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Papazachariou V, Fernández-Juárez V, Parfrey LW, Riemann L. Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters. MICROBIAL ECOLOGY 2024; 87:106. [PMID: 39141097 PMCID: PMC11324715 DOI: 10.1007/s00248-024-02424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g-1 dw h-1) and 15 (light, 194.6 nmol N g-1 dw h-1). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.
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Affiliation(s)
- Vasiliki Papazachariou
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
- Center for Volatile Interactions, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Victor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, Department of Botany, and Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
- Center for Volatile Interactions, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Nowruzi B, Hutarova L, Vešelenyiova D, Metcalf JS. Characterization of Neowestiellopsis persica A1387 (Hapalosiphonaceae) based on the cpcA, psbA, rpoC1, nifH and nifD gene sequences. BMC Ecol Evol 2024; 24:57. [PMID: 38711016 PMCID: PMC11075313 DOI: 10.1186/s12862-024-02244-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Complex descriptions of new strains of cyanobacteria appear very frequently. The main importance of these descriptions concerns potential new substances that they could synthesise, as well as their different properties as a result of their different ecological niches. The main gene used for these descriptions is 16 S with ITS or whole genome sequencing. Neowestiellopsis persica represents a unique example of the influence of ecology on morphological changes, with almost identical 16 S identity. Although our previously described Neowestiellopsis persica strain A1387 was characterized by 16 S analysis, we used different molecular markers to provide a way to separate strains of this genus that are closely related at the genetic level. MATERIALS AND METHODS In order to conduct an in-depth study, several molecular markers, namely psbA, rpoC1, nifD, nifH and cpcA were sequenced and studied in Neowestiellopsis persica strain A1387. RESULTS The results of the phylogenetic analysis, based on cpcA, showed that the studied strain A 1387 falls into a separate clade than N. persica, indicating that this signature sequence could be a useful molecular marker for phylogenetic separation of similar strains isolated in the future. CONCLUSIONS Analysis of strain A1387 based on gene differences confirmed that it is a Neowestiellopsis strain. The morphological changes observed in the previous study could be due to different ecological and cultivation conditions compared to the type species. At the same time, the sequences obtained have increased our understanding of this species and will help in the future to better identify strains belonging to the genus Neowestiellopsis.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biotechnology, Science and Research Branch, Islamic Azad University, Daneshgah Blvd, Simon Bulivar Blvd, Tehran, Iran.
| | - Lenka Hutarova
- Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Dominika Vešelenyiova
- Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - James S Metcalf
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
- Brain Chemistry Labs, Box 3464, Jackson, WY, 83001, USA
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Luz R, Cordeiro R, Kaštovský J, Johansen JR, Dias E, Fonseca A, Urbatzka R, Vasconcelos V, Gonçalves V. Description of four new filamentous cyanobacterial taxa from freshwater habitats in the Azores Archipelago. JOURNAL OF PHYCOLOGY 2023; 59:1323-1338. [PMID: 37843041 DOI: 10.1111/jpy.13396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
Simple filamentous cyanobacteria comprise a diverse and polyphyletic group of species, primarily in the orders Leptolyngbyales and Oscillatoriales, that need more sampling to improve their taxonomy. Oceanic islands, such as the Azores archipelago, present unique habitats and biogeographic conditions that harbor an unknown range of diversity of microorganisms. Filamentous cyanobacteria isolated from aquatic habitats in the Azores and maintained in the BACA culture collection were described using morphology, both light and transmission electron microscopy, ecology, and genetic data of the 16S rRNA gene sequences and 16S-23S Internal Transcribed Spacer (ITS) rRNA region secondary structure. Our analyses revealed two new monophyletic genera: Tumidithrix elongata gen. sp. nov. (Pseudanabaenaceae) and Radiculonema aquaticum gen. sp. nov. (Leptolyngbyaceae). In addition, two new species Leptodesmis lacustris sp. nov. (Leptolyngbyaceae) and Pycnacronema lacustrum sp. nov. (Wilmottiaceae) are reported as the first aquatic species for these genera. The description of these new taxa and the genetic study of an isolate of Leptodesmis alaskaensis from the Azores followed the polyphasic approach, identifying diacritical features. Our results reinforce the need for taxonomic studies on cyanobacteria from less-studied habits and geographic regions, which have a potential for new taxa description.
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Affiliation(s)
- Rúben Luz
- Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, Ponta Delgada, Portugal
| | - Rita Cordeiro
- Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, Ponta Delgada, Portugal
| | - Jan Kaštovský
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jeffrey R Johansen
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Biology, John Carroll University, University Heights, Ohio, USA
| | - Elisabete Dias
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, Ponta Delgada, Portugal
| | - Amélia Fonseca
- Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, Ponta Delgada, Portugal
| | - Ralph Urbatzka
- Interdisciplinary Centre of Marine and Environmental Research - CIIMAR/CIMAR, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research - CIIMAR/CIMAR, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Vítor Gonçalves
- Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, Ponta Delgada, Portugal
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McGregor GB, Sendall BC, Niiyama Y, Tuji A, Willis A. Chrysosporum ovalisporum is synonymous with the true-branching cyanobacterium Umezakia natans (Nostocales/Aphanizomenonaceae). JOURNAL OF PHYCOLOGY 2023; 59:326-341. [PMID: 36680435 DOI: 10.1111/jpy.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/11/2022] [Accepted: 12/18/2022] [Indexed: 05/28/2023]
Abstract
True branching is a facultative characteristic only known from two cyanobacteria in the Aphanizomenonaceae, Umezakia natans and Dolichospermum brachiatum. In both cases, its expression has been associated with environmental stress, and its practical use as a diacritical feature has been previously evaluated. In this study, we undertook further evaluation of the phylogeny of Umezakia natans and its relationship to Chrysosporum ovalisporum as a previous study suggested the two were potentially congeneric. We used combined morphological, phylogenetic, and phylogenomic approaches to determine their relatedness using new strains available from a broad geographic range. Phylogenetic analysis based on 16S rRNA gene sequences showed that Australian C. ovalisporum and Japanese U. natans strains clustered together with accessions of C. ovalisporum originating from Australia, Israel, and Spain, with high p-distance similarity values (99.5%-99.9%). Additionally, differences between the two species in the 16S-23S ITS region was low (0%-2.5%). The average nucleotide identity of the U. natans and C. ovalisporum strains was also high (ANI of > 99.5 and AF > 0.9) and supported a genus-level separation from Chrysosporum bergii (83 ANI between clusters). Furthermore, in culture, strains of both species grown in vitamin-free media showed facultative true branching, a feature not previously known in C. ovalisporum. Collectively, the results support unification of C. ovalisporum and U. natans according to the principle of priority as Umezakia ovalisporum.
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Affiliation(s)
- Glenn B McGregor
- Queensland Department of Environment and Science, Brisbane, Australia
| | - Barbara C Sendall
- Queensland Department of Health, Forensic and Scientific Services, Coopers Plains, Australia
| | - Yuko Niiyama
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
| | - Akihiro Tuji
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
| | - Anusuya Willis
- Australian National Algae Culture Collection, National Collections and Marine Infrastructure, CSIRO, Hobart, Tasmania, Australia
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Strunecký O, Ivanova AP, Mareš J. An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis. JOURNAL OF PHYCOLOGY 2023; 59:12-51. [PMID: 36443823 DOI: 10.1111/jpy.13304] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/16/2022] [Indexed: 06/15/2023]
Abstract
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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Affiliation(s)
- Otakar Strunecký
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05, České Budějovice, Czech Republic
| | - Anna Pavlovna Ivanova
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05, České Budějovice, Czech Republic
| | - Jan Mareš
- Biology Centre of the CAS, Institute of Hydrobiology, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
- Faculty of Science, Department of Botany, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
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Kumar N, Saraf A, Pal S, Mishra D, Singh P, Johansen JR. Circumscription of Fulbrightiella gen. nov. and Sherwoodiella gen. nov., Two Novel Genera in the Calotrichaceae (Nostocales, Cyanobacteria). JOURNAL OF PHYCOLOGY 2023; 59:204-220. [PMID: 36331047 DOI: 10.1111/jpy.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regard to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S-23S internal transcribed spacer (ITS). The strains fell into two clades formerly identified as Calothrix from freshwater and brackish habitats. Based on both morphology and ecology, they differed from the type species of Calothrix, C. confervicola, which is marine, has wide trichomes with short cells, and narrows abruptly to a hyaline hair. The first clade grouped species with heteropolar filaments widened at the base and narrowed gradually toward the apex but not ending in a hair, with basal heterocytes that are formed in series as the apically placed heterocytes senesce; this clade is being named Fulbrightiella gen. nov., with two named species, F. bharadwajae sp. nov. and F. oahuensis sp. nov. The second clade was comprised of a single species with isopolar trichomes that are untapering as hormogonia, but which widen midfilament and taper toward both ends following growth. These trichomes develop pairs of heterocyte mid-filament, causing fragmentation into heteropolar trichomes with basal heterocytes and ends that taper, but not to a hair. This clade consists of a single species at present, Sherwoodiella mauiensis. With this action, four clades in the Calotrichaceae have been named: Macrochaete, Dulcicalothrix, Fulbrightiella, and Sherwoodiella. Calothrix sensu stricto is truly marine, morphologically distinct, and unsequenced; finding and sequencing the generitype for Calothrix remains as the most important and unfinished task in the revision of the Calotrichaceae.
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Affiliation(s)
- Naresh Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | | | - Sagarika Pal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Deeksha Mishra
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Prashant Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, University of South Bohemia, Branišovská 1760, Ceske Budějovice, 370 05, Czech Republic
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Maltseva S, Kezlya E, Krivova Z, Gusev E, Kulikovskiy M, Maltsev Y. Phylogeny and fatty acid profiles of Aliinostoc vietnamicum sp. nov. (cyanobacteria) from the soils of Vietnam. JOURNAL OF PHYCOLOGY 2022; 58:789-803. [PMID: 36054495 DOI: 10.1111/jpy.13283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
A new cyanobacterial species of Aliinostoc, A. vietnamicum sp. nov., is recorded in the tropical forest soil from the Cát Tiên National Park, Vietnam. The analysis is based on morphological characters, 16S rDNA phylogeny, ITS secondary structure, and fatty acid composition analysis. Aliinostoc vietnamicum differed from the other species of the genus by the size and shape of vegetative cells, size of akinetes and heterocytes, and presence of granular polyphosphate inclusions in vegetative cells. The evolutionary distance matrix based on the 16S rRNA gene shared 96.2-98.2% similarities with other Aliinostoc sequences. The phylogeny inferred by maximum likelihood and Bayesian inference placed A. vietnamicum in the Aliinostoc clade, within the Nostocaceae. For the first time, fatty acid composition analysis was obtained for a member of the genus Aliinostoc with cultivation time experiments. α-linolenic (27.54-37.75%), palmitic (13.87-22.65%), and stearic (10.08-20.27%) acids were the dominant fatty acids when cultured during the exponential growth phase, as well as during stationary. This is the first finding of a strain with such a high content of stearic acid among cyanobacteria with Nostoc-like morphology.
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Affiliation(s)
- Svetlana Maltseva
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Elena Kezlya
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Zinaida Krivova
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Evgeniy Gusev
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Maxim Kulikovskiy
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Yevhen Maltsev
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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Gaysina LA, Johansen JR, Saraf A, Allaguvatova RZ, Pal S, Singh P. Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils. DIVERSITY 2022. [DOI: 10.3390/d14080620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica sp. nov., in accordance with the International Code of Nomenclature for algae, fungi, and plants. This work continues the rapid expansion of the description of new taxa of cyanobacteria, and particularly demonstrates a coming phase in cyanobacterial taxonomy in which the discovery of new species in recently described genera rapidly increases our understanding of the diversity in this phylum.
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