Recognizing novel cyanobacterial diversity in marine benthic mats, with the description of Sirenicapillariaceaefam. nov., two new genera,Sirenicapillaria gen. nov. andTigrinifilum gen. nov., and seven new species

Berthold, David E.; Lefler, Forrest W.; Laughinghouse, Haywood Dail

doi:10.1080/00318884.2021.2006589

Cited by 17 publications

(21 citation statements)

References 47 publications

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“…These benthic species typically possess gas vesicles, and they are capable of nitrogen fixation, resembling the notoriously reported planktic oceanic nitrogen fixer Trichodesmium, which also clusters in this group. We have noticed two recent reports published after our phylogenetic trees for the current article were already finished, including the description of new families of marine benthic cyanobacteria, Vermifilaceae and Sirenicapillariaceae (Berthold et al 2021(Berthold et al , 2022. The new families in these studies were based exclusively on 16S rRNA gene data and seemed to be intermixed with Microcoleaceae as defined in our current study (Fig.…”

supporting

confidence: 50%

“…We have noticed two recent reports published after our phylogenetic trees for the current article were already finished, including the description of new families of marine benthic cyanobacteria, Vermifilaceae and Sirenicapillariaceae (Berthold et al. 2021, 2022). The new families in these studies were based exclusively on 16S rRNA gene data and seemed to be intermixed with Microcoleaceae as defined in our current study (Fig.…”

Section: Resultsmentioning

confidence: 94%

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An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Strunecký

Ivanova

Mareš

2023

Journal of Phycology

125

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Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well‐described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.

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supporting

confidence: 50%

Section: Resultsmentioning

confidence: 94%

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Strunecký

Ivanova

Mareš

2023

Journal of Phycology

125

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“…Application of 16S rRNA gene phylogenies has resulted in hundreds of new taxa being described in the last two decades, either as novel taxa or revising previously polyphyletic taxa (Komárek et al, 2014;Mai et al, 2018). While much effort has focused on revising the genus and species ranks, orders and families have recently received more attention (Berthold et al, 2021(Berthold et al, , 2022Komárek et al, 2020;Mai et al, 2018) as many of the current ranks were artifacts of morphology-based taxonomy. Several works (e.g., Berthold et al, 2021Berthold et al, , 2022Bonthond et al, 2021;Mareš, 2018;Sendall & McGregor, 2018), noted the polyphyletic nature of these ranks using both 16S rRNA gene and phylogenomic analyses.…”

Section: E T H O D S a R T I C L Ementioning

confidence: 99%

“…While much effort has focused on revising the genus and species ranks, orders and families have recently received more attention (Berthold et al, 2021(Berthold et al, , 2022Komárek et al, 2020;Mai et al, 2018) as many of the current ranks were artifacts of morphology-based taxonomy. Several works (e.g., Berthold et al, 2021Berthold et al, , 2022Bonthond et al, 2021;Mareš, 2018;Sendall & McGregor, 2018), noted the polyphyletic nature of these ranks using both 16S rRNA gene and phylogenomic analyses. Recently, Strunecký et al (2022) revised the cyanobacterial orders and families based on phylogenomic analyses, enhancing our understanding and resolving the polyphyly of these ranks.…”

Section: E T H O D S a R T I C L Ementioning

confidence: 99%

Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Lefler

Berthold

Laughinghouse

2023

Journal of Phycology

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Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well‐known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full‐length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.

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“…Активне застосування комплексного підходу з широким залученням молекулярнофілогенетичних даних, розроблення нової класифікаційної схеми, покликаної відобразити еволюційну історію групи, спираючись на монофілетичні таксони ціанобактерій (Komárek et al, 2014), спричинило глибокі зміни в їхній систематиці. Щороку описують десятки нових родів і видів, з'являються й зникають нові родини та порядки (Komárkova et al, 2013;Hauer et al, 2014;Moreira et al, 2017;Mai et al, 2018;Komárek et al, 2020;Johansen et al, 2021;Pietrasiak et al, 2021;Bertold et al, 2022;Cheng et al, 2022). Крім того, протягом останніх 20 років українські альгологи активно продовжували флористичні та таксономічні дослідження, у т. ч. із залученням молекулярних методів, значно розширивши список видів ціанобактерій і таксономічну структуру флори (Kostikov, Golub, 2007;Sadogurskaya, 2007;Vinogradova, Darienko, 2008;Kovalenko, 2009;Nesterova, 2010;Vinogradova, Mikhailiuk, 2010;Gerasimiuk, 2011;Yarmoshenko et al, 2012;Voitsekhovich, 2013;Mikhailiuk et al, 2016Mikhailiuk et al, , 2018Vinogradova, 2016а;Beresovska, 2017;Vinogradova et al, 2017;Romanenko et al, 2020;Mikhailiuk, Vinogradova, 2022).…”

Section: вступunclassified

Cyanobacteria of Ukraine: actual diversity, trends of taxonomic changes, features of zonal and ectopic distribution

Vinogradova¹

2022

Algologia

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The paper presents the results of a critical taxonomic revision of the list of cyanobacteria of Ukraine and the analyzis of their zonal, ecological and typological distribution. The list includes 766 species from 150 genera. They belong to the class Cyanophyceae Schaftner, four subclasses, 7 orders and 46 families. The subclass Oscillatoriophycideae (4 orders, 21 families, 65 genera, 333 species) is characterized by the greatest species and taxonomic diversity. The leading orders are Synechococcales (34.1%), Nostocales (26.8%) and Oscillatoriales (25.5%). Genera Phormidium Kütz. ex Gomont (7.3% of species), Leptolyngbya Anagn. et Komárek (5.4%), Calothrix C.Agardh ex Bornet et Flahault (3.8%) and Oscillatoria Vaucher ex Gomont (3.7%) lead in species richness. The obtained results are significantly different from the generalized data on the species and taxonomic diversity of cyanobacteria of Ukraine as of 2005. The growth of generic and species diversity is partly related to nomenclature and taxonomic changes; 7 genera and 50 species are new floristic records, revealed including using molecular methods. The distribution of cyanobacteria on the territory of Ukraine has specific features. The highest diversity and uniqueness of the species composition is characteristic of the Steppe zone of Ukraine: 539 species from 124 genera of Cyanophyceae. Of these, 101 species and 11 genera were recorded only within this zone. The ecological spectrum of Ukrainian cyanoflora consists of freshwater (66.3%), marine (14.5%), terrestrial (9.5%) species, as well as species with a wide ecological amplitude (7.3%), brackish water (4.1%) and eurytopic (1.4%) species. The representation of species in different habitat types varies widely. Most species were found in rivers (56.5% of the total list), lakes (38.0%), ponds (34.6%) and reservoirs (29.4%). Among continental water bodies, swamps have the most peculiar species composition (9.8% of species are found only here). Floodplain water bodies have the least specific species composition (0.5%). Among non-aquatic habitats, the largest number of species was found in soils (excluding saline): 179 species from 55 genera, 15.6% of species occur only in this type of habitats. In the Ukrainian sectors of the Black and Azov seas, 228 species from 80 genera of cyanobacteria were found, of which 41 species (17.9%) were not registered in other types of habitats. 43 species are widespread in Ukraine. They include the water bloom agents Dolichospermum spiroides (Kleb.) Wacklin et al., Microcystis flosaquae (Wittrock) Kirchn. and M. viridis (A.Braun in Rabenh.) which most often occur in reservoirs of the plain part of Ukraine.

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Recognizing novel cyanobacterial diversity in marine benthic mats, with the description of Sirenicapillariaceaefam. nov., two new genera,Sirenicapillaria gen. nov. andTigrinifilum gen. nov., and seven new species

Cited by 17 publications

References 47 publications

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Cyanobacteria of Ukraine: actual diversity, trends of taxonomic changes, features of zonal and ectopic distribution

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