In addition to SILVA 138.2, we also provide files with GSR-DB as the bacterial database
The family Prochlorococcaceae has proven to be a headache for curation and now has its taxonomy modeled after GTDB R220 with some minor changes, see below. There have been several provisional genera (i.e., GTDB names) added. See the Taxonomy_V1.3.xlsx files for more in depth information.
Greatly reduced the number of sequences, primarily in over represented genera (e.g., Dolichospermum, Prochlorococcus, etc) to reduce redundancy. This "Should" help with classification, especially with the difficult groups (e.g., ADA-Aphanizomenon/Dolichospermum/Anabaena)
GTDB R220 changes for CyanoSeq V1.3:
WH-5701 and MW101C3 = Regnicoccus
NIES-981 = Ciimarium
RCC307 = Inmanicoccus
Synechococcus_D = Lacustricoccus
Aphanocapsa_A feldmannii, Regnicoccus frigidus, Cyanobium_A sp013205255 were excluded as their placement in the 16S rRNA phylogeny is weird, likely due to these being pulled from MAGs.
Almyronema, Ciimarium, Cyanoarbor, Limnonema, Egbenema, Komarkovaeasiopsis, Gansulinema, Karukerafilum, Radiculonema, Copelandiella, Azorthrix, Pseudocalidococcus, Phayaothrix, Trichothermofontia, Monilinema, Floridaenema, Venetifunis, Ahomia, Parathermosynechococcus, Candidatus Sivonenia, Sphaerothrix, Reofilinostoc, Okeanomitos, Thermospirulina
All taxa from the family Aerosakkonemataceae were moved to the novel order "Aerosakkonematales" based on phylogenomic analyses from our accepted paper in J Phycol, DOI pending. This also resulted in the description of Floridaenema, thus provisional genus "Oscillatoriaceae_X" and what we previously considered "Phormidium" have been with reclassified as Floridaenema.
Funiculus tenuis is now Konicacronema tenuis and Parifilum solicrustae is now Pycnacronema solicrustae (Jusko and Johansen 2023 DOI: 10.1111/jpy.13411)
Leptothermofonsia species were transferred into Kovacikia (Kaštovský et al. https://doi.org/10.3390/d15090975)
Rivulariaceae_XX is now Phayaothrix
Gloeobacteraceae_X is now Candidatus_Sivonenia
Prochlorococcaceae_XX is now NIES-981 based on GTDBR220 addition
Leptolyngbyaceae_XXX is now split between Copelandiella and Khargia
Sphaerothrix and Almyronema are very close on the tree, ignoring for now but deserves more attention
The Class "Candidatus-Melainabacteria" was renamed to "Vampirovibrionophyceae" as per Strunecký and Mareš 2023
Brunnivagina was not included as the analyses was done on a single partial 16S rRNA fragment. Genomic analyses was not conducted despite availability. Genomic evidence does not support the erection of this genus.
Kaštovský et al. (https://doi.org/10.3390/d15090975) also concluded that Plectolyngbya should be syn with Leptolyngbya, however we retain Plectolyngbya as our analyses do not support their conclusion.
The manuscript was accept in the Journal of Phycology (yay), but open access is expensive (not yay). Contact me for a copy!
Taxonomy file was update to include the type/reference strain for each genus. In the case of provisional genera or a genus with an unsequenced type, the provided information is what we are considering the reference strain.
Anathece sequences were transfered to Cyanobium due to high similarity between the types strains. Cyanobium takes principle of priority. This also increases the number of assigned ASVs for the freshwater Prochlorococcaceae in our tests
Phylum name was changed to Cyanobacteriota
Chrysosporum ovalisporum was changed to Umezakia ovalisporum, C. bergii remain unchanged
Chroococcidiopsidaceae_X was changed to Soropora
Leptolyngbyaceae_X was changed to Monilinema
Leptolyngbyaceae_XX was changed to Apatinema
Leptolyngbyaceae_XXXXX was changed to Romeriopsis
Geitlerinema was incorrectly placed in the Oscillatoriales, this has been resolved
Spirirestis, Microlinema, Cyanodorina, Microcrocis, Khargia
Insularia was found to be monophyletic with, and >97.8% similar to, Thainema. Thus, this was included in the database as Thainema.
Microcoleusiopsis was found to be monophyletic, and >99.8% similar to Arthrospira. Thus, this was included in the database as Arthrospira.
Calothrix reevaluated based on Kumar et al. 2022, seems like no known Calothrix sequences exist. Fulbrightiella and Sherwoodiella replace Calothrix Romeriopsis replaces Leptolyngbyaceae_XXXXX Apatinema replaces Leptolyngbyaceae_XX
Radiocystis*, Edaphophycus, Zarconia, Neocylindrospermum, Prochlorotrichaceae_X
Radiocystis: No valid publications, but these three strains form a monophyletic clade. However, these sequences come from trusted cyanobacterial taxonomists. Future works should aim to validate this genus.