure 1, the stria density is equal to (54.3 µm) (10) / 21, or 3.9 striae in 10 µm of circumference.

Stria count is based on the number of striae in a chord of the valve face. In Figure 2, the chord crosses 5 striae, giving a count of 5 in 10 µm.


One of possibly many scientific names belonging to a taxon. Two types of synonyms are considered here. Homotypic synonyms are based on the exact same type specimen, or holotype. Homotypic synonyms are declared through a ‘nomenclatural act’, that is, published in the scientific literature following the formal rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). For example, Achnanthes minutissima was transferred to the genus Achnanthidium and renamed Achnanthidium minutissimum. These two names are homotypic, nomenclatural, or objective, synonyms.

Heterotypic synonyms are based on different type specimens. These synonyms rely on the opinions of taxonomists rather than on the formal, nomenclatural rules. For example, Gomphonema louisiananum was first described by Kalinsky (1984). Later, this same diatom was described as Gomphonema patrickii by Kociolek and Stoermer (1995), using a different type specimen. These two names are heterotypic, or subjective, synonyms.

This web flora emphasizes objective synonyms. Expert contributors and reviewers determine the relevant objective synonyms to include on each species page and list them under the heading, SYNONYMS. We consider the relevant synonyms to be those that analysts might typically encounter. We also include names that we consider to be subjective synonyms under the heading, REPORTED AS. This heading also includes errors in identification published in various floras.