Diatoms

Universal coordinate method for locating light-microscope specimens

by David Williams

Authors: Frithjof A.S. Sterrenburg, Paul Hamilton & David Williams

A description is provided of a universally applicable method of locating specimens under the light microscope, which... more A description is provided of a universally applicable method of locating specimens under the light microscope, which is precisely reproducible, regardless of the brand or type of instrument used. For this method, two conditions must be met: (1) the instrument should have a graduated mechanical stage, and (2) the procedure must be rigorously standardised, as described.

Rimet F. and Bouchez A. 2012. Life-forms, cell-sizes and ecological guilds of diatoms in European rivers. Knowledge and Management of Aquatic Ecosystems. accepted

by Frederic Rimet

Comparative analysis of diatom genomes reveals substantial differences in the organization of carbonpartitioning pathways

by Raffaela Abbriano

A major challenge in the development of microalgal strains for large-scale production is the optimization of biomass... more A major challenge in the development of microalgal strains for large-scale production is the optimization of biomass accumulation and production of fuel-relevant molecules such as triacylglycerol. Selecting targets for genetic manipulation approaches will require a fundamental understanding of the organization and regulation of carbon metabolic pathways in these organisms. Functional genomic and metabolomics data is becoming easier to obtain and process, however interpreting the significance of these data in a physiological context is challenging since the metabolic framework of all microalgae remains poorly understood. Owing to a complex evolutionary history, diatoms differ substantially from many other photosynthetic organisms in their intracellular compartmentation and the organization of their carbonpartitioning pathways. A comparative analysis of the genes involved in carbonpartitioning metabolism from Thalassiosira pseudonana, Phaeodactylum tricornutum, and Fragilariopsis cylindrus revealed that diatoms have conserved the lower half of glycolysis in the mitochondria, the upper half of glycolysis (including key regulatory enzymes) in the cytosol, and several mitochondrial carbon partitioning enzymes. However, some substantial differences exist between the three diatoms investigated, including the translocation of metabolic pathways to different compartments, selective maintenance and horizontal acquisition of genes, and differential gene family expansions. A key finding is that metabolite transport between intracellular compartments is likely to play a substantial role in the regulation of carbon flux. Analysis of the carbonpartitioning components in the mitochondria suggests an important role of this organelle as a carbon flux regulator in diatoms. Differences between the analyzed species are specific examples of how diatoms may have modified their carbonpartitioning pathways to adapt to environmental niches during the diversification of the group. This comparative analysis highlights how even core central pathways can be modified considerably within a single algal group, and enables the identification of suitable targets for genetic engineering to enhance biofuel precursor production.

The place of diatoms in the biofuels industry

by Raffaela Abbriano

In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development... more In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development of microalgal biofuels. Diatoms are highly diverse and have substantial evolutionarily-based differences in cellular organization and metabolic processes relative to chlorophytes. Diatoms have tremendous ecological success, with typically higher productivity than other algal classes, which may relate to cellular factors discussed in this review. Diatoms can accumulate lipid equivalently or to a greater extent than other algal classes, and can rapidly induce triacylglycerol under Si limitation, avoiding the detrimental effects on photosynthesis, gene expression and protein content associated with N limitation. Diatoms have been grown on production scales for aquaculture for decades, produce value-added products and are amenable to omic and genetic manipulation approaches. In this article, we highlight beneficial attributes and address potential concerns of diatoms as biofuels research and production organisms, and encourage a greater emphasis on their development in the biofuels arena.

Briand J.F., Djeridi I., Jamet D., Coupé S, Bressya C., Molmeret M., Le Berre B., Rimet F., Bouchez A. & Blache Y., 2012. Pioneer marine biofilms on artificial surfaces including antifouling coatings immersed in two contrasting French Mediterranean coast sites. Biofouling, 28: 453-463.

by Frederic Rimet

Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways

by Sarah Smith

Co-authored with R. M. Abbriano and M. Hildebrand

A major challenge in the development of microalgal strains for large-scale production is the optimization of biomass... more A major challenge in the development of microalgal strains for large-scale production is the optimization of biomass accumulation and production of fuel-relevant molecules such as triacylglycerol. Selecting targets for genetic manipulation approaches will require a fundamental understanding of the organization and regulation of carbon metabolic pathways in these organisms. Functional genomic and metabolomics data is becoming easier to obtain and process, however interpreting the significance of these data in a physiological context is challenging since the metabolic framework of all microalgae remains poorly understood. Owing to a complex evolutionary history, diatoms differ substantially from many other photosynthetic organisms in their intracellular compartmentation and the organization of their carbon partitioning pathways. A comparative analysis of the genes involved in carbon partitioning metabolism from Thalassiosira pseudonana, Phaeodactylum tricornutum, and Fragilariopsis cylindrus revealed that diatoms have conserved the lower half of glycolysis in the mitochondria, the upper half of glycolysis (including key regulatory enzymes) in the cytosol, and several mitochondrial carbon partitioning enzymes. However, some substantial differences exist between the three diatoms investigated, including the translocation of metabolic pathways to different compartments, selective maintenance and horizontal acquisition of genes, and differential gene family expansions. A key finding is that metabolite transport between intracellular compartments is likely to play a substantial role in the regulation of carbon flux. Analysis of the carbon partitioning components in the mitochondria suggests an important role of this organelle as a carbon flux regulator in diatoms. Differences between the analyzed species are specific examples of how diatoms may have modified their carbon partitioning pathways to adapt to environmental niches during the diversification of the group. This comparative analysis highlights how even core central pathways can be modified considerably within a single algal group, and enables the identification of suitable targets for genetic engineering to enhance biofuel precursor production.

Two new species of Nitzschia (Bacillariophyta) from shallow wetlands of Peninsular India

by Karthick Balasubramanian

The majority of species belonging to the genus Nitzschia are distinguished by minute taxonomic features that are... more The majority of species belonging to the genus Nitzschia are distinguished by minute taxonomic features that are difficult to observe and document. Currently, geographical distributions for many species are recognized as cosmopolitan; in contrast endemic species are poorly documented and studied. Our study describes two new species of Nitzschia from shallow wetlands across the Bangalore urban district of peninsular India, Nitzschia taylorii, sp. nov. and Nitzschia williamsi, sp. nov. Morphological analyses of these new species were performed with light and scanning electron microscopy, and the ecology of inhabited wetlands are discussed briefly. New species records from urban polluted wetlands provide evidence for broadening taxonomic and ecological investigations of cosmopolitan genera like Nitzschia in the Southern Hemisphere.

Diatom dynamics in a long-lived mesoscale eddy in the northeast subarctic Pacific Ocean

by Tawnya Peterson

Karthick B, 2009. Genome sequencing of cells that live inside glass cages reveals their past history.

by Karthick Balasubramanian

Current Science, VOL. 96(3), 334-337.

Taxonomy and biogeography of some Surirella Turpin (Bacillariophyceae) taxa from Peninsular India

by Karthick Balasubramanian

B Karthick, PB Hamilton, JP Kociolek, 2012. Taxonomy and biogeography of some Surirella Turpin (Bacillariophyceae) taxa from Peninsular India. Beihefte zur Nova Hedwigia 141, 81-116

In this paper we reinvestigated seven Surirella species described or reported by Gandhi and two taxa which were not... more In this paper we reinvestigated seven Surirella species described or reported by Gandhi and two taxa which were not reported by Gandhi using his collections from Peninsular India. Among these, S. langebertalotii Karthick, Hamilton & Kociolek stat. & nom. nov. is a new name for Surirella robusta f. minor.
Surirella leyana Bramburger & Hamilton and S. pinnigera Bramburger & Hamilton were new records to India. Surirella lanceolata Gandhi is a synonym of the cosmopolitan species S. ovalis Brébisson 1838 and for the fi rst time the ultrastructural details of S. shyamae Gandhi, S. capronioides Gandhi, and Surirella capronii Brebisson & Kitton are presented. This study confi rms that members of Surirella show different levels of endemism, such as some being locally endemic, some regionally distributed and others cosmopolitan. It is also evident that Peninsular India and the Malay Archipelago share a similar regional diatom fl ora.

A new species of Pleurosigma from Western Ghats, South India

by Karthick Balasubramanian

B Karthick, JP Kociolek, 2012. A new species of Pleurosigma from Western Ghats, South India. Beihefte zur Nova Hedwigia 141, 117-124

A new species, Pleurosigma lange-bertalotii sp. nov., is studied with light and scanning electron microscopy and... more A new species, Pleurosigma lange-bertalotii sp. nov., is studied with light and scanning electron microscopy and described from Western Ghats, South India. The new species possesses transverse striae pattern on the external valve surface, but internal valve views show oblique striae patterns. At present the
species is assigned to the genus Pleurosigma due to the presence of oblique striation. The oblique striae pattern is continuous internally from the central nodule to the apices, and this helps to differentiate the new species from P. obscurum. The new taxon is observed only from a forested, low electrolytic stream from South Western Ghats, South India. Recent studies on diatoms suggest that the Indian sub continent is a major
geographic zone for many new diatoms, contributing to our understanding of the evolution of diatoms of this biogeographic region.

Karthick. B., Kociolek, J.P., Mahesh, M.K. and Ramachandra, T.V. 2011. The Diatom Genus Gomphonema Ehrenberg in India: Checklist and Description of Three New Species. Nova Hedwigia Vol. 93(1–2), 211–236.

by Karthick Balasubramanian

We have compiled a checklist of Gomphonema Ehrenberg taxa reported previously from India. From forty-nine references,... more We have compiled a checklist of Gomphonema Ehrenberg taxa reported previously from India. From forty-nine references, over 100 Gomphonema taxa have been reported, including 39 new taxon descriptions. In addition to these previous reports of Gomphonema taxa, we describe three new species, G. gandhii Karthick & Kociolek, sp. nov., G. difformum Karthick & Kociolek, sp. nov. and G. diminutum Karthick & Kociolek, sp. nov., all from hill streams of Western Ghats, India. Frustule morphology, as studied in light and scanning electron microscopy, is compared with that of other recently described Gomphonema species from Africa and Asia. All three Indian species have distinctly dilated proximal raphe ends, in addition to differentiated apical pore fields, septa, pseudosepta and a round external stigmal opening. Gomphonema gandhii is linear-lanceolate- clavate, has a wide axial area, and is 19–51 μm long, 3–7 μm broad. Gomphonema difformum is smaller than G. gandhii, and has a hyaline area around the headpole. Gomphonema diminuta is much smaller and narrower than the other two species. These species are distinct from their closest congeners by their sizes, shape and structure of the head pole, and striae densities. All these species were described from low nutrient, neutral, low ionic content streams of Western Ghats. As most other species described from tropical region these three species appear to be endemic to India. Moreover, within India they have hitherto only been found in Western Ghats, one of the twelve biodiversity hotspots of the World.

Karthick, B., Mahesh, M.K. and Ramachandra, T.V. 2011. Nestedness Pattern in Stream Diatom Assemblages of Central Western Ghats. Current Science. Vol. 100 (4), 552-558

by Karthick Balasubramanian

Community diversity and the population abundance of a particular group of species are controlled by immediate... more Community diversity and the population abundance of a particular group of species are controlled by immediate environment, inter- and intra-species interactions, landscape conditions, historical events and evolutionary processes. Nestedness is a measure of order in an ecological system, referring to the order in which the number of species is related to area or other factors. In this study we have studied the nestedness pattern in stream diatom assemblages in 24 stream sites of central Western Ghats, and report 98 taxa from the streams of central Western Ghats region. The communities show highly significant nested pattern. The Mantel test of matrix revealed a strong relationship between species assemblages and environmental conditions at the sites. A significant relationship between species assemblage and environmental condition was observed. Principal component analysis (PCA) indicated that environmental conditions differed markedly across the sampling sites, with the first three components explaining 78% of variance. Species composition of diatoms is significantly correlated with environmental distance across geographical extent. The current pattern suggests that micro-environment at regional levels influences the species composition of epilithic diatoms in streams. The nestedness shown by the diatom community was highly significant, even though it had a high proportion of idiosyncratic spe- cies, characterized with high numbers of cosmopolitan species, whereas the nested species were dominated by endemic species. PCA identifies ionic parameters and nutrients as the major features which determine the characteristics of the sampling sites. Hence the local water quality parameters are the major factors in deciding the diatom species assemblages.

Karthick, B. and Kociolek, J.P. 2011. Four new centric diatoms (Bacillariophyceae) from the Western Ghats, South India. Phytotaxa, Vol. 22: 25-40.

by Karthick Balasubramanian

Four new species, including two newly recorded genera of diatoms, are described from lentic habitats of Western Ghats,... more Four new species, including two newly recorded genera of diatoms, are described from lentic habitats of Western Ghats, South India. The new species are Pleurosira indica, Spicaticribra kodaikanaliana, Urosolenia curvata and U. extensa. Pleurosira indica and Spicaticribra kodaikanaliana were collected from Kodaikanal Lake in Tamil Nadu and the two Urosolenia species are collected from Hirebhasker Dam in Karnataka, India. Pleurosira indica differs from other members of the genus by the irregularly arranged areolae and c-shaped depressions associated with the rimoportulae. Spicaticribra kodaikanaliana lacks the large central openings found in S. kingstonii, but is otherwise very similar to this North American taxon. The two new Urosolenia species, U. extensa and U. curvata, have distinct shapes to their valves, unlike other previously described species of the genus. All of these new species were observed with light and scanning electron microscopes, and we discuss their systematic positions.

Karthick, B., Taylor, Jonathan Charles, Mahesh, M. K. and Ramachandra, T. V., 2010. Protocols for Collection, Preservation and Enumeration of Diatoms from Aquatic Habitats for Water Quality Monitoring in India. The IUP Journal of Soil and Water Sciences, Vol. 3, No. 1, pp. 25-60.

by Karthick Balasubramanian

Diatoms have become important organisms for monitoring freshwaters and their value has been recognised in Europe,... more Diatoms have become important organisms for monitoring freshwaters and their value has been recognised in Europe, American and African continents. If India is to include diatoms in the current suite of bioindicators, then thorough testing of diatom-based techniques is required. This paper provides guidance on methods through all stages of diatom collection from different habitats from streams and lakes, preparation and examination for the purposes of water quality assessment that can be adapted to most aquatic ecosystems in India.

Karthick B., Toyoda, K., Ramachandra, T.V. & Williams, D.M., 2009. A note on the identity of Ceratoneis iyengarii Gonzalves & Gandhi (Fragilario-phyceae, Bacillariophyta).

by Karthick Balasubramanian

Diatom Research, volume 24(1), 233-236

Ramachandra T V., Durga Madhab Mahapatra, Karthick B., Richard Gordon, 2009. Milking Diatoms for Sustainable Energy: Biochemical Engineering vs Gasoline Secreting Diatom Solar Panels.

by Karthick Balasubramanian

Ind. Eng. Chem. Res., 2009, 48 (19), pp 8769–8788

In the face of increasing CO2 emissions from conventional energy (gasoline), and the anticipated scarcity of crude... more In the face of increasing CO2 emissions from conventional energy (gasoline), and the anticipated scarcity of crude oil, a worldwide effort is underway for cost-effective renewable alternative energy sources. Here, we review a simple line of reasoning: (a) geologists claim that much crude oil comes from diatoms; (b) diatoms do indeed make oil; (c) agriculturists claim that diatoms could make 10−200 times as much oil per hectare as oil seeds; and (d) therefore, sustainable energy could be made from diatoms. In this communication, we propose ways of harvesting oil from diatoms, using biochemical engineering and also a new solar panel approach that utilizes genomically modifiable aspects of diatom biology, offering the prospect of “milking” diatoms for sustainable energy by altering them to actively secrete oil products. Secretion by and milking of diatoms may provide a way around the puzzle of how to make algae that both grow quickly and have a very high oil content.

The place of diatoms in the biofuels industry

by Sarah Smith

Co-authored with M. Hildebrand (first author), A. K. Davis, J. C. Traller, and R. Abbriano, published in the journal 'Biofuels' in March 2012

In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development... more In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development of microalgal biofuels. Diatoms are highly diverse and have substantial evolutionarily-based differences in cellular organization and metabolic processes relative to chlorophytes. Diatoms have tremendous ecological success, with typically higher productivity than other algal classes, which may relate to cellular factors discussed in this review. Diatoms can accumulate lipid equivalently or to a greater extent than other algal classes, and can rapidly induce triacylglycerol under Si limitation, avoiding the detrimental effects on photosynthesis, gene expression and protein content associated with N limitation. Diatoms have been grown on production scales for aquaculture for decades, produce value-added products and are amenable to omic and genetic manipulation approaches. In this article, we highlight beneficial attributes and address potential concerns of diatoms as biofuels research and production organisms, and encourage a greater emphasis on their development in the biofuels arena.

Kermarrec L., Ector L., Bouchez A., Rimet F. & Hoffmann L. 2011. A preliminary phylogenetic analysis of the Cymbellales based on 18S rDNA gene sequencing. Diatom Research, 26: 305-315.

by Frederic Rimet

Kermarrec L., Bouchez A., Rimet F. and Humbert J.F. 2012. Using a polyphasic approach to explore the diversity and geographical distribution of the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta). Protist, in revision.

by Frederic Rimet