Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS.

Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.

Draft Genome Assembly of the Bloom-Forming Cyanobacterium Nodularia spumigena Strain CENA596 in Shrimp Production Ponds.

We report here the draft genome assembly of the brackish cyanobacterium Nodularia spumigena strain CENA596 isolated from a shrimp production pond in Rio Grande do Sul, Brazil. The draft genome consists of 291 contigs with a total size of 5,189,679 bp. Secondary metabolite annotations resulted in several predicted gene clusters, including those responsible for encoding the hepatotoxin nodularin.

Asterionellopsis tropicalis (Bacillariophyceae): a new tropical species found in diatom accumulations.

The diatom Asterionellopsis glacialis sensu lato forms high-density patches in the surf zone of some sandy beaches worldwide and was until recently considered a cosmopolitan species. With the recent description of four cryptic species, the identity of specimens found in these accumulations remains uncertain. In this study, diatom patches were sampled from two sandy beaches of the Brazilian coast: one tropical (Futuro Beach, 3° S; 38° W) and one subtropical (Cassino Beach, 32° S; 52° W). Fine structure of frustules and the sequencing of three phylogenetic markers revealed the subtropical strains to be A. guyunusae and the tropical strains to be a new species, here described as Asterionellopsis tropicalis sp. nov. A. tropicalis was differentiated morphologically by the number of striae in 10 µm at the foot pole and head (39-44; 38-45, respectively), from A. lenisilicea (46-55; 46-64), A. maritima (46-51; 46-60), and A. thurstonii (42-58; 55-70). The number of striae at the head region of the valvocopula (10 µm) helped to distinguish A. tropicalis (56-62) from A. guyunusae (61-64), but A. tropicalis was morphologically undistinguishable from A. glacialis. The sequence divergence from other identified Asterionellopsis species was 13%-16% (Cox1), 11%-12% (5.8S + ITS2) and 2%-6% (RbcL), and A. tropicalis formed a distinct monophyletic clade with high support in all analyzed phylogenetic trees (single or multi-locus). This work will aid in the understanding of the ecological and physiological diversity of diatom patches that are key to the trophic webs of sandy beaches.

Dinoflagelados (Peridiniales, Prorocentrales) do microplâncton na plataforma continental e talude do extremo sul do Brasil (inverno 2005, verão 2007) / Microplankton dinoflagellates (Peridiniales, Prorocentrales) at the continental shelf and slope in Southern Brasil (winter 2005, summer 2007)

Este estudo teve por objetivo identificar as morfo-espécies de dinoflagelados do microplâncton (>20 μm) das Ordens Peridiniales e Prorocentrales ao largo do Cabo de Santa Marta Grande, CSMG (SC, 28º 40' S) e Albardão-Chuí, AC (RS, 34º 40' S) durante dois cruzeiros oceanográficos: inverno de 2005 e verão de 2007. Amostras de plâncton foram coletadas através de arrastos verticais com rede de plâncton (20 μm), preservadas com formalina 4 por cento e analisadas ao microscópio invertido equipado com câmara digital. Quando necessário, a identificação de espécies de Peridiniales foi efetuada através do número e morfologia das placas da teca realçadas com Calco Flúor Branco MR2; espécies de Prorocentrales foram identificadas com base em seu tamanho, forma, presença de processos apicais, padrão dos poros e marcas na faixa intercalar. Foram identificadas 25 espécies, das quais Protoperidinium (11), Prorocentrum (6), Corythodinium (3), Podolampas (2), Oxytoxum (2) e Heterocapsa (1). Espécies de Prorocentrum apresentaram ampla distribuição na plataforma continental do extremo sul do Brasil, enquanto as espécies de Peridiniales foram observadas principalmente na região do Albardão-Chuí durante o inverno, sob a influência da Pluma do Río de la Plata. Oxytoxum milneri foi pela primeira vez registrada na região sul do País, e Protoperidinium cassum var. cassum, P. curtipes e Heterocapsa triquetra foram registradas pela primeira vez no Brasil.

This study aimed at identifying morpho-species of microplankton dinoflagellates (> 20 μm) of the order Peridiniales and Prorocentrales off Santa Marta Grande Cape, CSMG (SC, 28º 40' S) and Albardão-Chui, AC (RS, 34º 40' S) during oceanographic cruises conducted in winter 2005 and summer 2007. Plankton samples were obtained by vertical net (mesh size 20 μm) hauls preserved with formaldehyde 4 percent and analyzed using the inverted microscope equipped with a digital camera. The identification of Peridiniales species was based on the number and morphology of thecal plates enhanced with Calco Fluor White MR2 whenever necessary and the identification of Prorocentrales was based on cell size, shape, presence of apical processes, pore pattern and marks at the intercalary band. We identified 25 species, including Protoperidinium (11), Prorocentrum (6), Corythodinium (3), Podolampas (2), Oxytoxum (2) and Heterocapsa (1). Prorocentrum species were widely distributed on the continental shelf of southern Brazil, while Peridiniales species were mainly found off Albardão-Chui during winter, especially under the influence of the plume of La Plata River. Oxytoxum milneri was the first time recorded in southern Brazil, while Protoperidinium cassum var. cassum, P. curtipes and Heterocapsa triquetra, were first registered in Brazil.

Dinophysiales (Dinophyceae) no extremo Sul do Brasil (inverno de 2005, verão de 2007) / Dinophysiales (Dinophyceae) in the farthest Southern region of Brazil (Winter 2005, Summer 2007)

The dinoflagellates of the Dinophysiales order are a morphologically diverse and ecologically heterogeneous group that includes autotrophic, mixotrophic and heterotrophic species and others containing endosymbionts or phycotoxin producers. In this research Dinophysis, Ornithocercus, Histioneis and Amphisolenia species have been identified in both coastal and oceanic waters of the Southern region of Brazil next to Santa Marta Grande Cape, SC and Albardão-Chuí, RS. Vertical hauls were performed with plankton nets (20 µm) on board of the R. V. Atlântico Sul at 33 oceanographic stations sampled in August/September 2005 (Winter) and February 2007 (Summer). The plankton was fixed with formaldehyde (4 percent) and analyzed with the help of an inverted microscope. A total of 43 Dinophysiales species were identified, most of them widely distributed in the coastal, continental and oceanic areas such as Dinophysis acuminata, D. exigua, D. ovata and Histioneis hyalina in the Summer of 2007 and D. acuminata, D. caudata, D. fortii e D. schroederi in the Winter of 2005. The distribution of some species was restricted to the oceanic region under the influence of the Brazil Current as it was observed for Dinophysis dubia, D. exigua, D. schuetti, Histioneis para, Ornithocercus thumii and O. splendidus in the Winter of 2005 and D. similis, D. rapa, H. megalocopa, H. milneri, O. heteroporus and O. splendidus in the Summer of 2007. Six potentially toxic species were registered, Dinophysis acuminata, D. caudata, D. fortii, D. mitra, D. tripos and D. rotundata.

Os dinoflagelados da ordem Dinophysiales representam um grupo morfologicamente diverso e ecologicamente heterogêneo, incluindo espécies autotróficas, mixotróficas e heterotróficas, outras contendo endossimbiontes ou ainda produtoras de ficotoxinas. No presente trabalho, foram identificadas as espécies de Dinophysis, Ornithocercus, Histioneis e Amphisolenia em águas costeira e oceânica na região Sul do Brasil, ao largo do Cabo de Santa Marta Grande, SC e Albardão-Chuí, RS. Arrastos verticais foram realizados com rede de plâncton (20 µm) à bordo do N. O. Atlântico Sul em 33 estações oceanográficas visitadas em agosto/setembro de 2005 (inverno) e fevereiro de 2007 (verão). As amostras de plâncton foram fixadas com formol (4 por cento) e analisadas com o auxílio de microscópio invertido. Ao todo, 43 espécies de Dinophysiales foram identificadas, a maioria com ampla distribuição nas regiões costeira, de plataforma continental e oceânica, como Dinophysis acuminata, D. exigua, D. ovata e Histioneis hyalina no verão de 2007, e D. acuminata, D. caudata, D. fortii e D. schroederi no inverno de 2005. Algumas espécies apresentaram distribuição restrita à região oceânica, sob influência da Corrente do Brasil, como Dinophysis dubia, D. exigua, D. schuetti, Histioneis para, Ornithocercus thumii e O. splendidus no inverno de 2005, e D. similis, D. rapa, H. megalocopa, H. milneri, O. heteroporus e O. splendidus no verão de 2007. Seis espécies potencialmente tóxicas foram encontradas, Dinophysis acuminata, D. caudata, D. fortii, D. mitra, D. tripos e D. rotundata.

Chave dicotômica ilustrada para a identificação de espécies de Thalassiosira Cleve (diatomácea) no estuário da Lagoa dos Patos e área costeira adjacente (Rio Grande do Sul, Brasil) / Illustrated dichotomous key for the identification of Thalassiosira Cleve species (Bacillariophyceae) from Lagoa dos Patos estuary and adjacent areas (Rio Grande do Sul, Brazil)

O trabalho apresenta uma chave dicotômica e uma tabela comparativa com as dimensões e características diagnósticas para a identificação de dezessete espécies de Thalassiosira (diatomáceas), comumente observadas no estuário da Lagoa dos Patos e na área costeira adjacente à sua desembocadura (~32º S e 52º W). Para todas as espécies estudadas são fornecidas ilustrações e comentários sobre os detalhes morfológicos importantes para a sua identificação em microscopia óptica, bem como imagens em microscopia eletrônica de varredura (MEV).

The paper presents a dichotomous key and a comparative table summarizing dimension data and diagnostic characteristics of seventeen Thalassiosira species (diatoms) commonly found in Lagoa dos Patos estuary and the coastal adjacent area (~32º S and 52º W). For all studied species, optic microscope illustrations and comments on significant morphological features are provided, together with scanning electron microscopy images.

DIVERSITY AND MORPHOLOGY OF SKELETONEMA SPECIES IN SOUTHERN BRAZIL, SOUTHWESTERN ATLANTIC OCEAN(1).

We examined the morphology of Skeletonema species occurring in coastal waters of southern Brazil, on the basis of LM, SEM, and TEM analyses of six isolated strains and of 13 field samples from the Patos Lagoon estuary and the adjacent Cassino Beach. We concluded that the genus Skeletonema is highly diverse in coastal waters of southern Brazil, with the occurrence of four confirmed species: S. costatum, S. pseudocostatum, S. potamos, and S. tropicum. In addition, EM details must still be provided for S. menzelii, and genetic studies should be conducted to confirm the identity of S. cf. grethae and S. subsalsum. The high diversity in this geographic area can be attributed to the proximity of the Subtropical Convergence and to the freshwater ecosystems of Patos Lagoon and La Plata River that favor the presence of warm-, cold-, and brackish-water species.

Loricate Choanoflagellates from the South Atlantic coastal zone (~32 ºS) including the description of Diplotheca tricyclica sp. nov / Choanoflagelados Loricados da zona costeira do Atlântico Sul (~32 ºS) incluindo a descrição de Diplotheca tricyclica sp. nov

The biodiversity of marine heterotrophic protists is poorly known in the South Atlantic coastal zone (~32 ºS) especially regarding the nanoflagellates. The presence of loricate choanoflagellates was reported for the first time in the Patos Lagoon estuary and the adjacent coastal zone. Seventeen species of eleven genera of loricate choanoflagellates were observed between October 1998 and May 2000 in fixed water samples (lugol's solution + glutaraldehyde) in a JEM 100-SX transmission electron microscope. Most species were recorded in euhaline and mixopolyhaline waters during the spring and summer, none in autumn and a few (four) in winter. The absence of choanoflagellates at the more sheltered inshore stations is due freshwater influence, and at the beach station, probably due the strong wave action. The probably cosmopolitan species Pleurasiga minima, Cosmoeca norvegica, C. ventricosa and Parvicorbicula circularis were present in spring or summer in the estuary channel and coastal area while Stephanoeca diplocostata which apparently prefers lower temperature, was recorded in winter. Calotheca alata and Campyloacantha spinifera are mainly temperate species and were present in spring. The new species Diplotheca tricyclica was recorded at the estuary channel in the summer 1999, in high salinity water.

A biodiversidade de protistas heterotróficos é pouco conhecida na zona costeira do Atlântico Sul (~32 ºS), especialmente dos nanoflagelados. No presente estudo, foi registrada pela primeira vez a presença de coanoflagelados loricados no estuário da Lagoa dos Patos e na zona costeira adjacente. Dezessete espécies de onze gêneros de coanoflagelados loricados foram observadas em amostras de água fixadas (solução de lugol + glutaraldeido) coletadas entre outubro de 1998 e maio de 2000, e analisadas em microscópio de transmissão JEM 100-SX. A maior parte das espécies foi registrada em águas euhalinas e mixopolihalinas durante a primavera e o verão, nenhuma no outono e poucas (quatro) no inverno. A ausência de coanoflagelados nas estações mais protegidas deve-se a influência da água doce, e na estação da praia deve-se, provavelmente, a forte ação das ondas. As espécies, provavelmente cosmopolitas, Pleurasiga minima, Cosmoeca norvegica, C. ventricosa and Parvicorbicula circularis ocorreram na primavera ou no verão no canal principal do estuário e na área costeira, enquanto Stephanoeca diplocostata, que aparentemente prefere baixas temperaturas, foi registrada no inverno. Calotheca alata e Campyloacantha spinifera são principalmente de ambientes temperados e estiveram presentes na primavera. Uma espécie nova, Diplotheca tricyclica, foi registrada na área do canal principal do estuário, no verão de 1999, em águas de alta salinidade.

Morphology and ecology of the planktonic diatom Palmerina hardmaniana (Greville) Hasle in southern Brazil / Morfologia e ecologia de diatomácea planctônica Palmerina hardmaniana (Greville) Hasle no Sul do Brasil

The diatom Palmerina hardmaniana (Greville) Hasle presents a wide geographical distribution in neritic tropical and subtropical regions. In the present work we analyzed plankton samples collected monthly between 1995 and 2007 at the surf zone of Cassino Beach, RS (32º 12' S and 52º 10' W), and in winter 2005 and summer 2007 at the continental shelf and slope in southern Brazil, Santa Marta Grande Cape, SC and Albardão-Chuí, RS regions (28º 23'-33º 07' S and 48º 41'-52º 26' W). We present the detailed morphological description of P. hardmaniana, and the first study including electron scanning microscope observations for material from the southwestern Atlantic Ocean. The morphometric data confirm the identity of the species in all its ultra-structural details. Palmerina hardmaniana was only observed in summer-autumn months with low cell density (< 500 cells.L-1) at both Cassino Beach surf zone and coastal shelf stations. The warm water temperature (18-29 ºC) indicates the most probable origin of its inoculum are tropical/subtropical regions. Salinities of 23-36 and the relatively high silicate content indicate the importance of the terrestrial discharge during occasions when P. hardmaniana was observed, probably with influence on the nutrient availability. We emphasize that the species was not cited previously for Argentinean and Uruguayan waters and suggest that the southern Brazilian region is close to the southern geographical distribution limit of Palmerina hardmaniana in the southwestern Atlantic Ocean.

A diatomácea Palmerina hardmaniana (Greville) Hasle apresenta ampla distribuição geográfica em águas neríticas tropicais e subtropicais. No presente trabalho foram analisadas amostras de plâncton, coletadas mensalmente entre 1995 e 2007 na zona de rebentação da Praia do Cassino, RS (32º 12' S e 52º 10' W), e no inverno de 2005 e verão de 2007 na plataforma continental e talude do sul do Brasil, na região de Cabo de Santa Marta Grande, SC e Albardão-Chuí, RS (28º 23'-33º 07' S e 48º 41'-52º 26' W). Apresentamos a descrição detalhada de P. hardmaniana, como primeiro estudo com observações de microscopia eletrônica de varredura para material coletado em águas do Oceano Atlântico Sul Ocidental. Os dados morfológicos analisados confirmam a identificação da espécie em todos os seus detalhes estruturais. Palmerina hardmaniana somente foi observada nos meses de verão/outono, em baixa densidade (< 500 células.L-1) na zona de arrebentação da Praia do Cassino bem como em estações costeiras da plataforma continental. A temperatura quente da água (18-29 ºC), indica as águas tropicais/subtropicais como possível origem do inóculo de P. hardmaniana no verão-outono. A salinidade entre 23 e 36 e o teor relativamente alto de sílica também indicam a importância da descarga terrestre nas ocasiões de presença de P. hardmaniana, exercendo importante papel no suprimento de nutrientes. Salienta-se que a espécie não é citada em águas argentinas e uruguaias e assim, sugerimos que o extremo sul do Brasil representa aproximadamente o limite sul da distribuição geográfica de Palmerina hardmaniana no Oceano Atlântico Sul Ocidental.