Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences

Tragin, Margot; Santos, Adriana Lopes dos; Christen, Richard; Vaulot, Daniel

doi:10.1127/pip/2016/0059

Cited by 35 publications

(48 citation statements)

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“…For example, in the present study, the V9 region of the 18S rRNA gene failed to discriminate clades within Dolichomastigales (Supporting Information Fig. S9B), because there are only four Dolichomastigales V9 reference sequences against 69 for V4 (Tragin et al ., ). In the same way, obtaining accurate image of communities at stations which host rare or uncultured taxa is more difficult with V9 than with V4, because many sequences in public databases are short and do not extend to the end of the 18S rRNA gene.…”

Section: Concluding Remarks – What Is the Best Choice: V4 Or V9?mentioning

confidence: 97%

“…Then, we look in detail at the community composition at the Class level for photosynthetic groups. We finally focus on the contribution at each station of Chlorophyta classes and of Mamiellophyceae genera, for which a high quality reference sequence database has been recently reannotated (Tragin et al ., ) and which have been the subject of recent ecological studies in oceanic waters (Monier et al ., ; Simmons et al ., ; Clayton et al ., ).…”

Section: Introductionmentioning

confidence: 99%

“…The choice between V4 and V9 depends on the taxonomic levels as well as the specific groups targeted. It is necessary to make detailed comparisons of genetic distances for each targeted region between and within the groups of interest (Dunthorn et al, 2012;Pernice et al, 2013) and to determine whether reference sequences are available for the group of interest in the target region (Tragin et al, 2016). The sequencing platform may also have some impact: using the 454 technology, Behnke and colleagues (2011) showed that the sequencing error rate was taxon dependent, but V4 error rates were higher than for V9.…”

Section: Introductionmentioning

confidence: 99%

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Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Tragin

Zingone

Vaulot

2017

Environmental Microbiology

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We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically green algae (Chlorophyta). Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, V9 provided 20% more OTUs built at 97% identity than V4. 34% of the genera were found with both markers and, of the remnant, 22% were found only with V4 and 44% only with V9. For photosynthetic groups, V4 and V9 performed equally well to describe global communities at different taxonomic levels from the division to the genus and provided similar Chlorophyta distribution patterns. However, at lower taxonomic level, the V9 dataset failed for example to describe the diversity of Dolichomastigales (Chlorophyta, Mamiellophyceae) emphasizing the lack of V9 sequences for this group and the importance of the reference database for metabarcode analysis. We conclude that in order to address questions regarding specific groups (e.g., a given genus), it is necessary to choose the marker based not only on the genetic divergence within this group but also on the existence of reference sequences in databases.

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Section: Concluding Remarks – What Is the Best Choice: V4 Or V9?mentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Tragin

Zingone

Vaulot

2017

Environmental Microbiology

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“…The class Mamiellophyceae (Marin and Melkonian, 2010), corresponding to clade II , contains three important genera of marine pico-phytoplankton: Micromonas, Bathycoccus and Ostreococcus. They are typical of coastal waters Romari and Vaulot, 2004;Collado-Fabri et al, 2011) where they can form sporadic blooms (O'Kelly et al, 2003) but have also been observed in open oceanic waters (Foulon et al, 2008;Monier et al, 2012;Treusch et al, 2012;Vaulot et al, 2012). The genus Micromonas can be dominant in Arctic ecosystems (Lovejoy et al, 2007;Balzano et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

et al. 2016

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Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1-A7 and B1-B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.

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“…Este es el caso particular de las familias Scenedesmaceae y Chlorellaceae, cuyos miembros presentan similitudes mayores al 99 % en la secuencia estudiada, independientemente de su género y especie, resultado que ha sido reportado por otros autores para algas verdes (Tragin et al, 2016, Temraleeva et al, 2017. Es indispensable encontrar nuevas secuencias genéticas variables en microalgas que puedan ser utilizadas en conjunto con otras regiones conocidas (ITS, ADNr18S, rbcL, etc) para mejorar la capacidad de discriminación y lograr una identificación molecular más precisa.…”

Section: Cyanidium Caldariumunclassified

Identificación de una colección de microalgas aisladas de Costa Rica mediante secuenciación de ADNr 18S

et al. 2018

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RESUMENLas microalgas componen un diverso grupo polifilético de microorganismos fotosintéticos. Debido a su potencial biotecnológico, los estudios para aislar e identificar nuevas cepas han incrementado, por lo que es necesario el desarrollo de nuevas técnicas para su correcta identificación y clasificación. Utilizando herramientas de biología molecular, en este estudio se analizó el gen del ADNr 18S de 12 cepas microalgales aisladas de diferentes regiones de Costa Rica, resultando seis pertenecientes a la clase Trebouxiophyceae, tres a Chlorophyceae, dos a Prymnesiophyceae y una a Cyanidiophyceae. Este estudio reporta por primera vez la identificación molecular de cepas microalgales aisladas de Costa Rica, resaltando la diversidad de estos microorganismos en el país.Palabras clave: biotecnología microalgal, filogenia, identificación molecular. ABSTRACTMicroalgae integrate a diverse polyphyletic group of photosynthetic microorganisms. Due to its biotechnological potential, studies to isolate and identify new strains have increased, hence, it is necessary to develop new techniques for their correct identification and classification. Using molecular biology tools, this study analyzed the 18S rDNA gene from 12 microalgal strains isolated from different regions of Costa Rica, resulting in six strains belonging to the class Trebouxiophyceae, three to Chlorophyceae, two to Prymnesiophyceae and one to Cyanidiophyceae. This study reports for the first time the molecular identification of microalgal strains isolated from Costa Rica, highlighting the diversity of these microorganisms in the country.

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Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences

Cited by 35 publications

References 0 publications

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

Identificación de una colección de microalgas aisladas de Costa Rica mediante secuenciación de ADNr 18S

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