<i>Sodalinema</i>
Bibliographic record
Abstract
Abstract So.da.li.ne.ma. Gr. neut. n. nêma , filament; N.L. neut. n. Sodalinema , the name of the genus referring to alkaline‐saline habitats where this cyanobacterium was found (soda lake) and to the cyanobacterium morphology. The Phormidium genus has been described as one of the most difficult phylogenetic lineages to resolve, with over 200 identified species representing distinct polyphyletic groups, including multiple strains intermingled with the genus Sodalinema . In this article, we attempt to address this inconsistency by describing and differentiating the genus Sodalinema from the other taxonomic lineage previously named Phormidium , using the Genome Taxonomy Database as a framework for data‐driven classification. This genus contains 64 strains, including 5 strains with high‐quality isolate genomes, 9 strains with associated metagenome‐assembled genomes, and 50 additional strains represented by small subunit ribosomal RNA gene sequences. Many of these strains have been identified as having potential for biotechnological applications and grow in high‐density biofilms. Members of the Sodalinema genus are filamentous cyanobacterium with straight, cylindrical, and unbranched trichomes. They perform oxygenic photosynthesis, with some strains capable of nonheterocystous nitrogen fixation and phototaxis. Colonies typically exist in the form of biofilms or microbial mats, growing either attached or floating, and have been observed globally in a variety of habitats, ranging from freshwater, marine, and high‐salinity environments (1.6–234 g/l total salinity), pH from neutral to 11.2, and temperatures up to 50°C. Strains are commonly isolated from high‐salinity soda lakes or salt marshes with no identified biosynthesis of cyanobacterial toxins. DNA G + C content (mol %) : 51.1–53.4. Type species : Sodalinema komarekii Cellamare et al. 2018. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Sodalinema is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Cyanobacteriota / Cyanophyceae / Oscillatoriales / Oscillatoriaceae / Sodalinema The genus Sodalinema can also be recovered in the Genome Taxonomy Database (GTDB) as g__Sodalinema (version v220) ** . GTDB classification: d__Bacteria / p__Cyanobacteriota / c__Cyanobacteriia / o__Cyanobacteriales / f__Geitlerinemaceae / g__Sodalinema * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.787 | 0.694 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".