Diatom Research Papers - Academia.edu (original) (raw)

From field-collected samples, two Icelandic diatom species were studied under light and electron microscopy, resulting in a newly described species and an emended description with a nomenclatural status change. A discussion on the... more

From field-collected samples, two Icelandic diatom species were studied under light and electron microscopy, resulting in a newly described species and an emended description with a nomenclatural status change. A discussion on the morphological features of these taxa and their taxonomic affinities with related species is presented. Nitzschia imae is described from Blue Lagoon, south-west Iceland. The main diagnostic criteria include the presence of two differences morphotypes, one with obtusely rounded apices and the other with slightly asymmetrical valve outline and broadly rounded apices. Additionally, we propose an emended description for Hannaea arcus var. linearis since there is no concordance between morphometric features in the protologue and the type illustration.

The Upper Paraná River floodplain is one of the few remaining non-dammed stretches in Brazil. It has a typical fluvial dynamics represented by the flood pulse and a highly complex habitat, which allows the existence and maintenance of a... more

The Upper Paraná River floodplain is one of the few remaining non-dammed stretches in Brazil. It has a typical fluvial dynamics represented by the flood pulse and a highly complex habitat, which allows the existence and maintenance of a great biodiversity, including diatom species. As it happens in tropical lowland environments, also in this floodplain, the genus Eunotia is one of the most diverse and abundant diatom groups. Therefore, this study addresses morphologic and morphometric details of a new species and the most abundant Eunotia species in sediment cores from two wetland lakes. The morphological characteristics from each species were obtained through microscopy documentation of cell walls, and compared with other related species.

High-resolution images of phytoplankton cells such as diatoms or desmids, which are useful for monitoring water quality, can now be provided by digital microscopes, facilitating the automated analysis and identification of specimens.... more

High-resolution images of phytoplankton cells such as diatoms or desmids, which are useful for monitoring water quality, can now be provided by digital microscopes, facilitating the automated analysis and identification of specimens. Conventional approaches are based on optical microscopy; however, manual image analysis is impractical due to the huge diversity of this group of microalgae and its great morphological plasticity. As such, there is a need for automated recognition techniques for diagnostic tools (e.g. environmental monitoring networks, early warning systems) to improve the management of water resources and decision-making processes. Describing the entire workflow of a bioindicator system, from capture, analysis and identification to the determination of quality indices, this book provides insights into the current state-of-the-art in automatic identification systems in microscopy.

A comparison of freshwater and marine Gomphonema species has shown that the ecological separation is accompanied by a morphological one. They have only been assigned to the same genus because they all have heteropolar, cuneate cells,... more

A comparison of freshwater and marine Gomphonema species has shown that the ecological separation is accompanied by a morphological one. They have only been assigned to the same genus because they all have heteropolar, cuneate cells, which are attached to the substratum by a mucilage pad or stalk. The marine taxa can be split into four clusters, each of which

Correct identification of diatom taxa is indispensable for diatom-based water quality studies, as well as for biotechnological applications. Biological applications of taxonomy include the identification of taxa from particular specimens.... more

Correct identification of diatom taxa is indispensable for diatom-based water quality studies, as well as for biotechnological applications. Biological applications of taxonomy include the identification of taxa from particular specimens. In this regard, identification keys, that use a predetermined set of characters to identify a given individual, are not commonly employed by diatom specialists due to the extreme biological diversity found in this group of microalgae. This chapter reviews previous attempts of using taxonomic keys for diatom identification, highlighting the pros and cons of the use of this and similar methods. The main morphological features found in common freshwater diatom genera are briefly presented, together with an account of the historical development of technologies used for species description.

El presente trabajo supone una contribución al conocimiento de las diatomeas dulceacuícolas españolas. Se describe la diatomea Eunotia emmae sp. nov. a partir de muestras de algas epífitas recogidas en una laguna somera oligo-mesotrófica... more

El presente trabajo supone una contribución al conocimiento de las diatomeas dulceacuícolas españolas. Se describe la diatomea Eunotia emmae sp. nov. a partir de muestras de algas epífitas recogidas en una laguna somera oligo-mesotrófica de la provincia de León. La muestra fue tomada y procesada siguiendo los protocolos comunes para diatomeas lacustres. Las características morfológicas y ultraestructurales de este nuevo taxón se detallan e ilustran mediante imágenes de microscopía óptica y electrónica. La diagnosis diferencial con otras especies afines muestra que la combinación de caracteres de E. emmae (principalmente la forma biconvexa de la valva y un conspicuo sternum) es única. Abstract This work aims at contributing to the knowledge of Spanish freshwater diatoms. The diatom Eunotia emmae sp. nov. is described from samples of epiphytic algae collected in a shallow, oligo-mesotrophic lake from the province of Leon (Spain). The sample was taken and processed following the usual protocols for lacustrine diatoms. Morphological and ultrastructural features of this new taxon are detailed and illustrated by means of light and scanning electron microscopy images. Differential diagnosis against related species shows that the combination of features in E. emmae (mainly the presence of biconvex valves and a conspicuous sternum) is unique.

A cross-check of botanical names databases revealed the presence of 19 cases of homonymy which are hereby resolved by proposing replacement names. Most cases concern diatom genera (Bacillariophyta) names which are preoccupied by... more

A cross-check of botanical names databases revealed the presence of 19 cases of homonymy which are hereby resolved by proposing replacement names. Most cases concern diatom genera (Bacillariophyta) names which are preoccupied by spermatophytes. While Loranthella nom. nov. (Spermatophyta, Loranthaceae) and Ochradiscus nom. nov. (Spermatophyta, Resedaceae) are proposed as new names for spermatophytes, new diatom names are proposed for genera that are currently placed in the families Amphipleuraceae, Coscinodiscaceae, Hemiaulaceae, Hemidiscaceae, Melosiraceae, Metascolionei-daceae nom. nov., Naviculaceae, Pyxillaceae, Stictodiscaceae and Surirellaceae. With one exception (i.e. Eileencoxia nom. nov.) all remaining diatom genera that are discussed in the present paper are marine and/or fossil elements. The particulari-ties of each case are briefly discussed. A total of one hundred and three new combinations are proposed.

In the Adamello-Brenta Regional Park (Trentino, Italy), the diatom communities of 30 mountain springs, 15 on crystalline and 15 on carbonate substratum, were studied between 1993 and 1996. Two of them, one from each substratum type, were... more

In the Adamello-Brenta Regional Park (Trentino, Italy), the diatom communities of 30 mountain springs, 15 on crystalline and 15 on carbonate substratum, were studied between 1993 and 1996. Two of them, one from each substratum type, were sampled monthly for a more detailed investigation of seasonal changes in community structure. The diatom flora of these springs consisted of 250 diatom taxa and showed similarities with springs and headwater stream diatom communities from different geographic areas. Characteristic spring taxa (crenophiles) were present, but included mainly subdominant and rare taxa. Diatom taxa numbers were similar to those found for mountain streams with the lowest values found for stones in carbonate springs; nevertheless the community structure of epilithic and epiphytic samples was found to be similar and more or less constant over the seasons. By numerical methods, diatom communities were clearly related to a pH gradient. A group of species, located at the lower end of this gradient, is typical of anthropogenetically acidified running waters.

The species Chamaepinnularia schauppiana was described in 1996 on the basis of LM observations. An investigation of specimens using the SEM was, however, considered necessary to be completely sure about the allocation of the new species... more

The species Chamaepinnularia schauppiana was described in 1996 on the basis of LM observations. An investigation of specimens using the SEM was, however, considered necessary to be completely sure about the allocation of the new species to Chamaepinnularia. These SEM observations were carried out during an investigation of materials sampled from shallow pools in the Danta di Cadore mires (south-eastern Alps, Italy). SEM micrographs allowed a detailed description of the ultrastructure (in particular, the peculiar grooves on the axial and central area, and the sub-marginal position of the silica bridges dividing the striae into two foramina), and definitively confirming the genus allocation. Moreover, useful information on habitat and substrata preference of this rather rare species was also provided.

Epiphytic diatom communities on macroalgae from Iceland coastal waters were investigated during July 2005. Ten species of seaweeds have been collected belonging to brown, red and green algae. The analysis of epiphytic diatom community was... more

Epiphytic diatom communities on macroalgae from Iceland coastal waters were investigated during July 2005. Ten species of seaweeds have been collected belonging to brown, red and green algae. The analysis of epiphytic diatom community was carried out under scanning electron microscopy. The epiphytic diatom abundances varied from 7 ± 5 to 7524 ± 3491 cells mm−2. Erect growth forms were the most abundant, representing

The present study refers to the effect of metal pollution on diatoms by describing a new form of teratology. The samples were collected in the Abrud River, located in a mining area from Romania, where an unreported type of deformity is... more

The present study refers to the effect of metal pollution on diatoms by describing a new form of teratology. The samples were collected in the Abrud River, located in a mining area from Romania, where an unreported type of deformity is observed in the diatoms Achnanthidium sp. pl. This kind of teratology has been found in the 20.5\% of individuals of the population and affects the cingulum, in particular to the valvocopula, by becoming markedly undulate.

Diatoms, a kind of algae microorganisms with several species, are quite useful for water quality determination, one of the hottest topics in applied biology nowadays. At the same time, deep learning and convolutional neural networks (CNN)... more

Diatoms, a kind of algae microorganisms with several species, are quite useful for water quality determination, one of the hottest topics in applied biology nowadays. At the same time, deep learning and convolutional neural networks (CNN) are becoming an extensively used technique for image classification in a variety of problems. This paper approaches diatom classification with this technique, in order to demonstrate whether it is suitable for solving the classification problem. An extensive dataset was specifically collected (80 types, 100 samples/type) for this study. The dataset covers different illumination conditions and it was computationally augmented to more than 160,000 samples. After that, CNNs were applied over datasets pre-processed with different image processing techniques. An overall accuracy of 99% is obtained for the 80-class problem and different kinds of images (brightfield, normalized). Results were compared to previous presented classification techniques with different number of samples. As far as the authors know, this is the first time that CNNs are applied to diatom classification.

The centric diatom order Thalassiosirales includes all diatoms with a fultoportula (strutted process), a feature now recognized as a synapomorphy for the lineage. Within Thalassiosirales, Thalassiosira is perhaps the most taxonomically... more

The centric diatom order Thalassiosirales includes all diatoms with a fultoportula (strutted process), a feature now recognized as a synapomorphy for the lineage. Within Thalassiosirales, Thalassiosira is perhaps the most taxonomically and morphologically diverse genus, and at least two distinct morphological groups have been recognized within it. Group “A” Thalassiosira species, which include the type species, T. nordenskioeldii, have short inward and long outward extensions of the strutted processes and a labiate process on the valve mantle. Group “B” species have exceptionally long inward and reduced outward extensions of the strutted processes, and a labiate process on the valve face. We collected and cultured Thalassiosira ritscheri, which has a combination of group A and B characters. It has a labiate process on the valve face and reduced outward extensions of the strutted processes. We show for the first time that T. ritscheri has short inward, A-type extensions of the strutted processes. A phylogenetic interpretation of these conditions suggests a close relationship between T. ritscheri and the traditionally held group “B” species. Species diagnosed by the autapomorphic condition of a labiate process away from the valve mantle, including many group “B” Thalassiosira species, are transferred into Shionodiscus gen. nov.

A population of an unknown Psammothidium species (Bacillariophyta, Achnanthidiaceae) was found in core sediments collected from Cimera Lake, an oligotrophic, undisturbed mountain lake in Central Spain (Gredos mountain range). The... more

A population of an unknown Psammothidium species (Bacillariophyta, Achnanthidiaceae) was found in core sediments collected from Cimera Lake, an oligotrophic, undisturbed mountain lake in Central Spain (Gredos mountain range). The morphology and ultrastructure of this taxon is hereby documented in detail by means of light (LM) and scanning electron (SEM) micrographs. Morphologically, the closest taxon is P. levanderi, and the type of this species is analyzed here to provide a differential diagnosis. A comparison with other similar small Psammothidium species with an elliptic outline show that the combination of features exhibited by this taxon is unique and it is thus described here as Psammothidium toroi sp. nov.

A new benthic freshwater diatom, Fragilaria rinoi Almeida & C.Delgado sp. nov., is described from river periphyton samples in Portugal. Fragilaria rinoi sp. nov. is illustrated and discussed based on populations collected from the Vouga,... more

A new benthic freshwater diatom, Fragilaria rinoi Almeida & C.Delgado sp. nov., is described from river periphyton samples in Portugal. Fragilaria rinoi sp. nov. is illustrated and discussed based on populations collected from the Vouga, Mondego and Lis river basins in central Portugal and compared with the type material of Fragilaria vaucheriae (Kütz.) J.B.Petersen. The morphological features of the new diatom species are documented through light and scanning electron micrographs, including a comparative analysis with related species of the genus (F. candidagilae Almeida, C.Delgado, Novais & S.Blanco, F. intermedia Grunow in Van Heurck, F. neointermedia Tuji & D.M.Williams, F. recapitellata Lange-Bert. & Metzeltin, F. perminuta (Grunow) Lange-Bert., F. vaucheriae and F. microvaucheriae C.E.Wetzel & Ector). Fragilaria rinoi sp. nov. is characterized by solitary cells without spines, lanceolate valves with slightly rostrate apices, a narrow, linear axial area, and a large, unilateral central area. Fragilaria rinoi sp. nov. may be confused with F. microvaucheriae in terms of length, striae density and outline, although a morphometric analysis revealed that F. rinoi sp. nov. is significantly wider. Fragilaria rinoi sp. nov. is present in rivers with high dissolved oxygen concentrations, medium to high conductivity, neutral to slightly alkaline pH and high mean values of nitrates and ammonium.

The aim of this paper is to present the distribution of Decussata hexagona, a new species in diatom flora of Serbia. Seventy-two diatom samples were collected from six localities along the Vrla and Rasina Rivers during 2011 and 2012.... more

The aim of this paper is to present the distribution of Decussata hexagona, a new species in diatom flora of Serbia. Seventy-two diatom samples were collected from six localities along the Vrla and Rasina Rivers during 2011 and 2012. Decussata hexagona was recorded with single specimens or low relative abundance (0.3%) from epilithic communities in seven samples from the Vrla River and in one sample from the Rasina River. It was recorded in unusual epilithic habitats of running neutral to low-alkaline waters with low ion content.

Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected,... more

Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected, with annotations provided by an expert diatomist. In this work, a comparison of the classical state-of-the-art general purpose methods along with two different deep learning approaches is carried out. The classical methods are based on Viola-Jones and scale and curvature invariant ridge object detectors. The deep learning based methods are Semantic Segmentation and YOLO. This is the first time that Viola-Jones and Semantic Segmentation techniques are applied and compared for diatom segmentation in microscopic images containing several taxon shells. While all methods provide relatively good results in specific species, the deep learning approaches are consistently better in terms of sensitivity and specificity (up to 0.99 for some taxa) and up to 0.86 precision.

... of Marine Botany, University of Goteborg, Carl Skottsbergs Gata 22, S-413 19 Goteborg, SwedenLinda K. Medlin Dept. ... The frustule is more or less straight, rectangular; the apices are slightly attenuated or produced; the corners... more

... of Marine Botany, University of Goteborg, Carl Skottsbergs Gata 22, S-413 19 Goteborg, SwedenLinda K. Medlin Dept. ... The frustule is more or less straight, rectangular; the apices are slightly attenuated or produced; the corners *liman (French): silt, liman (Russian): bay, gulf. ...

Las diatomeas son un grupo de algas microsc{\'{o}}picas extremadamente diversificado que viven en los ecosistemas acu{\'{a}}ticos de todo el mundo, a pesar de lo cual los estudios sobre estos organismos en la regi{\'{o}}n del Estrecho son... more

Las diatomeas son un grupo de algas microsc{\'{o}}picas extremadamente diversificado que viven en los ecosistemas acu{\'{a}}ticos de todo el mundo, a pesar de lo cual los estudios sobre estos organismos en la regi{\'{o}}n del Estrecho son escasos. Esta monograf{\'{i}}a presenta el primer estudio sistem{\'{a}}tico sobre las diatomeas de Ceuta, describiendo m{\'{a}}s de 250 especies encontradas durante muestreos efectuados en ambientes tanto dulceacu{\'{i}}colas como costeros. Adem{\'{a}}s de su inter{\'{e}}s taxon{\'{o}}mico y biogeogr{\'{a}}fico, las diatomeas ceut{\'{i}}es se revelan como unos excelentes bioindicadores de la calidad del agua en los ecosistemas que habitan.

Ohrid and Prespa lakes belong to a group of ancient lakes having an age of ca. 3 million years. Both lakes are characterized by a highly diverse diatom flora and endemism. Recent studies on the diatom flora led to the description of... more

Ohrid and Prespa lakes belong to a group of ancient lakes having an age of ca. 3 million years. Both lakes are characterized by a highly diverse diatom flora and endemism. Recent studies on the diatom flora led to the description of several new taxa. Observations on taxa closely related to the Sellaphora bacillum (Ehrenberg) Mereschkowsky complex showed the presence of two previously undescribed species. In this study, two new species, Sellaphora krsticii sp. nov. and Sellaphora perbacilloides sp. nov., are described. Furthermore a new combination, Sellaphora bacilloides (Hustedt) Levkov, Krstic & Nakov comb. nov. is proposed.

ABSTRACT Objective. The effect of cryopreservation on the proximate composition of microalgae Chaetoceros calcitrans was evaluated. Materials and methods. C. calcitrans was cultured and cryopreserved using 5% (v/v) dimethylsulfoxide as... more

ABSTRACT
Objective. The effect of cryopreservation on the proximate composition of microalgae Chaetoceros calcitrans was evaluated. Materials and methods. C. calcitrans was cultured and cryopreserved using 5% (v/v) dimethylsulfoxide as cryoprotectant. The freezing was controlled at a rate of 3°C/min, up to -60°C and then the microalgae were immersed in liquid nitrogen (-196°C). After storage in liquid nitrogen, microalgae were rapidly thawed out and subcultured. The percentage of proteins, lipids and carbohydrates was analyzed using absorption spectrophotometry and the organic matter was studied by gravimetric analysis. Results. There was no significant variation between the proximate composition of C. calcitrans cryopreserved and the controls (p>0.05). Conclusion. Our results show that, despite low cell recovery after the preservation of this organism at low temperatures, there is no apparent loss of nutritional characteristics caused by the storing process at low temperatures.

This paper deals with automatic taxa identification based on machine learning methods. The aim is therefore to automatically classify diatoms, in terms of pattern recognition terminology. Diatoms are a kind of algae microorganism with... more

This paper deals with automatic taxa identification based on machine learning methods. The aim is therefore to automatically classify diatoms, in terms of pattern recognition terminology. Diatoms are a kind of algae microorganism with high biodiversity at the species level, which are useful for water quality assessment. The most relevant features for diatom description and classification have been selected using an extensive dataset of 80 taxa with a minimum of 100 samples/taxon augmented to 300 samples/taxon. In addition to published morphological, statistical and textural descriptors, a new textural descriptor, Local Binary Patterns (LBP), to characterize the diatom’s valves, and a log Gabor implementation not tested before for this purpose are introduced in this paper. Results show an overall accuracy of 98.11% using bagging decision trees and combinations of descriptors. Finally, some phycological features of diatoms that are still difficult to integrate in computer systems are discussed for future work.

High altitude rivers in European mountains show a large diversity of benthic diatom assemblages. Diatoms were studied from rivers of the Alps, the Pyrenees, the Massif-Central and the Iberic system. The study area spread across four... more

High altitude rivers in European mountains show a large diversity of benthic diatom assemblages. Diatoms were studied from rivers of the Alps, the Pyrenees, the Massif-Central and the Iberic system. The study area spread across four countries, Italy, France, Switzerland and Spain. Since 2000, the European Water Framework Directive (WFD) has required the assessment of stream quality using bioindicators and any deviation from reference conditions measured. References for each river type and for each bioindicator, such as diatoms, are in the process of being defined.System A is a typological system proposed by the WFD, in which ecoregions spread over several countries were defined. The first aim of this study was to assess the importance of these ecoregions for diatoms compared to other environmental factors. To reduce the heterogeneity of the diatom assemblages due to the river continuum and also pollution, only the rivers higher than 800 meters were selected. These rivers include a majority of sites that are only slightly polluted, or not at all. In total 261 sampling sites were considered from four ecoregions: the Iberic region, the Pyrenees, the Alps and the Western Highlands. The sampling sites were characterized by differences in geology, distance from the source and altitudes. Statistical analysis showed that geographic ecoregions of system A and geology were the most important environmental descriptors for diatoms. Distance from the source and altitude were less important and pollution was the least important parameter.The second aim was to describe and to typify the main diatom assemblages of these European mountains. Eight clusters gathered into four main groups were identified. Group I was mainly recorded in the Alps and the Pyrenees; group II had in common its close proximity to the source; group III was often found in the Western Highlands on crystalline geology, and group IV was present in all ecoregions and included weakly polluted streams. Some suggestions for the improvement of the ecoregions based on benthic diatoms were given in the conclusion.

Gomphonema alavariense sp. nov. is a new freshwater diatom described in Portugal from phytobenthos samples in an urban pond located in Aveiro (Portugal). This new diatom is illustrated and discussed based on different samples collected in... more

Gomphonema alavariense sp. nov. is a new freshwater diatom described in Portugal from phytobenthos samples in an urban pond located in Aveiro (Portugal). This new diatom is illustrated and discussed based on different samples collected in July August 2017 from Santo Ant{\'{o}}nio Park pond in the city centre. This taxon was compared with other Gomphonema taxa and the morphological features are documented through light and scanning electron micrographs. Gomphonema alavariense sp. nov. is characterized by showing solitary cells, rhombic-lanceolate to lanceolate valves with rounded apices, a narrow, linear axial area, and slightly asymmetrical central area. This taxon may be confused with G. affine var. rhombicum in terms of length, striae density and outline. Gomphonema alavariense sp. nov. was present in freshwater with low dissolved oxygen concentrations, high conductivity, neutral to slightly alkaline pH and high nitrate concentrations.