Global radiation in a rare biosphere soil diatom.

Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms.

Exploring Diversity, Taxonomy and Phylogeny of Diatoms (Bacillariophyta) from Marine Habitats. Novel Taxa with Internal Costae.

In many marine littoral and sublittoral benthic habitats, we find small diatoms with few features resolvable with light microscopy (LM) other than internal costae across their valves. While classically those internal costae have defined their identification and classification, the use of electron microscopy and of molecular data have started to reveal the true diversity of unrelated forms and genera (e.g., Anaulus, Eunotogramma, Hustedtiella, or Plagiogramma) which possess these structures. Here we describe the new genus Ambo, in an attempt to clarify some of the polyphyly of taxa with internal costa by formally transferring Anaulus balticus, Anaulus simonsenii, and Plagiogramma tenuissimum as well as Ambo gallaeciae, described here. Related to this, we attempt to document and characterize the genus Anaulus itself, which was formally described by Ehrenberg with an illustration. A search by LM of mica designated by Ehrenberg as the holotype of Anaulus scalaris, the generitype of Anaulus, failed to recover a specimen which adequately describes the genus to the exclusion of other genera with internal costa. We also present morphological and molecular data for Anaulus creticus and suggest a new genus-Ceratanaulus-to reflect the distinct morphological and molecular characters we documented.

Protists and other organisms on a minute snail periostracum / Protistas e outros organismos em um pequeno periostracum de caracol

Abstract Since the foundation of the Malacological Center in 1980, Universidad Centro Americana (UCA), Managua-Nicaragua, has been monitoring and collecting the marine, terrestrial, fluvial and lake mollusk population of the country. Many specimens have been photographed by Scanning Electronic Microscope (SEM), and in one of these, observation of the hairy periostracum reveals a seemingly thriving population of minute protists in possible symbiosis with their host. Adequate magnification and comparison with previous studies allowed the determination of these hosts as diatoms, testaceous amoebae, yeast, phacus, spores and other undetermined organisms which occur in tropical forests on rocks, trees and leaves. Here illustrated are diatoms and other organisms detected for the first time on the periostracum of a tropical rainforest mollusk.

Resumo Desde a fundação do Centro Malacológico em 1980, a Universidad Central Americana (UCA), Manágua-Nicarágua, vem acompanhando e coletando a população de moluscos marinhos, terrestres, fluviais e lagoas do país. Muitos espécimes foram fotografados pelo microscópio eletrônico de varredura (SEM) e, em um deles, a observação do periostracum peludo revela uma população aparentemente próspera de protistas de minuto em possível simbiose com o hospedeiro. A ampliação adequada e a comparação com estudos anteriores permitem a determinação dessas diatomáceas, amebas testaceas, leveduras, phacus, esporos e outros organismos indeterminados que ocorrem em florestas tropicais em rochas, árvores e folhas. Aqui estão as diatomeas e outros organismos pela primeira vez detectados no periostracum de um molusco tropical.

Temporal changes in biological traits of diatom communities in response to an oil spill in a subtropical river.

Diatom growth strategies, which are used as a proxy to analyze disturbances and environmental impacts, can also provide reliable information about environmental gradients. In this study, we used diatom communities and biological traits to assess the structure of epilithic diatoms after an oil spill in a large tributary of the Iguaçu River (Paraná, Brazil). Epilithon and water samples were taken on July 12th, 2004, and after an unexpected oil spill, on the following days: 09/19, 10/03, and 10/13/2004. We observed that the spill caused a distinct shift in both diatom composition and guild group. Diversity decreased and pollution-tolerant diatoms of the motile group became dominant in response to the elevated nutrient levels and reduced light. Tube-forming diatoms, which are strong competitors for light, dominated the epilithon 24 days after the oil spill. Both diatom guilds and growth forms were successfully used to predict the environmental conditions. While diatom guilds responded to disturbances along a temporal gradient, changes inside the guilds were the main factor for understanding the environmental gradient.

Different iron storage strategies among bloom-forming diatoms.

Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.

Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation.

Diatoms are a highly successful group of photosynthetic protists that often thrive under adverse environmental conditions. Members of the genus Pseudo-nitzschia are ecologically important diatoms which are able to subsist during periods of chronic iron limitation and form dense blooms following iron fertilization events. The cellular strategies within diatoms that orchestrate these physiological responses to variable iron concentrations remain largely uncharacterized. Using a combined transcriptomic and proteomic approach, we explore the exceptional ability of a diatom isolated from the iron-limited Northeast Pacific Ocean to reorganize its intracellular processes as a function of iron. We compared the molecular responses of Pseudo-nitzschia granii observed under iron-replete and iron-limited growth conditions to those of other model diatoms. Iron-coordinated molecular responses demonstrated some agreement between gene expression and protein abundance, including iron-starvation-induced-proteins, a putative iron transport system and components of photosynthesis and the Calvin cycle. Pseudo-nitzschia granii distinctly differentially expresses genes encoding proteins involved in iron-independent photosynthetic electron transport, urea acquisition and vitamin synthesis. We show that P. granii is unique among studied diatoms in its physiology stemming from distinct cellular responses, which may underlie its ability to subsist in low iron regions and rapidly bloom to outcompete other diatom taxa following iron enrichment.

Structure and Development of the Auxospore in Ardissonea crystallina (C. Agardh) Grunow Demonstrates Another Way for a Centric to Look Like a Pennate.

Reproductive development in Ardissonea crystallina revealed a unique mode of enlargement involving a combination of novel and known structures. In light microscopy, auxospores of this elongated polar centric diatom were superficially similar to the auxospores of pennates. With SEM we found three different components in the auxospore wall. In the youngest, nearly spherical cell-stage, the wall consisted only of a delicate veil containing minute siliceous spherules. Incunabular elements developed underneath this layer. Second, a previously unknown form of specifically modified incunabular scales shaped the subsequent ellipsoidal-capsule auxospore stage. Third, there was a clear contribution of scales to the development of scaly transverse perizonial bands (or scaly bands, for brevity). Such bands, although noted by previous researchers, have not been fully appreciated for the evolutionary information they may convey: possibly common among polar centrics but not pennates. Finally, we propose maintaining the term transverse perizonium to refer to these bands in polar diatoms, but to introduce the differentiation of scaly bands described here from pinnate bands (currently known as typical of pennates). Further research into band types among polar centrics may provide new insights into the relationship between the groups within polar centrics that are currently unresolved by molecular methods.

Identification of benthic diatoms isolated from the eastern tidal flats of the Yellow Sea: Comparison between morphological and molecular approaches.

Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene. Based on the traditional morphological identification system, the 61 isolated strains were classified into 52 previously known taxa from 13 genera. However, 17 strains could not be classified as known species by morphological analyses, suggesting a hidden diversity of benthic diatoms. The Blast search on NCBI's Genebank indicated that the reference sequences for most of the species were absent for the benthic diatoms. Of the two genetic markers, the rbcL genes were more divergent than the 18S rRNA genes. Furthermore, a long branch attraction artefact was found in the 18S rRNA phylogeny. These results suggest that the rbcL gene is a more appropriate genetic marker for identification and classification of benthic diatoms. Considering their high diversity and simple shapes, and thus the difficulty associated with morphological classification of benthic diatoms, a molecular approach could provide a relatively easy and reliable classification system. However, this study suggests that more effort should be made to construct a reliable database containing polyphasic taxonomic data for diatom classification.

Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy.

The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.

Response of phytoplankton to an experimental fish culture in net cages in a subtropical reservoir / Resposta do fitoplâncton ao cultivo experimental de peixes em tanques-rede em um reservatório subtropical

Abstract This study aimed to evaluate nutrients concentration and spatial-temporal changes in phytoplankton biovolume during an experimental fish culture in net cages in a lateral arm of Salto Caxias reservoir, Brazil. Two sampling stations were placed in the affected lateral arm and other two in a cageless lateral arm. Neither abiotic variables nor phytoplankton biovolume presented significant differences between the treatments. Only temporal changes were confirmed by the analysis performed. Both lateral arms were classified as oligotrophic, reflecting low influence of the net cages. Phytoplankton growth seems to be limited by nitrogen. Biovolume values were, in general, low and five major functional groups were recognized (E, F, G, K and P). In summer higher biovolume values were observed and representatives of Chlorophyceae and Cyanobacteria belonging to the functional groups F and K, respectively, were the most important. In winter phytoplankton was mainly composed by Bacillariophyceae taxa from P group. G group was also restricted to winter and E group occurred in winter and summer. The variations recorded in phytoplankton structure appear to have been mainly influenced by seasonal changes in temperature, precipitation and nutrients availability. The effects of net cages on the abiotic variables and phytoplankton biovolume appear to have been small, probably due to the small number of net cages employed and the system dilution capacity. However, a permanent monitoring of phytoplankton is recommended, since this environment has a carrying capacity, from which the trophic state may increase.

Resumo Este estudo objetivou avaliar alterações nas variáveis abióticas e no biovolume fitoplanctônico durante o cultivo experimental de peixes em tanques-rede em um braço lateral do reservatório de Salto Caxias, Brasil. Foram selecionadas duas estações de amostragem no braço com tanques-rede e outras duas em um braço sem tanques. As variáveis abióticas e o biovolume fitoplanctônico não apresentaram diferenças significativas entre os locais estudados. Apenas mudanças temporais foram confirmadas pelas análises utilizadas. Os dois braços laterais foram classificados como oligotróficos, refletindo a baixa influência dos tanques-rede. O crescimento do fitoplâncton parece ter sido limitado principalmente por nitrogênio. Os valores de biovolume foram, em geral, baixos e cinco principais grupos funcionais foram observados (E, F, G, K e P). No verão, os maiores valores de biovolume foram observados e representantes de Chlorophyceae e Cyanobacteria dos grupos funcionais F e K, respectivamente, se destacaram. No inverno, o fitoplâncton foi composto principalmente por táxons de Bacillariophyceae do grupo P. O grupo G também foi restrito ao inverno e o grupo E ocorreu no inverno e verão. As variações registradas na estrutura do fitoplâncton parecem ter sido principalmente influenciadas pelas mudanças sazonais de temperatura, precipitação e disponibilidade de nutrientes. Os efeitos dos tanques-rede sobre as variáveis abióticas e biovolume fitoplanctônico parecem ter sido pequenos, provavelmente devido ao pequeno número de tanques utilizados e a capacidade de diluição do sistema. Entretanto, o monitoramento permanente do fitoplâncton é recomendado, uma vez que este ambiente possui uma capacidade de suporte, a partir da qual o estado trófico pode aumentar.

Composition of diatom communities and their contribution to plankton biomass in the naturally iron-fertilized region of Kerguelen in the Southern Ocean.

In the naturally iron-fertilized surface waters of the northern Kerguelen Plateau region, the early spring diatom community composition and contribution to plankton carbon biomass were investigated and compared with the high nutrient, low chlorophyll (HNLC) surrounding waters. The large iron-induced blooms were dominated by small diatom species belonging to the genera Chaetoceros (Hyalochaete) and Thalassiosira, which rapidly responded to the onset of favorable light-conditions in the meander of the Polar Front. In comparison, the iron-limited HNLC area was typically characterized by autotrophic nanoeukaryote-dominated communities and by larger and more heavily silicified diatom species (e.g. Fragilariopsis spp.). Our results support the hypothesis that diatoms are valuable vectors of carbon export to depth in naturally iron-fertilized systems of the Southern Ocean. Furthermore, our results corroborate observations of the exported diatom assemblage from a sediment trap deployed in the iron-fertilized area, whereby the dominant Chaetoceros (Hyalochaete) cells were less efficiently exported than the less abundant, yet heavily silicified, cells of Thalassionema nitzschioides and Fragilariopsis kerguelensis Our observations emphasize the strong influence of species-specific diatom cell properties combined with trophic interactions on matter export efficiency, and illustrate the tight link between the specific composition of phytoplankton communities and the biogeochemical properties characterizing the study area.

Tolerancia de diez especies de diatomeas (Bacillariophyceae) a los factores físico-químicos del agua en el Río Sarapiquí, Costa Rica / The tolerance of ten diatom species (Bacillariophyceae) to water's physico-chemical factors in the Sarapiqui River, Costa Rica

ResumenLas diatomeas del bentos son el componente más estudiado del perifiton en los ríos de Costa Rica, sin embargo aún queda mucho por conocer sobre su ecología. Por eso en el presente estudio se analizó el perifiton en seis diferentes sitios en la cuenca medio del Río Sarapiquí en el 2010, 2011 y 2012. En cada uno de los muestreos se realizó el conteo de 400 frústulas, de las cuales se obtuvo la abundancia relativa de las especies: Achnanthidium exiguum, Coconneis placentula, Cymbella tumida, Luticola goeppertiana, Luticola ventricosa, Navicula symmetrica, Nitzchia clausii, Nupela praecipua, Reimeria sinuata y Synedra goulardi. Esta información fue relacionada con los datos físico químicos (oxígeno disuelto, temperatura, conductividad, total de sedimentos en suspensión, turbidez, pH y alcalinidad) medidos en cada uno de los sitios. Con el propósito de observar las relaciones entre los diferentes sitios dentro de la cuenca, se utilizó un análisis de correspondencia canónica (ACC), lo que permitió distinguir tres sectores de acuerdo a la altitud. Estos sectores se diferencian en el tipo de sustrato, cobertura riparia vegetal y parámetros físico-químicos, lo que propicia diferencias en la composición de especies de diatomeas entre ellos. Se obtuvieron los valores óptimos calculados y tolerancia calculada para cada una de las especies. Los resultados obtenidos indican que las especies: A. exiguum, R. sinuata,L. ventricosa y C. tumida, dominan en aguas limpias, oxigenadas y baja temperatura. Las especies N. praecipua, S. goulardi, C. placentula, L. goeppertiana, N. clausii y N. symmetrica se encuentran en aguas cálidas, alta turbidez y poco oxigenadas. Las especies A. exiguum, R. sinuata, prevalecen en sitios con agua alcalina y baja conductividad y las especies N. symmetrica, C. tumida y L. ventricosa presentan una relación positiva con la conductividad y el pH de las aguas. Las especies estudiadas mostraron buenos indicios de su valor como indicadores de calidad del agua, sin embargo, debido a diferencias de interpretación por varios autores, es necesario realizar más estudios en otras cuencas hidrográficas en el país.

Abstract The tolerance of ten diatom species (Bacillariophyceae) to water's physico-chemical factors in the Sarapiqui River, Costa Rica. Benthic diatoms are the periphyton component most studied in Costa Rican rivers, yet there is still much to be known about their ecology. This study aims to contribute to this knowledge. Periphyton samples from six locations along the middle reach of Sarapiquí river and some of its tributaries were taken and analyzed from 2010 to 2012. A total count of 400 frustules was performed in each sample to obtain relative abundances of each species. Ten species, which were easily recognized at the light microscope, were analyzed here: Achnanthidium exiguum, Coconneis placentula, Cymbella tumida, Luticola goeppertiana, Luticola ventricosa, Navicula symmetrica, Nitzchia clausii, Nupela praecipua, Reimeria sinuata and Synedra goulardi. Their abundance was related to physico chemical data at each site for every sampling date (dissolved oxygen, temperature, conductivity, total suspended solids, turbidity, pH and alkalinity) with a canonical correspondence analysis (CCA) that allowed distinguishing three sectors along the river according to altitude. These sectors differed by substrate, riparian vegetation cover, and physic-chemical parameters, all of which resulted in differences in diatom species composition among them. Optimum values and tolerances form each environmental parameter were calculated for each species. Our results showed that A. exiguum, R. sinuata,L. ventricosa and C. tumida, were dominant in clean and well oxygenated waters with low temperatures. The species N. praecipua, S. goulardi, C. placentula, L. goeppertiana, N. clausii and N. symmetrica inhabited warm waters with high turbidity and low oxygen. The species A. exiguum, R. sinuata were dominant in sites with low alkalinity and conductivity, whereas species like N. symmetrica, C. tumida and L. ventricosa showed a positive relationship with conductivity and pH. The studied species showed good characteristics of their value as water quality indicators, yet due to different interpretations by several authors, it is necessary to perform further studies at more river basins in the country. Rev. Biol. Trop. 64 (1): 105-115. Epub 2016 March 01.

Auxosporulation in Paralia guyana MacGillivary (Bacillariophyta) and Possible New Insights into the Habit of the Earliest Diatoms.

BACKGROUND: Diatoms are one of the most ecologically important aquatic micro-eukaryotes. As a group unambiguously recognized as diatoms, they seem to have appeared relatively recently with a limited record of putative remains from oldest sediments. In contrast, molecular clock estimates for the earliest possible emergence of diatoms suggest a considerably older date. Depending on the analysis, Paralia and Leptocylindrus have been recovered within the basal molecular divergences of diatoms. Thus these genera may be in the position to inform on characters that the earliest diatoms possessed. FINDINGS: Here we present auxospore development and structure of initial and post-auxospore cells in a representative of the ancient non-polar centric genus Paralia. Their initial frustules showed unusual, but not unprecedented, spore-like morphology. Similarly, initial frustules of Leptocylindrus have been long considered resting spores and a unique peculiarity of this genus. However, even though spore-like in appearance, initial cells of Paralia readily resumed mitotic divisions. In addition, Paralia post-auxospore cells underwent several rounds of mitoses in a multi-step process of building a typical, "perfect" vegetative valve. This degree of heteromorphy immediately post-auxosporulation is thus far unknown among the diatoms. IMPLICATIONS: A spore-related origin of diatoms has already been considered, most recently in the form of the "multiplate diploid cyst" hypothesis. Our discovery that the initial cells in some of the most ancient diatom lineages are structurally spore-like is consistent with that hypothesis because the earliest diatoms may be expected to look somewhat similar to their ancestors. We speculate that because the earliest diatoms may have appeared less diatom-like and more spore-like, they could have gone unrecognized as such in the Triassic/Jurassic sediments. If correct, diatoms may indeed be much older than the fossil record indicates, and possibly more in line with some molecular clock predictions.

Molecular phylogeny of Amphora sensu lato (Bacillariophyta): an investigation into the monophyly and classification of the amphoroid diatoms.

Amphora sensu lato encompasses a large group of raphid diatoms, diverse in both form and ecology. The defining feature of this group has been an extreme asymmetry of the valve mantle and girdle bands, bringing both faces of the cell onto a single plane. Although this 'amphoroid' structure has long been the diagnostic feature and thus considered 'conservative' for the group, many have argued that the diversity of forms presently assigned to Amphora likely does not represent a monophyletic group. With the exception of several taxonomic transfers and the recent elevation of Halamphora to the level of genus, much of Amphora classification has remained unchanged for over 100 years. This study presents a phylogenetic analysis of Amphora s.l. based on a concatenated molecular alignment including the nuclear marker SSU rDNA and the chloroplast markers rbcL and psbC. These results are discussed within the framework of the current classification system of Amphora and Halamphora and lay the groundwork for a taxonomic revision of the group based on monophyly. The results of this analysis demonstrate that the genus Amphora is polyphyletic and that lineages assigned to the genus are distributed widely across the raphid diatom tree of life. The feature of amphoroid symmetry appears to have evolved independently several times. We discuss the nature of conservative characters in the raphid diatoms and their usefulness as a guide to phylogenetic relationships.

Nupela species (Naviculales: Bacillariophyceae) from Colombian lowland waters including N. acaciensis nov. sp. and N. catatumbensis nov. sp. / Especies de Nupela (Naviculales: Bacillariophyceae) en aguas de tierras bajas de Colombia que incluyen a N. acaciensis nov. sp. y N. catatumbensis nov. sp.

The genus Nupela comprises ca. 50 species that generally have a distribution restricted by bioclimatic frontiers. As part of an integrated analysis of the diatom flora of Colombia, in this study we focused our interest on the genus Nupela from lowland waters. Periphyton samples were collected from 150 sites of lotic water bodies in Colombia, taking into account hidrogeomorfological variability. In each sampling station, periphyton samples were obtained by scraping, and temperature, pH, dissolved oxygen and conductivity variables were measured. Samples were processed by both light microscopy (LM; Carl Zeiss Axio Scope.A1) and scanning electron microscopy (SEM; FEI-Quanta 450 and a Jeol JSM-6360 LV). The genus Nupela was found in 28 sites. Five taxa were identified, described and illustrated from tropical or subtropical environments: N. lesothensis, N. praecipua y N. subpallavicinii; these were new records for Colombia, and N. acaciensis and N. catatumbensis two new species for science. N. acaciensis is characterized by raphe branches of both valves equally long combined with cymbelloid symmetry, striae built by 2 transapically elongated areolae that delimit a longitudinal line at each hemivalve. N. catatumbensis is characterized by the presence of a well developed raphe in both valves; valves lanceolate with subcapitated to capitated ends and cymbelloid symmetry, striae built by 3-4 transapically elongated areolae, interestriae elevated as transapical ribs and internal proximal raphe ends hook-shaped. The genus Nupela was widely distributed in the studied basins but showed different distribution patterns: N. acaciensis and N. subpallavicini had a restricted distribution, while N. catatumbensis, N. lesothensis and N. praecipua had a wider distribution, and were collected in sites with significant variations in their ecomorphology, altitude, temperature, pH and electrolyte content.

El género Nupela comprende alrededor de 50 especies que tienen en general una distribución restringida por fronteras bioclimáticas. Como parte de un estudio integral de la flora diatomológica de Colombia, en este trabajo focalizamos nuestro interés en el género Nupela en cuerpos de agua de tierras bajas. Muestras de perifiton fueron recolectadas en 150 sitios en cuerpos de agua lóticos seleccionados por su variabilidad hidrogeomorfológica. En cada estación de muestreo se obtuvieron muestras por raspado de varios sustratos, y adicionalmente se registraron: temperatura, pH, oxígeno disuelto y conductividad. Las muestras fueron procesadas para su análisis con microscopio óptico (MO, Carl Zeiss Axio Scope. A1) y de barrido (MEB; FEI- Quanta 450 and a Jeol JSM-6360 LV). El género Nupela fue hallado en 28 sitios. Cinco especies fueron identificadas, descritas e ilustradas, tres de ellas: N. lesothensis, N. praecipua y N. subpallavicinii fueron descritas para ambientes tropicales y subtropicales y representan nuevas citas para Colombia. Además fueron descritas N. acaciensis y N. catatumbensis, dos especies nuevas para la ciencia. N. acaciensis se caracteriza por poseer rafe desarrollado en ambas valvas, simetría cymbelloide, estrías formadas por dos aréolas transapicalmente alargadas que definen una línea longitudinal en cada hemivalva. N. catatumbensis se caracteriza poseer rafe desarrollado en ambas valvas. Valvas lanceoladas con extremos subcapitados a capitados y simetría cymbelloide. Estrías formadas por 3-4 aréolas transapicalmente alargadas, interestrías elevadas a modo de costillas transapicales y extremos proximales internos del rafe en forma de gancho. El género Nupela estuvo ampliamente representado en el área de estudio, sin embargo, las especies mostraron diferentes patrones de distribución. N. acaciensis y N. subpallavicini estuvieron presentes en una única cuenca, mientras que N. catatumbensis, N. lesothensis y N. praecipua presentaron una distribución más amplia, y fueron recolectadas en sitios con variaciones significativas en ecomorfología, altitud, temperatura, pH y contenido electrolítico.

New records of amphoroid diatoms (Bacillariophyceae) from Cachoeira River, Northeast Brazil / Novas ocorrências de diatomáceas anforóides (Bacillariophyceae) no Rio Cachoeira, nordeste do Brasil

Amphoroid taxa have been revised in recent decades. Many species formerly assigned to Amphora have been transferred to other recently proposed genera, as Seminavis (Naviculaceae) and Halamphora (Catenulaceae). In Brazil, there are few studies focused on amphoroid taxonomy. This study presents a taxonomic investigation of five uncommon amphoroid taxa from Brazilian diatom flora: Seminavis pusilla, S. strigosa, Amphora ectorii, Halamphora ghanensis and Halamphora sp. Seminavis strigosa is identical in valve morphology and morphometrical data to Amphora twenteana, and its synonymy is proposed. Seminavis pusilla, poorly found in Brazilian waters, has expanded its distribution. Halamphora ghanensis is a new record to American continent while Amphora ectorii are new to Brazilian aquatic systems. Halamphora sp. has distinct ultrastructural features in relation to similar species and is probably new for science.

Táxons anforóides foram revisados nas últimas décadas. Várias espécies, previamente atribuídas a Amphora, foram transferidas para outros gêneros recentemente propostos, tais como Seminavis (Naviculaceae) e Halamphora (Catenulaceae). No Brasil, há poucos estudos com foco na taxonomia das diatomáceas anforóides. Este estudo apresenta uma investigação taxonômica de cinco táxons do grupo, incomuns na diatomoflora brasileira: Seminavis pusilla, S. strigosa, Amphora ectorii, Halamphora ghanensis e Halamphora sp. Seminavis strigosa é idêntica em morfologia e métrica da valva à Amphora twenteana, e a sinonimização destas espécies é proposta. Seminavis pusilla, raramente encontrada em águas brasileiras, tem a sua distribuição ampliada. Halamphora ghanensis é um novo registro para o continente Americano, enquanto Amphora ectorii é uma novidade para sistemas aquáticos brasileiros. Halamphora sp. possui características ultraestruturais distintas em relação a espécies similares e provavelmente seja uma nova espécie para a ciência.

Inferring phylogenetic networks from gene order data.

Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

Phytoplankton assemblages in lateral lagoons of a large tropical reservoir / Assembleias fitoplanctônicas em lagoas laterais de um reservatório tropical de grande porte

This study aimed to analyse the composition and ecological attributes of the phytoplankton assemblages in four lateral lagoons and in the main channel of Rosana Reservoir (Paranapanema River, SE Brazil). Fieldwork was carried out in September and November/2004 and January, March, May and August/2005. A total of 283 taxa was identified. Zygnemaphyta was the most specious group, followed by Chlorophyta and Bacillariophyta. Higher richness, abundance and biomass were observed in the lagoons when compared with the river-reservoir sampling point, especially during the rainy period. Cryptophyceae and Bacillariophyceae dominated numerically. Cryptomonas brasiliensis Castro, Bicudo and Bicudo was the main species of the phytoplankton in terms of abundance and frequency of occurrence. The dynamics of the most important taxa are discussed and the results showed that the phytoplankton assemblages are mainly influenced by meteorological factors and nutrient availability (the main driving forces). Correlation analyses indicated that the assemblage abundance was limited by nutrient (nitrogen and phosphorus). The phytoplankton abundance influenced positively the zooplankton abundance, what indicates the prevalence of bottom-up control routes in the lateral lagoons system. The results validate the hypotheses that lateral lagoons have a prominent ecological role on the phytoplankton diversity, as already previously demonstrated for fish and zooplankton. Therefore, the incorporation of the lateral lagoons in environmental programmes should be a target strategy for the conservation of the regional aquatic biota, minimising the negative impact of the dam.

O objetivo deste estudo foi analisar a composição e os atributos ecológicos das assembleias fitoplanctônicas de quatro lagoas marginais e canal principal do Reservatório de Rosana (SE, Brasil). Os trabalhos de campo foram realizados em setembro e novembro de 2004, e janeiro, março, maio e agosto de 2005. O número total de táxons identificados foi de 283. Zygnemaphyta foi o grupo com maior número de espécies, seguido por Chlorophyta e Bacillariophyta. Maior riqueza, abundância e biomassa foram observadas nas lagoas, quando comparadas ao canal do rio-reservatório, especialmente durante o período chuvoso. Cryptophyceae e Bacillariophyceae dominaram numericamente as assembleias. Cryptomonas brasiliensis Castro, Bicudo e Bicudo foi a principal espécie do fitoplâncton, em termos de abundância e frequência de ocorrência. Os resultados mostraram que as assembleias fitoplanctônicas são influenciadas principalmente pelos fatores meteorológicos e nutrientes (funções de força). Análises de correlação mostraram que a abundância do fitoplâncton foi limitada por nutrientes (nitrogênio e fósforo). Por sua vez, a abundância fitoplanctônica influenciou positivamente a abundância do zooplâncton, o que indica a predominância de mecanismos de controle ascendente no sistema de lagoas laterais. Os resultados validaram a hipótese, assim como já havia sido demonstrado para peixes e zooplâncton, de que as lagoas laterais têm um proeminente papel na diversidade do fitoplâncton. A incorporação das lagoas laterais em programas ambientais seria uma boa estratégia para a conservação da biota aquática regional, minimizando o impacto negativo do represamento.

Modern carbonate microbialites from an asbestos open pit pond, Yukon, Canada.

Microbialites were discovered in an open pit pond at an abandoned asbestos mine near Clinton Creek, Yukon, Canada. These microbialites are extremely young and presumably began forming soon after the mine closed in 1978. Detailed characterization of the periphyton and microbialites using light and scanning electron microscopy was coupled with mineralogical and isotopic analyses to investigate the mechanisms by which these microbialites formed. The microbialites are columnar in form (cm scale), have an internal spherulitic fabric (mm scale), and are mostly made of aragonite, which is supersaturated in the subsaline pond water. Initial precipitation is seen as acicular aragonite crystals nucleating onto microbial biomass and detrital particles. Continued precipitation entombs benthic diatoms (e.g. Brachysira vitrea), filamentous algae (e.g. Oedogonium sp.), dinoflagellates, and cyanobacteria. The presence of phototrophs at spherulite centers strongly suggests that these microbes play an important initial role in aragonite precipitation. Substantial growth of individual spherulites occurs abiotically through periodic precipitation of aragonite that forms concentric laminations around spherulite centers while pauses in spherulite growth allow for colonization by microbes. Aragonite associated with biomass (δ(13)C = -4.6‰ VPDB) showed a (13)C-enrichment of 0.8‰ relative to aragonite exhibiting no biomass (δ(13)C = -5.4‰ VPDB), which suggests a modest removal of isotopically light dissolved inorganic carbon by phototrophs. The combination of a low sedimentation rate, high calcification rate, and low microbial growth rate appears to result in the formation of these microbialites. The formation of microbialites at an historic mine site demonstrates that an anthropogenically constructed environment can foster microbial carbonate formation.

In situ assessment of periphyton recovery in a river contaminated by pesticides.

Recovery of bacterial and eukaryotic communities in biofilms naturally grown on stones was studied for 9 weeks after transferring them from a pesticide polluted downstream site of the river Morcille (Beaujolais, France) to a non-contaminated upstream site. Site-specific periphyton present on stones at both the down- and the upstream sampling site were collected to analyze the site-specific colonization. Throughout the experiment, structural and functional parameters were analyzed for the periphyton transferred and for the site-specific up- and downstream periphyton. Comparison between these three communities allowed quantifying recovery of the transferred one. Denaturing Gradient Gel Electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments were used to assess prokaryotic and eukaryotic microbial community composition, respectively. Microscopy counts allowed characterizing the diatom taxa abundances. The sensitivity of the microalgal communities towards diuron and copper was investigated at the laboratory by short-term photosynthesis inhibition assays. The functional reaction of the bacterial communities towards copper was assessed by short-term respiration inhibition assays. The structure of transferred eukaryotic, bacterial and diatom communities was more similar to the structure of the downstream communities than to upstream ones even after 9 weeks acclimatization in particular for the bacterial community. In the same way, the community tolerance towards diuron and copper, as estimated by the EC50 values, was intermediate for the transferred biofilms compared to the local up- or downstream biofilm, even after 9 weeks of acclimatization. These results strongly suggest slow recovery, likely to be linked to long lasting exposure of pesticides and in particular copper adsorbed to the biofilm matrices and to the toughness for pioneer microorganisms to invade mature biofilms.